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' => 'HOM05D001729', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '375', 'num_species' => '42' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'Ah.07g204710' => 'amhyb', 'AUR62006001' => 'cqu', 'AUR62006002' => 'cqu', 'AUR62006003' => 'cqu', 'AUR62015641' => 'cqu', 'AUR62027174' => 'cqu', 'AUR62035623' => 'cqu', 'AUR62035624' => 'cqu', 'AUR62035625' => 'cqu', 'AUR62035626' => 'cqu', 'CAN.G1110.53' => 'can', 'CANSAT80G0415' => 'cansat', 'Ca_21364_v3' => 'car', 'COL.COLO4_30693' => 'col', 'COL.COLO4_30694' => 'col', 'COL.COLO4_30695' => 'col', 'COL.COLO4_30696' => 'col', 'COL.COLO4_34020' => 'col', 'DCAR_004585' => 'dca', 'Dinv04029' => 'din', 'Dinv34857' => 'din', 'Duzib147G0011' => 'dzi', 'Duzib170G0599' => 'dzi', 'Duzib192G1051' => 'dzi', 'FAN01G0708' => 'fan', 'FAN01G0742' => 'fan', 'FAN02G0048' => 'fan', 'FAN02G0583' => 'fan', 'FAN02G0688' => 'fan', 'FAN02G1588' => 'fan', 'FAN02G2194' => 'fan', 'FAN02G2750' => 'fan', 'FAN02G3094' => 'fan', 'FAN02G3887' => 'fan', 'FAN02G3911' => 'fan', 'FAN02G3994' => 'fan', 'FAN02G4432' => 'fan', 'FAN02G4556' => 'fan', 'FAN03G1977' => 'fan', 'FAN03G2781' => 'fan', 'FAN03G2850' => 'fan', 'FAN03G3155' => 'fan', 'FAN04G2487' => 'fan', 'FAN05G0208' => 'fan', 'FAN05G0656' => 'fan', 'FAN05G0696' => 'fan', 'FAN05G0810' => 'fan', 'FAN05G1447' => 'fan', 'FAN05G2640' => 'fan', 'FAN05G2911' => 'fan', 'FAN05G3901' => 'fan', 'FAN05G4859' => 'fan', 'FAN05G4861' => 'fan', 'FAN05G4988' => 'fan', 'FAN05G5187' => 'fan', 'FAN05G5452' => 'fan', 'FAN05G5500' => 'fan', 'FAN05G5688' => 'fan', 'FAN06G0177' => 'fan', 'FAN06G0675' => 'fan', 'FAN06G1290' => 'fan', 'FAN06G2191' => 'fan', 'FAN06G2405' => 'fan', 'FAN06G3231' => 'fan', 'FAN06G3932' => 'fan', 'FAN07G0163' => 'fan', 'FAN07G0471' => 'fan', 'FAN07G1354' => 'fan', 'FAN08G0338' => 'fan', 'FAN08G1373' => 'fan', 'FAN08G2539' => 'fan', 'FAN08G2728' => 'fan', 'FAN09G0608' => 'fan', 'FAN09G1136' => 'fan', 'FAN09G1958' => 'fan', 'FAN09G2508' => 'fan', 'FAN09G2597' => 'fan', 'FAN09G2658' => 'fan', 'FAN09G2757' => 'fan', 'FAN09G2983' => 'fan', 'FAN09G3130' => 'fan', 'FAN09G3565' => 'fan', 'FAN09G3613' => 'fan', 'FAN09G4011' => 'fan', 'FAN09G4239' => 'fan', 'FAN09G4277' => 'fan', 'FAN09G4720' => 'fan', 'FAN11G0139' => 'fan', 'FAN11G1727' => 'fan', 'FAN11G2672' => 'fan', 'FAN11G2795' => 'fan', 'FAN11G3238' => 'fan', 'FAN11G3734' => 'fan', 'FAN12G0631' => 'fan', 'FAN12G2239' => 'fan', 'FAN12G2308' => 'fan', 'FAN12G2569' => 'fan', 'FAN12G2623' => 'fan', 'FAN13G3182' => 'fan', 'FAN14G0053' => 'fan', 'FAN14G0370' => 'fan', 'FAN14G0382' => 'fan', 'FAN14G0421' => 'fan', 'FAN14G0866' => 'fan', 'FAN14G1187' => 'fan', 'FAN14G1727' => 'fan', 'FAN14G1791' => 'fan', 'FAN14G2361' => 'fan', 'FAN14G2668' => 'fan', 'FAN14G2770' => 'fan', 'FAN14G2874' => 'fan', 'FAN14G3193' => 'fan', 'FAN14G3624' => 'fan', 'FAN14G3676' => 'fan', 'FAN14G3807' => 'fan', 'FAN14G4082' => 'fan', 'FAN14G4342' => 'fan', 'FAN14G4985' => 'fan', 'FAN14G5126' => 'fan', 'FAN14G5781' => 'fan', 'FAN14G5808' => 'fan', 'FAN14G5949' => 'fan', 'FAN15G0828' => 'fan', 'FAN15G1054' => 'fan', 'FAN15G2023' => 'fan', 'FAN15G2506' => 'fan', 'FAN16G0128' => 'fan', 'FAN16G0249' => 'fan', 'FAN16G0429' => 'fan', 'FAN16G1493' => 'fan', 'FAN16G2210' => 'fan', 'FAN16G2506' => 'fan', 'FAN18G1542' => 'fan', 'FAN18G4057' => 'fan', 'FAN19G0745' => 'fan', 'FAN19G1216' => 'fan', 'FAN19G1733' => 'fan', 'FAN20G0258' => 'fan', 'FAN20G1095' => 'fan', 'FAN20G1557' => 'fan', 'FAN21G0302' => 'fan', 'FAN21G0519' => 'fan', 'FAN21G0970' => 'fan', 'FAN21G1159' => 'fan', 'FAN21G1312' => 'fan', 'FAN21G1440' => 'fan', 'FAN21G1715' => 'fan', 'FAN23G1584' => 'fan', 'FAN24G0045' => 'fan', 'FAN24G0053' => 'fan', 'FAN24G1500' => 'fan', 'FAN24G1817' => 'fan', 'FAN24G2147' => 'fan', 'FAN24G2236' => 'fan', 'FAN24G2446' => 'fan', 'FAN24G2684' => 'fan', 'FAN25G0187' => 'fan', 'FAN25G0505' => 'fan', 'FAN25G0589' => 'fan', 'FAN25G3663' => 'fan', 'FAN26G1025' => 'fan', 'FAN26G2860' => 'fan', 'FAN27G1329' => 'fan', 'FAN27G3392' => 'fan', 'FvH4_1g02011' => 'fve', 'FvH4_1g06511' => 'fve', 'FvH4_2g19900' => 'fve', 'FvH4_2g19920' => 'fve', 'FvH4_2g24261' => 'fve', 'FvH4_2g24270' => 'fve', 'FvH4_2g24631' => 'fve', 'FvH4_2g30622' => 'fve', 'FvH4_3g12920' => 'fve', 'FvH4_3g30171' => 'fve', 'FvH4_3g35490' => 'fve', 'FvH4_3g43682' => 'fve', 'FvH4_3g43730' => 'fve', 'FvH4_3g43732' => 'fve', 'FvH4_3g43751' => 'fve', 'FvH4_3g43752' => 'fve', 'FvH4_3g43770' => 'fve', 'FvH4_3g44471' => 'fve', 'FvH4_3g44510' => 'fve', 'FvH4_3g44582' => 'fve', 'FvH4_4g16921' => 'fve', 'FvH4_4g17121' => 'fve', 'FvH4_4g17782' => 'fve', 'FvH4_4g17783' => 'fve', 'FvH4_4g18120' => 'fve', 'FvH4_4g31310' => 'fve', 'FvH4_4g35052' => 'fve', 'FvH4_5g30862' => 'fve', 'FvH4_6g01541' => 'fve', 'FvH4_6g02021' => 'fve', 'FvH4_6g02041' => 'fve', 'FvH4_6g02071' => 'fve', 'FvH4_6g02171' => 'fve', 'FvH4_6g03181' => 'fve', 'FvH4_6g03182' => 'fve', 'FvH4_6g03221' => 'fve', 'FvH4_6g03380' => 'fve', 'FvH4_6g05201' => 'fve', 'FvH4_6g05203' => 'fve', 'FvH4_6g20231' => 'fve', 'FvH4_6g31981' => 'fve', 'FvH4_6g32061' => 'fve', 'FvH4_6g37041' => 'fve', 'FvH4_6g37932' => 'fve', 'FvH4_6g38731' => 'fve', 'FvH4_6g39370' => 'fve', 'FvH4_6g39371' => 'fve', 'FvH4_6g40891' => 'fve', 'FvH4_6g40892' => 'fve', 'FvH4_6g43143' => 'fve', 'FvH4_6g45251' => 'fve', 'FvH4_6g45260' => 'fve', 'FvH4_6g45291' => 'fve', 'FvH4_6g45890' => 'fve', 'FvH4_6g46240' => 'fve', 'FvH4_6g46241' => 'fve', 'FvH4_6g46242' => 'fve', 'FvH4_6g46260' => 'fve', 'FvH4_6g46280' => 'fve', 'FvH4_6g46380' => 'fve', 'FvH4_7g12841' => 'fve', 'FvH4_7g31431' => 'fve', 'Glyma.09G075900' => 'gma', 'Gohir.A09G096401' => 'ghi', 'Gohir.D09G096101' => 'ghi', 'Gorai.006G112800' => 'gra', 'HanXRQChr04g0121411' => 'han', 'Hund15878' => 'sun', 'Lj2A1107G68' => 'lonja', 'Lj2A630G63' => 'lonja', 'Lj2A946T25' => 'lonja', 'Lj2C714T1' => 'lonja', 'Lj2C966T3' => 'lonja', 'Lj2C966T4' => 'lonja', 'Lj4g0002979' => 'lja', 'Lsat_1_v5_gn_5_30901' => 'lsa', 'Lsat_1_v5_gn_5_31100' => 'lsa', 'Lsat_1_v5_gn_5_38600' => 'lsa', 'Lsat_1_v5_gn_6_92061' => 'lsa', 'Manes.05G071301' => 'mes', 'MD02G1008700' => 'mdo', 'MD02G1008900' => 'mdo', 'MD03G1256400' => 'mdo', 'MD04G1180900' => 'mdo', 'MD04G1181000' => 'mdo', 'MD04G1181200' => 'mdo', 'MD05G1244200' => 'mdo', 'MD05G1324200' => 'mdo', 'MD09G1201600' => 'mdo', 'MD10G1000600' => 'mdo', 'MD14G1026900' => 'mdo', 'MD14G1187900' => 'mdo', 'MD15G1017800' => 'mdo', 'MD15G1018100' => 'mdo', 'Medtr4g124160' => 'mtr', 'Migut.L01260' => 'egut', 'Nitab4.5_0000008g0440' => 'nta', 'Nitab4.5_0000207g0170' => 'nta', 'Nitab4.5_0007671g0030' => 'nta', 'Nitab4.5_0010853g0020' => 'nta', 'Oeu057656.1' => 'oeu', 'PGSC0003DMG400005638' => 'stu', 'PGSC0003DMG400005639' => 'stu', 'Phvul.009G222800' => 'pvu', 'Potri.009G132400' => 'ptr', 'Potri.009G163001' => 'ptr', 'Potri.011G000700' => 'ptr', 'Potri.011G004800' => 'ptr', 'Prupe.1G509300' => 'ppe', 'Prupe.1G509700' => 'ppe', 'Prupe.1G510400' => 'ppe', 'Prupe.1G510700' => 'ppe', 'Prupe.1G512600' => 'ppe', 'Prupe.2G073200' => 'ppe', 'Prupe.3G059500' => 'ppe', 'Prupe.3G059600' => 'ppe', 'Prupe.3G246100' => 'ppe', 'Prupe.3G265100' => 'ppe', 'Prupe.4G034700' => 'ppe', 'Prupe.4G052100' => 'ppe', 'Prupe.4G053600' => 'ppe', 'Prupe.5G068800' => 'ppe', 'Prupe.5G070600' => 'ppe', 'Prupe.6G075400' => 'ppe', 'Prupe.6G075500' => 'ppe', 'Prupe.6G076400' => 'ppe', 'Prupe.8G110700' => 'ppe', 'Psat4g020960' => 'psa', 'PSO135G0788' => 'pso', 'PSO210G6463' => 'pso', 'PSO384G0370' => 'pso', 'PSO386G0056' => 'pso', 'QL01p006048' => 'qlo', 'QL02p054283' => 'qlo', 'QL05p008000' => 'qlo', 'QL05p008212' => 'qlo', 'QL05p008950' => 'qlo', 'QL05p009042' => 'qlo', 'QL05p009518' => 'qlo', 'QL05p012589' => 'qlo', 'QL05p012608' => 'qlo', 'QL05p012650' => 'qlo', 'QL05p012667' => 'qlo', 'QL05p014501' => 'qlo', 'QL05p052800' => 'qlo', 'QL05p065010' => 'qlo', 'QL05p074156' => 'qlo', 'QL05p074160' => 'qlo', 'QL05p074174' => 'qlo', 'QL05p074178' => 'qlo', 'QL05p074214' => 'qlo', 'QL06p001050' => 'qlo', 'QL06p001056' => 'qlo', 'QL06p006093' => 'qlo', 'QL06p006111' => 'qlo', 'QL07p019784' => 'qlo', 'QL07p019801' => 'qlo', 'QL07p036110' => 'qlo', 'QL07p036134' => 'qlo', 'QL07p036147' => 'qlo', 'QL07p036156' => 'qlo', 'QL07p036300' => 'qlo', 'QL07p036320' => 'qlo', 'QL08p014547' => 'qlo', 'QL08p014551' => 'qlo', 'QL08p043319' => 'qlo', 'QL08p043324' => 'qlo', 'QL11p009094' => 'qlo', 'RcHm_v2.0_Chr1g0380481' => 'rch', 'RcHm_v2.0_Chr2g0089331' => 'rch', 'RcHm_v2.0_Chr2g0123691' => 'rch', 'RcHm_v2.0_Chr2g0151111' => 'rch', 'RcHm_v2.0_Chr2g0163011' => 'rch', 'RcHm_v2.0_Chr2g0163051' => 'rch', 'RcHm_v2.0_Chr2g0164671' => 'rch', 'RcHm_v2.0_Chr2g0164681' => 'rch', 'RcHm_v2.0_Chr2g0164721' => 'rch', 'RcHm_v2.0_Chr3g0449911' => 'rch', 'RcHm_v2.0_Chr3g0450211' => 'rch', 'RcHm_v2.0_Chr3g0457271' => 'rch', 'RcHm_v2.0_Chr5g0018111' => 'rch', 'RcHm_v2.0_Chr5g0021011' => 'rch', 'RcHm_v2.0_Chr5g0081171' => 'rch', 'RcHm_v2.0_Chr5g0081211' => 'rch', 'RcHm_v2.0_Chr6g0275871' => 'rch', 'RcHm_v2.0_Chr6g0276071' => 'rch', 'RcHm_v2.0_Chr6g0285591' => 'rch', 'RcHm_v2.0_Chr6g0291931' => 'rch', 'RcHm_v2.0_Chr6g0292091' => 'rch', 'RcHm_v2.0_Chr6g0292271' => 'rch', 'RcHm_v2.0_Chr7g0221261' => 'rch', 'Rhsim08G0219900' => 'rsi', 'Rhsim08G0220200' => 'rsi', 'Rhsim08G0237800' => 'rsi', 'Rhsim08G0238800' => 'rsi', 'Sabra09G0102700' => 'sbr', 'Sabra09G0127200' => 'sbr', 'Sabra11G0003700' => 'sbr', 'Sabra15G0014700' => 'sbr', 'Sc19g0000590' => 'sci', 'Sc19g0001870' => 'sci', 'SGA_v2.0_scaffold1G00346' => 'sas', 'SGA_v2.0_scaffold1G00575' => 'sas', 'SGA_v2.0_scaffold1G00761' => 'sas', 'SGA_v2.0_scaffold232G43501' => 'sas', 'TAR625G1137' => 'tar', 'Thecc.03G222100' => 'tca', 'TPR.G12691' => 'tpr', 'TWI34G0727' => 'twi', 'TWI36G0117' => 'twi', 'VMungo1309G0868' => 'vmu' ), 'gf_id' => 'HOM05D001729', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001729' ), 'data_identifier' => 'HOM05D001729', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001729', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '375', 'num_species' => '42' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'Ah.07g204710' => 'amhyb', 'AUR62006001' => 'cqu', 'AUR62006002' => 'cqu', 'AUR62006003' => 'cqu', 'AUR62015641' => 'cqu', 'AUR62027174' => 'cqu', 'AUR62035623' => 'cqu', 'AUR62035624' => 'cqu', 'AUR62035625' => 'cqu', 'AUR62035626' => 'cqu', 'CAN.G1110.53' => 'can', 'CANSAT80G0415' => 'cansat', 'Ca_21364_v3' => 'car', 'COL.COLO4_30693' => 'col', 'COL.COLO4_30694' => 'col', 'COL.COLO4_30695' => 'col', 'COL.COLO4_30696' => 'col', 'COL.COLO4_34020' => 'col', 'DCAR_004585' => 'dca', 'Dinv04029' => 'din', 'Dinv34857' => 'din', 'Duzib147G0011' => 'dzi', 'Duzib170G0599' => 'dzi', 'Duzib192G1051' => 'dzi', 'FAN01G0708' => 'fan', 'FAN01G0742' => 'fan', 'FAN02G0048' => 'fan', 'FAN02G0583' => 'fan', 'FAN02G0688' => 'fan', 'FAN02G1588' => 'fan', 'FAN02G2194' => 'fan', 'FAN02G2750' => 'fan', 'FAN02G3094' => 'fan', 'FAN02G3887' => 'fan', 'FAN02G3911' => 'fan', 'FAN02G3994' => 'fan', 'FAN02G4432' => 'fan', 'FAN02G4556' => 'fan', 'FAN03G1977' => 'fan', 'FAN03G2781' => 'fan', 'FAN03G2850' => 'fan', 'FAN03G3155' => 'fan', 'FAN04G2487' => 'fan', 'FAN05G0208' => 'fan', 'FAN05G0656' => 'fan', 'FAN05G0696' => 'fan', 'FAN05G0810' => 'fan', 'FAN05G1447' => 'fan', 'FAN05G2640' => 'fan', 'FAN05G2911' => 'fan', 'FAN05G3901' => 'fan', 'FAN05G4859' => 'fan', 'FAN05G4861' => 'fan', 'FAN05G4988' => 'fan', 'FAN05G5187' => 'fan', 'FAN05G5452' => 'fan', 'FAN05G5500' => 'fan', 'FAN05G5688' => 'fan', 'FAN06G0177' => 'fan', 'FAN06G0675' => 'fan', 'FAN06G1290' => 'fan', 'FAN06G2191' => 'fan', 'FAN06G2405' => 'fan', 'FAN06G3231' => 'fan', 'FAN06G3932' => 'fan', 'FAN07G0163' => 'fan', 'FAN07G0471' => 'fan', 'FAN07G1354' => 'fan', 'FAN08G0338' => 'fan', 'FAN08G1373' => 'fan', 'FAN08G2539' => 'fan', 'FAN08G2728' => 'fan', 'FAN09G0608' => 'fan', 'FAN09G1136' => 'fan', 'FAN09G1958' => 'fan', 'FAN09G2508' => 'fan', 'FAN09G2597' => 'fan', 'FAN09G2658' => 'fan', 'FAN09G2757' => 'fan', 'FAN09G2983' => 'fan', 'FAN09G3130' => 'fan', 'FAN09G3565' => 'fan', 'FAN09G3613' => 'fan', 'FAN09G4011' => 'fan', 'FAN09G4239' => 'fan', 'FAN09G4277' => 'fan', 'FAN09G4720' => 'fan', 'FAN11G0139' => 'fan', 'FAN11G1727' => 'fan', 'FAN11G2672' => 'fan', 'FAN11G2795' => 'fan', 'FAN11G3238' => 'fan', 'FAN11G3734' => 'fan', 'FAN12G0631' => 'fan', 'FAN12G2239' => 'fan', 'FAN12G2308' => 'fan', 'FAN12G2569' => 'fan', 'FAN12G2623' => 'fan', 'FAN13G3182' => 'fan', 'FAN14G0053' => 'fan', 'FAN14G0370' => 'fan', 'FAN14G0382' => 'fan', 'FAN14G0421' => 'fan', 'FAN14G0866' => 'fan', 'FAN14G1187' => 'fan', 'FAN14G1727' => 'fan', 'FAN14G1791' => 'fan', 'FAN14G2361' => 'fan', 'FAN14G2668' => 'fan', 'FAN14G2770' => 'fan', 'FAN14G2874' => 'fan', 'FAN14G3193' => 'fan', 'FAN14G3624' => 'fan', 'FAN14G3676' => 'fan', 'FAN14G3807' => 'fan', 'FAN14G4082' => 'fan', 'FAN14G4342' => 'fan', 'FAN14G4985' => 'fan', 'FAN14G5126' => 'fan', 'FAN14G5781' => 'fan', 'FAN14G5808' => 'fan', 'FAN14G5949' => 'fan', 'FAN15G0828' => 'fan', 'FAN15G1054' => 'fan', 'FAN15G2023' => 'fan', 'FAN15G2506' => 'fan', 'FAN16G0128' => 'fan', 'FAN16G0249' => 'fan', 'FAN16G0429' => 'fan', 'FAN16G1493' => 'fan', 'FAN16G2210' => 'fan', 'FAN16G2506' => 'fan', 'FAN18G1542' => 'fan', 'FAN18G4057' => 'fan', 'FAN19G0745' => 'fan', 'FAN19G1216' => 'fan', 'FAN19G1733' => 'fan', 'FAN20G0258' => 'fan', 'FAN20G1095' => 'fan', 'FAN20G1557' => 'fan', 'FAN21G0302' => 'fan', 'FAN21G0519' => 'fan', 'FAN21G0970' => 'fan', 'FAN21G1159' => 'fan', 'FAN21G1312' => 'fan', 'FAN21G1440' => 'fan', 'FAN21G1715' => 'fan', 'FAN23G1584' => 'fan', 'FAN24G0045' => 'fan', 'FAN24G0053' => 'fan', 'FAN24G1500' => 'fan', 'FAN24G1817' => 'fan', 'FAN24G2147' => 'fan', 'FAN24G2236' => 'fan', 'FAN24G2446' => 'fan', 'FAN24G2684' => 'fan', 'FAN25G0187' => 'fan', 'FAN25G0505' => 'fan', 'FAN25G0589' => 'fan', 'FAN25G3663' => 'fan', 'FAN26G1025' => 'fan', 'FAN26G2860' => 'fan', 'FAN27G1329' => 'fan', 'FAN27G3392' => 'fan', 'FvH4_1g02011' => 'fve', 'FvH4_1g06511' => 'fve', 'FvH4_2g19900' => 'fve', 'FvH4_2g19920' => 'fve', 'FvH4_2g24261' => 'fve', 'FvH4_2g24270' => 'fve', 'FvH4_2g24631' => 'fve', 'FvH4_2g30622' => 'fve', 'FvH4_3g12920' => 'fve', 'FvH4_3g30171' => 'fve', 'FvH4_3g35490' => 'fve', 'FvH4_3g43682' => 'fve', 'FvH4_3g43730' => 'fve', 'FvH4_3g43732' => 'fve', 'FvH4_3g43751' => 'fve', 'FvH4_3g43752' => 'fve', 'FvH4_3g43770' => 'fve', 'FvH4_3g44471' => 'fve', 'FvH4_3g44510' => 'fve', 'FvH4_3g44582' => 'fve', 'FvH4_4g16921' => 'fve', 'FvH4_4g17121' => 'fve', 'FvH4_4g17782' => 'fve', 'FvH4_4g17783' => 'fve', 'FvH4_4g18120' => 'fve', 'FvH4_4g31310' => 'fve', 'FvH4_4g35052' => 'fve', 'FvH4_5g30862' => 'fve', 'FvH4_6g01541' => 'fve', 'FvH4_6g02021' => 'fve', 'FvH4_6g02041' => 'fve', 'FvH4_6g02071' => 'fve', 'FvH4_6g02171' => 'fve', 'FvH4_6g03181' => 'fve', 'FvH4_6g03182' => 'fve', 'FvH4_6g03221' => 'fve', 'FvH4_6g03380' => 'fve', 'FvH4_6g05201' => 'fve', 'FvH4_6g05203' => 'fve', 'FvH4_6g20231' => 'fve', 'FvH4_6g31981' => 'fve', 'FvH4_6g32061' => 'fve', 'FvH4_6g37041' => 'fve', 'FvH4_6g37932' => 'fve', 'FvH4_6g38731' => 'fve', 'FvH4_6g39370' => 'fve', 'FvH4_6g39371' => 'fve', 'FvH4_6g40891' => 'fve', 'FvH4_6g40892' => 'fve', 'FvH4_6g43143' => 'fve', 'FvH4_6g45251' => 'fve', 'FvH4_6g45260' => 'fve', 'FvH4_6g45291' => 'fve', 'FvH4_6g45890' => 'fve', 'FvH4_6g46240' => 'fve', 'FvH4_6g46241' => 'fve', 'FvH4_6g46242' => 'fve', 'FvH4_6g46260' => 'fve', 'FvH4_6g46280' => 'fve', 'FvH4_6g46380' => 'fve', 'FvH4_7g12841' => 'fve', 'FvH4_7g31431' => 'fve', 'Glyma.09G075900' => 'gma', 'Gohir.A09G096401' => 'ghi', 'Gohir.D09G096101' => 'ghi', 'Gorai.006G112800' => 'gra', 'HanXRQChr04g0121411' => 'han', 'Hund15878' => 'sun', 'Lj2A1107G68' => 'lonja', 'Lj2A630G63' => 'lonja', 'Lj2A946T25' => 'lonja', 'Lj2C714T1' => 'lonja', 'Lj2C966T3' => 'lonja', 'Lj2C966T4' => 'lonja', 'Lj4g0002979' => 'lja', 'Lsat_1_v5_gn_5_30901' => 'lsa', 'Lsat_1_v5_gn_5_31100' => 'lsa', 'Lsat_1_v5_gn_5_38600' => 'lsa', 'Lsat_1_v5_gn_6_92061' => 'lsa', 'Manes.05G071301' => 'mes', 'MD02G1008700' => 'mdo', 'MD02G1008900' => 'mdo', 'MD03G1256400' => 'mdo', 'MD04G1180900' => 'mdo', 'MD04G1181000' => 'mdo', 'MD04G1181200' => 'mdo', 'MD05G1244200' => 'mdo', 'MD05G1324200' => 'mdo', 'MD09G1201600' => 'mdo', 'MD10G1000600' => 'mdo', 'MD14G1026900' => 'mdo', 'MD14G1187900' => 'mdo', 'MD15G1017800' => 'mdo', 'MD15G1018100' => 'mdo', 'Medtr4g124160' => 'mtr', 'Migut.L01260' => 'egut', 'Nitab4.5_0000008g0440' => 'nta', 'Nitab4.5_0000207g0170' => 'nta', 'Nitab4.5_0007671g0030' => 'nta', 'Nitab4.5_0010853g0020' => 'nta', 'Oeu057656.1' => 'oeu', 'PGSC0003DMG400005638' => 'stu', 'PGSC0003DMG400005639' => 'stu', 'Phvul.009G222800' => 'pvu', 'Potri.009G132400' => 'ptr', 'Potri.009G163001' => 'ptr', 'Potri.011G000700' => 'ptr', 'Potri.011G004800' => 'ptr', 'Prupe.1G509300' => 'ppe', 'Prupe.1G509700' => 'ppe', 'Prupe.1G510400' => 'ppe', 'Prupe.1G510700' => 'ppe', 'Prupe.1G512600' => 'ppe', 'Prupe.2G073200' => 'ppe', 'Prupe.3G059500' => 'ppe', 'Prupe.3G059600' => 'ppe', 'Prupe.3G246100' => 'ppe', 'Prupe.3G265100' => 'ppe', 'Prupe.4G034700' => 'ppe', 'Prupe.4G052100' => 'ppe', 'Prupe.4G053600' => 'ppe', 'Prupe.5G068800' => 'ppe', 'Prupe.5G070600' => 'ppe', 'Prupe.6G075400' => 'ppe', 'Prupe.6G075500' => 'ppe', 'Prupe.6G076400' => 'ppe', 'Prupe.8G110700' => 'ppe', 'Psat4g020960' => 'psa', 'PSO135G0788' => 'pso', 'PSO210G6463' => 'pso', 'PSO384G0370' => 'pso', 'PSO386G0056' => 'pso', 'QL01p006048' => 'qlo', 'QL02p054283' => 'qlo', 'QL05p008000' => 'qlo', 'QL05p008212' => 'qlo', 'QL05p008950' => 'qlo', 'QL05p009042' => 'qlo', 'QL05p009518' => 'qlo', 'QL05p012589' => 'qlo', 'QL05p012608' => 'qlo', 'QL05p012650' => 'qlo', 'QL05p012667' => 'qlo', 'QL05p014501' => 'qlo', 'QL05p052800' => 'qlo', 'QL05p065010' => 'qlo', 'QL05p074156' => 'qlo', 'QL05p074160' => 'qlo', 'QL05p074174' => 'qlo', 'QL05p074178' => 'qlo', 'QL05p074214' => 'qlo', 'QL06p001050' => 'qlo', 'QL06p001056' => 'qlo', 'QL06p006093' => 'qlo', 'QL06p006111' => 'qlo', 'QL07p019784' => 'qlo', 'QL07p019801' => 'qlo', 'QL07p036110' => 'qlo', 'QL07p036134' => 'qlo', 'QL07p036147' => 'qlo', 'QL07p036156' => 'qlo', 'QL07p036300' => 'qlo', 'QL07p036320' => 'qlo', 'QL08p014547' => 'qlo', 'QL08p014551' => 'qlo', 'QL08p043319' => 'qlo', 'QL08p043324' => 'qlo', 'QL11p009094' => 'qlo', 'RcHm_v2.0_Chr1g0380481' => 'rch', 'RcHm_v2.0_Chr2g0089331' => 'rch', 'RcHm_v2.0_Chr2g0123691' => 'rch', 'RcHm_v2.0_Chr2g0151111' => 'rch', 'RcHm_v2.0_Chr2g0163011' => 'rch', 'RcHm_v2.0_Chr2g0163051' => 'rch', 'RcHm_v2.0_Chr2g0164671' => 'rch', 'RcHm_v2.0_Chr2g0164681' => 'rch', 'RcHm_v2.0_Chr2g0164721' => 'rch', 'RcHm_v2.0_Chr3g0449911' => 'rch', 'RcHm_v2.0_Chr3g0450211' => 'rch', 'RcHm_v2.0_Chr3g0457271' => 'rch', 'RcHm_v2.0_Chr5g0018111' => 'rch', 'RcHm_v2.0_Chr5g0021011' => 'rch', 'RcHm_v2.0_Chr5g0081171' => 'rch', 'RcHm_v2.0_Chr5g0081211' => 'rch', 'RcHm_v2.0_Chr6g0275871' => 'rch', 'RcHm_v2.0_Chr6g0276071' => 'rch', 'RcHm_v2.0_Chr6g0285591' => 'rch', 'RcHm_v2.0_Chr6g0291931' => 'rch', 'RcHm_v2.0_Chr6g0292091' => 'rch', 'RcHm_v2.0_Chr6g0292271' => 'rch', 'RcHm_v2.0_Chr7g0221261' => 'rch', 'Rhsim08G0219900' => 'rsi', 'Rhsim08G0220200' => 'rsi', 'Rhsim08G0237800' => 'rsi', 'Rhsim08G0238800' => 'rsi', 'Sabra09G0102700' => 'sbr', 'Sabra09G0127200' => 'sbr', 'Sabra11G0003700' => 'sbr', 'Sabra15G0014700' => 'sbr', 'Sc19g0000590' => 'sci', 'Sc19g0001870' => 'sci', 'SGA_v2.0_scaffold1G00346' => 'sas', 'SGA_v2.0_scaffold1G00575' => 'sas', 'SGA_v2.0_scaffold1G00761' => 'sas', 'SGA_v2.0_scaffold232G43501' => 'sas', 'TAR625G1137' => 'tar', 'Thecc.03G222100' => 'tca', 'TPR.G12691' => 'tpr', 'TWI34G0727' => 'twi', 'TWI36G0117' => 'twi', 'VMungo1309G0868' => 'vmu' ) $gf_id = 'HOM05D001729' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001729' ) $data_identifier = 'HOM05D001729' $data_type = 'gf_id' $species_gene_counts = array( 'amhyb' => (int) 1, 'cqu' => (int) 9, 'can' => (int) 1, 'cansat' => (int) 1, 'car' => (int) 1, 'col' => (int) 5, 'dca' => (int) 1, 'din' => (int) 2, 'dzi' => (int) 3, 'fan' => (int) 140, 'fve' => (int) 62, 'gma' => (int) 1, 'ghi' => (int) 2, 'gra' => (int) 1, 'han' => (int) 1, 'sun' => (int) 1, 'lonja' => (int) 6, 'lja' => (int) 1, 'lsa' => (int) 4, 'mes' => (int) 1, 'mdo' => (int) 14, 'mtr' => (int) 1, 'egut' => (int) 1, 'nta' => (int) 4, 'oeu' => (int) 1, 'stu' => (int) 2, 'pvu' => (int) 1, 'ptr' => (int) 4, 'ppe' => (int) 19, 'psa' => (int) 1, 'pso' => (int) 4, 'qlo' => (int) 36, 'rch' => (int) 23, 'rsi' => (int) 4, 'sbr' => (int) 4, 'sci' => (int) 2, 'sas' => (int) 4, 'tar' => (int) 1, 'tca' => (int) 1, 'tpr' => (int) 1, 'twi' => (int) 2, 'vmu' => (int) 1 ) $gf_gene_species = 'vmu' $gf_gene_id = 'VMungo1309G0868' $species_info = array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ) $local_species = 'amhyb' $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' => 'HOM05D001729', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '375', 'num_species' => '42' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'Ah.07g204710' => 'amhyb', 'AUR62006001' => 'cqu', 'AUR62006002' => 'cqu', 'AUR62006003' => 'cqu', 'AUR62015641' => 'cqu', 'AUR62027174' => 'cqu', 'AUR62035623' => 'cqu', 'AUR62035624' => 'cqu', 'AUR62035625' => 'cqu', 'AUR62035626' => 'cqu', 'CAN.G1110.53' => 'can', 'CANSAT80G0415' => 'cansat', 'Ca_21364_v3' => 'car', 'COL.COLO4_30693' => 'col', 'COL.COLO4_30694' => 'col', 'COL.COLO4_30695' => 'col', 'COL.COLO4_30696' => 'col', 'COL.COLO4_34020' => 'col', 'DCAR_004585' => 'dca', 'Dinv04029' => 'din', 'Dinv34857' => 'din', 'Duzib147G0011' => 'dzi', 'Duzib170G0599' => 'dzi', 'Duzib192G1051' => 'dzi', 'FAN01G0708' => 'fan', 'FAN01G0742' => 'fan', 'FAN02G0048' => 'fan', 'FAN02G0583' => 'fan', 'FAN02G0688' => 'fan', 'FAN02G1588' => 'fan', 'FAN02G2194' => 'fan', 'FAN02G2750' => 'fan', 'FAN02G3094' => 'fan', 'FAN02G3887' => 'fan', 'FAN02G3911' => 'fan', 'FAN02G3994' => 'fan', 'FAN02G4432' => 'fan', 'FAN02G4556' => 'fan', 'FAN03G1977' => 'fan', 'FAN03G2781' => 'fan', 'FAN03G2850' => 'fan', 'FAN03G3155' => 'fan', 'FAN04G2487' => 'fan', 'FAN05G0208' => 'fan', 'FAN05G0656' => 'fan', 'FAN05G0696' => 'fan', 'FAN05G0810' => 'fan', 'FAN05G1447' => 'fan', 'FAN05G2640' => 'fan', 'FAN05G2911' => 'fan', 'FAN05G3901' => 'fan', 'FAN05G4859' => 'fan', 'FAN05G4861' => 'fan', 'FAN05G4988' => 'fan', 'FAN05G5187' => 'fan', 'FAN05G5452' => 'fan', 'FAN05G5500' => 'fan', 'FAN05G5688' => 'fan', 'FAN06G0177' => 'fan', 'FAN06G0675' => 'fan', 'FAN06G1290' => 'fan', 'FAN06G2191' => 'fan', 'FAN06G2405' => 'fan', 'FAN06G3231' => 'fan', 'FAN06G3932' => 'fan', 'FAN07G0163' => 'fan', 'FAN07G0471' => 'fan', 'FAN07G1354' => 'fan', 'FAN08G0338' => 'fan', 'FAN08G1373' => 'fan', 'FAN08G2539' => 'fan', 'FAN08G2728' => 'fan', 'FAN09G0608' => 'fan', 'FAN09G1136' => 'fan', 'FAN09G1958' => 'fan', 'FAN09G2508' => 'fan', 'FAN09G2597' => 'fan', 'FAN09G2658' => 'fan', 'FAN09G2757' => 'fan', 'FAN09G2983' => 'fan', 'FAN09G3130' => 'fan', 'FAN09G3565' => 'fan', 'FAN09G3613' => 'fan', 'FAN09G4011' => 'fan', 'FAN09G4239' => 'fan', 'FAN09G4277' => 'fan', 'FAN09G4720' => 'fan', 'FAN11G0139' => 'fan', 'FAN11G1727' => 'fan', 'FAN11G2672' => 'fan', 'FAN11G2795' => 'fan', 'FAN11G3238' => 'fan', 'FAN11G3734' => 'fan', 'FAN12G0631' => 'fan', 'FAN12G2239' => 'fan', 'FAN12G2308' => 'fan', 'FAN12G2569' => 'fan', 'FAN12G2623' => 'fan', 'FAN13G3182' => 'fan', 'FAN14G0053' => 'fan', 'FAN14G0370' => 'fan', 'FAN14G0382' => 'fan', 'FAN14G0421' => 'fan', 'FAN14G0866' => 'fan', 'FAN14G1187' => 'fan', 'FAN14G1727' => 'fan', 'FAN14G1791' => 'fan', 'FAN14G2361' => 'fan', 'FAN14G2668' => 'fan', 'FAN14G2770' => 'fan', 'FAN14G2874' => 'fan', 'FAN14G3193' => 'fan', 'FAN14G3624' => 'fan', 'FAN14G3676' => 'fan', 'FAN14G3807' => 'fan', 'FAN14G4082' => 'fan', 'FAN14G4342' => 'fan', 'FAN14G4985' => 'fan', 'FAN14G5126' => 'fan', 'FAN14G5781' => 'fan', 'FAN14G5808' => 'fan', 'FAN14G5949' => 'fan', 'FAN15G0828' => 'fan', 'FAN15G1054' => 'fan', 'FAN15G2023' => 'fan', 'FAN15G2506' => 'fan', 'FAN16G0128' => 'fan', 'FAN16G0249' => 'fan', 'FAN16G0429' => 'fan', 'FAN16G1493' => 'fan', 'FAN16G2210' => 'fan', 'FAN16G2506' => 'fan', 'FAN18G1542' => 'fan', 'FAN18G4057' => 'fan', 'FAN19G0745' => 'fan', 'FAN19G1216' => 'fan', 'FAN19G1733' => 'fan', 'FAN20G0258' => 'fan', 'FAN20G1095' => 'fan', 'FAN20G1557' => 'fan', 'FAN21G0302' => 'fan', 'FAN21G0519' => 'fan', 'FAN21G0970' => 'fan', 'FAN21G1159' => 'fan', 'FAN21G1312' => 'fan', 'FAN21G1440' => 'fan', 'FAN21G1715' => 'fan', 'FAN23G1584' => 'fan', 'FAN24G0045' => 'fan', 'FAN24G0053' => 'fan', 'FAN24G1500' => 'fan', 'FAN24G1817' => 'fan', 'FAN24G2147' => 'fan', 'FAN24G2236' => 'fan', 'FAN24G2446' => 'fan', 'FAN24G2684' => 'fan', 'FAN25G0187' => 'fan', 'FAN25G0505' => 'fan', 'FAN25G0589' => 'fan', 'FAN25G3663' => 'fan', 'FAN26G1025' => 'fan', 'FAN26G2860' => 'fan', 'FAN27G1329' => 'fan', 'FAN27G3392' => 'fan', 'FvH4_1g02011' => 'fve', 'FvH4_1g06511' => 'fve', 'FvH4_2g19900' => 'fve', 'FvH4_2g19920' => 'fve', 'FvH4_2g24261' => 'fve', 'FvH4_2g24270' => 'fve', 'FvH4_2g24631' => 'fve', 'FvH4_2g30622' => 'fve', 'FvH4_3g12920' => 'fve', 'FvH4_3g30171' => 'fve', 'FvH4_3g35490' => 'fve', 'FvH4_3g43682' => 'fve', 'FvH4_3g43730' => 'fve', 'FvH4_3g43732' => 'fve', 'FvH4_3g43751' => 'fve', 'FvH4_3g43752' => 'fve', 'FvH4_3g43770' => 'fve', 'FvH4_3g44471' => 'fve', 'FvH4_3g44510' => 'fve', 'FvH4_3g44582' => 'fve', 'FvH4_4g16921' => 'fve', 'FvH4_4g17121' => 'fve', 'FvH4_4g17782' => 'fve', 'FvH4_4g17783' => 'fve', 'FvH4_4g18120' => 'fve', 'FvH4_4g31310' => 'fve', 'FvH4_4g35052' => 'fve', 'FvH4_5g30862' => 'fve', 'FvH4_6g01541' => 'fve', 'FvH4_6g02021' => 'fve', 'FvH4_6g02041' => 'fve', 'FvH4_6g02071' => 'fve', 'FvH4_6g02171' => 'fve', 'FvH4_6g03181' => 'fve', 'FvH4_6g03182' => 'fve', 'FvH4_6g03221' => 'fve', 'FvH4_6g03380' => 'fve', 'FvH4_6g05201' => 'fve', 'FvH4_6g05203' => 'fve', 'FvH4_6g20231' => 'fve', 'FvH4_6g31981' => 'fve', 'FvH4_6g32061' => 'fve', 'FvH4_6g37041' => 'fve', 'FvH4_6g37932' => 'fve', 'FvH4_6g38731' => 'fve', 'FvH4_6g39370' => 'fve', 'FvH4_6g39371' => 'fve', 'FvH4_6g40891' => 'fve', 'FvH4_6g40892' => 'fve', 'FvH4_6g43143' => 'fve', 'FvH4_6g45251' => 'fve', 'FvH4_6g45260' => 'fve', 'FvH4_6g45291' => 'fve', 'FvH4_6g45890' => 'fve', 'FvH4_6g46240' => 'fve', 'FvH4_6g46241' => 'fve', 'FvH4_6g46242' => 'fve', 'FvH4_6g46260' => 'fve', 'FvH4_6g46280' => 'fve', 'FvH4_6g46380' => 'fve', 'FvH4_7g12841' => 'fve', 'FvH4_7g31431' => 'fve', 'Glyma.09G075900' => 'gma', 'Gohir.A09G096401' => 'ghi', 'Gohir.D09G096101' => 'ghi', 'Gorai.006G112800' => 'gra', 'HanXRQChr04g0121411' => 'han', 'Hund15878' => 'sun', 'Lj2A1107G68' => 'lonja', 'Lj2A630G63' => 'lonja', 'Lj2A946T25' => 'lonja', 'Lj2C714T1' => 'lonja', 'Lj2C966T3' => 'lonja', 'Lj2C966T4' => 'lonja', 'Lj4g0002979' => 'lja', 'Lsat_1_v5_gn_5_30901' => 'lsa', 'Lsat_1_v5_gn_5_31100' => 'lsa', 'Lsat_1_v5_gn_5_38600' => 'lsa', 'Lsat_1_v5_gn_6_92061' => 'lsa', 'Manes.05G071301' => 'mes', 'MD02G1008700' => 'mdo', 'MD02G1008900' => 'mdo', 'MD03G1256400' => 'mdo', 'MD04G1180900' => 'mdo', 'MD04G1181000' => 'mdo', 'MD04G1181200' => 'mdo', 'MD05G1244200' => 'mdo', 'MD05G1324200' => 'mdo', 'MD09G1201600' => 'mdo', 'MD10G1000600' => 'mdo', 'MD14G1026900' => 'mdo', 'MD14G1187900' => 'mdo', 'MD15G1017800' => 'mdo', 'MD15G1018100' => 'mdo', 'Medtr4g124160' => 'mtr', 'Migut.L01260' => 'egut', 'Nitab4.5_0000008g0440' => 'nta', 'Nitab4.5_0000207g0170' => 'nta', 'Nitab4.5_0007671g0030' => 'nta', 'Nitab4.5_0010853g0020' => 'nta', 'Oeu057656.1' => 'oeu', 'PGSC0003DMG400005638' => 'stu', 'PGSC0003DMG400005639' => 'stu', 'Phvul.009G222800' => 'pvu', 'Potri.009G132400' => 'ptr', 'Potri.009G163001' => 'ptr', 'Potri.011G000700' => 'ptr', 'Potri.011G004800' => 'ptr', 'Prupe.1G509300' => 'ppe', 'Prupe.1G509700' => 'ppe', 'Prupe.1G510400' => 'ppe', 'Prupe.1G510700' => 'ppe', 'Prupe.1G512600' => 'ppe', 'Prupe.2G073200' => 'ppe', 'Prupe.3G059500' => 'ppe', 'Prupe.3G059600' => 'ppe', 'Prupe.3G246100' => 'ppe', 'Prupe.3G265100' => 'ppe', 'Prupe.4G034700' => 'ppe', 'Prupe.4G052100' => 'ppe', 'Prupe.4G053600' => 'ppe', 'Prupe.5G068800' => 'ppe', 'Prupe.5G070600' => 'ppe', 'Prupe.6G075400' => 'ppe', 'Prupe.6G075500' => 'ppe', 'Prupe.6G076400' => 'ppe', 'Prupe.8G110700' => 'ppe', 'Psat4g020960' => 'psa', 'PSO135G0788' => 'pso', 'PSO210G6463' => 'pso', 'PSO384G0370' => 'pso', 'PSO386G0056' => 'pso', 'QL01p006048' => 'qlo', 'QL02p054283' => 'qlo', 'QL05p008000' => 'qlo', 'QL05p008212' => 'qlo', 'QL05p008950' => 'qlo', 'QL05p009042' => 'qlo', 'QL05p009518' => 'qlo', 'QL05p012589' => 'qlo', 'QL05p012608' => 'qlo', 'QL05p012650' => 'qlo', 'QL05p012667' => 'qlo', 'QL05p014501' => 'qlo', 'QL05p052800' => 'qlo', 'QL05p065010' => 'qlo', 'QL05p074156' => 'qlo', 'QL05p074160' => 'qlo', 'QL05p074174' => 'qlo', 'QL05p074178' => 'qlo', 'QL05p074214' => 'qlo', 'QL06p001050' => 'qlo', 'QL06p001056' => 'qlo', 'QL06p006093' => 'qlo', 'QL06p006111' => 'qlo', 'QL07p019784' => 'qlo', 'QL07p019801' => 'qlo', 'QL07p036110' => 'qlo', 'QL07p036134' => 'qlo', 'QL07p036147' => 'qlo', 'QL07p036156' => 'qlo', 'QL07p036300' => 'qlo', 'QL07p036320' => 'qlo', 'QL08p014547' => 'qlo', 'QL08p014551' => 'qlo', 'QL08p043319' => 'qlo', 'QL08p043324' => 'qlo', 'QL11p009094' => 'qlo', 'RcHm_v2.0_Chr1g0380481' => 'rch', 'RcHm_v2.0_Chr2g0089331' => 'rch', 'RcHm_v2.0_Chr2g0123691' => 'rch', 'RcHm_v2.0_Chr2g0151111' => 'rch', 'RcHm_v2.0_Chr2g0163011' => 'rch', 'RcHm_v2.0_Chr2g0163051' => 'rch', 'RcHm_v2.0_Chr2g0164671' => 'rch', 'RcHm_v2.0_Chr2g0164681' => 'rch', 'RcHm_v2.0_Chr2g0164721' => 'rch', 'RcHm_v2.0_Chr3g0449911' => 'rch', 'RcHm_v2.0_Chr3g0450211' => 'rch', 'RcHm_v2.0_Chr3g0457271' => 'rch', 'RcHm_v2.0_Chr5g0018111' => 'rch', 'RcHm_v2.0_Chr5g0021011' => 'rch', 'RcHm_v2.0_Chr5g0081171' => 'rch', 'RcHm_v2.0_Chr5g0081211' => 'rch', 'RcHm_v2.0_Chr6g0275871' => 'rch', 'RcHm_v2.0_Chr6g0276071' => 'rch', 'RcHm_v2.0_Chr6g0285591' => 'rch', 'RcHm_v2.0_Chr6g0291931' => 'rch', 'RcHm_v2.0_Chr6g0292091' => 'rch', 'RcHm_v2.0_Chr6g0292271' => 'rch', 'RcHm_v2.0_Chr7g0221261' => 'rch', 'Rhsim08G0219900' => 'rsi', 'Rhsim08G0220200' => 'rsi', 'Rhsim08G0237800' => 'rsi', 'Rhsim08G0238800' => 'rsi', 'Sabra09G0102700' => 'sbr', 'Sabra09G0127200' => 'sbr', 'Sabra11G0003700' => 'sbr', 'Sabra15G0014700' => 'sbr', 'Sc19g0000590' => 'sci', 'Sc19g0001870' => 'sci', 'SGA_v2.0_scaffold1G00346' => 'sas', 'SGA_v2.0_scaffold1G00575' => 'sas', 'SGA_v2.0_scaffold1G00761' => 'sas', 'SGA_v2.0_scaffold232G43501' => 'sas', 'TAR625G1137' => 'tar', 'Thecc.03G222100' => 'tca', 'TPR.G12691' => 'tpr', 'TWI34G0727' => 'twi', 'TWI36G0117' => 'twi', 'VMungo1309G0868' => 'vmu' ), 'gf_id' => 'HOM05D001729', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001729' ), 'data_identifier' => 'HOM05D001729', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001729', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '375', 'num_species' => '42' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'Ah.07g204710' => 'amhyb', 'AUR62006001' => 'cqu', 'AUR62006002' => 'cqu', 'AUR62006003' => 'cqu', 'AUR62015641' => 'cqu', 'AUR62027174' => 'cqu', 'AUR62035623' => 'cqu', 'AUR62035624' => 'cqu', 'AUR62035625' => 'cqu', 'AUR62035626' => 'cqu', 'CAN.G1110.53' => 'can', 'CANSAT80G0415' => 'cansat', 'Ca_21364_v3' => 'car', 'COL.COLO4_30693' => 'col', 'COL.COLO4_30694' => 'col', 'COL.COLO4_30695' => 'col', 'COL.COLO4_30696' => 'col', 'COL.COLO4_34020' => 'col', 'DCAR_004585' => 'dca', 'Dinv04029' => 'din', 'Dinv34857' => 'din', 'Duzib147G0011' => 'dzi', 'Duzib170G0599' => 'dzi', 'Duzib192G1051' => 'dzi', 'FAN01G0708' => 'fan', 'FAN01G0742' => 'fan', 'FAN02G0048' => 'fan', 'FAN02G0583' => 'fan', 'FAN02G0688' => 'fan', 'FAN02G1588' => 'fan', 'FAN02G2194' => 'fan', 'FAN02G2750' => 'fan', 'FAN02G3094' => 'fan', 'FAN02G3887' => 'fan', 'FAN02G3911' => 'fan', 'FAN02G3994' => 'fan', 'FAN02G4432' => 'fan', 'FAN02G4556' => 'fan', 'FAN03G1977' => 'fan', 'FAN03G2781' => 'fan', 'FAN03G2850' => 'fan', 'FAN03G3155' => 'fan', 'FAN04G2487' => 'fan', 'FAN05G0208' => 'fan', 'FAN05G0656' => 'fan', 'FAN05G0696' => 'fan', 'FAN05G0810' => 'fan', 'FAN05G1447' => 'fan', 'FAN05G2640' => 'fan', 'FAN05G2911' => 'fan', 'FAN05G3901' => 'fan', 'FAN05G4859' => 'fan', 'FAN05G4861' => 'fan', 'FAN05G4988' => 'fan', 'FAN05G5187' => 'fan', 'FAN05G5452' => 'fan', 'FAN05G5500' => 'fan', 'FAN05G5688' => 'fan', 'FAN06G0177' => 'fan', 'FAN06G0675' => 'fan', 'FAN06G1290' => 'fan', 'FAN06G2191' => 'fan', 'FAN06G2405' => 'fan', 'FAN06G3231' => 'fan', 'FAN06G3932' => 'fan', 'FAN07G0163' => 'fan', 'FAN07G0471' => 'fan', 'FAN07G1354' => 'fan', 'FAN08G0338' => 'fan', 'FAN08G1373' => 'fan', 'FAN08G2539' => 'fan', 'FAN08G2728' => 'fan', 'FAN09G0608' => 'fan', 'FAN09G1136' => 'fan', 'FAN09G1958' => 'fan', 'FAN09G2508' => 'fan', 'FAN09G2597' => 'fan', 'FAN09G2658' => 'fan', 'FAN09G2757' => 'fan', 'FAN09G2983' => 'fan', 'FAN09G3130' => 'fan', 'FAN09G3565' => 'fan', 'FAN09G3613' => 'fan', 'FAN09G4011' => 'fan', 'FAN09G4239' => 'fan', 'FAN09G4277' => 'fan', 'FAN09G4720' => 'fan', 'FAN11G0139' => 'fan', 'FAN11G1727' => 'fan', 'FAN11G2672' => 'fan', 'FAN11G2795' => 'fan', 'FAN11G3238' => 'fan', 'FAN11G3734' => 'fan', 'FAN12G0631' => 'fan', 'FAN12G2239' => 'fan', 'FAN12G2308' => 'fan', 'FAN12G2569' => 'fan', 'FAN12G2623' => 'fan', 'FAN13G3182' => 'fan', 'FAN14G0053' => 'fan', 'FAN14G0370' => 'fan', 'FAN14G0382' => 'fan', 'FAN14G0421' => 'fan', 'FAN14G0866' => 'fan', 'FAN14G1187' => 'fan', 'FAN14G1727' => 'fan', 'FAN14G1791' => 'fan', 'FAN14G2361' => 'fan', 'FAN14G2668' => 'fan', 'FAN14G2770' => 'fan', 'FAN14G2874' => 'fan', 'FAN14G3193' => 'fan', 'FAN14G3624' => 'fan', 'FAN14G3676' => 'fan', 'FAN14G3807' => 'fan', 'FAN14G4082' => 'fan', 'FAN14G4342' => 'fan', 'FAN14G4985' => 'fan', 'FAN14G5126' => 'fan', 'FAN14G5781' => 'fan', 'FAN14G5808' => 'fan', 'FAN14G5949' => 'fan', 'FAN15G0828' => 'fan', 'FAN15G1054' => 'fan', 'FAN15G2023' => 'fan', 'FAN15G2506' => 'fan', 'FAN16G0128' => 'fan', 'FAN16G0249' => 'fan', 'FAN16G0429' => 'fan', 'FAN16G1493' => 'fan', 'FAN16G2210' => 'fan', 'FAN16G2506' => 'fan', 'FAN18G1542' => 'fan', 'FAN18G4057' => 'fan', 'FAN19G0745' => 'fan', 'FAN19G1216' => 'fan', 'FAN19G1733' => 'fan', 'FAN20G0258' => 'fan', 'FAN20G1095' => 'fan', 'FAN20G1557' => 'fan', 'FAN21G0302' => 'fan', 'FAN21G0519' => 'fan', 'FAN21G0970' => 'fan', 'FAN21G1159' => 'fan', 'FAN21G1312' => 'fan', 'FAN21G1440' => 'fan', 'FAN21G1715' => 'fan', 'FAN23G1584' => 'fan', 'FAN24G0045' => 'fan', 'FAN24G0053' => 'fan', 'FAN24G1500' => 'fan', 'FAN24G1817' => 'fan', 'FAN24G2147' => 'fan', 'FAN24G2236' => 'fan', 'FAN24G2446' => 'fan', 'FAN24G2684' => 'fan', 'FAN25G0187' => 'fan', 'FAN25G0505' => 'fan', 'FAN25G0589' => 'fan', 'FAN25G3663' => 'fan', 'FAN26G1025' => 'fan', 'FAN26G2860' => 'fan', 'FAN27G1329' => 'fan', 'FAN27G3392' => 'fan', 'FvH4_1g02011' => 'fve', 'FvH4_1g06511' => 'fve', 'FvH4_2g19900' => 'fve', 'FvH4_2g19920' => 'fve', 'FvH4_2g24261' => 'fve', 'FvH4_2g24270' => 'fve', 'FvH4_2g24631' => 'fve', 'FvH4_2g30622' => 'fve', 'FvH4_3g12920' => 'fve', 'FvH4_3g30171' => 'fve', 'FvH4_3g35490' => 'fve', 'FvH4_3g43682' => 'fve', 'FvH4_3g43730' => 'fve', 'FvH4_3g43732' => 'fve', 'FvH4_3g43751' => 'fve', 'FvH4_3g43752' => 'fve', 'FvH4_3g43770' => 'fve', 'FvH4_3g44471' => 'fve', 'FvH4_3g44510' => 'fve', 'FvH4_3g44582' => 'fve', 'FvH4_4g16921' => 'fve', 'FvH4_4g17121' => 'fve', 'FvH4_4g17782' => 'fve', 'FvH4_4g17783' => 'fve', 'FvH4_4g18120' => 'fve', 'FvH4_4g31310' => 'fve', 'FvH4_4g35052' => 'fve', 'FvH4_5g30862' => 'fve', 'FvH4_6g01541' => 'fve', 'FvH4_6g02021' => 'fve', 'FvH4_6g02041' => 'fve', 'FvH4_6g02071' => 'fve', 'FvH4_6g02171' => 'fve', 'FvH4_6g03181' => 'fve', 'FvH4_6g03182' => 'fve', 'FvH4_6g03221' => 'fve', 'FvH4_6g03380' => 'fve', 'FvH4_6g05201' => 'fve', 'FvH4_6g05203' => 'fve', 'FvH4_6g20231' => 'fve', 'FvH4_6g31981' => 'fve', 'FvH4_6g32061' => 'fve', 'FvH4_6g37041' => 'fve', 'FvH4_6g37932' => 'fve', 'FvH4_6g38731' => 'fve', 'FvH4_6g39370' => 'fve', 'FvH4_6g39371' => 'fve', 'FvH4_6g40891' => 'fve', 'FvH4_6g40892' => 'fve', 'FvH4_6g43143' => 'fve', 'FvH4_6g45251' => 'fve', 'FvH4_6g45260' => 'fve', 'FvH4_6g45291' => 'fve', 'FvH4_6g45890' => 'fve', 'FvH4_6g46240' => 'fve', 'FvH4_6g46241' => 'fve', 'FvH4_6g46242' => 'fve', 'FvH4_6g46260' => 'fve', 'FvH4_6g46280' => 'fve', 'FvH4_6g46380' => 'fve', 'FvH4_7g12841' => 'fve', 'FvH4_7g31431' => 'fve', 'Glyma.09G075900' => 'gma', 'Gohir.A09G096401' => 'ghi', 'Gohir.D09G096101' => 'ghi', 'Gorai.006G112800' => 'gra', 'HanXRQChr04g0121411' => 'han', 'Hund15878' => 'sun', 'Lj2A1107G68' => 'lonja', 'Lj2A630G63' => 'lonja', 'Lj2A946T25' => 'lonja', 'Lj2C714T1' => 'lonja', 'Lj2C966T3' => 'lonja', 'Lj2C966T4' => 'lonja', 'Lj4g0002979' => 'lja', 'Lsat_1_v5_gn_5_30901' => 'lsa', 'Lsat_1_v5_gn_5_31100' => 'lsa', 'Lsat_1_v5_gn_5_38600' => 'lsa', 'Lsat_1_v5_gn_6_92061' => 'lsa', 'Manes.05G071301' => 'mes', 'MD02G1008700' => 'mdo', 'MD02G1008900' => 'mdo', 'MD03G1256400' => 'mdo', 'MD04G1180900' => 'mdo', 'MD04G1181000' => 'mdo', 'MD04G1181200' => 'mdo', 'MD05G1244200' => 'mdo', 'MD05G1324200' => 'mdo', 'MD09G1201600' => 'mdo', 'MD10G1000600' => 'mdo', 'MD14G1026900' => 'mdo', 'MD14G1187900' => 'mdo', 'MD15G1017800' => 'mdo', 'MD15G1018100' => 'mdo', 'Medtr4g124160' => 'mtr', 'Migut.L01260' => 'egut', 'Nitab4.5_0000008g0440' => 'nta', 'Nitab4.5_0000207g0170' => 'nta', 'Nitab4.5_0007671g0030' => 'nta', 'Nitab4.5_0010853g0020' => 'nta', 'Oeu057656.1' => 'oeu', 'PGSC0003DMG400005638' => 'stu', 'PGSC0003DMG400005639' => 'stu', 'Phvul.009G222800' => 'pvu', 'Potri.009G132400' => 'ptr', 'Potri.009G163001' => 'ptr', 'Potri.011G000700' => 'ptr', 'Potri.011G004800' => 'ptr', 'Prupe.1G509300' => 'ppe', 'Prupe.1G509700' => 'ppe', 'Prupe.1G510400' => 'ppe', 'Prupe.1G510700' => 'ppe', 'Prupe.1G512600' => 'ppe', 'Prupe.2G073200' => 'ppe', 'Prupe.3G059500' => 'ppe', 'Prupe.3G059600' => 'ppe', 'Prupe.3G246100' => 'ppe', 'Prupe.3G265100' => 'ppe', 'Prupe.4G034700' => 'ppe', 'Prupe.4G052100' => 'ppe', 'Prupe.4G053600' => 'ppe', 'Prupe.5G068800' => 'ppe', 'Prupe.5G070600' => 'ppe', 'Prupe.6G075400' => 'ppe', 'Prupe.6G075500' => 'ppe', 'Prupe.6G076400' => 'ppe', 'Prupe.8G110700' => 'ppe', 'Psat4g020960' => 'psa', 'PSO135G0788' => 'pso', 'PSO210G6463' => 'pso', 'PSO384G0370' => 'pso', 'PSO386G0056' => 'pso', 'QL01p006048' => 'qlo', 'QL02p054283' => 'qlo', 'QL05p008000' => 'qlo', 'QL05p008212' => 'qlo', 'QL05p008950' => 'qlo', 'QL05p009042' => 'qlo', 'QL05p009518' => 'qlo', 'QL05p012589' => 'qlo', 'QL05p012608' => 'qlo', 'QL05p012650' => 'qlo', 'QL05p012667' => 'qlo', 'QL05p014501' => 'qlo', 'QL05p052800' => 'qlo', 'QL05p065010' => 'qlo', 'QL05p074156' => 'qlo', 'QL05p074160' => 'qlo', 'QL05p074174' => 'qlo', 'QL05p074178' => 'qlo', 'QL05p074214' => 'qlo', 'QL06p001050' => 'qlo', 'QL06p001056' => 'qlo', 'QL06p006093' => 'qlo', 'QL06p006111' => 'qlo', 'QL07p019784' => 'qlo', 'QL07p019801' => 'qlo', 'QL07p036110' => 'qlo', 'QL07p036134' => 'qlo', 'QL07p036147' => 'qlo', 'QL07p036156' => 'qlo', 'QL07p036300' => 'qlo', 'QL07p036320' => 'qlo', 'QL08p014547' => 'qlo', 'QL08p014551' => 'qlo', 'QL08p043319' => 'qlo', 'QL08p043324' => 'qlo', 'QL11p009094' => 'qlo', 'RcHm_v2.0_Chr1g0380481' => 'rch', 'RcHm_v2.0_Chr2g0089331' => 'rch', 'RcHm_v2.0_Chr2g0123691' => 'rch', 'RcHm_v2.0_Chr2g0151111' => 'rch', 'RcHm_v2.0_Chr2g0163011' => 'rch', 'RcHm_v2.0_Chr2g0163051' => 'rch', 'RcHm_v2.0_Chr2g0164671' => 'rch', 'RcHm_v2.0_Chr2g0164681' => 'rch', 'RcHm_v2.0_Chr2g0164721' => 'rch', 'RcHm_v2.0_Chr3g0449911' => 'rch', 'RcHm_v2.0_Chr3g0450211' => 'rch', 'RcHm_v2.0_Chr3g0457271' => 'rch', 'RcHm_v2.0_Chr5g0018111' => 'rch', 'RcHm_v2.0_Chr5g0021011' => 'rch', 'RcHm_v2.0_Chr5g0081171' => 'rch', 'RcHm_v2.0_Chr5g0081211' => 'rch', 'RcHm_v2.0_Chr6g0275871' => 'rch', 'RcHm_v2.0_Chr6g0276071' => 'rch', 'RcHm_v2.0_Chr6g0285591' => 'rch', 'RcHm_v2.0_Chr6g0291931' => 'rch', 'RcHm_v2.0_Chr6g0292091' => 'rch', 'RcHm_v2.0_Chr6g0292271' => 'rch', 'RcHm_v2.0_Chr7g0221261' => 'rch', 'Rhsim08G0219900' => 'rsi', 'Rhsim08G0220200' => 'rsi', 'Rhsim08G0237800' => 'rsi', 'Rhsim08G0238800' => 'rsi', 'Sabra09G0102700' => 'sbr', 'Sabra09G0127200' => 'sbr', 'Sabra11G0003700' => 'sbr', 'Sabra15G0014700' => 'sbr', 'Sc19g0000590' => 'sci', 'Sc19g0001870' => 'sci', 'SGA_v2.0_scaffold1G00346' => 'sas', 'SGA_v2.0_scaffold1G00575' => 'sas', 'SGA_v2.0_scaffold1G00761' => 'sas', 'SGA_v2.0_scaffold232G43501' => 'sas', 'TAR625G1137' => 'tar', 'Thecc.03G222100' => 'tca', 'TPR.G12691' => 'tpr', 'TWI34G0727' => 'twi', 'TWI36G0117' => 'twi', 'VMungo1309G0868' => 'vmu' ) $gf_id = 'HOM05D001729' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001729' ) $data_identifier = 'HOM05D001729' $data_type = 'gf_id' $species_gene_counts = array( 'amhyb' => (int) 1, 'cqu' => (int) 9, 'can' => (int) 1, 'cansat' => (int) 1, 'car' => (int) 1, 'col' => (int) 5, 'dca' => (int) 1, 'din' => (int) 2, 'dzi' => (int) 3, 'fan' => (int) 140, 'fve' => (int) 62, 'gma' => (int) 1, 'ghi' => (int) 2, 'gra' => (int) 1, 'han' => (int) 1, 'sun' => (int) 1, 'lonja' => (int) 6, 'lja' => (int) 1, 'lsa' => (int) 4, 'mes' => (int) 1, 'mdo' => (int) 14, 'mtr' => (int) 1, 'egut' => (int) 1, 'nta' => (int) 4, 'oeu' => (int) 1, 'stu' => (int) 2, 'pvu' => (int) 1, 'ptr' => (int) 4, 'ppe' => (int) 19, 'psa' => (int) 1, 'pso' => (int) 4, 'qlo' => (int) 36, 'rch' => (int) 23, 'rsi' => (int) 4, 'sbr' => (int) 4, 'sci' => (int) 2, 'sas' => (int) 4, 'tar' => (int) 1, 'tca' => (int) 1, 'tpr' => (int) 1, 'twi' => (int) 2, 'vmu' => (int) 1 ) $gf_gene_species = 'vmu' $gf_gene_id = 'VMungo1309G0868' $species_info = array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ) $local_species = 'amhyb' $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' => 'HOM05D001729', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '375', 'num_species' => '42' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'Ah.07g204710' => 'amhyb', 'AUR62006001' => 'cqu', 'AUR62006002' => 'cqu', 'AUR62006003' => 'cqu', 'AUR62015641' => 'cqu', 'AUR62027174' => 'cqu', 'AUR62035623' => 'cqu', 'AUR62035624' => 'cqu', 'AUR62035625' => 'cqu', 'AUR62035626' => 'cqu', 'CAN.G1110.53' => 'can', 'CANSAT80G0415' => 'cansat', 'Ca_21364_v3' => 'car', 'COL.COLO4_30693' => 'col', 'COL.COLO4_30694' => 'col', 'COL.COLO4_30695' => 'col', 'COL.COLO4_30696' => 'col', 'COL.COLO4_34020' => 'col', 'DCAR_004585' => 'dca', 'Dinv04029' => 'din', 'Dinv34857' => 'din', 'Duzib147G0011' => 'dzi', 'Duzib170G0599' => 'dzi', 'Duzib192G1051' => 'dzi', 'FAN01G0708' => 'fan', 'FAN01G0742' => 'fan', 'FAN02G0048' => 'fan', 'FAN02G0583' => 'fan', 'FAN02G0688' => 'fan', 'FAN02G1588' => 'fan', 'FAN02G2194' => 'fan', 'FAN02G2750' => 'fan', 'FAN02G3094' => 'fan', 'FAN02G3887' => 'fan', 'FAN02G3911' => 'fan', 'FAN02G3994' => 'fan', 'FAN02G4432' => 'fan', 'FAN02G4556' => 'fan', 'FAN03G1977' => 'fan', 'FAN03G2781' => 'fan', 'FAN03G2850' => 'fan', 'FAN03G3155' => 'fan', 'FAN04G2487' => 'fan', 'FAN05G0208' => 'fan', 'FAN05G0656' => 'fan', 'FAN05G0696' => 'fan', 'FAN05G0810' => 'fan', 'FAN05G1447' => 'fan', 'FAN05G2640' => 'fan', 'FAN05G2911' => 'fan', 'FAN05G3901' => 'fan', 'FAN05G4859' => 'fan', 'FAN05G4861' => 'fan', 'FAN05G4988' => 'fan', 'FAN05G5187' => 'fan', 'FAN05G5452' => 'fan', 'FAN05G5500' => 'fan', 'FAN05G5688' => 'fan', 'FAN06G0177' => 'fan', 'FAN06G0675' => 'fan', 'FAN06G1290' => 'fan', 'FAN06G2191' => 'fan', 'FAN06G2405' => 'fan', 'FAN06G3231' => 'fan', 'FAN06G3932' => 'fan', 'FAN07G0163' => 'fan', 'FAN07G0471' => 'fan', 'FAN07G1354' => 'fan', 'FAN08G0338' => 'fan', 'FAN08G1373' => 'fan', 'FAN08G2539' => 'fan', 'FAN08G2728' => 'fan', 'FAN09G0608' => 'fan', 'FAN09G1136' => 'fan', 'FAN09G1958' => 'fan', 'FAN09G2508' => 'fan', 'FAN09G2597' => 'fan', 'FAN09G2658' => 'fan', 'FAN09G2757' => 'fan', 'FAN09G2983' => 'fan', 'FAN09G3130' => 'fan', 'FAN09G3565' => 'fan', 'FAN09G3613' => 'fan', 'FAN09G4011' => 'fan', 'FAN09G4239' => 'fan', 'FAN09G4277' => 'fan', 'FAN09G4720' => 'fan', 'FAN11G0139' => 'fan', 'FAN11G1727' => 'fan', 'FAN11G2672' => 'fan', 'FAN11G2795' => 'fan', 'FAN11G3238' => 'fan', 'FAN11G3734' => 'fan', 'FAN12G0631' => 'fan', 'FAN12G2239' => 'fan', 'FAN12G2308' => 'fan', 'FAN12G2569' => 'fan', 'FAN12G2623' => 'fan', 'FAN13G3182' => 'fan', 'FAN14G0053' => 'fan', 'FAN14G0370' => 'fan', 'FAN14G0382' => 'fan', 'FAN14G0421' => 'fan', 'FAN14G0866' => 'fan', 'FAN14G1187' => 'fan', 'FAN14G1727' => 'fan', 'FAN14G1791' => 'fan', 'FAN14G2361' => 'fan', 'FAN14G2668' => 'fan', 'FAN14G2770' => 'fan', 'FAN14G2874' => 'fan', 'FAN14G3193' => 'fan', 'FAN14G3624' => 'fan', 'FAN14G3676' => 'fan', 'FAN14G3807' => 'fan', 'FAN14G4082' => 'fan', 'FAN14G4342' => 'fan', 'FAN14G4985' => 'fan', 'FAN14G5126' => 'fan', 'FAN14G5781' => 'fan', 'FAN14G5808' => 'fan', 'FAN14G5949' => 'fan', 'FAN15G0828' => 'fan', 'FAN15G1054' => 'fan', 'FAN15G2023' => 'fan', 'FAN15G2506' => 'fan', 'FAN16G0128' => 'fan', 'FAN16G0249' => 'fan', 'FAN16G0429' => 'fan', 'FAN16G1493' => 'fan', 'FAN16G2210' => 'fan', 'FAN16G2506' => 'fan', 'FAN18G1542' => 'fan', 'FAN18G4057' => 'fan', 'FAN19G0745' => 'fan', 'FAN19G1216' => 'fan', 'FAN19G1733' => 'fan', 'FAN20G0258' => 'fan', 'FAN20G1095' => 'fan', 'FAN20G1557' => 'fan', 'FAN21G0302' => 'fan', 'FAN21G0519' => 'fan', 'FAN21G0970' => 'fan', 'FAN21G1159' => 'fan', 'FAN21G1312' => 'fan', 'FAN21G1440' => 'fan', 'FAN21G1715' => 'fan', 'FAN23G1584' => 'fan', 'FAN24G0045' => 'fan', 'FAN24G0053' => 'fan', 'FAN24G1500' => 'fan', 'FAN24G1817' => 'fan', 'FAN24G2147' => 'fan', 'FAN24G2236' => 'fan', 'FAN24G2446' => 'fan', 'FAN24G2684' => 'fan', 'FAN25G0187' => 'fan', 'FAN25G0505' => 'fan', 'FAN25G0589' => 'fan', 'FAN25G3663' => 'fan', 'FAN26G1025' => 'fan', 'FAN26G2860' => 'fan', 'FAN27G1329' => 'fan', 'FAN27G3392' => 'fan', 'FvH4_1g02011' => 'fve', 'FvH4_1g06511' => 'fve', 'FvH4_2g19900' => 'fve', 'FvH4_2g19920' => 'fve', 'FvH4_2g24261' => 'fve', 'FvH4_2g24270' => 'fve', 'FvH4_2g24631' => 'fve', 'FvH4_2g30622' => 'fve', 'FvH4_3g12920' => 'fve', 'FvH4_3g30171' => 'fve', 'FvH4_3g35490' => 'fve', 'FvH4_3g43682' => 'fve', 'FvH4_3g43730' => 'fve', 'FvH4_3g43732' => 'fve', 'FvH4_3g43751' => 'fve', 'FvH4_3g43752' => 'fve', 'FvH4_3g43770' => 'fve', 'FvH4_3g44471' => 'fve', 'FvH4_3g44510' => 'fve', 'FvH4_3g44582' => 'fve', 'FvH4_4g16921' => 'fve', 'FvH4_4g17121' => 'fve', 'FvH4_4g17782' => 'fve', 'FvH4_4g17783' => 'fve', 'FvH4_4g18120' => 'fve', 'FvH4_4g31310' => 'fve', 'FvH4_4g35052' => 'fve', 'FvH4_5g30862' => 'fve', 'FvH4_6g01541' => 'fve', 'FvH4_6g02021' => 'fve', 'FvH4_6g02041' => 'fve', 'FvH4_6g02071' => 'fve', 'FvH4_6g02171' => 'fve', 'FvH4_6g03181' => 'fve', 'FvH4_6g03182' => 'fve', 'FvH4_6g03221' => 'fve', 'FvH4_6g03380' => 'fve', 'FvH4_6g05201' => 'fve', 'FvH4_6g05203' => 'fve', 'FvH4_6g20231' => 'fve', 'FvH4_6g31981' => 'fve', 'FvH4_6g32061' => 'fve', 'FvH4_6g37041' => 'fve', 'FvH4_6g37932' => 'fve', 'FvH4_6g38731' => 'fve', 'FvH4_6g39370' => 'fve', 'FvH4_6g39371' => 'fve', 'FvH4_6g40891' => 'fve', 'FvH4_6g40892' => 'fve', 'FvH4_6g43143' => 'fve', 'FvH4_6g45251' => 'fve', 'FvH4_6g45260' => 'fve', 'FvH4_6g45291' => 'fve', 'FvH4_6g45890' => 'fve', 'FvH4_6g46240' => 'fve', 'FvH4_6g46241' => 'fve', 'FvH4_6g46242' => 'fve', 'FvH4_6g46260' => 'fve', 'FvH4_6g46280' => 'fve', 'FvH4_6g46380' => 'fve', 'FvH4_7g12841' => 'fve', 'FvH4_7g31431' => 'fve', 'Glyma.09G075900' => 'gma', 'Gohir.A09G096401' => 'ghi', 'Gohir.D09G096101' => 'ghi', 'Gorai.006G112800' => 'gra', 'HanXRQChr04g0121411' => 'han', 'Hund15878' => 'sun', 'Lj2A1107G68' => 'lonja', 'Lj2A630G63' => 'lonja', 'Lj2A946T25' => 'lonja', 'Lj2C714T1' => 'lonja', 'Lj2C966T3' => 'lonja', 'Lj2C966T4' => 'lonja', 'Lj4g0002979' => 'lja', 'Lsat_1_v5_gn_5_30901' => 'lsa', 'Lsat_1_v5_gn_5_31100' => 'lsa', 'Lsat_1_v5_gn_5_38600' => 'lsa', 'Lsat_1_v5_gn_6_92061' => 'lsa', 'Manes.05G071301' => 'mes', 'MD02G1008700' => 'mdo', 'MD02G1008900' => 'mdo', 'MD03G1256400' => 'mdo', 'MD04G1180900' => 'mdo', 'MD04G1181000' => 'mdo', 'MD04G1181200' => 'mdo', 'MD05G1244200' => 'mdo', 'MD05G1324200' => 'mdo', 'MD09G1201600' => 'mdo', 'MD10G1000600' => 'mdo', 'MD14G1026900' => 'mdo', 'MD14G1187900' => 'mdo', 'MD15G1017800' => 'mdo', 'MD15G1018100' => 'mdo', 'Medtr4g124160' => 'mtr', 'Migut.L01260' => 'egut', 'Nitab4.5_0000008g0440' => 'nta', 'Nitab4.5_0000207g0170' => 'nta', 'Nitab4.5_0007671g0030' => 'nta', 'Nitab4.5_0010853g0020' => 'nta', 'Oeu057656.1' => 'oeu', 'PGSC0003DMG400005638' => 'stu', 'PGSC0003DMG400005639' => 'stu', 'Phvul.009G222800' => 'pvu', 'Potri.009G132400' => 'ptr', 'Potri.009G163001' => 'ptr', 'Potri.011G000700' => 'ptr', 'Potri.011G004800' => 'ptr', 'Prupe.1G509300' => 'ppe', 'Prupe.1G509700' => 'ppe', 'Prupe.1G510400' => 'ppe', 'Prupe.1G510700' => 'ppe', 'Prupe.1G512600' => 'ppe', 'Prupe.2G073200' => 'ppe', 'Prupe.3G059500' => 'ppe', 'Prupe.3G059600' => 'ppe', 'Prupe.3G246100' => 'ppe', 'Prupe.3G265100' => 'ppe', 'Prupe.4G034700' => 'ppe', 'Prupe.4G052100' => 'ppe', 'Prupe.4G053600' => 'ppe', 'Prupe.5G068800' => 'ppe', 'Prupe.5G070600' => 'ppe', 'Prupe.6G075400' => 'ppe', 'Prupe.6G075500' => 'ppe', 'Prupe.6G076400' => 'ppe', 'Prupe.8G110700' => 'ppe', 'Psat4g020960' => 'psa', 'PSO135G0788' => 'pso', 'PSO210G6463' => 'pso', 'PSO384G0370' => 'pso', 'PSO386G0056' => 'pso', 'QL01p006048' => 'qlo', 'QL02p054283' => 'qlo', 'QL05p008000' => 'qlo', 'QL05p008212' => 'qlo', 'QL05p008950' => 'qlo', 'QL05p009042' => 'qlo', 'QL05p009518' => 'qlo', 'QL05p012589' => 'qlo', 'QL05p012608' => 'qlo', 'QL05p012650' => 'qlo', 'QL05p012667' => 'qlo', 'QL05p014501' => 'qlo', 'QL05p052800' => 'qlo', 'QL05p065010' => 'qlo', 'QL05p074156' => 'qlo', 'QL05p074160' => 'qlo', 'QL05p074174' => 'qlo', 'QL05p074178' => 'qlo', 'QL05p074214' => 'qlo', 'QL06p001050' => 'qlo', 'QL06p001056' => 'qlo', 'QL06p006093' => 'qlo', 'QL06p006111' => 'qlo', 'QL07p019784' => 'qlo', 'QL07p019801' => 'qlo', 'QL07p036110' => 'qlo', 'QL07p036134' => 'qlo', 'QL07p036147' => 'qlo', 'QL07p036156' => 'qlo', 'QL07p036300' => 'qlo', 'QL07p036320' => 'qlo', 'QL08p014547' => 'qlo', 'QL08p014551' => 'qlo', 'QL08p043319' => 'qlo', 'QL08p043324' => 'qlo', 'QL11p009094' => 'qlo', 'RcHm_v2.0_Chr1g0380481' => 'rch', 'RcHm_v2.0_Chr2g0089331' => 'rch', 'RcHm_v2.0_Chr2g0123691' => 'rch', 'RcHm_v2.0_Chr2g0151111' => 'rch', 'RcHm_v2.0_Chr2g0163011' => 'rch', 'RcHm_v2.0_Chr2g0163051' => 'rch', 'RcHm_v2.0_Chr2g0164671' => 'rch', 'RcHm_v2.0_Chr2g0164681' => 'rch', 'RcHm_v2.0_Chr2g0164721' => 'rch', 'RcHm_v2.0_Chr3g0449911' => 'rch', 'RcHm_v2.0_Chr3g0450211' => 'rch', 'RcHm_v2.0_Chr3g0457271' => 'rch', 'RcHm_v2.0_Chr5g0018111' => 'rch', 'RcHm_v2.0_Chr5g0021011' => 'rch', 'RcHm_v2.0_Chr5g0081171' => 'rch', 'RcHm_v2.0_Chr5g0081211' => 'rch', 'RcHm_v2.0_Chr6g0275871' => 'rch', 'RcHm_v2.0_Chr6g0276071' => 'rch', 'RcHm_v2.0_Chr6g0285591' => 'rch', 'RcHm_v2.0_Chr6g0291931' => 'rch', 'RcHm_v2.0_Chr6g0292091' => 'rch', 'RcHm_v2.0_Chr6g0292271' => 'rch', 'RcHm_v2.0_Chr7g0221261' => 'rch', 'Rhsim08G0219900' => 'rsi', 'Rhsim08G0220200' => 'rsi', 'Rhsim08G0237800' => 'rsi', 'Rhsim08G0238800' => 'rsi', 'Sabra09G0102700' => 'sbr', 'Sabra09G0127200' => 'sbr', 'Sabra11G0003700' => 'sbr', 'Sabra15G0014700' => 'sbr', 'Sc19g0000590' => 'sci', 'Sc19g0001870' => 'sci', 'SGA_v2.0_scaffold1G00346' => 'sas', 'SGA_v2.0_scaffold1G00575' => 'sas', 'SGA_v2.0_scaffold1G00761' => 'sas', 'SGA_v2.0_scaffold232G43501' => 'sas', 'TAR625G1137' => 'tar', 'Thecc.03G222100' => 'tca', 'TPR.G12691' => 'tpr', 'TWI34G0727' => 'twi', 'TWI36G0117' => 'twi', 'VMungo1309G0868' => 'vmu' ), 'gf_id' => 'HOM05D001729', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001729' ), 'data_identifier' => 'HOM05D001729', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001729', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '375', 'num_species' => '42' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'Ah.07g204710' => 'amhyb', 'AUR62006001' => 'cqu', 'AUR62006002' => 'cqu', 'AUR62006003' => 'cqu', 'AUR62015641' => 'cqu', 'AUR62027174' => 'cqu', 'AUR62035623' => 'cqu', 'AUR62035624' => 'cqu', 'AUR62035625' => 'cqu', 'AUR62035626' => 'cqu', 'CAN.G1110.53' => 'can', 'CANSAT80G0415' => 'cansat', 'Ca_21364_v3' => 'car', 'COL.COLO4_30693' => 'col', 'COL.COLO4_30694' => 'col', 'COL.COLO4_30695' => 'col', 'COL.COLO4_30696' => 'col', 'COL.COLO4_34020' => 'col', 'DCAR_004585' => 'dca', 'Dinv04029' => 'din', 'Dinv34857' => 'din', 'Duzib147G0011' => 'dzi', 'Duzib170G0599' => 'dzi', 'Duzib192G1051' => 'dzi', 'FAN01G0708' => 'fan', 'FAN01G0742' => 'fan', 'FAN02G0048' => 'fan', 'FAN02G0583' => 'fan', 'FAN02G0688' => 'fan', 'FAN02G1588' => 'fan', 'FAN02G2194' => 'fan', 'FAN02G2750' => 'fan', 'FAN02G3094' => 'fan', 'FAN02G3887' => 'fan', 'FAN02G3911' => 'fan', 'FAN02G3994' => 'fan', 'FAN02G4432' => 'fan', 'FAN02G4556' => 'fan', 'FAN03G1977' => 'fan', 'FAN03G2781' => 'fan', 'FAN03G2850' => 'fan', 'FAN03G3155' => 'fan', 'FAN04G2487' => 'fan', 'FAN05G0208' => 'fan', 'FAN05G0656' => 'fan', 'FAN05G0696' => 'fan', 'FAN05G0810' => 'fan', 'FAN05G1447' => 'fan', 'FAN05G2640' => 'fan', 'FAN05G2911' => 'fan', 'FAN05G3901' => 'fan', 'FAN05G4859' => 'fan', 'FAN05G4861' => 'fan', 'FAN05G4988' => 'fan', 'FAN05G5187' => 'fan', 'FAN05G5452' => 'fan', 'FAN05G5500' => 'fan', 'FAN05G5688' => 'fan', 'FAN06G0177' => 'fan', 'FAN06G0675' => 'fan', 'FAN06G1290' => 'fan', 'FAN06G2191' => 'fan', 'FAN06G2405' => 'fan', 'FAN06G3231' => 'fan', 'FAN06G3932' => 'fan', 'FAN07G0163' => 'fan', 'FAN07G0471' => 'fan', 'FAN07G1354' => 'fan', 'FAN08G0338' => 'fan', 'FAN08G1373' => 'fan', 'FAN08G2539' => 'fan', 'FAN08G2728' => 'fan', 'FAN09G0608' => 'fan', 'FAN09G1136' => 'fan', 'FAN09G1958' => 'fan', 'FAN09G2508' => 'fan', 'FAN09G2597' => 'fan', 'FAN09G2658' => 'fan', 'FAN09G2757' => 'fan', 'FAN09G2983' => 'fan', 'FAN09G3130' => 'fan', 'FAN09G3565' => 'fan', 'FAN09G3613' => 'fan', 'FAN09G4011' => 'fan', 'FAN09G4239' => 'fan', 'FAN09G4277' => 'fan', 'FAN09G4720' => 'fan', 'FAN11G0139' => 'fan', 'FAN11G1727' => 'fan', 'FAN11G2672' => 'fan', 'FAN11G2795' => 'fan', 'FAN11G3238' => 'fan', 'FAN11G3734' => 'fan', 'FAN12G0631' => 'fan', 'FAN12G2239' => 'fan', 'FAN12G2308' => 'fan', 'FAN12G2569' => 'fan', 'FAN12G2623' => 'fan', 'FAN13G3182' => 'fan', 'FAN14G0053' => 'fan', 'FAN14G0370' => 'fan', 'FAN14G0382' => 'fan', 'FAN14G0421' => 'fan', 'FAN14G0866' => 'fan', 'FAN14G1187' => 'fan', 'FAN14G1727' => 'fan', 'FAN14G1791' => 'fan', 'FAN14G2361' => 'fan', 'FAN14G2668' => 'fan', 'FAN14G2770' => 'fan', 'FAN14G2874' => 'fan', 'FAN14G3193' => 'fan', 'FAN14G3624' => 'fan', 'FAN14G3676' => 'fan', 'FAN14G3807' => 'fan', 'FAN14G4082' => 'fan', 'FAN14G4342' => 'fan', 'FAN14G4985' => 'fan', 'FAN14G5126' => 'fan', 'FAN14G5781' => 'fan', 'FAN14G5808' => 'fan', 'FAN14G5949' => 'fan', 'FAN15G0828' => 'fan', 'FAN15G1054' => 'fan', 'FAN15G2023' => 'fan', 'FAN15G2506' => 'fan', 'FAN16G0128' => 'fan', 'FAN16G0249' => 'fan', 'FAN16G0429' => 'fan', 'FAN16G1493' => 'fan', 'FAN16G2210' => 'fan', 'FAN16G2506' => 'fan', 'FAN18G1542' => 'fan', 'FAN18G4057' => 'fan', 'FAN19G0745' => 'fan', 'FAN19G1216' => 'fan', 'FAN19G1733' => 'fan', 'FAN20G0258' => 'fan', 'FAN20G1095' => 'fan', 'FAN20G1557' => 'fan', 'FAN21G0302' => 'fan', 'FAN21G0519' => 'fan', 'FAN21G0970' => 'fan', 'FAN21G1159' => 'fan', 'FAN21G1312' => 'fan', 'FAN21G1440' => 'fan', 'FAN21G1715' => 'fan', 'FAN23G1584' => 'fan', 'FAN24G0045' => 'fan', 'FAN24G0053' => 'fan', 'FAN24G1500' => 'fan', 'FAN24G1817' => 'fan', 'FAN24G2147' => 'fan', 'FAN24G2236' => 'fan', 'FAN24G2446' => 'fan', 'FAN24G2684' => 'fan', 'FAN25G0187' => 'fan', 'FAN25G0505' => 'fan', 'FAN25G0589' => 'fan', 'FAN25G3663' => 'fan', 'FAN26G1025' => 'fan', 'FAN26G2860' => 'fan', 'FAN27G1329' => 'fan', 'FAN27G3392' => 'fan', 'FvH4_1g02011' => 'fve', 'FvH4_1g06511' => 'fve', 'FvH4_2g19900' => 'fve', 'FvH4_2g19920' => 'fve', 'FvH4_2g24261' => 'fve', 'FvH4_2g24270' => 'fve', 'FvH4_2g24631' => 'fve', 'FvH4_2g30622' => 'fve', 'FvH4_3g12920' => 'fve', 'FvH4_3g30171' => 'fve', 'FvH4_3g35490' => 'fve', 'FvH4_3g43682' => 'fve', 'FvH4_3g43730' => 'fve', 'FvH4_3g43732' => 'fve', 'FvH4_3g43751' => 'fve', 'FvH4_3g43752' => 'fve', 'FvH4_3g43770' => 'fve', 'FvH4_3g44471' => 'fve', 'FvH4_3g44510' => 'fve', 'FvH4_3g44582' => 'fve', 'FvH4_4g16921' => 'fve', 'FvH4_4g17121' => 'fve', 'FvH4_4g17782' => 'fve', 'FvH4_4g17783' => 'fve', 'FvH4_4g18120' => 'fve', 'FvH4_4g31310' => 'fve', 'FvH4_4g35052' => 'fve', 'FvH4_5g30862' => 'fve', 'FvH4_6g01541' => 'fve', 'FvH4_6g02021' => 'fve', 'FvH4_6g02041' => 'fve', 'FvH4_6g02071' => 'fve', 'FvH4_6g02171' => 'fve', 'FvH4_6g03181' => 'fve', 'FvH4_6g03182' => 'fve', 'FvH4_6g03221' => 'fve', 'FvH4_6g03380' => 'fve', 'FvH4_6g05201' => 'fve', 'FvH4_6g05203' => 'fve', 'FvH4_6g20231' => 'fve', 'FvH4_6g31981' => 'fve', 'FvH4_6g32061' => 'fve', 'FvH4_6g37041' => 'fve', 'FvH4_6g37932' => 'fve', 'FvH4_6g38731' => 'fve', 'FvH4_6g39370' => 'fve', 'FvH4_6g39371' => 'fve', 'FvH4_6g40891' => 'fve', 'FvH4_6g40892' => 'fve', 'FvH4_6g43143' => 'fve', 'FvH4_6g45251' => 'fve', 'FvH4_6g45260' => 'fve', 'FvH4_6g45291' => 'fve', 'FvH4_6g45890' => 'fve', 'FvH4_6g46240' => 'fve', 'FvH4_6g46241' => 'fve', 'FvH4_6g46242' => 'fve', 'FvH4_6g46260' => 'fve', 'FvH4_6g46280' => 'fve', 'FvH4_6g46380' => 'fve', 'FvH4_7g12841' => 'fve', 'FvH4_7g31431' => 'fve', 'Glyma.09G075900' => 'gma', 'Gohir.A09G096401' => 'ghi', 'Gohir.D09G096101' => 'ghi', 'Gorai.006G112800' => 'gra', 'HanXRQChr04g0121411' => 'han', 'Hund15878' => 'sun', 'Lj2A1107G68' => 'lonja', 'Lj2A630G63' => 'lonja', 'Lj2A946T25' => 'lonja', 'Lj2C714T1' => 'lonja', 'Lj2C966T3' => 'lonja', 'Lj2C966T4' => 'lonja', 'Lj4g0002979' => 'lja', 'Lsat_1_v5_gn_5_30901' => 'lsa', 'Lsat_1_v5_gn_5_31100' => 'lsa', 'Lsat_1_v5_gn_5_38600' => 'lsa', 'Lsat_1_v5_gn_6_92061' => 'lsa', 'Manes.05G071301' => 'mes', 'MD02G1008700' => 'mdo', 'MD02G1008900' => 'mdo', 'MD03G1256400' => 'mdo', 'MD04G1180900' => 'mdo', 'MD04G1181000' => 'mdo', 'MD04G1181200' => 'mdo', 'MD05G1244200' => 'mdo', 'MD05G1324200' => 'mdo', 'MD09G1201600' => 'mdo', 'MD10G1000600' => 'mdo', 'MD14G1026900' => 'mdo', 'MD14G1187900' => 'mdo', 'MD15G1017800' => 'mdo', 'MD15G1018100' => 'mdo', 'Medtr4g124160' => 'mtr', 'Migut.L01260' => 'egut', 'Nitab4.5_0000008g0440' => 'nta', 'Nitab4.5_0000207g0170' => 'nta', 'Nitab4.5_0007671g0030' => 'nta', 'Nitab4.5_0010853g0020' => 'nta', 'Oeu057656.1' => 'oeu', 'PGSC0003DMG400005638' => 'stu', 'PGSC0003DMG400005639' => 'stu', 'Phvul.009G222800' => 'pvu', 'Potri.009G132400' => 'ptr', 'Potri.009G163001' => 'ptr', 'Potri.011G000700' => 'ptr', 'Potri.011G004800' => 'ptr', 'Prupe.1G509300' => 'ppe', 'Prupe.1G509700' => 'ppe', 'Prupe.1G510400' => 'ppe', 'Prupe.1G510700' => 'ppe', 'Prupe.1G512600' => 'ppe', 'Prupe.2G073200' => 'ppe', 'Prupe.3G059500' => 'ppe', 'Prupe.3G059600' => 'ppe', 'Prupe.3G246100' => 'ppe', 'Prupe.3G265100' => 'ppe', 'Prupe.4G034700' => 'ppe', 'Prupe.4G052100' => 'ppe', 'Prupe.4G053600' => 'ppe', 'Prupe.5G068800' => 'ppe', 'Prupe.5G070600' => 'ppe', 'Prupe.6G075400' => 'ppe', 'Prupe.6G075500' => 'ppe', 'Prupe.6G076400' => 'ppe', 'Prupe.8G110700' => 'ppe', 'Psat4g020960' => 'psa', 'PSO135G0788' => 'pso', 'PSO210G6463' => 'pso', 'PSO384G0370' => 'pso', 'PSO386G0056' => 'pso', 'QL01p006048' => 'qlo', 'QL02p054283' => 'qlo', 'QL05p008000' => 'qlo', 'QL05p008212' => 'qlo', 'QL05p008950' => 'qlo', 'QL05p009042' => 'qlo', 'QL05p009518' => 'qlo', 'QL05p012589' => 'qlo', 'QL05p012608' => 'qlo', 'QL05p012650' => 'qlo', 'QL05p012667' => 'qlo', 'QL05p014501' => 'qlo', 'QL05p052800' => 'qlo', 'QL05p065010' => 'qlo', 'QL05p074156' => 'qlo', 'QL05p074160' => 'qlo', 'QL05p074174' => 'qlo', 'QL05p074178' => 'qlo', 'QL05p074214' => 'qlo', 'QL06p001050' => 'qlo', 'QL06p001056' => 'qlo', 'QL06p006093' => 'qlo', 'QL06p006111' => 'qlo', 'QL07p019784' => 'qlo', 'QL07p019801' => 'qlo', 'QL07p036110' => 'qlo', 'QL07p036134' => 'qlo', 'QL07p036147' => 'qlo', 'QL07p036156' => 'qlo', 'QL07p036300' => 'qlo', 'QL07p036320' => 'qlo', 'QL08p014547' => 'qlo', 'QL08p014551' => 'qlo', 'QL08p043319' => 'qlo', 'QL08p043324' => 'qlo', 'QL11p009094' => 'qlo', 'RcHm_v2.0_Chr1g0380481' => 'rch', 'RcHm_v2.0_Chr2g0089331' => 'rch', 'RcHm_v2.0_Chr2g0123691' => 'rch', 'RcHm_v2.0_Chr2g0151111' => 'rch', 'RcHm_v2.0_Chr2g0163011' => 'rch', 'RcHm_v2.0_Chr2g0163051' => 'rch', 'RcHm_v2.0_Chr2g0164671' => 'rch', 'RcHm_v2.0_Chr2g0164681' => 'rch', 'RcHm_v2.0_Chr2g0164721' => 'rch', 'RcHm_v2.0_Chr3g0449911' => 'rch', 'RcHm_v2.0_Chr3g0450211' => 'rch', 'RcHm_v2.0_Chr3g0457271' => 'rch', 'RcHm_v2.0_Chr5g0018111' => 'rch', 'RcHm_v2.0_Chr5g0021011' => 'rch', 'RcHm_v2.0_Chr5g0081171' => 'rch', 'RcHm_v2.0_Chr5g0081211' => 'rch', 'RcHm_v2.0_Chr6g0275871' => 'rch', 'RcHm_v2.0_Chr6g0276071' => 'rch', 'RcHm_v2.0_Chr6g0285591' => 'rch', 'RcHm_v2.0_Chr6g0291931' => 'rch', 'RcHm_v2.0_Chr6g0292091' => 'rch', 'RcHm_v2.0_Chr6g0292271' => 'rch', 'RcHm_v2.0_Chr7g0221261' => 'rch', 'Rhsim08G0219900' => 'rsi', 'Rhsim08G0220200' => 'rsi', 'Rhsim08G0237800' => 'rsi', 'Rhsim08G0238800' => 'rsi', 'Sabra09G0102700' => 'sbr', 'Sabra09G0127200' => 'sbr', 'Sabra11G0003700' => 'sbr', 'Sabra15G0014700' => 'sbr', 'Sc19g0000590' => 'sci', 'Sc19g0001870' => 'sci', 'SGA_v2.0_scaffold1G00346' => 'sas', 'SGA_v2.0_scaffold1G00575' => 'sas', 'SGA_v2.0_scaffold1G00761' => 'sas', 'SGA_v2.0_scaffold232G43501' => 'sas', 'TAR625G1137' => 'tar', 'Thecc.03G222100' => 'tca', 'TPR.G12691' => 'tpr', 'TWI34G0727' => 'twi', 'TWI36G0117' => 'twi', 'VMungo1309G0868' => 'vmu' ) $gf_id = 'HOM05D001729' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001729' ) $data_identifier = 'HOM05D001729' $data_type = 'gf_id' $species_gene_counts = array( 'amhyb' => (int) 1, 'cqu' => (int) 9, 'can' => (int) 1, 'cansat' => (int) 1, 'car' => (int) 1, 'col' => (int) 5, 'dca' => (int) 1, 'din' => (int) 2, 'dzi' => (int) 3, 'fan' => (int) 140, 'fve' => (int) 62, 'gma' => (int) 1, 'ghi' => (int) 2, 'gra' => (int) 1, 'han' => (int) 1, 'sun' => (int) 1, 'lonja' => (int) 6, 'lja' => (int) 1, 'lsa' => (int) 4, 'mes' => (int) 1, 'mdo' => (int) 14, 'mtr' => (int) 1, 'egut' => (int) 1, 'nta' => (int) 4, 'oeu' => (int) 1, 'stu' => (int) 2, 'pvu' => (int) 1, 'ptr' => (int) 4, 'ppe' => (int) 19, 'psa' => (int) 1, 'pso' => (int) 4, 'qlo' => (int) 36, 'rch' => (int) 23, 'rsi' => (int) 4, 'sbr' => (int) 4, 'sci' => (int) 2, 'sas' => (int) 4, 'tar' => (int) 1, 'tca' => (int) 1, 'tpr' => (int) 1, 'twi' => (int) 2, 'vmu' => (int) 1 ) $gf_gene_species = 'vmu' $gf_gene_id = 'VMungo1309G0868' $species_info = array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ) $local_species = 'cansat' $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' => 'HOM05D001729', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '375', 'num_species' => '42' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'Ah.07g204710' => 'amhyb', 'AUR62006001' => 'cqu', 'AUR62006002' => 'cqu', 'AUR62006003' => 'cqu', 'AUR62015641' => 'cqu', 'AUR62027174' => 'cqu', 'AUR62035623' => 'cqu', 'AUR62035624' => 'cqu', 'AUR62035625' => 'cqu', 'AUR62035626' => 'cqu', 'CAN.G1110.53' => 'can', 'CANSAT80G0415' => 'cansat', 'Ca_21364_v3' => 'car', 'COL.COLO4_30693' => 'col', 'COL.COLO4_30694' => 'col', 'COL.COLO4_30695' => 'col', 'COL.COLO4_30696' => 'col', 'COL.COLO4_34020' => 'col', 'DCAR_004585' => 'dca', 'Dinv04029' => 'din', 'Dinv34857' => 'din', 'Duzib147G0011' => 'dzi', 'Duzib170G0599' => 'dzi', 'Duzib192G1051' => 'dzi', 'FAN01G0708' => 'fan', 'FAN01G0742' => 'fan', 'FAN02G0048' => 'fan', 'FAN02G0583' => 'fan', 'FAN02G0688' => 'fan', 'FAN02G1588' => 'fan', 'FAN02G2194' => 'fan', 'FAN02G2750' => 'fan', 'FAN02G3094' => 'fan', 'FAN02G3887' => 'fan', 'FAN02G3911' => 'fan', 'FAN02G3994' => 'fan', 'FAN02G4432' => 'fan', 'FAN02G4556' => 'fan', 'FAN03G1977' => 'fan', 'FAN03G2781' => 'fan', 'FAN03G2850' => 'fan', 'FAN03G3155' => 'fan', 'FAN04G2487' => 'fan', 'FAN05G0208' => 'fan', 'FAN05G0656' => 'fan', 'FAN05G0696' => 'fan', 'FAN05G0810' => 'fan', 'FAN05G1447' => 'fan', 'FAN05G2640' => 'fan', 'FAN05G2911' => 'fan', 'FAN05G3901' => 'fan', 'FAN05G4859' => 'fan', 'FAN05G4861' => 'fan', 'FAN05G4988' => 'fan', 'FAN05G5187' => 'fan', 'FAN05G5452' => 'fan', 'FAN05G5500' => 'fan', 'FAN05G5688' => 'fan', 'FAN06G0177' => 'fan', 'FAN06G0675' => 'fan', 'FAN06G1290' => 'fan', 'FAN06G2191' => 'fan', 'FAN06G2405' => 'fan', 'FAN06G3231' => 'fan', 'FAN06G3932' => 'fan', 'FAN07G0163' => 'fan', 'FAN07G0471' => 'fan', 'FAN07G1354' => 'fan', 'FAN08G0338' => 'fan', 'FAN08G1373' => 'fan', 'FAN08G2539' => 'fan', 'FAN08G2728' => 'fan', 'FAN09G0608' => 'fan', 'FAN09G1136' => 'fan', 'FAN09G1958' => 'fan', 'FAN09G2508' => 'fan', 'FAN09G2597' => 'fan', 'FAN09G2658' => 'fan', 'FAN09G2757' => 'fan', 'FAN09G2983' => 'fan', 'FAN09G3130' => 'fan', 'FAN09G3565' => 'fan', 'FAN09G3613' => 'fan', 'FAN09G4011' => 'fan', 'FAN09G4239' => 'fan', 'FAN09G4277' => 'fan', 'FAN09G4720' => 'fan', 'FAN11G0139' => 'fan', 'FAN11G1727' => 'fan', 'FAN11G2672' => 'fan', 'FAN11G2795' => 'fan', 'FAN11G3238' => 'fan', 'FAN11G3734' => 'fan', 'FAN12G0631' => 'fan', 'FAN12G2239' => 'fan', 'FAN12G2308' => 'fan', 'FAN12G2569' => 'fan', 'FAN12G2623' => 'fan', 'FAN13G3182' => 'fan', 'FAN14G0053' => 'fan', 'FAN14G0370' => 'fan', 'FAN14G0382' => 'fan', 'FAN14G0421' => 'fan', 'FAN14G0866' => 'fan', 'FAN14G1187' => 'fan', 'FAN14G1727' => 'fan', 'FAN14G1791' => 'fan', 'FAN14G2361' => 'fan', 'FAN14G2668' => 'fan', 'FAN14G2770' => 'fan', 'FAN14G2874' => 'fan', 'FAN14G3193' => 'fan', 'FAN14G3624' => 'fan', 'FAN14G3676' => 'fan', 'FAN14G3807' => 'fan', 'FAN14G4082' => 'fan', 'FAN14G4342' => 'fan', 'FAN14G4985' => 'fan', 'FAN14G5126' => 'fan', 'FAN14G5781' => 'fan', 'FAN14G5808' => 'fan', 'FAN14G5949' => 'fan', 'FAN15G0828' => 'fan', 'FAN15G1054' => 'fan', 'FAN15G2023' => 'fan', 'FAN15G2506' => 'fan', 'FAN16G0128' => 'fan', 'FAN16G0249' => 'fan', 'FAN16G0429' => 'fan', 'FAN16G1493' => 'fan', 'FAN16G2210' => 'fan', 'FAN16G2506' => 'fan', 'FAN18G1542' => 'fan', 'FAN18G4057' => 'fan', 'FAN19G0745' => 'fan', 'FAN19G1216' => 'fan', 'FAN19G1733' => 'fan', 'FAN20G0258' => 'fan', 'FAN20G1095' => 'fan', 'FAN20G1557' => 'fan', 'FAN21G0302' => 'fan', 'FAN21G0519' => 'fan', 'FAN21G0970' => 'fan', 'FAN21G1159' => 'fan', 'FAN21G1312' => 'fan', 'FAN21G1440' => 'fan', 'FAN21G1715' => 'fan', 'FAN23G1584' => 'fan', 'FAN24G0045' => 'fan', 'FAN24G0053' => 'fan', 'FAN24G1500' => 'fan', 'FAN24G1817' => 'fan', 'FAN24G2147' => 'fan', 'FAN24G2236' => 'fan', 'FAN24G2446' => 'fan', 'FAN24G2684' => 'fan', 'FAN25G0187' => 'fan', 'FAN25G0505' => 'fan', 'FAN25G0589' => 'fan', 'FAN25G3663' => 'fan', 'FAN26G1025' => 'fan', 'FAN26G2860' => 'fan', 'FAN27G1329' => 'fan', 'FAN27G3392' => 'fan', 'FvH4_1g02011' => 'fve', 'FvH4_1g06511' => 'fve', 'FvH4_2g19900' => 'fve', 'FvH4_2g19920' => 'fve', 'FvH4_2g24261' => 'fve', 'FvH4_2g24270' => 'fve', 'FvH4_2g24631' => 'fve', 'FvH4_2g30622' => 'fve', 'FvH4_3g12920' => 'fve', 'FvH4_3g30171' => 'fve', 'FvH4_3g35490' => 'fve', 'FvH4_3g43682' => 'fve', 'FvH4_3g43730' => 'fve', 'FvH4_3g43732' => 'fve', 'FvH4_3g43751' => 'fve', 'FvH4_3g43752' => 'fve', 'FvH4_3g43770' => 'fve', 'FvH4_3g44471' => 'fve', 'FvH4_3g44510' => 'fve', 'FvH4_3g44582' => 'fve', 'FvH4_4g16921' => 'fve', 'FvH4_4g17121' => 'fve', 'FvH4_4g17782' => 'fve', 'FvH4_4g17783' => 'fve', 'FvH4_4g18120' => 'fve', 'FvH4_4g31310' => 'fve', 'FvH4_4g35052' => 'fve', 'FvH4_5g30862' => 'fve', 'FvH4_6g01541' => 'fve', 'FvH4_6g02021' => 'fve', 'FvH4_6g02041' => 'fve', 'FvH4_6g02071' => 'fve', 'FvH4_6g02171' => 'fve', 'FvH4_6g03181' => 'fve', 'FvH4_6g03182' => 'fve', 'FvH4_6g03221' => 'fve', 'FvH4_6g03380' => 'fve', 'FvH4_6g05201' => 'fve', 'FvH4_6g05203' => 'fve', 'FvH4_6g20231' => 'fve', 'FvH4_6g31981' => 'fve', 'FvH4_6g32061' => 'fve', 'FvH4_6g37041' => 'fve', 'FvH4_6g37932' => 'fve', 'FvH4_6g38731' => 'fve', 'FvH4_6g39370' => 'fve', 'FvH4_6g39371' => 'fve', 'FvH4_6g40891' => 'fve', 'FvH4_6g40892' => 'fve', 'FvH4_6g43143' => 'fve', 'FvH4_6g45251' => 'fve', 'FvH4_6g45260' => 'fve', 'FvH4_6g45291' => 'fve', 'FvH4_6g45890' => 'fve', 'FvH4_6g46240' => 'fve', 'FvH4_6g46241' => 'fve', 'FvH4_6g46242' => 'fve', 'FvH4_6g46260' => 'fve', 'FvH4_6g46280' => 'fve', 'FvH4_6g46380' => 'fve', 'FvH4_7g12841' => 'fve', 'FvH4_7g31431' => 'fve', 'Glyma.09G075900' => 'gma', 'Gohir.A09G096401' => 'ghi', 'Gohir.D09G096101' => 'ghi', 'Gorai.006G112800' => 'gra', 'HanXRQChr04g0121411' => 'han', 'Hund15878' => 'sun', 'Lj2A1107G68' => 'lonja', 'Lj2A630G63' => 'lonja', 'Lj2A946T25' => 'lonja', 'Lj2C714T1' => 'lonja', 'Lj2C966T3' => 'lonja', 'Lj2C966T4' => 'lonja', 'Lj4g0002979' => 'lja', 'Lsat_1_v5_gn_5_30901' => 'lsa', 'Lsat_1_v5_gn_5_31100' => 'lsa', 'Lsat_1_v5_gn_5_38600' => 'lsa', 'Lsat_1_v5_gn_6_92061' => 'lsa', 'Manes.05G071301' => 'mes', 'MD02G1008700' => 'mdo', 'MD02G1008900' => 'mdo', 'MD03G1256400' => 'mdo', 'MD04G1180900' => 'mdo', 'MD04G1181000' => 'mdo', 'MD04G1181200' => 'mdo', 'MD05G1244200' => 'mdo', 'MD05G1324200' => 'mdo', 'MD09G1201600' => 'mdo', 'MD10G1000600' => 'mdo', 'MD14G1026900' => 'mdo', 'MD14G1187900' => 'mdo', 'MD15G1017800' => 'mdo', 'MD15G1018100' => 'mdo', 'Medtr4g124160' => 'mtr', 'Migut.L01260' => 'egut', 'Nitab4.5_0000008g0440' => 'nta', 'Nitab4.5_0000207g0170' => 'nta', 'Nitab4.5_0007671g0030' => 'nta', 'Nitab4.5_0010853g0020' => 'nta', 'Oeu057656.1' => 'oeu', 'PGSC0003DMG400005638' => 'stu', 'PGSC0003DMG400005639' => 'stu', 'Phvul.009G222800' => 'pvu', 'Potri.009G132400' => 'ptr', 'Potri.009G163001' => 'ptr', 'Potri.011G000700' => 'ptr', 'Potri.011G004800' => 'ptr', 'Prupe.1G509300' => 'ppe', 'Prupe.1G509700' => 'ppe', 'Prupe.1G510400' => 'ppe', 'Prupe.1G510700' => 'ppe', 'Prupe.1G512600' => 'ppe', 'Prupe.2G073200' => 'ppe', 'Prupe.3G059500' => 'ppe', 'Prupe.3G059600' => 'ppe', 'Prupe.3G246100' => 'ppe', 'Prupe.3G265100' => 'ppe', 'Prupe.4G034700' => 'ppe', 'Prupe.4G052100' => 'ppe', 'Prupe.4G053600' => 'ppe', 'Prupe.5G068800' => 'ppe', 'Prupe.5G070600' => 'ppe', 'Prupe.6G075400' => 'ppe', 'Prupe.6G075500' => 'ppe', 'Prupe.6G076400' => 'ppe', 'Prupe.8G110700' => 'ppe', 'Psat4g020960' => 'psa', 'PSO135G0788' => 'pso', 'PSO210G6463' => 'pso', 'PSO384G0370' => 'pso', 'PSO386G0056' => 'pso', 'QL01p006048' => 'qlo', 'QL02p054283' => 'qlo', 'QL05p008000' => 'qlo', 'QL05p008212' => 'qlo', 'QL05p008950' => 'qlo', 'QL05p009042' => 'qlo', 'QL05p009518' => 'qlo', 'QL05p012589' => 'qlo', 'QL05p012608' => 'qlo', 'QL05p012650' => 'qlo', 'QL05p012667' => 'qlo', 'QL05p014501' => 'qlo', 'QL05p052800' => 'qlo', 'QL05p065010' => 'qlo', 'QL05p074156' => 'qlo', 'QL05p074160' => 'qlo', 'QL05p074174' => 'qlo', 'QL05p074178' => 'qlo', 'QL05p074214' => 'qlo', 'QL06p001050' => 'qlo', 'QL06p001056' => 'qlo', 'QL06p006093' => 'qlo', 'QL06p006111' => 'qlo', 'QL07p019784' => 'qlo', 'QL07p019801' => 'qlo', 'QL07p036110' => 'qlo', 'QL07p036134' => 'qlo', 'QL07p036147' => 'qlo', 'QL07p036156' => 'qlo', 'QL07p036300' => 'qlo', 'QL07p036320' => 'qlo', 'QL08p014547' => 'qlo', 'QL08p014551' => 'qlo', 'QL08p043319' => 'qlo', 'QL08p043324' => 'qlo', 'QL11p009094' => 'qlo', 'RcHm_v2.0_Chr1g0380481' => 'rch', 'RcHm_v2.0_Chr2g0089331' => 'rch', 'RcHm_v2.0_Chr2g0123691' => 'rch', 'RcHm_v2.0_Chr2g0151111' => 'rch', 'RcHm_v2.0_Chr2g0163011' => 'rch', 'RcHm_v2.0_Chr2g0163051' => 'rch', 'RcHm_v2.0_Chr2g0164671' => 'rch', 'RcHm_v2.0_Chr2g0164681' => 'rch', 'RcHm_v2.0_Chr2g0164721' => 'rch', 'RcHm_v2.0_Chr3g0449911' => 'rch', 'RcHm_v2.0_Chr3g0450211' => 'rch', 'RcHm_v2.0_Chr3g0457271' => 'rch', 'RcHm_v2.0_Chr5g0018111' => 'rch', 'RcHm_v2.0_Chr5g0021011' => 'rch', 'RcHm_v2.0_Chr5g0081171' => 'rch', 'RcHm_v2.0_Chr5g0081211' => 'rch', 'RcHm_v2.0_Chr6g0275871' => 'rch', 'RcHm_v2.0_Chr6g0276071' => 'rch', 'RcHm_v2.0_Chr6g0285591' => 'rch', 'RcHm_v2.0_Chr6g0291931' => 'rch', 'RcHm_v2.0_Chr6g0292091' => 'rch', 'RcHm_v2.0_Chr6g0292271' => 'rch', 'RcHm_v2.0_Chr7g0221261' => 'rch', 'Rhsim08G0219900' => 'rsi', 'Rhsim08G0220200' => 'rsi', 'Rhsim08G0237800' => 'rsi', 'Rhsim08G0238800' => 'rsi', 'Sabra09G0102700' => 'sbr', 'Sabra09G0127200' => 'sbr', 'Sabra11G0003700' => 'sbr', 'Sabra15G0014700' => 'sbr', 'Sc19g0000590' => 'sci', 'Sc19g0001870' => 'sci', 'SGA_v2.0_scaffold1G00346' => 'sas', 'SGA_v2.0_scaffold1G00575' => 'sas', 'SGA_v2.0_scaffold1G00761' => 'sas', 'SGA_v2.0_scaffold232G43501' => 'sas', 'TAR625G1137' => 'tar', 'Thecc.03G222100' => 'tca', 'TPR.G12691' => 'tpr', 'TWI34G0727' => 'twi', 'TWI36G0117' => 'twi', 'VMungo1309G0868' => 'vmu' ), 'gf_id' => 'HOM05D001729', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001729' ), 'data_identifier' => 'HOM05D001729', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001729', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '375', 'num_species' => '42' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'Ah.07g204710' => 'amhyb', 'AUR62006001' => 'cqu', 'AUR62006002' => 'cqu', 'AUR62006003' => 'cqu', 'AUR62015641' => 'cqu', 'AUR62027174' => 'cqu', 'AUR62035623' => 'cqu', 'AUR62035624' => 'cqu', 'AUR62035625' => 'cqu', 'AUR62035626' => 'cqu', 'CAN.G1110.53' => 'can', 'CANSAT80G0415' => 'cansat', 'Ca_21364_v3' => 'car', 'COL.COLO4_30693' => 'col', 'COL.COLO4_30694' => 'col', 'COL.COLO4_30695' => 'col', 'COL.COLO4_30696' => 'col', 'COL.COLO4_34020' => 'col', 'DCAR_004585' => 'dca', 'Dinv04029' => 'din', 'Dinv34857' => 'din', 'Duzib147G0011' => 'dzi', 'Duzib170G0599' => 'dzi', 'Duzib192G1051' => 'dzi', 'FAN01G0708' => 'fan', 'FAN01G0742' => 'fan', 'FAN02G0048' => 'fan', 'FAN02G0583' => 'fan', 'FAN02G0688' => 'fan', 'FAN02G1588' => 'fan', 'FAN02G2194' => 'fan', 'FAN02G2750' => 'fan', 'FAN02G3094' => 'fan', 'FAN02G3887' => 'fan', 'FAN02G3911' => 'fan', 'FAN02G3994' => 'fan', 'FAN02G4432' => 'fan', 'FAN02G4556' => 'fan', 'FAN03G1977' => 'fan', 'FAN03G2781' => 'fan', 'FAN03G2850' => 'fan', 'FAN03G3155' => 'fan', 'FAN04G2487' => 'fan', 'FAN05G0208' => 'fan', 'FAN05G0656' => 'fan', 'FAN05G0696' => 'fan', 'FAN05G0810' => 'fan', 'FAN05G1447' => 'fan', 'FAN05G2640' => 'fan', 'FAN05G2911' => 'fan', 'FAN05G3901' => 'fan', 'FAN05G4859' => 'fan', 'FAN05G4861' => 'fan', 'FAN05G4988' => 'fan', 'FAN05G5187' => 'fan', 'FAN05G5452' => 'fan', 'FAN05G5500' => 'fan', 'FAN05G5688' => 'fan', 'FAN06G0177' => 'fan', 'FAN06G0675' => 'fan', 'FAN06G1290' => 'fan', 'FAN06G2191' => 'fan', 'FAN06G2405' => 'fan', 'FAN06G3231' => 'fan', 'FAN06G3932' => 'fan', 'FAN07G0163' => 'fan', 'FAN07G0471' => 'fan', 'FAN07G1354' => 'fan', 'FAN08G0338' => 'fan', 'FAN08G1373' => 'fan', 'FAN08G2539' => 'fan', 'FAN08G2728' => 'fan', 'FAN09G0608' => 'fan', 'FAN09G1136' => 'fan', 'FAN09G1958' => 'fan', 'FAN09G2508' => 'fan', 'FAN09G2597' => 'fan', 'FAN09G2658' => 'fan', 'FAN09G2757' => 'fan', 'FAN09G2983' => 'fan', 'FAN09G3130' => 'fan', 'FAN09G3565' => 'fan', 'FAN09G3613' => 'fan', 'FAN09G4011' => 'fan', 'FAN09G4239' => 'fan', 'FAN09G4277' => 'fan', 'FAN09G4720' => 'fan', 'FAN11G0139' => 'fan', 'FAN11G1727' => 'fan', 'FAN11G2672' => 'fan', 'FAN11G2795' => 'fan', 'FAN11G3238' => 'fan', 'FAN11G3734' => 'fan', 'FAN12G0631' => 'fan', 'FAN12G2239' => 'fan', 'FAN12G2308' => 'fan', 'FAN12G2569' => 'fan', 'FAN12G2623' => 'fan', 'FAN13G3182' => 'fan', 'FAN14G0053' => 'fan', 'FAN14G0370' => 'fan', 'FAN14G0382' => 'fan', 'FAN14G0421' => 'fan', 'FAN14G0866' => 'fan', 'FAN14G1187' => 'fan', 'FAN14G1727' => 'fan', 'FAN14G1791' => 'fan', 'FAN14G2361' => 'fan', 'FAN14G2668' => 'fan', 'FAN14G2770' => 'fan', 'FAN14G2874' => 'fan', 'FAN14G3193' => 'fan', 'FAN14G3624' => 'fan', 'FAN14G3676' => 'fan', 'FAN14G3807' => 'fan', 'FAN14G4082' => 'fan', 'FAN14G4342' => 'fan', 'FAN14G4985' => 'fan', 'FAN14G5126' => 'fan', 'FAN14G5781' => 'fan', 'FAN14G5808' => 'fan', 'FAN14G5949' => 'fan', 'FAN15G0828' => 'fan', 'FAN15G1054' => 'fan', 'FAN15G2023' => 'fan', 'FAN15G2506' => 'fan', 'FAN16G0128' => 'fan', 'FAN16G0249' => 'fan', 'FAN16G0429' => 'fan', 'FAN16G1493' => 'fan', 'FAN16G2210' => 'fan', 'FAN16G2506' => 'fan', 'FAN18G1542' => 'fan', 'FAN18G4057' => 'fan', 'FAN19G0745' => 'fan', 'FAN19G1216' => 'fan', 'FAN19G1733' => 'fan', 'FAN20G0258' => 'fan', 'FAN20G1095' => 'fan', 'FAN20G1557' => 'fan', 'FAN21G0302' => 'fan', 'FAN21G0519' => 'fan', 'FAN21G0970' => 'fan', 'FAN21G1159' => 'fan', 'FAN21G1312' => 'fan', 'FAN21G1440' => 'fan', 'FAN21G1715' => 'fan', 'FAN23G1584' => 'fan', 'FAN24G0045' => 'fan', 'FAN24G0053' => 'fan', 'FAN24G1500' => 'fan', 'FAN24G1817' => 'fan', 'FAN24G2147' => 'fan', 'FAN24G2236' => 'fan', 'FAN24G2446' => 'fan', 'FAN24G2684' => 'fan', 'FAN25G0187' => 'fan', 'FAN25G0505' => 'fan', 'FAN25G0589' => 'fan', 'FAN25G3663' => 'fan', 'FAN26G1025' => 'fan', 'FAN26G2860' => 'fan', 'FAN27G1329' => 'fan', 'FAN27G3392' => 'fan', 'FvH4_1g02011' => 'fve', 'FvH4_1g06511' => 'fve', 'FvH4_2g19900' => 'fve', 'FvH4_2g19920' => 'fve', 'FvH4_2g24261' => 'fve', 'FvH4_2g24270' => 'fve', 'FvH4_2g24631' => 'fve', 'FvH4_2g30622' => 'fve', 'FvH4_3g12920' => 'fve', 'FvH4_3g30171' => 'fve', 'FvH4_3g35490' => 'fve', 'FvH4_3g43682' => 'fve', 'FvH4_3g43730' => 'fve', 'FvH4_3g43732' => 'fve', 'FvH4_3g43751' => 'fve', 'FvH4_3g43752' => 'fve', 'FvH4_3g43770' => 'fve', 'FvH4_3g44471' => 'fve', 'FvH4_3g44510' => 'fve', 'FvH4_3g44582' => 'fve', 'FvH4_4g16921' => 'fve', 'FvH4_4g17121' => 'fve', 'FvH4_4g17782' => 'fve', 'FvH4_4g17783' => 'fve', 'FvH4_4g18120' => 'fve', 'FvH4_4g31310' => 'fve', 'FvH4_4g35052' => 'fve', 'FvH4_5g30862' => 'fve', 'FvH4_6g01541' => 'fve', 'FvH4_6g02021' => 'fve', 'FvH4_6g02041' => 'fve', 'FvH4_6g02071' => 'fve', 'FvH4_6g02171' => 'fve', 'FvH4_6g03181' => 'fve', 'FvH4_6g03182' => 'fve', 'FvH4_6g03221' => 'fve', 'FvH4_6g03380' => 'fve', 'FvH4_6g05201' => 'fve', 'FvH4_6g05203' => 'fve', 'FvH4_6g20231' => 'fve', 'FvH4_6g31981' => 'fve', 'FvH4_6g32061' => 'fve', 'FvH4_6g37041' => 'fve', 'FvH4_6g37932' => 'fve', 'FvH4_6g38731' => 'fve', 'FvH4_6g39370' => 'fve', 'FvH4_6g39371' => 'fve', 'FvH4_6g40891' => 'fve', 'FvH4_6g40892' => 'fve', 'FvH4_6g43143' => 'fve', 'FvH4_6g45251' => 'fve', 'FvH4_6g45260' => 'fve', 'FvH4_6g45291' => 'fve', 'FvH4_6g45890' => 'fve', 'FvH4_6g46240' => 'fve', 'FvH4_6g46241' => 'fve', 'FvH4_6g46242' => 'fve', 'FvH4_6g46260' => 'fve', 'FvH4_6g46280' => 'fve', 'FvH4_6g46380' => 'fve', 'FvH4_7g12841' => 'fve', 'FvH4_7g31431' => 'fve', 'Glyma.09G075900' => 'gma', 'Gohir.A09G096401' => 'ghi', 'Gohir.D09G096101' => 'ghi', 'Gorai.006G112800' => 'gra', 'HanXRQChr04g0121411' => 'han', 'Hund15878' => 'sun', 'Lj2A1107G68' => 'lonja', 'Lj2A630G63' => 'lonja', 'Lj2A946T25' => 'lonja', 'Lj2C714T1' => 'lonja', 'Lj2C966T3' => 'lonja', 'Lj2C966T4' => 'lonja', 'Lj4g0002979' => 'lja', 'Lsat_1_v5_gn_5_30901' => 'lsa', 'Lsat_1_v5_gn_5_31100' => 'lsa', 'Lsat_1_v5_gn_5_38600' => 'lsa', 'Lsat_1_v5_gn_6_92061' => 'lsa', 'Manes.05G071301' => 'mes', 'MD02G1008700' => 'mdo', 'MD02G1008900' => 'mdo', 'MD03G1256400' => 'mdo', 'MD04G1180900' => 'mdo', 'MD04G1181000' => 'mdo', 'MD04G1181200' => 'mdo', 'MD05G1244200' => 'mdo', 'MD05G1324200' => 'mdo', 'MD09G1201600' => 'mdo', 'MD10G1000600' => 'mdo', 'MD14G1026900' => 'mdo', 'MD14G1187900' => 'mdo', 'MD15G1017800' => 'mdo', 'MD15G1018100' => 'mdo', 'Medtr4g124160' => 'mtr', 'Migut.L01260' => 'egut', 'Nitab4.5_0000008g0440' => 'nta', 'Nitab4.5_0000207g0170' => 'nta', 'Nitab4.5_0007671g0030' => 'nta', 'Nitab4.5_0010853g0020' => 'nta', 'Oeu057656.1' => 'oeu', 'PGSC0003DMG400005638' => 'stu', 'PGSC0003DMG400005639' => 'stu', 'Phvul.009G222800' => 'pvu', 'Potri.009G132400' => 'ptr', 'Potri.009G163001' => 'ptr', 'Potri.011G000700' => 'ptr', 'Potri.011G004800' => 'ptr', 'Prupe.1G509300' => 'ppe', 'Prupe.1G509700' => 'ppe', 'Prupe.1G510400' => 'ppe', 'Prupe.1G510700' => 'ppe', 'Prupe.1G512600' => 'ppe', 'Prupe.2G073200' => 'ppe', 'Prupe.3G059500' => 'ppe', 'Prupe.3G059600' => 'ppe', 'Prupe.3G246100' => 'ppe', 'Prupe.3G265100' => 'ppe', 'Prupe.4G034700' => 'ppe', 'Prupe.4G052100' => 'ppe', 'Prupe.4G053600' => 'ppe', 'Prupe.5G068800' => 'ppe', 'Prupe.5G070600' => 'ppe', 'Prupe.6G075400' => 'ppe', 'Prupe.6G075500' => 'ppe', 'Prupe.6G076400' => 'ppe', 'Prupe.8G110700' => 'ppe', 'Psat4g020960' => 'psa', 'PSO135G0788' => 'pso', 'PSO210G6463' => 'pso', 'PSO384G0370' => 'pso', 'PSO386G0056' => 'pso', 'QL01p006048' => 'qlo', 'QL02p054283' => 'qlo', 'QL05p008000' => 'qlo', 'QL05p008212' => 'qlo', 'QL05p008950' => 'qlo', 'QL05p009042' => 'qlo', 'QL05p009518' => 'qlo', 'QL05p012589' => 'qlo', 'QL05p012608' => 'qlo', 'QL05p012650' => 'qlo', 'QL05p012667' => 'qlo', 'QL05p014501' => 'qlo', 'QL05p052800' => 'qlo', 'QL05p065010' => 'qlo', 'QL05p074156' => 'qlo', 'QL05p074160' => 'qlo', 'QL05p074174' => 'qlo', 'QL05p074178' => 'qlo', 'QL05p074214' => 'qlo', 'QL06p001050' => 'qlo', 'QL06p001056' => 'qlo', 'QL06p006093' => 'qlo', 'QL06p006111' => 'qlo', 'QL07p019784' => 'qlo', 'QL07p019801' => 'qlo', 'QL07p036110' => 'qlo', 'QL07p036134' => 'qlo', 'QL07p036147' => 'qlo', 'QL07p036156' => 'qlo', 'QL07p036300' => 'qlo', 'QL07p036320' => 'qlo', 'QL08p014547' => 'qlo', 'QL08p014551' => 'qlo', 'QL08p043319' => 'qlo', 'QL08p043324' => 'qlo', 'QL11p009094' => 'qlo', 'RcHm_v2.0_Chr1g0380481' => 'rch', 'RcHm_v2.0_Chr2g0089331' => 'rch', 'RcHm_v2.0_Chr2g0123691' => 'rch', 'RcHm_v2.0_Chr2g0151111' => 'rch', 'RcHm_v2.0_Chr2g0163011' => 'rch', 'RcHm_v2.0_Chr2g0163051' => 'rch', 'RcHm_v2.0_Chr2g0164671' => 'rch', 'RcHm_v2.0_Chr2g0164681' => 'rch', 'RcHm_v2.0_Chr2g0164721' => 'rch', 'RcHm_v2.0_Chr3g0449911' => 'rch', 'RcHm_v2.0_Chr3g0450211' => 'rch', 'RcHm_v2.0_Chr3g0457271' => 'rch', 'RcHm_v2.0_Chr5g0018111' => 'rch', 'RcHm_v2.0_Chr5g0021011' => 'rch', 'RcHm_v2.0_Chr5g0081171' => 'rch', 'RcHm_v2.0_Chr5g0081211' => 'rch', 'RcHm_v2.0_Chr6g0275871' => 'rch', 'RcHm_v2.0_Chr6g0276071' => 'rch', 'RcHm_v2.0_Chr6g0285591' => 'rch', 'RcHm_v2.0_Chr6g0291931' => 'rch', 'RcHm_v2.0_Chr6g0292091' => 'rch', 'RcHm_v2.0_Chr6g0292271' => 'rch', 'RcHm_v2.0_Chr7g0221261' => 'rch', 'Rhsim08G0219900' => 'rsi', 'Rhsim08G0220200' => 'rsi', 'Rhsim08G0237800' => 'rsi', 'Rhsim08G0238800' => 'rsi', 'Sabra09G0102700' => 'sbr', 'Sabra09G0127200' => 'sbr', 'Sabra11G0003700' => 'sbr', 'Sabra15G0014700' => 'sbr', 'Sc19g0000590' => 'sci', 'Sc19g0001870' => 'sci', 'SGA_v2.0_scaffold1G00346' => 'sas', 'SGA_v2.0_scaffold1G00575' => 'sas', 'SGA_v2.0_scaffold1G00761' => 'sas', 'SGA_v2.0_scaffold232G43501' => 'sas', 'TAR625G1137' => 'tar', 'Thecc.03G222100' => 'tca', 'TPR.G12691' => 'tpr', 'TWI34G0727' => 'twi', 'TWI36G0117' => 'twi', 'VMungo1309G0868' => 'vmu' ) $gf_id = 'HOM05D001729' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001729' ) $data_identifier = 'HOM05D001729' $data_type = 'gf_id' $species_gene_counts = array( 'amhyb' => (int) 1, 'cqu' => (int) 9, 'can' => (int) 1, 'cansat' => (int) 1, 'car' => (int) 1, 'col' => (int) 5, 'dca' => (int) 1, 'din' => (int) 2, 'dzi' => (int) 3, 'fan' => (int) 140, 'fve' => (int) 62, 'gma' => (int) 1, 'ghi' => (int) 2, 'gra' => (int) 1, 'han' => (int) 1, 'sun' => (int) 1, 'lonja' => (int) 6, 'lja' => (int) 1, 'lsa' => (int) 4, 'mes' => (int) 1, 'mdo' => (int) 14, 'mtr' => (int) 1, 'egut' => (int) 1, 'nta' => (int) 4, 'oeu' => (int) 1, 'stu' => (int) 2, 'pvu' => (int) 1, 'ptr' => (int) 4, 'ppe' => (int) 19, 'psa' => (int) 1, 'pso' => (int) 4, 'qlo' => (int) 36, 'rch' => (int) 23, 'rsi' => (int) 4, 'sbr' => (int) 4, 'sci' => (int) 2, 'sas' => (int) 4, 'tar' => (int) 1, 'tca' => (int) 1, 'tpr' => (int) 1, 'twi' => (int) 2, 'vmu' => (int) 1 ) $gf_gene_species = 'vmu' $gf_gene_id = 'VMungo1309G0868' $species_info = array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ) $local_species = 'cansat' $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' => 'HOM05D001729', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '375', 'num_species' => '42' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'Ah.07g204710' => 'amhyb', 'AUR62006001' => 'cqu', 'AUR62006002' => 'cqu', 'AUR62006003' => 'cqu', 'AUR62015641' => 'cqu', 'AUR62027174' => 'cqu', 'AUR62035623' => 'cqu', 'AUR62035624' => 'cqu', 'AUR62035625' => 'cqu', 'AUR62035626' => 'cqu', 'CAN.G1110.53' => 'can', 'CANSAT80G0415' => 'cansat', 'Ca_21364_v3' => 'car', 'COL.COLO4_30693' => 'col', 'COL.COLO4_30694' => 'col', 'COL.COLO4_30695' => 'col', 'COL.COLO4_30696' => 'col', 'COL.COLO4_34020' => 'col', 'DCAR_004585' => 'dca', 'Dinv04029' => 'din', 'Dinv34857' => 'din', 'Duzib147G0011' => 'dzi', 'Duzib170G0599' => 'dzi', 'Duzib192G1051' => 'dzi', 'FAN01G0708' => 'fan', 'FAN01G0742' => 'fan', 'FAN02G0048' => 'fan', 'FAN02G0583' => 'fan', 'FAN02G0688' => 'fan', 'FAN02G1588' => 'fan', 'FAN02G2194' => 'fan', 'FAN02G2750' => 'fan', 'FAN02G3094' => 'fan', 'FAN02G3887' => 'fan', 'FAN02G3911' => 'fan', 'FAN02G3994' => 'fan', 'FAN02G4432' => 'fan', 'FAN02G4556' => 'fan', 'FAN03G1977' => 'fan', 'FAN03G2781' => 'fan', 'FAN03G2850' => 'fan', 'FAN03G3155' => 'fan', 'FAN04G2487' => 'fan', 'FAN05G0208' => 'fan', 'FAN05G0656' => 'fan', 'FAN05G0696' => 'fan', 'FAN05G0810' => 'fan', 'FAN05G1447' => 'fan', 'FAN05G2640' => 'fan', 'FAN05G2911' => 'fan', 'FAN05G3901' => 'fan', 'FAN05G4859' => 'fan', 'FAN05G4861' => 'fan', 'FAN05G4988' => 'fan', 'FAN05G5187' => 'fan', 'FAN05G5452' => 'fan', 'FAN05G5500' => 'fan', 'FAN05G5688' => 'fan', 'FAN06G0177' => 'fan', 'FAN06G0675' => 'fan', 'FAN06G1290' => 'fan', 'FAN06G2191' => 'fan', 'FAN06G2405' => 'fan', 'FAN06G3231' => 'fan', 'FAN06G3932' => 'fan', 'FAN07G0163' => 'fan', 'FAN07G0471' => 'fan', 'FAN07G1354' => 'fan', 'FAN08G0338' => 'fan', 'FAN08G1373' => 'fan', 'FAN08G2539' => 'fan', 'FAN08G2728' => 'fan', 'FAN09G0608' => 'fan', 'FAN09G1136' => 'fan', 'FAN09G1958' => 'fan', 'FAN09G2508' => 'fan', 'FAN09G2597' => 'fan', 'FAN09G2658' => 'fan', 'FAN09G2757' => 'fan', 'FAN09G2983' => 'fan', 'FAN09G3130' => 'fan', 'FAN09G3565' => 'fan', 'FAN09G3613' => 'fan', 'FAN09G4011' => 'fan', 'FAN09G4239' => 'fan', 'FAN09G4277' => 'fan', 'FAN09G4720' => 'fan', 'FAN11G0139' => 'fan', 'FAN11G1727' => 'fan', 'FAN11G2672' => 'fan', 'FAN11G2795' => 'fan', 'FAN11G3238' => 'fan', 'FAN11G3734' => 'fan', 'FAN12G0631' => 'fan', 'FAN12G2239' => 'fan', 'FAN12G2308' => 'fan', 'FAN12G2569' => 'fan', 'FAN12G2623' => 'fan', 'FAN13G3182' => 'fan', 'FAN14G0053' => 'fan', 'FAN14G0370' => 'fan', 'FAN14G0382' => 'fan', 'FAN14G0421' => 'fan', 'FAN14G0866' => 'fan', 'FAN14G1187' => 'fan', 'FAN14G1727' => 'fan', 'FAN14G1791' => 'fan', 'FAN14G2361' => 'fan', 'FAN14G2668' => 'fan', 'FAN14G2770' => 'fan', 'FAN14G2874' => 'fan', 'FAN14G3193' => 'fan', 'FAN14G3624' => 'fan', 'FAN14G3676' => 'fan', 'FAN14G3807' => 'fan', 'FAN14G4082' => 'fan', 'FAN14G4342' => 'fan', 'FAN14G4985' => 'fan', 'FAN14G5126' => 'fan', 'FAN14G5781' => 'fan', 'FAN14G5808' => 'fan', 'FAN14G5949' => 'fan', 'FAN15G0828' => 'fan', 'FAN15G1054' => 'fan', 'FAN15G2023' => 'fan', 'FAN15G2506' => 'fan', 'FAN16G0128' => 'fan', 'FAN16G0249' => 'fan', 'FAN16G0429' => 'fan', 'FAN16G1493' => 'fan', 'FAN16G2210' => 'fan', 'FAN16G2506' => 'fan', 'FAN18G1542' => 'fan', 'FAN18G4057' => 'fan', 'FAN19G0745' => 'fan', 'FAN19G1216' => 'fan', 'FAN19G1733' => 'fan', 'FAN20G0258' => 'fan', 'FAN20G1095' => 'fan', 'FAN20G1557' => 'fan', 'FAN21G0302' => 'fan', 'FAN21G0519' => 'fan', 'FAN21G0970' => 'fan', 'FAN21G1159' => 'fan', 'FAN21G1312' => 'fan', 'FAN21G1440' => 'fan', 'FAN21G1715' => 'fan', 'FAN23G1584' => 'fan', 'FAN24G0045' => 'fan', 'FAN24G0053' => 'fan', 'FAN24G1500' => 'fan', 'FAN24G1817' => 'fan', 'FAN24G2147' => 'fan', 'FAN24G2236' => 'fan', 'FAN24G2446' => 'fan', 'FAN24G2684' => 'fan', 'FAN25G0187' => 'fan', 'FAN25G0505' => 'fan', 'FAN25G0589' => 'fan', 'FAN25G3663' => 'fan', 'FAN26G1025' => 'fan', 'FAN26G2860' => 'fan', 'FAN27G1329' => 'fan', 'FAN27G3392' => 'fan', 'FvH4_1g02011' => 'fve', 'FvH4_1g06511' => 'fve', 'FvH4_2g19900' => 'fve', 'FvH4_2g19920' => 'fve', 'FvH4_2g24261' => 'fve', 'FvH4_2g24270' => 'fve', 'FvH4_2g24631' => 'fve', 'FvH4_2g30622' => 'fve', 'FvH4_3g12920' => 'fve', 'FvH4_3g30171' => 'fve', 'FvH4_3g35490' => 'fve', 'FvH4_3g43682' => 'fve', 'FvH4_3g43730' => 'fve', 'FvH4_3g43732' => 'fve', 'FvH4_3g43751' => 'fve', 'FvH4_3g43752' => 'fve', 'FvH4_3g43770' => 'fve', 'FvH4_3g44471' => 'fve', 'FvH4_3g44510' => 'fve', 'FvH4_3g44582' => 'fve', 'FvH4_4g16921' => 'fve', 'FvH4_4g17121' => 'fve', 'FvH4_4g17782' => 'fve', 'FvH4_4g17783' => 'fve', 'FvH4_4g18120' => 'fve', 'FvH4_4g31310' => 'fve', 'FvH4_4g35052' => 'fve', 'FvH4_5g30862' => 'fve', 'FvH4_6g01541' => 'fve', 'FvH4_6g02021' => 'fve', 'FvH4_6g02041' => 'fve', 'FvH4_6g02071' => 'fve', 'FvH4_6g02171' => 'fve', 'FvH4_6g03181' => 'fve', 'FvH4_6g03182' => 'fve', 'FvH4_6g03221' => 'fve', 'FvH4_6g03380' => 'fve', 'FvH4_6g05201' => 'fve', 'FvH4_6g05203' => 'fve', 'FvH4_6g20231' => 'fve', 'FvH4_6g31981' => 'fve', 'FvH4_6g32061' => 'fve', 'FvH4_6g37041' => 'fve', 'FvH4_6g37932' => 'fve', 'FvH4_6g38731' => 'fve', 'FvH4_6g39370' => 'fve', 'FvH4_6g39371' => 'fve', 'FvH4_6g40891' => 'fve', 'FvH4_6g40892' => 'fve', 'FvH4_6g43143' => 'fve', 'FvH4_6g45251' => 'fve', 'FvH4_6g45260' => 'fve', 'FvH4_6g45291' => 'fve', 'FvH4_6g45890' => 'fve', 'FvH4_6g46240' => 'fve', 'FvH4_6g46241' => 'fve', 'FvH4_6g46242' => 'fve', 'FvH4_6g46260' => 'fve', 'FvH4_6g46280' => 'fve', 'FvH4_6g46380' => 'fve', 'FvH4_7g12841' => 'fve', 'FvH4_7g31431' => 'fve', 'Glyma.09G075900' => 'gma', 'Gohir.A09G096401' => 'ghi', 'Gohir.D09G096101' => 'ghi', 'Gorai.006G112800' => 'gra', 'HanXRQChr04g0121411' => 'han', 'Hund15878' => 'sun', 'Lj2A1107G68' => 'lonja', 'Lj2A630G63' => 'lonja', 'Lj2A946T25' => 'lonja', 'Lj2C714T1' => 'lonja', 'Lj2C966T3' => 'lonja', 'Lj2C966T4' => 'lonja', 'Lj4g0002979' => 'lja', 'Lsat_1_v5_gn_5_30901' => 'lsa', 'Lsat_1_v5_gn_5_31100' => 'lsa', 'Lsat_1_v5_gn_5_38600' => 'lsa', 'Lsat_1_v5_gn_6_92061' => 'lsa', 'Manes.05G071301' => 'mes', 'MD02G1008700' => 'mdo', 'MD02G1008900' => 'mdo', 'MD03G1256400' => 'mdo', 'MD04G1180900' => 'mdo', 'MD04G1181000' => 'mdo', 'MD04G1181200' => 'mdo', 'MD05G1244200' => 'mdo', 'MD05G1324200' => 'mdo', 'MD09G1201600' => 'mdo', 'MD10G1000600' => 'mdo', 'MD14G1026900' => 'mdo', 'MD14G1187900' => 'mdo', 'MD15G1017800' => 'mdo', 'MD15G1018100' => 'mdo', 'Medtr4g124160' => 'mtr', 'Migut.L01260' => 'egut', 'Nitab4.5_0000008g0440' => 'nta', 'Nitab4.5_0000207g0170' => 'nta', 'Nitab4.5_0007671g0030' => 'nta', 'Nitab4.5_0010853g0020' => 'nta', 'Oeu057656.1' => 'oeu', 'PGSC0003DMG400005638' => 'stu', 'PGSC0003DMG400005639' => 'stu', 'Phvul.009G222800' => 'pvu', 'Potri.009G132400' => 'ptr', 'Potri.009G163001' => 'ptr', 'Potri.011G000700' => 'ptr', 'Potri.011G004800' => 'ptr', 'Prupe.1G509300' => 'ppe', 'Prupe.1G509700' => 'ppe', 'Prupe.1G510400' => 'ppe', 'Prupe.1G510700' => 'ppe', 'Prupe.1G512600' => 'ppe', 'Prupe.2G073200' => 'ppe', 'Prupe.3G059500' => 'ppe', 'Prupe.3G059600' => 'ppe', 'Prupe.3G246100' => 'ppe', 'Prupe.3G265100' => 'ppe', 'Prupe.4G034700' => 'ppe', 'Prupe.4G052100' => 'ppe', 'Prupe.4G053600' => 'ppe', 'Prupe.5G068800' => 'ppe', 'Prupe.5G070600' => 'ppe', 'Prupe.6G075400' => 'ppe', 'Prupe.6G075500' => 'ppe', 'Prupe.6G076400' => 'ppe', 'Prupe.8G110700' => 'ppe', 'Psat4g020960' => 'psa', 'PSO135G0788' => 'pso', 'PSO210G6463' => 'pso', 'PSO384G0370' => 'pso', 'PSO386G0056' => 'pso', 'QL01p006048' => 'qlo', 'QL02p054283' => 'qlo', 'QL05p008000' => 'qlo', 'QL05p008212' => 'qlo', 'QL05p008950' => 'qlo', 'QL05p009042' => 'qlo', 'QL05p009518' => 'qlo', 'QL05p012589' => 'qlo', 'QL05p012608' => 'qlo', 'QL05p012650' => 'qlo', 'QL05p012667' => 'qlo', 'QL05p014501' => 'qlo', 'QL05p052800' => 'qlo', 'QL05p065010' => 'qlo', 'QL05p074156' => 'qlo', 'QL05p074160' => 'qlo', 'QL05p074174' => 'qlo', 'QL05p074178' => 'qlo', 'QL05p074214' => 'qlo', 'QL06p001050' => 'qlo', 'QL06p001056' => 'qlo', 'QL06p006093' => 'qlo', 'QL06p006111' => 'qlo', 'QL07p019784' => 'qlo', 'QL07p019801' => 'qlo', 'QL07p036110' => 'qlo', 'QL07p036134' => 'qlo', 'QL07p036147' => 'qlo', 'QL07p036156' => 'qlo', 'QL07p036300' => 'qlo', 'QL07p036320' => 'qlo', 'QL08p014547' => 'qlo', 'QL08p014551' => 'qlo', 'QL08p043319' => 'qlo', 'QL08p043324' => 'qlo', 'QL11p009094' => 'qlo', 'RcHm_v2.0_Chr1g0380481' => 'rch', 'RcHm_v2.0_Chr2g0089331' => 'rch', 'RcHm_v2.0_Chr2g0123691' => 'rch', 'RcHm_v2.0_Chr2g0151111' => 'rch', 'RcHm_v2.0_Chr2g0163011' => 'rch', 'RcHm_v2.0_Chr2g0163051' => 'rch', 'RcHm_v2.0_Chr2g0164671' => 'rch', 'RcHm_v2.0_Chr2g0164681' => 'rch', 'RcHm_v2.0_Chr2g0164721' => 'rch', 'RcHm_v2.0_Chr3g0449911' => 'rch', 'RcHm_v2.0_Chr3g0450211' => 'rch', 'RcHm_v2.0_Chr3g0457271' => 'rch', 'RcHm_v2.0_Chr5g0018111' => 'rch', 'RcHm_v2.0_Chr5g0021011' => 'rch', 'RcHm_v2.0_Chr5g0081171' => 'rch', 'RcHm_v2.0_Chr5g0081211' => 'rch', 'RcHm_v2.0_Chr6g0275871' => 'rch', 'RcHm_v2.0_Chr6g0276071' => 'rch', 'RcHm_v2.0_Chr6g0285591' => 'rch', 'RcHm_v2.0_Chr6g0291931' => 'rch', 'RcHm_v2.0_Chr6g0292091' => 'rch', 'RcHm_v2.0_Chr6g0292271' => 'rch', 'RcHm_v2.0_Chr7g0221261' => 'rch', 'Rhsim08G0219900' => 'rsi', 'Rhsim08G0220200' => 'rsi', 'Rhsim08G0237800' => 'rsi', 'Rhsim08G0238800' => 'rsi', 'Sabra09G0102700' => 'sbr', 'Sabra09G0127200' => 'sbr', 'Sabra11G0003700' => 'sbr', 'Sabra15G0014700' => 'sbr', 'Sc19g0000590' => 'sci', 'Sc19g0001870' => 'sci', 'SGA_v2.0_scaffold1G00346' => 'sas', 'SGA_v2.0_scaffold1G00575' => 'sas', 'SGA_v2.0_scaffold1G00761' => 'sas', 'SGA_v2.0_scaffold232G43501' => 'sas', 'TAR625G1137' => 'tar', 'Thecc.03G222100' => 'tca', 'TPR.G12691' => 'tpr', 'TWI34G0727' => 'twi', 'TWI36G0117' => 'twi', 'VMungo1309G0868' => 'vmu' ), 'gf_id' => 'HOM05D001729', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001729' ), 'data_identifier' => 'HOM05D001729', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001729', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '375', 'num_species' => '42' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'Ah.07g204710' => 'amhyb', 'AUR62006001' => 'cqu', 'AUR62006002' => 'cqu', 'AUR62006003' => 'cqu', 'AUR62015641' => 'cqu', 'AUR62027174' => 'cqu', 'AUR62035623' => 'cqu', 'AUR62035624' => 'cqu', 'AUR62035625' => 'cqu', 'AUR62035626' => 'cqu', 'CAN.G1110.53' => 'can', 'CANSAT80G0415' => 'cansat', 'Ca_21364_v3' => 'car', 'COL.COLO4_30693' => 'col', 'COL.COLO4_30694' => 'col', 'COL.COLO4_30695' => 'col', 'COL.COLO4_30696' => 'col', 'COL.COLO4_34020' => 'col', 'DCAR_004585' => 'dca', 'Dinv04029' => 'din', 'Dinv34857' => 'din', 'Duzib147G0011' => 'dzi', 'Duzib170G0599' => 'dzi', 'Duzib192G1051' => 'dzi', 'FAN01G0708' => 'fan', 'FAN01G0742' => 'fan', 'FAN02G0048' => 'fan', 'FAN02G0583' => 'fan', 'FAN02G0688' => 'fan', 'FAN02G1588' => 'fan', 'FAN02G2194' => 'fan', 'FAN02G2750' => 'fan', 'FAN02G3094' => 'fan', 'FAN02G3887' => 'fan', 'FAN02G3911' => 'fan', 'FAN02G3994' => 'fan', 'FAN02G4432' => 'fan', 'FAN02G4556' => 'fan', 'FAN03G1977' => 'fan', 'FAN03G2781' => 'fan', 'FAN03G2850' => 'fan', 'FAN03G3155' => 'fan', 'FAN04G2487' => 'fan', 'FAN05G0208' => 'fan', 'FAN05G0656' => 'fan', 'FAN05G0696' => 'fan', 'FAN05G0810' => 'fan', 'FAN05G1447' => 'fan', 'FAN05G2640' => 'fan', 'FAN05G2911' => 'fan', 'FAN05G3901' => 'fan', 'FAN05G4859' => 'fan', 'FAN05G4861' => 'fan', 'FAN05G4988' => 'fan', 'FAN05G5187' => 'fan', 'FAN05G5452' => 'fan', 'FAN05G5500' => 'fan', 'FAN05G5688' => 'fan', 'FAN06G0177' => 'fan', 'FAN06G0675' => 'fan', 'FAN06G1290' => 'fan', 'FAN06G2191' => 'fan', 'FAN06G2405' => 'fan', 'FAN06G3231' => 'fan', 'FAN06G3932' => 'fan', 'FAN07G0163' => 'fan', 'FAN07G0471' => 'fan', 'FAN07G1354' => 'fan', 'FAN08G0338' => 'fan', 'FAN08G1373' => 'fan', 'FAN08G2539' => 'fan', 'FAN08G2728' => 'fan', 'FAN09G0608' => 'fan', 'FAN09G1136' => 'fan', 'FAN09G1958' => 'fan', 'FAN09G2508' => 'fan', 'FAN09G2597' => 'fan', 'FAN09G2658' => 'fan', 'FAN09G2757' => 'fan', 'FAN09G2983' => 'fan', 'FAN09G3130' => 'fan', 'FAN09G3565' => 'fan', 'FAN09G3613' => 'fan', 'FAN09G4011' => 'fan', 'FAN09G4239' => 'fan', 'FAN09G4277' => 'fan', 'FAN09G4720' => 'fan', 'FAN11G0139' => 'fan', 'FAN11G1727' => 'fan', 'FAN11G2672' => 'fan', 'FAN11G2795' => 'fan', 'FAN11G3238' => 'fan', 'FAN11G3734' => 'fan', 'FAN12G0631' => 'fan', 'FAN12G2239' => 'fan', 'FAN12G2308' => 'fan', 'FAN12G2569' => 'fan', 'FAN12G2623' => 'fan', 'FAN13G3182' => 'fan', 'FAN14G0053' => 'fan', 'FAN14G0370' => 'fan', 'FAN14G0382' => 'fan', 'FAN14G0421' => 'fan', 'FAN14G0866' => 'fan', 'FAN14G1187' => 'fan', 'FAN14G1727' => 'fan', 'FAN14G1791' => 'fan', 'FAN14G2361' => 'fan', 'FAN14G2668' => 'fan', 'FAN14G2770' => 'fan', 'FAN14G2874' => 'fan', 'FAN14G3193' => 'fan', 'FAN14G3624' => 'fan', 'FAN14G3676' => 'fan', 'FAN14G3807' => 'fan', 'FAN14G4082' => 'fan', 'FAN14G4342' => 'fan', 'FAN14G4985' => 'fan', 'FAN14G5126' => 'fan', 'FAN14G5781' => 'fan', 'FAN14G5808' => 'fan', 'FAN14G5949' => 'fan', 'FAN15G0828' => 'fan', 'FAN15G1054' => 'fan', 'FAN15G2023' => 'fan', 'FAN15G2506' => 'fan', 'FAN16G0128' => 'fan', 'FAN16G0249' => 'fan', 'FAN16G0429' => 'fan', 'FAN16G1493' => 'fan', 'FAN16G2210' => 'fan', 'FAN16G2506' => 'fan', 'FAN18G1542' => 'fan', 'FAN18G4057' => 'fan', 'FAN19G0745' => 'fan', 'FAN19G1216' => 'fan', 'FAN19G1733' => 'fan', 'FAN20G0258' => 'fan', 'FAN20G1095' => 'fan', 'FAN20G1557' => 'fan', 'FAN21G0302' => 'fan', 'FAN21G0519' => 'fan', 'FAN21G0970' => 'fan', 'FAN21G1159' => 'fan', 'FAN21G1312' => 'fan', 'FAN21G1440' => 'fan', 'FAN21G1715' => 'fan', 'FAN23G1584' => 'fan', 'FAN24G0045' => 'fan', 'FAN24G0053' => 'fan', 'FAN24G1500' => 'fan', 'FAN24G1817' => 'fan', 'FAN24G2147' => 'fan', 'FAN24G2236' => 'fan', 'FAN24G2446' => 'fan', 'FAN24G2684' => 'fan', 'FAN25G0187' => 'fan', 'FAN25G0505' => 'fan', 'FAN25G0589' => 'fan', 'FAN25G3663' => 'fan', 'FAN26G1025' => 'fan', 'FAN26G2860' => 'fan', 'FAN27G1329' => 'fan', 'FAN27G3392' => 'fan', 'FvH4_1g02011' => 'fve', 'FvH4_1g06511' => 'fve', 'FvH4_2g19900' => 'fve', 'FvH4_2g19920' => 'fve', 'FvH4_2g24261' => 'fve', 'FvH4_2g24270' => 'fve', 'FvH4_2g24631' => 'fve', 'FvH4_2g30622' => 'fve', 'FvH4_3g12920' => 'fve', 'FvH4_3g30171' => 'fve', 'FvH4_3g35490' => 'fve', 'FvH4_3g43682' => 'fve', 'FvH4_3g43730' => 'fve', 'FvH4_3g43732' => 'fve', 'FvH4_3g43751' => 'fve', 'FvH4_3g43752' => 'fve', 'FvH4_3g43770' => 'fve', 'FvH4_3g44471' => 'fve', 'FvH4_3g44510' => 'fve', 'FvH4_3g44582' => 'fve', 'FvH4_4g16921' => 'fve', 'FvH4_4g17121' => 'fve', 'FvH4_4g17782' => 'fve', 'FvH4_4g17783' => 'fve', 'FvH4_4g18120' => 'fve', 'FvH4_4g31310' => 'fve', 'FvH4_4g35052' => 'fve', 'FvH4_5g30862' => 'fve', 'FvH4_6g01541' => 'fve', 'FvH4_6g02021' => 'fve', 'FvH4_6g02041' => 'fve', 'FvH4_6g02071' => 'fve', 'FvH4_6g02171' => 'fve', 'FvH4_6g03181' => 'fve', 'FvH4_6g03182' => 'fve', 'FvH4_6g03221' => 'fve', 'FvH4_6g03380' => 'fve', 'FvH4_6g05201' => 'fve', 'FvH4_6g05203' => 'fve', 'FvH4_6g20231' => 'fve', 'FvH4_6g31981' => 'fve', 'FvH4_6g32061' => 'fve', 'FvH4_6g37041' => 'fve', 'FvH4_6g37932' => 'fve', 'FvH4_6g38731' => 'fve', 'FvH4_6g39370' => 'fve', 'FvH4_6g39371' => 'fve', 'FvH4_6g40891' => 'fve', 'FvH4_6g40892' => 'fve', 'FvH4_6g43143' => 'fve', 'FvH4_6g45251' => 'fve', 'FvH4_6g45260' => 'fve', 'FvH4_6g45291' => 'fve', 'FvH4_6g45890' => 'fve', 'FvH4_6g46240' => 'fve', 'FvH4_6g46241' => 'fve', 'FvH4_6g46242' => 'fve', 'FvH4_6g46260' => 'fve', 'FvH4_6g46280' => 'fve', 'FvH4_6g46380' => 'fve', 'FvH4_7g12841' => 'fve', 'FvH4_7g31431' => 'fve', 'Glyma.09G075900' => 'gma', 'Gohir.A09G096401' => 'ghi', 'Gohir.D09G096101' => 'ghi', 'Gorai.006G112800' => 'gra', 'HanXRQChr04g0121411' => 'han', 'Hund15878' => 'sun', 'Lj2A1107G68' => 'lonja', 'Lj2A630G63' => 'lonja', 'Lj2A946T25' => 'lonja', 'Lj2C714T1' => 'lonja', 'Lj2C966T3' => 'lonja', 'Lj2C966T4' => 'lonja', 'Lj4g0002979' => 'lja', 'Lsat_1_v5_gn_5_30901' => 'lsa', 'Lsat_1_v5_gn_5_31100' => 'lsa', 'Lsat_1_v5_gn_5_38600' => 'lsa', 'Lsat_1_v5_gn_6_92061' => 'lsa', 'Manes.05G071301' => 'mes', 'MD02G1008700' => 'mdo', 'MD02G1008900' => 'mdo', 'MD03G1256400' => 'mdo', 'MD04G1180900' => 'mdo', 'MD04G1181000' => 'mdo', 'MD04G1181200' => 'mdo', 'MD05G1244200' => 'mdo', 'MD05G1324200' => 'mdo', 'MD09G1201600' => 'mdo', 'MD10G1000600' => 'mdo', 'MD14G1026900' => 'mdo', 'MD14G1187900' => 'mdo', 'MD15G1017800' => 'mdo', 'MD15G1018100' => 'mdo', 'Medtr4g124160' => 'mtr', 'Migut.L01260' => 'egut', 'Nitab4.5_0000008g0440' => 'nta', 'Nitab4.5_0000207g0170' => 'nta', 'Nitab4.5_0007671g0030' => 'nta', 'Nitab4.5_0010853g0020' => 'nta', 'Oeu057656.1' => 'oeu', 'PGSC0003DMG400005638' => 'stu', 'PGSC0003DMG400005639' => 'stu', 'Phvul.009G222800' => 'pvu', 'Potri.009G132400' => 'ptr', 'Potri.009G163001' => 'ptr', 'Potri.011G000700' => 'ptr', 'Potri.011G004800' => 'ptr', 'Prupe.1G509300' => 'ppe', 'Prupe.1G509700' => 'ppe', 'Prupe.1G510400' => 'ppe', 'Prupe.1G510700' => 'ppe', 'Prupe.1G512600' => 'ppe', 'Prupe.2G073200' => 'ppe', 'Prupe.3G059500' => 'ppe', 'Prupe.3G059600' => 'ppe', 'Prupe.3G246100' => 'ppe', 'Prupe.3G265100' => 'ppe', 'Prupe.4G034700' => 'ppe', 'Prupe.4G052100' => 'ppe', 'Prupe.4G053600' => 'ppe', 'Prupe.5G068800' => 'ppe', 'Prupe.5G070600' => 'ppe', 'Prupe.6G075400' => 'ppe', 'Prupe.6G075500' => 'ppe', 'Prupe.6G076400' => 'ppe', 'Prupe.8G110700' => 'ppe', 'Psat4g020960' => 'psa', 'PSO135G0788' => 'pso', 'PSO210G6463' => 'pso', 'PSO384G0370' => 'pso', 'PSO386G0056' => 'pso', 'QL01p006048' => 'qlo', 'QL02p054283' => 'qlo', 'QL05p008000' => 'qlo', 'QL05p008212' => 'qlo', 'QL05p008950' => 'qlo', 'QL05p009042' => 'qlo', 'QL05p009518' => 'qlo', 'QL05p012589' => 'qlo', 'QL05p012608' => 'qlo', 'QL05p012650' => 'qlo', 'QL05p012667' => 'qlo', 'QL05p014501' => 'qlo', 'QL05p052800' => 'qlo', 'QL05p065010' => 'qlo', 'QL05p074156' => 'qlo', 'QL05p074160' => 'qlo', 'QL05p074174' => 'qlo', 'QL05p074178' => 'qlo', 'QL05p074214' => 'qlo', 'QL06p001050' => 'qlo', 'QL06p001056' => 'qlo', 'QL06p006093' => 'qlo', 'QL06p006111' => 'qlo', 'QL07p019784' => 'qlo', 'QL07p019801' => 'qlo', 'QL07p036110' => 'qlo', 'QL07p036134' => 'qlo', 'QL07p036147' => 'qlo', 'QL07p036156' => 'qlo', 'QL07p036300' => 'qlo', 'QL07p036320' => 'qlo', 'QL08p014547' => 'qlo', 'QL08p014551' => 'qlo', 'QL08p043319' => 'qlo', 'QL08p043324' => 'qlo', 'QL11p009094' => 'qlo', 'RcHm_v2.0_Chr1g0380481' => 'rch', 'RcHm_v2.0_Chr2g0089331' => 'rch', 'RcHm_v2.0_Chr2g0123691' => 'rch', 'RcHm_v2.0_Chr2g0151111' => 'rch', 'RcHm_v2.0_Chr2g0163011' => 'rch', 'RcHm_v2.0_Chr2g0163051' => 'rch', 'RcHm_v2.0_Chr2g0164671' => 'rch', 'RcHm_v2.0_Chr2g0164681' => 'rch', 'RcHm_v2.0_Chr2g0164721' => 'rch', 'RcHm_v2.0_Chr3g0449911' => 'rch', 'RcHm_v2.0_Chr3g0450211' => 'rch', 'RcHm_v2.0_Chr3g0457271' => 'rch', 'RcHm_v2.0_Chr5g0018111' => 'rch', 'RcHm_v2.0_Chr5g0021011' => 'rch', 'RcHm_v2.0_Chr5g0081171' => 'rch', 'RcHm_v2.0_Chr5g0081211' => 'rch', 'RcHm_v2.0_Chr6g0275871' => 'rch', 'RcHm_v2.0_Chr6g0276071' => 'rch', 'RcHm_v2.0_Chr6g0285591' => 'rch', 'RcHm_v2.0_Chr6g0291931' => 'rch', 'RcHm_v2.0_Chr6g0292091' => 'rch', 'RcHm_v2.0_Chr6g0292271' => 'rch', 'RcHm_v2.0_Chr7g0221261' => 'rch', 'Rhsim08G0219900' => 'rsi', 'Rhsim08G0220200' => 'rsi', 'Rhsim08G0237800' => 'rsi', 'Rhsim08G0238800' => 'rsi', 'Sabra09G0102700' => 'sbr', 'Sabra09G0127200' => 'sbr', 'Sabra11G0003700' => 'sbr', 'Sabra15G0014700' => 'sbr', 'Sc19g0000590' => 'sci', 'Sc19g0001870' => 'sci', 'SGA_v2.0_scaffold1G00346' => 'sas', 'SGA_v2.0_scaffold1G00575' => 'sas', 'SGA_v2.0_scaffold1G00761' => 'sas', 'SGA_v2.0_scaffold232G43501' => 'sas', 'TAR625G1137' => 'tar', 'Thecc.03G222100' => 'tca', 'TPR.G12691' => 'tpr', 'TWI34G0727' => 'twi', 'TWI36G0117' => 'twi', 'VMungo1309G0868' => 'vmu' ) $gf_id = 'HOM05D001729' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001729' ) $data_identifier = 'HOM05D001729' $data_type = 'gf_id' $species_gene_counts = array( 'amhyb' => (int) 1, 'cqu' => (int) 9, 'can' => (int) 1, 'cansat' => (int) 1, 'car' => (int) 1, 'col' => (int) 5, 'dca' => (int) 1, 'din' => (int) 2, 'dzi' => (int) 3, 'fan' => (int) 140, 'fve' => (int) 62, 'gma' => (int) 1, 'ghi' => (int) 2, 'gra' => (int) 1, 'han' => (int) 1, 'sun' => (int) 1, 'lonja' => (int) 6, 'lja' => (int) 1, 'lsa' => (int) 4, 'mes' => (int) 1, 'mdo' => (int) 14, 'mtr' => (int) 1, 'egut' => (int) 1, 'nta' => (int) 4, 'oeu' => (int) 1, 'stu' => (int) 2, 'pvu' => (int) 1, 'ptr' => (int) 4, 'ppe' => (int) 19, 'psa' => (int) 1, 'pso' => (int) 4, 'qlo' => (int) 36, 'rch' => (int) 23, 'rsi' => (int) 4, 'sbr' => (int) 4, 'sci' => (int) 2, 'sas' => (int) 4, 'tar' => (int) 1, 'tca' => (int) 1, 'tpr' => (int) 1, 'twi' => (int) 2, 'vmu' => (int) 1 ) $gf_gene_species = 'vmu' $gf_gene_id = 'VMungo1309G0868' $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' => 'HOM05D001729', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '375', 'num_species' => '42' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'Ah.07g204710' => 'amhyb', 'AUR62006001' => 'cqu', 'AUR62006002' => 'cqu', 'AUR62006003' => 'cqu', 'AUR62015641' => 'cqu', 'AUR62027174' => 'cqu', 'AUR62035623' => 'cqu', 'AUR62035624' => 'cqu', 'AUR62035625' => 'cqu', 'AUR62035626' => 'cqu', 'CAN.G1110.53' => 'can', 'CANSAT80G0415' => 'cansat', 'Ca_21364_v3' => 'car', 'COL.COLO4_30693' => 'col', 'COL.COLO4_30694' => 'col', 'COL.COLO4_30695' => 'col', 'COL.COLO4_30696' => 'col', 'COL.COLO4_34020' => 'col', 'DCAR_004585' => 'dca', 'Dinv04029' => 'din', 'Dinv34857' => 'din', 'Duzib147G0011' => 'dzi', 'Duzib170G0599' => 'dzi', 'Duzib192G1051' => 'dzi', 'FAN01G0708' => 'fan', 'FAN01G0742' => 'fan', 'FAN02G0048' => 'fan', 'FAN02G0583' => 'fan', 'FAN02G0688' => 'fan', 'FAN02G1588' => 'fan', 'FAN02G2194' => 'fan', 'FAN02G2750' => 'fan', 'FAN02G3094' => 'fan', 'FAN02G3887' => 'fan', 'FAN02G3911' => 'fan', 'FAN02G3994' => 'fan', 'FAN02G4432' => 'fan', 'FAN02G4556' => 'fan', 'FAN03G1977' => 'fan', 'FAN03G2781' => 'fan', 'FAN03G2850' => 'fan', 'FAN03G3155' => 'fan', 'FAN04G2487' => 'fan', 'FAN05G0208' => 'fan', 'FAN05G0656' => 'fan', 'FAN05G0696' => 'fan', 'FAN05G0810' => 'fan', 'FAN05G1447' => 'fan', 'FAN05G2640' => 'fan', 'FAN05G2911' => 'fan', 'FAN05G3901' => 'fan', 'FAN05G4859' => 'fan', 'FAN05G4861' => 'fan', 'FAN05G4988' => 'fan', 'FAN05G5187' => 'fan', 'FAN05G5452' => 'fan', 'FAN05G5500' => 'fan', 'FAN05G5688' => 'fan', 'FAN06G0177' => 'fan', 'FAN06G0675' => 'fan', 'FAN06G1290' => 'fan', 'FAN06G2191' => 'fan', 'FAN06G2405' => 'fan', 'FAN06G3231' => 'fan', 'FAN06G3932' => 'fan', 'FAN07G0163' => 'fan', 'FAN07G0471' => 'fan', 'FAN07G1354' => 'fan', 'FAN08G0338' => 'fan', 'FAN08G1373' => 'fan', 'FAN08G2539' => 'fan', 'FAN08G2728' => 'fan', 'FAN09G0608' => 'fan', 'FAN09G1136' => 'fan', 'FAN09G1958' => 'fan', 'FAN09G2508' => 'fan', 'FAN09G2597' => 'fan', 'FAN09G2658' => 'fan', 'FAN09G2757' => 'fan', 'FAN09G2983' => 'fan', 'FAN09G3130' => 'fan', 'FAN09G3565' => 'fan', 'FAN09G3613' => 'fan', 'FAN09G4011' => 'fan', 'FAN09G4239' => 'fan', 'FAN09G4277' => 'fan', 'FAN09G4720' => 'fan', 'FAN11G0139' => 'fan', 'FAN11G1727' => 'fan', 'FAN11G2672' => 'fan', 'FAN11G2795' => 'fan', 'FAN11G3238' => 'fan', 'FAN11G3734' => 'fan', 'FAN12G0631' => 'fan', 'FAN12G2239' => 'fan', 'FAN12G2308' => 'fan', 'FAN12G2569' => 'fan', 'FAN12G2623' => 'fan', 'FAN13G3182' => 'fan', 'FAN14G0053' => 'fan', 'FAN14G0370' => 'fan', 'FAN14G0382' => 'fan', 'FAN14G0421' => 'fan', 'FAN14G0866' => 'fan', 'FAN14G1187' => 'fan', 'FAN14G1727' => 'fan', 'FAN14G1791' => 'fan', 'FAN14G2361' => 'fan', 'FAN14G2668' => 'fan', 'FAN14G2770' => 'fan', 'FAN14G2874' => 'fan', 'FAN14G3193' => 'fan', 'FAN14G3624' => 'fan', 'FAN14G3676' => 'fan', 'FAN14G3807' => 'fan', 'FAN14G4082' => 'fan', 'FAN14G4342' => 'fan', 'FAN14G4985' => 'fan', 'FAN14G5126' => 'fan', 'FAN14G5781' => 'fan', 'FAN14G5808' => 'fan', 'FAN14G5949' => 'fan', 'FAN15G0828' => 'fan', 'FAN15G1054' => 'fan', 'FAN15G2023' => 'fan', 'FAN15G2506' => 'fan', 'FAN16G0128' => 'fan', 'FAN16G0249' => 'fan', 'FAN16G0429' => 'fan', 'FAN16G1493' => 'fan', 'FAN16G2210' => 'fan', 'FAN16G2506' => 'fan', 'FAN18G1542' => 'fan', 'FAN18G4057' => 'fan', 'FAN19G0745' => 'fan', 'FAN19G1216' => 'fan', 'FAN19G1733' => 'fan', 'FAN20G0258' => 'fan', 'FAN20G1095' => 'fan', 'FAN20G1557' => 'fan', 'FAN21G0302' => 'fan', 'FAN21G0519' => 'fan', 'FAN21G0970' => 'fan', 'FAN21G1159' => 'fan', 'FAN21G1312' => 'fan', 'FAN21G1440' => 'fan', 'FAN21G1715' => 'fan', 'FAN23G1584' => 'fan', 'FAN24G0045' => 'fan', 'FAN24G0053' => 'fan', 'FAN24G1500' => 'fan', 'FAN24G1817' => 'fan', 'FAN24G2147' => 'fan', 'FAN24G2236' => 'fan', 'FAN24G2446' => 'fan', 'FAN24G2684' => 'fan', 'FAN25G0187' => 'fan', 'FAN25G0505' => 'fan', 'FAN25G0589' => 'fan', 'FAN25G3663' => 'fan', 'FAN26G1025' => 'fan', 'FAN26G2860' => 'fan', 'FAN27G1329' => 'fan', 'FAN27G3392' => 'fan', 'FvH4_1g02011' => 'fve', 'FvH4_1g06511' => 'fve', 'FvH4_2g19900' => 'fve', 'FvH4_2g19920' => 'fve', 'FvH4_2g24261' => 'fve', 'FvH4_2g24270' => 'fve', 'FvH4_2g24631' => 'fve', 'FvH4_2g30622' => 'fve', 'FvH4_3g12920' => 'fve', 'FvH4_3g30171' => 'fve', 'FvH4_3g35490' => 'fve', 'FvH4_3g43682' => 'fve', 'FvH4_3g43730' => 'fve', 'FvH4_3g43732' => 'fve', 'FvH4_3g43751' => 'fve', 'FvH4_3g43752' => 'fve', 'FvH4_3g43770' => 'fve', 'FvH4_3g44471' => 'fve', 'FvH4_3g44510' => 'fve', 'FvH4_3g44582' => 'fve', 'FvH4_4g16921' => 'fve', 'FvH4_4g17121' => 'fve', 'FvH4_4g17782' => 'fve', 'FvH4_4g17783' => 'fve', 'FvH4_4g18120' => 'fve', 'FvH4_4g31310' => 'fve', 'FvH4_4g35052' => 'fve', 'FvH4_5g30862' => 'fve', 'FvH4_6g01541' => 'fve', 'FvH4_6g02021' => 'fve', 'FvH4_6g02041' => 'fve', 'FvH4_6g02071' => 'fve', 'FvH4_6g02171' => 'fve', 'FvH4_6g03181' => 'fve', 'FvH4_6g03182' => 'fve', 'FvH4_6g03221' => 'fve', 'FvH4_6g03380' => 'fve', 'FvH4_6g05201' => 'fve', 'FvH4_6g05203' => 'fve', 'FvH4_6g20231' => 'fve', 'FvH4_6g31981' => 'fve', 'FvH4_6g32061' => 'fve', 'FvH4_6g37041' => 'fve', 'FvH4_6g37932' => 'fve', 'FvH4_6g38731' => 'fve', 'FvH4_6g39370' => 'fve', 'FvH4_6g39371' => 'fve', 'FvH4_6g40891' => 'fve', 'FvH4_6g40892' => 'fve', 'FvH4_6g43143' => 'fve', 'FvH4_6g45251' => 'fve', 'FvH4_6g45260' => 'fve', 'FvH4_6g45291' => 'fve', 'FvH4_6g45890' => 'fve', 'FvH4_6g46240' => 'fve', 'FvH4_6g46241' => 'fve', 'FvH4_6g46242' => 'fve', 'FvH4_6g46260' => 'fve', 'FvH4_6g46280' => 'fve', 'FvH4_6g46380' => 'fve', 'FvH4_7g12841' => 'fve', 'FvH4_7g31431' => 'fve', 'Glyma.09G075900' => 'gma', 'Gohir.A09G096401' => 'ghi', 'Gohir.D09G096101' => 'ghi', 'Gorai.006G112800' => 'gra', 'HanXRQChr04g0121411' => 'han', 'Hund15878' => 'sun', 'Lj2A1107G68' => 'lonja', 'Lj2A630G63' => 'lonja', 'Lj2A946T25' => 'lonja', 'Lj2C714T1' => 'lonja', 'Lj2C966T3' => 'lonja', 'Lj2C966T4' => 'lonja', 'Lj4g0002979' => 'lja', 'Lsat_1_v5_gn_5_30901' => 'lsa', 'Lsat_1_v5_gn_5_31100' => 'lsa', 'Lsat_1_v5_gn_5_38600' => 'lsa', 'Lsat_1_v5_gn_6_92061' => 'lsa', 'Manes.05G071301' => 'mes', 'MD02G1008700' => 'mdo', 'MD02G1008900' => 'mdo', 'MD03G1256400' => 'mdo', 'MD04G1180900' => 'mdo', 'MD04G1181000' => 'mdo', 'MD04G1181200' => 'mdo', 'MD05G1244200' => 'mdo', 'MD05G1324200' => 'mdo', 'MD09G1201600' => 'mdo', 'MD10G1000600' => 'mdo', 'MD14G1026900' => 'mdo', 'MD14G1187900' => 'mdo', 'MD15G1017800' => 'mdo', 'MD15G1018100' => 'mdo', 'Medtr4g124160' => 'mtr', 'Migut.L01260' => 'egut', 'Nitab4.5_0000008g0440' => 'nta', 'Nitab4.5_0000207g0170' => 'nta', 'Nitab4.5_0007671g0030' => 'nta', 'Nitab4.5_0010853g0020' => 'nta', 'Oeu057656.1' => 'oeu', 'PGSC0003DMG400005638' => 'stu', 'PGSC0003DMG400005639' => 'stu', 'Phvul.009G222800' => 'pvu', 'Potri.009G132400' => 'ptr', 'Potri.009G163001' => 'ptr', 'Potri.011G000700' => 'ptr', 'Potri.011G004800' => 'ptr', 'Prupe.1G509300' => 'ppe', 'Prupe.1G509700' => 'ppe', 'Prupe.1G510400' => 'ppe', 'Prupe.1G510700' => 'ppe', 'Prupe.1G512600' => 'ppe', 'Prupe.2G073200' => 'ppe', 'Prupe.3G059500' => 'ppe', 'Prupe.3G059600' => 'ppe', 'Prupe.3G246100' => 'ppe', 'Prupe.3G265100' => 'ppe', 'Prupe.4G034700' => 'ppe', 'Prupe.4G052100' => 'ppe', 'Prupe.4G053600' => 'ppe', 'Prupe.5G068800' => 'ppe', 'Prupe.5G070600' => 'ppe', 'Prupe.6G075400' => 'ppe', 'Prupe.6G075500' => 'ppe', 'Prupe.6G076400' => 'ppe', 'Prupe.8G110700' => 'ppe', 'Psat4g020960' => 'psa', 'PSO135G0788' => 'pso', 'PSO210G6463' => 'pso', 'PSO384G0370' => 'pso', 'PSO386G0056' => 'pso', 'QL01p006048' => 'qlo', 'QL02p054283' => 'qlo', 'QL05p008000' => 'qlo', 'QL05p008212' => 'qlo', 'QL05p008950' => 'qlo', 'QL05p009042' => 'qlo', 'QL05p009518' => 'qlo', 'QL05p012589' => 'qlo', 'QL05p012608' => 'qlo', 'QL05p012650' => 'qlo', 'QL05p012667' => 'qlo', 'QL05p014501' => 'qlo', 'QL05p052800' => 'qlo', 'QL05p065010' => 'qlo', 'QL05p074156' => 'qlo', 'QL05p074160' => 'qlo', 'QL05p074174' => 'qlo', 'QL05p074178' => 'qlo', 'QL05p074214' => 'qlo', 'QL06p001050' => 'qlo', 'QL06p001056' => 'qlo', 'QL06p006093' => 'qlo', 'QL06p006111' => 'qlo', 'QL07p019784' => 'qlo', 'QL07p019801' => 'qlo', 'QL07p036110' => 'qlo', 'QL07p036134' => 'qlo', 'QL07p036147' => 'qlo', 'QL07p036156' => 'qlo', 'QL07p036300' => 'qlo', 'QL07p036320' => 'qlo', 'QL08p014547' => 'qlo', 'QL08p014551' => 'qlo', 'QL08p043319' => 'qlo', 'QL08p043324' => 'qlo', 'QL11p009094' => 'qlo', 'RcHm_v2.0_Chr1g0380481' => 'rch', 'RcHm_v2.0_Chr2g0089331' => 'rch', 'RcHm_v2.0_Chr2g0123691' => 'rch', 'RcHm_v2.0_Chr2g0151111' => 'rch', 'RcHm_v2.0_Chr2g0163011' => 'rch', 'RcHm_v2.0_Chr2g0163051' => 'rch', 'RcHm_v2.0_Chr2g0164671' => 'rch', 'RcHm_v2.0_Chr2g0164681' => 'rch', 'RcHm_v2.0_Chr2g0164721' => 'rch', 'RcHm_v2.0_Chr3g0449911' => 'rch', 'RcHm_v2.0_Chr3g0450211' => 'rch', 'RcHm_v2.0_Chr3g0457271' => 'rch', 'RcHm_v2.0_Chr5g0018111' => 'rch', 'RcHm_v2.0_Chr5g0021011' => 'rch', 'RcHm_v2.0_Chr5g0081171' => 'rch', 'RcHm_v2.0_Chr5g0081211' => 'rch', 'RcHm_v2.0_Chr6g0275871' => 'rch', 'RcHm_v2.0_Chr6g0276071' => 'rch', 'RcHm_v2.0_Chr6g0285591' => 'rch', 'RcHm_v2.0_Chr6g0291931' => 'rch', 'RcHm_v2.0_Chr6g0292091' => 'rch', 'RcHm_v2.0_Chr6g0292271' => 'rch', 'RcHm_v2.0_Chr7g0221261' => 'rch', 'Rhsim08G0219900' => 'rsi', 'Rhsim08G0220200' => 'rsi', 'Rhsim08G0237800' => 'rsi', 'Rhsim08G0238800' => 'rsi', 'Sabra09G0102700' => 'sbr', 'Sabra09G0127200' => 'sbr', 'Sabra11G0003700' => 'sbr', 'Sabra15G0014700' => 'sbr', 'Sc19g0000590' => 'sci', 'Sc19g0001870' => 'sci', 'SGA_v2.0_scaffold1G00346' => 'sas', 'SGA_v2.0_scaffold1G00575' => 'sas', 'SGA_v2.0_scaffold1G00761' => 'sas', 'SGA_v2.0_scaffold232G43501' => 'sas', 'TAR625G1137' => 'tar', 'Thecc.03G222100' => 'tca', 'TPR.G12691' => 'tpr', 'TWI34G0727' => 'twi', 'TWI36G0117' => 'twi', 'VMungo1309G0868' => 'vmu' ), 'gf_id' => 'HOM05D001729', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001729' ), 'data_identifier' => 'HOM05D001729', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001729', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '375', 'num_species' => '42' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'Ah.07g204710' => 'amhyb', 'AUR62006001' => 'cqu', 'AUR62006002' => 'cqu', 'AUR62006003' => 'cqu', 'AUR62015641' => 'cqu', 'AUR62027174' => 'cqu', 'AUR62035623' => 'cqu', 'AUR62035624' => 'cqu', 'AUR62035625' => 'cqu', 'AUR62035626' => 'cqu', 'CAN.G1110.53' => 'can', 'CANSAT80G0415' => 'cansat', 'Ca_21364_v3' => 'car', 'COL.COLO4_30693' => 'col', 'COL.COLO4_30694' => 'col', 'COL.COLO4_30695' => 'col', 'COL.COLO4_30696' => 'col', 'COL.COLO4_34020' => 'col', 'DCAR_004585' => 'dca', 'Dinv04029' => 'din', 'Dinv34857' => 'din', 'Duzib147G0011' => 'dzi', 'Duzib170G0599' => 'dzi', 'Duzib192G1051' => 'dzi', 'FAN01G0708' => 'fan', 'FAN01G0742' => 'fan', 'FAN02G0048' => 'fan', 'FAN02G0583' => 'fan', 'FAN02G0688' => 'fan', 'FAN02G1588' => 'fan', 'FAN02G2194' => 'fan', 'FAN02G2750' => 'fan', 'FAN02G3094' => 'fan', 'FAN02G3887' => 'fan', 'FAN02G3911' => 'fan', 'FAN02G3994' => 'fan', 'FAN02G4432' => 'fan', 'FAN02G4556' => 'fan', 'FAN03G1977' => 'fan', 'FAN03G2781' => 'fan', 'FAN03G2850' => 'fan', 'FAN03G3155' => 'fan', 'FAN04G2487' => 'fan', 'FAN05G0208' => 'fan', 'FAN05G0656' => 'fan', 'FAN05G0696' => 'fan', 'FAN05G0810' => 'fan', 'FAN05G1447' => 'fan', 'FAN05G2640' => 'fan', 'FAN05G2911' => 'fan', 'FAN05G3901' => 'fan', 'FAN05G4859' => 'fan', 'FAN05G4861' => 'fan', 'FAN05G4988' => 'fan', 'FAN05G5187' => 'fan', 'FAN05G5452' => 'fan', 'FAN05G5500' => 'fan', 'FAN05G5688' => 'fan', 'FAN06G0177' => 'fan', 'FAN06G0675' => 'fan', 'FAN06G1290' => 'fan', 'FAN06G2191' => 'fan', 'FAN06G2405' => 'fan', 'FAN06G3231' => 'fan', 'FAN06G3932' => 'fan', 'FAN07G0163' => 'fan', 'FAN07G0471' => 'fan', 'FAN07G1354' => 'fan', 'FAN08G0338' => 'fan', 'FAN08G1373' => 'fan', 'FAN08G2539' => 'fan', 'FAN08G2728' => 'fan', 'FAN09G0608' => 'fan', 'FAN09G1136' => 'fan', 'FAN09G1958' => 'fan', 'FAN09G2508' => 'fan', 'FAN09G2597' => 'fan', 'FAN09G2658' => 'fan', 'FAN09G2757' => 'fan', 'FAN09G2983' => 'fan', 'FAN09G3130' => 'fan', 'FAN09G3565' => 'fan', 'FAN09G3613' => 'fan', 'FAN09G4011' => 'fan', 'FAN09G4239' => 'fan', 'FAN09G4277' => 'fan', 'FAN09G4720' => 'fan', 'FAN11G0139' => 'fan', 'FAN11G1727' => 'fan', 'FAN11G2672' => 'fan', 'FAN11G2795' => 'fan', 'FAN11G3238' => 'fan', 'FAN11G3734' => 'fan', 'FAN12G0631' => 'fan', 'FAN12G2239' => 'fan', 'FAN12G2308' => 'fan', 'FAN12G2569' => 'fan', 'FAN12G2623' => 'fan', 'FAN13G3182' => 'fan', 'FAN14G0053' => 'fan', 'FAN14G0370' => 'fan', 'FAN14G0382' => 'fan', 'FAN14G0421' => 'fan', 'FAN14G0866' => 'fan', 'FAN14G1187' => 'fan', 'FAN14G1727' => 'fan', 'FAN14G1791' => 'fan', 'FAN14G2361' => 'fan', 'FAN14G2668' => 'fan', 'FAN14G2770' => 'fan', 'FAN14G2874' => 'fan', 'FAN14G3193' => 'fan', 'FAN14G3624' => 'fan', 'FAN14G3676' => 'fan', 'FAN14G3807' => 'fan', 'FAN14G4082' => 'fan', 'FAN14G4342' => 'fan', 'FAN14G4985' => 'fan', 'FAN14G5126' => 'fan', 'FAN14G5781' => 'fan', 'FAN14G5808' => 'fan', 'FAN14G5949' => 'fan', 'FAN15G0828' => 'fan', 'FAN15G1054' => 'fan', 'FAN15G2023' => 'fan', 'FAN15G2506' => 'fan', 'FAN16G0128' => 'fan', 'FAN16G0249' => 'fan', 'FAN16G0429' => 'fan', 'FAN16G1493' => 'fan', 'FAN16G2210' => 'fan', 'FAN16G2506' => 'fan', 'FAN18G1542' => 'fan', 'FAN18G4057' => 'fan', 'FAN19G0745' => 'fan', 'FAN19G1216' => 'fan', 'FAN19G1733' => 'fan', 'FAN20G0258' => 'fan', 'FAN20G1095' => 'fan', 'FAN20G1557' => 'fan', 'FAN21G0302' => 'fan', 'FAN21G0519' => 'fan', 'FAN21G0970' => 'fan', 'FAN21G1159' => 'fan', 'FAN21G1312' => 'fan', 'FAN21G1440' => 'fan', 'FAN21G1715' => 'fan', 'FAN23G1584' => 'fan', 'FAN24G0045' => 'fan', 'FAN24G0053' => 'fan', 'FAN24G1500' => 'fan', 'FAN24G1817' => 'fan', 'FAN24G2147' => 'fan', 'FAN24G2236' => 'fan', 'FAN24G2446' => 'fan', 'FAN24G2684' => 'fan', 'FAN25G0187' => 'fan', 'FAN25G0505' => 'fan', 'FAN25G0589' => 'fan', 'FAN25G3663' => 'fan', 'FAN26G1025' => 'fan', 'FAN26G2860' => 'fan', 'FAN27G1329' => 'fan', 'FAN27G3392' => 'fan', 'FvH4_1g02011' => 'fve', 'FvH4_1g06511' => 'fve', 'FvH4_2g19900' => 'fve', 'FvH4_2g19920' => 'fve', 'FvH4_2g24261' => 'fve', 'FvH4_2g24270' => 'fve', 'FvH4_2g24631' => 'fve', 'FvH4_2g30622' => 'fve', 'FvH4_3g12920' => 'fve', 'FvH4_3g30171' => 'fve', 'FvH4_3g35490' => 'fve', 'FvH4_3g43682' => 'fve', 'FvH4_3g43730' => 'fve', 'FvH4_3g43732' => 'fve', 'FvH4_3g43751' => 'fve', 'FvH4_3g43752' => 'fve', 'FvH4_3g43770' => 'fve', 'FvH4_3g44471' => 'fve', 'FvH4_3g44510' => 'fve', 'FvH4_3g44582' => 'fve', 'FvH4_4g16921' => 'fve', 'FvH4_4g17121' => 'fve', 'FvH4_4g17782' => 'fve', 'FvH4_4g17783' => 'fve', 'FvH4_4g18120' => 'fve', 'FvH4_4g31310' => 'fve', 'FvH4_4g35052' => 'fve', 'FvH4_5g30862' => 'fve', 'FvH4_6g01541' => 'fve', 'FvH4_6g02021' => 'fve', 'FvH4_6g02041' => 'fve', 'FvH4_6g02071' => 'fve', 'FvH4_6g02171' => 'fve', 'FvH4_6g03181' => 'fve', 'FvH4_6g03182' => 'fve', 'FvH4_6g03221' => 'fve', 'FvH4_6g03380' => 'fve', 'FvH4_6g05201' => 'fve', 'FvH4_6g05203' => 'fve', 'FvH4_6g20231' => 'fve', 'FvH4_6g31981' => 'fve', 'FvH4_6g32061' => 'fve', 'FvH4_6g37041' => 'fve', 'FvH4_6g37932' => 'fve', 'FvH4_6g38731' => 'fve', 'FvH4_6g39370' => 'fve', 'FvH4_6g39371' => 'fve', 'FvH4_6g40891' => 'fve', 'FvH4_6g40892' => 'fve', 'FvH4_6g43143' => 'fve', 'FvH4_6g45251' => 'fve', 'FvH4_6g45260' => 'fve', 'FvH4_6g45291' => 'fve', 'FvH4_6g45890' => 'fve', 'FvH4_6g46240' => 'fve', 'FvH4_6g46241' => 'fve', 'FvH4_6g46242' => 'fve', 'FvH4_6g46260' => 'fve', 'FvH4_6g46280' => 'fve', 'FvH4_6g46380' => 'fve', 'FvH4_7g12841' => 'fve', 'FvH4_7g31431' => 'fve', 'Glyma.09G075900' => 'gma', 'Gohir.A09G096401' => 'ghi', 'Gohir.D09G096101' => 'ghi', 'Gorai.006G112800' => 'gra', 'HanXRQChr04g0121411' => 'han', 'Hund15878' => 'sun', 'Lj2A1107G68' => 'lonja', 'Lj2A630G63' => 'lonja', 'Lj2A946T25' => 'lonja', 'Lj2C714T1' => 'lonja', 'Lj2C966T3' => 'lonja', 'Lj2C966T4' => 'lonja', 'Lj4g0002979' => 'lja', 'Lsat_1_v5_gn_5_30901' => 'lsa', 'Lsat_1_v5_gn_5_31100' => 'lsa', 'Lsat_1_v5_gn_5_38600' => 'lsa', 'Lsat_1_v5_gn_6_92061' => 'lsa', 'Manes.05G071301' => 'mes', 'MD02G1008700' => 'mdo', 'MD02G1008900' => 'mdo', 'MD03G1256400' => 'mdo', 'MD04G1180900' => 'mdo', 'MD04G1181000' => 'mdo', 'MD04G1181200' => 'mdo', 'MD05G1244200' => 'mdo', 'MD05G1324200' => 'mdo', 'MD09G1201600' => 'mdo', 'MD10G1000600' => 'mdo', 'MD14G1026900' => 'mdo', 'MD14G1187900' => 'mdo', 'MD15G1017800' => 'mdo', 'MD15G1018100' => 'mdo', 'Medtr4g124160' => 'mtr', 'Migut.L01260' => 'egut', 'Nitab4.5_0000008g0440' => 'nta', 'Nitab4.5_0000207g0170' => 'nta', 'Nitab4.5_0007671g0030' => 'nta', 'Nitab4.5_0010853g0020' => 'nta', 'Oeu057656.1' => 'oeu', 'PGSC0003DMG400005638' => 'stu', 'PGSC0003DMG400005639' => 'stu', 'Phvul.009G222800' => 'pvu', 'Potri.009G132400' => 'ptr', 'Potri.009G163001' => 'ptr', 'Potri.011G000700' => 'ptr', 'Potri.011G004800' => 'ptr', 'Prupe.1G509300' => 'ppe', 'Prupe.1G509700' => 'ppe', 'Prupe.1G510400' => 'ppe', 'Prupe.1G510700' => 'ppe', 'Prupe.1G512600' => 'ppe', 'Prupe.2G073200' => 'ppe', 'Prupe.3G059500' => 'ppe', 'Prupe.3G059600' => 'ppe', 'Prupe.3G246100' => 'ppe', 'Prupe.3G265100' => 'ppe', 'Prupe.4G034700' => 'ppe', 'Prupe.4G052100' => 'ppe', 'Prupe.4G053600' => 'ppe', 'Prupe.5G068800' => 'ppe', 'Prupe.5G070600' => 'ppe', 'Prupe.6G075400' => 'ppe', 'Prupe.6G075500' => 'ppe', 'Prupe.6G076400' => 'ppe', 'Prupe.8G110700' => 'ppe', 'Psat4g020960' => 'psa', 'PSO135G0788' => 'pso', 'PSO210G6463' => 'pso', 'PSO384G0370' => 'pso', 'PSO386G0056' => 'pso', 'QL01p006048' => 'qlo', 'QL02p054283' => 'qlo', 'QL05p008000' => 'qlo', 'QL05p008212' => 'qlo', 'QL05p008950' => 'qlo', 'QL05p009042' => 'qlo', 'QL05p009518' => 'qlo', 'QL05p012589' => 'qlo', 'QL05p012608' => 'qlo', 'QL05p012650' => 'qlo', 'QL05p012667' => 'qlo', 'QL05p014501' => 'qlo', 'QL05p052800' => 'qlo', 'QL05p065010' => 'qlo', 'QL05p074156' => 'qlo', 'QL05p074160' => 'qlo', 'QL05p074174' => 'qlo', 'QL05p074178' => 'qlo', 'QL05p074214' => 'qlo', 'QL06p001050' => 'qlo', 'QL06p001056' => 'qlo', 'QL06p006093' => 'qlo', 'QL06p006111' => 'qlo', 'QL07p019784' => 'qlo', 'QL07p019801' => 'qlo', 'QL07p036110' => 'qlo', 'QL07p036134' => 'qlo', 'QL07p036147' => 'qlo', 'QL07p036156' => 'qlo', 'QL07p036300' => 'qlo', 'QL07p036320' => 'qlo', 'QL08p014547' => 'qlo', 'QL08p014551' => 'qlo', 'QL08p043319' => 'qlo', 'QL08p043324' => 'qlo', 'QL11p009094' => 'qlo', 'RcHm_v2.0_Chr1g0380481' => 'rch', 'RcHm_v2.0_Chr2g0089331' => 'rch', 'RcHm_v2.0_Chr2g0123691' => 'rch', 'RcHm_v2.0_Chr2g0151111' => 'rch', 'RcHm_v2.0_Chr2g0163011' => 'rch', 'RcHm_v2.0_Chr2g0163051' => 'rch', 'RcHm_v2.0_Chr2g0164671' => 'rch', 'RcHm_v2.0_Chr2g0164681' => 'rch', 'RcHm_v2.0_Chr2g0164721' => 'rch', 'RcHm_v2.0_Chr3g0449911' => 'rch', 'RcHm_v2.0_Chr3g0450211' => 'rch', 'RcHm_v2.0_Chr3g0457271' => 'rch', 'RcHm_v2.0_Chr5g0018111' => 'rch', 'RcHm_v2.0_Chr5g0021011' => 'rch', 'RcHm_v2.0_Chr5g0081171' => 'rch', 'RcHm_v2.0_Chr5g0081211' => 'rch', 'RcHm_v2.0_Chr6g0275871' => 'rch', 'RcHm_v2.0_Chr6g0276071' => 'rch', 'RcHm_v2.0_Chr6g0285591' => 'rch', 'RcHm_v2.0_Chr6g0291931' => 'rch', 'RcHm_v2.0_Chr6g0292091' => 'rch', 'RcHm_v2.0_Chr6g0292271' => 'rch', 'RcHm_v2.0_Chr7g0221261' => 'rch', 'Rhsim08G0219900' => 'rsi', 'Rhsim08G0220200' => 'rsi', 'Rhsim08G0237800' => 'rsi', 'Rhsim08G0238800' => 'rsi', 'Sabra09G0102700' => 'sbr', 'Sabra09G0127200' => 'sbr', 'Sabra11G0003700' => 'sbr', 'Sabra15G0014700' => 'sbr', 'Sc19g0000590' => 'sci', 'Sc19g0001870' => 'sci', 'SGA_v2.0_scaffold1G00346' => 'sas', 'SGA_v2.0_scaffold1G00575' => 'sas', 'SGA_v2.0_scaffold1G00761' => 'sas', 'SGA_v2.0_scaffold232G43501' => 'sas', 'TAR625G1137' => 'tar', 'Thecc.03G222100' => 'tca', 'TPR.G12691' => 'tpr', 'TWI34G0727' => 'twi', 'TWI36G0117' => 'twi', 'VMungo1309G0868' => 'vmu' ) $gf_id = 'HOM05D001729' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001729' ) $data_identifier = 'HOM05D001729' $data_type = 'gf_id' $species_gene_counts = array( 'amhyb' => (int) 1, 'cqu' => (int) 9, 'can' => (int) 1, 'cansat' => (int) 1, 'car' => (int) 1, 'col' => (int) 5, 'dca' => (int) 1, 'din' => (int) 2, 'dzi' => (int) 3, 'fan' => (int) 140, 'fve' => (int) 62, 'gma' => (int) 1, 'ghi' => (int) 2, 'gra' => (int) 1, 'han' => (int) 1, 'sun' => (int) 1, 'lonja' => (int) 6, 'lja' => (int) 1, 'lsa' => (int) 4, 'mes' => (int) 1, 'mdo' => (int) 14, 'mtr' => (int) 1, 'egut' => (int) 1, 'nta' => (int) 4, 'oeu' => (int) 1, 'stu' => (int) 2, 'pvu' => (int) 1, 'ptr' => (int) 4, 'ppe' => (int) 19, 'psa' => (int) 1, 'pso' => (int) 4, 'qlo' => (int) 36, 'rch' => (int) 23, 'rsi' => (int) 4, 'sbr' => (int) 4, 'sci' => (int) 2, 'sas' => (int) 4, 'tar' => (int) 1, 'tca' => (int) 1, 'tpr' => (int) 1, 'twi' => (int) 2, 'vmu' => (int) 1 ) $gf_gene_species = 'vmu' $gf_gene_id = 'VMungo1309G0868' $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' => 'HOM05D001729', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '375', 'num_species' => '42' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'Ah.07g204710' => 'amhyb', 'AUR62006001' => 'cqu', 'AUR62006002' => 'cqu', 'AUR62006003' => 'cqu', 'AUR62015641' => 'cqu', 'AUR62027174' => 'cqu', 'AUR62035623' => 'cqu', 'AUR62035624' => 'cqu', 'AUR62035625' => 'cqu', 'AUR62035626' => 'cqu', 'CAN.G1110.53' => 'can', 'CANSAT80G0415' => 'cansat', 'Ca_21364_v3' => 'car', 'COL.COLO4_30693' => 'col', 'COL.COLO4_30694' => 'col', 'COL.COLO4_30695' => 'col', 'COL.COLO4_30696' => 'col', 'COL.COLO4_34020' => 'col', 'DCAR_004585' => 'dca', 'Dinv04029' => 'din', 'Dinv34857' => 'din', 'Duzib147G0011' => 'dzi', 'Duzib170G0599' => 'dzi', 'Duzib192G1051' => 'dzi', 'FAN01G0708' => 'fan', 'FAN01G0742' => 'fan', 'FAN02G0048' => 'fan', 'FAN02G0583' => 'fan', 'FAN02G0688' => 'fan', 'FAN02G1588' => 'fan', 'FAN02G2194' => 'fan', 'FAN02G2750' => 'fan', 'FAN02G3094' => 'fan', 'FAN02G3887' => 'fan', 'FAN02G3911' => 'fan', 'FAN02G3994' => 'fan', 'FAN02G4432' => 'fan', 'FAN02G4556' => 'fan', 'FAN03G1977' => 'fan', 'FAN03G2781' => 'fan', 'FAN03G2850' => 'fan', 'FAN03G3155' => 'fan', 'FAN04G2487' => 'fan', 'FAN05G0208' => 'fan', 'FAN05G0656' => 'fan', 'FAN05G0696' => 'fan', 'FAN05G0810' => 'fan', 'FAN05G1447' => 'fan', 'FAN05G2640' => 'fan', 'FAN05G2911' => 'fan', 'FAN05G3901' => 'fan', 'FAN05G4859' => 'fan', 'FAN05G4861' => 'fan', 'FAN05G4988' => 'fan', 'FAN05G5187' => 'fan', 'FAN05G5452' => 'fan', 'FAN05G5500' => 'fan', 'FAN05G5688' => 'fan', 'FAN06G0177' => 'fan', 'FAN06G0675' => 'fan', 'FAN06G1290' => 'fan', 'FAN06G2191' => 'fan', 'FAN06G2405' => 'fan', 'FAN06G3231' => 'fan', 'FAN06G3932' => 'fan', 'FAN07G0163' => 'fan', 'FAN07G0471' => 'fan', 'FAN07G1354' => 'fan', 'FAN08G0338' => 'fan', 'FAN08G1373' => 'fan', 'FAN08G2539' => 'fan', 'FAN08G2728' => 'fan', 'FAN09G0608' => 'fan', 'FAN09G1136' => 'fan', 'FAN09G1958' => 'fan', 'FAN09G2508' => 'fan', 'FAN09G2597' => 'fan', 'FAN09G2658' => 'fan', 'FAN09G2757' => 'fan', 'FAN09G2983' => 'fan', 'FAN09G3130' => 'fan', 'FAN09G3565' => 'fan', 'FAN09G3613' => 'fan', 'FAN09G4011' => 'fan', 'FAN09G4239' => 'fan', 'FAN09G4277' => 'fan', 'FAN09G4720' => 'fan', 'FAN11G0139' => 'fan', 'FAN11G1727' => 'fan', 'FAN11G2672' => 'fan', 'FAN11G2795' => 'fan', 'FAN11G3238' => 'fan', 'FAN11G3734' => 'fan', 'FAN12G0631' => 'fan', 'FAN12G2239' => 'fan', 'FAN12G2308' => 'fan', 'FAN12G2569' => 'fan', 'FAN12G2623' => 'fan', 'FAN13G3182' => 'fan', 'FAN14G0053' => 'fan', 'FAN14G0370' => 'fan', 'FAN14G0382' => 'fan', 'FAN14G0421' => 'fan', 'FAN14G0866' => 'fan', 'FAN14G1187' => 'fan', 'FAN14G1727' => 'fan', 'FAN14G1791' => 'fan', 'FAN14G2361' => 'fan', 'FAN14G2668' => 'fan', 'FAN14G2770' => 'fan', 'FAN14G2874' => 'fan', 'FAN14G3193' => 'fan', 'FAN14G3624' => 'fan', 'FAN14G3676' => 'fan', 'FAN14G3807' => 'fan', 'FAN14G4082' => 'fan', 'FAN14G4342' => 'fan', 'FAN14G4985' => 'fan', 'FAN14G5126' => 'fan', 'FAN14G5781' => 'fan', 'FAN14G5808' => 'fan', 'FAN14G5949' => 'fan', 'FAN15G0828' => 'fan', 'FAN15G1054' => 'fan', 'FAN15G2023' => 'fan', 'FAN15G2506' => 'fan', 'FAN16G0128' => 'fan', 'FAN16G0249' => 'fan', 'FAN16G0429' => 'fan', 'FAN16G1493' => 'fan', 'FAN16G2210' => 'fan', 'FAN16G2506' => 'fan', 'FAN18G1542' => 'fan', 'FAN18G4057' => 'fan', 'FAN19G0745' => 'fan', 'FAN19G1216' => 'fan', 'FAN19G1733' => 'fan', 'FAN20G0258' => 'fan', 'FAN20G1095' => 'fan', 'FAN20G1557' => 'fan', 'FAN21G0302' => 'fan', 'FAN21G0519' => 'fan', 'FAN21G0970' => 'fan', 'FAN21G1159' => 'fan', 'FAN21G1312' => 'fan', 'FAN21G1440' => 'fan', 'FAN21G1715' => 'fan', 'FAN23G1584' => 'fan', 'FAN24G0045' => 'fan', 'FAN24G0053' => 'fan', 'FAN24G1500' => 'fan', 'FAN24G1817' => 'fan', 'FAN24G2147' => 'fan', 'FAN24G2236' => 'fan', 'FAN24G2446' => 'fan', 'FAN24G2684' => 'fan', 'FAN25G0187' => 'fan', 'FAN25G0505' => 'fan', 'FAN25G0589' => 'fan', 'FAN25G3663' => 'fan', 'FAN26G1025' => 'fan', 'FAN26G2860' => 'fan', 'FAN27G1329' => 'fan', 'FAN27G3392' => 'fan', 'FvH4_1g02011' => 'fve', 'FvH4_1g06511' => 'fve', 'FvH4_2g19900' => 'fve', 'FvH4_2g19920' => 'fve', 'FvH4_2g24261' => 'fve', 'FvH4_2g24270' => 'fve', 'FvH4_2g24631' => 'fve', 'FvH4_2g30622' => 'fve', 'FvH4_3g12920' => 'fve', 'FvH4_3g30171' => 'fve', 'FvH4_3g35490' => 'fve', 'FvH4_3g43682' => 'fve', 'FvH4_3g43730' => 'fve', 'FvH4_3g43732' => 'fve', 'FvH4_3g43751' => 'fve', 'FvH4_3g43752' => 'fve', 'FvH4_3g43770' => 'fve', 'FvH4_3g44471' => 'fve', 'FvH4_3g44510' => 'fve', 'FvH4_3g44582' => 'fve', 'FvH4_4g16921' => 'fve', 'FvH4_4g17121' => 'fve', 'FvH4_4g17782' => 'fve', 'FvH4_4g17783' => 'fve', 'FvH4_4g18120' => 'fve', 'FvH4_4g31310' => 'fve', 'FvH4_4g35052' => 'fve', 'FvH4_5g30862' => 'fve', 'FvH4_6g01541' => 'fve', 'FvH4_6g02021' => 'fve', 'FvH4_6g02041' => 'fve', 'FvH4_6g02071' => 'fve', 'FvH4_6g02171' => 'fve', 'FvH4_6g03181' => 'fve', 'FvH4_6g03182' => 'fve', 'FvH4_6g03221' => 'fve', 'FvH4_6g03380' => 'fve', 'FvH4_6g05201' => 'fve', 'FvH4_6g05203' => 'fve', 'FvH4_6g20231' => 'fve', 'FvH4_6g31981' => 'fve', 'FvH4_6g32061' => 'fve', 'FvH4_6g37041' => 'fve', 'FvH4_6g37932' => 'fve', 'FvH4_6g38731' => 'fve', 'FvH4_6g39370' => 'fve', 'FvH4_6g39371' => 'fve', 'FvH4_6g40891' => 'fve', 'FvH4_6g40892' => 'fve', 'FvH4_6g43143' => 'fve', 'FvH4_6g45251' => 'fve', 'FvH4_6g45260' => 'fve', 'FvH4_6g45291' => 'fve', 'FvH4_6g45890' => 'fve', 'FvH4_6g46240' => 'fve', 'FvH4_6g46241' => 'fve', 'FvH4_6g46242' => 'fve', 'FvH4_6g46260' => 'fve', 'FvH4_6g46280' => 'fve', 'FvH4_6g46380' => 'fve', 'FvH4_7g12841' => 'fve', 'FvH4_7g31431' => 'fve', 'Glyma.09G075900' => 'gma', 'Gohir.A09G096401' => 'ghi', 'Gohir.D09G096101' => 'ghi', 'Gorai.006G112800' => 'gra', 'HanXRQChr04g0121411' => 'han', 'Hund15878' => 'sun', 'Lj2A1107G68' => 'lonja', 'Lj2A630G63' => 'lonja', 'Lj2A946T25' => 'lonja', 'Lj2C714T1' => 'lonja', 'Lj2C966T3' => 'lonja', 'Lj2C966T4' => 'lonja', 'Lj4g0002979' => 'lja', 'Lsat_1_v5_gn_5_30901' => 'lsa', 'Lsat_1_v5_gn_5_31100' => 'lsa', 'Lsat_1_v5_gn_5_38600' => 'lsa', 'Lsat_1_v5_gn_6_92061' => 'lsa', 'Manes.05G071301' => 'mes', 'MD02G1008700' => 'mdo', 'MD02G1008900' => 'mdo', 'MD03G1256400' => 'mdo', 'MD04G1180900' => 'mdo', 'MD04G1181000' => 'mdo', 'MD04G1181200' => 'mdo', 'MD05G1244200' => 'mdo', 'MD05G1324200' => 'mdo', 'MD09G1201600' => 'mdo', 'MD10G1000600' => 'mdo', 'MD14G1026900' => 'mdo', 'MD14G1187900' => 'mdo', 'MD15G1017800' => 'mdo', 'MD15G1018100' => 'mdo', 'Medtr4g124160' => 'mtr', 'Migut.L01260' => 'egut', 'Nitab4.5_0000008g0440' => 'nta', 'Nitab4.5_0000207g0170' => 'nta', 'Nitab4.5_0007671g0030' => 'nta', 'Nitab4.5_0010853g0020' => 'nta', 'Oeu057656.1' => 'oeu', 'PGSC0003DMG400005638' => 'stu', 'PGSC0003DMG400005639' => 'stu', 'Phvul.009G222800' => 'pvu', 'Potri.009G132400' => 'ptr', 'Potri.009G163001' => 'ptr', 'Potri.011G000700' => 'ptr', 'Potri.011G004800' => 'ptr', 'Prupe.1G509300' => 'ppe', 'Prupe.1G509700' => 'ppe', 'Prupe.1G510400' => 'ppe', 'Prupe.1G510700' => 'ppe', 'Prupe.1G512600' => 'ppe', 'Prupe.2G073200' => 'ppe', 'Prupe.3G059500' => 'ppe', 'Prupe.3G059600' => 'ppe', 'Prupe.3G246100' => 'ppe', 'Prupe.3G265100' => 'ppe', 'Prupe.4G034700' => 'ppe', 'Prupe.4G052100' => 'ppe', 'Prupe.4G053600' => 'ppe', 'Prupe.5G068800' => 'ppe', 'Prupe.5G070600' => 'ppe', 'Prupe.6G075400' => 'ppe', 'Prupe.6G075500' => 'ppe', 'Prupe.6G076400' => 'ppe', 'Prupe.8G110700' => 'ppe', 'Psat4g020960' => 'psa', 'PSO135G0788' => 'pso', 'PSO210G6463' => 'pso', 'PSO384G0370' => 'pso', 'PSO386G0056' => 'pso', 'QL01p006048' => 'qlo', 'QL02p054283' => 'qlo', 'QL05p008000' => 'qlo', 'QL05p008212' => 'qlo', 'QL05p008950' => 'qlo', 'QL05p009042' => 'qlo', 'QL05p009518' => 'qlo', 'QL05p012589' => 'qlo', 'QL05p012608' => 'qlo', 'QL05p012650' => 'qlo', 'QL05p012667' => 'qlo', 'QL05p014501' => 'qlo', 'QL05p052800' => 'qlo', 'QL05p065010' => 'qlo', 'QL05p074156' => 'qlo', 'QL05p074160' => 'qlo', 'QL05p074174' => 'qlo', 'QL05p074178' => 'qlo', 'QL05p074214' => 'qlo', 'QL06p001050' => 'qlo', 'QL06p001056' => 'qlo', 'QL06p006093' => 'qlo', 'QL06p006111' => 'qlo', 'QL07p019784' => 'qlo', 'QL07p019801' => 'qlo', 'QL07p036110' => 'qlo', 'QL07p036134' => 'qlo', 'QL07p036147' => 'qlo', 'QL07p036156' => 'qlo', 'QL07p036300' => 'qlo', 'QL07p036320' => 'qlo', 'QL08p014547' => 'qlo', 'QL08p014551' => 'qlo', 'QL08p043319' => 'qlo', 'QL08p043324' => 'qlo', 'QL11p009094' => 'qlo', 'RcHm_v2.0_Chr1g0380481' => 'rch', 'RcHm_v2.0_Chr2g0089331' => 'rch', 'RcHm_v2.0_Chr2g0123691' => 'rch', 'RcHm_v2.0_Chr2g0151111' => 'rch', 'RcHm_v2.0_Chr2g0163011' => 'rch', 'RcHm_v2.0_Chr2g0163051' => 'rch', 'RcHm_v2.0_Chr2g0164671' => 'rch', 'RcHm_v2.0_Chr2g0164681' => 'rch', 'RcHm_v2.0_Chr2g0164721' => 'rch', 'RcHm_v2.0_Chr3g0449911' => 'rch', 'RcHm_v2.0_Chr3g0450211' => 'rch', 'RcHm_v2.0_Chr3g0457271' => 'rch', 'RcHm_v2.0_Chr5g0018111' => 'rch', 'RcHm_v2.0_Chr5g0021011' => 'rch', 'RcHm_v2.0_Chr5g0081171' => 'rch', 'RcHm_v2.0_Chr5g0081211' => 'rch', 'RcHm_v2.0_Chr6g0275871' => 'rch', 'RcHm_v2.0_Chr6g0276071' => 'rch', 'RcHm_v2.0_Chr6g0285591' => 'rch', 'RcHm_v2.0_Chr6g0291931' => 'rch', 'RcHm_v2.0_Chr6g0292091' => 'rch', 'RcHm_v2.0_Chr6g0292271' => 'rch', 'RcHm_v2.0_Chr7g0221261' => 'rch', 'Rhsim08G0219900' => 'rsi', 'Rhsim08G0220200' => 'rsi', 'Rhsim08G0237800' => 'rsi', 'Rhsim08G0238800' => 'rsi', 'Sabra09G0102700' => 'sbr', 'Sabra09G0127200' => 'sbr', 'Sabra11G0003700' => 'sbr', 'Sabra15G0014700' => 'sbr', 'Sc19g0000590' => 'sci', 'Sc19g0001870' => 'sci', 'SGA_v2.0_scaffold1G00346' => 'sas', 'SGA_v2.0_scaffold1G00575' => 'sas', 'SGA_v2.0_scaffold1G00761' => 'sas', 'SGA_v2.0_scaffold232G43501' => 'sas', 'TAR625G1137' => 'tar', 'Thecc.03G222100' => 'tca', 'TPR.G12691' => 'tpr', 'TWI34G0727' => 'twi', 'TWI36G0117' => 'twi', 'VMungo1309G0868' => 'vmu' ), 'gf_id' => 'HOM05D001729', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001729' ), 'data_identifier' => 'HOM05D001729', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001729', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '375', 'num_species' => '42' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'Ah.07g204710' => 'amhyb', 'AUR62006001' => 'cqu', 'AUR62006002' => 'cqu', 'AUR62006003' => 'cqu', 'AUR62015641' => 'cqu', 'AUR62027174' => 'cqu', 'AUR62035623' => 'cqu', 'AUR62035624' => 'cqu', 'AUR62035625' => 'cqu', 'AUR62035626' => 'cqu', 'CAN.G1110.53' => 'can', 'CANSAT80G0415' => 'cansat', 'Ca_21364_v3' => 'car', 'COL.COLO4_30693' => 'col', 'COL.COLO4_30694' => 'col', 'COL.COLO4_30695' => 'col', 'COL.COLO4_30696' => 'col', 'COL.COLO4_34020' => 'col', 'DCAR_004585' => 'dca', 'Dinv04029' => 'din', 'Dinv34857' => 'din', 'Duzib147G0011' => 'dzi', 'Duzib170G0599' => 'dzi', 'Duzib192G1051' => 'dzi', 'FAN01G0708' => 'fan', 'FAN01G0742' => 'fan', 'FAN02G0048' => 'fan', 'FAN02G0583' => 'fan', 'FAN02G0688' => 'fan', 'FAN02G1588' => 'fan', 'FAN02G2194' => 'fan', 'FAN02G2750' => 'fan', 'FAN02G3094' => 'fan', 'FAN02G3887' => 'fan', 'FAN02G3911' => 'fan', 'FAN02G3994' => 'fan', 'FAN02G4432' => 'fan', 'FAN02G4556' => 'fan', 'FAN03G1977' => 'fan', 'FAN03G2781' => 'fan', 'FAN03G2850' => 'fan', 'FAN03G3155' => 'fan', 'FAN04G2487' => 'fan', 'FAN05G0208' => 'fan', 'FAN05G0656' => 'fan', 'FAN05G0696' => 'fan', 'FAN05G0810' => 'fan', 'FAN05G1447' => 'fan', 'FAN05G2640' => 'fan', 'FAN05G2911' => 'fan', 'FAN05G3901' => 'fan', 'FAN05G4859' => 'fan', 'FAN05G4861' => 'fan', 'FAN05G4988' => 'fan', 'FAN05G5187' => 'fan', 'FAN05G5452' => 'fan', 'FAN05G5500' => 'fan', 'FAN05G5688' => 'fan', 'FAN06G0177' => 'fan', 'FAN06G0675' => 'fan', 'FAN06G1290' => 'fan', 'FAN06G2191' => 'fan', 'FAN06G2405' => 'fan', 'FAN06G3231' => 'fan', 'FAN06G3932' => 'fan', 'FAN07G0163' => 'fan', 'FAN07G0471' => 'fan', 'FAN07G1354' => 'fan', 'FAN08G0338' => 'fan', 'FAN08G1373' => 'fan', 'FAN08G2539' => 'fan', 'FAN08G2728' => 'fan', 'FAN09G0608' => 'fan', 'FAN09G1136' => 'fan', 'FAN09G1958' => 'fan', 'FAN09G2508' => 'fan', 'FAN09G2597' => 'fan', 'FAN09G2658' => 'fan', 'FAN09G2757' => 'fan', 'FAN09G2983' => 'fan', 'FAN09G3130' => 'fan', 'FAN09G3565' => 'fan', 'FAN09G3613' => 'fan', 'FAN09G4011' => 'fan', 'FAN09G4239' => 'fan', 'FAN09G4277' => 'fan', 'FAN09G4720' => 'fan', 'FAN11G0139' => 'fan', 'FAN11G1727' => 'fan', 'FAN11G2672' => 'fan', 'FAN11G2795' => 'fan', 'FAN11G3238' => 'fan', 'FAN11G3734' => 'fan', 'FAN12G0631' => 'fan', 'FAN12G2239' => 'fan', 'FAN12G2308' => 'fan', 'FAN12G2569' => 'fan', 'FAN12G2623' => 'fan', 'FAN13G3182' => 'fan', 'FAN14G0053' => 'fan', 'FAN14G0370' => 'fan', 'FAN14G0382' => 'fan', 'FAN14G0421' => 'fan', 'FAN14G0866' => 'fan', 'FAN14G1187' => 'fan', 'FAN14G1727' => 'fan', 'FAN14G1791' => 'fan', 'FAN14G2361' => 'fan', 'FAN14G2668' => 'fan', 'FAN14G2770' => 'fan', 'FAN14G2874' => 'fan', 'FAN14G3193' => 'fan', 'FAN14G3624' => 'fan', 'FAN14G3676' => 'fan', 'FAN14G3807' => 'fan', 'FAN14G4082' => 'fan', 'FAN14G4342' => 'fan', 'FAN14G4985' => 'fan', 'FAN14G5126' => 'fan', 'FAN14G5781' => 'fan', 'FAN14G5808' => 'fan', 'FAN14G5949' => 'fan', 'FAN15G0828' => 'fan', 'FAN15G1054' => 'fan', 'FAN15G2023' => 'fan', 'FAN15G2506' => 'fan', 'FAN16G0128' => 'fan', 'FAN16G0249' => 'fan', 'FAN16G0429' => 'fan', 'FAN16G1493' => 'fan', 'FAN16G2210' => 'fan', 'FAN16G2506' => 'fan', 'FAN18G1542' => 'fan', 'FAN18G4057' => 'fan', 'FAN19G0745' => 'fan', 'FAN19G1216' => 'fan', 'FAN19G1733' => 'fan', 'FAN20G0258' => 'fan', 'FAN20G1095' => 'fan', 'FAN20G1557' => 'fan', 'FAN21G0302' => 'fan', 'FAN21G0519' => 'fan', 'FAN21G0970' => 'fan', 'FAN21G1159' => 'fan', 'FAN21G1312' => 'fan', 'FAN21G1440' => 'fan', 'FAN21G1715' => 'fan', 'FAN23G1584' => 'fan', 'FAN24G0045' => 'fan', 'FAN24G0053' => 'fan', 'FAN24G1500' => 'fan', 'FAN24G1817' => 'fan', 'FAN24G2147' => 'fan', 'FAN24G2236' => 'fan', 'FAN24G2446' => 'fan', 'FAN24G2684' => 'fan', 'FAN25G0187' => 'fan', 'FAN25G0505' => 'fan', 'FAN25G0589' => 'fan', 'FAN25G3663' => 'fan', 'FAN26G1025' => 'fan', 'FAN26G2860' => 'fan', 'FAN27G1329' => 'fan', 'FAN27G3392' => 'fan', 'FvH4_1g02011' => 'fve', 'FvH4_1g06511' => 'fve', 'FvH4_2g19900' => 'fve', 'FvH4_2g19920' => 'fve', 'FvH4_2g24261' => 'fve', 'FvH4_2g24270' => 'fve', 'FvH4_2g24631' => 'fve', 'FvH4_2g30622' => 'fve', 'FvH4_3g12920' => 'fve', 'FvH4_3g30171' => 'fve', 'FvH4_3g35490' => 'fve', 'FvH4_3g43682' => 'fve', 'FvH4_3g43730' => 'fve', 'FvH4_3g43732' => 'fve', 'FvH4_3g43751' => 'fve', 'FvH4_3g43752' => 'fve', 'FvH4_3g43770' => 'fve', 'FvH4_3g44471' => 'fve', 'FvH4_3g44510' => 'fve', 'FvH4_3g44582' => 'fve', 'FvH4_4g16921' => 'fve', 'FvH4_4g17121' => 'fve', 'FvH4_4g17782' => 'fve', 'FvH4_4g17783' => 'fve', 'FvH4_4g18120' => 'fve', 'FvH4_4g31310' => 'fve', 'FvH4_4g35052' => 'fve', 'FvH4_5g30862' => 'fve', 'FvH4_6g01541' => 'fve', 'FvH4_6g02021' => 'fve', 'FvH4_6g02041' => 'fve', 'FvH4_6g02071' => 'fve', 'FvH4_6g02171' => 'fve', 'FvH4_6g03181' => 'fve', 'FvH4_6g03182' => 'fve', 'FvH4_6g03221' => 'fve', 'FvH4_6g03380' => 'fve', 'FvH4_6g05201' => 'fve', 'FvH4_6g05203' => 'fve', 'FvH4_6g20231' => 'fve', 'FvH4_6g31981' => 'fve', 'FvH4_6g32061' => 'fve', 'FvH4_6g37041' => 'fve', 'FvH4_6g37932' => 'fve', 'FvH4_6g38731' => 'fve', 'FvH4_6g39370' => 'fve', 'FvH4_6g39371' => 'fve', 'FvH4_6g40891' => 'fve', 'FvH4_6g40892' => 'fve', 'FvH4_6g43143' => 'fve', 'FvH4_6g45251' => 'fve', 'FvH4_6g45260' => 'fve', 'FvH4_6g45291' => 'fve', 'FvH4_6g45890' => 'fve', 'FvH4_6g46240' => 'fve', 'FvH4_6g46241' => 'fve', 'FvH4_6g46242' => 'fve', 'FvH4_6g46260' => 'fve', 'FvH4_6g46280' => 'fve', 'FvH4_6g46380' => 'fve', 'FvH4_7g12841' => 'fve', 'FvH4_7g31431' => 'fve', 'Glyma.09G075900' => 'gma', 'Gohir.A09G096401' => 'ghi', 'Gohir.D09G096101' => 'ghi', 'Gorai.006G112800' => 'gra', 'HanXRQChr04g0121411' => 'han', 'Hund15878' => 'sun', 'Lj2A1107G68' => 'lonja', 'Lj2A630G63' => 'lonja', 'Lj2A946T25' => 'lonja', 'Lj2C714T1' => 'lonja', 'Lj2C966T3' => 'lonja', 'Lj2C966T4' => 'lonja', 'Lj4g0002979' => 'lja', 'Lsat_1_v5_gn_5_30901' => 'lsa', 'Lsat_1_v5_gn_5_31100' => 'lsa', 'Lsat_1_v5_gn_5_38600' => 'lsa', 'Lsat_1_v5_gn_6_92061' => 'lsa', 'Manes.05G071301' => 'mes', 'MD02G1008700' => 'mdo', 'MD02G1008900' => 'mdo', 'MD03G1256400' => 'mdo', 'MD04G1180900' => 'mdo', 'MD04G1181000' => 'mdo', 'MD04G1181200' => 'mdo', 'MD05G1244200' => 'mdo', 'MD05G1324200' => 'mdo', 'MD09G1201600' => 'mdo', 'MD10G1000600' => 'mdo', 'MD14G1026900' => 'mdo', 'MD14G1187900' => 'mdo', 'MD15G1017800' => 'mdo', 'MD15G1018100' => 'mdo', 'Medtr4g124160' => 'mtr', 'Migut.L01260' => 'egut', 'Nitab4.5_0000008g0440' => 'nta', 'Nitab4.5_0000207g0170' => 'nta', 'Nitab4.5_0007671g0030' => 'nta', 'Nitab4.5_0010853g0020' => 'nta', 'Oeu057656.1' => 'oeu', 'PGSC0003DMG400005638' => 'stu', 'PGSC0003DMG400005639' => 'stu', 'Phvul.009G222800' => 'pvu', 'Potri.009G132400' => 'ptr', 'Potri.009G163001' => 'ptr', 'Potri.011G000700' => 'ptr', 'Potri.011G004800' => 'ptr', 'Prupe.1G509300' => 'ppe', 'Prupe.1G509700' => 'ppe', 'Prupe.1G510400' => 'ppe', 'Prupe.1G510700' => 'ppe', 'Prupe.1G512600' => 'ppe', 'Prupe.2G073200' => 'ppe', 'Prupe.3G059500' => 'ppe', 'Prupe.3G059600' => 'ppe', 'Prupe.3G246100' => 'ppe', 'Prupe.3G265100' => 'ppe', 'Prupe.4G034700' => 'ppe', 'Prupe.4G052100' => 'ppe', 'Prupe.4G053600' => 'ppe', 'Prupe.5G068800' => 'ppe', 'Prupe.5G070600' => 'ppe', 'Prupe.6G075400' => 'ppe', 'Prupe.6G075500' => 'ppe', 'Prupe.6G076400' => 'ppe', 'Prupe.8G110700' => 'ppe', 'Psat4g020960' => 'psa', 'PSO135G0788' => 'pso', 'PSO210G6463' => 'pso', 'PSO384G0370' => 'pso', 'PSO386G0056' => 'pso', 'QL01p006048' => 'qlo', 'QL02p054283' => 'qlo', 'QL05p008000' => 'qlo', 'QL05p008212' => 'qlo', 'QL05p008950' => 'qlo', 'QL05p009042' => 'qlo', 'QL05p009518' => 'qlo', 'QL05p012589' => 'qlo', 'QL05p012608' => 'qlo', 'QL05p012650' => 'qlo', 'QL05p012667' => 'qlo', 'QL05p014501' => 'qlo', 'QL05p052800' => 'qlo', 'QL05p065010' => 'qlo', 'QL05p074156' => 'qlo', 'QL05p074160' => 'qlo', 'QL05p074174' => 'qlo', 'QL05p074178' => 'qlo', 'QL05p074214' => 'qlo', 'QL06p001050' => 'qlo', 'QL06p001056' => 'qlo', 'QL06p006093' => 'qlo', 'QL06p006111' => 'qlo', 'QL07p019784' => 'qlo', 'QL07p019801' => 'qlo', 'QL07p036110' => 'qlo', 'QL07p036134' => 'qlo', 'QL07p036147' => 'qlo', 'QL07p036156' => 'qlo', 'QL07p036300' => 'qlo', 'QL07p036320' => 'qlo', 'QL08p014547' => 'qlo', 'QL08p014551' => 'qlo', 'QL08p043319' => 'qlo', 'QL08p043324' => 'qlo', 'QL11p009094' => 'qlo', 'RcHm_v2.0_Chr1g0380481' => 'rch', 'RcHm_v2.0_Chr2g0089331' => 'rch', 'RcHm_v2.0_Chr2g0123691' => 'rch', 'RcHm_v2.0_Chr2g0151111' => 'rch', 'RcHm_v2.0_Chr2g0163011' => 'rch', 'RcHm_v2.0_Chr2g0163051' => 'rch', 'RcHm_v2.0_Chr2g0164671' => 'rch', 'RcHm_v2.0_Chr2g0164681' => 'rch', 'RcHm_v2.0_Chr2g0164721' => 'rch', 'RcHm_v2.0_Chr3g0449911' => 'rch', 'RcHm_v2.0_Chr3g0450211' => 'rch', 'RcHm_v2.0_Chr3g0457271' => 'rch', 'RcHm_v2.0_Chr5g0018111' => 'rch', 'RcHm_v2.0_Chr5g0021011' => 'rch', 'RcHm_v2.0_Chr5g0081171' => 'rch', 'RcHm_v2.0_Chr5g0081211' => 'rch', 'RcHm_v2.0_Chr6g0275871' => 'rch', 'RcHm_v2.0_Chr6g0276071' => 'rch', 'RcHm_v2.0_Chr6g0285591' => 'rch', 'RcHm_v2.0_Chr6g0291931' => 'rch', 'RcHm_v2.0_Chr6g0292091' => 'rch', 'RcHm_v2.0_Chr6g0292271' => 'rch', 'RcHm_v2.0_Chr7g0221261' => 'rch', 'Rhsim08G0219900' => 'rsi', 'Rhsim08G0220200' => 'rsi', 'Rhsim08G0237800' => 'rsi', 'Rhsim08G0238800' => 'rsi', 'Sabra09G0102700' => 'sbr', 'Sabra09G0127200' => 'sbr', 'Sabra11G0003700' => 'sbr', 'Sabra15G0014700' => 'sbr', 'Sc19g0000590' => 'sci', 'Sc19g0001870' => 'sci', 'SGA_v2.0_scaffold1G00346' => 'sas', 'SGA_v2.0_scaffold1G00575' => 'sas', 'SGA_v2.0_scaffold1G00761' => 'sas', 'SGA_v2.0_scaffold232G43501' => 'sas', 'TAR625G1137' => 'tar', 'Thecc.03G222100' => 'tca', 'TPR.G12691' => 'tpr', 'TWI34G0727' => 'twi', 'TWI36G0117' => 'twi', 'VMungo1309G0868' => 'vmu' ) $gf_id = 'HOM05D001729' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001729' ) $data_identifier = 'HOM05D001729' $data_type = 'gf_id' $species_gene_counts = array( 'amhyb' => (int) 1, 'cqu' => (int) 9, 'can' => (int) 1, 'cansat' => (int) 1, 'car' => (int) 1, 'col' => (int) 5, 'dca' => (int) 1, 'din' => (int) 2, 'dzi' => (int) 3, 'fan' => (int) 140, 'fve' => (int) 62, 'gma' => (int) 1, 'ghi' => (int) 2, 'gra' => (int) 1, 'han' => (int) 1, 'sun' => (int) 1, 'lonja' => (int) 6, 'lja' => (int) 1, 'lsa' => (int) 4, 'mes' => (int) 1, 'mdo' => (int) 14, 'mtr' => (int) 1, 'egut' => (int) 1, 'nta' => (int) 4, 'oeu' => (int) 1, 'stu' => (int) 2, 'pvu' => (int) 1, 'ptr' => (int) 4, 'ppe' => (int) 19, 'psa' => (int) 1, 'pso' => (int) 4, 'qlo' => (int) 36, 'rch' => (int) 23, 'rsi' => (int) 4, 'sbr' => (int) 4, 'sci' => (int) 2, 'sas' => (int) 4, 'tar' => (int) 1, 'tca' => (int) 1, 'tpr' => (int) 1, 'twi' => (int) 2, 'vmu' => (int) 1 ) $gf_gene_species = 'vmu' $gf_gene_id = 'VMungo1309G0868' $species_info = array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ) $local_species = 'cqu' $disabled = '' $selected = '' $num_hits = (int) 0include - APP/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp, line 33 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933 View::_renderElement() - CORE/Cake/View/View.php, line 1224 View::element() - CORE/Cake/View/View.php, line 418 include - APP/View/Elements/analysis/phylogenetics_module/gf_data_settings.ctp, line 37 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933 View::_renderElement() - CORE/Cake/View/View.php, line 1224 View::element() - CORE/Cake/View/View.php, line 418 include - APP/View/Elements/analysis/phylogenetics_module/parameter_selection.ctp, line 64 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933 View::_renderElement() - CORE/Cake/View/View.php, line 1224 View::element() - CORE/Cake/View/View.php, line 418 include - APP/View/Analysis/custom_tree_creation.ctp, line 27 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933
$viewFile = '/www/bioinformatics01_ro/plaza/_dev_instances/feedback/app/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp' $dataForView = array( 'sidebar_info' => array( 'gf_id' => 'HOM05D001729', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '375', 'num_species' => '42' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'Ah.07g204710' => 'amhyb', 'AUR62006001' => 'cqu', 'AUR62006002' => 'cqu', 'AUR62006003' => 'cqu', 'AUR62015641' => 'cqu', 'AUR62027174' => 'cqu', 'AUR62035623' => 'cqu', 'AUR62035624' => 'cqu', 'AUR62035625' => 'cqu', 'AUR62035626' => 'cqu', 'CAN.G1110.53' => 'can', 'CANSAT80G0415' => 'cansat', 'Ca_21364_v3' => 'car', 'COL.COLO4_30693' => 'col', 'COL.COLO4_30694' => 'col', 'COL.COLO4_30695' => 'col', 'COL.COLO4_30696' => 'col', 'COL.COLO4_34020' => 'col', 'DCAR_004585' => 'dca', 'Dinv04029' => 'din', 'Dinv34857' => 'din', 'Duzib147G0011' => 'dzi', 'Duzib170G0599' => 'dzi', 'Duzib192G1051' => 'dzi', 'FAN01G0708' => 'fan', 'FAN01G0742' => 'fan', 'FAN02G0048' => 'fan', 'FAN02G0583' => 'fan', 'FAN02G0688' => 'fan', 'FAN02G1588' => 'fan', 'FAN02G2194' => 'fan', 'FAN02G2750' => 'fan', 'FAN02G3094' => 'fan', 'FAN02G3887' => 'fan', 'FAN02G3911' => 'fan', 'FAN02G3994' => 'fan', 'FAN02G4432' => 'fan', 'FAN02G4556' => 'fan', 'FAN03G1977' => 'fan', 'FAN03G2781' => 'fan', 'FAN03G2850' => 'fan', 'FAN03G3155' => 'fan', 'FAN04G2487' => 'fan', 'FAN05G0208' => 'fan', 'FAN05G0656' => 'fan', 'FAN05G0696' => 'fan', 'FAN05G0810' => 'fan', 'FAN05G1447' => 'fan', 'FAN05G2640' => 'fan', 'FAN05G2911' => 'fan', 'FAN05G3901' => 'fan', 'FAN05G4859' => 'fan', 'FAN05G4861' => 'fan', 'FAN05G4988' => 'fan', 'FAN05G5187' => 'fan', 'FAN05G5452' => 'fan', 'FAN05G5500' => 'fan', 'FAN05G5688' => 'fan', 'FAN06G0177' => 'fan', 'FAN06G0675' => 'fan', 'FAN06G1290' => 'fan', 'FAN06G2191' => 'fan', 'FAN06G2405' => 'fan', 'FAN06G3231' => 'fan', 'FAN06G3932' => 'fan', 'FAN07G0163' => 'fan', 'FAN07G0471' => 'fan', 'FAN07G1354' => 'fan', 'FAN08G0338' => 'fan', 'FAN08G1373' => 'fan', 'FAN08G2539' => 'fan', 'FAN08G2728' => 'fan', 'FAN09G0608' => 'fan', 'FAN09G1136' => 'fan', 'FAN09G1958' => 'fan', 'FAN09G2508' => 'fan', 'FAN09G2597' => 'fan', 'FAN09G2658' => 'fan', 'FAN09G2757' => 'fan', 'FAN09G2983' => 'fan', 'FAN09G3130' => 'fan', 'FAN09G3565' => 'fan', 'FAN09G3613' => 'fan', 'FAN09G4011' => 'fan', 'FAN09G4239' => 'fan', 'FAN09G4277' => 'fan', 'FAN09G4720' => 'fan', 'FAN11G0139' => 'fan', 'FAN11G1727' => 'fan', 'FAN11G2672' => 'fan', 'FAN11G2795' => 'fan', 'FAN11G3238' => 'fan', 'FAN11G3734' => 'fan', 'FAN12G0631' => 'fan', 'FAN12G2239' => 'fan', 'FAN12G2308' => 'fan', 'FAN12G2569' => 'fan', 'FAN12G2623' => 'fan', 'FAN13G3182' => 'fan', 'FAN14G0053' => 'fan', 'FAN14G0370' => 'fan', 'FAN14G0382' => 'fan', 'FAN14G0421' => 'fan', 'FAN14G0866' => 'fan', 'FAN14G1187' => 'fan', 'FAN14G1727' => 'fan', 'FAN14G1791' => 'fan', 'FAN14G2361' => 'fan', 'FAN14G2668' => 'fan', 'FAN14G2770' => 'fan', 'FAN14G2874' => 'fan', 'FAN14G3193' => 'fan', 'FAN14G3624' => 'fan', 'FAN14G3676' => 'fan', 'FAN14G3807' => 'fan', 'FAN14G4082' => 'fan', 'FAN14G4342' => 'fan', 'FAN14G4985' => 'fan', 'FAN14G5126' => 'fan', 'FAN14G5781' => 'fan', 'FAN14G5808' => 'fan', 'FAN14G5949' => 'fan', 'FAN15G0828' => 'fan', 'FAN15G1054' => 'fan', 'FAN15G2023' => 'fan', 'FAN15G2506' => 'fan', 'FAN16G0128' => 'fan', 'FAN16G0249' => 'fan', 'FAN16G0429' => 'fan', 'FAN16G1493' => 'fan', 'FAN16G2210' => 'fan', 'FAN16G2506' => 'fan', 'FAN18G1542' => 'fan', 'FAN18G4057' => 'fan', 'FAN19G0745' => 'fan', 'FAN19G1216' => 'fan', 'FAN19G1733' => 'fan', 'FAN20G0258' => 'fan', 'FAN20G1095' => 'fan', 'FAN20G1557' => 'fan', 'FAN21G0302' => 'fan', 'FAN21G0519' => 'fan', 'FAN21G0970' => 'fan', 'FAN21G1159' => 'fan', 'FAN21G1312' => 'fan', 'FAN21G1440' => 'fan', 'FAN21G1715' => 'fan', 'FAN23G1584' => 'fan', 'FAN24G0045' => 'fan', 'FAN24G0053' => 'fan', 'FAN24G1500' => 'fan', 'FAN24G1817' => 'fan', 'FAN24G2147' => 'fan', 'FAN24G2236' => 'fan', 'FAN24G2446' => 'fan', 'FAN24G2684' => 'fan', 'FAN25G0187' => 'fan', 'FAN25G0505' => 'fan', 'FAN25G0589' => 'fan', 'FAN25G3663' => 'fan', 'FAN26G1025' => 'fan', 'FAN26G2860' => 'fan', 'FAN27G1329' => 'fan', 'FAN27G3392' => 'fan', 'FvH4_1g02011' => 'fve', 'FvH4_1g06511' => 'fve', 'FvH4_2g19900' => 'fve', 'FvH4_2g19920' => 'fve', 'FvH4_2g24261' => 'fve', 'FvH4_2g24270' => 'fve', 'FvH4_2g24631' => 'fve', 'FvH4_2g30622' => 'fve', 'FvH4_3g12920' => 'fve', 'FvH4_3g30171' => 'fve', 'FvH4_3g35490' => 'fve', 'FvH4_3g43682' => 'fve', 'FvH4_3g43730' => 'fve', 'FvH4_3g43732' => 'fve', 'FvH4_3g43751' => 'fve', 'FvH4_3g43752' => 'fve', 'FvH4_3g43770' => 'fve', 'FvH4_3g44471' => 'fve', 'FvH4_3g44510' => 'fve', 'FvH4_3g44582' => 'fve', 'FvH4_4g16921' => 'fve', 'FvH4_4g17121' => 'fve', 'FvH4_4g17782' => 'fve', 'FvH4_4g17783' => 'fve', 'FvH4_4g18120' => 'fve', 'FvH4_4g31310' => 'fve', 'FvH4_4g35052' => 'fve', 'FvH4_5g30862' => 'fve', 'FvH4_6g01541' => 'fve', 'FvH4_6g02021' => 'fve', 'FvH4_6g02041' => 'fve', 'FvH4_6g02071' => 'fve', 'FvH4_6g02171' => 'fve', 'FvH4_6g03181' => 'fve', 'FvH4_6g03182' => 'fve', 'FvH4_6g03221' => 'fve', 'FvH4_6g03380' => 'fve', 'FvH4_6g05201' => 'fve', 'FvH4_6g05203' => 'fve', 'FvH4_6g20231' => 'fve', 'FvH4_6g31981' => 'fve', 'FvH4_6g32061' => 'fve', 'FvH4_6g37041' => 'fve', 'FvH4_6g37932' => 'fve', 'FvH4_6g38731' => 'fve', 'FvH4_6g39370' => 'fve', 'FvH4_6g39371' => 'fve', 'FvH4_6g40891' => 'fve', 'FvH4_6g40892' => 'fve', 'FvH4_6g43143' => 'fve', 'FvH4_6g45251' => 'fve', 'FvH4_6g45260' => 'fve', 'FvH4_6g45291' => 'fve', 'FvH4_6g45890' => 'fve', 'FvH4_6g46240' => 'fve', 'FvH4_6g46241' => 'fve', 'FvH4_6g46242' => 'fve', 'FvH4_6g46260' => 'fve', 'FvH4_6g46280' => 'fve', 'FvH4_6g46380' => 'fve', 'FvH4_7g12841' => 'fve', 'FvH4_7g31431' => 'fve', 'Glyma.09G075900' => 'gma', 'Gohir.A09G096401' => 'ghi', 'Gohir.D09G096101' => 'ghi', 'Gorai.006G112800' => 'gra', 'HanXRQChr04g0121411' => 'han', 'Hund15878' => 'sun', 'Lj2A1107G68' => 'lonja', 'Lj2A630G63' => 'lonja', 'Lj2A946T25' => 'lonja', 'Lj2C714T1' => 'lonja', 'Lj2C966T3' => 'lonja', 'Lj2C966T4' => 'lonja', 'Lj4g0002979' => 'lja', 'Lsat_1_v5_gn_5_30901' => 'lsa', 'Lsat_1_v5_gn_5_31100' => 'lsa', 'Lsat_1_v5_gn_5_38600' => 'lsa', 'Lsat_1_v5_gn_6_92061' => 'lsa', 'Manes.05G071301' => 'mes', 'MD02G1008700' => 'mdo', 'MD02G1008900' => 'mdo', 'MD03G1256400' => 'mdo', 'MD04G1180900' => 'mdo', 'MD04G1181000' => 'mdo', 'MD04G1181200' => 'mdo', 'MD05G1244200' => 'mdo', 'MD05G1324200' => 'mdo', 'MD09G1201600' => 'mdo', 'MD10G1000600' => 'mdo', 'MD14G1026900' => 'mdo', 'MD14G1187900' => 'mdo', 'MD15G1017800' => 'mdo', 'MD15G1018100' => 'mdo', 'Medtr4g124160' => 'mtr', 'Migut.L01260' => 'egut', 'Nitab4.5_0000008g0440' => 'nta', 'Nitab4.5_0000207g0170' => 'nta', 'Nitab4.5_0007671g0030' => 'nta', 'Nitab4.5_0010853g0020' => 'nta', 'Oeu057656.1' => 'oeu', 'PGSC0003DMG400005638' => 'stu', 'PGSC0003DMG400005639' => 'stu', 'Phvul.009G222800' => 'pvu', 'Potri.009G132400' => 'ptr', 'Potri.009G163001' => 'ptr', 'Potri.011G000700' => 'ptr', 'Potri.011G004800' => 'ptr', 'Prupe.1G509300' => 'ppe', 'Prupe.1G509700' => 'ppe', 'Prupe.1G510400' => 'ppe', 'Prupe.1G510700' => 'ppe', 'Prupe.1G512600' => 'ppe', 'Prupe.2G073200' => 'ppe', 'Prupe.3G059500' => 'ppe', 'Prupe.3G059600' => 'ppe', 'Prupe.3G246100' => 'ppe', 'Prupe.3G265100' => 'ppe', 'Prupe.4G034700' => 'ppe', 'Prupe.4G052100' => 'ppe', 'Prupe.4G053600' => 'ppe', 'Prupe.5G068800' => 'ppe', 'Prupe.5G070600' => 'ppe', 'Prupe.6G075400' => 'ppe', 'Prupe.6G075500' => 'ppe', 'Prupe.6G076400' => 'ppe', 'Prupe.8G110700' => 'ppe', 'Psat4g020960' => 'psa', 'PSO135G0788' => 'pso', 'PSO210G6463' => 'pso', 'PSO384G0370' => 'pso', 'PSO386G0056' => 'pso', 'QL01p006048' => 'qlo', 'QL02p054283' => 'qlo', 'QL05p008000' => 'qlo', 'QL05p008212' => 'qlo', 'QL05p008950' => 'qlo', 'QL05p009042' => 'qlo', 'QL05p009518' => 'qlo', 'QL05p012589' => 'qlo', 'QL05p012608' => 'qlo', 'QL05p012650' => 'qlo', 'QL05p012667' => 'qlo', 'QL05p014501' => 'qlo', 'QL05p052800' => 'qlo', 'QL05p065010' => 'qlo', 'QL05p074156' => 'qlo', 'QL05p074160' => 'qlo', 'QL05p074174' => 'qlo', 'QL05p074178' => 'qlo', 'QL05p074214' => 'qlo', 'QL06p001050' => 'qlo', 'QL06p001056' => 'qlo', 'QL06p006093' => 'qlo', 'QL06p006111' => 'qlo', 'QL07p019784' => 'qlo', 'QL07p019801' => 'qlo', 'QL07p036110' => 'qlo', 'QL07p036134' => 'qlo', 'QL07p036147' => 'qlo', 'QL07p036156' => 'qlo', 'QL07p036300' => 'qlo', 'QL07p036320' => 'qlo', 'QL08p014547' => 'qlo', 'QL08p014551' => 'qlo', 'QL08p043319' => 'qlo', 'QL08p043324' => 'qlo', 'QL11p009094' => 'qlo', 'RcHm_v2.0_Chr1g0380481' => 'rch', 'RcHm_v2.0_Chr2g0089331' => 'rch', 'RcHm_v2.0_Chr2g0123691' => 'rch', 'RcHm_v2.0_Chr2g0151111' => 'rch', 'RcHm_v2.0_Chr2g0163011' => 'rch', 'RcHm_v2.0_Chr2g0163051' => 'rch', 'RcHm_v2.0_Chr2g0164671' => 'rch', 'RcHm_v2.0_Chr2g0164681' => 'rch', 'RcHm_v2.0_Chr2g0164721' => 'rch', 'RcHm_v2.0_Chr3g0449911' => 'rch', 'RcHm_v2.0_Chr3g0450211' => 'rch', 'RcHm_v2.0_Chr3g0457271' => 'rch', 'RcHm_v2.0_Chr5g0018111' => 'rch', 'RcHm_v2.0_Chr5g0021011' => 'rch', 'RcHm_v2.0_Chr5g0081171' => 'rch', 'RcHm_v2.0_Chr5g0081211' => 'rch', 'RcHm_v2.0_Chr6g0275871' => 'rch', 'RcHm_v2.0_Chr6g0276071' => 'rch', 'RcHm_v2.0_Chr6g0285591' => 'rch', 'RcHm_v2.0_Chr6g0291931' => 'rch', 'RcHm_v2.0_Chr6g0292091' => 'rch', 'RcHm_v2.0_Chr6g0292271' => 'rch', 'RcHm_v2.0_Chr7g0221261' => 'rch', 'Rhsim08G0219900' => 'rsi', 'Rhsim08G0220200' => 'rsi', 'Rhsim08G0237800' => 'rsi', 'Rhsim08G0238800' => 'rsi', 'Sabra09G0102700' => 'sbr', 'Sabra09G0127200' => 'sbr', 'Sabra11G0003700' => 'sbr', 'Sabra15G0014700' => 'sbr', 'Sc19g0000590' => 'sci', 'Sc19g0001870' => 'sci', 'SGA_v2.0_scaffold1G00346' => 'sas', 'SGA_v2.0_scaffold1G00575' => 'sas', 'SGA_v2.0_scaffold1G00761' => 'sas', 'SGA_v2.0_scaffold232G43501' => 'sas', 'TAR625G1137' => 'tar', 'Thecc.03G222100' => 'tca', 'TPR.G12691' => 'tpr', 'TWI34G0727' => 'twi', 'TWI36G0117' => 'twi', 'VMungo1309G0868' => 'vmu' ), 'gf_id' => 'HOM05D001729', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001729' ), 'data_identifier' => 'HOM05D001729', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001729', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '375', 'num_species' => '42' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'Ah.07g204710' => 'amhyb', 'AUR62006001' => 'cqu', 'AUR62006002' => 'cqu', 'AUR62006003' => 'cqu', 'AUR62015641' => 'cqu', 'AUR62027174' => 'cqu', 'AUR62035623' => 'cqu', 'AUR62035624' => 'cqu', 'AUR62035625' => 'cqu', 'AUR62035626' => 'cqu', 'CAN.G1110.53' => 'can', 'CANSAT80G0415' => 'cansat', 'Ca_21364_v3' => 'car', 'COL.COLO4_30693' => 'col', 'COL.COLO4_30694' => 'col', 'COL.COLO4_30695' => 'col', 'COL.COLO4_30696' => 'col', 'COL.COLO4_34020' => 'col', 'DCAR_004585' => 'dca', 'Dinv04029' => 'din', 'Dinv34857' => 'din', 'Duzib147G0011' => 'dzi', 'Duzib170G0599' => 'dzi', 'Duzib192G1051' => 'dzi', 'FAN01G0708' => 'fan', 'FAN01G0742' => 'fan', 'FAN02G0048' => 'fan', 'FAN02G0583' => 'fan', 'FAN02G0688' => 'fan', 'FAN02G1588' => 'fan', 'FAN02G2194' => 'fan', 'FAN02G2750' => 'fan', 'FAN02G3094' => 'fan', 'FAN02G3887' => 'fan', 'FAN02G3911' => 'fan', 'FAN02G3994' => 'fan', 'FAN02G4432' => 'fan', 'FAN02G4556' => 'fan', 'FAN03G1977' => 'fan', 'FAN03G2781' => 'fan', 'FAN03G2850' => 'fan', 'FAN03G3155' => 'fan', 'FAN04G2487' => 'fan', 'FAN05G0208' => 'fan', 'FAN05G0656' => 'fan', 'FAN05G0696' => 'fan', 'FAN05G0810' => 'fan', 'FAN05G1447' => 'fan', 'FAN05G2640' => 'fan', 'FAN05G2911' => 'fan', 'FAN05G3901' => 'fan', 'FAN05G4859' => 'fan', 'FAN05G4861' => 'fan', 'FAN05G4988' => 'fan', 'FAN05G5187' => 'fan', 'FAN05G5452' => 'fan', 'FAN05G5500' => 'fan', 'FAN05G5688' => 'fan', 'FAN06G0177' => 'fan', 'FAN06G0675' => 'fan', 'FAN06G1290' => 'fan', 'FAN06G2191' => 'fan', 'FAN06G2405' => 'fan', 'FAN06G3231' => 'fan', 'FAN06G3932' => 'fan', 'FAN07G0163' => 'fan', 'FAN07G0471' => 'fan', 'FAN07G1354' => 'fan', 'FAN08G0338' => 'fan', 'FAN08G1373' => 'fan', 'FAN08G2539' => 'fan', 'FAN08G2728' => 'fan', 'FAN09G0608' => 'fan', 'FAN09G1136' => 'fan', 'FAN09G1958' => 'fan', 'FAN09G2508' => 'fan', 'FAN09G2597' => 'fan', 'FAN09G2658' => 'fan', 'FAN09G2757' => 'fan', 'FAN09G2983' => 'fan', 'FAN09G3130' => 'fan', 'FAN09G3565' => 'fan', 'FAN09G3613' => 'fan', 'FAN09G4011' => 'fan', 'FAN09G4239' => 'fan', 'FAN09G4277' => 'fan', 'FAN09G4720' => 'fan', 'FAN11G0139' => 'fan', 'FAN11G1727' => 'fan', 'FAN11G2672' => 'fan', 'FAN11G2795' => 'fan', 'FAN11G3238' => 'fan', 'FAN11G3734' => 'fan', 'FAN12G0631' => 'fan', 'FAN12G2239' => 'fan', 'FAN12G2308' => 'fan', 'FAN12G2569' => 'fan', 'FAN12G2623' => 'fan', 'FAN13G3182' => 'fan', 'FAN14G0053' => 'fan', 'FAN14G0370' => 'fan', 'FAN14G0382' => 'fan', 'FAN14G0421' => 'fan', 'FAN14G0866' => 'fan', 'FAN14G1187' => 'fan', 'FAN14G1727' => 'fan', 'FAN14G1791' => 'fan', 'FAN14G2361' => 'fan', 'FAN14G2668' => 'fan', 'FAN14G2770' => 'fan', 'FAN14G2874' => 'fan', 'FAN14G3193' => 'fan', 'FAN14G3624' => 'fan', 'FAN14G3676' => 'fan', 'FAN14G3807' => 'fan', 'FAN14G4082' => 'fan', 'FAN14G4342' => 'fan', 'FAN14G4985' => 'fan', 'FAN14G5126' => 'fan', 'FAN14G5781' => 'fan', 'FAN14G5808' => 'fan', 'FAN14G5949' => 'fan', 'FAN15G0828' => 'fan', 'FAN15G1054' => 'fan', 'FAN15G2023' => 'fan', 'FAN15G2506' => 'fan', 'FAN16G0128' => 'fan', 'FAN16G0249' => 'fan', 'FAN16G0429' => 'fan', 'FAN16G1493' => 'fan', 'FAN16G2210' => 'fan', 'FAN16G2506' => 'fan', 'FAN18G1542' => 'fan', 'FAN18G4057' => 'fan', 'FAN19G0745' => 'fan', 'FAN19G1216' => 'fan', 'FAN19G1733' => 'fan', 'FAN20G0258' => 'fan', 'FAN20G1095' => 'fan', 'FAN20G1557' => 'fan', 'FAN21G0302' => 'fan', 'FAN21G0519' => 'fan', 'FAN21G0970' => 'fan', 'FAN21G1159' => 'fan', 'FAN21G1312' => 'fan', 'FAN21G1440' => 'fan', 'FAN21G1715' => 'fan', 'FAN23G1584' => 'fan', 'FAN24G0045' => 'fan', 'FAN24G0053' => 'fan', 'FAN24G1500' => 'fan', 'FAN24G1817' => 'fan', 'FAN24G2147' => 'fan', 'FAN24G2236' => 'fan', 'FAN24G2446' => 'fan', 'FAN24G2684' => 'fan', 'FAN25G0187' => 'fan', 'FAN25G0505' => 'fan', 'FAN25G0589' => 'fan', 'FAN25G3663' => 'fan', 'FAN26G1025' => 'fan', 'FAN26G2860' => 'fan', 'FAN27G1329' => 'fan', 'FAN27G3392' => 'fan', 'FvH4_1g02011' => 'fve', 'FvH4_1g06511' => 'fve', 'FvH4_2g19900' => 'fve', 'FvH4_2g19920' => 'fve', 'FvH4_2g24261' => 'fve', 'FvH4_2g24270' => 'fve', 'FvH4_2g24631' => 'fve', 'FvH4_2g30622' => 'fve', 'FvH4_3g12920' => 'fve', 'FvH4_3g30171' => 'fve', 'FvH4_3g35490' => 'fve', 'FvH4_3g43682' => 'fve', 'FvH4_3g43730' => 'fve', 'FvH4_3g43732' => 'fve', 'FvH4_3g43751' => 'fve', 'FvH4_3g43752' => 'fve', 'FvH4_3g43770' => 'fve', 'FvH4_3g44471' => 'fve', 'FvH4_3g44510' => 'fve', 'FvH4_3g44582' => 'fve', 'FvH4_4g16921' => 'fve', 'FvH4_4g17121' => 'fve', 'FvH4_4g17782' => 'fve', 'FvH4_4g17783' => 'fve', 'FvH4_4g18120' => 'fve', 'FvH4_4g31310' => 'fve', 'FvH4_4g35052' => 'fve', 'FvH4_5g30862' => 'fve', 'FvH4_6g01541' => 'fve', 'FvH4_6g02021' => 'fve', 'FvH4_6g02041' => 'fve', 'FvH4_6g02071' => 'fve', 'FvH4_6g02171' => 'fve', 'FvH4_6g03181' => 'fve', 'FvH4_6g03182' => 'fve', 'FvH4_6g03221' => 'fve', 'FvH4_6g03380' => 'fve', 'FvH4_6g05201' => 'fve', 'FvH4_6g05203' => 'fve', 'FvH4_6g20231' => 'fve', 'FvH4_6g31981' => 'fve', 'FvH4_6g32061' => 'fve', 'FvH4_6g37041' => 'fve', 'FvH4_6g37932' => 'fve', 'FvH4_6g38731' => 'fve', 'FvH4_6g39370' => 'fve', 'FvH4_6g39371' => 'fve', 'FvH4_6g40891' => 'fve', 'FvH4_6g40892' => 'fve', 'FvH4_6g43143' => 'fve', 'FvH4_6g45251' => 'fve', 'FvH4_6g45260' => 'fve', 'FvH4_6g45291' => 'fve', 'FvH4_6g45890' => 'fve', 'FvH4_6g46240' => 'fve', 'FvH4_6g46241' => 'fve', 'FvH4_6g46242' => 'fve', 'FvH4_6g46260' => 'fve', 'FvH4_6g46280' => 'fve', 'FvH4_6g46380' => 'fve', 'FvH4_7g12841' => 'fve', 'FvH4_7g31431' => 'fve', 'Glyma.09G075900' => 'gma', 'Gohir.A09G096401' => 'ghi', 'Gohir.D09G096101' => 'ghi', 'Gorai.006G112800' => 'gra', 'HanXRQChr04g0121411' => 'han', 'Hund15878' => 'sun', 'Lj2A1107G68' => 'lonja', 'Lj2A630G63' => 'lonja', 'Lj2A946T25' => 'lonja', 'Lj2C714T1' => 'lonja', 'Lj2C966T3' => 'lonja', 'Lj2C966T4' => 'lonja', 'Lj4g0002979' => 'lja', 'Lsat_1_v5_gn_5_30901' => 'lsa', 'Lsat_1_v5_gn_5_31100' => 'lsa', 'Lsat_1_v5_gn_5_38600' => 'lsa', 'Lsat_1_v5_gn_6_92061' => 'lsa', 'Manes.05G071301' => 'mes', 'MD02G1008700' => 'mdo', 'MD02G1008900' => 'mdo', 'MD03G1256400' => 'mdo', 'MD04G1180900' => 'mdo', 'MD04G1181000' => 'mdo', 'MD04G1181200' => 'mdo', 'MD05G1244200' => 'mdo', 'MD05G1324200' => 'mdo', 'MD09G1201600' => 'mdo', 'MD10G1000600' => 'mdo', 'MD14G1026900' => 'mdo', 'MD14G1187900' => 'mdo', 'MD15G1017800' => 'mdo', 'MD15G1018100' => 'mdo', 'Medtr4g124160' => 'mtr', 'Migut.L01260' => 'egut', 'Nitab4.5_0000008g0440' => 'nta', 'Nitab4.5_0000207g0170' => 'nta', 'Nitab4.5_0007671g0030' => 'nta', 'Nitab4.5_0010853g0020' => 'nta', 'Oeu057656.1' => 'oeu', 'PGSC0003DMG400005638' => 'stu', 'PGSC0003DMG400005639' => 'stu', 'Phvul.009G222800' => 'pvu', 'Potri.009G132400' => 'ptr', 'Potri.009G163001' => 'ptr', 'Potri.011G000700' => 'ptr', 'Potri.011G004800' => 'ptr', 'Prupe.1G509300' => 'ppe', 'Prupe.1G509700' => 'ppe', 'Prupe.1G510400' => 'ppe', 'Prupe.1G510700' => 'ppe', 'Prupe.1G512600' => 'ppe', 'Prupe.2G073200' => 'ppe', 'Prupe.3G059500' => 'ppe', 'Prupe.3G059600' => 'ppe', 'Prupe.3G246100' => 'ppe', 'Prupe.3G265100' => 'ppe', 'Prupe.4G034700' => 'ppe', 'Prupe.4G052100' => 'ppe', 'Prupe.4G053600' => 'ppe', 'Prupe.5G068800' => 'ppe', 'Prupe.5G070600' => 'ppe', 'Prupe.6G075400' => 'ppe', 'Prupe.6G075500' => 'ppe', 'Prupe.6G076400' => 'ppe', 'Prupe.8G110700' => 'ppe', 'Psat4g020960' => 'psa', 'PSO135G0788' => 'pso', 'PSO210G6463' => 'pso', 'PSO384G0370' => 'pso', 'PSO386G0056' => 'pso', 'QL01p006048' => 'qlo', 'QL02p054283' => 'qlo', 'QL05p008000' => 'qlo', 'QL05p008212' => 'qlo', 'QL05p008950' => 'qlo', 'QL05p009042' => 'qlo', 'QL05p009518' => 'qlo', 'QL05p012589' => 'qlo', 'QL05p012608' => 'qlo', 'QL05p012650' => 'qlo', 'QL05p012667' => 'qlo', 'QL05p014501' => 'qlo', 'QL05p052800' => 'qlo', 'QL05p065010' => 'qlo', 'QL05p074156' => 'qlo', 'QL05p074160' => 'qlo', 'QL05p074174' => 'qlo', 'QL05p074178' => 'qlo', 'QL05p074214' => 'qlo', 'QL06p001050' => 'qlo', 'QL06p001056' => 'qlo', 'QL06p006093' => 'qlo', 'QL06p006111' => 'qlo', 'QL07p019784' => 'qlo', 'QL07p019801' => 'qlo', 'QL07p036110' => 'qlo', 'QL07p036134' => 'qlo', 'QL07p036147' => 'qlo', 'QL07p036156' => 'qlo', 'QL07p036300' => 'qlo', 'QL07p036320' => 'qlo', 'QL08p014547' => 'qlo', 'QL08p014551' => 'qlo', 'QL08p043319' => 'qlo', 'QL08p043324' => 'qlo', 'QL11p009094' => 'qlo', 'RcHm_v2.0_Chr1g0380481' => 'rch', 'RcHm_v2.0_Chr2g0089331' => 'rch', 'RcHm_v2.0_Chr2g0123691' => 'rch', 'RcHm_v2.0_Chr2g0151111' => 'rch', 'RcHm_v2.0_Chr2g0163011' => 'rch', 'RcHm_v2.0_Chr2g0163051' => 'rch', 'RcHm_v2.0_Chr2g0164671' => 'rch', 'RcHm_v2.0_Chr2g0164681' => 'rch', 'RcHm_v2.0_Chr2g0164721' => 'rch', 'RcHm_v2.0_Chr3g0449911' => 'rch', 'RcHm_v2.0_Chr3g0450211' => 'rch', 'RcHm_v2.0_Chr3g0457271' => 'rch', 'RcHm_v2.0_Chr5g0018111' => 'rch', 'RcHm_v2.0_Chr5g0021011' => 'rch', 'RcHm_v2.0_Chr5g0081171' => 'rch', 'RcHm_v2.0_Chr5g0081211' => 'rch', 'RcHm_v2.0_Chr6g0275871' => 'rch', 'RcHm_v2.0_Chr6g0276071' => 'rch', 'RcHm_v2.0_Chr6g0285591' => 'rch', 'RcHm_v2.0_Chr6g0291931' => 'rch', 'RcHm_v2.0_Chr6g0292091' => 'rch', 'RcHm_v2.0_Chr6g0292271' => 'rch', 'RcHm_v2.0_Chr7g0221261' => 'rch', 'Rhsim08G0219900' => 'rsi', 'Rhsim08G0220200' => 'rsi', 'Rhsim08G0237800' => 'rsi', 'Rhsim08G0238800' => 'rsi', 'Sabra09G0102700' => 'sbr', 'Sabra09G0127200' => 'sbr', 'Sabra11G0003700' => 'sbr', 'Sabra15G0014700' => 'sbr', 'Sc19g0000590' => 'sci', 'Sc19g0001870' => 'sci', 'SGA_v2.0_scaffold1G00346' => 'sas', 'SGA_v2.0_scaffold1G00575' => 'sas', 'SGA_v2.0_scaffold1G00761' => 'sas', 'SGA_v2.0_scaffold232G43501' => 'sas', 'TAR625G1137' => 'tar', 'Thecc.03G222100' => 'tca', 'TPR.G12691' => 'tpr', 'TWI34G0727' => 'twi', 'TWI36G0117' => 'twi', 'VMungo1309G0868' => 'vmu' ) $gf_id = 'HOM05D001729' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001729' ) $data_identifier = 'HOM05D001729' $data_type = 'gf_id' $species_gene_counts = array( 'amhyb' => (int) 1, 'cqu' => (int) 9, 'can' => (int) 1, 'cansat' => (int) 1, 'car' => (int) 1, 'col' => (int) 5, 'dca' => (int) 1, 'din' => (int) 2, 'dzi' => (int) 3, 'fan' => (int) 140, 'fve' => (int) 62, 'gma' => (int) 1, 'ghi' => (int) 2, 'gra' => (int) 1, 'han' => (int) 1, 'sun' => (int) 1, 'lonja' => (int) 6, 'lja' => (int) 1, 'lsa' => (int) 4, 'mes' => (int) 1, 'mdo' => (int) 14, 'mtr' => (int) 1, 'egut' => (int) 1, 'nta' => (int) 4, 'oeu' => (int) 1, 'stu' => (int) 2, 'pvu' => (int) 1, 'ptr' => (int) 4, 'ppe' => (int) 19, 'psa' => (int) 1, 'pso' => (int) 4, 'qlo' => (int) 36, 'rch' => (int) 23, 'rsi' => (int) 4, 'sbr' => (int) 4, 'sci' => (int) 2, 'sas' => (int) 4, 'tar' => (int) 1, 'tca' => (int) 1, 'tpr' => (int) 1, 'twi' => (int) 2, 'vmu' => (int) 1 ) $gf_gene_species = 'vmu' $gf_gene_id = 'VMungo1309G0868' $species_info = array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ) $local_species = 'cqu' $disabled = '' $selected = '' $num_hits = (int) 0
Warning (2): count(): Parameter must be an array or an object that implements Countable [APP/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp, line 33]Code Context $disabled = (!array_key_exists($local_species,$species_gene_counts))?"disabled":""; $selected = (isset($selected_species) && array_key_exists($local_species,$selected_species))?"checked='checked'":""; $num_hits = (array_key_exists($local_species,$species_gene_counts))?count($species_gene_counts[$local_species]):0; $viewFile = '/www/bioinformatics01_ro/plaza/_dev_instances/feedback/app/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp' $dataForView = array( 'sidebar_info' => array( 'gf_id' => 'HOM05D001729', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '375', 'num_species' => '42' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'Ah.07g204710' => 'amhyb', 'AUR62006001' => 'cqu', 'AUR62006002' => 'cqu', 'AUR62006003' => 'cqu', 'AUR62015641' => 'cqu', 'AUR62027174' => 'cqu', 'AUR62035623' => 'cqu', 'AUR62035624' => 'cqu', 'AUR62035625' => 'cqu', 'AUR62035626' => 'cqu', 'CAN.G1110.53' => 'can', 'CANSAT80G0415' => 'cansat', 'Ca_21364_v3' => 'car', 'COL.COLO4_30693' => 'col', 'COL.COLO4_30694' => 'col', 'COL.COLO4_30695' => 'col', 'COL.COLO4_30696' => 'col', 'COL.COLO4_34020' => 'col', 'DCAR_004585' => 'dca', 'Dinv04029' => 'din', 'Dinv34857' => 'din', 'Duzib147G0011' => 'dzi', 'Duzib170G0599' => 'dzi', 'Duzib192G1051' => 'dzi', 'FAN01G0708' => 'fan', 'FAN01G0742' => 'fan', 'FAN02G0048' => 'fan', 'FAN02G0583' => 'fan', 'FAN02G0688' => 'fan', 'FAN02G1588' => 'fan', 'FAN02G2194' => 'fan', 'FAN02G2750' => 'fan', 'FAN02G3094' => 'fan', 'FAN02G3887' => 'fan', 'FAN02G3911' => 'fan', 'FAN02G3994' => 'fan', 'FAN02G4432' => 'fan', 'FAN02G4556' => 'fan', 'FAN03G1977' => 'fan', 'FAN03G2781' => 'fan', 'FAN03G2850' => 'fan', 'FAN03G3155' => 'fan', 'FAN04G2487' => 'fan', 'FAN05G0208' => 'fan', 'FAN05G0656' => 'fan', 'FAN05G0696' => 'fan', 'FAN05G0810' => 'fan', 'FAN05G1447' => 'fan', 'FAN05G2640' => 'fan', 'FAN05G2911' => 'fan', 'FAN05G3901' => 'fan', 'FAN05G4859' => 'fan', 'FAN05G4861' => 'fan', 'FAN05G4988' => 'fan', 'FAN05G5187' => 'fan', 'FAN05G5452' => 'fan', 'FAN05G5500' => 'fan', 'FAN05G5688' => 'fan', 'FAN06G0177' => 'fan', 'FAN06G0675' => 'fan', 'FAN06G1290' => 'fan', 'FAN06G2191' => 'fan', 'FAN06G2405' => 'fan', 'FAN06G3231' => 'fan', 'FAN06G3932' => 'fan', 'FAN07G0163' => 'fan', 'FAN07G0471' => 'fan', 'FAN07G1354' => 'fan', 'FAN08G0338' => 'fan', 'FAN08G1373' => 'fan', 'FAN08G2539' => 'fan', 'FAN08G2728' => 'fan', 'FAN09G0608' => 'fan', 'FAN09G1136' => 'fan', 'FAN09G1958' => 'fan', 'FAN09G2508' => 'fan', 'FAN09G2597' => 'fan', 'FAN09G2658' => 'fan', 'FAN09G2757' => 'fan', 'FAN09G2983' => 'fan', 'FAN09G3130' => 'fan', 'FAN09G3565' => 'fan', 'FAN09G3613' => 'fan', 'FAN09G4011' => 'fan', 'FAN09G4239' => 'fan', 'FAN09G4277' => 'fan', 'FAN09G4720' => 'fan', 'FAN11G0139' => 'fan', 'FAN11G1727' => 'fan', 'FAN11G2672' => 'fan', 'FAN11G2795' => 'fan', 'FAN11G3238' => 'fan', 'FAN11G3734' => 'fan', 'FAN12G0631' => 'fan', 'FAN12G2239' => 'fan', 'FAN12G2308' => 'fan', 'FAN12G2569' => 'fan', 'FAN12G2623' => 'fan', 'FAN13G3182' => 'fan', 'FAN14G0053' => 'fan', 'FAN14G0370' => 'fan', 'FAN14G0382' => 'fan', 'FAN14G0421' => 'fan', 'FAN14G0866' => 'fan', 'FAN14G1187' => 'fan', 'FAN14G1727' => 'fan', 'FAN14G1791' => 'fan', 'FAN14G2361' => 'fan', 'FAN14G2668' => 'fan', 'FAN14G2770' => 'fan', 'FAN14G2874' => 'fan', 'FAN14G3193' => 'fan', 'FAN14G3624' => 'fan', 'FAN14G3676' => 'fan', 'FAN14G3807' => 'fan', 'FAN14G4082' => 'fan', 'FAN14G4342' => 'fan', 'FAN14G4985' => 'fan', 'FAN14G5126' => 'fan', 'FAN14G5781' => 'fan', 'FAN14G5808' => 'fan', 'FAN14G5949' => 'fan', 'FAN15G0828' => 'fan', 'FAN15G1054' => 'fan', 'FAN15G2023' => 'fan', 'FAN15G2506' => 'fan', 'FAN16G0128' => 'fan', 'FAN16G0249' => 'fan', 'FAN16G0429' => 'fan', 'FAN16G1493' => 'fan', 'FAN16G2210' => 'fan', 'FAN16G2506' => 'fan', 'FAN18G1542' => 'fan', 'FAN18G4057' => 'fan', 'FAN19G0745' => 'fan', 'FAN19G1216' => 'fan', 'FAN19G1733' => 'fan', 'FAN20G0258' => 'fan', 'FAN20G1095' => 'fan', 'FAN20G1557' => 'fan', 'FAN21G0302' => 'fan', 'FAN21G0519' => 'fan', 'FAN21G0970' => 'fan', 'FAN21G1159' => 'fan', 'FAN21G1312' => 'fan', 'FAN21G1440' => 'fan', 'FAN21G1715' => 'fan', 'FAN23G1584' => 'fan', 'FAN24G0045' => 'fan', 'FAN24G0053' => 'fan', 'FAN24G1500' => 'fan', 'FAN24G1817' => 'fan', 'FAN24G2147' => 'fan', 'FAN24G2236' => 'fan', 'FAN24G2446' => 'fan', 'FAN24G2684' => 'fan', 'FAN25G0187' => 'fan', 'FAN25G0505' => 'fan', 'FAN25G0589' => 'fan', 'FAN25G3663' => 'fan', 'FAN26G1025' => 'fan', 'FAN26G2860' => 'fan', 'FAN27G1329' => 'fan', 'FAN27G3392' => 'fan', 'FvH4_1g02011' => 'fve', 'FvH4_1g06511' => 'fve', 'FvH4_2g19900' => 'fve', 'FvH4_2g19920' => 'fve', 'FvH4_2g24261' => 'fve', 'FvH4_2g24270' => 'fve', 'FvH4_2g24631' => 'fve', 'FvH4_2g30622' => 'fve', 'FvH4_3g12920' => 'fve', 'FvH4_3g30171' => 'fve', 'FvH4_3g35490' => 'fve', 'FvH4_3g43682' => 'fve', 'FvH4_3g43730' => 'fve', 'FvH4_3g43732' => 'fve', 'FvH4_3g43751' => 'fve', 'FvH4_3g43752' => 'fve', 'FvH4_3g43770' => 'fve', 'FvH4_3g44471' => 'fve', 'FvH4_3g44510' => 'fve', 'FvH4_3g44582' => 'fve', 'FvH4_4g16921' => 'fve', 'FvH4_4g17121' => 'fve', 'FvH4_4g17782' => 'fve', 'FvH4_4g17783' => 'fve', 'FvH4_4g18120' => 'fve', 'FvH4_4g31310' => 'fve', 'FvH4_4g35052' => 'fve', 'FvH4_5g30862' => 'fve', 'FvH4_6g01541' => 'fve', 'FvH4_6g02021' => 'fve', 'FvH4_6g02041' => 'fve', 'FvH4_6g02071' => 'fve', 'FvH4_6g02171' => 'fve', 'FvH4_6g03181' => 'fve', 'FvH4_6g03182' => 'fve', 'FvH4_6g03221' => 'fve', 'FvH4_6g03380' => 'fve', 'FvH4_6g05201' => 'fve', 'FvH4_6g05203' => 'fve', 'FvH4_6g20231' => 'fve', 'FvH4_6g31981' => 'fve', 'FvH4_6g32061' => 'fve', 'FvH4_6g37041' => 'fve', 'FvH4_6g37932' => 'fve', 'FvH4_6g38731' => 'fve', 'FvH4_6g39370' => 'fve', 'FvH4_6g39371' => 'fve', 'FvH4_6g40891' => 'fve', 'FvH4_6g40892' => 'fve', 'FvH4_6g43143' => 'fve', 'FvH4_6g45251' => 'fve', 'FvH4_6g45260' => 'fve', 'FvH4_6g45291' => 'fve', 'FvH4_6g45890' => 'fve', 'FvH4_6g46240' => 'fve', 'FvH4_6g46241' => 'fve', 'FvH4_6g46242' => 'fve', 'FvH4_6g46260' => 'fve', 'FvH4_6g46280' => 'fve', 'FvH4_6g46380' => 'fve', 'FvH4_7g12841' => 'fve', 'FvH4_7g31431' => 'fve', 'Glyma.09G075900' => 'gma', 'Gohir.A09G096401' => 'ghi', 'Gohir.D09G096101' => 'ghi', 'Gorai.006G112800' => 'gra', 'HanXRQChr04g0121411' => 'han', 'Hund15878' => 'sun', 'Lj2A1107G68' => 'lonja', 'Lj2A630G63' => 'lonja', 'Lj2A946T25' => 'lonja', 'Lj2C714T1' => 'lonja', 'Lj2C966T3' => 'lonja', 'Lj2C966T4' => 'lonja', 'Lj4g0002979' => 'lja', 'Lsat_1_v5_gn_5_30901' => 'lsa', 'Lsat_1_v5_gn_5_31100' => 'lsa', 'Lsat_1_v5_gn_5_38600' => 'lsa', 'Lsat_1_v5_gn_6_92061' => 'lsa', 'Manes.05G071301' => 'mes', 'MD02G1008700' => 'mdo', 'MD02G1008900' => 'mdo', 'MD03G1256400' => 'mdo', 'MD04G1180900' => 'mdo', 'MD04G1181000' => 'mdo', 'MD04G1181200' => 'mdo', 'MD05G1244200' => 'mdo', 'MD05G1324200' => 'mdo', 'MD09G1201600' => 'mdo', 'MD10G1000600' => 'mdo', 'MD14G1026900' => 'mdo', 'MD14G1187900' => 'mdo', 'MD15G1017800' => 'mdo', 'MD15G1018100' => 'mdo', 'Medtr4g124160' => 'mtr', 'Migut.L01260' => 'egut', 'Nitab4.5_0000008g0440' => 'nta', 'Nitab4.5_0000207g0170' => 'nta', 'Nitab4.5_0007671g0030' => 'nta', 'Nitab4.5_0010853g0020' => 'nta', 'Oeu057656.1' => 'oeu', 'PGSC0003DMG400005638' => 'stu', 'PGSC0003DMG400005639' => 'stu', 'Phvul.009G222800' => 'pvu', 'Potri.009G132400' => 'ptr', 'Potri.009G163001' => 'ptr', 'Potri.011G000700' => 'ptr', 'Potri.011G004800' => 'ptr', 'Prupe.1G509300' => 'ppe', 'Prupe.1G509700' => 'ppe', 'Prupe.1G510400' => 'ppe', 'Prupe.1G510700' => 'ppe', 'Prupe.1G512600' => 'ppe', 'Prupe.2G073200' => 'ppe', 'Prupe.3G059500' => 'ppe', 'Prupe.3G059600' => 'ppe', 'Prupe.3G246100' => 'ppe', 'Prupe.3G265100' => 'ppe', 'Prupe.4G034700' => 'ppe', 'Prupe.4G052100' => 'ppe', 'Prupe.4G053600' => 'ppe', 'Prupe.5G068800' => 'ppe', 'Prupe.5G070600' => 'ppe', 'Prupe.6G075400' => 'ppe', 'Prupe.6G075500' => 'ppe', 'Prupe.6G076400' => 'ppe', 'Prupe.8G110700' => 'ppe', 'Psat4g020960' => 'psa', 'PSO135G0788' => 'pso', 'PSO210G6463' => 'pso', 'PSO384G0370' => 'pso', 'PSO386G0056' => 'pso', 'QL01p006048' => 'qlo', 'QL02p054283' => 'qlo', 'QL05p008000' => 'qlo', 'QL05p008212' => 'qlo', 'QL05p008950' => 'qlo', 'QL05p009042' => 'qlo', 'QL05p009518' => 'qlo', 'QL05p012589' => 'qlo', 'QL05p012608' => 'qlo', 'QL05p012650' => 'qlo', 'QL05p012667' => 'qlo', 'QL05p014501' => 'qlo', 'QL05p052800' => 'qlo', 'QL05p065010' => 'qlo', 'QL05p074156' => 'qlo', 'QL05p074160' => 'qlo', 'QL05p074174' => 'qlo', 'QL05p074178' => 'qlo', 'QL05p074214' => 'qlo', 'QL06p001050' => 'qlo', 'QL06p001056' => 'qlo', 'QL06p006093' => 'qlo', 'QL06p006111' => 'qlo', 'QL07p019784' => 'qlo', 'QL07p019801' => 'qlo', 'QL07p036110' => 'qlo', 'QL07p036134' => 'qlo', 'QL07p036147' => 'qlo', 'QL07p036156' => 'qlo', 'QL07p036300' => 'qlo', 'QL07p036320' => 'qlo', 'QL08p014547' => 'qlo', 'QL08p014551' => 'qlo', 'QL08p043319' => 'qlo', 'QL08p043324' => 'qlo', 'QL11p009094' => 'qlo', 'RcHm_v2.0_Chr1g0380481' => 'rch', 'RcHm_v2.0_Chr2g0089331' => 'rch', 'RcHm_v2.0_Chr2g0123691' => 'rch', 'RcHm_v2.0_Chr2g0151111' => 'rch', 'RcHm_v2.0_Chr2g0163011' => 'rch', 'RcHm_v2.0_Chr2g0163051' => 'rch', 'RcHm_v2.0_Chr2g0164671' => 'rch', 'RcHm_v2.0_Chr2g0164681' => 'rch', 'RcHm_v2.0_Chr2g0164721' => 'rch', 'RcHm_v2.0_Chr3g0449911' => 'rch', 'RcHm_v2.0_Chr3g0450211' => 'rch', 'RcHm_v2.0_Chr3g0457271' => 'rch', 'RcHm_v2.0_Chr5g0018111' => 'rch', 'RcHm_v2.0_Chr5g0021011' => 'rch', 'RcHm_v2.0_Chr5g0081171' => 'rch', 'RcHm_v2.0_Chr5g0081211' => 'rch', 'RcHm_v2.0_Chr6g0275871' => 'rch', 'RcHm_v2.0_Chr6g0276071' => 'rch', 'RcHm_v2.0_Chr6g0285591' => 'rch', 'RcHm_v2.0_Chr6g0291931' => 'rch', 'RcHm_v2.0_Chr6g0292091' => 'rch', 'RcHm_v2.0_Chr6g0292271' => 'rch', 'RcHm_v2.0_Chr7g0221261' => 'rch', 'Rhsim08G0219900' => 'rsi', 'Rhsim08G0220200' => 'rsi', 'Rhsim08G0237800' => 'rsi', 'Rhsim08G0238800' => 'rsi', 'Sabra09G0102700' => 'sbr', 'Sabra09G0127200' => 'sbr', 'Sabra11G0003700' => 'sbr', 'Sabra15G0014700' => 'sbr', 'Sc19g0000590' => 'sci', 'Sc19g0001870' => 'sci', 'SGA_v2.0_scaffold1G00346' => 'sas', 'SGA_v2.0_scaffold1G00575' => 'sas', 'SGA_v2.0_scaffold1G00761' => 'sas', 'SGA_v2.0_scaffold232G43501' => 'sas', 'TAR625G1137' => 'tar', 'Thecc.03G222100' => 'tca', 'TPR.G12691' => 'tpr', 'TWI34G0727' => 'twi', 'TWI36G0117' => 'twi', 'VMungo1309G0868' => 'vmu' ), 'gf_id' => 'HOM05D001729', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001729' ), 'data_identifier' => 'HOM05D001729', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001729', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '375', 'num_species' => '42' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'Ah.07g204710' => 'amhyb', 'AUR62006001' => 'cqu', 'AUR62006002' => 'cqu', 'AUR62006003' => 'cqu', 'AUR62015641' => 'cqu', 'AUR62027174' => 'cqu', 'AUR62035623' => 'cqu', 'AUR62035624' => 'cqu', 'AUR62035625' => 'cqu', 'AUR62035626' => 'cqu', 'CAN.G1110.53' => 'can', 'CANSAT80G0415' => 'cansat', 'Ca_21364_v3' => 'car', 'COL.COLO4_30693' => 'col', 'COL.COLO4_30694' => 'col', 'COL.COLO4_30695' => 'col', 'COL.COLO4_30696' => 'col', 'COL.COLO4_34020' => 'col', 'DCAR_004585' => 'dca', 'Dinv04029' => 'din', 'Dinv34857' => 'din', 'Duzib147G0011' => 'dzi', 'Duzib170G0599' => 'dzi', 'Duzib192G1051' => 'dzi', 'FAN01G0708' => 'fan', 'FAN01G0742' => 'fan', 'FAN02G0048' => 'fan', 'FAN02G0583' => 'fan', 'FAN02G0688' => 'fan', 'FAN02G1588' => 'fan', 'FAN02G2194' => 'fan', 'FAN02G2750' => 'fan', 'FAN02G3094' => 'fan', 'FAN02G3887' => 'fan', 'FAN02G3911' => 'fan', 'FAN02G3994' => 'fan', 'FAN02G4432' => 'fan', 'FAN02G4556' => 'fan', 'FAN03G1977' => 'fan', 'FAN03G2781' => 'fan', 'FAN03G2850' => 'fan', 'FAN03G3155' => 'fan', 'FAN04G2487' => 'fan', 'FAN05G0208' => 'fan', 'FAN05G0656' => 'fan', 'FAN05G0696' => 'fan', 'FAN05G0810' => 'fan', 'FAN05G1447' => 'fan', 'FAN05G2640' => 'fan', 'FAN05G2911' => 'fan', 'FAN05G3901' => 'fan', 'FAN05G4859' => 'fan', 'FAN05G4861' => 'fan', 'FAN05G4988' => 'fan', 'FAN05G5187' => 'fan', 'FAN05G5452' => 'fan', 'FAN05G5500' => 'fan', 'FAN05G5688' => 'fan', 'FAN06G0177' => 'fan', 'FAN06G0675' => 'fan', 'FAN06G1290' => 'fan', 'FAN06G2191' => 'fan', 'FAN06G2405' => 'fan', 'FAN06G3231' => 'fan', 'FAN06G3932' => 'fan', 'FAN07G0163' => 'fan', 'FAN07G0471' => 'fan', 'FAN07G1354' => 'fan', 'FAN08G0338' => 'fan', 'FAN08G1373' => 'fan', 'FAN08G2539' => 'fan', 'FAN08G2728' => 'fan', 'FAN09G0608' => 'fan', 'FAN09G1136' => 'fan', 'FAN09G1958' => 'fan', 'FAN09G2508' => 'fan', 'FAN09G2597' => 'fan', 'FAN09G2658' => 'fan', 'FAN09G2757' => 'fan', 'FAN09G2983' => 'fan', 'FAN09G3130' => 'fan', 'FAN09G3565' => 'fan', 'FAN09G3613' => 'fan', 'FAN09G4011' => 'fan', 'FAN09G4239' => 'fan', 'FAN09G4277' => 'fan', 'FAN09G4720' => 'fan', 'FAN11G0139' => 'fan', 'FAN11G1727' => 'fan', 'FAN11G2672' => 'fan', 'FAN11G2795' => 'fan', 'FAN11G3238' => 'fan', 'FAN11G3734' => 'fan', 'FAN12G0631' => 'fan', 'FAN12G2239' => 'fan', 'FAN12G2308' => 'fan', 'FAN12G2569' => 'fan', 'FAN12G2623' => 'fan', 'FAN13G3182' => 'fan', 'FAN14G0053' => 'fan', 'FAN14G0370' => 'fan', 'FAN14G0382' => 'fan', 'FAN14G0421' => 'fan', 'FAN14G0866' => 'fan', 'FAN14G1187' => 'fan', 'FAN14G1727' => 'fan', 'FAN14G1791' => 'fan', 'FAN14G2361' => 'fan', 'FAN14G2668' => 'fan', 'FAN14G2770' => 'fan', 'FAN14G2874' => 'fan', 'FAN14G3193' => 'fan', 'FAN14G3624' => 'fan', 'FAN14G3676' => 'fan', 'FAN14G3807' => 'fan', 'FAN14G4082' => 'fan', 'FAN14G4342' => 'fan', 'FAN14G4985' => 'fan', 'FAN14G5126' => 'fan', 'FAN14G5781' => 'fan', 'FAN14G5808' => 'fan', 'FAN14G5949' => 'fan', 'FAN15G0828' => 'fan', 'FAN15G1054' => 'fan', 'FAN15G2023' => 'fan', 'FAN15G2506' => 'fan', 'FAN16G0128' => 'fan', 'FAN16G0249' => 'fan', 'FAN16G0429' => 'fan', 'FAN16G1493' => 'fan', 'FAN16G2210' => 'fan', 'FAN16G2506' => 'fan', 'FAN18G1542' => 'fan', 'FAN18G4057' => 'fan', 'FAN19G0745' => 'fan', 'FAN19G1216' => 'fan', 'FAN19G1733' => 'fan', 'FAN20G0258' => 'fan', 'FAN20G1095' => 'fan', 'FAN20G1557' => 'fan', 'FAN21G0302' => 'fan', 'FAN21G0519' => 'fan', 'FAN21G0970' => 'fan', 'FAN21G1159' => 'fan', 'FAN21G1312' => 'fan', 'FAN21G1440' => 'fan', 'FAN21G1715' => 'fan', 'FAN23G1584' => 'fan', 'FAN24G0045' => 'fan', 'FAN24G0053' => 'fan', 'FAN24G1500' => 'fan', 'FAN24G1817' => 'fan', 'FAN24G2147' => 'fan', 'FAN24G2236' => 'fan', 'FAN24G2446' => 'fan', 'FAN24G2684' => 'fan', 'FAN25G0187' => 'fan', 'FAN25G0505' => 'fan', 'FAN25G0589' => 'fan', 'FAN25G3663' => 'fan', 'FAN26G1025' => 'fan', 'FAN26G2860' => 'fan', 'FAN27G1329' => 'fan', 'FAN27G3392' => 'fan', 'FvH4_1g02011' => 'fve', 'FvH4_1g06511' => 'fve', 'FvH4_2g19900' => 'fve', 'FvH4_2g19920' => 'fve', 'FvH4_2g24261' => 'fve', 'FvH4_2g24270' => 'fve', 'FvH4_2g24631' => 'fve', 'FvH4_2g30622' => 'fve', 'FvH4_3g12920' => 'fve', 'FvH4_3g30171' => 'fve', 'FvH4_3g35490' => 'fve', 'FvH4_3g43682' => 'fve', 'FvH4_3g43730' => 'fve', 'FvH4_3g43732' => 'fve', 'FvH4_3g43751' => 'fve', 'FvH4_3g43752' => 'fve', 'FvH4_3g43770' => 'fve', 'FvH4_3g44471' => 'fve', 'FvH4_3g44510' => 'fve', 'FvH4_3g44582' => 'fve', 'FvH4_4g16921' => 'fve', 'FvH4_4g17121' => 'fve', 'FvH4_4g17782' => 'fve', 'FvH4_4g17783' => 'fve', 'FvH4_4g18120' => 'fve', 'FvH4_4g31310' => 'fve', 'FvH4_4g35052' => 'fve', 'FvH4_5g30862' => 'fve', 'FvH4_6g01541' => 'fve', 'FvH4_6g02021' => 'fve', 'FvH4_6g02041' => 'fve', 'FvH4_6g02071' => 'fve', 'FvH4_6g02171' => 'fve', 'FvH4_6g03181' => 'fve', 'FvH4_6g03182' => 'fve', 'FvH4_6g03221' => 'fve', 'FvH4_6g03380' => 'fve', 'FvH4_6g05201' => 'fve', 'FvH4_6g05203' => 'fve', 'FvH4_6g20231' => 'fve', 'FvH4_6g31981' => 'fve', 'FvH4_6g32061' => 'fve', 'FvH4_6g37041' => 'fve', 'FvH4_6g37932' => 'fve', 'FvH4_6g38731' => 'fve', 'FvH4_6g39370' => 'fve', 'FvH4_6g39371' => 'fve', 'FvH4_6g40891' => 'fve', 'FvH4_6g40892' => 'fve', 'FvH4_6g43143' => 'fve', 'FvH4_6g45251' => 'fve', 'FvH4_6g45260' => 'fve', 'FvH4_6g45291' => 'fve', 'FvH4_6g45890' => 'fve', 'FvH4_6g46240' => 'fve', 'FvH4_6g46241' => 'fve', 'FvH4_6g46242' => 'fve', 'FvH4_6g46260' => 'fve', 'FvH4_6g46280' => 'fve', 'FvH4_6g46380' => 'fve', 'FvH4_7g12841' => 'fve', 'FvH4_7g31431' => 'fve', 'Glyma.09G075900' => 'gma', 'Gohir.A09G096401' => 'ghi', 'Gohir.D09G096101' => 'ghi', 'Gorai.006G112800' => 'gra', 'HanXRQChr04g0121411' => 'han', 'Hund15878' => 'sun', 'Lj2A1107G68' => 'lonja', 'Lj2A630G63' => 'lonja', 'Lj2A946T25' => 'lonja', 'Lj2C714T1' => 'lonja', 'Lj2C966T3' => 'lonja', 'Lj2C966T4' => 'lonja', 'Lj4g0002979' => 'lja', 'Lsat_1_v5_gn_5_30901' => 'lsa', 'Lsat_1_v5_gn_5_31100' => 'lsa', 'Lsat_1_v5_gn_5_38600' => 'lsa', 'Lsat_1_v5_gn_6_92061' => 'lsa', 'Manes.05G071301' => 'mes', 'MD02G1008700' => 'mdo', 'MD02G1008900' => 'mdo', 'MD03G1256400' => 'mdo', 'MD04G1180900' => 'mdo', 'MD04G1181000' => 'mdo', 'MD04G1181200' => 'mdo', 'MD05G1244200' => 'mdo', 'MD05G1324200' => 'mdo', 'MD09G1201600' => 'mdo', 'MD10G1000600' => 'mdo', 'MD14G1026900' => 'mdo', 'MD14G1187900' => 'mdo', 'MD15G1017800' => 'mdo', 'MD15G1018100' => 'mdo', 'Medtr4g124160' => 'mtr', 'Migut.L01260' => 'egut', 'Nitab4.5_0000008g0440' => 'nta', 'Nitab4.5_0000207g0170' => 'nta', 'Nitab4.5_0007671g0030' => 'nta', 'Nitab4.5_0010853g0020' => 'nta', 'Oeu057656.1' => 'oeu', 'PGSC0003DMG400005638' => 'stu', 'PGSC0003DMG400005639' => 'stu', 'Phvul.009G222800' => 'pvu', 'Potri.009G132400' => 'ptr', 'Potri.009G163001' => 'ptr', 'Potri.011G000700' => 'ptr', 'Potri.011G004800' => 'ptr', 'Prupe.1G509300' => 'ppe', 'Prupe.1G509700' => 'ppe', 'Prupe.1G510400' => 'ppe', 'Prupe.1G510700' => 'ppe', 'Prupe.1G512600' => 'ppe', 'Prupe.2G073200' => 'ppe', 'Prupe.3G059500' => 'ppe', 'Prupe.3G059600' => 'ppe', 'Prupe.3G246100' => 'ppe', 'Prupe.3G265100' => 'ppe', 'Prupe.4G034700' => 'ppe', 'Prupe.4G052100' => 'ppe', 'Prupe.4G053600' => 'ppe', 'Prupe.5G068800' => 'ppe', 'Prupe.5G070600' => 'ppe', 'Prupe.6G075400' => 'ppe', 'Prupe.6G075500' => 'ppe', 'Prupe.6G076400' => 'ppe', 'Prupe.8G110700' => 'ppe', 'Psat4g020960' => 'psa', 'PSO135G0788' => 'pso', 'PSO210G6463' => 'pso', 'PSO384G0370' => 'pso', 'PSO386G0056' => 'pso', 'QL01p006048' => 'qlo', 'QL02p054283' => 'qlo', 'QL05p008000' => 'qlo', 'QL05p008212' => 'qlo', 'QL05p008950' => 'qlo', 'QL05p009042' => 'qlo', 'QL05p009518' => 'qlo', 'QL05p012589' => 'qlo', 'QL05p012608' => 'qlo', 'QL05p012650' => 'qlo', 'QL05p012667' => 'qlo', 'QL05p014501' => 'qlo', 'QL05p052800' => 'qlo', 'QL05p065010' => 'qlo', 'QL05p074156' => 'qlo', 'QL05p074160' => 'qlo', 'QL05p074174' => 'qlo', 'QL05p074178' => 'qlo', 'QL05p074214' => 'qlo', 'QL06p001050' => 'qlo', 'QL06p001056' => 'qlo', 'QL06p006093' => 'qlo', 'QL06p006111' => 'qlo', 'QL07p019784' => 'qlo', 'QL07p019801' => 'qlo', 'QL07p036110' => 'qlo', 'QL07p036134' => 'qlo', 'QL07p036147' => 'qlo', 'QL07p036156' => 'qlo', 'QL07p036300' => 'qlo', 'QL07p036320' => 'qlo', 'QL08p014547' => 'qlo', 'QL08p014551' => 'qlo', 'QL08p043319' => 'qlo', 'QL08p043324' => 'qlo', 'QL11p009094' => 'qlo', 'RcHm_v2.0_Chr1g0380481' => 'rch', 'RcHm_v2.0_Chr2g0089331' => 'rch', 'RcHm_v2.0_Chr2g0123691' => 'rch', 'RcHm_v2.0_Chr2g0151111' => 'rch', 'RcHm_v2.0_Chr2g0163011' => 'rch', 'RcHm_v2.0_Chr2g0163051' => 'rch', 'RcHm_v2.0_Chr2g0164671' => 'rch', 'RcHm_v2.0_Chr2g0164681' => 'rch', 'RcHm_v2.0_Chr2g0164721' => 'rch', 'RcHm_v2.0_Chr3g0449911' => 'rch', 'RcHm_v2.0_Chr3g0450211' => 'rch', 'RcHm_v2.0_Chr3g0457271' => 'rch', 'RcHm_v2.0_Chr5g0018111' => 'rch', 'RcHm_v2.0_Chr5g0021011' => 'rch', 'RcHm_v2.0_Chr5g0081171' => 'rch', 'RcHm_v2.0_Chr5g0081211' => 'rch', 'RcHm_v2.0_Chr6g0275871' => 'rch', 'RcHm_v2.0_Chr6g0276071' => 'rch', 'RcHm_v2.0_Chr6g0285591' => 'rch', 'RcHm_v2.0_Chr6g0291931' => 'rch', 'RcHm_v2.0_Chr6g0292091' => 'rch', 'RcHm_v2.0_Chr6g0292271' => 'rch', 'RcHm_v2.0_Chr7g0221261' => 'rch', 'Rhsim08G0219900' => 'rsi', 'Rhsim08G0220200' => 'rsi', 'Rhsim08G0237800' => 'rsi', 'Rhsim08G0238800' => 'rsi', 'Sabra09G0102700' => 'sbr', 'Sabra09G0127200' => 'sbr', 'Sabra11G0003700' => 'sbr', 'Sabra15G0014700' => 'sbr', 'Sc19g0000590' => 'sci', 'Sc19g0001870' => 'sci', 'SGA_v2.0_scaffold1G00346' => 'sas', 'SGA_v2.0_scaffold1G00575' => 'sas', 'SGA_v2.0_scaffold1G00761' => 'sas', 'SGA_v2.0_scaffold232G43501' => 'sas', 'TAR625G1137' => 'tar', 'Thecc.03G222100' => 'tca', 'TPR.G12691' => 'tpr', 'TWI34G0727' => 'twi', 'TWI36G0117' => 'twi', 'VMungo1309G0868' => 'vmu' ) $gf_id = 'HOM05D001729' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001729' ) $data_identifier = 'HOM05D001729' $data_type = 'gf_id' $species_gene_counts = array( 'amhyb' => (int) 1, 'cqu' => (int) 9, 'can' => (int) 1, 'cansat' => (int) 1, 'car' => (int) 1, 'col' => (int) 5, 'dca' => (int) 1, 'din' => (int) 2, 'dzi' => (int) 3, 'fan' => (int) 140, 'fve' => (int) 62, 'gma' => (int) 1, 'ghi' => (int) 2, 'gra' => (int) 1, 'han' => (int) 1, 'sun' => (int) 1, 'lonja' => (int) 6, 'lja' => (int) 1, 'lsa' => (int) 4, 'mes' => (int) 1, 'mdo' => (int) 14, 'mtr' => (int) 1, 'egut' => (int) 1, 'nta' => (int) 4, 'oeu' => (int) 1, 'stu' => (int) 2, 'pvu' => (int) 1, 'ptr' => (int) 4, 'ppe' => (int) 19, 'psa' => (int) 1, 'pso' => (int) 4, 'qlo' => (int) 36, 'rch' => (int) 23, 'rsi' => (int) 4, 'sbr' => (int) 4, 'sci' => (int) 2, 'sas' => (int) 4, 'tar' => (int) 1, 'tca' => (int) 1, 'tpr' => (int) 1, 'twi' => (int) 2, 'vmu' => (int) 1 ) $gf_gene_species = 'vmu' $gf_gene_id = 'VMungo1309G0868' $species_info = array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ) $local_species = 'car' $disabled = '' $selected = '' $num_hits = (int) 0include - APP/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp, line 33 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933 View::_renderElement() - CORE/Cake/View/View.php, line 1224 View::element() - CORE/Cake/View/View.php, line 418 include - APP/View/Elements/analysis/phylogenetics_module/gf_data_settings.ctp, line 37 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933 View::_renderElement() - CORE/Cake/View/View.php, line 1224 View::element() - CORE/Cake/View/View.php, line 418 include - APP/View/Elements/analysis/phylogenetics_module/parameter_selection.ctp, line 64 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933 View::_renderElement() - CORE/Cake/View/View.php, line 1224 View::element() - CORE/Cake/View/View.php, line 418 include - APP/View/Analysis/custom_tree_creation.ctp, line 27 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933
$viewFile = '/www/bioinformatics01_ro/plaza/_dev_instances/feedback/app/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp' $dataForView = array( 'sidebar_info' => array( 'gf_id' => 'HOM05D001729', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '375', 'num_species' => '42' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'Ah.07g204710' => 'amhyb', 'AUR62006001' => 'cqu', 'AUR62006002' => 'cqu', 'AUR62006003' => 'cqu', 'AUR62015641' => 'cqu', 'AUR62027174' => 'cqu', 'AUR62035623' => 'cqu', 'AUR62035624' => 'cqu', 'AUR62035625' => 'cqu', 'AUR62035626' => 'cqu', 'CAN.G1110.53' => 'can', 'CANSAT80G0415' => 'cansat', 'Ca_21364_v3' => 'car', 'COL.COLO4_30693' => 'col', 'COL.COLO4_30694' => 'col', 'COL.COLO4_30695' => 'col', 'COL.COLO4_30696' => 'col', 'COL.COLO4_34020' => 'col', 'DCAR_004585' => 'dca', 'Dinv04029' => 'din', 'Dinv34857' => 'din', 'Duzib147G0011' => 'dzi', 'Duzib170G0599' => 'dzi', 'Duzib192G1051' => 'dzi', 'FAN01G0708' => 'fan', 'FAN01G0742' => 'fan', 'FAN02G0048' => 'fan', 'FAN02G0583' => 'fan', 'FAN02G0688' => 'fan', 'FAN02G1588' => 'fan', 'FAN02G2194' => 'fan', 'FAN02G2750' => 'fan', 'FAN02G3094' => 'fan', 'FAN02G3887' => 'fan', 'FAN02G3911' => 'fan', 'FAN02G3994' => 'fan', 'FAN02G4432' => 'fan', 'FAN02G4556' => 'fan', 'FAN03G1977' => 'fan', 'FAN03G2781' => 'fan', 'FAN03G2850' => 'fan', 'FAN03G3155' => 'fan', 'FAN04G2487' => 'fan', 'FAN05G0208' => 'fan', 'FAN05G0656' => 'fan', 'FAN05G0696' => 'fan', 'FAN05G0810' => 'fan', 'FAN05G1447' => 'fan', 'FAN05G2640' => 'fan', 'FAN05G2911' => 'fan', 'FAN05G3901' => 'fan', 'FAN05G4859' => 'fan', 'FAN05G4861' => 'fan', 'FAN05G4988' => 'fan', 'FAN05G5187' => 'fan', 'FAN05G5452' => 'fan', 'FAN05G5500' => 'fan', 'FAN05G5688' => 'fan', 'FAN06G0177' => 'fan', 'FAN06G0675' => 'fan', 'FAN06G1290' => 'fan', 'FAN06G2191' => 'fan', 'FAN06G2405' => 'fan', 'FAN06G3231' => 'fan', 'FAN06G3932' => 'fan', 'FAN07G0163' => 'fan', 'FAN07G0471' => 'fan', 'FAN07G1354' => 'fan', 'FAN08G0338' => 'fan', 'FAN08G1373' => 'fan', 'FAN08G2539' => 'fan', 'FAN08G2728' => 'fan', 'FAN09G0608' => 'fan', 'FAN09G1136' => 'fan', 'FAN09G1958' => 'fan', 'FAN09G2508' => 'fan', 'FAN09G2597' => 'fan', 'FAN09G2658' => 'fan', 'FAN09G2757' => 'fan', 'FAN09G2983' => 'fan', 'FAN09G3130' => 'fan', 'FAN09G3565' => 'fan', 'FAN09G3613' => 'fan', 'FAN09G4011' => 'fan', 'FAN09G4239' => 'fan', 'FAN09G4277' => 'fan', 'FAN09G4720' => 'fan', 'FAN11G0139' => 'fan', 'FAN11G1727' => 'fan', 'FAN11G2672' => 'fan', 'FAN11G2795' => 'fan', 'FAN11G3238' => 'fan', 'FAN11G3734' => 'fan', 'FAN12G0631' => 'fan', 'FAN12G2239' => 'fan', 'FAN12G2308' => 'fan', 'FAN12G2569' => 'fan', 'FAN12G2623' => 'fan', 'FAN13G3182' => 'fan', 'FAN14G0053' => 'fan', 'FAN14G0370' => 'fan', 'FAN14G0382' => 'fan', 'FAN14G0421' => 'fan', 'FAN14G0866' => 'fan', 'FAN14G1187' => 'fan', 'FAN14G1727' => 'fan', 'FAN14G1791' => 'fan', 'FAN14G2361' => 'fan', 'FAN14G2668' => 'fan', 'FAN14G2770' => 'fan', 'FAN14G2874' => 'fan', 'FAN14G3193' => 'fan', 'FAN14G3624' => 'fan', 'FAN14G3676' => 'fan', 'FAN14G3807' => 'fan', 'FAN14G4082' => 'fan', 'FAN14G4342' => 'fan', 'FAN14G4985' => 'fan', 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'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 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'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001729' ), 'data_identifier' => 'HOM05D001729', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001729', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '375', 'num_species' => '42' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'Ah.07g204710' => 'amhyb', 'AUR62006001' => 'cqu', 'AUR62006002' => 'cqu', 'AUR62006003' => 'cqu', 'AUR62015641' => 'cqu', 'AUR62027174' => 'cqu', 'AUR62035623' => 'cqu', 'AUR62035624' => 'cqu', 'AUR62035625' => 'cqu', 'AUR62035626' => 'cqu', 'CAN.G1110.53' => 'can', 'CANSAT80G0415' => 'cansat', 'Ca_21364_v3' => 'car', 'COL.COLO4_30693' => 'col', 'COL.COLO4_30694' => 'col', 'COL.COLO4_30695' => 'col', 'COL.COLO4_30696' => 'col', 'COL.COLO4_34020' => 'col', 'DCAR_004585' => 'dca', 'Dinv04029' => 'din', 'Dinv34857' => 'din', 'Duzib147G0011' => 'dzi', 'Duzib170G0599' => 'dzi', 'Duzib192G1051' => 'dzi', 'FAN01G0708' => 'fan', 'FAN01G0742' => 'fan', 'FAN02G0048' => 'fan', 'FAN02G0583' => 'fan', 'FAN02G0688' => 'fan', 'FAN02G1588' => 'fan', 'FAN02G2194' => 'fan', 'FAN02G2750' => 'fan', 'FAN02G3094' => 'fan', 'FAN02G3887' => 'fan', 'FAN02G3911' => 'fan', 'FAN02G3994' => 'fan', 'FAN02G4432' => 'fan', 'FAN02G4556' => 'fan', 'FAN03G1977' => 'fan', 'FAN03G2781' => 'fan', 'FAN03G2850' => 'fan', 'FAN03G3155' => 'fan', 'FAN04G2487' => 'fan', 'FAN05G0208' => 'fan', 'FAN05G0656' => 'fan', 'FAN05G0696' => 'fan', 'FAN05G0810' => 'fan', 'FAN05G1447' => 'fan', 'FAN05G2640' => 'fan', 'FAN05G2911' => 'fan', 'FAN05G3901' => 'fan', 'FAN05G4859' => 'fan', 'FAN05G4861' => 'fan', 'FAN05G4988' => 'fan', 'FAN05G5187' => 'fan', 'FAN05G5452' => 'fan', 'FAN05G5500' => 'fan', 'FAN05G5688' => 'fan', 'FAN06G0177' => 'fan', 'FAN06G0675' => 'fan', 'FAN06G1290' => 'fan', 'FAN06G2191' => 'fan', 'FAN06G2405' => 'fan', 'FAN06G3231' => 'fan', 'FAN06G3932' => 'fan', 'FAN07G0163' => 'fan', 'FAN07G0471' => 'fan', 'FAN07G1354' => 'fan', 'FAN08G0338' => 'fan', 'FAN08G1373' => 'fan', 'FAN08G2539' => 'fan', 'FAN08G2728' => 'fan', 'FAN09G0608' => 'fan', 'FAN09G1136' => 'fan', 'FAN09G1958' => 'fan', 'FAN09G2508' => 'fan', 'FAN09G2597' => 'fan', 'FAN09G2658' => 'fan', 'FAN09G2757' => 'fan', 'FAN09G2983' => 'fan', 'FAN09G3130' => 'fan', 'FAN09G3565' => 'fan', 'FAN09G3613' => 'fan', 'FAN09G4011' => 'fan', 'FAN09G4239' => 'fan', 'FAN09G4277' => 'fan', 'FAN09G4720' => 'fan', 'FAN11G0139' => 'fan', 'FAN11G1727' => 'fan', 'FAN11G2672' => 'fan', 'FAN11G2795' => 'fan', 'FAN11G3238' => 'fan', 'FAN11G3734' => 'fan', 'FAN12G0631' => 'fan', 'FAN12G2239' => 'fan', 'FAN12G2308' => 'fan', 'FAN12G2569' => 'fan', 'FAN12G2623' => 'fan', 'FAN13G3182' => 'fan', 'FAN14G0053' => 'fan', 'FAN14G0370' => 'fan', 'FAN14G0382' => 'fan', 'FAN14G0421' => 'fan', 'FAN14G0866' => 'fan', 'FAN14G1187' => 'fan', 'FAN14G1727' => 'fan', 'FAN14G1791' => 'fan', 'FAN14G2361' => 'fan', 'FAN14G2668' => 'fan', 'FAN14G2770' => 'fan', 'FAN14G2874' => 'fan', 'FAN14G3193' => 'fan', 'FAN14G3624' => 'fan', 'FAN14G3676' => 'fan', 'FAN14G3807' => 'fan', 'FAN14G4082' => 'fan', 'FAN14G4342' => 'fan', 'FAN14G4985' => 'fan', 'FAN14G5126' => 'fan', 'FAN14G5781' => 'fan', 'FAN14G5808' => 'fan', 'FAN14G5949' => 'fan', 'FAN15G0828' => 'fan', 'FAN15G1054' => 'fan', 'FAN15G2023' => 'fan', 'FAN15G2506' => 'fan', 'FAN16G0128' => 'fan', 'FAN16G0249' => 'fan', 'FAN16G0429' => 'fan', 'FAN16G1493' => 'fan', 'FAN16G2210' => 'fan', 'FAN16G2506' => 'fan', 'FAN18G1542' => 'fan', 'FAN18G4057' => 'fan', 'FAN19G0745' => 'fan', 'FAN19G1216' => 'fan', 'FAN19G1733' => 'fan', 'FAN20G0258' => 'fan', 'FAN20G1095' => 'fan', 'FAN20G1557' => 'fan', 'FAN21G0302' => 'fan', 'FAN21G0519' => 'fan', 'FAN21G0970' => 'fan', 'FAN21G1159' => 'fan', 'FAN21G1312' => 'fan', 'FAN21G1440' => 'fan', 'FAN21G1715' => 'fan', 'FAN23G1584' => 'fan', 'FAN24G0045' => 'fan', 'FAN24G0053' => 'fan', 'FAN24G1500' => 'fan', 'FAN24G1817' => 'fan', 'FAN24G2147' => 'fan', 'FAN24G2236' => 'fan', 'FAN24G2446' => 'fan', 'FAN24G2684' => 'fan', 'FAN25G0187' => 'fan', 'FAN25G0505' => 'fan', 'FAN25G0589' => 'fan', 'FAN25G3663' => 'fan', 'FAN26G1025' => 'fan', 'FAN26G2860' => 'fan', 'FAN27G1329' => 'fan', 'FAN27G3392' => 'fan', 'FvH4_1g02011' => 'fve', 'FvH4_1g06511' => 'fve', 'FvH4_2g19900' => 'fve', 'FvH4_2g19920' => 'fve', 'FvH4_2g24261' => 'fve', 'FvH4_2g24270' => 'fve', 'FvH4_2g24631' => 'fve', 'FvH4_2g30622' => 'fve', 'FvH4_3g12920' => 'fve', 'FvH4_3g30171' => 'fve', 'FvH4_3g35490' => 'fve', 'FvH4_3g43682' => 'fve', 'FvH4_3g43730' => 'fve', 'FvH4_3g43732' => 'fve', 'FvH4_3g43751' => 'fve', 'FvH4_3g43752' => 'fve', 'FvH4_3g43770' => 'fve', 'FvH4_3g44471' => 'fve', 'FvH4_3g44510' => 'fve', 'FvH4_3g44582' => 'fve', 'FvH4_4g16921' => 'fve', 'FvH4_4g17121' => 'fve', 'FvH4_4g17782' => 'fve', 'FvH4_4g17783' => 'fve', 'FvH4_4g18120' => 'fve', 'FvH4_4g31310' => 'fve', 'FvH4_4g35052' => 'fve', 'FvH4_5g30862' => 'fve', 'FvH4_6g01541' => 'fve', 'FvH4_6g02021' => 'fve', 'FvH4_6g02041' => 'fve', 'FvH4_6g02071' => 'fve', 'FvH4_6g02171' => 'fve', 'FvH4_6g03181' => 'fve', 'FvH4_6g03182' => 'fve', 'FvH4_6g03221' => 'fve', 'FvH4_6g03380' => 'fve', 'FvH4_6g05201' => 'fve', 'FvH4_6g05203' => 'fve', 'FvH4_6g20231' => 'fve', 'FvH4_6g31981' => 'fve', 'FvH4_6g32061' => 'fve', 'FvH4_6g37041' => 'fve', 'FvH4_6g37932' => 'fve', 'FvH4_6g38731' => 'fve', 'FvH4_6g39370' => 'fve', 'FvH4_6g39371' => 'fve', 'FvH4_6g40891' => 'fve', 'FvH4_6g40892' => 'fve', 'FvH4_6g43143' => 'fve', 'FvH4_6g45251' => 'fve', 'FvH4_6g45260' => 'fve', 'FvH4_6g45291' => 'fve', 'FvH4_6g45890' => 'fve', 'FvH4_6g46240' => 'fve', 'FvH4_6g46241' => 'fve', 'FvH4_6g46242' => 'fve', 'FvH4_6g46260' => 'fve', 'FvH4_6g46280' => 'fve', 'FvH4_6g46380' => 'fve', 'FvH4_7g12841' => 'fve', 'FvH4_7g31431' => 'fve', 'Glyma.09G075900' => 'gma', 'Gohir.A09G096401' => 'ghi', 'Gohir.D09G096101' => 'ghi', 'Gorai.006G112800' => 'gra', 'HanXRQChr04g0121411' => 'han', 'Hund15878' => 'sun', 'Lj2A1107G68' => 'lonja', 'Lj2A630G63' => 'lonja', 'Lj2A946T25' => 'lonja', 'Lj2C714T1' => 'lonja', 'Lj2C966T3' => 'lonja', 'Lj2C966T4' => 'lonja', 'Lj4g0002979' => 'lja', 'Lsat_1_v5_gn_5_30901' => 'lsa', 'Lsat_1_v5_gn_5_31100' => 'lsa', 'Lsat_1_v5_gn_5_38600' => 'lsa', 'Lsat_1_v5_gn_6_92061' => 'lsa', 'Manes.05G071301' => 'mes', 'MD02G1008700' => 'mdo', 'MD02G1008900' => 'mdo', 'MD03G1256400' => 'mdo', 'MD04G1180900' => 'mdo', 'MD04G1181000' => 'mdo', 'MD04G1181200' => 'mdo', 'MD05G1244200' => 'mdo', 'MD05G1324200' => 'mdo', 'MD09G1201600' => 'mdo', 'MD10G1000600' => 'mdo', 'MD14G1026900' => 'mdo', 'MD14G1187900' => 'mdo', 'MD15G1017800' => 'mdo', 'MD15G1018100' => 'mdo', 'Medtr4g124160' => 'mtr', 'Migut.L01260' => 'egut', 'Nitab4.5_0000008g0440' => 'nta', 'Nitab4.5_0000207g0170' => 'nta', 'Nitab4.5_0007671g0030' => 'nta', 'Nitab4.5_0010853g0020' => 'nta', 'Oeu057656.1' => 'oeu', 'PGSC0003DMG400005638' => 'stu', 'PGSC0003DMG400005639' => 'stu', 'Phvul.009G222800' => 'pvu', 'Potri.009G132400' => 'ptr', 'Potri.009G163001' => 'ptr', 'Potri.011G000700' => 'ptr', 'Potri.011G004800' => 'ptr', 'Prupe.1G509300' => 'ppe', 'Prupe.1G509700' => 'ppe', 'Prupe.1G510400' => 'ppe', 'Prupe.1G510700' => 'ppe', 'Prupe.1G512600' => 'ppe', 'Prupe.2G073200' => 'ppe', 'Prupe.3G059500' => 'ppe', 'Prupe.3G059600' => 'ppe', 'Prupe.3G246100' => 'ppe', 'Prupe.3G265100' => 'ppe', 'Prupe.4G034700' => 'ppe', 'Prupe.4G052100' => 'ppe', 'Prupe.4G053600' => 'ppe', 'Prupe.5G068800' => 'ppe', 'Prupe.5G070600' => 'ppe', 'Prupe.6G075400' => 'ppe', 'Prupe.6G075500' => 'ppe', 'Prupe.6G076400' => 'ppe', 'Prupe.8G110700' => 'ppe', 'Psat4g020960' => 'psa', 'PSO135G0788' => 'pso', 'PSO210G6463' => 'pso', 'PSO384G0370' => 'pso', 'PSO386G0056' => 'pso', 'QL01p006048' => 'qlo', 'QL02p054283' => 'qlo', 'QL05p008000' => 'qlo', 'QL05p008212' => 'qlo', 'QL05p008950' => 'qlo', 'QL05p009042' => 'qlo', 'QL05p009518' => 'qlo', 'QL05p012589' => 'qlo', 'QL05p012608' => 'qlo', 'QL05p012650' => 'qlo', 'QL05p012667' => 'qlo', 'QL05p014501' => 'qlo', 'QL05p052800' => 'qlo', 'QL05p065010' => 'qlo', 'QL05p074156' => 'qlo', 'QL05p074160' => 'qlo', 'QL05p074174' => 'qlo', 'QL05p074178' => 'qlo', 'QL05p074214' => 'qlo', 'QL06p001050' => 'qlo', 'QL06p001056' => 'qlo', 'QL06p006093' => 'qlo', 'QL06p006111' => 'qlo', 'QL07p019784' => 'qlo', 'QL07p019801' => 'qlo', 'QL07p036110' => 'qlo', 'QL07p036134' => 'qlo', 'QL07p036147' => 'qlo', 'QL07p036156' => 'qlo', 'QL07p036300' => 'qlo', 'QL07p036320' => 'qlo', 'QL08p014547' => 'qlo', 'QL08p014551' => 'qlo', 'QL08p043319' => 'qlo', 'QL08p043324' => 'qlo', 'QL11p009094' => 'qlo', 'RcHm_v2.0_Chr1g0380481' => 'rch', 'RcHm_v2.0_Chr2g0089331' => 'rch', 'RcHm_v2.0_Chr2g0123691' => 'rch', 'RcHm_v2.0_Chr2g0151111' => 'rch', 'RcHm_v2.0_Chr2g0163011' => 'rch', 'RcHm_v2.0_Chr2g0163051' => 'rch', 'RcHm_v2.0_Chr2g0164671' => 'rch', 'RcHm_v2.0_Chr2g0164681' => 'rch', 'RcHm_v2.0_Chr2g0164721' => 'rch', 'RcHm_v2.0_Chr3g0449911' => 'rch', 'RcHm_v2.0_Chr3g0450211' => 'rch', 'RcHm_v2.0_Chr3g0457271' => 'rch', 'RcHm_v2.0_Chr5g0018111' => 'rch', 'RcHm_v2.0_Chr5g0021011' => 'rch', 'RcHm_v2.0_Chr5g0081171' => 'rch', 'RcHm_v2.0_Chr5g0081211' => 'rch', 'RcHm_v2.0_Chr6g0275871' => 'rch', 'RcHm_v2.0_Chr6g0276071' => 'rch', 'RcHm_v2.0_Chr6g0285591' => 'rch', 'RcHm_v2.0_Chr6g0291931' => 'rch', 'RcHm_v2.0_Chr6g0292091' => 'rch', 'RcHm_v2.0_Chr6g0292271' => 'rch', 'RcHm_v2.0_Chr7g0221261' => 'rch', 'Rhsim08G0219900' => 'rsi', 'Rhsim08G0220200' => 'rsi', 'Rhsim08G0237800' => 'rsi', 'Rhsim08G0238800' => 'rsi', 'Sabra09G0102700' => 'sbr', 'Sabra09G0127200' => 'sbr', 'Sabra11G0003700' => 'sbr', 'Sabra15G0014700' => 'sbr', 'Sc19g0000590' => 'sci', 'Sc19g0001870' => 'sci', 'SGA_v2.0_scaffold1G00346' => 'sas', 'SGA_v2.0_scaffold1G00575' => 'sas', 'SGA_v2.0_scaffold1G00761' => 'sas', 'SGA_v2.0_scaffold232G43501' => 'sas', 'TAR625G1137' => 'tar', 'Thecc.03G222100' => 'tca', 'TPR.G12691' => 'tpr', 'TWI34G0727' => 'twi', 'TWI36G0117' => 'twi', 'VMungo1309G0868' => 'vmu' ) $gf_id = 'HOM05D001729' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001729' ) $data_identifier = 'HOM05D001729' $data_type = 'gf_id' $species_gene_counts = array( 'amhyb' => (int) 1, 'cqu' => (int) 9, 'can' => (int) 1, 'cansat' => (int) 1, 'car' => (int) 1, 'col' => (int) 5, 'dca' => (int) 1, 'din' => (int) 2, 'dzi' => (int) 3, 'fan' => (int) 140, 'fve' => (int) 62, 'gma' => (int) 1, 'ghi' => (int) 2, 'gra' => (int) 1, 'han' => (int) 1, 'sun' => (int) 1, 'lonja' => (int) 6, 'lja' => (int) 1, 'lsa' => (int) 4, 'mes' => (int) 1, 'mdo' => (int) 14, 'mtr' => (int) 1, 'egut' => (int) 1, 'nta' => (int) 4, 'oeu' => (int) 1, 'stu' => (int) 2, 'pvu' => (int) 1, 'ptr' => (int) 4, 'ppe' => (int) 19, 'psa' => (int) 1, 'pso' => (int) 4, 'qlo' => (int) 36, 'rch' => (int) 23, 'rsi' => (int) 4, 'sbr' => (int) 4, 'sci' => (int) 2, 'sas' => (int) 4, 'tar' => (int) 1, 'tca' => (int) 1, 'tpr' => (int) 1, 'twi' => (int) 2, 'vmu' => (int) 1 ) $gf_gene_species = 'vmu' $gf_gene_id = 'VMungo1309G0868' $species_info = array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ) $local_species = 'car' $disabled = '' $selected = '' $num_hits = (int) 0
Warning (2): count(): Parameter must be an array or an object that implements Countable [APP/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp, line 33]Code Context $disabled = (!array_key_exists($local_species,$species_gene_counts))?"disabled":""; $selected = (isset($selected_species) && array_key_exists($local_species,$selected_species))?"checked='checked'":""; $num_hits = (array_key_exists($local_species,$species_gene_counts))?count($species_gene_counts[$local_species]):0; $viewFile = '/www/bioinformatics01_ro/plaza/_dev_instances/feedback/app/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp' $dataForView = array( 'sidebar_info' => array( 'gf_id' => 'HOM05D001729', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '375', 'num_species' => '42' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'Ah.07g204710' => 'amhyb', 'AUR62006001' => 'cqu', 'AUR62006002' => 'cqu', 'AUR62006003' => 'cqu', 'AUR62015641' => 'cqu', 'AUR62027174' => 'cqu', 'AUR62035623' => 'cqu', 'AUR62035624' => 'cqu', 'AUR62035625' => 'cqu', 'AUR62035626' => 'cqu', 'CAN.G1110.53' => 'can', 'CANSAT80G0415' => 'cansat', 'Ca_21364_v3' => 'car', 'COL.COLO4_30693' => 'col', 'COL.COLO4_30694' => 'col', 'COL.COLO4_30695' => 'col', 'COL.COLO4_30696' => 'col', 'COL.COLO4_34020' => 'col', 'DCAR_004585' => 'dca', 'Dinv04029' => 'din', 'Dinv34857' => 'din', 'Duzib147G0011' => 'dzi', 'Duzib170G0599' => 'dzi', 'Duzib192G1051' => 'dzi', 'FAN01G0708' => 'fan', 'FAN01G0742' => 'fan', 'FAN02G0048' => 'fan', 'FAN02G0583' => 'fan', 'FAN02G0688' => 'fan', 'FAN02G1588' => 'fan', 'FAN02G2194' => 'fan', 'FAN02G2750' => 'fan', 'FAN02G3094' => 'fan', 'FAN02G3887' => 'fan', 'FAN02G3911' => 'fan', 'FAN02G3994' => 'fan', 'FAN02G4432' => 'fan', 'FAN02G4556' => 'fan', 'FAN03G1977' => 'fan', 'FAN03G2781' => 'fan', 'FAN03G2850' => 'fan', 'FAN03G3155' => 'fan', 'FAN04G2487' => 'fan', 'FAN05G0208' => 'fan', 'FAN05G0656' => 'fan', 'FAN05G0696' => 'fan', 'FAN05G0810' => 'fan', 'FAN05G1447' => 'fan', 'FAN05G2640' => 'fan', 'FAN05G2911' => 'fan', 'FAN05G3901' => 'fan', 'FAN05G4859' => 'fan', 'FAN05G4861' => 'fan', 'FAN05G4988' => 'fan', 'FAN05G5187' => 'fan', 'FAN05G5452' => 'fan', 'FAN05G5500' => 'fan', 'FAN05G5688' => 'fan', 'FAN06G0177' => 'fan', 'FAN06G0675' => 'fan', 'FAN06G1290' => 'fan', 'FAN06G2191' => 'fan', 'FAN06G2405' => 'fan', 'FAN06G3231' => 'fan', 'FAN06G3932' => 'fan', 'FAN07G0163' => 'fan', 'FAN07G0471' => 'fan', 'FAN07G1354' => 'fan', 'FAN08G0338' => 'fan', 'FAN08G1373' => 'fan', 'FAN08G2539' => 'fan', 'FAN08G2728' => 'fan', 'FAN09G0608' => 'fan', 'FAN09G1136' => 'fan', 'FAN09G1958' => 'fan', 'FAN09G2508' => 'fan', 'FAN09G2597' => 'fan', 'FAN09G2658' => 'fan', 'FAN09G2757' => 'fan', 'FAN09G2983' => 'fan', 'FAN09G3130' => 'fan', 'FAN09G3565' => 'fan', 'FAN09G3613' => 'fan', 'FAN09G4011' => 'fan', 'FAN09G4239' => 'fan', 'FAN09G4277' => 'fan', 'FAN09G4720' => 'fan', 'FAN11G0139' => 'fan', 'FAN11G1727' => 'fan', 'FAN11G2672' => 'fan', 'FAN11G2795' => 'fan', 'FAN11G3238' => 'fan', 'FAN11G3734' => 'fan', 'FAN12G0631' => 'fan', 'FAN12G2239' => 'fan', 'FAN12G2308' => 'fan', 'FAN12G2569' => 'fan', 'FAN12G2623' => 'fan', 'FAN13G3182' => 'fan', 'FAN14G0053' => 'fan', 'FAN14G0370' => 'fan', 'FAN14G0382' => 'fan', 'FAN14G0421' => 'fan', 'FAN14G0866' => 'fan', 'FAN14G1187' => 'fan', 'FAN14G1727' => 'fan', 'FAN14G1791' => 'fan', 'FAN14G2361' => 'fan', 'FAN14G2668' => 'fan', 'FAN14G2770' => 'fan', 'FAN14G2874' => 'fan', 'FAN14G3193' => 'fan', 'FAN14G3624' => 'fan', 'FAN14G3676' => 'fan', 'FAN14G3807' => 'fan', 'FAN14G4082' => 'fan', 'FAN14G4342' => 'fan', 'FAN14G4985' => 'fan', 'FAN14G5126' => 'fan', 'FAN14G5781' => 'fan', 'FAN14G5808' => 'fan', 'FAN14G5949' => 'fan', 'FAN15G0828' => 'fan', 'FAN15G1054' => 'fan', 'FAN15G2023' => 'fan', 'FAN15G2506' => 'fan', 'FAN16G0128' => 'fan', 'FAN16G0249' => 'fan', 'FAN16G0429' => 'fan', 'FAN16G1493' => 'fan', 'FAN16G2210' => 'fan', 'FAN16G2506' => 'fan', 'FAN18G1542' => 'fan', 'FAN18G4057' => 'fan', 'FAN19G0745' => 'fan', 'FAN19G1216' => 'fan', 'FAN19G1733' => 'fan', 'FAN20G0258' => 'fan', 'FAN20G1095' => 'fan', 'FAN20G1557' => 'fan', 'FAN21G0302' => 'fan', 'FAN21G0519' => 'fan', 'FAN21G0970' => 'fan', 'FAN21G1159' => 'fan', 'FAN21G1312' => 'fan', 'FAN21G1440' => 'fan', 'FAN21G1715' => 'fan', 'FAN23G1584' => 'fan', 'FAN24G0045' => 'fan', 'FAN24G0053' => 'fan', 'FAN24G1500' => 'fan', 'FAN24G1817' => 'fan', 'FAN24G2147' => 'fan', 'FAN24G2236' => 'fan', 'FAN24G2446' => 'fan', 'FAN24G2684' => 'fan', 'FAN25G0187' => 'fan', 'FAN25G0505' => 'fan', 'FAN25G0589' => 'fan', 'FAN25G3663' => 'fan', 'FAN26G1025' => 'fan', 'FAN26G2860' => 'fan', 'FAN27G1329' => 'fan', 'FAN27G3392' => 'fan', 'FvH4_1g02011' => 'fve', 'FvH4_1g06511' => 'fve', 'FvH4_2g19900' => 'fve', 'FvH4_2g19920' => 'fve', 'FvH4_2g24261' => 'fve', 'FvH4_2g24270' => 'fve', 'FvH4_2g24631' => 'fve', 'FvH4_2g30622' => 'fve', 'FvH4_3g12920' => 'fve', 'FvH4_3g30171' => 'fve', 'FvH4_3g35490' => 'fve', 'FvH4_3g43682' => 'fve', 'FvH4_3g43730' => 'fve', 'FvH4_3g43732' => 'fve', 'FvH4_3g43751' => 'fve', 'FvH4_3g43752' => 'fve', 'FvH4_3g43770' => 'fve', 'FvH4_3g44471' => 'fve', 'FvH4_3g44510' => 'fve', 'FvH4_3g44582' => 'fve', 'FvH4_4g16921' => 'fve', 'FvH4_4g17121' => 'fve', 'FvH4_4g17782' => 'fve', 'FvH4_4g17783' => 'fve', 'FvH4_4g18120' => 'fve', 'FvH4_4g31310' => 'fve', 'FvH4_4g35052' => 'fve', 'FvH4_5g30862' => 'fve', 'FvH4_6g01541' => 'fve', 'FvH4_6g02021' => 'fve', 'FvH4_6g02041' => 'fve', 'FvH4_6g02071' => 'fve', 'FvH4_6g02171' => 'fve', 'FvH4_6g03181' => 'fve', 'FvH4_6g03182' => 'fve', 'FvH4_6g03221' => 'fve', 'FvH4_6g03380' => 'fve', 'FvH4_6g05201' => 'fve', 'FvH4_6g05203' => 'fve', 'FvH4_6g20231' => 'fve', 'FvH4_6g31981' => 'fve', 'FvH4_6g32061' => 'fve', 'FvH4_6g37041' => 'fve', 'FvH4_6g37932' => 'fve', 'FvH4_6g38731' => 'fve', 'FvH4_6g39370' => 'fve', 'FvH4_6g39371' => 'fve', 'FvH4_6g40891' => 'fve', 'FvH4_6g40892' => 'fve', 'FvH4_6g43143' => 'fve', 'FvH4_6g45251' => 'fve', 'FvH4_6g45260' => 'fve', 'FvH4_6g45291' => 'fve', 'FvH4_6g45890' => 'fve', 'FvH4_6g46240' => 'fve', 'FvH4_6g46241' => 'fve', 'FvH4_6g46242' => 'fve', 'FvH4_6g46260' => 'fve', 'FvH4_6g46280' => 'fve', 'FvH4_6g46380' => 'fve', 'FvH4_7g12841' => 'fve', 'FvH4_7g31431' => 'fve', 'Glyma.09G075900' => 'gma', 'Gohir.A09G096401' => 'ghi', 'Gohir.D09G096101' => 'ghi', 'Gorai.006G112800' => 'gra', 'HanXRQChr04g0121411' => 'han', 'Hund15878' => 'sun', 'Lj2A1107G68' => 'lonja', 'Lj2A630G63' => 'lonja', 'Lj2A946T25' => 'lonja', 'Lj2C714T1' => 'lonja', 'Lj2C966T3' => 'lonja', 'Lj2C966T4' => 'lonja', 'Lj4g0002979' => 'lja', 'Lsat_1_v5_gn_5_30901' => 'lsa', 'Lsat_1_v5_gn_5_31100' => 'lsa', 'Lsat_1_v5_gn_5_38600' => 'lsa', 'Lsat_1_v5_gn_6_92061' => 'lsa', 'Manes.05G071301' => 'mes', 'MD02G1008700' => 'mdo', 'MD02G1008900' => 'mdo', 'MD03G1256400' => 'mdo', 'MD04G1180900' => 'mdo', 'MD04G1181000' => 'mdo', 'MD04G1181200' => 'mdo', 'MD05G1244200' => 'mdo', 'MD05G1324200' => 'mdo', 'MD09G1201600' => 'mdo', 'MD10G1000600' => 'mdo', 'MD14G1026900' => 'mdo', 'MD14G1187900' => 'mdo', 'MD15G1017800' => 'mdo', 'MD15G1018100' => 'mdo', 'Medtr4g124160' => 'mtr', 'Migut.L01260' => 'egut', 'Nitab4.5_0000008g0440' => 'nta', 'Nitab4.5_0000207g0170' => 'nta', 'Nitab4.5_0007671g0030' => 'nta', 'Nitab4.5_0010853g0020' => 'nta', 'Oeu057656.1' => 'oeu', 'PGSC0003DMG400005638' => 'stu', 'PGSC0003DMG400005639' => 'stu', 'Phvul.009G222800' => 'pvu', 'Potri.009G132400' => 'ptr', 'Potri.009G163001' => 'ptr', 'Potri.011G000700' => 'ptr', 'Potri.011G004800' => 'ptr', 'Prupe.1G509300' => 'ppe', 'Prupe.1G509700' => 'ppe', 'Prupe.1G510400' => 'ppe', 'Prupe.1G510700' => 'ppe', 'Prupe.1G512600' => 'ppe', 'Prupe.2G073200' => 'ppe', 'Prupe.3G059500' => 'ppe', 'Prupe.3G059600' => 'ppe', 'Prupe.3G246100' => 'ppe', 'Prupe.3G265100' => 'ppe', 'Prupe.4G034700' => 'ppe', 'Prupe.4G052100' => 'ppe', 'Prupe.4G053600' => 'ppe', 'Prupe.5G068800' => 'ppe', 'Prupe.5G070600' => 'ppe', 'Prupe.6G075400' => 'ppe', 'Prupe.6G075500' => 'ppe', 'Prupe.6G076400' => 'ppe', 'Prupe.8G110700' => 'ppe', 'Psat4g020960' => 'psa', 'PSO135G0788' => 'pso', 'PSO210G6463' => 'pso', 'PSO384G0370' => 'pso', 'PSO386G0056' => 'pso', 'QL01p006048' => 'qlo', 'QL02p054283' => 'qlo', 'QL05p008000' => 'qlo', 'QL05p008212' => 'qlo', 'QL05p008950' => 'qlo', 'QL05p009042' => 'qlo', 'QL05p009518' => 'qlo', 'QL05p012589' => 'qlo', 'QL05p012608' => 'qlo', 'QL05p012650' => 'qlo', 'QL05p012667' => 'qlo', 'QL05p014501' => 'qlo', 'QL05p052800' => 'qlo', 'QL05p065010' => 'qlo', 'QL05p074156' => 'qlo', 'QL05p074160' => 'qlo', 'QL05p074174' => 'qlo', 'QL05p074178' => 'qlo', 'QL05p074214' => 'qlo', 'QL06p001050' => 'qlo', 'QL06p001056' => 'qlo', 'QL06p006093' => 'qlo', 'QL06p006111' => 'qlo', 'QL07p019784' => 'qlo', 'QL07p019801' => 'qlo', 'QL07p036110' => 'qlo', 'QL07p036134' => 'qlo', 'QL07p036147' => 'qlo', 'QL07p036156' => 'qlo', 'QL07p036300' => 'qlo', 'QL07p036320' => 'qlo', 'QL08p014547' => 'qlo', 'QL08p014551' => 'qlo', 'QL08p043319' => 'qlo', 'QL08p043324' => 'qlo', 'QL11p009094' => 'qlo', 'RcHm_v2.0_Chr1g0380481' => 'rch', 'RcHm_v2.0_Chr2g0089331' => 'rch', 'RcHm_v2.0_Chr2g0123691' => 'rch', 'RcHm_v2.0_Chr2g0151111' => 'rch', 'RcHm_v2.0_Chr2g0163011' => 'rch', 'RcHm_v2.0_Chr2g0163051' => 'rch', 'RcHm_v2.0_Chr2g0164671' => 'rch', 'RcHm_v2.0_Chr2g0164681' => 'rch', 'RcHm_v2.0_Chr2g0164721' => 'rch', 'RcHm_v2.0_Chr3g0449911' => 'rch', 'RcHm_v2.0_Chr3g0450211' => 'rch', 'RcHm_v2.0_Chr3g0457271' => 'rch', 'RcHm_v2.0_Chr5g0018111' => 'rch', 'RcHm_v2.0_Chr5g0021011' => 'rch', 'RcHm_v2.0_Chr5g0081171' => 'rch', 'RcHm_v2.0_Chr5g0081211' => 'rch', 'RcHm_v2.0_Chr6g0275871' => 'rch', 'RcHm_v2.0_Chr6g0276071' => 'rch', 'RcHm_v2.0_Chr6g0285591' => 'rch', 'RcHm_v2.0_Chr6g0291931' => 'rch', 'RcHm_v2.0_Chr6g0292091' => 'rch', 'RcHm_v2.0_Chr6g0292271' => 'rch', 'RcHm_v2.0_Chr7g0221261' => 'rch', 'Rhsim08G0219900' => 'rsi', 'Rhsim08G0220200' => 'rsi', 'Rhsim08G0237800' => 'rsi', 'Rhsim08G0238800' => 'rsi', 'Sabra09G0102700' => 'sbr', 'Sabra09G0127200' => 'sbr', 'Sabra11G0003700' => 'sbr', 'Sabra15G0014700' => 'sbr', 'Sc19g0000590' => 'sci', 'Sc19g0001870' => 'sci', 'SGA_v2.0_scaffold1G00346' => 'sas', 'SGA_v2.0_scaffold1G00575' => 'sas', 'SGA_v2.0_scaffold1G00761' => 'sas', 'SGA_v2.0_scaffold232G43501' => 'sas', 'TAR625G1137' => 'tar', 'Thecc.03G222100' => 'tca', 'TPR.G12691' => 'tpr', 'TWI34G0727' => 'twi', 'TWI36G0117' => 'twi', 'VMungo1309G0868' => 'vmu' ), 'gf_id' => 'HOM05D001729', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001729' ), 'data_identifier' => 'HOM05D001729', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001729', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '375', 'num_species' => '42' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'Ah.07g204710' => 'amhyb', 'AUR62006001' => 'cqu', 'AUR62006002' => 'cqu', 'AUR62006003' => 'cqu', 'AUR62015641' => 'cqu', 'AUR62027174' => 'cqu', 'AUR62035623' => 'cqu', 'AUR62035624' => 'cqu', 'AUR62035625' => 'cqu', 'AUR62035626' => 'cqu', 'CAN.G1110.53' => 'can', 'CANSAT80G0415' => 'cansat', 'Ca_21364_v3' => 'car', 'COL.COLO4_30693' => 'col', 'COL.COLO4_30694' => 'col', 'COL.COLO4_30695' => 'col', 'COL.COLO4_30696' => 'col', 'COL.COLO4_34020' => 'col', 'DCAR_004585' => 'dca', 'Dinv04029' => 'din', 'Dinv34857' => 'din', 'Duzib147G0011' => 'dzi', 'Duzib170G0599' => 'dzi', 'Duzib192G1051' => 'dzi', 'FAN01G0708' => 'fan', 'FAN01G0742' => 'fan', 'FAN02G0048' => 'fan', 'FAN02G0583' => 'fan', 'FAN02G0688' => 'fan', 'FAN02G1588' => 'fan', 'FAN02G2194' => 'fan', 'FAN02G2750' => 'fan', 'FAN02G3094' => 'fan', 'FAN02G3887' => 'fan', 'FAN02G3911' => 'fan', 'FAN02G3994' => 'fan', 'FAN02G4432' => 'fan', 'FAN02G4556' => 'fan', 'FAN03G1977' => 'fan', 'FAN03G2781' => 'fan', 'FAN03G2850' => 'fan', 'FAN03G3155' => 'fan', 'FAN04G2487' => 'fan', 'FAN05G0208' => 'fan', 'FAN05G0656' => 'fan', 'FAN05G0696' => 'fan', 'FAN05G0810' => 'fan', 'FAN05G1447' => 'fan', 'FAN05G2640' => 'fan', 'FAN05G2911' => 'fan', 'FAN05G3901' => 'fan', 'FAN05G4859' => 'fan', 'FAN05G4861' => 'fan', 'FAN05G4988' => 'fan', 'FAN05G5187' => 'fan', 'FAN05G5452' => 'fan', 'FAN05G5500' => 'fan', 'FAN05G5688' => 'fan', 'FAN06G0177' => 'fan', 'FAN06G0675' => 'fan', 'FAN06G1290' => 'fan', 'FAN06G2191' => 'fan', 'FAN06G2405' => 'fan', 'FAN06G3231' => 'fan', 'FAN06G3932' => 'fan', 'FAN07G0163' => 'fan', 'FAN07G0471' => 'fan', 'FAN07G1354' => 'fan', 'FAN08G0338' => 'fan', 'FAN08G1373' => 'fan', 'FAN08G2539' => 'fan', 'FAN08G2728' => 'fan', 'FAN09G0608' => 'fan', 'FAN09G1136' => 'fan', 'FAN09G1958' => 'fan', 'FAN09G2508' => 'fan', 'FAN09G2597' => 'fan', 'FAN09G2658' => 'fan', 'FAN09G2757' => 'fan', 'FAN09G2983' => 'fan', 'FAN09G3130' => 'fan', 'FAN09G3565' => 'fan', 'FAN09G3613' => 'fan', 'FAN09G4011' => 'fan', 'FAN09G4239' => 'fan', 'FAN09G4277' => 'fan', 'FAN09G4720' => 'fan', 'FAN11G0139' => 'fan', 'FAN11G1727' => 'fan', 'FAN11G2672' => 'fan', 'FAN11G2795' => 'fan', 'FAN11G3238' => 'fan', 'FAN11G3734' => 'fan', 'FAN12G0631' => 'fan', 'FAN12G2239' => 'fan', 'FAN12G2308' => 'fan', 'FAN12G2569' => 'fan', 'FAN12G2623' => 'fan', 'FAN13G3182' => 'fan', 'FAN14G0053' => 'fan', 'FAN14G0370' => 'fan', 'FAN14G0382' => 'fan', 'FAN14G0421' => 'fan', 'FAN14G0866' => 'fan', 'FAN14G1187' => 'fan', 'FAN14G1727' => 'fan', 'FAN14G1791' => 'fan', 'FAN14G2361' => 'fan', 'FAN14G2668' => 'fan', 'FAN14G2770' => 'fan', 'FAN14G2874' => 'fan', 'FAN14G3193' => 'fan', 'FAN14G3624' => 'fan', 'FAN14G3676' => 'fan', 'FAN14G3807' => 'fan', 'FAN14G4082' => 'fan', 'FAN14G4342' => 'fan', 'FAN14G4985' => 'fan', 'FAN14G5126' => 'fan', 'FAN14G5781' => 'fan', 'FAN14G5808' => 'fan', 'FAN14G5949' => 'fan', 'FAN15G0828' => 'fan', 'FAN15G1054' => 'fan', 'FAN15G2023' => 'fan', 'FAN15G2506' => 'fan', 'FAN16G0128' => 'fan', 'FAN16G0249' => 'fan', 'FAN16G0429' => 'fan', 'FAN16G1493' => 'fan', 'FAN16G2210' => 'fan', 'FAN16G2506' => 'fan', 'FAN18G1542' => 'fan', 'FAN18G4057' => 'fan', 'FAN19G0745' => 'fan', 'FAN19G1216' => 'fan', 'FAN19G1733' => 'fan', 'FAN20G0258' => 'fan', 'FAN20G1095' => 'fan', 'FAN20G1557' => 'fan', 'FAN21G0302' => 'fan', 'FAN21G0519' => 'fan', 'FAN21G0970' => 'fan', 'FAN21G1159' => 'fan', 'FAN21G1312' => 'fan', 'FAN21G1440' => 'fan', 'FAN21G1715' => 'fan', 'FAN23G1584' => 'fan', 'FAN24G0045' => 'fan', 'FAN24G0053' => 'fan', 'FAN24G1500' => 'fan', 'FAN24G1817' => 'fan', 'FAN24G2147' => 'fan', 'FAN24G2236' => 'fan', 'FAN24G2446' => 'fan', 'FAN24G2684' => 'fan', 'FAN25G0187' => 'fan', 'FAN25G0505' => 'fan', 'FAN25G0589' => 'fan', 'FAN25G3663' => 'fan', 'FAN26G1025' => 'fan', 'FAN26G2860' => 'fan', 'FAN27G1329' => 'fan', 'FAN27G3392' => 'fan', 'FvH4_1g02011' => 'fve', 'FvH4_1g06511' => 'fve', 'FvH4_2g19900' => 'fve', 'FvH4_2g19920' => 'fve', 'FvH4_2g24261' => 'fve', 'FvH4_2g24270' => 'fve', 'FvH4_2g24631' => 'fve', 'FvH4_2g30622' => 'fve', 'FvH4_3g12920' => 'fve', 'FvH4_3g30171' => 'fve', 'FvH4_3g35490' => 'fve', 'FvH4_3g43682' => 'fve', 'FvH4_3g43730' => 'fve', 'FvH4_3g43732' => 'fve', 'FvH4_3g43751' => 'fve', 'FvH4_3g43752' => 'fve', 'FvH4_3g43770' => 'fve', 'FvH4_3g44471' => 'fve', 'FvH4_3g44510' => 'fve', 'FvH4_3g44582' => 'fve', 'FvH4_4g16921' => 'fve', 'FvH4_4g17121' => 'fve', 'FvH4_4g17782' => 'fve', 'FvH4_4g17783' => 'fve', 'FvH4_4g18120' => 'fve', 'FvH4_4g31310' => 'fve', 'FvH4_4g35052' => 'fve', 'FvH4_5g30862' => 'fve', 'FvH4_6g01541' => 'fve', 'FvH4_6g02021' => 'fve', 'FvH4_6g02041' => 'fve', 'FvH4_6g02071' => 'fve', 'FvH4_6g02171' => 'fve', 'FvH4_6g03181' => 'fve', 'FvH4_6g03182' => 'fve', 'FvH4_6g03221' => 'fve', 'FvH4_6g03380' => 'fve', 'FvH4_6g05201' => 'fve', 'FvH4_6g05203' => 'fve', 'FvH4_6g20231' => 'fve', 'FvH4_6g31981' => 'fve', 'FvH4_6g32061' => 'fve', 'FvH4_6g37041' => 'fve', 'FvH4_6g37932' => 'fve', 'FvH4_6g38731' => 'fve', 'FvH4_6g39370' => 'fve', 'FvH4_6g39371' => 'fve', 'FvH4_6g40891' => 'fve', 'FvH4_6g40892' => 'fve', 'FvH4_6g43143' => 'fve', 'FvH4_6g45251' => 'fve', 'FvH4_6g45260' => 'fve', 'FvH4_6g45291' => 'fve', 'FvH4_6g45890' => 'fve', 'FvH4_6g46240' => 'fve', 'FvH4_6g46241' => 'fve', 'FvH4_6g46242' => 'fve', 'FvH4_6g46260' => 'fve', 'FvH4_6g46280' => 'fve', 'FvH4_6g46380' => 'fve', 'FvH4_7g12841' => 'fve', 'FvH4_7g31431' => 'fve', 'Glyma.09G075900' => 'gma', 'Gohir.A09G096401' => 'ghi', 'Gohir.D09G096101' => 'ghi', 'Gorai.006G112800' => 'gra', 'HanXRQChr04g0121411' => 'han', 'Hund15878' => 'sun', 'Lj2A1107G68' => 'lonja', 'Lj2A630G63' => 'lonja', 'Lj2A946T25' => 'lonja', 'Lj2C714T1' => 'lonja', 'Lj2C966T3' => 'lonja', 'Lj2C966T4' => 'lonja', 'Lj4g0002979' => 'lja', 'Lsat_1_v5_gn_5_30901' => 'lsa', 'Lsat_1_v5_gn_5_31100' => 'lsa', 'Lsat_1_v5_gn_5_38600' => 'lsa', 'Lsat_1_v5_gn_6_92061' => 'lsa', 'Manes.05G071301' => 'mes', 'MD02G1008700' => 'mdo', 'MD02G1008900' => 'mdo', 'MD03G1256400' => 'mdo', 'MD04G1180900' => 'mdo', 'MD04G1181000' => 'mdo', 'MD04G1181200' => 'mdo', 'MD05G1244200' => 'mdo', 'MD05G1324200' => 'mdo', 'MD09G1201600' => 'mdo', 'MD10G1000600' => 'mdo', 'MD14G1026900' => 'mdo', 'MD14G1187900' => 'mdo', 'MD15G1017800' => 'mdo', 'MD15G1018100' => 'mdo', 'Medtr4g124160' => 'mtr', 'Migut.L01260' => 'egut', 'Nitab4.5_0000008g0440' => 'nta', 'Nitab4.5_0000207g0170' => 'nta', 'Nitab4.5_0007671g0030' => 'nta', 'Nitab4.5_0010853g0020' => 'nta', 'Oeu057656.1' => 'oeu', 'PGSC0003DMG400005638' => 'stu', 'PGSC0003DMG400005639' => 'stu', 'Phvul.009G222800' => 'pvu', 'Potri.009G132400' => 'ptr', 'Potri.009G163001' => 'ptr', 'Potri.011G000700' => 'ptr', 'Potri.011G004800' => 'ptr', 'Prupe.1G509300' => 'ppe', 'Prupe.1G509700' => 'ppe', 'Prupe.1G510400' => 'ppe', 'Prupe.1G510700' => 'ppe', 'Prupe.1G512600' => 'ppe', 'Prupe.2G073200' => 'ppe', 'Prupe.3G059500' => 'ppe', 'Prupe.3G059600' => 'ppe', 'Prupe.3G246100' => 'ppe', 'Prupe.3G265100' => 'ppe', 'Prupe.4G034700' => 'ppe', 'Prupe.4G052100' => 'ppe', 'Prupe.4G053600' => 'ppe', 'Prupe.5G068800' => 'ppe', 'Prupe.5G070600' => 'ppe', 'Prupe.6G075400' => 'ppe', 'Prupe.6G075500' => 'ppe', 'Prupe.6G076400' => 'ppe', 'Prupe.8G110700' => 'ppe', 'Psat4g020960' => 'psa', 'PSO135G0788' => 'pso', 'PSO210G6463' => 'pso', 'PSO384G0370' => 'pso', 'PSO386G0056' => 'pso', 'QL01p006048' => 'qlo', 'QL02p054283' => 'qlo', 'QL05p008000' => 'qlo', 'QL05p008212' => 'qlo', 'QL05p008950' => 'qlo', 'QL05p009042' => 'qlo', 'QL05p009518' => 'qlo', 'QL05p012589' => 'qlo', 'QL05p012608' => 'qlo', 'QL05p012650' => 'qlo', 'QL05p012667' => 'qlo', 'QL05p014501' => 'qlo', 'QL05p052800' => 'qlo', 'QL05p065010' => 'qlo', 'QL05p074156' => 'qlo', 'QL05p074160' => 'qlo', 'QL05p074174' => 'qlo', 'QL05p074178' => 'qlo', 'QL05p074214' => 'qlo', 'QL06p001050' => 'qlo', 'QL06p001056' => 'qlo', 'QL06p006093' => 'qlo', 'QL06p006111' => 'qlo', 'QL07p019784' => 'qlo', 'QL07p019801' => 'qlo', 'QL07p036110' => 'qlo', 'QL07p036134' => 'qlo', 'QL07p036147' => 'qlo', 'QL07p036156' => 'qlo', 'QL07p036300' => 'qlo', 'QL07p036320' => 'qlo', 'QL08p014547' => 'qlo', 'QL08p014551' => 'qlo', 'QL08p043319' => 'qlo', 'QL08p043324' => 'qlo', 'QL11p009094' => 'qlo', 'RcHm_v2.0_Chr1g0380481' => 'rch', 'RcHm_v2.0_Chr2g0089331' => 'rch', 'RcHm_v2.0_Chr2g0123691' => 'rch', 'RcHm_v2.0_Chr2g0151111' => 'rch', 'RcHm_v2.0_Chr2g0163011' => 'rch', 'RcHm_v2.0_Chr2g0163051' => 'rch', 'RcHm_v2.0_Chr2g0164671' => 'rch', 'RcHm_v2.0_Chr2g0164681' => 'rch', 'RcHm_v2.0_Chr2g0164721' => 'rch', 'RcHm_v2.0_Chr3g0449911' => 'rch', 'RcHm_v2.0_Chr3g0450211' => 'rch', 'RcHm_v2.0_Chr3g0457271' => 'rch', 'RcHm_v2.0_Chr5g0018111' => 'rch', 'RcHm_v2.0_Chr5g0021011' => 'rch', 'RcHm_v2.0_Chr5g0081171' => 'rch', 'RcHm_v2.0_Chr5g0081211' => 'rch', 'RcHm_v2.0_Chr6g0275871' => 'rch', 'RcHm_v2.0_Chr6g0276071' => 'rch', 'RcHm_v2.0_Chr6g0285591' => 'rch', 'RcHm_v2.0_Chr6g0291931' => 'rch', 'RcHm_v2.0_Chr6g0292091' => 'rch', 'RcHm_v2.0_Chr6g0292271' => 'rch', 'RcHm_v2.0_Chr7g0221261' => 'rch', 'Rhsim08G0219900' => 'rsi', 'Rhsim08G0220200' => 'rsi', 'Rhsim08G0237800' => 'rsi', 'Rhsim08G0238800' => 'rsi', 'Sabra09G0102700' => 'sbr', 'Sabra09G0127200' => 'sbr', 'Sabra11G0003700' => 'sbr', 'Sabra15G0014700' => 'sbr', 'Sc19g0000590' => 'sci', 'Sc19g0001870' => 'sci', 'SGA_v2.0_scaffold1G00346' => 'sas', 'SGA_v2.0_scaffold1G00575' => 'sas', 'SGA_v2.0_scaffold1G00761' => 'sas', 'SGA_v2.0_scaffold232G43501' => 'sas', 'TAR625G1137' => 'tar', 'Thecc.03G222100' => 'tca', 'TPR.G12691' => 'tpr', 'TWI34G0727' => 'twi', 'TWI36G0117' => 'twi', 'VMungo1309G0868' => 'vmu' ) $gf_id = 'HOM05D001729' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001729' ) $data_identifier = 'HOM05D001729' $data_type = 'gf_id' $species_gene_counts = array( 'amhyb' => (int) 1, 'cqu' => (int) 9, 'can' => (int) 1, 'cansat' => (int) 1, 'car' => (int) 1, 'col' => (int) 5, 'dca' => (int) 1, 'din' => (int) 2, 'dzi' => (int) 3, 'fan' => (int) 140, 'fve' => (int) 62, 'gma' => (int) 1, 'ghi' => (int) 2, 'gra' => (int) 1, 'han' => (int) 1, 'sun' => (int) 1, 'lonja' => (int) 6, 'lja' => (int) 1, 'lsa' => (int) 4, 'mes' => (int) 1, 'mdo' => (int) 14, 'mtr' => (int) 1, 'egut' => (int) 1, 'nta' => (int) 4, 'oeu' => (int) 1, 'stu' => (int) 2, 'pvu' => (int) 1, 'ptr' => (int) 4, 'ppe' => (int) 19, 'psa' => (int) 1, 'pso' => (int) 4, 'qlo' => (int) 36, 'rch' => (int) 23, 'rsi' => (int) 4, 'sbr' => (int) 4, 'sci' => (int) 2, 'sas' => (int) 4, 'tar' => (int) 1, 'tca' => (int) 1, 'tpr' => (int) 1, 'twi' => (int) 2, 'vmu' => (int) 1 ) $gf_gene_species = 'vmu' $gf_gene_id = 'VMungo1309G0868' $species_info = array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ) $local_species = 'col' $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' => 'HOM05D001729', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '375', 'num_species' => '42' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'Ah.07g204710' => 'amhyb', 'AUR62006001' => 'cqu', 'AUR62006002' => 'cqu', 'AUR62006003' => 'cqu', 'AUR62015641' => 'cqu', 'AUR62027174' => 'cqu', 'AUR62035623' => 'cqu', 'AUR62035624' => 'cqu', 'AUR62035625' => 'cqu', 'AUR62035626' => 'cqu', 'CAN.G1110.53' => 'can', 'CANSAT80G0415' => 'cansat', 'Ca_21364_v3' => 'car', 'COL.COLO4_30693' => 'col', 'COL.COLO4_30694' => 'col', 'COL.COLO4_30695' => 'col', 'COL.COLO4_30696' => 'col', 'COL.COLO4_34020' => 'col', 'DCAR_004585' => 'dca', 'Dinv04029' => 'din', 'Dinv34857' => 'din', 'Duzib147G0011' => 'dzi', 'Duzib170G0599' => 'dzi', 'Duzib192G1051' => 'dzi', 'FAN01G0708' => 'fan', 'FAN01G0742' => 'fan', 'FAN02G0048' => 'fan', 'FAN02G0583' => 'fan', 'FAN02G0688' => 'fan', 'FAN02G1588' => 'fan', 'FAN02G2194' => 'fan', 'FAN02G2750' => 'fan', 'FAN02G3094' => 'fan', 'FAN02G3887' => 'fan', 'FAN02G3911' => 'fan', 'FAN02G3994' => 'fan', 'FAN02G4432' => 'fan', 'FAN02G4556' => 'fan', 'FAN03G1977' => 'fan', 'FAN03G2781' => 'fan', 'FAN03G2850' => 'fan', 'FAN03G3155' => 'fan', 'FAN04G2487' => 'fan', 'FAN05G0208' => 'fan', 'FAN05G0656' => 'fan', 'FAN05G0696' => 'fan', 'FAN05G0810' => 'fan', 'FAN05G1447' => 'fan', 'FAN05G2640' => 'fan', 'FAN05G2911' => 'fan', 'FAN05G3901' => 'fan', 'FAN05G4859' => 'fan', 'FAN05G4861' => 'fan', 'FAN05G4988' => 'fan', 'FAN05G5187' => 'fan', 'FAN05G5452' => 'fan', 'FAN05G5500' => 'fan', 'FAN05G5688' => 'fan', 'FAN06G0177' => 'fan', 'FAN06G0675' => 'fan', 'FAN06G1290' => 'fan', 'FAN06G2191' => 'fan', 'FAN06G2405' => 'fan', 'FAN06G3231' => 'fan', 'FAN06G3932' => 'fan', 'FAN07G0163' => 'fan', 'FAN07G0471' => 'fan', 'FAN07G1354' => 'fan', 'FAN08G0338' => 'fan', 'FAN08G1373' => 'fan', 'FAN08G2539' => 'fan', 'FAN08G2728' => 'fan', 'FAN09G0608' => 'fan', 'FAN09G1136' => 'fan', 'FAN09G1958' => 'fan', 'FAN09G2508' => 'fan', 'FAN09G2597' => 'fan', 'FAN09G2658' => 'fan', 'FAN09G2757' => 'fan', 'FAN09G2983' => 'fan', 'FAN09G3130' => 'fan', 'FAN09G3565' => 'fan', 'FAN09G3613' => 'fan', 'FAN09G4011' => 'fan', 'FAN09G4239' => 'fan', 'FAN09G4277' => 'fan', 'FAN09G4720' => 'fan', 'FAN11G0139' => 'fan', 'FAN11G1727' => 'fan', 'FAN11G2672' => 'fan', 'FAN11G2795' => 'fan', 'FAN11G3238' => 'fan', 'FAN11G3734' => 'fan', 'FAN12G0631' => 'fan', 'FAN12G2239' => 'fan', 'FAN12G2308' => 'fan', 'FAN12G2569' => 'fan', 'FAN12G2623' => 'fan', 'FAN13G3182' => 'fan', 'FAN14G0053' => 'fan', 'FAN14G0370' => 'fan', 'FAN14G0382' => 'fan', 'FAN14G0421' => 'fan', 'FAN14G0866' => 'fan', 'FAN14G1187' => 'fan', 'FAN14G1727' => 'fan', 'FAN14G1791' => 'fan', 'FAN14G2361' => 'fan', 'FAN14G2668' => 'fan', 'FAN14G2770' => 'fan', 'FAN14G2874' => 'fan', 'FAN14G3193' => 'fan', 'FAN14G3624' => 'fan', 'FAN14G3676' => 'fan', 'FAN14G3807' => 'fan', 'FAN14G4082' => 'fan', 'FAN14G4342' => 'fan', 'FAN14G4985' => 'fan', 'FAN14G5126' => 'fan', 'FAN14G5781' => 'fan', 'FAN14G5808' => 'fan', 'FAN14G5949' => 'fan', 'FAN15G0828' => 'fan', 'FAN15G1054' => 'fan', 'FAN15G2023' => 'fan', 'FAN15G2506' => 'fan', 'FAN16G0128' => 'fan', 'FAN16G0249' => 'fan', 'FAN16G0429' => 'fan', 'FAN16G1493' => 'fan', 'FAN16G2210' => 'fan', 'FAN16G2506' => 'fan', 'FAN18G1542' => 'fan', 'FAN18G4057' => 'fan', 'FAN19G0745' => 'fan', 'FAN19G1216' => 'fan', 'FAN19G1733' => 'fan', 'FAN20G0258' => 'fan', 'FAN20G1095' => 'fan', 'FAN20G1557' => 'fan', 'FAN21G0302' => 'fan', 'FAN21G0519' => 'fan', 'FAN21G0970' => 'fan', 'FAN21G1159' => 'fan', 'FAN21G1312' => 'fan', 'FAN21G1440' => 'fan', 'FAN21G1715' => 'fan', 'FAN23G1584' => 'fan', 'FAN24G0045' => 'fan', 'FAN24G0053' => 'fan', 'FAN24G1500' => 'fan', 'FAN24G1817' => 'fan', 'FAN24G2147' => 'fan', 'FAN24G2236' => 'fan', 'FAN24G2446' => 'fan', 'FAN24G2684' => 'fan', 'FAN25G0187' => 'fan', 'FAN25G0505' => 'fan', 'FAN25G0589' => 'fan', 'FAN25G3663' => 'fan', 'FAN26G1025' => 'fan', 'FAN26G2860' => 'fan', 'FAN27G1329' => 'fan', 'FAN27G3392' => 'fan', 'FvH4_1g02011' => 'fve', 'FvH4_1g06511' => 'fve', 'FvH4_2g19900' => 'fve', 'FvH4_2g19920' => 'fve', 'FvH4_2g24261' => 'fve', 'FvH4_2g24270' => 'fve', 'FvH4_2g24631' => 'fve', 'FvH4_2g30622' => 'fve', 'FvH4_3g12920' => 'fve', 'FvH4_3g30171' => 'fve', 'FvH4_3g35490' => 'fve', 'FvH4_3g43682' => 'fve', 'FvH4_3g43730' => 'fve', 'FvH4_3g43732' => 'fve', 'FvH4_3g43751' => 'fve', 'FvH4_3g43752' => 'fve', 'FvH4_3g43770' => 'fve', 'FvH4_3g44471' => 'fve', 'FvH4_3g44510' => 'fve', 'FvH4_3g44582' => 'fve', 'FvH4_4g16921' => 'fve', 'FvH4_4g17121' => 'fve', 'FvH4_4g17782' => 'fve', 'FvH4_4g17783' => 'fve', 'FvH4_4g18120' => 'fve', 'FvH4_4g31310' => 'fve', 'FvH4_4g35052' => 'fve', 'FvH4_5g30862' => 'fve', 'FvH4_6g01541' => 'fve', 'FvH4_6g02021' => 'fve', 'FvH4_6g02041' => 'fve', 'FvH4_6g02071' => 'fve', 'FvH4_6g02171' => 'fve', 'FvH4_6g03181' => 'fve', 'FvH4_6g03182' => 'fve', 'FvH4_6g03221' => 'fve', 'FvH4_6g03380' => 'fve', 'FvH4_6g05201' => 'fve', 'FvH4_6g05203' => 'fve', 'FvH4_6g20231' => 'fve', 'FvH4_6g31981' => 'fve', 'FvH4_6g32061' => 'fve', 'FvH4_6g37041' => 'fve', 'FvH4_6g37932' => 'fve', 'FvH4_6g38731' => 'fve', 'FvH4_6g39370' => 'fve', 'FvH4_6g39371' => 'fve', 'FvH4_6g40891' => 'fve', 'FvH4_6g40892' => 'fve', 'FvH4_6g43143' => 'fve', 'FvH4_6g45251' => 'fve', 'FvH4_6g45260' => 'fve', 'FvH4_6g45291' => 'fve', 'FvH4_6g45890' => 'fve', 'FvH4_6g46240' => 'fve', 'FvH4_6g46241' => 'fve', 'FvH4_6g46242' => 'fve', 'FvH4_6g46260' => 'fve', 'FvH4_6g46280' => 'fve', 'FvH4_6g46380' => 'fve', 'FvH4_7g12841' => 'fve', 'FvH4_7g31431' => 'fve', 'Glyma.09G075900' => 'gma', 'Gohir.A09G096401' => 'ghi', 'Gohir.D09G096101' => 'ghi', 'Gorai.006G112800' => 'gra', 'HanXRQChr04g0121411' => 'han', 'Hund15878' => 'sun', 'Lj2A1107G68' => 'lonja', 'Lj2A630G63' => 'lonja', 'Lj2A946T25' => 'lonja', 'Lj2C714T1' => 'lonja', 'Lj2C966T3' => 'lonja', 'Lj2C966T4' => 'lonja', 'Lj4g0002979' => 'lja', 'Lsat_1_v5_gn_5_30901' => 'lsa', 'Lsat_1_v5_gn_5_31100' => 'lsa', 'Lsat_1_v5_gn_5_38600' => 'lsa', 'Lsat_1_v5_gn_6_92061' => 'lsa', 'Manes.05G071301' => 'mes', 'MD02G1008700' => 'mdo', 'MD02G1008900' => 'mdo', 'MD03G1256400' => 'mdo', 'MD04G1180900' => 'mdo', 'MD04G1181000' => 'mdo', 'MD04G1181200' => 'mdo', 'MD05G1244200' => 'mdo', 'MD05G1324200' => 'mdo', 'MD09G1201600' => 'mdo', 'MD10G1000600' => 'mdo', 'MD14G1026900' => 'mdo', 'MD14G1187900' => 'mdo', 'MD15G1017800' => 'mdo', 'MD15G1018100' => 'mdo', 'Medtr4g124160' => 'mtr', 'Migut.L01260' => 'egut', 'Nitab4.5_0000008g0440' => 'nta', 'Nitab4.5_0000207g0170' => 'nta', 'Nitab4.5_0007671g0030' => 'nta', 'Nitab4.5_0010853g0020' => 'nta', 'Oeu057656.1' => 'oeu', 'PGSC0003DMG400005638' => 'stu', 'PGSC0003DMG400005639' => 'stu', 'Phvul.009G222800' => 'pvu', 'Potri.009G132400' => 'ptr', 'Potri.009G163001' => 'ptr', 'Potri.011G000700' => 'ptr', 'Potri.011G004800' => 'ptr', 'Prupe.1G509300' => 'ppe', 'Prupe.1G509700' => 'ppe', 'Prupe.1G510400' => 'ppe', 'Prupe.1G510700' => 'ppe', 'Prupe.1G512600' => 'ppe', 'Prupe.2G073200' => 'ppe', 'Prupe.3G059500' => 'ppe', 'Prupe.3G059600' => 'ppe', 'Prupe.3G246100' => 'ppe', 'Prupe.3G265100' => 'ppe', 'Prupe.4G034700' => 'ppe', 'Prupe.4G052100' => 'ppe', 'Prupe.4G053600' => 'ppe', 'Prupe.5G068800' => 'ppe', 'Prupe.5G070600' => 'ppe', 'Prupe.6G075400' => 'ppe', 'Prupe.6G075500' => 'ppe', 'Prupe.6G076400' => 'ppe', 'Prupe.8G110700' => 'ppe', 'Psat4g020960' => 'psa', 'PSO135G0788' => 'pso', 'PSO210G6463' => 'pso', 'PSO384G0370' => 'pso', 'PSO386G0056' => 'pso', 'QL01p006048' => 'qlo', 'QL02p054283' => 'qlo', 'QL05p008000' => 'qlo', 'QL05p008212' => 'qlo', 'QL05p008950' => 'qlo', 'QL05p009042' => 'qlo', 'QL05p009518' => 'qlo', 'QL05p012589' => 'qlo', 'QL05p012608' => 'qlo', 'QL05p012650' => 'qlo', 'QL05p012667' => 'qlo', 'QL05p014501' => 'qlo', 'QL05p052800' => 'qlo', 'QL05p065010' => 'qlo', 'QL05p074156' => 'qlo', 'QL05p074160' => 'qlo', 'QL05p074174' => 'qlo', 'QL05p074178' => 'qlo', 'QL05p074214' => 'qlo', 'QL06p001050' => 'qlo', 'QL06p001056' => 'qlo', 'QL06p006093' => 'qlo', 'QL06p006111' => 'qlo', 'QL07p019784' => 'qlo', 'QL07p019801' => 'qlo', 'QL07p036110' => 'qlo', 'QL07p036134' => 'qlo', 'QL07p036147' => 'qlo', 'QL07p036156' => 'qlo', 'QL07p036300' => 'qlo', 'QL07p036320' => 'qlo', 'QL08p014547' => 'qlo', 'QL08p014551' => 'qlo', 'QL08p043319' => 'qlo', 'QL08p043324' => 'qlo', 'QL11p009094' => 'qlo', 'RcHm_v2.0_Chr1g0380481' => 'rch', 'RcHm_v2.0_Chr2g0089331' => 'rch', 'RcHm_v2.0_Chr2g0123691' => 'rch', 'RcHm_v2.0_Chr2g0151111' => 'rch', 'RcHm_v2.0_Chr2g0163011' => 'rch', 'RcHm_v2.0_Chr2g0163051' => 'rch', 'RcHm_v2.0_Chr2g0164671' => 'rch', 'RcHm_v2.0_Chr2g0164681' => 'rch', 'RcHm_v2.0_Chr2g0164721' => 'rch', 'RcHm_v2.0_Chr3g0449911' => 'rch', 'RcHm_v2.0_Chr3g0450211' => 'rch', 'RcHm_v2.0_Chr3g0457271' => 'rch', 'RcHm_v2.0_Chr5g0018111' => 'rch', 'RcHm_v2.0_Chr5g0021011' => 'rch', 'RcHm_v2.0_Chr5g0081171' => 'rch', 'RcHm_v2.0_Chr5g0081211' => 'rch', 'RcHm_v2.0_Chr6g0275871' => 'rch', 'RcHm_v2.0_Chr6g0276071' => 'rch', 'RcHm_v2.0_Chr6g0285591' => 'rch', 'RcHm_v2.0_Chr6g0291931' => 'rch', 'RcHm_v2.0_Chr6g0292091' => 'rch', 'RcHm_v2.0_Chr6g0292271' => 'rch', 'RcHm_v2.0_Chr7g0221261' => 'rch', 'Rhsim08G0219900' => 'rsi', 'Rhsim08G0220200' => 'rsi', 'Rhsim08G0237800' => 'rsi', 'Rhsim08G0238800' => 'rsi', 'Sabra09G0102700' => 'sbr', 'Sabra09G0127200' => 'sbr', 'Sabra11G0003700' => 'sbr', 'Sabra15G0014700' => 'sbr', 'Sc19g0000590' => 'sci', 'Sc19g0001870' => 'sci', 'SGA_v2.0_scaffold1G00346' => 'sas', 'SGA_v2.0_scaffold1G00575' => 'sas', 'SGA_v2.0_scaffold1G00761' => 'sas', 'SGA_v2.0_scaffold232G43501' => 'sas', 'TAR625G1137' => 'tar', 'Thecc.03G222100' => 'tca', 'TPR.G12691' => 'tpr', 'TWI34G0727' => 'twi', 'TWI36G0117' => 'twi', 'VMungo1309G0868' => 'vmu' ), 'gf_id' => 'HOM05D001729', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001729' ), 'data_identifier' => 'HOM05D001729', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001729', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '375', 'num_species' => '42' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'Ah.07g204710' => 'amhyb', 'AUR62006001' => 'cqu', 'AUR62006002' => 'cqu', 'AUR62006003' => 'cqu', 'AUR62015641' => 'cqu', 'AUR62027174' => 'cqu', 'AUR62035623' => 'cqu', 'AUR62035624' => 'cqu', 'AUR62035625' => 'cqu', 'AUR62035626' => 'cqu', 'CAN.G1110.53' => 'can', 'CANSAT80G0415' => 'cansat', 'Ca_21364_v3' => 'car', 'COL.COLO4_30693' => 'col', 'COL.COLO4_30694' => 'col', 'COL.COLO4_30695' => 'col', 'COL.COLO4_30696' => 'col', 'COL.COLO4_34020' => 'col', 'DCAR_004585' => 'dca', 'Dinv04029' => 'din', 'Dinv34857' => 'din', 'Duzib147G0011' => 'dzi', 'Duzib170G0599' => 'dzi', 'Duzib192G1051' => 'dzi', 'FAN01G0708' => 'fan', 'FAN01G0742' => 'fan', 'FAN02G0048' => 'fan', 'FAN02G0583' => 'fan', 'FAN02G0688' => 'fan', 'FAN02G1588' => 'fan', 'FAN02G2194' => 'fan', 'FAN02G2750' => 'fan', 'FAN02G3094' => 'fan', 'FAN02G3887' => 'fan', 'FAN02G3911' => 'fan', 'FAN02G3994' => 'fan', 'FAN02G4432' => 'fan', 'FAN02G4556' => 'fan', 'FAN03G1977' => 'fan', 'FAN03G2781' => 'fan', 'FAN03G2850' => 'fan', 'FAN03G3155' => 'fan', 'FAN04G2487' => 'fan', 'FAN05G0208' => 'fan', 'FAN05G0656' => 'fan', 'FAN05G0696' => 'fan', 'FAN05G0810' => 'fan', 'FAN05G1447' => 'fan', 'FAN05G2640' => 'fan', 'FAN05G2911' => 'fan', 'FAN05G3901' => 'fan', 'FAN05G4859' => 'fan', 'FAN05G4861' => 'fan', 'FAN05G4988' => 'fan', 'FAN05G5187' => 'fan', 'FAN05G5452' => 'fan', 'FAN05G5500' => 'fan', 'FAN05G5688' => 'fan', 'FAN06G0177' => 'fan', 'FAN06G0675' => 'fan', 'FAN06G1290' => 'fan', 'FAN06G2191' => 'fan', 'FAN06G2405' => 'fan', 'FAN06G3231' => 'fan', 'FAN06G3932' => 'fan', 'FAN07G0163' => 'fan', 'FAN07G0471' => 'fan', 'FAN07G1354' => 'fan', 'FAN08G0338' => 'fan', 'FAN08G1373' => 'fan', 'FAN08G2539' => 'fan', 'FAN08G2728' => 'fan', 'FAN09G0608' => 'fan', 'FAN09G1136' => 'fan', 'FAN09G1958' => 'fan', 'FAN09G2508' => 'fan', 'FAN09G2597' => 'fan', 'FAN09G2658' => 'fan', 'FAN09G2757' => 'fan', 'FAN09G2983' => 'fan', 'FAN09G3130' => 'fan', 'FAN09G3565' => 'fan', 'FAN09G3613' => 'fan', 'FAN09G4011' => 'fan', 'FAN09G4239' => 'fan', 'FAN09G4277' => 'fan', 'FAN09G4720' => 'fan', 'FAN11G0139' => 'fan', 'FAN11G1727' => 'fan', 'FAN11G2672' => 'fan', 'FAN11G2795' => 'fan', 'FAN11G3238' => 'fan', 'FAN11G3734' => 'fan', 'FAN12G0631' => 'fan', 'FAN12G2239' => 'fan', 'FAN12G2308' => 'fan', 'FAN12G2569' => 'fan', 'FAN12G2623' => 'fan', 'FAN13G3182' => 'fan', 'FAN14G0053' => 'fan', 'FAN14G0370' => 'fan', 'FAN14G0382' => 'fan', 'FAN14G0421' => 'fan', 'FAN14G0866' => 'fan', 'FAN14G1187' => 'fan', 'FAN14G1727' => 'fan', 'FAN14G1791' => 'fan', 'FAN14G2361' => 'fan', 'FAN14G2668' => 'fan', 'FAN14G2770' => 'fan', 'FAN14G2874' => 'fan', 'FAN14G3193' => 'fan', 'FAN14G3624' => 'fan', 'FAN14G3676' => 'fan', 'FAN14G3807' => 'fan', 'FAN14G4082' => 'fan', 'FAN14G4342' => 'fan', 'FAN14G4985' => 'fan', 'FAN14G5126' => 'fan', 'FAN14G5781' => 'fan', 'FAN14G5808' => 'fan', 'FAN14G5949' => 'fan', 'FAN15G0828' => 'fan', 'FAN15G1054' => 'fan', 'FAN15G2023' => 'fan', 'FAN15G2506' => 'fan', 'FAN16G0128' => 'fan', 'FAN16G0249' => 'fan', 'FAN16G0429' => 'fan', 'FAN16G1493' => 'fan', 'FAN16G2210' => 'fan', 'FAN16G2506' => 'fan', 'FAN18G1542' => 'fan', 'FAN18G4057' => 'fan', 'FAN19G0745' => 'fan', 'FAN19G1216' => 'fan', 'FAN19G1733' => 'fan', 'FAN20G0258' => 'fan', 'FAN20G1095' => 'fan', 'FAN20G1557' => 'fan', 'FAN21G0302' => 'fan', 'FAN21G0519' => 'fan', 'FAN21G0970' => 'fan', 'FAN21G1159' => 'fan', 'FAN21G1312' => 'fan', 'FAN21G1440' => 'fan', 'FAN21G1715' => 'fan', 'FAN23G1584' => 'fan', 'FAN24G0045' => 'fan', 'FAN24G0053' => 'fan', 'FAN24G1500' => 'fan', 'FAN24G1817' => 'fan', 'FAN24G2147' => 'fan', 'FAN24G2236' => 'fan', 'FAN24G2446' => 'fan', 'FAN24G2684' => 'fan', 'FAN25G0187' => 'fan', 'FAN25G0505' => 'fan', 'FAN25G0589' => 'fan', 'FAN25G3663' => 'fan', 'FAN26G1025' => 'fan', 'FAN26G2860' => 'fan', 'FAN27G1329' => 'fan', 'FAN27G3392' => 'fan', 'FvH4_1g02011' => 'fve', 'FvH4_1g06511' => 'fve', 'FvH4_2g19900' => 'fve', 'FvH4_2g19920' => 'fve', 'FvH4_2g24261' => 'fve', 'FvH4_2g24270' => 'fve', 'FvH4_2g24631' => 'fve', 'FvH4_2g30622' => 'fve', 'FvH4_3g12920' => 'fve', 'FvH4_3g30171' => 'fve', 'FvH4_3g35490' => 'fve', 'FvH4_3g43682' => 'fve', 'FvH4_3g43730' => 'fve', 'FvH4_3g43732' => 'fve', 'FvH4_3g43751' => 'fve', 'FvH4_3g43752' => 'fve', 'FvH4_3g43770' => 'fve', 'FvH4_3g44471' => 'fve', 'FvH4_3g44510' => 'fve', 'FvH4_3g44582' => 'fve', 'FvH4_4g16921' => 'fve', 'FvH4_4g17121' => 'fve', 'FvH4_4g17782' => 'fve', 'FvH4_4g17783' => 'fve', 'FvH4_4g18120' => 'fve', 'FvH4_4g31310' => 'fve', 'FvH4_4g35052' => 'fve', 'FvH4_5g30862' => 'fve', 'FvH4_6g01541' => 'fve', 'FvH4_6g02021' => 'fve', 'FvH4_6g02041' => 'fve', 'FvH4_6g02071' => 'fve', 'FvH4_6g02171' => 'fve', 'FvH4_6g03181' => 'fve', 'FvH4_6g03182' => 'fve', 'FvH4_6g03221' => 'fve', 'FvH4_6g03380' => 'fve', 'FvH4_6g05201' => 'fve', 'FvH4_6g05203' => 'fve', 'FvH4_6g20231' => 'fve', 'FvH4_6g31981' => 'fve', 'FvH4_6g32061' => 'fve', 'FvH4_6g37041' => 'fve', 'FvH4_6g37932' => 'fve', 'FvH4_6g38731' => 'fve', 'FvH4_6g39370' => 'fve', 'FvH4_6g39371' => 'fve', 'FvH4_6g40891' => 'fve', 'FvH4_6g40892' => 'fve', 'FvH4_6g43143' => 'fve', 'FvH4_6g45251' => 'fve', 'FvH4_6g45260' => 'fve', 'FvH4_6g45291' => 'fve', 'FvH4_6g45890' => 'fve', 'FvH4_6g46240' => 'fve', 'FvH4_6g46241' => 'fve', 'FvH4_6g46242' => 'fve', 'FvH4_6g46260' => 'fve', 'FvH4_6g46280' => 'fve', 'FvH4_6g46380' => 'fve', 'FvH4_7g12841' => 'fve', 'FvH4_7g31431' => 'fve', 'Glyma.09G075900' => 'gma', 'Gohir.A09G096401' => 'ghi', 'Gohir.D09G096101' => 'ghi', 'Gorai.006G112800' => 'gra', 'HanXRQChr04g0121411' => 'han', 'Hund15878' => 'sun', 'Lj2A1107G68' => 'lonja', 'Lj2A630G63' => 'lonja', 'Lj2A946T25' => 'lonja', 'Lj2C714T1' => 'lonja', 'Lj2C966T3' => 'lonja', 'Lj2C966T4' => 'lonja', 'Lj4g0002979' => 'lja', 'Lsat_1_v5_gn_5_30901' => 'lsa', 'Lsat_1_v5_gn_5_31100' => 'lsa', 'Lsat_1_v5_gn_5_38600' => 'lsa', 'Lsat_1_v5_gn_6_92061' => 'lsa', 'Manes.05G071301' => 'mes', 'MD02G1008700' => 'mdo', 'MD02G1008900' => 'mdo', 'MD03G1256400' => 'mdo', 'MD04G1180900' => 'mdo', 'MD04G1181000' => 'mdo', 'MD04G1181200' => 'mdo', 'MD05G1244200' => 'mdo', 'MD05G1324200' => 'mdo', 'MD09G1201600' => 'mdo', 'MD10G1000600' => 'mdo', 'MD14G1026900' => 'mdo', 'MD14G1187900' => 'mdo', 'MD15G1017800' => 'mdo', 'MD15G1018100' => 'mdo', 'Medtr4g124160' => 'mtr', 'Migut.L01260' => 'egut', 'Nitab4.5_0000008g0440' => 'nta', 'Nitab4.5_0000207g0170' => 'nta', 'Nitab4.5_0007671g0030' => 'nta', 'Nitab4.5_0010853g0020' => 'nta', 'Oeu057656.1' => 'oeu', 'PGSC0003DMG400005638' => 'stu', 'PGSC0003DMG400005639' => 'stu', 'Phvul.009G222800' => 'pvu', 'Potri.009G132400' => 'ptr', 'Potri.009G163001' => 'ptr', 'Potri.011G000700' => 'ptr', 'Potri.011G004800' => 'ptr', 'Prupe.1G509300' => 'ppe', 'Prupe.1G509700' => 'ppe', 'Prupe.1G510400' => 'ppe', 'Prupe.1G510700' => 'ppe', 'Prupe.1G512600' => 'ppe', 'Prupe.2G073200' => 'ppe', 'Prupe.3G059500' => 'ppe', 'Prupe.3G059600' => 'ppe', 'Prupe.3G246100' => 'ppe', 'Prupe.3G265100' => 'ppe', 'Prupe.4G034700' => 'ppe', 'Prupe.4G052100' => 'ppe', 'Prupe.4G053600' => 'ppe', 'Prupe.5G068800' => 'ppe', 'Prupe.5G070600' => 'ppe', 'Prupe.6G075400' => 'ppe', 'Prupe.6G075500' => 'ppe', 'Prupe.6G076400' => 'ppe', 'Prupe.8G110700' => 'ppe', 'Psat4g020960' => 'psa', 'PSO135G0788' => 'pso', 'PSO210G6463' => 'pso', 'PSO384G0370' => 'pso', 'PSO386G0056' => 'pso', 'QL01p006048' => 'qlo', 'QL02p054283' => 'qlo', 'QL05p008000' => 'qlo', 'QL05p008212' => 'qlo', 'QL05p008950' => 'qlo', 'QL05p009042' => 'qlo', 'QL05p009518' => 'qlo', 'QL05p012589' => 'qlo', 'QL05p012608' => 'qlo', 'QL05p012650' => 'qlo', 'QL05p012667' => 'qlo', 'QL05p014501' => 'qlo', 'QL05p052800' => 'qlo', 'QL05p065010' => 'qlo', 'QL05p074156' => 'qlo', 'QL05p074160' => 'qlo', 'QL05p074174' => 'qlo', 'QL05p074178' => 'qlo', 'QL05p074214' => 'qlo', 'QL06p001050' => 'qlo', 'QL06p001056' => 'qlo', 'QL06p006093' => 'qlo', 'QL06p006111' => 'qlo', 'QL07p019784' => 'qlo', 'QL07p019801' => 'qlo', 'QL07p036110' => 'qlo', 'QL07p036134' => 'qlo', 'QL07p036147' => 'qlo', 'QL07p036156' => 'qlo', 'QL07p036300' => 'qlo', 'QL07p036320' => 'qlo', 'QL08p014547' => 'qlo', 'QL08p014551' => 'qlo', 'QL08p043319' => 'qlo', 'QL08p043324' => 'qlo', 'QL11p009094' => 'qlo', 'RcHm_v2.0_Chr1g0380481' => 'rch', 'RcHm_v2.0_Chr2g0089331' => 'rch', 'RcHm_v2.0_Chr2g0123691' => 'rch', 'RcHm_v2.0_Chr2g0151111' => 'rch', 'RcHm_v2.0_Chr2g0163011' => 'rch', 'RcHm_v2.0_Chr2g0163051' => 'rch', 'RcHm_v2.0_Chr2g0164671' => 'rch', 'RcHm_v2.0_Chr2g0164681' => 'rch', 'RcHm_v2.0_Chr2g0164721' => 'rch', 'RcHm_v2.0_Chr3g0449911' => 'rch', 'RcHm_v2.0_Chr3g0450211' => 'rch', 'RcHm_v2.0_Chr3g0457271' => 'rch', 'RcHm_v2.0_Chr5g0018111' => 'rch', 'RcHm_v2.0_Chr5g0021011' => 'rch', 'RcHm_v2.0_Chr5g0081171' => 'rch', 'RcHm_v2.0_Chr5g0081211' => 'rch', 'RcHm_v2.0_Chr6g0275871' => 'rch', 'RcHm_v2.0_Chr6g0276071' => 'rch', 'RcHm_v2.0_Chr6g0285591' => 'rch', 'RcHm_v2.0_Chr6g0291931' => 'rch', 'RcHm_v2.0_Chr6g0292091' => 'rch', 'RcHm_v2.0_Chr6g0292271' => 'rch', 'RcHm_v2.0_Chr7g0221261' => 'rch', 'Rhsim08G0219900' => 'rsi', 'Rhsim08G0220200' => 'rsi', 'Rhsim08G0237800' => 'rsi', 'Rhsim08G0238800' => 'rsi', 'Sabra09G0102700' => 'sbr', 'Sabra09G0127200' => 'sbr', 'Sabra11G0003700' => 'sbr', 'Sabra15G0014700' => 'sbr', 'Sc19g0000590' => 'sci', 'Sc19g0001870' => 'sci', 'SGA_v2.0_scaffold1G00346' => 'sas', 'SGA_v2.0_scaffold1G00575' => 'sas', 'SGA_v2.0_scaffold1G00761' => 'sas', 'SGA_v2.0_scaffold232G43501' => 'sas', 'TAR625G1137' => 'tar', 'Thecc.03G222100' => 'tca', 'TPR.G12691' => 'tpr', 'TWI34G0727' => 'twi', 'TWI36G0117' => 'twi', 'VMungo1309G0868' => 'vmu' ) $gf_id = 'HOM05D001729' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001729' ) $data_identifier = 'HOM05D001729' $data_type = 'gf_id' $species_gene_counts = array( 'amhyb' => (int) 1, 'cqu' => (int) 9, 'can' => (int) 1, 'cansat' => (int) 1, 'car' => (int) 1, 'col' => (int) 5, 'dca' => (int) 1, 'din' => (int) 2, 'dzi' => (int) 3, 'fan' => (int) 140, 'fve' => (int) 62, 'gma' => (int) 1, 'ghi' => (int) 2, 'gra' => (int) 1, 'han' => (int) 1, 'sun' => (int) 1, 'lonja' => (int) 6, 'lja' => (int) 1, 'lsa' => (int) 4, 'mes' => (int) 1, 'mdo' => (int) 14, 'mtr' => (int) 1, 'egut' => (int) 1, 'nta' => (int) 4, 'oeu' => (int) 1, 'stu' => (int) 2, 'pvu' => (int) 1, 'ptr' => (int) 4, 'ppe' => (int) 19, 'psa' => (int) 1, 'pso' => (int) 4, 'qlo' => (int) 36, 'rch' => (int) 23, 'rsi' => (int) 4, 'sbr' => (int) 4, 'sci' => (int) 2, 'sas' => (int) 4, 'tar' => (int) 1, 'tca' => (int) 1, 'tpr' => (int) 1, 'twi' => (int) 2, 'vmu' => (int) 1 ) $gf_gene_species = 'vmu' $gf_gene_id = 'VMungo1309G0868' $species_info = array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ) $local_species = 'col' $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' => 'HOM05D001729', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '375', 'num_species' => '42' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'Ah.07g204710' => 'amhyb', 'AUR62006001' => 'cqu', 'AUR62006002' => 'cqu', 'AUR62006003' => 'cqu', 'AUR62015641' => 'cqu', 'AUR62027174' => 'cqu', 'AUR62035623' => 'cqu', 'AUR62035624' => 'cqu', 'AUR62035625' => 'cqu', 'AUR62035626' => 'cqu', 'CAN.G1110.53' => 'can', 'CANSAT80G0415' => 'cansat', 'Ca_21364_v3' => 'car', 'COL.COLO4_30693' => 'col', 'COL.COLO4_30694' => 'col', 'COL.COLO4_30695' => 'col', 'COL.COLO4_30696' => 'col', 'COL.COLO4_34020' => 'col', 'DCAR_004585' => 'dca', 'Dinv04029' => 'din', 'Dinv34857' => 'din', 'Duzib147G0011' => 'dzi', 'Duzib170G0599' => 'dzi', 'Duzib192G1051' => 'dzi', 'FAN01G0708' => 'fan', 'FAN01G0742' => 'fan', 'FAN02G0048' => 'fan', 'FAN02G0583' => 'fan', 'FAN02G0688' => 'fan', 'FAN02G1588' => 'fan', 'FAN02G2194' => 'fan', 'FAN02G2750' => 'fan', 'FAN02G3094' => 'fan', 'FAN02G3887' => 'fan', 'FAN02G3911' => 'fan', 'FAN02G3994' => 'fan', 'FAN02G4432' => 'fan', 'FAN02G4556' => 'fan', 'FAN03G1977' => 'fan', 'FAN03G2781' => 'fan', 'FAN03G2850' => 'fan', 'FAN03G3155' => 'fan', 'FAN04G2487' => 'fan', 'FAN05G0208' => 'fan', 'FAN05G0656' => 'fan', 'FAN05G0696' => 'fan', 'FAN05G0810' => 'fan', 'FAN05G1447' => 'fan', 'FAN05G2640' => 'fan', 'FAN05G2911' => 'fan', 'FAN05G3901' => 'fan', 'FAN05G4859' => 'fan', 'FAN05G4861' => 'fan', 'FAN05G4988' => 'fan', 'FAN05G5187' => 'fan', 'FAN05G5452' => 'fan', 'FAN05G5500' => 'fan', 'FAN05G5688' => 'fan', 'FAN06G0177' => 'fan', 'FAN06G0675' => 'fan', 'FAN06G1290' => 'fan', 'FAN06G2191' => 'fan', 'FAN06G2405' => 'fan', 'FAN06G3231' => 'fan', 'FAN06G3932' => 'fan', 'FAN07G0163' => 'fan', 'FAN07G0471' => 'fan', 'FAN07G1354' => 'fan', 'FAN08G0338' => 'fan', 'FAN08G1373' => 'fan', 'FAN08G2539' => 'fan', 'FAN08G2728' => 'fan', 'FAN09G0608' => 'fan', 'FAN09G1136' => 'fan', 'FAN09G1958' => 'fan', 'FAN09G2508' => 'fan', 'FAN09G2597' => 'fan', 'FAN09G2658' => 'fan', 'FAN09G2757' => 'fan', 'FAN09G2983' => 'fan', 'FAN09G3130' => 'fan', 'FAN09G3565' => 'fan', 'FAN09G3613' => 'fan', 'FAN09G4011' => 'fan', 'FAN09G4239' => 'fan', 'FAN09G4277' => 'fan', 'FAN09G4720' => 'fan', 'FAN11G0139' => 'fan', 'FAN11G1727' => 'fan', 'FAN11G2672' => 'fan', 'FAN11G2795' => 'fan', 'FAN11G3238' => 'fan', 'FAN11G3734' => 'fan', 'FAN12G0631' => 'fan', 'FAN12G2239' => 'fan', 'FAN12G2308' => 'fan', 'FAN12G2569' => 'fan', 'FAN12G2623' => 'fan', 'FAN13G3182' => 'fan', 'FAN14G0053' => 'fan', 'FAN14G0370' => 'fan', 'FAN14G0382' => 'fan', 'FAN14G0421' => 'fan', 'FAN14G0866' => 'fan', 'FAN14G1187' => 'fan', 'FAN14G1727' => 'fan', 'FAN14G1791' => 'fan', 'FAN14G2361' => 'fan', 'FAN14G2668' => 'fan', 'FAN14G2770' => 'fan', 'FAN14G2874' => 'fan', 'FAN14G3193' => 'fan', 'FAN14G3624' => 'fan', 'FAN14G3676' => 'fan', 'FAN14G3807' => 'fan', 'FAN14G4082' => 'fan', 'FAN14G4342' => 'fan', 'FAN14G4985' => 'fan', 'FAN14G5126' => 'fan', 'FAN14G5781' => 'fan', 'FAN14G5808' => 'fan', 'FAN14G5949' => 'fan', 'FAN15G0828' => 'fan', 'FAN15G1054' => 'fan', 'FAN15G2023' => 'fan', 'FAN15G2506' => 'fan', 'FAN16G0128' => 'fan', 'FAN16G0249' => 'fan', 'FAN16G0429' => 'fan', 'FAN16G1493' => 'fan', 'FAN16G2210' => 'fan', 'FAN16G2506' => 'fan', 'FAN18G1542' => 'fan', 'FAN18G4057' => 'fan', 'FAN19G0745' => 'fan', 'FAN19G1216' => 'fan', 'FAN19G1733' => 'fan', 'FAN20G0258' => 'fan', 'FAN20G1095' => 'fan', 'FAN20G1557' => 'fan', 'FAN21G0302' => 'fan', 'FAN21G0519' => 'fan', 'FAN21G0970' => 'fan', 'FAN21G1159' => 'fan', 'FAN21G1312' => 'fan', 'FAN21G1440' => 'fan', 'FAN21G1715' => 'fan', 'FAN23G1584' => 'fan', 'FAN24G0045' => 'fan', 'FAN24G0053' => 'fan', 'FAN24G1500' => 'fan', 'FAN24G1817' => 'fan', 'FAN24G2147' => 'fan', 'FAN24G2236' => 'fan', 'FAN24G2446' => 'fan', 'FAN24G2684' => 'fan', 'FAN25G0187' => 'fan', 'FAN25G0505' => 'fan', 'FAN25G0589' => 'fan', 'FAN25G3663' => 'fan', 'FAN26G1025' => 'fan', 'FAN26G2860' => 'fan', 'FAN27G1329' => 'fan', 'FAN27G3392' => 'fan', 'FvH4_1g02011' => 'fve', 'FvH4_1g06511' => 'fve', 'FvH4_2g19900' => 'fve', 'FvH4_2g19920' => 'fve', 'FvH4_2g24261' => 'fve', 'FvH4_2g24270' => 'fve', 'FvH4_2g24631' => 'fve', 'FvH4_2g30622' => 'fve', 'FvH4_3g12920' => 'fve', 'FvH4_3g30171' => 'fve', 'FvH4_3g35490' => 'fve', 'FvH4_3g43682' => 'fve', 'FvH4_3g43730' => 'fve', 'FvH4_3g43732' => 'fve', 'FvH4_3g43751' => 'fve', 'FvH4_3g43752' => 'fve', 'FvH4_3g43770' => 'fve', 'FvH4_3g44471' => 'fve', 'FvH4_3g44510' => 'fve', 'FvH4_3g44582' => 'fve', 'FvH4_4g16921' => 'fve', 'FvH4_4g17121' => 'fve', 'FvH4_4g17782' => 'fve', 'FvH4_4g17783' => 'fve', 'FvH4_4g18120' => 'fve', 'FvH4_4g31310' => 'fve', 'FvH4_4g35052' => 'fve', 'FvH4_5g30862' => 'fve', 'FvH4_6g01541' => 'fve', 'FvH4_6g02021' => 'fve', 'FvH4_6g02041' => 'fve', 'FvH4_6g02071' => 'fve', 'FvH4_6g02171' => 'fve', 'FvH4_6g03181' => 'fve', 'FvH4_6g03182' => 'fve', 'FvH4_6g03221' => 'fve', 'FvH4_6g03380' => 'fve', 'FvH4_6g05201' => 'fve', 'FvH4_6g05203' => 'fve', 'FvH4_6g20231' => 'fve', 'FvH4_6g31981' => 'fve', 'FvH4_6g32061' => 'fve', 'FvH4_6g37041' => 'fve', 'FvH4_6g37932' => 'fve', 'FvH4_6g38731' => 'fve', 'FvH4_6g39370' => 'fve', 'FvH4_6g39371' => 'fve', 'FvH4_6g40891' => 'fve', 'FvH4_6g40892' => 'fve', 'FvH4_6g43143' => 'fve', 'FvH4_6g45251' => 'fve', 'FvH4_6g45260' => 'fve', 'FvH4_6g45291' => 'fve', 'FvH4_6g45890' => 'fve', 'FvH4_6g46240' => 'fve', 'FvH4_6g46241' => 'fve', 'FvH4_6g46242' => 'fve', 'FvH4_6g46260' => 'fve', 'FvH4_6g46280' => 'fve', 'FvH4_6g46380' => 'fve', 'FvH4_7g12841' => 'fve', 'FvH4_7g31431' => 'fve', 'Glyma.09G075900' => 'gma', 'Gohir.A09G096401' => 'ghi', 'Gohir.D09G096101' => 'ghi', 'Gorai.006G112800' => 'gra', 'HanXRQChr04g0121411' => 'han', 'Hund15878' => 'sun', 'Lj2A1107G68' => 'lonja', 'Lj2A630G63' => 'lonja', 'Lj2A946T25' => 'lonja', 'Lj2C714T1' => 'lonja', 'Lj2C966T3' => 'lonja', 'Lj2C966T4' => 'lonja', 'Lj4g0002979' => 'lja', 'Lsat_1_v5_gn_5_30901' => 'lsa', 'Lsat_1_v5_gn_5_31100' => 'lsa', 'Lsat_1_v5_gn_5_38600' => 'lsa', 'Lsat_1_v5_gn_6_92061' => 'lsa', 'Manes.05G071301' => 'mes', 'MD02G1008700' => 'mdo', 'MD02G1008900' => 'mdo', 'MD03G1256400' => 'mdo', 'MD04G1180900' => 'mdo', 'MD04G1181000' => 'mdo', 'MD04G1181200' => 'mdo', 'MD05G1244200' => 'mdo', 'MD05G1324200' => 'mdo', 'MD09G1201600' => 'mdo', 'MD10G1000600' => 'mdo', 'MD14G1026900' => 'mdo', 'MD14G1187900' => 'mdo', 'MD15G1017800' => 'mdo', 'MD15G1018100' => 'mdo', 'Medtr4g124160' => 'mtr', 'Migut.L01260' => 'egut', 'Nitab4.5_0000008g0440' => 'nta', 'Nitab4.5_0000207g0170' => 'nta', 'Nitab4.5_0007671g0030' => 'nta', 'Nitab4.5_0010853g0020' => 'nta', 'Oeu057656.1' => 'oeu', 'PGSC0003DMG400005638' => 'stu', 'PGSC0003DMG400005639' => 'stu', 'Phvul.009G222800' => 'pvu', 'Potri.009G132400' => 'ptr', 'Potri.009G163001' => 'ptr', 'Potri.011G000700' => 'ptr', 'Potri.011G004800' => 'ptr', 'Prupe.1G509300' => 'ppe', 'Prupe.1G509700' => 'ppe', 'Prupe.1G510400' => 'ppe', 'Prupe.1G510700' => 'ppe', 'Prupe.1G512600' => 'ppe', 'Prupe.2G073200' => 'ppe', 'Prupe.3G059500' => 'ppe', 'Prupe.3G059600' => 'ppe', 'Prupe.3G246100' => 'ppe', 'Prupe.3G265100' => 'ppe', 'Prupe.4G034700' => 'ppe', 'Prupe.4G052100' => 'ppe', 'Prupe.4G053600' => 'ppe', 'Prupe.5G068800' => 'ppe', 'Prupe.5G070600' => 'ppe', 'Prupe.6G075400' => 'ppe', 'Prupe.6G075500' => 'ppe', 'Prupe.6G076400' => 'ppe', 'Prupe.8G110700' => 'ppe', 'Psat4g020960' => 'psa', 'PSO135G0788' => 'pso', 'PSO210G6463' => 'pso', 'PSO384G0370' => 'pso', 'PSO386G0056' => 'pso', 'QL01p006048' => 'qlo', 'QL02p054283' => 'qlo', 'QL05p008000' => 'qlo', 'QL05p008212' => 'qlo', 'QL05p008950' => 'qlo', 'QL05p009042' => 'qlo', 'QL05p009518' => 'qlo', 'QL05p012589' => 'qlo', 'QL05p012608' => 'qlo', 'QL05p012650' => 'qlo', 'QL05p012667' => 'qlo', 'QL05p014501' => 'qlo', 'QL05p052800' => 'qlo', 'QL05p065010' => 'qlo', 'QL05p074156' => 'qlo', 'QL05p074160' => 'qlo', 'QL05p074174' => 'qlo', 'QL05p074178' => 'qlo', 'QL05p074214' => 'qlo', 'QL06p001050' => 'qlo', 'QL06p001056' => 'qlo', 'QL06p006093' => 'qlo', 'QL06p006111' => 'qlo', 'QL07p019784' => 'qlo', 'QL07p019801' => 'qlo', 'QL07p036110' => 'qlo', 'QL07p036134' => 'qlo', 'QL07p036147' => 'qlo', 'QL07p036156' => 'qlo', 'QL07p036300' => 'qlo', 'QL07p036320' => 'qlo', 'QL08p014547' => 'qlo', 'QL08p014551' => 'qlo', 'QL08p043319' => 'qlo', 'QL08p043324' => 'qlo', 'QL11p009094' => 'qlo', 'RcHm_v2.0_Chr1g0380481' => 'rch', 'RcHm_v2.0_Chr2g0089331' => 'rch', 'RcHm_v2.0_Chr2g0123691' => 'rch', 'RcHm_v2.0_Chr2g0151111' => 'rch', 'RcHm_v2.0_Chr2g0163011' => 'rch', 'RcHm_v2.0_Chr2g0163051' => 'rch', 'RcHm_v2.0_Chr2g0164671' => 'rch', 'RcHm_v2.0_Chr2g0164681' => 'rch', 'RcHm_v2.0_Chr2g0164721' => 'rch', 'RcHm_v2.0_Chr3g0449911' => 'rch', 'RcHm_v2.0_Chr3g0450211' => 'rch', 'RcHm_v2.0_Chr3g0457271' => 'rch', 'RcHm_v2.0_Chr5g0018111' => 'rch', 'RcHm_v2.0_Chr5g0021011' => 'rch', 'RcHm_v2.0_Chr5g0081171' => 'rch', 'RcHm_v2.0_Chr5g0081211' => 'rch', 'RcHm_v2.0_Chr6g0275871' => 'rch', 'RcHm_v2.0_Chr6g0276071' => 'rch', 'RcHm_v2.0_Chr6g0285591' => 'rch', 'RcHm_v2.0_Chr6g0291931' => 'rch', 'RcHm_v2.0_Chr6g0292091' => 'rch', 'RcHm_v2.0_Chr6g0292271' => 'rch', 'RcHm_v2.0_Chr7g0221261' => 'rch', 'Rhsim08G0219900' => 'rsi', 'Rhsim08G0220200' => 'rsi', 'Rhsim08G0237800' => 'rsi', 'Rhsim08G0238800' => 'rsi', 'Sabra09G0102700' => 'sbr', 'Sabra09G0127200' => 'sbr', 'Sabra11G0003700' => 'sbr', 'Sabra15G0014700' => 'sbr', 'Sc19g0000590' => 'sci', 'Sc19g0001870' => 'sci', 'SGA_v2.0_scaffold1G00346' => 'sas', 'SGA_v2.0_scaffold1G00575' => 'sas', 'SGA_v2.0_scaffold1G00761' => 'sas', 'SGA_v2.0_scaffold232G43501' => 'sas', 'TAR625G1137' => 'tar', 'Thecc.03G222100' => 'tca', 'TPR.G12691' => 'tpr', 'TWI34G0727' => 'twi', 'TWI36G0117' => 'twi', 'VMungo1309G0868' => 'vmu' ), 'gf_id' => 'HOM05D001729', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001729' ), 'data_identifier' => 'HOM05D001729', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001729', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '375', 'num_species' => '42' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'Ah.07g204710' => 'amhyb', 'AUR62006001' => 'cqu', 'AUR62006002' => 'cqu', 'AUR62006003' => 'cqu', 'AUR62015641' => 'cqu', 'AUR62027174' => 'cqu', 'AUR62035623' => 'cqu', 'AUR62035624' => 'cqu', 'AUR62035625' => 'cqu', 'AUR62035626' => 'cqu', 'CAN.G1110.53' => 'can', 'CANSAT80G0415' => 'cansat', 'Ca_21364_v3' => 'car', 'COL.COLO4_30693' => 'col', 'COL.COLO4_30694' => 'col', 'COL.COLO4_30695' => 'col', 'COL.COLO4_30696' => 'col', 'COL.COLO4_34020' => 'col', 'DCAR_004585' => 'dca', 'Dinv04029' => 'din', 'Dinv34857' => 'din', 'Duzib147G0011' => 'dzi', 'Duzib170G0599' => 'dzi', 'Duzib192G1051' => 'dzi', 'FAN01G0708' => 'fan', 'FAN01G0742' => 'fan', 'FAN02G0048' => 'fan', 'FAN02G0583' => 'fan', 'FAN02G0688' => 'fan', 'FAN02G1588' => 'fan', 'FAN02G2194' => 'fan', 'FAN02G2750' => 'fan', 'FAN02G3094' => 'fan', 'FAN02G3887' => 'fan', 'FAN02G3911' => 'fan', 'FAN02G3994' => 'fan', 'FAN02G4432' => 'fan', 'FAN02G4556' => 'fan', 'FAN03G1977' => 'fan', 'FAN03G2781' => 'fan', 'FAN03G2850' => 'fan', 'FAN03G3155' => 'fan', 'FAN04G2487' => 'fan', 'FAN05G0208' => 'fan', 'FAN05G0656' => 'fan', 'FAN05G0696' => 'fan', 'FAN05G0810' => 'fan', 'FAN05G1447' => 'fan', 'FAN05G2640' => 'fan', 'FAN05G2911' => 'fan', 'FAN05G3901' => 'fan', 'FAN05G4859' => 'fan', 'FAN05G4861' => 'fan', 'FAN05G4988' => 'fan', 'FAN05G5187' => 'fan', 'FAN05G5452' => 'fan', 'FAN05G5500' => 'fan', 'FAN05G5688' => 'fan', 'FAN06G0177' => 'fan', 'FAN06G0675' => 'fan', 'FAN06G1290' => 'fan', 'FAN06G2191' => 'fan', 'FAN06G2405' => 'fan', 'FAN06G3231' => 'fan', 'FAN06G3932' => 'fan', 'FAN07G0163' => 'fan', 'FAN07G0471' => 'fan', 'FAN07G1354' => 'fan', 'FAN08G0338' => 'fan', 'FAN08G1373' => 'fan', 'FAN08G2539' => 'fan', 'FAN08G2728' => 'fan', 'FAN09G0608' => 'fan', 'FAN09G1136' => 'fan', 'FAN09G1958' => 'fan', 'FAN09G2508' => 'fan', 'FAN09G2597' => 'fan', 'FAN09G2658' => 'fan', 'FAN09G2757' => 'fan', 'FAN09G2983' => 'fan', 'FAN09G3130' => 'fan', 'FAN09G3565' => 'fan', 'FAN09G3613' => 'fan', 'FAN09G4011' => 'fan', 'FAN09G4239' => 'fan', 'FAN09G4277' => 'fan', 'FAN09G4720' => 'fan', 'FAN11G0139' => 'fan', 'FAN11G1727' => 'fan', 'FAN11G2672' => 'fan', 'FAN11G2795' => 'fan', 'FAN11G3238' => 'fan', 'FAN11G3734' => 'fan', 'FAN12G0631' => 'fan', 'FAN12G2239' => 'fan', 'FAN12G2308' => 'fan', 'FAN12G2569' => 'fan', 'FAN12G2623' => 'fan', 'FAN13G3182' => 'fan', 'FAN14G0053' => 'fan', 'FAN14G0370' => 'fan', 'FAN14G0382' => 'fan', 'FAN14G0421' => 'fan', 'FAN14G0866' => 'fan', 'FAN14G1187' => 'fan', 'FAN14G1727' => 'fan', 'FAN14G1791' => 'fan', 'FAN14G2361' => 'fan', 'FAN14G2668' => 'fan', 'FAN14G2770' => 'fan', 'FAN14G2874' => 'fan', 'FAN14G3193' => 'fan', 'FAN14G3624' => 'fan', 'FAN14G3676' => 'fan', 'FAN14G3807' => 'fan', 'FAN14G4082' => 'fan', 'FAN14G4342' => 'fan', 'FAN14G4985' => 'fan', 'FAN14G5126' => 'fan', 'FAN14G5781' => 'fan', 'FAN14G5808' => 'fan', 'FAN14G5949' => 'fan', 'FAN15G0828' => 'fan', 'FAN15G1054' => 'fan', 'FAN15G2023' => 'fan', 'FAN15G2506' => 'fan', 'FAN16G0128' => 'fan', 'FAN16G0249' => 'fan', 'FAN16G0429' => 'fan', 'FAN16G1493' => 'fan', 'FAN16G2210' => 'fan', 'FAN16G2506' => 'fan', 'FAN18G1542' => 'fan', 'FAN18G4057' => 'fan', 'FAN19G0745' => 'fan', 'FAN19G1216' => 'fan', 'FAN19G1733' => 'fan', 'FAN20G0258' => 'fan', 'FAN20G1095' => 'fan', 'FAN20G1557' => 'fan', 'FAN21G0302' => 'fan', 'FAN21G0519' => 'fan', 'FAN21G0970' => 'fan', 'FAN21G1159' => 'fan', 'FAN21G1312' => 'fan', 'FAN21G1440' => 'fan', 'FAN21G1715' => 'fan', 'FAN23G1584' => 'fan', 'FAN24G0045' => 'fan', 'FAN24G0053' => 'fan', 'FAN24G1500' => 'fan', 'FAN24G1817' => 'fan', 'FAN24G2147' => 'fan', 'FAN24G2236' => 'fan', 'FAN24G2446' => 'fan', 'FAN24G2684' => 'fan', 'FAN25G0187' => 'fan', 'FAN25G0505' => 'fan', 'FAN25G0589' => 'fan', 'FAN25G3663' => 'fan', 'FAN26G1025' => 'fan', 'FAN26G2860' => 'fan', 'FAN27G1329' => 'fan', 'FAN27G3392' => 'fan', 'FvH4_1g02011' => 'fve', 'FvH4_1g06511' => 'fve', 'FvH4_2g19900' => 'fve', 'FvH4_2g19920' => 'fve', 'FvH4_2g24261' => 'fve', 'FvH4_2g24270' => 'fve', 'FvH4_2g24631' => 'fve', 'FvH4_2g30622' => 'fve', 'FvH4_3g12920' => 'fve', 'FvH4_3g30171' => 'fve', 'FvH4_3g35490' => 'fve', 'FvH4_3g43682' => 'fve', 'FvH4_3g43730' => 'fve', 'FvH4_3g43732' => 'fve', 'FvH4_3g43751' => 'fve', 'FvH4_3g43752' => 'fve', 'FvH4_3g43770' => 'fve', 'FvH4_3g44471' => 'fve', 'FvH4_3g44510' => 'fve', 'FvH4_3g44582' => 'fve', 'FvH4_4g16921' => 'fve', 'FvH4_4g17121' => 'fve', 'FvH4_4g17782' => 'fve', 'FvH4_4g17783' => 'fve', 'FvH4_4g18120' => 'fve', 'FvH4_4g31310' => 'fve', 'FvH4_4g35052' => 'fve', 'FvH4_5g30862' => 'fve', 'FvH4_6g01541' => 'fve', 'FvH4_6g02021' => 'fve', 'FvH4_6g02041' => 'fve', 'FvH4_6g02071' => 'fve', 'FvH4_6g02171' => 'fve', 'FvH4_6g03181' => 'fve', 'FvH4_6g03182' => 'fve', 'FvH4_6g03221' => 'fve', 'FvH4_6g03380' => 'fve', 'FvH4_6g05201' => 'fve', 'FvH4_6g05203' => 'fve', 'FvH4_6g20231' => 'fve', 'FvH4_6g31981' => 'fve', 'FvH4_6g32061' => 'fve', 'FvH4_6g37041' => 'fve', 'FvH4_6g37932' => 'fve', 'FvH4_6g38731' => 'fve', 'FvH4_6g39370' => 'fve', 'FvH4_6g39371' => 'fve', 'FvH4_6g40891' => 'fve', 'FvH4_6g40892' => 'fve', 'FvH4_6g43143' => 'fve', 'FvH4_6g45251' => 'fve', 'FvH4_6g45260' => 'fve', 'FvH4_6g45291' => 'fve', 'FvH4_6g45890' => 'fve', 'FvH4_6g46240' => 'fve', 'FvH4_6g46241' => 'fve', 'FvH4_6g46242' => 'fve', 'FvH4_6g46260' => 'fve', 'FvH4_6g46280' => 'fve', 'FvH4_6g46380' => 'fve', 'FvH4_7g12841' => 'fve', 'FvH4_7g31431' => 'fve', 'Glyma.09G075900' => 'gma', 'Gohir.A09G096401' => 'ghi', 'Gohir.D09G096101' => 'ghi', 'Gorai.006G112800' => 'gra', 'HanXRQChr04g0121411' => 'han', 'Hund15878' => 'sun', 'Lj2A1107G68' => 'lonja', 'Lj2A630G63' => 'lonja', 'Lj2A946T25' => 'lonja', 'Lj2C714T1' => 'lonja', 'Lj2C966T3' => 'lonja', 'Lj2C966T4' => 'lonja', 'Lj4g0002979' => 'lja', 'Lsat_1_v5_gn_5_30901' => 'lsa', 'Lsat_1_v5_gn_5_31100' => 'lsa', 'Lsat_1_v5_gn_5_38600' => 'lsa', 'Lsat_1_v5_gn_6_92061' => 'lsa', 'Manes.05G071301' => 'mes', 'MD02G1008700' => 'mdo', 'MD02G1008900' => 'mdo', 'MD03G1256400' => 'mdo', 'MD04G1180900' => 'mdo', 'MD04G1181000' => 'mdo', 'MD04G1181200' => 'mdo', 'MD05G1244200' => 'mdo', 'MD05G1324200' => 'mdo', 'MD09G1201600' => 'mdo', 'MD10G1000600' => 'mdo', 'MD14G1026900' => 'mdo', 'MD14G1187900' => 'mdo', 'MD15G1017800' => 'mdo', 'MD15G1018100' => 'mdo', 'Medtr4g124160' => 'mtr', 'Migut.L01260' => 'egut', 'Nitab4.5_0000008g0440' => 'nta', 'Nitab4.5_0000207g0170' => 'nta', 'Nitab4.5_0007671g0030' => 'nta', 'Nitab4.5_0010853g0020' => 'nta', 'Oeu057656.1' => 'oeu', 'PGSC0003DMG400005638' => 'stu', 'PGSC0003DMG400005639' => 'stu', 'Phvul.009G222800' => 'pvu', 'Potri.009G132400' => 'ptr', 'Potri.009G163001' => 'ptr', 'Potri.011G000700' => 'ptr', 'Potri.011G004800' => 'ptr', 'Prupe.1G509300' => 'ppe', 'Prupe.1G509700' => 'ppe', 'Prupe.1G510400' => 'ppe', 'Prupe.1G510700' => 'ppe', 'Prupe.1G512600' => 'ppe', 'Prupe.2G073200' => 'ppe', 'Prupe.3G059500' => 'ppe', 'Prupe.3G059600' => 'ppe', 'Prupe.3G246100' => 'ppe', 'Prupe.3G265100' => 'ppe', 'Prupe.4G034700' => 'ppe', 'Prupe.4G052100' => 'ppe', 'Prupe.4G053600' => 'ppe', 'Prupe.5G068800' => 'ppe', 'Prupe.5G070600' => 'ppe', 'Prupe.6G075400' => 'ppe', 'Prupe.6G075500' => 'ppe', 'Prupe.6G076400' => 'ppe', 'Prupe.8G110700' => 'ppe', 'Psat4g020960' => 'psa', 'PSO135G0788' => 'pso', 'PSO210G6463' => 'pso', 'PSO384G0370' => 'pso', 'PSO386G0056' => 'pso', 'QL01p006048' => 'qlo', 'QL02p054283' => 'qlo', 'QL05p008000' => 'qlo', 'QL05p008212' => 'qlo', 'QL05p008950' => 'qlo', 'QL05p009042' => 'qlo', 'QL05p009518' => 'qlo', 'QL05p012589' => 'qlo', 'QL05p012608' => 'qlo', 'QL05p012650' => 'qlo', 'QL05p012667' => 'qlo', 'QL05p014501' => 'qlo', 'QL05p052800' => 'qlo', 'QL05p065010' => 'qlo', 'QL05p074156' => 'qlo', 'QL05p074160' => 'qlo', 'QL05p074174' => 'qlo', 'QL05p074178' => 'qlo', 'QL05p074214' => 'qlo', 'QL06p001050' => 'qlo', 'QL06p001056' => 'qlo', 'QL06p006093' => 'qlo', 'QL06p006111' => 'qlo', 'QL07p019784' => 'qlo', 'QL07p019801' => 'qlo', 'QL07p036110' => 'qlo', 'QL07p036134' => 'qlo', 'QL07p036147' => 'qlo', 'QL07p036156' => 'qlo', 'QL07p036300' => 'qlo', 'QL07p036320' => 'qlo', 'QL08p014547' => 'qlo', 'QL08p014551' => 'qlo', 'QL08p043319' => 'qlo', 'QL08p043324' => 'qlo', 'QL11p009094' => 'qlo', 'RcHm_v2.0_Chr1g0380481' => 'rch', 'RcHm_v2.0_Chr2g0089331' => 'rch', 'RcHm_v2.0_Chr2g0123691' => 'rch', 'RcHm_v2.0_Chr2g0151111' => 'rch', 'RcHm_v2.0_Chr2g0163011' => 'rch', 'RcHm_v2.0_Chr2g0163051' => 'rch', 'RcHm_v2.0_Chr2g0164671' => 'rch', 'RcHm_v2.0_Chr2g0164681' => 'rch', 'RcHm_v2.0_Chr2g0164721' => 'rch', 'RcHm_v2.0_Chr3g0449911' => 'rch', 'RcHm_v2.0_Chr3g0450211' => 'rch', 'RcHm_v2.0_Chr3g0457271' => 'rch', 'RcHm_v2.0_Chr5g0018111' => 'rch', 'RcHm_v2.0_Chr5g0021011' => 'rch', 'RcHm_v2.0_Chr5g0081171' => 'rch', 'RcHm_v2.0_Chr5g0081211' => 'rch', 'RcHm_v2.0_Chr6g0275871' => 'rch', 'RcHm_v2.0_Chr6g0276071' => 'rch', 'RcHm_v2.0_Chr6g0285591' => 'rch', 'RcHm_v2.0_Chr6g0291931' => 'rch', 'RcHm_v2.0_Chr6g0292091' => 'rch', 'RcHm_v2.0_Chr6g0292271' => 'rch', 'RcHm_v2.0_Chr7g0221261' => 'rch', 'Rhsim08G0219900' => 'rsi', 'Rhsim08G0220200' => 'rsi', 'Rhsim08G0237800' => 'rsi', 'Rhsim08G0238800' => 'rsi', 'Sabra09G0102700' => 'sbr', 'Sabra09G0127200' => 'sbr', 'Sabra11G0003700' => 'sbr', 'Sabra15G0014700' => 'sbr', 'Sc19g0000590' => 'sci', 'Sc19g0001870' => 'sci', 'SGA_v2.0_scaffold1G00346' => 'sas', 'SGA_v2.0_scaffold1G00575' => 'sas', 'SGA_v2.0_scaffold1G00761' => 'sas', 'SGA_v2.0_scaffold232G43501' => 'sas', 'TAR625G1137' => 'tar', 'Thecc.03G222100' => 'tca', 'TPR.G12691' => 'tpr', 'TWI34G0727' => 'twi', 'TWI36G0117' => 'twi', 'VMungo1309G0868' => 'vmu' ) $gf_id = 'HOM05D001729' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001729' ) $data_identifier = 'HOM05D001729' $data_type = 'gf_id' $species_gene_counts = array( 'amhyb' => (int) 1, 'cqu' => (int) 9, 'can' => (int) 1, 'cansat' => (int) 1, 'car' => (int) 1, 'col' => (int) 5, 'dca' => (int) 1, 'din' => (int) 2, 'dzi' => (int) 3, 'fan' => (int) 140, 'fve' => (int) 62, 'gma' => (int) 1, 'ghi' => (int) 2, 'gra' => (int) 1, 'han' => (int) 1, 'sun' => (int) 1, 'lonja' => (int) 6, 'lja' => (int) 1, 'lsa' => (int) 4, 'mes' => (int) 1, 'mdo' => (int) 14, 'mtr' => (int) 1, 'egut' => (int) 1, 'nta' => (int) 4, 'oeu' => (int) 1, 'stu' => (int) 2, 'pvu' => (int) 1, 'ptr' => (int) 4, 'ppe' => (int) 19, 'psa' => (int) 1, 'pso' => (int) 4, 'qlo' => (int) 36, 'rch' => (int) 23, 'rsi' => (int) 4, 'sbr' => (int) 4, 'sci' => (int) 2, 'sas' => (int) 4, 'tar' => (int) 1, 'tca' => (int) 1, 'tpr' => (int) 1, 'twi' => (int) 2, 'vmu' => (int) 1 ) $gf_gene_species = 'vmu' $gf_gene_id = 'VMungo1309G0868' $species_info = array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ) $local_species = 'dca' $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' => 'HOM05D001729', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '375', 'num_species' => '42' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'Ah.07g204710' => 'amhyb', 'AUR62006001' => 'cqu', 'AUR62006002' => 'cqu', 'AUR62006003' => 'cqu', 'AUR62015641' => 'cqu', 'AUR62027174' => 'cqu', 'AUR62035623' => 'cqu', 'AUR62035624' => 'cqu', 'AUR62035625' => 'cqu', 'AUR62035626' => 'cqu', 'CAN.G1110.53' => 'can', 'CANSAT80G0415' => 'cansat', 'Ca_21364_v3' => 'car', 'COL.COLO4_30693' => 'col', 'COL.COLO4_30694' => 'col', 'COL.COLO4_30695' => 'col', 'COL.COLO4_30696' => 'col', 'COL.COLO4_34020' => 'col', 'DCAR_004585' => 'dca', 'Dinv04029' => 'din', 'Dinv34857' => 'din', 'Duzib147G0011' => 'dzi', 'Duzib170G0599' => 'dzi', 'Duzib192G1051' => 'dzi', 'FAN01G0708' => 'fan', 'FAN01G0742' => 'fan', 'FAN02G0048' => 'fan', 'FAN02G0583' => 'fan', 'FAN02G0688' => 'fan', 'FAN02G1588' => 'fan', 'FAN02G2194' => 'fan', 'FAN02G2750' => 'fan', 'FAN02G3094' => 'fan', 'FAN02G3887' => 'fan', 'FAN02G3911' => 'fan', 'FAN02G3994' => 'fan', 'FAN02G4432' => 'fan', 'FAN02G4556' => 'fan', 'FAN03G1977' => 'fan', 'FAN03G2781' => 'fan', 'FAN03G2850' => 'fan', 'FAN03G3155' => 'fan', 'FAN04G2487' => 'fan', 'FAN05G0208' => 'fan', 'FAN05G0656' => 'fan', 'FAN05G0696' => 'fan', 'FAN05G0810' => 'fan', 'FAN05G1447' => 'fan', 'FAN05G2640' => 'fan', 'FAN05G2911' => 'fan', 'FAN05G3901' => 'fan', 'FAN05G4859' => 'fan', 'FAN05G4861' => 'fan', 'FAN05G4988' => 'fan', 'FAN05G5187' => 'fan', 'FAN05G5452' => 'fan', 'FAN05G5500' => 'fan', 'FAN05G5688' => 'fan', 'FAN06G0177' => 'fan', 'FAN06G0675' => 'fan', 'FAN06G1290' => 'fan', 'FAN06G2191' => 'fan', 'FAN06G2405' => 'fan', 'FAN06G3231' => 'fan', 'FAN06G3932' => 'fan', 'FAN07G0163' => 'fan', 'FAN07G0471' => 'fan', 'FAN07G1354' => 'fan', 'FAN08G0338' => 'fan', 'FAN08G1373' => 'fan', 'FAN08G2539' => 'fan', 'FAN08G2728' => 'fan', 'FAN09G0608' => 'fan', 'FAN09G1136' => 'fan', 'FAN09G1958' => 'fan', 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'FAN14G5126' => 'fan', 'FAN14G5781' => 'fan', 'FAN14G5808' => 'fan', 'FAN14G5949' => 'fan', 'FAN15G0828' => 'fan', 'FAN15G1054' => 'fan', 'FAN15G2023' => 'fan', 'FAN15G2506' => 'fan', 'FAN16G0128' => 'fan', 'FAN16G0249' => 'fan', 'FAN16G0429' => 'fan', 'FAN16G1493' => 'fan', 'FAN16G2210' => 'fan', 'FAN16G2506' => 'fan', 'FAN18G1542' => 'fan', 'FAN18G4057' => 'fan', 'FAN19G0745' => 'fan', 'FAN19G1216' => 'fan', 'FAN19G1733' => 'fan', 'FAN20G0258' => 'fan', 'FAN20G1095' => 'fan', 'FAN20G1557' => 'fan', 'FAN21G0302' => 'fan', 'FAN21G0519' => 'fan', 'FAN21G0970' => 'fan', 'FAN21G1159' => 'fan', 'FAN21G1312' => 'fan', 'FAN21G1440' => 'fan', 'FAN21G1715' => 'fan', 'FAN23G1584' => 'fan', 'FAN24G0045' => 'fan', 'FAN24G0053' => 'fan', 'FAN24G1500' => 'fan', 'FAN24G1817' => 'fan', 'FAN24G2147' => 'fan', 'FAN24G2236' => 'fan', 'FAN24G2446' => 'fan', 'FAN24G2684' => 'fan', 'FAN25G0187' => 'fan', 'FAN25G0505' => 'fan', 'FAN25G0589' => 'fan', 'FAN25G3663' => 'fan', 'FAN26G1025' => 'fan', 'FAN26G2860' => 'fan', 'FAN27G1329' => 'fan', 'FAN27G3392' => 'fan', 'FvH4_1g02011' => 'fve', 'FvH4_1g06511' => 'fve', 'FvH4_2g19900' => 'fve', 'FvH4_2g19920' => 'fve', 'FvH4_2g24261' => 'fve', 'FvH4_2g24270' => 'fve', 'FvH4_2g24631' => 'fve', 'FvH4_2g30622' => 'fve', 'FvH4_3g12920' => 'fve', 'FvH4_3g30171' => 'fve', 'FvH4_3g35490' => 'fve', 'FvH4_3g43682' => 'fve', 'FvH4_3g43730' => 'fve', 'FvH4_3g43732' => 'fve', 'FvH4_3g43751' => 'fve', 'FvH4_3g43752' => 'fve', 'FvH4_3g43770' => 'fve', 'FvH4_3g44471' => 'fve', 'FvH4_3g44510' => 'fve', 'FvH4_3g44582' => 'fve', 'FvH4_4g16921' => 'fve', 'FvH4_4g17121' => 'fve', 'FvH4_4g17782' => 'fve', 'FvH4_4g17783' => 'fve', 'FvH4_4g18120' => 'fve', 'FvH4_4g31310' => 'fve', 'FvH4_4g35052' => 'fve', 'FvH4_5g30862' => 'fve', 'FvH4_6g01541' => 'fve', 'FvH4_6g02021' => 'fve', 'FvH4_6g02041' => 'fve', 'FvH4_6g02071' => 'fve', 'FvH4_6g02171' => 'fve', 'FvH4_6g03181' => 'fve', 'FvH4_6g03182' => 'fve', 'FvH4_6g03221' => 'fve', 'FvH4_6g03380' => 'fve', 'FvH4_6g05201' => 'fve', 'FvH4_6g05203' => 'fve', 'FvH4_6g20231' => 'fve', 'FvH4_6g31981' => 'fve', 'FvH4_6g32061' => 'fve', 'FvH4_6g37041' => 'fve', 'FvH4_6g37932' => 'fve', 'FvH4_6g38731' => 'fve', 'FvH4_6g39370' => 'fve', 'FvH4_6g39371' => 'fve', 'FvH4_6g40891' => 'fve', 'FvH4_6g40892' => 'fve', 'FvH4_6g43143' => 'fve', 'FvH4_6g45251' => 'fve', 'FvH4_6g45260' => 'fve', 'FvH4_6g45291' => 'fve', 'FvH4_6g45890' => 'fve', 'FvH4_6g46240' => 'fve', 'FvH4_6g46241' => 'fve', 'FvH4_6g46242' => 'fve', 'FvH4_6g46260' => 'fve', 'FvH4_6g46280' => 'fve', 'FvH4_6g46380' => 'fve', 'FvH4_7g12841' => 'fve', 'FvH4_7g31431' => 'fve', 'Glyma.09G075900' => 'gma', 'Gohir.A09G096401' => 'ghi', 'Gohir.D09G096101' => 'ghi', 'Gorai.006G112800' => 'gra', 'HanXRQChr04g0121411' => 'han', 'Hund15878' => 'sun', 'Lj2A1107G68' => 'lonja', 'Lj2A630G63' => 'lonja', 'Lj2A946T25' => 'lonja', 'Lj2C714T1' => 'lonja', 'Lj2C966T3' => 'lonja', 'Lj2C966T4' => 'lonja', 'Lj4g0002979' => 'lja', 'Lsat_1_v5_gn_5_30901' => 'lsa', 'Lsat_1_v5_gn_5_31100' => 'lsa', 'Lsat_1_v5_gn_5_38600' => 'lsa', 'Lsat_1_v5_gn_6_92061' => 'lsa', 'Manes.05G071301' => 'mes', 'MD02G1008700' => 'mdo', 'MD02G1008900' => 'mdo', 'MD03G1256400' => 'mdo', 'MD04G1180900' => 'mdo', 'MD04G1181000' => 'mdo', 'MD04G1181200' => 'mdo', 'MD05G1244200' => 'mdo', 'MD05G1324200' => 'mdo', 'MD09G1201600' => 'mdo', 'MD10G1000600' => 'mdo', 'MD14G1026900' => 'mdo', 'MD14G1187900' => 'mdo', 'MD15G1017800' => 'mdo', 'MD15G1018100' => 'mdo', 'Medtr4g124160' => 'mtr', 'Migut.L01260' => 'egut', 'Nitab4.5_0000008g0440' => 'nta', 'Nitab4.5_0000207g0170' => 'nta', 'Nitab4.5_0007671g0030' => 'nta', 'Nitab4.5_0010853g0020' => 'nta', 'Oeu057656.1' => 'oeu', 'PGSC0003DMG400005638' => 'stu', 'PGSC0003DMG400005639' => 'stu', 'Phvul.009G222800' => 'pvu', 'Potri.009G132400' => 'ptr', 'Potri.009G163001' => 'ptr', 'Potri.011G000700' => 'ptr', 'Potri.011G004800' => 'ptr', 'Prupe.1G509300' => 'ppe', 'Prupe.1G509700' => 'ppe', 'Prupe.1G510400' => 'ppe', 'Prupe.1G510700' => 'ppe', 'Prupe.1G512600' => 'ppe', 'Prupe.2G073200' => 'ppe', 'Prupe.3G059500' => 'ppe', 'Prupe.3G059600' => 'ppe', 'Prupe.3G246100' => 'ppe', 'Prupe.3G265100' => 'ppe', 'Prupe.4G034700' => 'ppe', 'Prupe.4G052100' => 'ppe', 'Prupe.4G053600' => 'ppe', 'Prupe.5G068800' => 'ppe', 'Prupe.5G070600' => 'ppe', 'Prupe.6G075400' => 'ppe', 'Prupe.6G075500' => 'ppe', 'Prupe.6G076400' => 'ppe', 'Prupe.8G110700' => 'ppe', 'Psat4g020960' => 'psa', 'PSO135G0788' => 'pso', 'PSO210G6463' => 'pso', 'PSO384G0370' => 'pso', 'PSO386G0056' => 'pso', 'QL01p006048' => 'qlo', 'QL02p054283' => 'qlo', 'QL05p008000' => 'qlo', 'QL05p008212' => 'qlo', 'QL05p008950' => 'qlo', 'QL05p009042' => 'qlo', 'QL05p009518' => 'qlo', 'QL05p012589' => 'qlo', 'QL05p012608' => 'qlo', 'QL05p012650' => 'qlo', 'QL05p012667' => 'qlo', 'QL05p014501' => 'qlo', 'QL05p052800' => 'qlo', 'QL05p065010' => 'qlo', 'QL05p074156' => 'qlo', 'QL05p074160' => 'qlo', 'QL05p074174' => 'qlo', 'QL05p074178' => 'qlo', 'QL05p074214' => 'qlo', 'QL06p001050' => 'qlo', 'QL06p001056' => 'qlo', 'QL06p006093' => 'qlo', 'QL06p006111' => 'qlo', 'QL07p019784' => 'qlo', 'QL07p019801' => 'qlo', 'QL07p036110' => 'qlo', 'QL07p036134' => 'qlo', 'QL07p036147' => 'qlo', 'QL07p036156' => 'qlo', 'QL07p036300' => 'qlo', 'QL07p036320' => 'qlo', 'QL08p014547' => 'qlo', 'QL08p014551' => 'qlo', 'QL08p043319' => 'qlo', 'QL08p043324' => 'qlo', 'QL11p009094' => 'qlo', 'RcHm_v2.0_Chr1g0380481' => 'rch', 'RcHm_v2.0_Chr2g0089331' => 'rch', 'RcHm_v2.0_Chr2g0123691' => 'rch', 'RcHm_v2.0_Chr2g0151111' => 'rch', 'RcHm_v2.0_Chr2g0163011' => 'rch', 'RcHm_v2.0_Chr2g0163051' => 'rch', 'RcHm_v2.0_Chr2g0164671' => 'rch', 'RcHm_v2.0_Chr2g0164681' => 'rch', 'RcHm_v2.0_Chr2g0164721' => 'rch', 'RcHm_v2.0_Chr3g0449911' => 'rch', 'RcHm_v2.0_Chr3g0450211' => 'rch', 'RcHm_v2.0_Chr3g0457271' => 'rch', 'RcHm_v2.0_Chr5g0018111' => 'rch', 'RcHm_v2.0_Chr5g0021011' => 'rch', 'RcHm_v2.0_Chr5g0081171' => 'rch', 'RcHm_v2.0_Chr5g0081211' => 'rch', 'RcHm_v2.0_Chr6g0275871' => 'rch', 'RcHm_v2.0_Chr6g0276071' => 'rch', 'RcHm_v2.0_Chr6g0285591' => 'rch', 'RcHm_v2.0_Chr6g0291931' => 'rch', 'RcHm_v2.0_Chr6g0292091' => 'rch', 'RcHm_v2.0_Chr6g0292271' => 'rch', 'RcHm_v2.0_Chr7g0221261' => 'rch', 'Rhsim08G0219900' => 'rsi', 'Rhsim08G0220200' => 'rsi', 'Rhsim08G0237800' => 'rsi', 'Rhsim08G0238800' => 'rsi', 'Sabra09G0102700' => 'sbr', 'Sabra09G0127200' => 'sbr', 'Sabra11G0003700' => 'sbr', 'Sabra15G0014700' => 'sbr', 'Sc19g0000590' => 'sci', 'Sc19g0001870' => 'sci', 'SGA_v2.0_scaffold1G00346' => 'sas', 'SGA_v2.0_scaffold1G00575' => 'sas', 'SGA_v2.0_scaffold1G00761' => 'sas', 'SGA_v2.0_scaffold232G43501' => 'sas', 'TAR625G1137' => 'tar', 'Thecc.03G222100' => 'tca', 'TPR.G12691' => 'tpr', 'TWI34G0727' => 'twi', 'TWI36G0117' => 'twi', 'VMungo1309G0868' => 'vmu' ), 'gf_id' => 'HOM05D001729', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001729' ), 'data_identifier' => 'HOM05D001729', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001729', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '375', 'num_species' => '42' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'Ah.07g204710' => 'amhyb', 'AUR62006001' => 'cqu', 'AUR62006002' => 'cqu', 'AUR62006003' => 'cqu', 'AUR62015641' => 'cqu', 'AUR62027174' => 'cqu', 'AUR62035623' => 'cqu', 'AUR62035624' => 'cqu', 'AUR62035625' => 'cqu', 'AUR62035626' => 'cqu', 'CAN.G1110.53' => 'can', 'CANSAT80G0415' => 'cansat', 'Ca_21364_v3' => 'car', 'COL.COLO4_30693' => 'col', 'COL.COLO4_30694' => 'col', 'COL.COLO4_30695' => 'col', 'COL.COLO4_30696' => 'col', 'COL.COLO4_34020' => 'col', 'DCAR_004585' => 'dca', 'Dinv04029' => 'din', 'Dinv34857' => 'din', 'Duzib147G0011' => 'dzi', 'Duzib170G0599' => 'dzi', 'Duzib192G1051' => 'dzi', 'FAN01G0708' => 'fan', 'FAN01G0742' => 'fan', 'FAN02G0048' => 'fan', 'FAN02G0583' => 'fan', 'FAN02G0688' => 'fan', 'FAN02G1588' => 'fan', 'FAN02G2194' => 'fan', 'FAN02G2750' => 'fan', 'FAN02G3094' => 'fan', 'FAN02G3887' => 'fan', 'FAN02G3911' => 'fan', 'FAN02G3994' => 'fan', 'FAN02G4432' => 'fan', 'FAN02G4556' => 'fan', 'FAN03G1977' => 'fan', 'FAN03G2781' => 'fan', 'FAN03G2850' => 'fan', 'FAN03G3155' => 'fan', 'FAN04G2487' => 'fan', 'FAN05G0208' => 'fan', 'FAN05G0656' => 'fan', 'FAN05G0696' => 'fan', 'FAN05G0810' => 'fan', 'FAN05G1447' => 'fan', 'FAN05G2640' => 'fan', 'FAN05G2911' => 'fan', 'FAN05G3901' => 'fan', 'FAN05G4859' => 'fan', 'FAN05G4861' => 'fan', 'FAN05G4988' => 'fan', 'FAN05G5187' => 'fan', 'FAN05G5452' => 'fan', 'FAN05G5500' => 'fan', 'FAN05G5688' => 'fan', 'FAN06G0177' => 'fan', 'FAN06G0675' => 'fan', 'FAN06G1290' => 'fan', 'FAN06G2191' => 'fan', 'FAN06G2405' => 'fan', 'FAN06G3231' => 'fan', 'FAN06G3932' => 'fan', 'FAN07G0163' => 'fan', 'FAN07G0471' => 'fan', 'FAN07G1354' => 'fan', 'FAN08G0338' => 'fan', 'FAN08G1373' => 'fan', 'FAN08G2539' => 'fan', 'FAN08G2728' => 'fan', 'FAN09G0608' => 'fan', 'FAN09G1136' => 'fan', 'FAN09G1958' => 'fan', 'FAN09G2508' => 'fan', 'FAN09G2597' => 'fan', 'FAN09G2658' => 'fan', 'FAN09G2757' => 'fan', 'FAN09G2983' => 'fan', 'FAN09G3130' => 'fan', 'FAN09G3565' => 'fan', 'FAN09G3613' => 'fan', 'FAN09G4011' => 'fan', 'FAN09G4239' => 'fan', 'FAN09G4277' => 'fan', 'FAN09G4720' => 'fan', 'FAN11G0139' => 'fan', 'FAN11G1727' => 'fan', 'FAN11G2672' => 'fan', 'FAN11G2795' => 'fan', 'FAN11G3238' => 'fan', 'FAN11G3734' => 'fan', 'FAN12G0631' => 'fan', 'FAN12G2239' => 'fan', 'FAN12G2308' => 'fan', 'FAN12G2569' => 'fan', 'FAN12G2623' => 'fan', 'FAN13G3182' => 'fan', 'FAN14G0053' => 'fan', 'FAN14G0370' => 'fan', 'FAN14G0382' => 'fan', 'FAN14G0421' => 'fan', 'FAN14G0866' => 'fan', 'FAN14G1187' => 'fan', 'FAN14G1727' => 'fan', 'FAN14G1791' => 'fan', 'FAN14G2361' => 'fan', 'FAN14G2668' => 'fan', 'FAN14G2770' => 'fan', 'FAN14G2874' => 'fan', 'FAN14G3193' => 'fan', 'FAN14G3624' => 'fan', 'FAN14G3676' => 'fan', 'FAN14G3807' => 'fan', 'FAN14G4082' => 'fan', 'FAN14G4342' => 'fan', 'FAN14G4985' => 'fan', 'FAN14G5126' => 'fan', 'FAN14G5781' => 'fan', 'FAN14G5808' => 'fan', 'FAN14G5949' => 'fan', 'FAN15G0828' => 'fan', 'FAN15G1054' => 'fan', 'FAN15G2023' => 'fan', 'FAN15G2506' => 'fan', 'FAN16G0128' => 'fan', 'FAN16G0249' => 'fan', 'FAN16G0429' => 'fan', 'FAN16G1493' => 'fan', 'FAN16G2210' => 'fan', 'FAN16G2506' => 'fan', 'FAN18G1542' => 'fan', 'FAN18G4057' => 'fan', 'FAN19G0745' => 'fan', 'FAN19G1216' => 'fan', 'FAN19G1733' => 'fan', 'FAN20G0258' => 'fan', 'FAN20G1095' => 'fan', 'FAN20G1557' => 'fan', 'FAN21G0302' => 'fan', 'FAN21G0519' => 'fan', 'FAN21G0970' => 'fan', 'FAN21G1159' => 'fan', 'FAN21G1312' => 'fan', 'FAN21G1440' => 'fan', 'FAN21G1715' => 'fan', 'FAN23G1584' => 'fan', 'FAN24G0045' => 'fan', 'FAN24G0053' => 'fan', 'FAN24G1500' => 'fan', 'FAN24G1817' => 'fan', 'FAN24G2147' => 'fan', 'FAN24G2236' => 'fan', 'FAN24G2446' => 'fan', 'FAN24G2684' => 'fan', 'FAN25G0187' => 'fan', 'FAN25G0505' => 'fan', 'FAN25G0589' => 'fan', 'FAN25G3663' => 'fan', 'FAN26G1025' => 'fan', 'FAN26G2860' => 'fan', 'FAN27G1329' => 'fan', 'FAN27G3392' => 'fan', 'FvH4_1g02011' => 'fve', 'FvH4_1g06511' => 'fve', 'FvH4_2g19900' => 'fve', 'FvH4_2g19920' => 'fve', 'FvH4_2g24261' => 'fve', 'FvH4_2g24270' => 'fve', 'FvH4_2g24631' => 'fve', 'FvH4_2g30622' => 'fve', 'FvH4_3g12920' => 'fve', 'FvH4_3g30171' => 'fve', 'FvH4_3g35490' => 'fve', 'FvH4_3g43682' => 'fve', 'FvH4_3g43730' => 'fve', 'FvH4_3g43732' => 'fve', 'FvH4_3g43751' => 'fve', 'FvH4_3g43752' => 'fve', 'FvH4_3g43770' => 'fve', 'FvH4_3g44471' => 'fve', 'FvH4_3g44510' => 'fve', 'FvH4_3g44582' => 'fve', 'FvH4_4g16921' => 'fve', 'FvH4_4g17121' => 'fve', 'FvH4_4g17782' => 'fve', 'FvH4_4g17783' => 'fve', 'FvH4_4g18120' => 'fve', 'FvH4_4g31310' => 'fve', 'FvH4_4g35052' => 'fve', 'FvH4_5g30862' => 'fve', 'FvH4_6g01541' => 'fve', 'FvH4_6g02021' => 'fve', 'FvH4_6g02041' => 'fve', 'FvH4_6g02071' => 'fve', 'FvH4_6g02171' => 'fve', 'FvH4_6g03181' => 'fve', 'FvH4_6g03182' => 'fve', 'FvH4_6g03221' => 'fve', 'FvH4_6g03380' => 'fve', 'FvH4_6g05201' => 'fve', 'FvH4_6g05203' => 'fve', 'FvH4_6g20231' => 'fve', 'FvH4_6g31981' => 'fve', 'FvH4_6g32061' => 'fve', 'FvH4_6g37041' => 'fve', 'FvH4_6g37932' => 'fve', 'FvH4_6g38731' => 'fve', 'FvH4_6g39370' => 'fve', 'FvH4_6g39371' => 'fve', 'FvH4_6g40891' => 'fve', 'FvH4_6g40892' => 'fve', 'FvH4_6g43143' => 'fve', 'FvH4_6g45251' => 'fve', 'FvH4_6g45260' => 'fve', 'FvH4_6g45291' => 'fve', 'FvH4_6g45890' => 'fve', 'FvH4_6g46240' => 'fve', 'FvH4_6g46241' => 'fve', 'FvH4_6g46242' => 'fve', 'FvH4_6g46260' => 'fve', 'FvH4_6g46280' => 'fve', 'FvH4_6g46380' => 'fve', 'FvH4_7g12841' => 'fve', 'FvH4_7g31431' => 'fve', 'Glyma.09G075900' => 'gma', 'Gohir.A09G096401' => 'ghi', 'Gohir.D09G096101' => 'ghi', 'Gorai.006G112800' => 'gra', 'HanXRQChr04g0121411' => 'han', 'Hund15878' => 'sun', 'Lj2A1107G68' => 'lonja', 'Lj2A630G63' => 'lonja', 'Lj2A946T25' => 'lonja', 'Lj2C714T1' => 'lonja', 'Lj2C966T3' => 'lonja', 'Lj2C966T4' => 'lonja', 'Lj4g0002979' => 'lja', 'Lsat_1_v5_gn_5_30901' => 'lsa', 'Lsat_1_v5_gn_5_31100' => 'lsa', 'Lsat_1_v5_gn_5_38600' => 'lsa', 'Lsat_1_v5_gn_6_92061' => 'lsa', 'Manes.05G071301' => 'mes', 'MD02G1008700' => 'mdo', 'MD02G1008900' => 'mdo', 'MD03G1256400' => 'mdo', 'MD04G1180900' => 'mdo', 'MD04G1181000' => 'mdo', 'MD04G1181200' => 'mdo', 'MD05G1244200' => 'mdo', 'MD05G1324200' => 'mdo', 'MD09G1201600' => 'mdo', 'MD10G1000600' => 'mdo', 'MD14G1026900' => 'mdo', 'MD14G1187900' => 'mdo', 'MD15G1017800' => 'mdo', 'MD15G1018100' => 'mdo', 'Medtr4g124160' => 'mtr', 'Migut.L01260' => 'egut', 'Nitab4.5_0000008g0440' => 'nta', 'Nitab4.5_0000207g0170' => 'nta', 'Nitab4.5_0007671g0030' => 'nta', 'Nitab4.5_0010853g0020' => 'nta', 'Oeu057656.1' => 'oeu', 'PGSC0003DMG400005638' => 'stu', 'PGSC0003DMG400005639' => 'stu', 'Phvul.009G222800' => 'pvu', 'Potri.009G132400' => 'ptr', 'Potri.009G163001' => 'ptr', 'Potri.011G000700' => 'ptr', 'Potri.011G004800' => 'ptr', 'Prupe.1G509300' => 'ppe', 'Prupe.1G509700' => 'ppe', 'Prupe.1G510400' => 'ppe', 'Prupe.1G510700' => 'ppe', 'Prupe.1G512600' => 'ppe', 'Prupe.2G073200' => 'ppe', 'Prupe.3G059500' => 'ppe', 'Prupe.3G059600' => 'ppe', 'Prupe.3G246100' => 'ppe', 'Prupe.3G265100' => 'ppe', 'Prupe.4G034700' => 'ppe', 'Prupe.4G052100' => 'ppe', 'Prupe.4G053600' => 'ppe', 'Prupe.5G068800' => 'ppe', 'Prupe.5G070600' => 'ppe', 'Prupe.6G075400' => 'ppe', 'Prupe.6G075500' => 'ppe', 'Prupe.6G076400' => 'ppe', 'Prupe.8G110700' => 'ppe', 'Psat4g020960' => 'psa', 'PSO135G0788' => 'pso', 'PSO210G6463' => 'pso', 'PSO384G0370' => 'pso', 'PSO386G0056' => 'pso', 'QL01p006048' => 'qlo', 'QL02p054283' => 'qlo', 'QL05p008000' => 'qlo', 'QL05p008212' => 'qlo', 'QL05p008950' => 'qlo', 'QL05p009042' => 'qlo', 'QL05p009518' => 'qlo', 'QL05p012589' => 'qlo', 'QL05p012608' => 'qlo', 'QL05p012650' => 'qlo', 'QL05p012667' => 'qlo', 'QL05p014501' => 'qlo', 'QL05p052800' => 'qlo', 'QL05p065010' => 'qlo', 'QL05p074156' => 'qlo', 'QL05p074160' => 'qlo', 'QL05p074174' => 'qlo', 'QL05p074178' => 'qlo', 'QL05p074214' => 'qlo', 'QL06p001050' => 'qlo', 'QL06p001056' => 'qlo', 'QL06p006093' => 'qlo', 'QL06p006111' => 'qlo', 'QL07p019784' => 'qlo', 'QL07p019801' => 'qlo', 'QL07p036110' => 'qlo', 'QL07p036134' => 'qlo', 'QL07p036147' => 'qlo', 'QL07p036156' => 'qlo', 'QL07p036300' => 'qlo', 'QL07p036320' => 'qlo', 'QL08p014547' => 'qlo', 'QL08p014551' => 'qlo', 'QL08p043319' => 'qlo', 'QL08p043324' => 'qlo', 'QL11p009094' => 'qlo', 'RcHm_v2.0_Chr1g0380481' => 'rch', 'RcHm_v2.0_Chr2g0089331' => 'rch', 'RcHm_v2.0_Chr2g0123691' => 'rch', 'RcHm_v2.0_Chr2g0151111' => 'rch', 'RcHm_v2.0_Chr2g0163011' => 'rch', 'RcHm_v2.0_Chr2g0163051' => 'rch', 'RcHm_v2.0_Chr2g0164671' => 'rch', 'RcHm_v2.0_Chr2g0164681' => 'rch', 'RcHm_v2.0_Chr2g0164721' => 'rch', 'RcHm_v2.0_Chr3g0449911' => 'rch', 'RcHm_v2.0_Chr3g0450211' => 'rch', 'RcHm_v2.0_Chr3g0457271' => 'rch', 'RcHm_v2.0_Chr5g0018111' => 'rch', 'RcHm_v2.0_Chr5g0021011' => 'rch', 'RcHm_v2.0_Chr5g0081171' => 'rch', 'RcHm_v2.0_Chr5g0081211' => 'rch', 'RcHm_v2.0_Chr6g0275871' => 'rch', 'RcHm_v2.0_Chr6g0276071' => 'rch', 'RcHm_v2.0_Chr6g0285591' => 'rch', 'RcHm_v2.0_Chr6g0291931' => 'rch', 'RcHm_v2.0_Chr6g0292091' => 'rch', 'RcHm_v2.0_Chr6g0292271' => 'rch', 'RcHm_v2.0_Chr7g0221261' => 'rch', 'Rhsim08G0219900' => 'rsi', 'Rhsim08G0220200' => 'rsi', 'Rhsim08G0237800' => 'rsi', 'Rhsim08G0238800' => 'rsi', 'Sabra09G0102700' => 'sbr', 'Sabra09G0127200' => 'sbr', 'Sabra11G0003700' => 'sbr', 'Sabra15G0014700' => 'sbr', 'Sc19g0000590' => 'sci', 'Sc19g0001870' => 'sci', 'SGA_v2.0_scaffold1G00346' => 'sas', 'SGA_v2.0_scaffold1G00575' => 'sas', 'SGA_v2.0_scaffold1G00761' => 'sas', 'SGA_v2.0_scaffold232G43501' => 'sas', 'TAR625G1137' => 'tar', 'Thecc.03G222100' => 'tca', 'TPR.G12691' => 'tpr', 'TWI34G0727' => 'twi', 'TWI36G0117' => 'twi', 'VMungo1309G0868' => 'vmu' ) $gf_id = 'HOM05D001729' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001729' ) $data_identifier = 'HOM05D001729' $data_type = 'gf_id' $species_gene_counts = array( 'amhyb' => (int) 1, 'cqu' => (int) 9, 'can' => (int) 1, 'cansat' => (int) 1, 'car' => (int) 1, 'col' => (int) 5, 'dca' => (int) 1, 'din' => (int) 2, 'dzi' => (int) 3, 'fan' => (int) 140, 'fve' => (int) 62, 'gma' => (int) 1, 'ghi' => (int) 2, 'gra' => (int) 1, 'han' => (int) 1, 'sun' => (int) 1, 'lonja' => (int) 6, 'lja' => (int) 1, 'lsa' => (int) 4, 'mes' => (int) 1, 'mdo' => (int) 14, 'mtr' => (int) 1, 'egut' => (int) 1, 'nta' => (int) 4, 'oeu' => (int) 1, 'stu' => (int) 2, 'pvu' => (int) 1, 'ptr' => (int) 4, 'ppe' => (int) 19, 'psa' => (int) 1, 'pso' => (int) 4, 'qlo' => (int) 36, 'rch' => (int) 23, 'rsi' => (int) 4, 'sbr' => (int) 4, 'sci' => (int) 2, 'sas' => (int) 4, 'tar' => (int) 1, 'tca' => (int) 1, 'tpr' => (int) 1, 'twi' => (int) 2, 'vmu' => (int) 1 ) $gf_gene_species = 'vmu' $gf_gene_id = 'VMungo1309G0868' $species_info = array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ) $local_species = 'dca' $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' => 'HOM05D001729', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '375', 'num_species' => '42' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'Ah.07g204710' => 'amhyb', 'AUR62006001' => 'cqu', 'AUR62006002' => 'cqu', 'AUR62006003' => 'cqu', 'AUR62015641' => 'cqu', 'AUR62027174' => 'cqu', 'AUR62035623' => 'cqu', 'AUR62035624' => 'cqu', 'AUR62035625' => 'cqu', 'AUR62035626' => 'cqu', 'CAN.G1110.53' => 'can', 'CANSAT80G0415' => 'cansat', 'Ca_21364_v3' => 'car', 'COL.COLO4_30693' => 'col', 'COL.COLO4_30694' => 'col', 'COL.COLO4_30695' => 'col', 'COL.COLO4_30696' => 'col', 'COL.COLO4_34020' => 'col', 'DCAR_004585' => 'dca', 'Dinv04029' => 'din', 'Dinv34857' => 'din', 'Duzib147G0011' => 'dzi', 'Duzib170G0599' => 'dzi', 'Duzib192G1051' => 'dzi', 'FAN01G0708' => 'fan', 'FAN01G0742' => 'fan', 'FAN02G0048' => 'fan', 'FAN02G0583' => 'fan', 'FAN02G0688' => 'fan', 'FAN02G1588' => 'fan', 'FAN02G2194' => 'fan', 'FAN02G2750' => 'fan', 'FAN02G3094' => 'fan', 'FAN02G3887' => 'fan', 'FAN02G3911' => 'fan', 'FAN02G3994' => 'fan', 'FAN02G4432' => 'fan', 'FAN02G4556' => 'fan', 'FAN03G1977' => 'fan', 'FAN03G2781' => 'fan', 'FAN03G2850' => 'fan', 'FAN03G3155' => 'fan', 'FAN04G2487' => 'fan', 'FAN05G0208' => 'fan', 'FAN05G0656' => 'fan', 'FAN05G0696' => 'fan', 'FAN05G0810' => 'fan', 'FAN05G1447' => 'fan', 'FAN05G2640' => 'fan', 'FAN05G2911' => 'fan', 'FAN05G3901' => 'fan', 'FAN05G4859' => 'fan', 'FAN05G4861' => 'fan', 'FAN05G4988' => 'fan', 'FAN05G5187' => 'fan', 'FAN05G5452' => 'fan', 'FAN05G5500' => 'fan', 'FAN05G5688' => 'fan', 'FAN06G0177' => 'fan', 'FAN06G0675' => 'fan', 'FAN06G1290' => 'fan', 'FAN06G2191' => 'fan', 'FAN06G2405' => 'fan', 'FAN06G3231' => 'fan', 'FAN06G3932' => 'fan', 'FAN07G0163' => 'fan', 'FAN07G0471' => 'fan', 'FAN07G1354' => 'fan', 'FAN08G0338' => 'fan', 'FAN08G1373' => 'fan', 'FAN08G2539' => 'fan', 'FAN08G2728' => 'fan', 'FAN09G0608' => 'fan', 'FAN09G1136' => 'fan', 'FAN09G1958' => 'fan', 'FAN09G2508' => 'fan', 'FAN09G2597' => 'fan', 'FAN09G2658' => 'fan', 'FAN09G2757' => 'fan', 'FAN09G2983' => 'fan', 'FAN09G3130' => 'fan', 'FAN09G3565' => 'fan', 'FAN09G3613' => 'fan', 'FAN09G4011' => 'fan', 'FAN09G4239' => 'fan', 'FAN09G4277' => 'fan', 'FAN09G4720' => 'fan', 'FAN11G0139' => 'fan', 'FAN11G1727' => 'fan', 'FAN11G2672' => 'fan', 'FAN11G2795' => 'fan', 'FAN11G3238' => 'fan', 'FAN11G3734' => 'fan', 'FAN12G0631' => 'fan', 'FAN12G2239' => 'fan', 'FAN12G2308' => 'fan', 'FAN12G2569' => 'fan', 'FAN12G2623' => 'fan', 'FAN13G3182' => 'fan', 'FAN14G0053' => 'fan', 'FAN14G0370' => 'fan', 'FAN14G0382' => 'fan', 'FAN14G0421' => 'fan', 'FAN14G0866' => 'fan', 'FAN14G1187' => 'fan', 'FAN14G1727' => 'fan', 'FAN14G1791' => 'fan', 'FAN14G2361' => 'fan', 'FAN14G2668' => 'fan', 'FAN14G2770' => 'fan', 'FAN14G2874' => 'fan', 'FAN14G3193' => 'fan', 'FAN14G3624' => 'fan', 'FAN14G3676' => 'fan', 'FAN14G3807' => 'fan', 'FAN14G4082' => 'fan', 'FAN14G4342' => 'fan', 'FAN14G4985' => 'fan', 'FAN14G5126' => 'fan', 'FAN14G5781' => 'fan', 'FAN14G5808' => 'fan', 'FAN14G5949' => 'fan', 'FAN15G0828' => 'fan', 'FAN15G1054' => 'fan', 'FAN15G2023' => 'fan', 'FAN15G2506' => 'fan', 'FAN16G0128' => 'fan', 'FAN16G0249' => 'fan', 'FAN16G0429' => 'fan', 'FAN16G1493' => 'fan', 'FAN16G2210' => 'fan', 'FAN16G2506' => 'fan', 'FAN18G1542' => 'fan', 'FAN18G4057' => 'fan', 'FAN19G0745' => 'fan', 'FAN19G1216' => 'fan', 'FAN19G1733' => 'fan', 'FAN20G0258' => 'fan', 'FAN20G1095' => 'fan', 'FAN20G1557' => 'fan', 'FAN21G0302' => 'fan', 'FAN21G0519' => 'fan', 'FAN21G0970' => 'fan', 'FAN21G1159' => 'fan', 'FAN21G1312' => 'fan', 'FAN21G1440' => 'fan', 'FAN21G1715' => 'fan', 'FAN23G1584' => 'fan', 'FAN24G0045' => 'fan', 'FAN24G0053' => 'fan', 'FAN24G1500' => 'fan', 'FAN24G1817' => 'fan', 'FAN24G2147' => 'fan', 'FAN24G2236' => 'fan', 'FAN24G2446' => 'fan', 'FAN24G2684' => 'fan', 'FAN25G0187' => 'fan', 'FAN25G0505' => 'fan', 'FAN25G0589' => 'fan', 'FAN25G3663' => 'fan', 'FAN26G1025' => 'fan', 'FAN26G2860' => 'fan', 'FAN27G1329' => 'fan', 'FAN27G3392' => 'fan', 'FvH4_1g02011' => 'fve', 'FvH4_1g06511' => 'fve', 'FvH4_2g19900' => 'fve', 'FvH4_2g19920' => 'fve', 'FvH4_2g24261' => 'fve', 'FvH4_2g24270' => 'fve', 'FvH4_2g24631' => 'fve', 'FvH4_2g30622' => 'fve', 'FvH4_3g12920' => 'fve', 'FvH4_3g30171' => 'fve', 'FvH4_3g35490' => 'fve', 'FvH4_3g43682' => 'fve', 'FvH4_3g43730' => 'fve', 'FvH4_3g43732' => 'fve', 'FvH4_3g43751' => 'fve', 'FvH4_3g43752' => 'fve', 'FvH4_3g43770' => 'fve', 'FvH4_3g44471' => 'fve', 'FvH4_3g44510' => 'fve', 'FvH4_3g44582' => 'fve', 'FvH4_4g16921' => 'fve', 'FvH4_4g17121' => 'fve', 'FvH4_4g17782' => 'fve', 'FvH4_4g17783' => 'fve', 'FvH4_4g18120' => 'fve', 'FvH4_4g31310' => 'fve', 'FvH4_4g35052' => 'fve', 'FvH4_5g30862' => 'fve', 'FvH4_6g01541' => 'fve', 'FvH4_6g02021' => 'fve', 'FvH4_6g02041' => 'fve', 'FvH4_6g02071' => 'fve', 'FvH4_6g02171' => 'fve', 'FvH4_6g03181' => 'fve', 'FvH4_6g03182' => 'fve', 'FvH4_6g03221' => 'fve', 'FvH4_6g03380' => 'fve', 'FvH4_6g05201' => 'fve', 'FvH4_6g05203' => 'fve', 'FvH4_6g20231' => 'fve', 'FvH4_6g31981' => 'fve', 'FvH4_6g32061' => 'fve', 'FvH4_6g37041' => 'fve', 'FvH4_6g37932' => 'fve', 'FvH4_6g38731' => 'fve', 'FvH4_6g39370' => 'fve', 'FvH4_6g39371' => 'fve', 'FvH4_6g40891' => 'fve', 'FvH4_6g40892' => 'fve', 'FvH4_6g43143' => 'fve', 'FvH4_6g45251' => 'fve', 'FvH4_6g45260' => 'fve', 'FvH4_6g45291' => 'fve', 'FvH4_6g45890' => 'fve', 'FvH4_6g46240' => 'fve', 'FvH4_6g46241' => 'fve', 'FvH4_6g46242' => 'fve', 'FvH4_6g46260' => 'fve', 'FvH4_6g46280' => 'fve', 'FvH4_6g46380' => 'fve', 'FvH4_7g12841' => 'fve', 'FvH4_7g31431' => 'fve', 'Glyma.09G075900' => 'gma', 'Gohir.A09G096401' => 'ghi', 'Gohir.D09G096101' => 'ghi', 'Gorai.006G112800' => 'gra', 'HanXRQChr04g0121411' => 'han', 'Hund15878' => 'sun', 'Lj2A1107G68' => 'lonja', 'Lj2A630G63' => 'lonja', 'Lj2A946T25' => 'lonja', 'Lj2C714T1' => 'lonja', 'Lj2C966T3' => 'lonja', 'Lj2C966T4' => 'lonja', 'Lj4g0002979' => 'lja', 'Lsat_1_v5_gn_5_30901' => 'lsa', 'Lsat_1_v5_gn_5_31100' => 'lsa', 'Lsat_1_v5_gn_5_38600' => 'lsa', 'Lsat_1_v5_gn_6_92061' => 'lsa', 'Manes.05G071301' => 'mes', 'MD02G1008700' => 'mdo', 'MD02G1008900' => 'mdo', 'MD03G1256400' => 'mdo', 'MD04G1180900' => 'mdo', 'MD04G1181000' => 'mdo', 'MD04G1181200' => 'mdo', 'MD05G1244200' => 'mdo', 'MD05G1324200' => 'mdo', 'MD09G1201600' => 'mdo', 'MD10G1000600' => 'mdo', 'MD14G1026900' => 'mdo', 'MD14G1187900' => 'mdo', 'MD15G1017800' => 'mdo', 'MD15G1018100' => 'mdo', 'Medtr4g124160' => 'mtr', 'Migut.L01260' => 'egut', 'Nitab4.5_0000008g0440' => 'nta', 'Nitab4.5_0000207g0170' => 'nta', 'Nitab4.5_0007671g0030' => 'nta', 'Nitab4.5_0010853g0020' => 'nta', 'Oeu057656.1' => 'oeu', 'PGSC0003DMG400005638' => 'stu', 'PGSC0003DMG400005639' => 'stu', 'Phvul.009G222800' => 'pvu', 'Potri.009G132400' => 'ptr', 'Potri.009G163001' => 'ptr', 'Potri.011G000700' => 'ptr', 'Potri.011G004800' => 'ptr', 'Prupe.1G509300' => 'ppe', 'Prupe.1G509700' => 'ppe', 'Prupe.1G510400' => 'ppe', 'Prupe.1G510700' => 'ppe', 'Prupe.1G512600' => 'ppe', 'Prupe.2G073200' => 'ppe', 'Prupe.3G059500' => 'ppe', 'Prupe.3G059600' => 'ppe', 'Prupe.3G246100' => 'ppe', 'Prupe.3G265100' => 'ppe', 'Prupe.4G034700' => 'ppe', 'Prupe.4G052100' => 'ppe', 'Prupe.4G053600' => 'ppe', 'Prupe.5G068800' => 'ppe', 'Prupe.5G070600' => 'ppe', 'Prupe.6G075400' => 'ppe', 'Prupe.6G075500' => 'ppe', 'Prupe.6G076400' => 'ppe', 'Prupe.8G110700' => 'ppe', 'Psat4g020960' => 'psa', 'PSO135G0788' => 'pso', 'PSO210G6463' => 'pso', 'PSO384G0370' => 'pso', 'PSO386G0056' => 'pso', 'QL01p006048' => 'qlo', 'QL02p054283' => 'qlo', 'QL05p008000' => 'qlo', 'QL05p008212' => 'qlo', 'QL05p008950' => 'qlo', 'QL05p009042' => 'qlo', 'QL05p009518' => 'qlo', 'QL05p012589' => 'qlo', 'QL05p012608' => 'qlo', 'QL05p012650' => 'qlo', 'QL05p012667' => 'qlo', 'QL05p014501' => 'qlo', 'QL05p052800' => 'qlo', 'QL05p065010' => 'qlo', 'QL05p074156' => 'qlo', 'QL05p074160' => 'qlo', 'QL05p074174' => 'qlo', 'QL05p074178' => 'qlo', 'QL05p074214' => 'qlo', 'QL06p001050' => 'qlo', 'QL06p001056' => 'qlo', 'QL06p006093' => 'qlo', 'QL06p006111' => 'qlo', 'QL07p019784' => 'qlo', 'QL07p019801' => 'qlo', 'QL07p036110' => 'qlo', 'QL07p036134' => 'qlo', 'QL07p036147' => 'qlo', 'QL07p036156' => 'qlo', 'QL07p036300' => 'qlo', 'QL07p036320' => 'qlo', 'QL08p014547' => 'qlo', 'QL08p014551' => 'qlo', 'QL08p043319' => 'qlo', 'QL08p043324' => 'qlo', 'QL11p009094' => 'qlo', 'RcHm_v2.0_Chr1g0380481' => 'rch', 'RcHm_v2.0_Chr2g0089331' => 'rch', 'RcHm_v2.0_Chr2g0123691' => 'rch', 'RcHm_v2.0_Chr2g0151111' => 'rch', 'RcHm_v2.0_Chr2g0163011' => 'rch', 'RcHm_v2.0_Chr2g0163051' => 'rch', 'RcHm_v2.0_Chr2g0164671' => 'rch', 'RcHm_v2.0_Chr2g0164681' => 'rch', 'RcHm_v2.0_Chr2g0164721' => 'rch', 'RcHm_v2.0_Chr3g0449911' => 'rch', 'RcHm_v2.0_Chr3g0450211' => 'rch', 'RcHm_v2.0_Chr3g0457271' => 'rch', 'RcHm_v2.0_Chr5g0018111' => 'rch', 'RcHm_v2.0_Chr5g0021011' => 'rch', 'RcHm_v2.0_Chr5g0081171' => 'rch', 'RcHm_v2.0_Chr5g0081211' => 'rch', 'RcHm_v2.0_Chr6g0275871' => 'rch', 'RcHm_v2.0_Chr6g0276071' => 'rch', 'RcHm_v2.0_Chr6g0285591' => 'rch', 'RcHm_v2.0_Chr6g0291931' => 'rch', 'RcHm_v2.0_Chr6g0292091' => 'rch', 'RcHm_v2.0_Chr6g0292271' => 'rch', 'RcHm_v2.0_Chr7g0221261' => 'rch', 'Rhsim08G0219900' => 'rsi', 'Rhsim08G0220200' => 'rsi', 'Rhsim08G0237800' => 'rsi', 'Rhsim08G0238800' => 'rsi', 'Sabra09G0102700' => 'sbr', 'Sabra09G0127200' => 'sbr', 'Sabra11G0003700' => 'sbr', 'Sabra15G0014700' => 'sbr', 'Sc19g0000590' => 'sci', 'Sc19g0001870' => 'sci', 'SGA_v2.0_scaffold1G00346' => 'sas', 'SGA_v2.0_scaffold1G00575' => 'sas', 'SGA_v2.0_scaffold1G00761' => 'sas', 'SGA_v2.0_scaffold232G43501' => 'sas', 'TAR625G1137' => 'tar', 'Thecc.03G222100' => 'tca', 'TPR.G12691' => 'tpr', 'TWI34G0727' => 'twi', 'TWI36G0117' => 'twi', 'VMungo1309G0868' => 'vmu' ), 'gf_id' => 'HOM05D001729', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001729' ), 'data_identifier' => 'HOM05D001729', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001729', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '375', 'num_species' => '42' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'Ah.07g204710' => 'amhyb', 'AUR62006001' => 'cqu', 'AUR62006002' => 'cqu', 'AUR62006003' => 'cqu', 'AUR62015641' => 'cqu', 'AUR62027174' => 'cqu', 'AUR62035623' => 'cqu', 'AUR62035624' => 'cqu', 'AUR62035625' => 'cqu', 'AUR62035626' => 'cqu', 'CAN.G1110.53' => 'can', 'CANSAT80G0415' => 'cansat', 'Ca_21364_v3' => 'car', 'COL.COLO4_30693' => 'col', 'COL.COLO4_30694' => 'col', 'COL.COLO4_30695' => 'col', 'COL.COLO4_30696' => 'col', 'COL.COLO4_34020' => 'col', 'DCAR_004585' => 'dca', 'Dinv04029' => 'din', 'Dinv34857' => 'din', 'Duzib147G0011' => 'dzi', 'Duzib170G0599' => 'dzi', 'Duzib192G1051' => 'dzi', 'FAN01G0708' => 'fan', 'FAN01G0742' => 'fan', 'FAN02G0048' => 'fan', 'FAN02G0583' => 'fan', 'FAN02G0688' => 'fan', 'FAN02G1588' => 'fan', 'FAN02G2194' => 'fan', 'FAN02G2750' => 'fan', 'FAN02G3094' => 'fan', 'FAN02G3887' => 'fan', 'FAN02G3911' => 'fan', 'FAN02G3994' => 'fan', 'FAN02G4432' => 'fan', 'FAN02G4556' => 'fan', 'FAN03G1977' => 'fan', 'FAN03G2781' => 'fan', 'FAN03G2850' => 'fan', 'FAN03G3155' => 'fan', 'FAN04G2487' => 'fan', 'FAN05G0208' => 'fan', 'FAN05G0656' => 'fan', 'FAN05G0696' => 'fan', 'FAN05G0810' => 'fan', 'FAN05G1447' => 'fan', 'FAN05G2640' => 'fan', 'FAN05G2911' => 'fan', 'FAN05G3901' => 'fan', 'FAN05G4859' => 'fan', 'FAN05G4861' => 'fan', 'FAN05G4988' => 'fan', 'FAN05G5187' => 'fan', 'FAN05G5452' => 'fan', 'FAN05G5500' => 'fan', 'FAN05G5688' => 'fan', 'FAN06G0177' => 'fan', 'FAN06G0675' => 'fan', 'FAN06G1290' => 'fan', 'FAN06G2191' => 'fan', 'FAN06G2405' => 'fan', 'FAN06G3231' => 'fan', 'FAN06G3932' => 'fan', 'FAN07G0163' => 'fan', 'FAN07G0471' => 'fan', 'FAN07G1354' => 'fan', 'FAN08G0338' => 'fan', 'FAN08G1373' => 'fan', 'FAN08G2539' => 'fan', 'FAN08G2728' => 'fan', 'FAN09G0608' => 'fan', 'FAN09G1136' => 'fan', 'FAN09G1958' => 'fan', 'FAN09G2508' => 'fan', 'FAN09G2597' => 'fan', 'FAN09G2658' => 'fan', 'FAN09G2757' => 'fan', 'FAN09G2983' => 'fan', 'FAN09G3130' => 'fan', 'FAN09G3565' => 'fan', 'FAN09G3613' => 'fan', 'FAN09G4011' => 'fan', 'FAN09G4239' => 'fan', 'FAN09G4277' => 'fan', 'FAN09G4720' => 'fan', 'FAN11G0139' => 'fan', 'FAN11G1727' => 'fan', 'FAN11G2672' => 'fan', 'FAN11G2795' => 'fan', 'FAN11G3238' => 'fan', 'FAN11G3734' => 'fan', 'FAN12G0631' => 'fan', 'FAN12G2239' => 'fan', 'FAN12G2308' => 'fan', 'FAN12G2569' => 'fan', 'FAN12G2623' => 'fan', 'FAN13G3182' => 'fan', 'FAN14G0053' => 'fan', 'FAN14G0370' => 'fan', 'FAN14G0382' => 'fan', 'FAN14G0421' => 'fan', 'FAN14G0866' => 'fan', 'FAN14G1187' => 'fan', 'FAN14G1727' => 'fan', 'FAN14G1791' => 'fan', 'FAN14G2361' => 'fan', 'FAN14G2668' => 'fan', 'FAN14G2770' => 'fan', 'FAN14G2874' => 'fan', 'FAN14G3193' => 'fan', 'FAN14G3624' => 'fan', 'FAN14G3676' => 'fan', 'FAN14G3807' => 'fan', 'FAN14G4082' => 'fan', 'FAN14G4342' => 'fan', 'FAN14G4985' => 'fan', 'FAN14G5126' => 'fan', 'FAN14G5781' => 'fan', 'FAN14G5808' => 'fan', 'FAN14G5949' => 'fan', 'FAN15G0828' => 'fan', 'FAN15G1054' => 'fan', 'FAN15G2023' => 'fan', 'FAN15G2506' => 'fan', 'FAN16G0128' => 'fan', 'FAN16G0249' => 'fan', 'FAN16G0429' => 'fan', 'FAN16G1493' => 'fan', 'FAN16G2210' => 'fan', 'FAN16G2506' => 'fan', 'FAN18G1542' => 'fan', 'FAN18G4057' => 'fan', 'FAN19G0745' => 'fan', 'FAN19G1216' => 'fan', 'FAN19G1733' => 'fan', 'FAN20G0258' => 'fan', 'FAN20G1095' => 'fan', 'FAN20G1557' => 'fan', 'FAN21G0302' => 'fan', 'FAN21G0519' => 'fan', 'FAN21G0970' => 'fan', 'FAN21G1159' => 'fan', 'FAN21G1312' => 'fan', 'FAN21G1440' => 'fan', 'FAN21G1715' => 'fan', 'FAN23G1584' => 'fan', 'FAN24G0045' => 'fan', 'FAN24G0053' => 'fan', 'FAN24G1500' => 'fan', 'FAN24G1817' => 'fan', 'FAN24G2147' => 'fan', 'FAN24G2236' => 'fan', 'FAN24G2446' => 'fan', 'FAN24G2684' => 'fan', 'FAN25G0187' => 'fan', 'FAN25G0505' => 'fan', 'FAN25G0589' => 'fan', 'FAN25G3663' => 'fan', 'FAN26G1025' => 'fan', 'FAN26G2860' => 'fan', 'FAN27G1329' => 'fan', 'FAN27G3392' => 'fan', 'FvH4_1g02011' => 'fve', 'FvH4_1g06511' => 'fve', 'FvH4_2g19900' => 'fve', 'FvH4_2g19920' => 'fve', 'FvH4_2g24261' => 'fve', 'FvH4_2g24270' => 'fve', 'FvH4_2g24631' => 'fve', 'FvH4_2g30622' => 'fve', 'FvH4_3g12920' => 'fve', 'FvH4_3g30171' => 'fve', 'FvH4_3g35490' => 'fve', 'FvH4_3g43682' => 'fve', 'FvH4_3g43730' => 'fve', 'FvH4_3g43732' => 'fve', 'FvH4_3g43751' => 'fve', 'FvH4_3g43752' => 'fve', 'FvH4_3g43770' => 'fve', 'FvH4_3g44471' => 'fve', 'FvH4_3g44510' => 'fve', 'FvH4_3g44582' => 'fve', 'FvH4_4g16921' => 'fve', 'FvH4_4g17121' => 'fve', 'FvH4_4g17782' => 'fve', 'FvH4_4g17783' => 'fve', 'FvH4_4g18120' => 'fve', 'FvH4_4g31310' => 'fve', 'FvH4_4g35052' => 'fve', 'FvH4_5g30862' => 'fve', 'FvH4_6g01541' => 'fve', 'FvH4_6g02021' => 'fve', 'FvH4_6g02041' => 'fve', 'FvH4_6g02071' => 'fve', 'FvH4_6g02171' => 'fve', 'FvH4_6g03181' => 'fve', 'FvH4_6g03182' => 'fve', 'FvH4_6g03221' => 'fve', 'FvH4_6g03380' => 'fve', 'FvH4_6g05201' => 'fve', 'FvH4_6g05203' => 'fve', 'FvH4_6g20231' => 'fve', 'FvH4_6g31981' => 'fve', 'FvH4_6g32061' => 'fve', 'FvH4_6g37041' => 'fve', 'FvH4_6g37932' => 'fve', 'FvH4_6g38731' => 'fve', 'FvH4_6g39370' => 'fve', 'FvH4_6g39371' => 'fve', 'FvH4_6g40891' => 'fve', 'FvH4_6g40892' => 'fve', 'FvH4_6g43143' => 'fve', 'FvH4_6g45251' => 'fve', 'FvH4_6g45260' => 'fve', 'FvH4_6g45291' => 'fve', 'FvH4_6g45890' => 'fve', 'FvH4_6g46240' => 'fve', 'FvH4_6g46241' => 'fve', 'FvH4_6g46242' => 'fve', 'FvH4_6g46260' => 'fve', 'FvH4_6g46280' => 'fve', 'FvH4_6g46380' => 'fve', 'FvH4_7g12841' => 'fve', 'FvH4_7g31431' => 'fve', 'Glyma.09G075900' => 'gma', 'Gohir.A09G096401' => 'ghi', 'Gohir.D09G096101' => 'ghi', 'Gorai.006G112800' => 'gra', 'HanXRQChr04g0121411' => 'han', 'Hund15878' => 'sun', 'Lj2A1107G68' => 'lonja', 'Lj2A630G63' => 'lonja', 'Lj2A946T25' => 'lonja', 'Lj2C714T1' => 'lonja', 'Lj2C966T3' => 'lonja', 'Lj2C966T4' => 'lonja', 'Lj4g0002979' => 'lja', 'Lsat_1_v5_gn_5_30901' => 'lsa', 'Lsat_1_v5_gn_5_31100' => 'lsa', 'Lsat_1_v5_gn_5_38600' => 'lsa', 'Lsat_1_v5_gn_6_92061' => 'lsa', 'Manes.05G071301' => 'mes', 'MD02G1008700' => 'mdo', 'MD02G1008900' => 'mdo', 'MD03G1256400' => 'mdo', 'MD04G1180900' => 'mdo', 'MD04G1181000' => 'mdo', 'MD04G1181200' => 'mdo', 'MD05G1244200' => 'mdo', 'MD05G1324200' => 'mdo', 'MD09G1201600' => 'mdo', 'MD10G1000600' => 'mdo', 'MD14G1026900' => 'mdo', 'MD14G1187900' => 'mdo', 'MD15G1017800' => 'mdo', 'MD15G1018100' => 'mdo', 'Medtr4g124160' => 'mtr', 'Migut.L01260' => 'egut', 'Nitab4.5_0000008g0440' => 'nta', 'Nitab4.5_0000207g0170' => 'nta', 'Nitab4.5_0007671g0030' => 'nta', 'Nitab4.5_0010853g0020' => 'nta', 'Oeu057656.1' => 'oeu', 'PGSC0003DMG400005638' => 'stu', 'PGSC0003DMG400005639' => 'stu', 'Phvul.009G222800' => 'pvu', 'Potri.009G132400' => 'ptr', 'Potri.009G163001' => 'ptr', 'Potri.011G000700' => 'ptr', 'Potri.011G004800' => 'ptr', 'Prupe.1G509300' => 'ppe', 'Prupe.1G509700' => 'ppe', 'Prupe.1G510400' => 'ppe', 'Prupe.1G510700' => 'ppe', 'Prupe.1G512600' => 'ppe', 'Prupe.2G073200' => 'ppe', 'Prupe.3G059500' => 'ppe', 'Prupe.3G059600' => 'ppe', 'Prupe.3G246100' => 'ppe', 'Prupe.3G265100' => 'ppe', 'Prupe.4G034700' => 'ppe', 'Prupe.4G052100' => 'ppe', 'Prupe.4G053600' => 'ppe', 'Prupe.5G068800' => 'ppe', 'Prupe.5G070600' => 'ppe', 'Prupe.6G075400' => 'ppe', 'Prupe.6G075500' => 'ppe', 'Prupe.6G076400' => 'ppe', 'Prupe.8G110700' => 'ppe', 'Psat4g020960' => 'psa', 'PSO135G0788' => 'pso', 'PSO210G6463' => 'pso', 'PSO384G0370' => 'pso', 'PSO386G0056' => 'pso', 'QL01p006048' => 'qlo', 'QL02p054283' => 'qlo', 'QL05p008000' => 'qlo', 'QL05p008212' => 'qlo', 'QL05p008950' => 'qlo', 'QL05p009042' => 'qlo', 'QL05p009518' => 'qlo', 'QL05p012589' => 'qlo', 'QL05p012608' => 'qlo', 'QL05p012650' => 'qlo', 'QL05p012667' => 'qlo', 'QL05p014501' => 'qlo', 'QL05p052800' => 'qlo', 'QL05p065010' => 'qlo', 'QL05p074156' => 'qlo', 'QL05p074160' => 'qlo', 'QL05p074174' => 'qlo', 'QL05p074178' => 'qlo', 'QL05p074214' => 'qlo', 'QL06p001050' => 'qlo', 'QL06p001056' => 'qlo', 'QL06p006093' => 'qlo', 'QL06p006111' => 'qlo', 'QL07p019784' => 'qlo', 'QL07p019801' => 'qlo', 'QL07p036110' => 'qlo', 'QL07p036134' => 'qlo', 'QL07p036147' => 'qlo', 'QL07p036156' => 'qlo', 'QL07p036300' => 'qlo', 'QL07p036320' => 'qlo', 'QL08p014547' => 'qlo', 'QL08p014551' => 'qlo', 'QL08p043319' => 'qlo', 'QL08p043324' => 'qlo', 'QL11p009094' => 'qlo', 'RcHm_v2.0_Chr1g0380481' => 'rch', 'RcHm_v2.0_Chr2g0089331' => 'rch', 'RcHm_v2.0_Chr2g0123691' => 'rch', 'RcHm_v2.0_Chr2g0151111' => 'rch', 'RcHm_v2.0_Chr2g0163011' => 'rch', 'RcHm_v2.0_Chr2g0163051' => 'rch', 'RcHm_v2.0_Chr2g0164671' => 'rch', 'RcHm_v2.0_Chr2g0164681' => 'rch', 'RcHm_v2.0_Chr2g0164721' => 'rch', 'RcHm_v2.0_Chr3g0449911' => 'rch', 'RcHm_v2.0_Chr3g0450211' => 'rch', 'RcHm_v2.0_Chr3g0457271' => 'rch', 'RcHm_v2.0_Chr5g0018111' => 'rch', 'RcHm_v2.0_Chr5g0021011' => 'rch', 'RcHm_v2.0_Chr5g0081171' => 'rch', 'RcHm_v2.0_Chr5g0081211' => 'rch', 'RcHm_v2.0_Chr6g0275871' => 'rch', 'RcHm_v2.0_Chr6g0276071' => 'rch', 'RcHm_v2.0_Chr6g0285591' => 'rch', 'RcHm_v2.0_Chr6g0291931' => 'rch', 'RcHm_v2.0_Chr6g0292091' => 'rch', 'RcHm_v2.0_Chr6g0292271' => 'rch', 'RcHm_v2.0_Chr7g0221261' => 'rch', 'Rhsim08G0219900' => 'rsi', 'Rhsim08G0220200' => 'rsi', 'Rhsim08G0237800' => 'rsi', 'Rhsim08G0238800' => 'rsi', 'Sabra09G0102700' => 'sbr', 'Sabra09G0127200' => 'sbr', 'Sabra11G0003700' => 'sbr', 'Sabra15G0014700' => 'sbr', 'Sc19g0000590' => 'sci', 'Sc19g0001870' => 'sci', 'SGA_v2.0_scaffold1G00346' => 'sas', 'SGA_v2.0_scaffold1G00575' => 'sas', 'SGA_v2.0_scaffold1G00761' => 'sas', 'SGA_v2.0_scaffold232G43501' => 'sas', 'TAR625G1137' => 'tar', 'Thecc.03G222100' => 'tca', 'TPR.G12691' => 'tpr', 'TWI34G0727' => 'twi', 'TWI36G0117' => 'twi', 'VMungo1309G0868' => 'vmu' ) $gf_id = 'HOM05D001729' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001729' ) $data_identifier = 'HOM05D001729' $data_type = 'gf_id' $species_gene_counts = array( 'amhyb' => (int) 1, 'cqu' => (int) 9, 'can' => (int) 1, 'cansat' => (int) 1, 'car' => (int) 1, 'col' => (int) 5, 'dca' => (int) 1, 'din' => (int) 2, 'dzi' => (int) 3, 'fan' => (int) 140, 'fve' => (int) 62, 'gma' => (int) 1, 'ghi' => (int) 2, 'gra' => (int) 1, 'han' => (int) 1, 'sun' => (int) 1, 'lonja' => (int) 6, 'lja' => (int) 1, 'lsa' => (int) 4, 'mes' => (int) 1, 'mdo' => (int) 14, 'mtr' => (int) 1, 'egut' => (int) 1, 'nta' => (int) 4, 'oeu' => (int) 1, 'stu' => (int) 2, 'pvu' => (int) 1, 'ptr' => (int) 4, 'ppe' => (int) 19, 'psa' => (int) 1, 'pso' => (int) 4, 'qlo' => (int) 36, 'rch' => (int) 23, 'rsi' => (int) 4, 'sbr' => (int) 4, 'sci' => (int) 2, 'sas' => (int) 4, 'tar' => (int) 1, 'tca' => (int) 1, 'tpr' => (int) 1, 'twi' => (int) 2, 'vmu' => (int) 1 ) $gf_gene_species = 'vmu' $gf_gene_id = 'VMungo1309G0868' $species_info = array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ) $local_species = 'din' $disabled = '' $selected = '' $num_hits = (int) 1include - APP/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp, line 33 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933 View::_renderElement() - CORE/Cake/View/View.php, line 1224 View::element() - CORE/Cake/View/View.php, line 418 include - APP/View/Elements/analysis/phylogenetics_module/gf_data_settings.ctp, line 37 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933 View::_renderElement() - CORE/Cake/View/View.php, line 1224 View::element() - CORE/Cake/View/View.php, line 418 include - APP/View/Elements/analysis/phylogenetics_module/parameter_selection.ctp, line 64 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933 View::_renderElement() - CORE/Cake/View/View.php, line 1224 View::element() - CORE/Cake/View/View.php, line 418 include - APP/View/Analysis/custom_tree_creation.ctp, line 27 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933
$viewFile = '/www/bioinformatics01_ro/plaza/_dev_instances/feedback/app/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp' $dataForView = array( 'sidebar_info' => array( 'gf_id' => 'HOM05D001729', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '375', 'num_species' => '42' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'Ah.07g204710' => 'amhyb', 'AUR62006001' => 'cqu', 'AUR62006002' => 'cqu', 'AUR62006003' => 'cqu', 'AUR62015641' => 'cqu', 'AUR62027174' => 'cqu', 'AUR62035623' => 'cqu', 'AUR62035624' => 'cqu', 'AUR62035625' => 'cqu', 'AUR62035626' => 'cqu', 'CAN.G1110.53' => 'can', 'CANSAT80G0415' => 'cansat', 'Ca_21364_v3' => 'car', 'COL.COLO4_30693' => 'col', 'COL.COLO4_30694' => 'col', 'COL.COLO4_30695' => 'col', 'COL.COLO4_30696' => 'col', 'COL.COLO4_34020' => 'col', 'DCAR_004585' => 'dca', 'Dinv04029' => 'din', 'Dinv34857' => 'din', 'Duzib147G0011' => 'dzi', 'Duzib170G0599' => 'dzi', 'Duzib192G1051' => 'dzi', 'FAN01G0708' => 'fan', 'FAN01G0742' => 'fan', 'FAN02G0048' => 'fan', 'FAN02G0583' => 'fan', 'FAN02G0688' => 'fan', 'FAN02G1588' => 'fan', 'FAN02G2194' => 'fan', 'FAN02G2750' => 'fan', 'FAN02G3094' => 'fan', 'FAN02G3887' => 'fan', 'FAN02G3911' => 'fan', 'FAN02G3994' => 'fan', 'FAN02G4432' => 'fan', 'FAN02G4556' => 'fan', 'FAN03G1977' => 'fan', 'FAN03G2781' => 'fan', 'FAN03G2850' => 'fan', 'FAN03G3155' => 'fan', 'FAN04G2487' => 'fan', 'FAN05G0208' => 'fan', 'FAN05G0656' => 'fan', 'FAN05G0696' => 'fan', 'FAN05G0810' => 'fan', 'FAN05G1447' => 'fan', 'FAN05G2640' => 'fan', 'FAN05G2911' => 'fan', 'FAN05G3901' => 'fan', 'FAN05G4859' => 'fan', 'FAN05G4861' => 'fan', 'FAN05G4988' => 'fan', 'FAN05G5187' => 'fan', 'FAN05G5452' => 'fan', 'FAN05G5500' => 'fan', 'FAN05G5688' => 'fan', 'FAN06G0177' => 'fan', 'FAN06G0675' => 'fan', 'FAN06G1290' => 'fan', 'FAN06G2191' => 'fan', 'FAN06G2405' => 'fan', 'FAN06G3231' => 'fan', 'FAN06G3932' => 'fan', 'FAN07G0163' => 'fan', 'FAN07G0471' => 'fan', 'FAN07G1354' => 'fan', 'FAN08G0338' => 'fan', 'FAN08G1373' => 'fan', 'FAN08G2539' => 'fan', 'FAN08G2728' => 'fan', 'FAN09G0608' => 'fan', 'FAN09G1136' => 'fan', 'FAN09G1958' => 'fan', 'FAN09G2508' => 'fan', 'FAN09G2597' => 'fan', 'FAN09G2658' => 'fan', 'FAN09G2757' => 'fan', 'FAN09G2983' => 'fan', 'FAN09G3130' => 'fan', 'FAN09G3565' => 'fan', 'FAN09G3613' => 'fan', 'FAN09G4011' => 'fan', 'FAN09G4239' => 'fan', 'FAN09G4277' => 'fan', 'FAN09G4720' => 'fan', 'FAN11G0139' => 'fan', 'FAN11G1727' => 'fan', 'FAN11G2672' => 'fan', 'FAN11G2795' => 'fan', 'FAN11G3238' => 'fan', 'FAN11G3734' => 'fan', 'FAN12G0631' => 'fan', 'FAN12G2239' => 'fan', 'FAN12G2308' => 'fan', 'FAN12G2569' => 'fan', 'FAN12G2623' => 'fan', 'FAN13G3182' => 'fan', 'FAN14G0053' => 'fan', 'FAN14G0370' => 'fan', 'FAN14G0382' => 'fan', 'FAN14G0421' => 'fan', 'FAN14G0866' => 'fan', 'FAN14G1187' => 'fan', 'FAN14G1727' => 'fan', 'FAN14G1791' => 'fan', 'FAN14G2361' => 'fan', 'FAN14G2668' => 'fan', 'FAN14G2770' => 'fan', 'FAN14G2874' => 'fan', 'FAN14G3193' => 'fan', 'FAN14G3624' => 'fan', 'FAN14G3676' => 'fan', 'FAN14G3807' => 'fan', 'FAN14G4082' => 'fan', 'FAN14G4342' => 'fan', 'FAN14G4985' => 'fan', 'FAN14G5126' => 'fan', 'FAN14G5781' => 'fan', 'FAN14G5808' => 'fan', 'FAN14G5949' => 'fan', 'FAN15G0828' => 'fan', 'FAN15G1054' => 'fan', 'FAN15G2023' => 'fan', 'FAN15G2506' => 'fan', 'FAN16G0128' => 'fan', 'FAN16G0249' => 'fan', 'FAN16G0429' => 'fan', 'FAN16G1493' => 'fan', 'FAN16G2210' => 'fan', 'FAN16G2506' => 'fan', 'FAN18G1542' => 'fan', 'FAN18G4057' => 'fan', 'FAN19G0745' => 'fan', 'FAN19G1216' => 'fan', 'FAN19G1733' => 'fan', 'FAN20G0258' => 'fan', 'FAN20G1095' => 'fan', 'FAN20G1557' => 'fan', 'FAN21G0302' => 'fan', 'FAN21G0519' => 'fan', 'FAN21G0970' => 'fan', 'FAN21G1159' => 'fan', 'FAN21G1312' => 'fan', 'FAN21G1440' => 'fan', 'FAN21G1715' => 'fan', 'FAN23G1584' => 'fan', 'FAN24G0045' => 'fan', 'FAN24G0053' => 'fan', 'FAN24G1500' => 'fan', 'FAN24G1817' => 'fan', 'FAN24G2147' => 'fan', 'FAN24G2236' => 'fan', 'FAN24G2446' => 'fan', 'FAN24G2684' => 'fan', 'FAN25G0187' => 'fan', 'FAN25G0505' => 'fan', 'FAN25G0589' => 'fan', 'FAN25G3663' => 'fan', 'FAN26G1025' => 'fan', 'FAN26G2860' => 'fan', 'FAN27G1329' => 'fan', 'FAN27G3392' => 'fan', 'FvH4_1g02011' => 'fve', 'FvH4_1g06511' => 'fve', 'FvH4_2g19900' => 'fve', 'FvH4_2g19920' => 'fve', 'FvH4_2g24261' => 'fve', 'FvH4_2g24270' => 'fve', 'FvH4_2g24631' => 'fve', 'FvH4_2g30622' => 'fve', 'FvH4_3g12920' => 'fve', 'FvH4_3g30171' => 'fve', 'FvH4_3g35490' => 'fve', 'FvH4_3g43682' => 'fve', 'FvH4_3g43730' => 'fve', 'FvH4_3g43732' => 'fve', 'FvH4_3g43751' => 'fve', 'FvH4_3g43752' => 'fve', 'FvH4_3g43770' => 'fve', 'FvH4_3g44471' => 'fve', 'FvH4_3g44510' => 'fve', 'FvH4_3g44582' => 'fve', 'FvH4_4g16921' => 'fve', 'FvH4_4g17121' => 'fve', 'FvH4_4g17782' => 'fve', 'FvH4_4g17783' => 'fve', 'FvH4_4g18120' => 'fve', 'FvH4_4g31310' => 'fve', 'FvH4_4g35052' => 'fve', 'FvH4_5g30862' => 'fve', 'FvH4_6g01541' => 'fve', 'FvH4_6g02021' => 'fve', 'FvH4_6g02041' => 'fve', 'FvH4_6g02071' => 'fve', 'FvH4_6g02171' => 'fve', 'FvH4_6g03181' => 'fve', 'FvH4_6g03182' => 'fve', 'FvH4_6g03221' => 'fve', 'FvH4_6g03380' => 'fve', 'FvH4_6g05201' => 'fve', 'FvH4_6g05203' => 'fve', 'FvH4_6g20231' => 'fve', 'FvH4_6g31981' => 'fve', 'FvH4_6g32061' => 'fve', 'FvH4_6g37041' => 'fve', 'FvH4_6g37932' => 'fve', 'FvH4_6g38731' => 'fve', 'FvH4_6g39370' => 'fve', 'FvH4_6g39371' => 'fve', 'FvH4_6g40891' => 'fve', 'FvH4_6g40892' => 'fve', 'FvH4_6g43143' => 'fve', 'FvH4_6g45251' => 'fve', 'FvH4_6g45260' => 'fve', 'FvH4_6g45291' => 'fve', 'FvH4_6g45890' => 'fve', 'FvH4_6g46240' => 'fve', 'FvH4_6g46241' => 'fve', 'FvH4_6g46242' => 'fve', 'FvH4_6g46260' => 'fve', 'FvH4_6g46280' => 'fve', 'FvH4_6g46380' => 'fve', 'FvH4_7g12841' => 'fve', 'FvH4_7g31431' => 'fve', 'Glyma.09G075900' => 'gma', 'Gohir.A09G096401' => 'ghi', 'Gohir.D09G096101' => 'ghi', 'Gorai.006G112800' => 'gra', 'HanXRQChr04g0121411' => 'han', 'Hund15878' => 'sun', 'Lj2A1107G68' => 'lonja', 'Lj2A630G63' => 'lonja', 'Lj2A946T25' => 'lonja', 'Lj2C714T1' => 'lonja', 'Lj2C966T3' => 'lonja', 'Lj2C966T4' => 'lonja', 'Lj4g0002979' => 'lja', 'Lsat_1_v5_gn_5_30901' => 'lsa', 'Lsat_1_v5_gn_5_31100' => 'lsa', 'Lsat_1_v5_gn_5_38600' => 'lsa', 'Lsat_1_v5_gn_6_92061' => 'lsa', 'Manes.05G071301' => 'mes', 'MD02G1008700' => 'mdo', 'MD02G1008900' => 'mdo', 'MD03G1256400' => 'mdo', 'MD04G1180900' => 'mdo', 'MD04G1181000' => 'mdo', 'MD04G1181200' => 'mdo', 'MD05G1244200' => 'mdo', 'MD05G1324200' => 'mdo', 'MD09G1201600' => 'mdo', 'MD10G1000600' => 'mdo', 'MD14G1026900' => 'mdo', 'MD14G1187900' => 'mdo', 'MD15G1017800' => 'mdo', 'MD15G1018100' => 'mdo', 'Medtr4g124160' => 'mtr', 'Migut.L01260' => 'egut', 'Nitab4.5_0000008g0440' => 'nta', 'Nitab4.5_0000207g0170' => 'nta', 'Nitab4.5_0007671g0030' => 'nta', 'Nitab4.5_0010853g0020' => 'nta', 'Oeu057656.1' => 'oeu', 'PGSC0003DMG400005638' => 'stu', 'PGSC0003DMG400005639' => 'stu', 'Phvul.009G222800' => 'pvu', 'Potri.009G132400' => 'ptr', 'Potri.009G163001' => 'ptr', 'Potri.011G000700' => 'ptr', 'Potri.011G004800' => 'ptr', 'Prupe.1G509300' => 'ppe', 'Prupe.1G509700' => 'ppe', 'Prupe.1G510400' => 'ppe', 'Prupe.1G510700' => 'ppe', 'Prupe.1G512600' => 'ppe', 'Prupe.2G073200' => 'ppe', 'Prupe.3G059500' => 'ppe', 'Prupe.3G059600' => 'ppe', 'Prupe.3G246100' => 'ppe', 'Prupe.3G265100' => 'ppe', 'Prupe.4G034700' => 'ppe', 'Prupe.4G052100' => 'ppe', 'Prupe.4G053600' => 'ppe', 'Prupe.5G068800' => 'ppe', 'Prupe.5G070600' => 'ppe', 'Prupe.6G075400' => 'ppe', 'Prupe.6G075500' => 'ppe', 'Prupe.6G076400' => 'ppe', 'Prupe.8G110700' => 'ppe', 'Psat4g020960' => 'psa', 'PSO135G0788' => 'pso', 'PSO210G6463' => 'pso', 'PSO384G0370' => 'pso', 'PSO386G0056' => 'pso', 'QL01p006048' => 'qlo', 'QL02p054283' => 'qlo', 'QL05p008000' => 'qlo', 'QL05p008212' => 'qlo', 'QL05p008950' => 'qlo', 'QL05p009042' => 'qlo', 'QL05p009518' => 'qlo', 'QL05p012589' => 'qlo', 'QL05p012608' => 'qlo', 'QL05p012650' => 'qlo', 'QL05p012667' => 'qlo', 'QL05p014501' => 'qlo', 'QL05p052800' => 'qlo', 'QL05p065010' => 'qlo', 'QL05p074156' => 'qlo', 'QL05p074160' => 'qlo', 'QL05p074174' => 'qlo', 'QL05p074178' => 'qlo', 'QL05p074214' => 'qlo', 'QL06p001050' => 'qlo', 'QL06p001056' => 'qlo', 'QL06p006093' => 'qlo', 'QL06p006111' => 'qlo', 'QL07p019784' => 'qlo', 'QL07p019801' => 'qlo', 'QL07p036110' => 'qlo', 'QL07p036134' => 'qlo', 'QL07p036147' => 'qlo', 'QL07p036156' => 'qlo', 'QL07p036300' => 'qlo', 'QL07p036320' => 'qlo', 'QL08p014547' => 'qlo', 'QL08p014551' => 'qlo', 'QL08p043319' => 'qlo', 'QL08p043324' => 'qlo', 'QL11p009094' => 'qlo', 'RcHm_v2.0_Chr1g0380481' => 'rch', 'RcHm_v2.0_Chr2g0089331' => 'rch', 'RcHm_v2.0_Chr2g0123691' => 'rch', 'RcHm_v2.0_Chr2g0151111' => 'rch', 'RcHm_v2.0_Chr2g0163011' => 'rch', 'RcHm_v2.0_Chr2g0163051' => 'rch', 'RcHm_v2.0_Chr2g0164671' => 'rch', 'RcHm_v2.0_Chr2g0164681' => 'rch', 'RcHm_v2.0_Chr2g0164721' => 'rch', 'RcHm_v2.0_Chr3g0449911' => 'rch', 'RcHm_v2.0_Chr3g0450211' => 'rch', 'RcHm_v2.0_Chr3g0457271' => 'rch', 'RcHm_v2.0_Chr5g0018111' => 'rch', 'RcHm_v2.0_Chr5g0021011' => 'rch', 'RcHm_v2.0_Chr5g0081171' => 'rch', 'RcHm_v2.0_Chr5g0081211' => 'rch', 'RcHm_v2.0_Chr6g0275871' => 'rch', 'RcHm_v2.0_Chr6g0276071' => 'rch', 'RcHm_v2.0_Chr6g0285591' => 'rch', 'RcHm_v2.0_Chr6g0291931' => 'rch', 'RcHm_v2.0_Chr6g0292091' => 'rch', 'RcHm_v2.0_Chr6g0292271' => 'rch', 'RcHm_v2.0_Chr7g0221261' => 'rch', 'Rhsim08G0219900' => 'rsi', 'Rhsim08G0220200' => 'rsi', 'Rhsim08G0237800' => 'rsi', 'Rhsim08G0238800' => 'rsi', 'Sabra09G0102700' => 'sbr', 'Sabra09G0127200' => 'sbr', 'Sabra11G0003700' => 'sbr', 'Sabra15G0014700' => 'sbr', 'Sc19g0000590' => 'sci', 'Sc19g0001870' => 'sci', 'SGA_v2.0_scaffold1G00346' => 'sas', 'SGA_v2.0_scaffold1G00575' => 'sas', 'SGA_v2.0_scaffold1G00761' => 'sas', 'SGA_v2.0_scaffold232G43501' => 'sas', 'TAR625G1137' => 'tar', 'Thecc.03G222100' => 'tca', 'TPR.G12691' => 'tpr', 'TWI34G0727' => 'twi', 'TWI36G0117' => 'twi', 'VMungo1309G0868' => 'vmu' ), 'gf_id' => 'HOM05D001729', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001729' ), 'data_identifier' => 'HOM05D001729', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001729', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '375', 'num_species' => '42' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'Ah.07g204710' => 'amhyb', 'AUR62006001' => 'cqu', 'AUR62006002' => 'cqu', 'AUR62006003' => 'cqu', 'AUR62015641' => 'cqu', 'AUR62027174' => 'cqu', 'AUR62035623' => 'cqu', 'AUR62035624' => 'cqu', 'AUR62035625' => 'cqu', 'AUR62035626' => 'cqu', 'CAN.G1110.53' => 'can', 'CANSAT80G0415' => 'cansat', 'Ca_21364_v3' => 'car', 'COL.COLO4_30693' => 'col', 'COL.COLO4_30694' => 'col', 'COL.COLO4_30695' => 'col', 'COL.COLO4_30696' => 'col', 'COL.COLO4_34020' => 'col', 'DCAR_004585' => 'dca', 'Dinv04029' => 'din', 'Dinv34857' => 'din', 'Duzib147G0011' => 'dzi', 'Duzib170G0599' => 'dzi', 'Duzib192G1051' => 'dzi', 'FAN01G0708' => 'fan', 'FAN01G0742' => 'fan', 'FAN02G0048' => 'fan', 'FAN02G0583' => 'fan', 'FAN02G0688' => 'fan', 'FAN02G1588' => 'fan', 'FAN02G2194' => 'fan', 'FAN02G2750' => 'fan', 'FAN02G3094' => 'fan', 'FAN02G3887' => 'fan', 'FAN02G3911' => 'fan', 'FAN02G3994' => 'fan', 'FAN02G4432' => 'fan', 'FAN02G4556' => 'fan', 'FAN03G1977' => 'fan', 'FAN03G2781' => 'fan', 'FAN03G2850' => 'fan', 'FAN03G3155' => 'fan', 'FAN04G2487' => 'fan', 'FAN05G0208' => 'fan', 'FAN05G0656' => 'fan', 'FAN05G0696' => 'fan', 'FAN05G0810' => 'fan', 'FAN05G1447' => 'fan', 'FAN05G2640' => 'fan', 'FAN05G2911' => 'fan', 'FAN05G3901' => 'fan', 'FAN05G4859' => 'fan', 'FAN05G4861' => 'fan', 'FAN05G4988' => 'fan', 'FAN05G5187' => 'fan', 'FAN05G5452' => 'fan', 'FAN05G5500' => 'fan', 'FAN05G5688' => 'fan', 'FAN06G0177' => 'fan', 'FAN06G0675' => 'fan', 'FAN06G1290' => 'fan', 'FAN06G2191' => 'fan', 'FAN06G2405' => 'fan', 'FAN06G3231' => 'fan', 'FAN06G3932' => 'fan', 'FAN07G0163' => 'fan', 'FAN07G0471' => 'fan', 'FAN07G1354' => 'fan', 'FAN08G0338' => 'fan', 'FAN08G1373' => 'fan', 'FAN08G2539' => 'fan', 'FAN08G2728' => 'fan', 'FAN09G0608' => 'fan', 'FAN09G1136' => 'fan', 'FAN09G1958' => 'fan', 'FAN09G2508' => 'fan', 'FAN09G2597' => 'fan', 'FAN09G2658' => 'fan', 'FAN09G2757' => 'fan', 'FAN09G2983' => 'fan', 'FAN09G3130' => 'fan', 'FAN09G3565' => 'fan', 'FAN09G3613' => 'fan', 'FAN09G4011' => 'fan', 'FAN09G4239' => 'fan', 'FAN09G4277' => 'fan', 'FAN09G4720' => 'fan', 'FAN11G0139' => 'fan', 'FAN11G1727' => 'fan', 'FAN11G2672' => 'fan', 'FAN11G2795' => 'fan', 'FAN11G3238' => 'fan', 'FAN11G3734' => 'fan', 'FAN12G0631' => 'fan', 'FAN12G2239' => 'fan', 'FAN12G2308' => 'fan', 'FAN12G2569' => 'fan', 'FAN12G2623' => 'fan', 'FAN13G3182' => 'fan', 'FAN14G0053' => 'fan', 'FAN14G0370' => 'fan', 'FAN14G0382' => 'fan', 'FAN14G0421' => 'fan', 'FAN14G0866' => 'fan', 'FAN14G1187' => 'fan', 'FAN14G1727' => 'fan', 'FAN14G1791' => 'fan', 'FAN14G2361' => 'fan', 'FAN14G2668' => 'fan', 'FAN14G2770' => 'fan', 'FAN14G2874' => 'fan', 'FAN14G3193' => 'fan', 'FAN14G3624' => 'fan', 'FAN14G3676' => 'fan', 'FAN14G3807' => 'fan', 'FAN14G4082' => 'fan', 'FAN14G4342' => 'fan', 'FAN14G4985' => 'fan', 'FAN14G5126' => 'fan', 'FAN14G5781' => 'fan', 'FAN14G5808' => 'fan', 'FAN14G5949' => 'fan', 'FAN15G0828' => 'fan', 'FAN15G1054' => 'fan', 'FAN15G2023' => 'fan', 'FAN15G2506' => 'fan', 'FAN16G0128' => 'fan', 'FAN16G0249' => 'fan', 'FAN16G0429' => 'fan', 'FAN16G1493' => 'fan', 'FAN16G2210' => 'fan', 'FAN16G2506' => 'fan', 'FAN18G1542' => 'fan', 'FAN18G4057' => 'fan', 'FAN19G0745' => 'fan', 'FAN19G1216' => 'fan', 'FAN19G1733' => 'fan', 'FAN20G0258' => 'fan', 'FAN20G1095' => 'fan', 'FAN20G1557' => 'fan', 'FAN21G0302' => 'fan', 'FAN21G0519' => 'fan', 'FAN21G0970' => 'fan', 'FAN21G1159' => 'fan', 'FAN21G1312' => 'fan', 'FAN21G1440' => 'fan', 'FAN21G1715' => 'fan', 'FAN23G1584' => 'fan', 'FAN24G0045' => 'fan', 'FAN24G0053' => 'fan', 'FAN24G1500' => 'fan', 'FAN24G1817' => 'fan', 'FAN24G2147' => 'fan', 'FAN24G2236' => 'fan', 'FAN24G2446' => 'fan', 'FAN24G2684' => 'fan', 'FAN25G0187' => 'fan', 'FAN25G0505' => 'fan', 'FAN25G0589' => 'fan', 'FAN25G3663' => 'fan', 'FAN26G1025' => 'fan', 'FAN26G2860' => 'fan', 'FAN27G1329' => 'fan', 'FAN27G3392' => 'fan', 'FvH4_1g02011' => 'fve', 'FvH4_1g06511' => 'fve', 'FvH4_2g19900' => 'fve', 'FvH4_2g19920' => 'fve', 'FvH4_2g24261' => 'fve', 'FvH4_2g24270' => 'fve', 'FvH4_2g24631' => 'fve', 'FvH4_2g30622' => 'fve', 'FvH4_3g12920' => 'fve', 'FvH4_3g30171' => 'fve', 'FvH4_3g35490' => 'fve', 'FvH4_3g43682' => 'fve', 'FvH4_3g43730' => 'fve', 'FvH4_3g43732' => 'fve', 'FvH4_3g43751' => 'fve', 'FvH4_3g43752' => 'fve', 'FvH4_3g43770' => 'fve', 'FvH4_3g44471' => 'fve', 'FvH4_3g44510' => 'fve', 'FvH4_3g44582' => 'fve', 'FvH4_4g16921' => 'fve', 'FvH4_4g17121' => 'fve', 'FvH4_4g17782' => 'fve', 'FvH4_4g17783' => 'fve', 'FvH4_4g18120' => 'fve', 'FvH4_4g31310' => 'fve', 'FvH4_4g35052' => 'fve', 'FvH4_5g30862' => 'fve', 'FvH4_6g01541' => 'fve', 'FvH4_6g02021' => 'fve', 'FvH4_6g02041' => 'fve', 'FvH4_6g02071' => 'fve', 'FvH4_6g02171' => 'fve', 'FvH4_6g03181' => 'fve', 'FvH4_6g03182' => 'fve', 'FvH4_6g03221' => 'fve', 'FvH4_6g03380' => 'fve', 'FvH4_6g05201' => 'fve', 'FvH4_6g05203' => 'fve', 'FvH4_6g20231' => 'fve', 'FvH4_6g31981' => 'fve', 'FvH4_6g32061' => 'fve', 'FvH4_6g37041' => 'fve', 'FvH4_6g37932' => 'fve', 'FvH4_6g38731' => 'fve', 'FvH4_6g39370' => 'fve', 'FvH4_6g39371' => 'fve', 'FvH4_6g40891' => 'fve', 'FvH4_6g40892' => 'fve', 'FvH4_6g43143' => 'fve', 'FvH4_6g45251' => 'fve', 'FvH4_6g45260' => 'fve', 'FvH4_6g45291' => 'fve', 'FvH4_6g45890' => 'fve', 'FvH4_6g46240' => 'fve', 'FvH4_6g46241' => 'fve', 'FvH4_6g46242' => 'fve', 'FvH4_6g46260' => 'fve', 'FvH4_6g46280' => 'fve', 'FvH4_6g46380' => 'fve', 'FvH4_7g12841' => 'fve', 'FvH4_7g31431' => 'fve', 'Glyma.09G075900' => 'gma', 'Gohir.A09G096401' => 'ghi', 'Gohir.D09G096101' => 'ghi', 'Gorai.006G112800' => 'gra', 'HanXRQChr04g0121411' => 'han', 'Hund15878' => 'sun', 'Lj2A1107G68' => 'lonja', 'Lj2A630G63' => 'lonja', 'Lj2A946T25' => 'lonja', 'Lj2C714T1' => 'lonja', 'Lj2C966T3' => 'lonja', 'Lj2C966T4' => 'lonja', 'Lj4g0002979' => 'lja', 'Lsat_1_v5_gn_5_30901' => 'lsa', 'Lsat_1_v5_gn_5_31100' => 'lsa', 'Lsat_1_v5_gn_5_38600' => 'lsa', 'Lsat_1_v5_gn_6_92061' => 'lsa', 'Manes.05G071301' => 'mes', 'MD02G1008700' => 'mdo', 'MD02G1008900' => 'mdo', 'MD03G1256400' => 'mdo', 'MD04G1180900' => 'mdo', 'MD04G1181000' => 'mdo', 'MD04G1181200' => 'mdo', 'MD05G1244200' => 'mdo', 'MD05G1324200' => 'mdo', 'MD09G1201600' => 'mdo', 'MD10G1000600' => 'mdo', 'MD14G1026900' => 'mdo', 'MD14G1187900' => 'mdo', 'MD15G1017800' => 'mdo', 'MD15G1018100' => 'mdo', 'Medtr4g124160' => 'mtr', 'Migut.L01260' => 'egut', 'Nitab4.5_0000008g0440' => 'nta', 'Nitab4.5_0000207g0170' => 'nta', 'Nitab4.5_0007671g0030' => 'nta', 'Nitab4.5_0010853g0020' => 'nta', 'Oeu057656.1' => 'oeu', 'PGSC0003DMG400005638' => 'stu', 'PGSC0003DMG400005639' => 'stu', 'Phvul.009G222800' => 'pvu', 'Potri.009G132400' => 'ptr', 'Potri.009G163001' => 'ptr', 'Potri.011G000700' => 'ptr', 'Potri.011G004800' => 'ptr', 'Prupe.1G509300' => 'ppe', 'Prupe.1G509700' => 'ppe', 'Prupe.1G510400' => 'ppe', 'Prupe.1G510700' => 'ppe', 'Prupe.1G512600' => 'ppe', 'Prupe.2G073200' => 'ppe', 'Prupe.3G059500' => 'ppe', 'Prupe.3G059600' => 'ppe', 'Prupe.3G246100' => 'ppe', 'Prupe.3G265100' => 'ppe', 'Prupe.4G034700' => 'ppe', 'Prupe.4G052100' => 'ppe', 'Prupe.4G053600' => 'ppe', 'Prupe.5G068800' => 'ppe', 'Prupe.5G070600' => 'ppe', 'Prupe.6G075400' => 'ppe', 'Prupe.6G075500' => 'ppe', 'Prupe.6G076400' => 'ppe', 'Prupe.8G110700' => 'ppe', 'Psat4g020960' => 'psa', 'PSO135G0788' => 'pso', 'PSO210G6463' => 'pso', 'PSO384G0370' => 'pso', 'PSO386G0056' => 'pso', 'QL01p006048' => 'qlo', 'QL02p054283' => 'qlo', 'QL05p008000' => 'qlo', 'QL05p008212' => 'qlo', 'QL05p008950' => 'qlo', 'QL05p009042' => 'qlo', 'QL05p009518' => 'qlo', 'QL05p012589' => 'qlo', 'QL05p012608' => 'qlo', 'QL05p012650' => 'qlo', 'QL05p012667' => 'qlo', 'QL05p014501' => 'qlo', 'QL05p052800' => 'qlo', 'QL05p065010' => 'qlo', 'QL05p074156' => 'qlo', 'QL05p074160' => 'qlo', 'QL05p074174' => 'qlo', 'QL05p074178' => 'qlo', 'QL05p074214' => 'qlo', 'QL06p001050' => 'qlo', 'QL06p001056' => 'qlo', 'QL06p006093' => 'qlo', 'QL06p006111' => 'qlo', 'QL07p019784' => 'qlo', 'QL07p019801' => 'qlo', 'QL07p036110' => 'qlo', 'QL07p036134' => 'qlo', 'QL07p036147' => 'qlo', 'QL07p036156' => 'qlo', 'QL07p036300' => 'qlo', 'QL07p036320' => 'qlo', 'QL08p014547' => 'qlo', 'QL08p014551' => 'qlo', 'QL08p043319' => 'qlo', 'QL08p043324' => 'qlo', 'QL11p009094' => 'qlo', 'RcHm_v2.0_Chr1g0380481' => 'rch', 'RcHm_v2.0_Chr2g0089331' => 'rch', 'RcHm_v2.0_Chr2g0123691' => 'rch', 'RcHm_v2.0_Chr2g0151111' => 'rch', 'RcHm_v2.0_Chr2g0163011' => 'rch', 'RcHm_v2.0_Chr2g0163051' => 'rch', 'RcHm_v2.0_Chr2g0164671' => 'rch', 'RcHm_v2.0_Chr2g0164681' => 'rch', 'RcHm_v2.0_Chr2g0164721' => 'rch', 'RcHm_v2.0_Chr3g0449911' => 'rch', 'RcHm_v2.0_Chr3g0450211' => 'rch', 'RcHm_v2.0_Chr3g0457271' => 'rch', 'RcHm_v2.0_Chr5g0018111' => 'rch', 'RcHm_v2.0_Chr5g0021011' => 'rch', 'RcHm_v2.0_Chr5g0081171' => 'rch', 'RcHm_v2.0_Chr5g0081211' => 'rch', 'RcHm_v2.0_Chr6g0275871' => 'rch', 'RcHm_v2.0_Chr6g0276071' => 'rch', 'RcHm_v2.0_Chr6g0285591' => 'rch', 'RcHm_v2.0_Chr6g0291931' => 'rch', 'RcHm_v2.0_Chr6g0292091' => 'rch', 'RcHm_v2.0_Chr6g0292271' => 'rch', 'RcHm_v2.0_Chr7g0221261' => 'rch', 'Rhsim08G0219900' => 'rsi', 'Rhsim08G0220200' => 'rsi', 'Rhsim08G0237800' => 'rsi', 'Rhsim08G0238800' => 'rsi', 'Sabra09G0102700' => 'sbr', 'Sabra09G0127200' => 'sbr', 'Sabra11G0003700' => 'sbr', 'Sabra15G0014700' => 'sbr', 'Sc19g0000590' => 'sci', 'Sc19g0001870' => 'sci', 'SGA_v2.0_scaffold1G00346' => 'sas', 'SGA_v2.0_scaffold1G00575' => 'sas', 'SGA_v2.0_scaffold1G00761' => 'sas', 'SGA_v2.0_scaffold232G43501' => 'sas', 'TAR625G1137' => 'tar', 'Thecc.03G222100' => 'tca', 'TPR.G12691' => 'tpr', 'TWI34G0727' => 'twi', 'TWI36G0117' => 'twi', 'VMungo1309G0868' => 'vmu' ) $gf_id = 'HOM05D001729' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001729' ) $data_identifier = 'HOM05D001729' $data_type = 'gf_id' $species_gene_counts = array( 'amhyb' => (int) 1, 'cqu' => (int) 9, 'can' => (int) 1, 'cansat' => (int) 1, 'car' => (int) 1, 'col' => (int) 5, 'dca' => (int) 1, 'din' => (int) 2, 'dzi' => (int) 3, 'fan' => (int) 140, 'fve' => (int) 62, 'gma' => (int) 1, 'ghi' => (int) 2, 'gra' => (int) 1, 'han' => (int) 1, 'sun' => (int) 1, 'lonja' => (int) 6, 'lja' => (int) 1, 'lsa' => (int) 4, 'mes' => (int) 1, 'mdo' => (int) 14, 'mtr' => (int) 1, 'egut' => (int) 1, 'nta' => (int) 4, 'oeu' => (int) 1, 'stu' => (int) 2, 'pvu' => (int) 1, 'ptr' => (int) 4, 'ppe' => (int) 19, 'psa' => (int) 1, 'pso' => (int) 4, 'qlo' => (int) 36, 'rch' => (int) 23, 'rsi' => (int) 4, 'sbr' => (int) 4, 'sci' => (int) 2, 'sas' => (int) 4, 'tar' => (int) 1, 'tca' => (int) 1, 'tpr' => (int) 1, 'twi' => (int) 2, 'vmu' => (int) 1 ) $gf_gene_species = 'vmu' $gf_gene_id = 'VMungo1309G0868' $species_info = array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ) $local_species = 'din' $disabled = '' $selected = '' $num_hits = (int) 1
Warning (2): count(): Parameter must be an array or an object that implements Countable [APP/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp, line 33]Code Context $disabled = (!array_key_exists($local_species,$species_gene_counts))?"disabled":""; $selected = (isset($selected_species) && array_key_exists($local_species,$selected_species))?"checked='checked'":""; $num_hits = (array_key_exists($local_species,$species_gene_counts))?count($species_gene_counts[$local_species]):0; $viewFile = '/www/bioinformatics01_ro/plaza/_dev_instances/feedback/app/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp' $dataForView = array( 'sidebar_info' => array( 'gf_id' => 'HOM05D001729', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '375', 'num_species' => '42' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'Ah.07g204710' => 'amhyb', 'AUR62006001' => 'cqu', 'AUR62006002' => 'cqu', 'AUR62006003' => 'cqu', 'AUR62015641' => 'cqu', 'AUR62027174' => 'cqu', 'AUR62035623' => 'cqu', 'AUR62035624' => 'cqu', 'AUR62035625' => 'cqu', 'AUR62035626' => 'cqu', 'CAN.G1110.53' => 'can', 'CANSAT80G0415' => 'cansat', 'Ca_21364_v3' => 'car', 'COL.COLO4_30693' => 'col', 'COL.COLO4_30694' => 'col', 'COL.COLO4_30695' => 'col', 'COL.COLO4_30696' => 'col', 'COL.COLO4_34020' => 'col', 'DCAR_004585' => 'dca', 'Dinv04029' => 'din', 'Dinv34857' => 'din', 'Duzib147G0011' => 'dzi', 'Duzib170G0599' => 'dzi', 'Duzib192G1051' => 'dzi', 'FAN01G0708' => 'fan', 'FAN01G0742' => 'fan', 'FAN02G0048' => 'fan', 'FAN02G0583' => 'fan', 'FAN02G0688' => 'fan', 'FAN02G1588' => 'fan', 'FAN02G2194' => 'fan', 'FAN02G2750' => 'fan', 'FAN02G3094' => 'fan', 'FAN02G3887' => 'fan', 'FAN02G3911' => 'fan', 'FAN02G3994' => 'fan', 'FAN02G4432' => 'fan', 'FAN02G4556' => 'fan', 'FAN03G1977' => 'fan', 'FAN03G2781' => 'fan', 'FAN03G2850' => 'fan', 'FAN03G3155' => 'fan', 'FAN04G2487' => 'fan', 'FAN05G0208' => 'fan', 'FAN05G0656' => 'fan', 'FAN05G0696' => 'fan', 'FAN05G0810' => 'fan', 'FAN05G1447' => 'fan', 'FAN05G2640' => 'fan', 'FAN05G2911' => 'fan', 'FAN05G3901' => 'fan', 'FAN05G4859' => 'fan', 'FAN05G4861' => 'fan', 'FAN05G4988' => 'fan', 'FAN05G5187' => 'fan', 'FAN05G5452' => 'fan', 'FAN05G5500' => 'fan', 'FAN05G5688' => 'fan', 'FAN06G0177' => 'fan', 'FAN06G0675' => 'fan', 'FAN06G1290' => 'fan', 'FAN06G2191' => 'fan', 'FAN06G2405' => 'fan', 'FAN06G3231' => 'fan', 'FAN06G3932' => 'fan', 'FAN07G0163' => 'fan', 'FAN07G0471' => 'fan', 'FAN07G1354' => 'fan', 'FAN08G0338' => 'fan', 'FAN08G1373' => 'fan', 'FAN08G2539' => 'fan', 'FAN08G2728' => 'fan', 'FAN09G0608' => 'fan', 'FAN09G1136' => 'fan', 'FAN09G1958' => 'fan', 'FAN09G2508' => 'fan', 'FAN09G2597' => 'fan', 'FAN09G2658' => 'fan', 'FAN09G2757' => 'fan', 'FAN09G2983' => 'fan', 'FAN09G3130' => 'fan', 'FAN09G3565' => 'fan', 'FAN09G3613' => 'fan', 'FAN09G4011' => 'fan', 'FAN09G4239' => 'fan', 'FAN09G4277' => 'fan', 'FAN09G4720' => 'fan', 'FAN11G0139' => 'fan', 'FAN11G1727' => 'fan', 'FAN11G2672' => 'fan', 'FAN11G2795' => 'fan', 'FAN11G3238' => 'fan', 'FAN11G3734' => 'fan', 'FAN12G0631' => 'fan', 'FAN12G2239' => 'fan', 'FAN12G2308' => 'fan', 'FAN12G2569' => 'fan', 'FAN12G2623' => 'fan', 'FAN13G3182' => 'fan', 'FAN14G0053' => 'fan', 'FAN14G0370' => 'fan', 'FAN14G0382' => 'fan', 'FAN14G0421' => 'fan', 'FAN14G0866' => 'fan', 'FAN14G1187' => 'fan', 'FAN14G1727' => 'fan', 'FAN14G1791' => 'fan', 'FAN14G2361' => 'fan', 'FAN14G2668' => 'fan', 'FAN14G2770' => 'fan', 'FAN14G2874' => 'fan', 'FAN14G3193' => 'fan', 'FAN14G3624' => 'fan', 'FAN14G3676' => 'fan', 'FAN14G3807' => 'fan', 'FAN14G4082' => 'fan', 'FAN14G4342' => 'fan', 'FAN14G4985' => 'fan', 'FAN14G5126' => 'fan', 'FAN14G5781' => 'fan', 'FAN14G5808' => 'fan', 'FAN14G5949' => 'fan', 'FAN15G0828' => 'fan', 'FAN15G1054' => 'fan', 'FAN15G2023' => 'fan', 'FAN15G2506' => 'fan', 'FAN16G0128' => 'fan', 'FAN16G0249' => 'fan', 'FAN16G0429' => 'fan', 'FAN16G1493' => 'fan', 'FAN16G2210' => 'fan', 'FAN16G2506' => 'fan', 'FAN18G1542' => 'fan', 'FAN18G4057' => 'fan', 'FAN19G0745' => 'fan', 'FAN19G1216' => 'fan', 'FAN19G1733' => 'fan', 'FAN20G0258' => 'fan', 'FAN20G1095' => 'fan', 'FAN20G1557' => 'fan', 'FAN21G0302' => 'fan', 'FAN21G0519' => 'fan', 'FAN21G0970' => 'fan', 'FAN21G1159' => 'fan', 'FAN21G1312' => 'fan', 'FAN21G1440' => 'fan', 'FAN21G1715' => 'fan', 'FAN23G1584' => 'fan', 'FAN24G0045' => 'fan', 'FAN24G0053' => 'fan', 'FAN24G1500' => 'fan', 'FAN24G1817' => 'fan', 'FAN24G2147' => 'fan', 'FAN24G2236' => 'fan', 'FAN24G2446' => 'fan', 'FAN24G2684' => 'fan', 'FAN25G0187' => 'fan', 'FAN25G0505' => 'fan', 'FAN25G0589' => 'fan', 'FAN25G3663' => 'fan', 'FAN26G1025' => 'fan', 'FAN26G2860' => 'fan', 'FAN27G1329' => 'fan', 'FAN27G3392' => 'fan', 'FvH4_1g02011' => 'fve', 'FvH4_1g06511' => 'fve', 'FvH4_2g19900' => 'fve', 'FvH4_2g19920' => 'fve', 'FvH4_2g24261' => 'fve', 'FvH4_2g24270' => 'fve', 'FvH4_2g24631' => 'fve', 'FvH4_2g30622' => 'fve', 'FvH4_3g12920' => 'fve', 'FvH4_3g30171' => 'fve', 'FvH4_3g35490' => 'fve', 'FvH4_3g43682' => 'fve', 'FvH4_3g43730' => 'fve', 'FvH4_3g43732' => 'fve', 'FvH4_3g43751' => 'fve', 'FvH4_3g43752' => 'fve', 'FvH4_3g43770' => 'fve', 'FvH4_3g44471' => 'fve', 'FvH4_3g44510' => 'fve', 'FvH4_3g44582' => 'fve', 'FvH4_4g16921' => 'fve', 'FvH4_4g17121' => 'fve', 'FvH4_4g17782' => 'fve', 'FvH4_4g17783' => 'fve', 'FvH4_4g18120' => 'fve', 'FvH4_4g31310' => 'fve', 'FvH4_4g35052' => 'fve', 'FvH4_5g30862' => 'fve', 'FvH4_6g01541' => 'fve', 'FvH4_6g02021' => 'fve', 'FvH4_6g02041' => 'fve', 'FvH4_6g02071' => 'fve', 'FvH4_6g02171' => 'fve', 'FvH4_6g03181' => 'fve', 'FvH4_6g03182' => 'fve', 'FvH4_6g03221' => 'fve', 'FvH4_6g03380' => 'fve', 'FvH4_6g05201' => 'fve', 'FvH4_6g05203' => 'fve', 'FvH4_6g20231' => 'fve', 'FvH4_6g31981' => 'fve', 'FvH4_6g32061' => 'fve', 'FvH4_6g37041' => 'fve', 'FvH4_6g37932' => 'fve', 'FvH4_6g38731' => 'fve', 'FvH4_6g39370' => 'fve', 'FvH4_6g39371' => 'fve', 'FvH4_6g40891' => 'fve', 'FvH4_6g40892' => 'fve', 'FvH4_6g43143' => 'fve', 'FvH4_6g45251' => 'fve', 'FvH4_6g45260' => 'fve', 'FvH4_6g45291' => 'fve', 'FvH4_6g45890' => 'fve', 'FvH4_6g46240' => 'fve', 'FvH4_6g46241' => 'fve', 'FvH4_6g46242' => 'fve', 'FvH4_6g46260' => 'fve', 'FvH4_6g46280' => 'fve', 'FvH4_6g46380' => 'fve', 'FvH4_7g12841' => 'fve', 'FvH4_7g31431' => 'fve', 'Glyma.09G075900' => 'gma', 'Gohir.A09G096401' => 'ghi', 'Gohir.D09G096101' => 'ghi', 'Gorai.006G112800' => 'gra', 'HanXRQChr04g0121411' => 'han', 'Hund15878' => 'sun', 'Lj2A1107G68' => 'lonja', 'Lj2A630G63' => 'lonja', 'Lj2A946T25' => 'lonja', 'Lj2C714T1' => 'lonja', 'Lj2C966T3' => 'lonja', 'Lj2C966T4' => 'lonja', 'Lj4g0002979' => 'lja', 'Lsat_1_v5_gn_5_30901' => 'lsa', 'Lsat_1_v5_gn_5_31100' => 'lsa', 'Lsat_1_v5_gn_5_38600' => 'lsa', 'Lsat_1_v5_gn_6_92061' => 'lsa', 'Manes.05G071301' => 'mes', 'MD02G1008700' => 'mdo', 'MD02G1008900' => 'mdo', 'MD03G1256400' => 'mdo', 'MD04G1180900' => 'mdo', 'MD04G1181000' => 'mdo', 'MD04G1181200' => 'mdo', 'MD05G1244200' => 'mdo', 'MD05G1324200' => 'mdo', 'MD09G1201600' => 'mdo', 'MD10G1000600' => 'mdo', 'MD14G1026900' => 'mdo', 'MD14G1187900' => 'mdo', 'MD15G1017800' => 'mdo', 'MD15G1018100' => 'mdo', 'Medtr4g124160' => 'mtr', 'Migut.L01260' => 'egut', 'Nitab4.5_0000008g0440' => 'nta', 'Nitab4.5_0000207g0170' => 'nta', 'Nitab4.5_0007671g0030' => 'nta', 'Nitab4.5_0010853g0020' => 'nta', 'Oeu057656.1' => 'oeu', 'PGSC0003DMG400005638' => 'stu', 'PGSC0003DMG400005639' => 'stu', 'Phvul.009G222800' => 'pvu', 'Potri.009G132400' => 'ptr', 'Potri.009G163001' => 'ptr', 'Potri.011G000700' => 'ptr', 'Potri.011G004800' => 'ptr', 'Prupe.1G509300' => 'ppe', 'Prupe.1G509700' => 'ppe', 'Prupe.1G510400' => 'ppe', 'Prupe.1G510700' => 'ppe', 'Prupe.1G512600' => 'ppe', 'Prupe.2G073200' => 'ppe', 'Prupe.3G059500' => 'ppe', 'Prupe.3G059600' => 'ppe', 'Prupe.3G246100' => 'ppe', 'Prupe.3G265100' => 'ppe', 'Prupe.4G034700' => 'ppe', 'Prupe.4G052100' => 'ppe', 'Prupe.4G053600' => 'ppe', 'Prupe.5G068800' => 'ppe', 'Prupe.5G070600' => 'ppe', 'Prupe.6G075400' => 'ppe', 'Prupe.6G075500' => 'ppe', 'Prupe.6G076400' => 'ppe', 'Prupe.8G110700' => 'ppe', 'Psat4g020960' => 'psa', 'PSO135G0788' => 'pso', 'PSO210G6463' => 'pso', 'PSO384G0370' => 'pso', 'PSO386G0056' => 'pso', 'QL01p006048' => 'qlo', 'QL02p054283' => 'qlo', 'QL05p008000' => 'qlo', 'QL05p008212' => 'qlo', 'QL05p008950' => 'qlo', 'QL05p009042' => 'qlo', 'QL05p009518' => 'qlo', 'QL05p012589' => 'qlo', 'QL05p012608' => 'qlo', 'QL05p012650' => 'qlo', 'QL05p012667' => 'qlo', 'QL05p014501' => 'qlo', 'QL05p052800' => 'qlo', 'QL05p065010' => 'qlo', 'QL05p074156' => 'qlo', 'QL05p074160' => 'qlo', 'QL05p074174' => 'qlo', 'QL05p074178' => 'qlo', 'QL05p074214' => 'qlo', 'QL06p001050' => 'qlo', 'QL06p001056' => 'qlo', 'QL06p006093' => 'qlo', 'QL06p006111' => 'qlo', 'QL07p019784' => 'qlo', 'QL07p019801' => 'qlo', 'QL07p036110' => 'qlo', 'QL07p036134' => 'qlo', 'QL07p036147' => 'qlo', 'QL07p036156' => 'qlo', 'QL07p036300' => 'qlo', 'QL07p036320' => 'qlo', 'QL08p014547' => 'qlo', 'QL08p014551' => 'qlo', 'QL08p043319' => 'qlo', 'QL08p043324' => 'qlo', 'QL11p009094' => 'qlo', 'RcHm_v2.0_Chr1g0380481' => 'rch', 'RcHm_v2.0_Chr2g0089331' => 'rch', 'RcHm_v2.0_Chr2g0123691' => 'rch', 'RcHm_v2.0_Chr2g0151111' => 'rch', 'RcHm_v2.0_Chr2g0163011' => 'rch', 'RcHm_v2.0_Chr2g0163051' => 'rch', 'RcHm_v2.0_Chr2g0164671' => 'rch', 'RcHm_v2.0_Chr2g0164681' => 'rch', 'RcHm_v2.0_Chr2g0164721' => 'rch', 'RcHm_v2.0_Chr3g0449911' => 'rch', 'RcHm_v2.0_Chr3g0450211' => 'rch', 'RcHm_v2.0_Chr3g0457271' => 'rch', 'RcHm_v2.0_Chr5g0018111' => 'rch', 'RcHm_v2.0_Chr5g0021011' => 'rch', 'RcHm_v2.0_Chr5g0081171' => 'rch', 'RcHm_v2.0_Chr5g0081211' => 'rch', 'RcHm_v2.0_Chr6g0275871' => 'rch', 'RcHm_v2.0_Chr6g0276071' => 'rch', 'RcHm_v2.0_Chr6g0285591' => 'rch', 'RcHm_v2.0_Chr6g0291931' => 'rch', 'RcHm_v2.0_Chr6g0292091' => 'rch', 'RcHm_v2.0_Chr6g0292271' => 'rch', 'RcHm_v2.0_Chr7g0221261' => 'rch', 'Rhsim08G0219900' => 'rsi', 'Rhsim08G0220200' => 'rsi', 'Rhsim08G0237800' => 'rsi', 'Rhsim08G0238800' => 'rsi', 'Sabra09G0102700' => 'sbr', 'Sabra09G0127200' => 'sbr', 'Sabra11G0003700' => 'sbr', 'Sabra15G0014700' => 'sbr', 'Sc19g0000590' => 'sci', 'Sc19g0001870' => 'sci', 'SGA_v2.0_scaffold1G00346' => 'sas', 'SGA_v2.0_scaffold1G00575' => 'sas', 'SGA_v2.0_scaffold1G00761' => 'sas', 'SGA_v2.0_scaffold232G43501' => 'sas', 'TAR625G1137' => 'tar', 'Thecc.03G222100' => 'tca', 'TPR.G12691' => 'tpr', 'TWI34G0727' => 'twi', 'TWI36G0117' => 'twi', 'VMungo1309G0868' => 'vmu' ), 'gf_id' => 'HOM05D001729', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001729' ), 'data_identifier' => 'HOM05D001729', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001729', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '375', 'num_species' => '42' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'Ah.07g204710' => 'amhyb', 'AUR62006001' => 'cqu', 'AUR62006002' => 'cqu', 'AUR62006003' => 'cqu', 'AUR62015641' => 'cqu', 'AUR62027174' => 'cqu', 'AUR62035623' => 'cqu', 'AUR62035624' => 'cqu', 'AUR62035625' => 'cqu', 'AUR62035626' => 'cqu', 'CAN.G1110.53' => 'can', 'CANSAT80G0415' => 'cansat', 'Ca_21364_v3' => 'car', 'COL.COLO4_30693' => 'col', 'COL.COLO4_30694' => 'col', 'COL.COLO4_30695' => 'col', 'COL.COLO4_30696' => 'col', 'COL.COLO4_34020' => 'col', 'DCAR_004585' => 'dca', 'Dinv04029' => 'din', 'Dinv34857' => 'din', 'Duzib147G0011' => 'dzi', 'Duzib170G0599' => 'dzi', 'Duzib192G1051' => 'dzi', 'FAN01G0708' => 'fan', 'FAN01G0742' => 'fan', 'FAN02G0048' => 'fan', 'FAN02G0583' => 'fan', 'FAN02G0688' => 'fan', 'FAN02G1588' => 'fan', 'FAN02G2194' => 'fan', 'FAN02G2750' => 'fan', 'FAN02G3094' => 'fan', 'FAN02G3887' => 'fan', 'FAN02G3911' => 'fan', 'FAN02G3994' => 'fan', 'FAN02G4432' => 'fan', 'FAN02G4556' => 'fan', 'FAN03G1977' => 'fan', 'FAN03G2781' => 'fan', 'FAN03G2850' => 'fan', 'FAN03G3155' => 'fan', 'FAN04G2487' => 'fan', 'FAN05G0208' => 'fan', 'FAN05G0656' => 'fan', 'FAN05G0696' => 'fan', 'FAN05G0810' => 'fan', 'FAN05G1447' => 'fan', 'FAN05G2640' => 'fan', 'FAN05G2911' => 'fan', 'FAN05G3901' => 'fan', 'FAN05G4859' => 'fan', 'FAN05G4861' => 'fan', 'FAN05G4988' => 'fan', 'FAN05G5187' => 'fan', 'FAN05G5452' => 'fan', 'FAN05G5500' => 'fan', 'FAN05G5688' => 'fan', 'FAN06G0177' => 'fan', 'FAN06G0675' => 'fan', 'FAN06G1290' => 'fan', 'FAN06G2191' => 'fan', 'FAN06G2405' => 'fan', 'FAN06G3231' => 'fan', 'FAN06G3932' => 'fan', 'FAN07G0163' => 'fan', 'FAN07G0471' => 'fan', 'FAN07G1354' => 'fan', 'FAN08G0338' => 'fan', 'FAN08G1373' => 'fan', 'FAN08G2539' => 'fan', 'FAN08G2728' => 'fan', 'FAN09G0608' => 'fan', 'FAN09G1136' => 'fan', 'FAN09G1958' => 'fan', 'FAN09G2508' => 'fan', 'FAN09G2597' => 'fan', 'FAN09G2658' => 'fan', 'FAN09G2757' => 'fan', 'FAN09G2983' => 'fan', 'FAN09G3130' => 'fan', 'FAN09G3565' => 'fan', 'FAN09G3613' => 'fan', 'FAN09G4011' => 'fan', 'FAN09G4239' => 'fan', 'FAN09G4277' => 'fan', 'FAN09G4720' => 'fan', 'FAN11G0139' => 'fan', 'FAN11G1727' => 'fan', 'FAN11G2672' => 'fan', 'FAN11G2795' => 'fan', 'FAN11G3238' => 'fan', 'FAN11G3734' => 'fan', 'FAN12G0631' => 'fan', 'FAN12G2239' => 'fan', 'FAN12G2308' => 'fan', 'FAN12G2569' => 'fan', 'FAN12G2623' => 'fan', 'FAN13G3182' => 'fan', 'FAN14G0053' => 'fan', 'FAN14G0370' => 'fan', 'FAN14G0382' => 'fan', 'FAN14G0421' => 'fan', 'FAN14G0866' => 'fan', 'FAN14G1187' => 'fan', 'FAN14G1727' => 'fan', 'FAN14G1791' => 'fan', 'FAN14G2361' => 'fan', 'FAN14G2668' => 'fan', 'FAN14G2770' => 'fan', 'FAN14G2874' => 'fan', 'FAN14G3193' => 'fan', 'FAN14G3624' => 'fan', 'FAN14G3676' => 'fan', 'FAN14G3807' => 'fan', 'FAN14G4082' => 'fan', 'FAN14G4342' => 'fan', 'FAN14G4985' => 'fan', 'FAN14G5126' => 'fan', 'FAN14G5781' => 'fan', 'FAN14G5808' => 'fan', 'FAN14G5949' => 'fan', 'FAN15G0828' => 'fan', 'FAN15G1054' => 'fan', 'FAN15G2023' => 'fan', 'FAN15G2506' => 'fan', 'FAN16G0128' => 'fan', 'FAN16G0249' => 'fan', 'FAN16G0429' => 'fan', 'FAN16G1493' => 'fan', 'FAN16G2210' => 'fan', 'FAN16G2506' => 'fan', 'FAN18G1542' => 'fan', 'FAN18G4057' => 'fan', 'FAN19G0745' => 'fan', 'FAN19G1216' => 'fan', 'FAN19G1733' => 'fan', 'FAN20G0258' => 'fan', 'FAN20G1095' => 'fan', 'FAN20G1557' => 'fan', 'FAN21G0302' => 'fan', 'FAN21G0519' => 'fan', 'FAN21G0970' => 'fan', 'FAN21G1159' => 'fan', 'FAN21G1312' => 'fan', 'FAN21G1440' => 'fan', 'FAN21G1715' => 'fan', 'FAN23G1584' => 'fan', 'FAN24G0045' => 'fan', 'FAN24G0053' => 'fan', 'FAN24G1500' => 'fan', 'FAN24G1817' => 'fan', 'FAN24G2147' => 'fan', 'FAN24G2236' => 'fan', 'FAN24G2446' => 'fan', 'FAN24G2684' => 'fan', 'FAN25G0187' => 'fan', 'FAN25G0505' => 'fan', 'FAN25G0589' => 'fan', 'FAN25G3663' => 'fan', 'FAN26G1025' => 'fan', 'FAN26G2860' => 'fan', 'FAN27G1329' => 'fan', 'FAN27G3392' => 'fan', 'FvH4_1g02011' => 'fve', 'FvH4_1g06511' => 'fve', 'FvH4_2g19900' => 'fve', 'FvH4_2g19920' => 'fve', 'FvH4_2g24261' => 'fve', 'FvH4_2g24270' => 'fve', 'FvH4_2g24631' => 'fve', 'FvH4_2g30622' => 'fve', 'FvH4_3g12920' => 'fve', 'FvH4_3g30171' => 'fve', 'FvH4_3g35490' => 'fve', 'FvH4_3g43682' => 'fve', 'FvH4_3g43730' => 'fve', 'FvH4_3g43732' => 'fve', 'FvH4_3g43751' => 'fve', 'FvH4_3g43752' => 'fve', 'FvH4_3g43770' => 'fve', 'FvH4_3g44471' => 'fve', 'FvH4_3g44510' => 'fve', 'FvH4_3g44582' => 'fve', 'FvH4_4g16921' => 'fve', 'FvH4_4g17121' => 'fve', 'FvH4_4g17782' => 'fve', 'FvH4_4g17783' => 'fve', 'FvH4_4g18120' => 'fve', 'FvH4_4g31310' => 'fve', 'FvH4_4g35052' => 'fve', 'FvH4_5g30862' => 'fve', 'FvH4_6g01541' => 'fve', 'FvH4_6g02021' => 'fve', 'FvH4_6g02041' => 'fve', 'FvH4_6g02071' => 'fve', 'FvH4_6g02171' => 'fve', 'FvH4_6g03181' => 'fve', 'FvH4_6g03182' => 'fve', 'FvH4_6g03221' => 'fve', 'FvH4_6g03380' => 'fve', 'FvH4_6g05201' => 'fve', 'FvH4_6g05203' => 'fve', 'FvH4_6g20231' => 'fve', 'FvH4_6g31981' => 'fve', 'FvH4_6g32061' => 'fve', 'FvH4_6g37041' => 'fve', 'FvH4_6g37932' => 'fve', 'FvH4_6g38731' => 'fve', 'FvH4_6g39370' => 'fve', 'FvH4_6g39371' => 'fve', 'FvH4_6g40891' => 'fve', 'FvH4_6g40892' => 'fve', 'FvH4_6g43143' => 'fve', 'FvH4_6g45251' => 'fve', 'FvH4_6g45260' => 'fve', 'FvH4_6g45291' => 'fve', 'FvH4_6g45890' => 'fve', 'FvH4_6g46240' => 'fve', 'FvH4_6g46241' => 'fve', 'FvH4_6g46242' => 'fve', 'FvH4_6g46260' => 'fve', 'FvH4_6g46280' => 'fve', 'FvH4_6g46380' => 'fve', 'FvH4_7g12841' => 'fve', 'FvH4_7g31431' => 'fve', 'Glyma.09G075900' => 'gma', 'Gohir.A09G096401' => 'ghi', 'Gohir.D09G096101' => 'ghi', 'Gorai.006G112800' => 'gra', 'HanXRQChr04g0121411' => 'han', 'Hund15878' => 'sun', 'Lj2A1107G68' => 'lonja', 'Lj2A630G63' => 'lonja', 'Lj2A946T25' => 'lonja', 'Lj2C714T1' => 'lonja', 'Lj2C966T3' => 'lonja', 'Lj2C966T4' => 'lonja', 'Lj4g0002979' => 'lja', 'Lsat_1_v5_gn_5_30901' => 'lsa', 'Lsat_1_v5_gn_5_31100' => 'lsa', 'Lsat_1_v5_gn_5_38600' => 'lsa', 'Lsat_1_v5_gn_6_92061' => 'lsa', 'Manes.05G071301' => 'mes', 'MD02G1008700' => 'mdo', 'MD02G1008900' => 'mdo', 'MD03G1256400' => 'mdo', 'MD04G1180900' => 'mdo', 'MD04G1181000' => 'mdo', 'MD04G1181200' => 'mdo', 'MD05G1244200' => 'mdo', 'MD05G1324200' => 'mdo', 'MD09G1201600' => 'mdo', 'MD10G1000600' => 'mdo', 'MD14G1026900' => 'mdo', 'MD14G1187900' => 'mdo', 'MD15G1017800' => 'mdo', 'MD15G1018100' => 'mdo', 'Medtr4g124160' => 'mtr', 'Migut.L01260' => 'egut', 'Nitab4.5_0000008g0440' => 'nta', 'Nitab4.5_0000207g0170' => 'nta', 'Nitab4.5_0007671g0030' => 'nta', 'Nitab4.5_0010853g0020' => 'nta', 'Oeu057656.1' => 'oeu', 'PGSC0003DMG400005638' => 'stu', 'PGSC0003DMG400005639' => 'stu', 'Phvul.009G222800' => 'pvu', 'Potri.009G132400' => 'ptr', 'Potri.009G163001' => 'ptr', 'Potri.011G000700' => 'ptr', 'Potri.011G004800' => 'ptr', 'Prupe.1G509300' => 'ppe', 'Prupe.1G509700' => 'ppe', 'Prupe.1G510400' => 'ppe', 'Prupe.1G510700' => 'ppe', 'Prupe.1G512600' => 'ppe', 'Prupe.2G073200' => 'ppe', 'Prupe.3G059500' => 'ppe', 'Prupe.3G059600' => 'ppe', 'Prupe.3G246100' => 'ppe', 'Prupe.3G265100' => 'ppe', 'Prupe.4G034700' => 'ppe', 'Prupe.4G052100' => 'ppe', 'Prupe.4G053600' => 'ppe', 'Prupe.5G068800' => 'ppe', 'Prupe.5G070600' => 'ppe', 'Prupe.6G075400' => 'ppe', 'Prupe.6G075500' => 'ppe', 'Prupe.6G076400' => 'ppe', 'Prupe.8G110700' => 'ppe', 'Psat4g020960' => 'psa', 'PSO135G0788' => 'pso', 'PSO210G6463' => 'pso', 'PSO384G0370' => 'pso', 'PSO386G0056' => 'pso', 'QL01p006048' => 'qlo', 'QL02p054283' => 'qlo', 'QL05p008000' => 'qlo', 'QL05p008212' => 'qlo', 'QL05p008950' => 'qlo', 'QL05p009042' => 'qlo', 'QL05p009518' => 'qlo', 'QL05p012589' => 'qlo', 'QL05p012608' => 'qlo', 'QL05p012650' => 'qlo', 'QL05p012667' => 'qlo', 'QL05p014501' => 'qlo', 'QL05p052800' => 'qlo', 'QL05p065010' => 'qlo', 'QL05p074156' => 'qlo', 'QL05p074160' => 'qlo', 'QL05p074174' => 'qlo', 'QL05p074178' => 'qlo', 'QL05p074214' => 'qlo', 'QL06p001050' => 'qlo', 'QL06p001056' => 'qlo', 'QL06p006093' => 'qlo', 'QL06p006111' => 'qlo', 'QL07p019784' => 'qlo', 'QL07p019801' => 'qlo', 'QL07p036110' => 'qlo', 'QL07p036134' => 'qlo', 'QL07p036147' => 'qlo', 'QL07p036156' => 'qlo', 'QL07p036300' => 'qlo', 'QL07p036320' => 'qlo', 'QL08p014547' => 'qlo', 'QL08p014551' => 'qlo', 'QL08p043319' => 'qlo', 'QL08p043324' => 'qlo', 'QL11p009094' => 'qlo', 'RcHm_v2.0_Chr1g0380481' => 'rch', 'RcHm_v2.0_Chr2g0089331' => 'rch', 'RcHm_v2.0_Chr2g0123691' => 'rch', 'RcHm_v2.0_Chr2g0151111' => 'rch', 'RcHm_v2.0_Chr2g0163011' => 'rch', 'RcHm_v2.0_Chr2g0163051' => 'rch', 'RcHm_v2.0_Chr2g0164671' => 'rch', 'RcHm_v2.0_Chr2g0164681' => 'rch', 'RcHm_v2.0_Chr2g0164721' => 'rch', 'RcHm_v2.0_Chr3g0449911' => 'rch', 'RcHm_v2.0_Chr3g0450211' => 'rch', 'RcHm_v2.0_Chr3g0457271' => 'rch', 'RcHm_v2.0_Chr5g0018111' => 'rch', 'RcHm_v2.0_Chr5g0021011' => 'rch', 'RcHm_v2.0_Chr5g0081171' => 'rch', 'RcHm_v2.0_Chr5g0081211' => 'rch', 'RcHm_v2.0_Chr6g0275871' => 'rch', 'RcHm_v2.0_Chr6g0276071' => 'rch', 'RcHm_v2.0_Chr6g0285591' => 'rch', 'RcHm_v2.0_Chr6g0291931' => 'rch', 'RcHm_v2.0_Chr6g0292091' => 'rch', 'RcHm_v2.0_Chr6g0292271' => 'rch', 'RcHm_v2.0_Chr7g0221261' => 'rch', 'Rhsim08G0219900' => 'rsi', 'Rhsim08G0220200' => 'rsi', 'Rhsim08G0237800' => 'rsi', 'Rhsim08G0238800' => 'rsi', 'Sabra09G0102700' => 'sbr', 'Sabra09G0127200' => 'sbr', 'Sabra11G0003700' => 'sbr', 'Sabra15G0014700' => 'sbr', 'Sc19g0000590' => 'sci', 'Sc19g0001870' => 'sci', 'SGA_v2.0_scaffold1G00346' => 'sas', 'SGA_v2.0_scaffold1G00575' => 'sas', 'SGA_v2.0_scaffold1G00761' => 'sas', 'SGA_v2.0_scaffold232G43501' => 'sas', 'TAR625G1137' => 'tar', 'Thecc.03G222100' => 'tca', 'TPR.G12691' => 'tpr', 'TWI34G0727' => 'twi', 'TWI36G0117' => 'twi', 'VMungo1309G0868' => 'vmu' ) $gf_id = 'HOM05D001729' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001729' ) $data_identifier = 'HOM05D001729' $data_type = 'gf_id' $species_gene_counts = array( 'amhyb' => (int) 1, 'cqu' => (int) 9, 'can' => (int) 1, 'cansat' => (int) 1, 'car' => (int) 1, 'col' => (int) 5, 'dca' => (int) 1, 'din' => (int) 2, 'dzi' => (int) 3, 'fan' => (int) 140, 'fve' => (int) 62, 'gma' => (int) 1, 'ghi' => (int) 2, 'gra' => (int) 1, 'han' => (int) 1, 'sun' => (int) 1, 'lonja' => (int) 6, 'lja' => (int) 1, 'lsa' => (int) 4, 'mes' => (int) 1, 'mdo' => (int) 14, 'mtr' => (int) 1, 'egut' => (int) 1, 'nta' => (int) 4, 'oeu' => (int) 1, 'stu' => (int) 2, 'pvu' => (int) 1, 'ptr' => (int) 4, 'ppe' => (int) 19, 'psa' => (int) 1, 'pso' => (int) 4, 'qlo' => (int) 36, 'rch' => (int) 23, 'rsi' => (int) 4, 'sbr' => (int) 4, 'sci' => (int) 2, 'sas' => (int) 4, 'tar' => (int) 1, 'tca' => (int) 1, 'tpr' => (int) 1, 'twi' => (int) 2, 'vmu' => (int) 1 ) $gf_gene_species = 'vmu' $gf_gene_id = 'VMungo1309G0868' $species_info = array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ) $local_species = 'dzi' $disabled = '' $selected = '' $num_hits = (int) 1include - APP/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp, line 33 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933 View::_renderElement() - CORE/Cake/View/View.php, line 1224 View::element() - CORE/Cake/View/View.php, line 418 include - APP/View/Elements/analysis/phylogenetics_module/gf_data_settings.ctp, line 37 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933 View::_renderElement() - CORE/Cake/View/View.php, line 1224 View::element() - CORE/Cake/View/View.php, line 418 include - APP/View/Elements/analysis/phylogenetics_module/parameter_selection.ctp, line 64 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933 View::_renderElement() - CORE/Cake/View/View.php, line 1224 View::element() - CORE/Cake/View/View.php, line 418 include - APP/View/Analysis/custom_tree_creation.ctp, line 27 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933
$viewFile = '/www/bioinformatics01_ro/plaza/_dev_instances/feedback/app/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp' $dataForView = array( 'sidebar_info' => array( 'gf_id' => 'HOM05D001729', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '375', 'num_species' => '42' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'Ah.07g204710' => 'amhyb', 'AUR62006001' => 'cqu', 'AUR62006002' => 'cqu', 'AUR62006003' => 'cqu', 'AUR62015641' => 'cqu', 'AUR62027174' => 'cqu', 'AUR62035623' => 'cqu', 'AUR62035624' => 'cqu', 'AUR62035625' => 'cqu', 'AUR62035626' => 'cqu', 'CAN.G1110.53' => 'can', 'CANSAT80G0415' => 'cansat', 'Ca_21364_v3' => 'car', 'COL.COLO4_30693' => 'col', 'COL.COLO4_30694' => 'col', 'COL.COLO4_30695' => 'col', 'COL.COLO4_30696' => 'col', 'COL.COLO4_34020' => 'col', 'DCAR_004585' => 'dca', 'Dinv04029' => 'din', 'Dinv34857' => 'din', 'Duzib147G0011' => 'dzi', 'Duzib170G0599' => 'dzi', 'Duzib192G1051' => 'dzi', 'FAN01G0708' => 'fan', 'FAN01G0742' => 'fan', 'FAN02G0048' => 'fan', 'FAN02G0583' => 'fan', 'FAN02G0688' => 'fan', 'FAN02G1588' => 'fan', 'FAN02G2194' => 'fan', 'FAN02G2750' => 'fan', 'FAN02G3094' => 'fan', 'FAN02G3887' => 'fan', 'FAN02G3911' => 'fan', 'FAN02G3994' => 'fan', 'FAN02G4432' => 'fan', 'FAN02G4556' => 'fan', 'FAN03G1977' => 'fan', 'FAN03G2781' => 'fan', 'FAN03G2850' => 'fan', 'FAN03G3155' => 'fan', 'FAN04G2487' => 'fan', 'FAN05G0208' => 'fan', 'FAN05G0656' => 'fan', 'FAN05G0696' => 'fan', 'FAN05G0810' => 'fan', 'FAN05G1447' => 'fan', 'FAN05G2640' => 'fan', 'FAN05G2911' => 'fan', 'FAN05G3901' => 'fan', 'FAN05G4859' => 'fan', 'FAN05G4861' => 'fan', 'FAN05G4988' => 'fan', 'FAN05G5187' => 'fan', 'FAN05G5452' => 'fan', 'FAN05G5500' => 'fan', 'FAN05G5688' => 'fan', 'FAN06G0177' => 'fan', 'FAN06G0675' => 'fan', 'FAN06G1290' => 'fan', 'FAN06G2191' => 'fan', 'FAN06G2405' => 'fan', 'FAN06G3231' => 'fan', 'FAN06G3932' => 'fan', 'FAN07G0163' => 'fan', 'FAN07G0471' => 'fan', 'FAN07G1354' => 'fan', 'FAN08G0338' => 'fan', 'FAN08G1373' => 'fan', 'FAN08G2539' => 'fan', 'FAN08G2728' => 'fan', 'FAN09G0608' => 'fan', 'FAN09G1136' => 'fan', 'FAN09G1958' => 'fan', 'FAN09G2508' => 'fan', 'FAN09G2597' => 'fan', 'FAN09G2658' => 'fan', 'FAN09G2757' => 'fan', 'FAN09G2983' => 'fan', 'FAN09G3130' => 'fan', 'FAN09G3565' => 'fan', 'FAN09G3613' => 'fan', 'FAN09G4011' => 'fan', 'FAN09G4239' => 'fan', 'FAN09G4277' => 'fan', 'FAN09G4720' => 'fan', 'FAN11G0139' => 'fan', 'FAN11G1727' => 'fan', 'FAN11G2672' => 'fan', 'FAN11G2795' => 'fan', 'FAN11G3238' => 'fan', 'FAN11G3734' => 'fan', 'FAN12G0631' => 'fan', 'FAN12G2239' => 'fan', 'FAN12G2308' => 'fan', 'FAN12G2569' => 'fan', 'FAN12G2623' => 'fan', 'FAN13G3182' => 'fan', 'FAN14G0053' => 'fan', 'FAN14G0370' => 'fan', 'FAN14G0382' => 'fan', 'FAN14G0421' => 'fan', 'FAN14G0866' => 'fan', 'FAN14G1187' => 'fan', 'FAN14G1727' => 'fan', 'FAN14G1791' => 'fan', 'FAN14G2361' => 'fan', 'FAN14G2668' => 'fan', 'FAN14G2770' => 'fan', 'FAN14G2874' => 'fan', 'FAN14G3193' => 'fan', 'FAN14G3624' => 'fan', 'FAN14G3676' => 'fan', 'FAN14G3807' => 'fan', 'FAN14G4082' => 'fan', 'FAN14G4342' => 'fan', 'FAN14G4985' => 'fan', 'FAN14G5126' => 'fan', 'FAN14G5781' => 'fan', 'FAN14G5808' => 'fan', 'FAN14G5949' => 'fan', 'FAN15G0828' => 'fan', 'FAN15G1054' => 'fan', 'FAN15G2023' => 'fan', 'FAN15G2506' => 'fan', 'FAN16G0128' => 'fan', 'FAN16G0249' => 'fan', 'FAN16G0429' => 'fan', 'FAN16G1493' => 'fan', 'FAN16G2210' => 'fan', 'FAN16G2506' => 'fan', 'FAN18G1542' => 'fan', 'FAN18G4057' => 'fan', 'FAN19G0745' => 'fan', 'FAN19G1216' => 'fan', 'FAN19G1733' => 'fan', 'FAN20G0258' => 'fan', 'FAN20G1095' => 'fan', 'FAN20G1557' => 'fan', 'FAN21G0302' => 'fan', 'FAN21G0519' => 'fan', 'FAN21G0970' => 'fan', 'FAN21G1159' => 'fan', 'FAN21G1312' => 'fan', 'FAN21G1440' => 'fan', 'FAN21G1715' => 'fan', 'FAN23G1584' => 'fan', 'FAN24G0045' => 'fan', 'FAN24G0053' => 'fan', 'FAN24G1500' => 'fan', 'FAN24G1817' => 'fan', 'FAN24G2147' => 'fan', 'FAN24G2236' => 'fan', 'FAN24G2446' => 'fan', 'FAN24G2684' => 'fan', 'FAN25G0187' => 'fan', 'FAN25G0505' => 'fan', 'FAN25G0589' => 'fan', 'FAN25G3663' => 'fan', 'FAN26G1025' => 'fan', 'FAN26G2860' => 'fan', 'FAN27G1329' => 'fan', 'FAN27G3392' => 'fan', 'FvH4_1g02011' => 'fve', 'FvH4_1g06511' => 'fve', 'FvH4_2g19900' => 'fve', 'FvH4_2g19920' => 'fve', 'FvH4_2g24261' => 'fve', 'FvH4_2g24270' => 'fve', 'FvH4_2g24631' => 'fve', 'FvH4_2g30622' => 'fve', 'FvH4_3g12920' => 'fve', 'FvH4_3g30171' => 'fve', 'FvH4_3g35490' => 'fve', 'FvH4_3g43682' => 'fve', 'FvH4_3g43730' => 'fve', 'FvH4_3g43732' => 'fve', 'FvH4_3g43751' => 'fve', 'FvH4_3g43752' => 'fve', 'FvH4_3g43770' => 'fve', 'FvH4_3g44471' => 'fve', 'FvH4_3g44510' => 'fve', 'FvH4_3g44582' => 'fve', 'FvH4_4g16921' => 'fve', 'FvH4_4g17121' => 'fve', 'FvH4_4g17782' => 'fve', 'FvH4_4g17783' => 'fve', 'FvH4_4g18120' => 'fve', 'FvH4_4g31310' => 'fve', 'FvH4_4g35052' => 'fve', 'FvH4_5g30862' => 'fve', 'FvH4_6g01541' => 'fve', 'FvH4_6g02021' => 'fve', 'FvH4_6g02041' => 'fve', 'FvH4_6g02071' => 'fve', 'FvH4_6g02171' => 'fve', 'FvH4_6g03181' => 'fve', 'FvH4_6g03182' => 'fve', 'FvH4_6g03221' => 'fve', 'FvH4_6g03380' => 'fve', 'FvH4_6g05201' => 'fve', 'FvH4_6g05203' => 'fve', 'FvH4_6g20231' => 'fve', 'FvH4_6g31981' => 'fve', 'FvH4_6g32061' => 'fve', 'FvH4_6g37041' => 'fve', 'FvH4_6g37932' => 'fve', 'FvH4_6g38731' => 'fve', 'FvH4_6g39370' => 'fve', 'FvH4_6g39371' => 'fve', 'FvH4_6g40891' => 'fve', 'FvH4_6g40892' => 'fve', 'FvH4_6g43143' => 'fve', 'FvH4_6g45251' => 'fve', 'FvH4_6g45260' => 'fve', 'FvH4_6g45291' => 'fve', 'FvH4_6g45890' => 'fve', 'FvH4_6g46240' => 'fve', 'FvH4_6g46241' => 'fve', 'FvH4_6g46242' => 'fve', 'FvH4_6g46260' => 'fve', 'FvH4_6g46280' => 'fve', 'FvH4_6g46380' => 'fve', 'FvH4_7g12841' => 'fve', 'FvH4_7g31431' => 'fve', 'Glyma.09G075900' => 'gma', 'Gohir.A09G096401' => 'ghi', 'Gohir.D09G096101' => 'ghi', 'Gorai.006G112800' => 'gra', 'HanXRQChr04g0121411' => 'han', 'Hund15878' => 'sun', 'Lj2A1107G68' => 'lonja', 'Lj2A630G63' => 'lonja', 'Lj2A946T25' => 'lonja', 'Lj2C714T1' => 'lonja', 'Lj2C966T3' => 'lonja', 'Lj2C966T4' => 'lonja', 'Lj4g0002979' => 'lja', 'Lsat_1_v5_gn_5_30901' => 'lsa', 'Lsat_1_v5_gn_5_31100' => 'lsa', 'Lsat_1_v5_gn_5_38600' => 'lsa', 'Lsat_1_v5_gn_6_92061' => 'lsa', 'Manes.05G071301' => 'mes', 'MD02G1008700' => 'mdo', 'MD02G1008900' => 'mdo', 'MD03G1256400' => 'mdo', 'MD04G1180900' => 'mdo', 'MD04G1181000' => 'mdo', 'MD04G1181200' => 'mdo', 'MD05G1244200' => 'mdo', 'MD05G1324200' => 'mdo', 'MD09G1201600' => 'mdo', 'MD10G1000600' => 'mdo', 'MD14G1026900' => 'mdo', 'MD14G1187900' => 'mdo', 'MD15G1017800' => 'mdo', 'MD15G1018100' => 'mdo', 'Medtr4g124160' => 'mtr', 'Migut.L01260' => 'egut', 'Nitab4.5_0000008g0440' => 'nta', 'Nitab4.5_0000207g0170' => 'nta', 'Nitab4.5_0007671g0030' => 'nta', 'Nitab4.5_0010853g0020' => 'nta', 'Oeu057656.1' => 'oeu', 'PGSC0003DMG400005638' => 'stu', 'PGSC0003DMG400005639' => 'stu', 'Phvul.009G222800' => 'pvu', 'Potri.009G132400' => 'ptr', 'Potri.009G163001' => 'ptr', 'Potri.011G000700' => 'ptr', 'Potri.011G004800' => 'ptr', 'Prupe.1G509300' => 'ppe', 'Prupe.1G509700' => 'ppe', 'Prupe.1G510400' => 'ppe', 'Prupe.1G510700' => 'ppe', 'Prupe.1G512600' => 'ppe', 'Prupe.2G073200' => 'ppe', 'Prupe.3G059500' => 'ppe', 'Prupe.3G059600' => 'ppe', 'Prupe.3G246100' => 'ppe', 'Prupe.3G265100' => 'ppe', 'Prupe.4G034700' => 'ppe', 'Prupe.4G052100' => 'ppe', 'Prupe.4G053600' => 'ppe', 'Prupe.5G068800' => 'ppe', 'Prupe.5G070600' => 'ppe', 'Prupe.6G075400' => 'ppe', 'Prupe.6G075500' => 'ppe', 'Prupe.6G076400' => 'ppe', 'Prupe.8G110700' => 'ppe', 'Psat4g020960' => 'psa', 'PSO135G0788' => 'pso', 'PSO210G6463' => 'pso', 'PSO384G0370' => 'pso', 'PSO386G0056' => 'pso', 'QL01p006048' => 'qlo', 'QL02p054283' => 'qlo', 'QL05p008000' => 'qlo', 'QL05p008212' => 'qlo', 'QL05p008950' => 'qlo', 'QL05p009042' => 'qlo', 'QL05p009518' => 'qlo', 'QL05p012589' => 'qlo', 'QL05p012608' => 'qlo', 'QL05p012650' => 'qlo', 'QL05p012667' => 'qlo', 'QL05p014501' => 'qlo', 'QL05p052800' => 'qlo', 'QL05p065010' => 'qlo', 'QL05p074156' => 'qlo', 'QL05p074160' => 'qlo', 'QL05p074174' => 'qlo', 'QL05p074178' => 'qlo', 'QL05p074214' => 'qlo', 'QL06p001050' => 'qlo', 'QL06p001056' => 'qlo', 'QL06p006093' => 'qlo', 'QL06p006111' => 'qlo', 'QL07p019784' => 'qlo', 'QL07p019801' => 'qlo', 'QL07p036110' => 'qlo', 'QL07p036134' => 'qlo', 'QL07p036147' => 'qlo', 'QL07p036156' => 'qlo', 'QL07p036300' => 'qlo', 'QL07p036320' => 'qlo', 'QL08p014547' => 'qlo', 'QL08p014551' => 'qlo', 'QL08p043319' => 'qlo', 'QL08p043324' => 'qlo', 'QL11p009094' => 'qlo', 'RcHm_v2.0_Chr1g0380481' => 'rch', 'RcHm_v2.0_Chr2g0089331' => 'rch', 'RcHm_v2.0_Chr2g0123691' => 'rch', 'RcHm_v2.0_Chr2g0151111' => 'rch', 'RcHm_v2.0_Chr2g0163011' => 'rch', 'RcHm_v2.0_Chr2g0163051' => 'rch', 'RcHm_v2.0_Chr2g0164671' => 'rch', 'RcHm_v2.0_Chr2g0164681' => 'rch', 'RcHm_v2.0_Chr2g0164721' => 'rch', 'RcHm_v2.0_Chr3g0449911' => 'rch', 'RcHm_v2.0_Chr3g0450211' => 'rch', 'RcHm_v2.0_Chr3g0457271' => 'rch', 'RcHm_v2.0_Chr5g0018111' => 'rch', 'RcHm_v2.0_Chr5g0021011' => 'rch', 'RcHm_v2.0_Chr5g0081171' => 'rch', 'RcHm_v2.0_Chr5g0081211' => 'rch', 'RcHm_v2.0_Chr6g0275871' => 'rch', 'RcHm_v2.0_Chr6g0276071' => 'rch', 'RcHm_v2.0_Chr6g0285591' => 'rch', 'RcHm_v2.0_Chr6g0291931' => 'rch', 'RcHm_v2.0_Chr6g0292091' => 'rch', 'RcHm_v2.0_Chr6g0292271' => 'rch', 'RcHm_v2.0_Chr7g0221261' => 'rch', 'Rhsim08G0219900' => 'rsi', 'Rhsim08G0220200' => 'rsi', 'Rhsim08G0237800' => 'rsi', 'Rhsim08G0238800' => 'rsi', 'Sabra09G0102700' => 'sbr', 'Sabra09G0127200' => 'sbr', 'Sabra11G0003700' => 'sbr', 'Sabra15G0014700' => 'sbr', 'Sc19g0000590' => 'sci', 'Sc19g0001870' => 'sci', 'SGA_v2.0_scaffold1G00346' => 'sas', 'SGA_v2.0_scaffold1G00575' => 'sas', 'SGA_v2.0_scaffold1G00761' => 'sas', 'SGA_v2.0_scaffold232G43501' => 'sas', 'TAR625G1137' => 'tar', 'Thecc.03G222100' => 'tca', 'TPR.G12691' => 'tpr', 'TWI34G0727' => 'twi', 'TWI36G0117' => 'twi', 'VMungo1309G0868' => 'vmu' ), 'gf_id' => 'HOM05D001729', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001729' ), 'data_identifier' => 'HOM05D001729', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001729', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '375', 'num_species' => '42' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'Ah.07g204710' => 'amhyb', 'AUR62006001' => 'cqu', 'AUR62006002' => 'cqu', 'AUR62006003' => 'cqu', 'AUR62015641' => 'cqu', 'AUR62027174' => 'cqu', 'AUR62035623' => 'cqu', 'AUR62035624' => 'cqu', 'AUR62035625' => 'cqu', 'AUR62035626' => 'cqu', 'CAN.G1110.53' => 'can', 'CANSAT80G0415' => 'cansat', 'Ca_21364_v3' => 'car', 'COL.COLO4_30693' => 'col', 'COL.COLO4_30694' => 'col', 'COL.COLO4_30695' => 'col', 'COL.COLO4_30696' => 'col', 'COL.COLO4_34020' => 'col', 'DCAR_004585' => 'dca', 'Dinv04029' => 'din', 'Dinv34857' => 'din', 'Duzib147G0011' => 'dzi', 'Duzib170G0599' => 'dzi', 'Duzib192G1051' => 'dzi', 'FAN01G0708' => 'fan', 'FAN01G0742' => 'fan', 'FAN02G0048' => 'fan', 'FAN02G0583' => 'fan', 'FAN02G0688' => 'fan', 'FAN02G1588' => 'fan', 'FAN02G2194' => 'fan', 'FAN02G2750' => 'fan', 'FAN02G3094' => 'fan', 'FAN02G3887' => 'fan', 'FAN02G3911' => 'fan', 'FAN02G3994' => 'fan', 'FAN02G4432' => 'fan', 'FAN02G4556' => 'fan', 'FAN03G1977' => 'fan', 'FAN03G2781' => 'fan', 'FAN03G2850' => 'fan', 'FAN03G3155' => 'fan', 'FAN04G2487' => 'fan', 'FAN05G0208' => 'fan', 'FAN05G0656' => 'fan', 'FAN05G0696' => 'fan', 'FAN05G0810' => 'fan', 'FAN05G1447' => 'fan', 'FAN05G2640' => 'fan', 'FAN05G2911' => 'fan', 'FAN05G3901' => 'fan', 'FAN05G4859' => 'fan', 'FAN05G4861' => 'fan', 'FAN05G4988' => 'fan', 'FAN05G5187' => 'fan', 'FAN05G5452' => 'fan', 'FAN05G5500' => 'fan', 'FAN05G5688' => 'fan', 'FAN06G0177' => 'fan', 'FAN06G0675' => 'fan', 'FAN06G1290' => 'fan', 'FAN06G2191' => 'fan', 'FAN06G2405' => 'fan', 'FAN06G3231' => 'fan', 'FAN06G3932' => 'fan', 'FAN07G0163' => 'fan', 'FAN07G0471' => 'fan', 'FAN07G1354' => 'fan', 'FAN08G0338' => 'fan', 'FAN08G1373' => 'fan', 'FAN08G2539' => 'fan', 'FAN08G2728' => 'fan', 'FAN09G0608' => 'fan', 'FAN09G1136' => 'fan', 'FAN09G1958' => 'fan', 'FAN09G2508' => 'fan', 'FAN09G2597' => 'fan', 'FAN09G2658' => 'fan', 'FAN09G2757' => 'fan', 'FAN09G2983' => 'fan', 'FAN09G3130' => 'fan', 'FAN09G3565' => 'fan', 'FAN09G3613' => 'fan', 'FAN09G4011' => 'fan', 'FAN09G4239' => 'fan', 'FAN09G4277' => 'fan', 'FAN09G4720' => 'fan', 'FAN11G0139' => 'fan', 'FAN11G1727' => 'fan', 'FAN11G2672' => 'fan', 'FAN11G2795' => 'fan', 'FAN11G3238' => 'fan', 'FAN11G3734' => 'fan', 'FAN12G0631' => 'fan', 'FAN12G2239' => 'fan', 'FAN12G2308' => 'fan', 'FAN12G2569' => 'fan', 'FAN12G2623' => 'fan', 'FAN13G3182' => 'fan', 'FAN14G0053' => 'fan', 'FAN14G0370' => 'fan', 'FAN14G0382' => 'fan', 'FAN14G0421' => 'fan', 'FAN14G0866' => 'fan', 'FAN14G1187' => 'fan', 'FAN14G1727' => 'fan', 'FAN14G1791' => 'fan', 'FAN14G2361' => 'fan', 'FAN14G2668' => 'fan', 'FAN14G2770' => 'fan', 'FAN14G2874' => 'fan', 'FAN14G3193' => 'fan', 'FAN14G3624' => 'fan', 'FAN14G3676' => 'fan', 'FAN14G3807' => 'fan', 'FAN14G4082' => 'fan', 'FAN14G4342' => 'fan', 'FAN14G4985' => 'fan', 'FAN14G5126' => 'fan', 'FAN14G5781' => 'fan', 'FAN14G5808' => 'fan', 'FAN14G5949' => 'fan', 'FAN15G0828' => 'fan', 'FAN15G1054' => 'fan', 'FAN15G2023' => 'fan', 'FAN15G2506' => 'fan', 'FAN16G0128' => 'fan', 'FAN16G0249' => 'fan', 'FAN16G0429' => 'fan', 'FAN16G1493' => 'fan', 'FAN16G2210' => 'fan', 'FAN16G2506' => 'fan', 'FAN18G1542' => 'fan', 'FAN18G4057' => 'fan', 'FAN19G0745' => 'fan', 'FAN19G1216' => 'fan', 'FAN19G1733' => 'fan', 'FAN20G0258' => 'fan', 'FAN20G1095' => 'fan', 'FAN20G1557' => 'fan', 'FAN21G0302' => 'fan', 'FAN21G0519' => 'fan', 'FAN21G0970' => 'fan', 'FAN21G1159' => 'fan', 'FAN21G1312' => 'fan', 'FAN21G1440' => 'fan', 'FAN21G1715' => 'fan', 'FAN23G1584' => 'fan', 'FAN24G0045' => 'fan', 'FAN24G0053' => 'fan', 'FAN24G1500' => 'fan', 'FAN24G1817' => 'fan', 'FAN24G2147' => 'fan', 'FAN24G2236' => 'fan', 'FAN24G2446' => 'fan', 'FAN24G2684' => 'fan', 'FAN25G0187' => 'fan', 'FAN25G0505' => 'fan', 'FAN25G0589' => 'fan', 'FAN25G3663' => 'fan', 'FAN26G1025' => 'fan', 'FAN26G2860' => 'fan', 'FAN27G1329' => 'fan', 'FAN27G3392' => 'fan', 'FvH4_1g02011' => 'fve', 'FvH4_1g06511' => 'fve', 'FvH4_2g19900' => 'fve', 'FvH4_2g19920' => 'fve', 'FvH4_2g24261' => 'fve', 'FvH4_2g24270' => 'fve', 'FvH4_2g24631' => 'fve', 'FvH4_2g30622' => 'fve', 'FvH4_3g12920' => 'fve', 'FvH4_3g30171' => 'fve', 'FvH4_3g35490' => 'fve', 'FvH4_3g43682' => 'fve', 'FvH4_3g43730' => 'fve', 'FvH4_3g43732' => 'fve', 'FvH4_3g43751' => 'fve', 'FvH4_3g43752' => 'fve', 'FvH4_3g43770' => 'fve', 'FvH4_3g44471' => 'fve', 'FvH4_3g44510' => 'fve', 'FvH4_3g44582' => 'fve', 'FvH4_4g16921' => 'fve', 'FvH4_4g17121' => 'fve', 'FvH4_4g17782' => 'fve', 'FvH4_4g17783' => 'fve', 'FvH4_4g18120' => 'fve', 'FvH4_4g31310' => 'fve', 'FvH4_4g35052' => 'fve', 'FvH4_5g30862' => 'fve', 'FvH4_6g01541' => 'fve', 'FvH4_6g02021' => 'fve', 'FvH4_6g02041' => 'fve', 'FvH4_6g02071' => 'fve', 'FvH4_6g02171' => 'fve', 'FvH4_6g03181' => 'fve', 'FvH4_6g03182' => 'fve', 'FvH4_6g03221' => 'fve', 'FvH4_6g03380' => 'fve', 'FvH4_6g05201' => 'fve', 'FvH4_6g05203' => 'fve', 'FvH4_6g20231' => 'fve', 'FvH4_6g31981' => 'fve', 'FvH4_6g32061' => 'fve', 'FvH4_6g37041' => 'fve', 'FvH4_6g37932' => 'fve', 'FvH4_6g38731' => 'fve', 'FvH4_6g39370' => 'fve', 'FvH4_6g39371' => 'fve', 'FvH4_6g40891' => 'fve', 'FvH4_6g40892' => 'fve', 'FvH4_6g43143' => 'fve', 'FvH4_6g45251' => 'fve', 'FvH4_6g45260' => 'fve', 'FvH4_6g45291' => 'fve', 'FvH4_6g45890' => 'fve', 'FvH4_6g46240' => 'fve', 'FvH4_6g46241' => 'fve', 'FvH4_6g46242' => 'fve', 'FvH4_6g46260' => 'fve', 'FvH4_6g46280' => 'fve', 'FvH4_6g46380' => 'fve', 'FvH4_7g12841' => 'fve', 'FvH4_7g31431' => 'fve', 'Glyma.09G075900' => 'gma', 'Gohir.A09G096401' => 'ghi', 'Gohir.D09G096101' => 'ghi', 'Gorai.006G112800' => 'gra', 'HanXRQChr04g0121411' => 'han', 'Hund15878' => 'sun', 'Lj2A1107G68' => 'lonja', 'Lj2A630G63' => 'lonja', 'Lj2A946T25' => 'lonja', 'Lj2C714T1' => 'lonja', 'Lj2C966T3' => 'lonja', 'Lj2C966T4' => 'lonja', 'Lj4g0002979' => 'lja', 'Lsat_1_v5_gn_5_30901' => 'lsa', 'Lsat_1_v5_gn_5_31100' => 'lsa', 'Lsat_1_v5_gn_5_38600' => 'lsa', 'Lsat_1_v5_gn_6_92061' => 'lsa', 'Manes.05G071301' => 'mes', 'MD02G1008700' => 'mdo', 'MD02G1008900' => 'mdo', 'MD03G1256400' => 'mdo', 'MD04G1180900' => 'mdo', 'MD04G1181000' => 'mdo', 'MD04G1181200' => 'mdo', 'MD05G1244200' => 'mdo', 'MD05G1324200' => 'mdo', 'MD09G1201600' => 'mdo', 'MD10G1000600' => 'mdo', 'MD14G1026900' => 'mdo', 'MD14G1187900' => 'mdo', 'MD15G1017800' => 'mdo', 'MD15G1018100' => 'mdo', 'Medtr4g124160' => 'mtr', 'Migut.L01260' => 'egut', 'Nitab4.5_0000008g0440' => 'nta', 'Nitab4.5_0000207g0170' => 'nta', 'Nitab4.5_0007671g0030' => 'nta', 'Nitab4.5_0010853g0020' => 'nta', 'Oeu057656.1' => 'oeu', 'PGSC0003DMG400005638' => 'stu', 'PGSC0003DMG400005639' => 'stu', 'Phvul.009G222800' => 'pvu', 'Potri.009G132400' => 'ptr', 'Potri.009G163001' => 'ptr', 'Potri.011G000700' => 'ptr', 'Potri.011G004800' => 'ptr', 'Prupe.1G509300' => 'ppe', 'Prupe.1G509700' => 'ppe', 'Prupe.1G510400' => 'ppe', 'Prupe.1G510700' => 'ppe', 'Prupe.1G512600' => 'ppe', 'Prupe.2G073200' => 'ppe', 'Prupe.3G059500' => 'ppe', 'Prupe.3G059600' => 'ppe', 'Prupe.3G246100' => 'ppe', 'Prupe.3G265100' => 'ppe', 'Prupe.4G034700' => 'ppe', 'Prupe.4G052100' => 'ppe', 'Prupe.4G053600' => 'ppe', 'Prupe.5G068800' => 'ppe', 'Prupe.5G070600' => 'ppe', 'Prupe.6G075400' => 'ppe', 'Prupe.6G075500' => 'ppe', 'Prupe.6G076400' => 'ppe', 'Prupe.8G110700' => 'ppe', 'Psat4g020960' => 'psa', 'PSO135G0788' => 'pso', 'PSO210G6463' => 'pso', 'PSO384G0370' => 'pso', 'PSO386G0056' => 'pso', 'QL01p006048' => 'qlo', 'QL02p054283' => 'qlo', 'QL05p008000' => 'qlo', 'QL05p008212' => 'qlo', 'QL05p008950' => 'qlo', 'QL05p009042' => 'qlo', 'QL05p009518' => 'qlo', 'QL05p012589' => 'qlo', 'QL05p012608' => 'qlo', 'QL05p012650' => 'qlo', 'QL05p012667' => 'qlo', 'QL05p014501' => 'qlo', 'QL05p052800' => 'qlo', 'QL05p065010' => 'qlo', 'QL05p074156' => 'qlo', 'QL05p074160' => 'qlo', 'QL05p074174' => 'qlo', 'QL05p074178' => 'qlo', 'QL05p074214' => 'qlo', 'QL06p001050' => 'qlo', 'QL06p001056' => 'qlo', 'QL06p006093' => 'qlo', 'QL06p006111' => 'qlo', 'QL07p019784' => 'qlo', 'QL07p019801' => 'qlo', 'QL07p036110' => 'qlo', 'QL07p036134' => 'qlo', 'QL07p036147' => 'qlo', 'QL07p036156' => 'qlo', 'QL07p036300' => 'qlo', 'QL07p036320' => 'qlo', 'QL08p014547' => 'qlo', 'QL08p014551' => 'qlo', 'QL08p043319' => 'qlo', 'QL08p043324' => 'qlo', 'QL11p009094' => 'qlo', 'RcHm_v2.0_Chr1g0380481' => 'rch', 'RcHm_v2.0_Chr2g0089331' => 'rch', 'RcHm_v2.0_Chr2g0123691' => 'rch', 'RcHm_v2.0_Chr2g0151111' => 'rch', 'RcHm_v2.0_Chr2g0163011' => 'rch', 'RcHm_v2.0_Chr2g0163051' => 'rch', 'RcHm_v2.0_Chr2g0164671' => 'rch', 'RcHm_v2.0_Chr2g0164681' => 'rch', 'RcHm_v2.0_Chr2g0164721' => 'rch', 'RcHm_v2.0_Chr3g0449911' => 'rch', 'RcHm_v2.0_Chr3g0450211' => 'rch', 'RcHm_v2.0_Chr3g0457271' => 'rch', 'RcHm_v2.0_Chr5g0018111' => 'rch', 'RcHm_v2.0_Chr5g0021011' => 'rch', 'RcHm_v2.0_Chr5g0081171' => 'rch', 'RcHm_v2.0_Chr5g0081211' => 'rch', 'RcHm_v2.0_Chr6g0275871' => 'rch', 'RcHm_v2.0_Chr6g0276071' => 'rch', 'RcHm_v2.0_Chr6g0285591' => 'rch', 'RcHm_v2.0_Chr6g0291931' => 'rch', 'RcHm_v2.0_Chr6g0292091' => 'rch', 'RcHm_v2.0_Chr6g0292271' => 'rch', 'RcHm_v2.0_Chr7g0221261' => 'rch', 'Rhsim08G0219900' => 'rsi', 'Rhsim08G0220200' => 'rsi', 'Rhsim08G0237800' => 'rsi', 'Rhsim08G0238800' => 'rsi', 'Sabra09G0102700' => 'sbr', 'Sabra09G0127200' => 'sbr', 'Sabra11G0003700' => 'sbr', 'Sabra15G0014700' => 'sbr', 'Sc19g0000590' => 'sci', 'Sc19g0001870' => 'sci', 'SGA_v2.0_scaffold1G00346' => 'sas', 'SGA_v2.0_scaffold1G00575' => 'sas', 'SGA_v2.0_scaffold1G00761' => 'sas', 'SGA_v2.0_scaffold232G43501' => 'sas', 'TAR625G1137' => 'tar', 'Thecc.03G222100' => 'tca', 'TPR.G12691' => 'tpr', 'TWI34G0727' => 'twi', 'TWI36G0117' => 'twi', 'VMungo1309G0868' => 'vmu' ) $gf_id = 'HOM05D001729' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001729' ) $data_identifier = 'HOM05D001729' $data_type = 'gf_id' $species_gene_counts = array( 'amhyb' => (int) 1, 'cqu' => (int) 9, 'can' => (int) 1, 'cansat' => (int) 1, 'car' => (int) 1, 'col' => (int) 5, 'dca' => (int) 1, 'din' => (int) 2, 'dzi' => (int) 3, 'fan' => (int) 140, 'fve' => (int) 62, 'gma' => (int) 1, 'ghi' => (int) 2, 'gra' => (int) 1, 'han' => (int) 1, 'sun' => (int) 1, 'lonja' => (int) 6, 'lja' => (int) 1, 'lsa' => (int) 4, 'mes' => (int) 1, 'mdo' => (int) 14, 'mtr' => (int) 1, 'egut' => (int) 1, 'nta' => (int) 4, 'oeu' => (int) 1, 'stu' => (int) 2, 'pvu' => (int) 1, 'ptr' => (int) 4, 'ppe' => (int) 19, 'psa' => (int) 1, 'pso' => (int) 4, 'qlo' => (int) 36, 'rch' => (int) 23, 'rsi' => (int) 4, 'sbr' => (int) 4, 'sci' => (int) 2, 'sas' => (int) 4, 'tar' => (int) 1, 'tca' => (int) 1, 'tpr' => (int) 1, 'twi' => (int) 2, 'vmu' => (int) 1 ) $gf_gene_species = 'vmu' $gf_gene_id = 'VMungo1309G0868' $species_info = array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ) $local_species = 'dzi' $disabled = '' $selected = '' $num_hits = (int) 1
Warning (2): count(): Parameter must be an array or an object that implements Countable [APP/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp, line 33]Code Context $disabled = (!array_key_exists($local_species,$species_gene_counts))?"disabled":""; $selected = (isset($selected_species) && array_key_exists($local_species,$selected_species))?"checked='checked'":""; $num_hits = (array_key_exists($local_species,$species_gene_counts))?count($species_gene_counts[$local_species]):0; $viewFile = '/www/bioinformatics01_ro/plaza/_dev_instances/feedback/app/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp' $dataForView = array( 'sidebar_info' => array( 'gf_id' => 'HOM05D001729', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '375', 'num_species' => '42' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'Ah.07g204710' => 'amhyb', 'AUR62006001' => 'cqu', 'AUR62006002' => 'cqu', 'AUR62006003' => 'cqu', 'AUR62015641' => 'cqu', 'AUR62027174' => 'cqu', 'AUR62035623' => 'cqu', 'AUR62035624' => 'cqu', 'AUR62035625' => 'cqu', 'AUR62035626' => 'cqu', 'CAN.G1110.53' => 'can', 'CANSAT80G0415' => 'cansat', 'Ca_21364_v3' => 'car', 'COL.COLO4_30693' => 'col', 'COL.COLO4_30694' => 'col', 'COL.COLO4_30695' => 'col', 'COL.COLO4_30696' => 'col', 'COL.COLO4_34020' => 'col', 'DCAR_004585' => 'dca', 'Dinv04029' => 'din', 'Dinv34857' => 'din', 'Duzib147G0011' => 'dzi', 'Duzib170G0599' => 'dzi', 'Duzib192G1051' => 'dzi', 'FAN01G0708' => 'fan', 'FAN01G0742' => 'fan', 'FAN02G0048' => 'fan', 'FAN02G0583' => 'fan', 'FAN02G0688' => 'fan', 'FAN02G1588' => 'fan', 'FAN02G2194' => 'fan', 'FAN02G2750' => 'fan', 'FAN02G3094' => 'fan', 'FAN02G3887' => 'fan', 'FAN02G3911' => 'fan', 'FAN02G3994' => 'fan', 'FAN02G4432' => 'fan', 'FAN02G4556' => 'fan', 'FAN03G1977' => 'fan', 'FAN03G2781' => 'fan', 'FAN03G2850' => 'fan', 'FAN03G3155' => 'fan', 'FAN04G2487' => 'fan', 'FAN05G0208' => 'fan', 'FAN05G0656' => 'fan', 'FAN05G0696' => 'fan', 'FAN05G0810' => 'fan', 'FAN05G1447' => 'fan', 'FAN05G2640' => 'fan', 'FAN05G2911' => 'fan', 'FAN05G3901' => 'fan', 'FAN05G4859' => 'fan', 'FAN05G4861' => 'fan', 'FAN05G4988' => 'fan', 'FAN05G5187' => 'fan', 'FAN05G5452' => 'fan', 'FAN05G5500' => 'fan', 'FAN05G5688' => 'fan', 'FAN06G0177' => 'fan', 'FAN06G0675' => 'fan', 'FAN06G1290' => 'fan', 'FAN06G2191' => 'fan', 'FAN06G2405' => 'fan', 'FAN06G3231' => 'fan', 'FAN06G3932' => 'fan', 'FAN07G0163' => 'fan', 'FAN07G0471' => 'fan', 'FAN07G1354' => 'fan', 'FAN08G0338' => 'fan', 'FAN08G1373' => 'fan', 'FAN08G2539' => 'fan', 'FAN08G2728' => 'fan', 'FAN09G0608' => 'fan', 'FAN09G1136' => 'fan', 'FAN09G1958' => 'fan', 'FAN09G2508' => 'fan', 'FAN09G2597' => 'fan', 'FAN09G2658' => 'fan', 'FAN09G2757' => 'fan', 'FAN09G2983' => 'fan', 'FAN09G3130' => 'fan', 'FAN09G3565' => 'fan', 'FAN09G3613' => 'fan', 'FAN09G4011' => 'fan', 'FAN09G4239' => 'fan', 'FAN09G4277' => 'fan', 'FAN09G4720' => 'fan', 'FAN11G0139' => 'fan', 'FAN11G1727' => 'fan', 'FAN11G2672' => 'fan', 'FAN11G2795' => 'fan', 'FAN11G3238' => 'fan', 'FAN11G3734' => 'fan', 'FAN12G0631' => 'fan', 'FAN12G2239' => 'fan', 'FAN12G2308' => 'fan', 'FAN12G2569' => 'fan', 'FAN12G2623' => 'fan', 'FAN13G3182' => 'fan', 'FAN14G0053' => 'fan', 'FAN14G0370' => 'fan', 'FAN14G0382' => 'fan', 'FAN14G0421' => 'fan', 'FAN14G0866' => 'fan', 'FAN14G1187' => 'fan', 'FAN14G1727' => 'fan', 'FAN14G1791' => 'fan', 'FAN14G2361' => 'fan', 'FAN14G2668' => 'fan', 'FAN14G2770' => 'fan', 'FAN14G2874' => 'fan', 'FAN14G3193' => 'fan', 'FAN14G3624' => 'fan', 'FAN14G3676' => 'fan', 'FAN14G3807' => 'fan', 'FAN14G4082' => 'fan', 'FAN14G4342' => 'fan', 'FAN14G4985' => 'fan', 'FAN14G5126' => 'fan', 'FAN14G5781' => 'fan', 'FAN14G5808' => 'fan', 'FAN14G5949' => 'fan', 'FAN15G0828' => 'fan', 'FAN15G1054' => 'fan', 'FAN15G2023' => 'fan', 'FAN15G2506' => 'fan', 'FAN16G0128' => 'fan', 'FAN16G0249' => 'fan', 'FAN16G0429' => 'fan', 'FAN16G1493' => 'fan', 'FAN16G2210' => 'fan', 'FAN16G2506' => 'fan', 'FAN18G1542' => 'fan', 'FAN18G4057' => 'fan', 'FAN19G0745' => 'fan', 'FAN19G1216' => 'fan', 'FAN19G1733' => 'fan', 'FAN20G0258' => 'fan', 'FAN20G1095' => 'fan', 'FAN20G1557' => 'fan', 'FAN21G0302' => 'fan', 'FAN21G0519' => 'fan', 'FAN21G0970' => 'fan', 'FAN21G1159' => 'fan', 'FAN21G1312' => 'fan', 'FAN21G1440' => 'fan', 'FAN21G1715' => 'fan', 'FAN23G1584' => 'fan', 'FAN24G0045' => 'fan', 'FAN24G0053' => 'fan', 'FAN24G1500' => 'fan', 'FAN24G1817' => 'fan', 'FAN24G2147' => 'fan', 'FAN24G2236' => 'fan', 'FAN24G2446' => 'fan', 'FAN24G2684' => 'fan', 'FAN25G0187' => 'fan', 'FAN25G0505' => 'fan', 'FAN25G0589' => 'fan', 'FAN25G3663' => 'fan', 'FAN26G1025' => 'fan', 'FAN26G2860' => 'fan', 'FAN27G1329' => 'fan', 'FAN27G3392' => 'fan', 'FvH4_1g02011' => 'fve', 'FvH4_1g06511' => 'fve', 'FvH4_2g19900' => 'fve', 'FvH4_2g19920' => 'fve', 'FvH4_2g24261' => 'fve', 'FvH4_2g24270' => 'fve', 'FvH4_2g24631' => 'fve', 'FvH4_2g30622' => 'fve', 'FvH4_3g12920' => 'fve', 'FvH4_3g30171' => 'fve', 'FvH4_3g35490' => 'fve', 'FvH4_3g43682' => 'fve', 'FvH4_3g43730' => 'fve', 'FvH4_3g43732' => 'fve', 'FvH4_3g43751' => 'fve', 'FvH4_3g43752' => 'fve', 'FvH4_3g43770' => 'fve', 'FvH4_3g44471' => 'fve', 'FvH4_3g44510' => 'fve', 'FvH4_3g44582' => 'fve', 'FvH4_4g16921' => 'fve', 'FvH4_4g17121' => 'fve', 'FvH4_4g17782' => 'fve', 'FvH4_4g17783' => 'fve', 'FvH4_4g18120' => 'fve', 'FvH4_4g31310' => 'fve', 'FvH4_4g35052' => 'fve', 'FvH4_5g30862' => 'fve', 'FvH4_6g01541' => 'fve', 'FvH4_6g02021' => 'fve', 'FvH4_6g02041' => 'fve', 'FvH4_6g02071' => 'fve', 'FvH4_6g02171' => 'fve', 'FvH4_6g03181' => 'fve', 'FvH4_6g03182' => 'fve', 'FvH4_6g03221' => 'fve', 'FvH4_6g03380' => 'fve', 'FvH4_6g05201' => 'fve', 'FvH4_6g05203' => 'fve', 'FvH4_6g20231' => 'fve', 'FvH4_6g31981' => 'fve', 'FvH4_6g32061' => 'fve', 'FvH4_6g37041' => 'fve', 'FvH4_6g37932' => 'fve', 'FvH4_6g38731' => 'fve', 'FvH4_6g39370' => 'fve', 'FvH4_6g39371' => 'fve', 'FvH4_6g40891' => 'fve', 'FvH4_6g40892' => 'fve', 'FvH4_6g43143' => 'fve', 'FvH4_6g45251' => 'fve', 'FvH4_6g45260' => 'fve', 'FvH4_6g45291' => 'fve', 'FvH4_6g45890' => 'fve', 'FvH4_6g46240' => 'fve', 'FvH4_6g46241' => 'fve', 'FvH4_6g46242' => 'fve', 'FvH4_6g46260' => 'fve', 'FvH4_6g46280' => 'fve', 'FvH4_6g46380' => 'fve', 'FvH4_7g12841' => 'fve', 'FvH4_7g31431' => 'fve', 'Glyma.09G075900' => 'gma', 'Gohir.A09G096401' => 'ghi', 'Gohir.D09G096101' => 'ghi', 'Gorai.006G112800' => 'gra', 'HanXRQChr04g0121411' => 'han', 'Hund15878' => 'sun', 'Lj2A1107G68' => 'lonja', 'Lj2A630G63' => 'lonja', 'Lj2A946T25' => 'lonja', 'Lj2C714T1' => 'lonja', 'Lj2C966T3' => 'lonja', 'Lj2C966T4' => 'lonja', 'Lj4g0002979' => 'lja', 'Lsat_1_v5_gn_5_30901' => 'lsa', 'Lsat_1_v5_gn_5_31100' => 'lsa', 'Lsat_1_v5_gn_5_38600' => 'lsa', 'Lsat_1_v5_gn_6_92061' => 'lsa', 'Manes.05G071301' => 'mes', 'MD02G1008700' => 'mdo', 'MD02G1008900' => 'mdo', 'MD03G1256400' => 'mdo', 'MD04G1180900' => 'mdo', 'MD04G1181000' => 'mdo', 'MD04G1181200' => 'mdo', 'MD05G1244200' => 'mdo', 'MD05G1324200' => 'mdo', 'MD09G1201600' => 'mdo', 'MD10G1000600' => 'mdo', 'MD14G1026900' => 'mdo', 'MD14G1187900' => 'mdo', 'MD15G1017800' => 'mdo', 'MD15G1018100' => 'mdo', 'Medtr4g124160' => 'mtr', 'Migut.L01260' => 'egut', 'Nitab4.5_0000008g0440' => 'nta', 'Nitab4.5_0000207g0170' => 'nta', 'Nitab4.5_0007671g0030' => 'nta', 'Nitab4.5_0010853g0020' => 'nta', 'Oeu057656.1' => 'oeu', 'PGSC0003DMG400005638' => 'stu', 'PGSC0003DMG400005639' => 'stu', 'Phvul.009G222800' => 'pvu', 'Potri.009G132400' => 'ptr', 'Potri.009G163001' => 'ptr', 'Potri.011G000700' => 'ptr', 'Potri.011G004800' => 'ptr', 'Prupe.1G509300' => 'ppe', 'Prupe.1G509700' => 'ppe', 'Prupe.1G510400' => 'ppe', 'Prupe.1G510700' => 'ppe', 'Prupe.1G512600' => 'ppe', 'Prupe.2G073200' => 'ppe', 'Prupe.3G059500' => 'ppe', 'Prupe.3G059600' => 'ppe', 'Prupe.3G246100' => 'ppe', 'Prupe.3G265100' => 'ppe', 'Prupe.4G034700' => 'ppe', 'Prupe.4G052100' => 'ppe', 'Prupe.4G053600' => 'ppe', 'Prupe.5G068800' => 'ppe', 'Prupe.5G070600' => 'ppe', 'Prupe.6G075400' => 'ppe', 'Prupe.6G075500' => 'ppe', 'Prupe.6G076400' => 'ppe', 'Prupe.8G110700' => 'ppe', 'Psat4g020960' => 'psa', 'PSO135G0788' => 'pso', 'PSO210G6463' => 'pso', 'PSO384G0370' => 'pso', 'PSO386G0056' => 'pso', 'QL01p006048' => 'qlo', 'QL02p054283' => 'qlo', 'QL05p008000' => 'qlo', 'QL05p008212' => 'qlo', 'QL05p008950' => 'qlo', 'QL05p009042' => 'qlo', 'QL05p009518' => 'qlo', 'QL05p012589' => 'qlo', 'QL05p012608' => 'qlo', 'QL05p012650' => 'qlo', 'QL05p012667' => 'qlo', 'QL05p014501' => 'qlo', 'QL05p052800' => 'qlo', 'QL05p065010' => 'qlo', 'QL05p074156' => 'qlo', 'QL05p074160' => 'qlo', 'QL05p074174' => 'qlo', 'QL05p074178' => 'qlo', 'QL05p074214' => 'qlo', 'QL06p001050' => 'qlo', 'QL06p001056' => 'qlo', 'QL06p006093' => 'qlo', 'QL06p006111' => 'qlo', 'QL07p019784' => 'qlo', 'QL07p019801' => 'qlo', 'QL07p036110' => 'qlo', 'QL07p036134' => 'qlo', 'QL07p036147' => 'qlo', 'QL07p036156' => 'qlo', 'QL07p036300' => 'qlo', 'QL07p036320' => 'qlo', 'QL08p014547' => 'qlo', 'QL08p014551' => 'qlo', 'QL08p043319' => 'qlo', 'QL08p043324' => 'qlo', 'QL11p009094' => 'qlo', 'RcHm_v2.0_Chr1g0380481' => 'rch', 'RcHm_v2.0_Chr2g0089331' => 'rch', 'RcHm_v2.0_Chr2g0123691' => 'rch', 'RcHm_v2.0_Chr2g0151111' => 'rch', 'RcHm_v2.0_Chr2g0163011' => 'rch', 'RcHm_v2.0_Chr2g0163051' => 'rch', 'RcHm_v2.0_Chr2g0164671' => 'rch', 'RcHm_v2.0_Chr2g0164681' => 'rch', 'RcHm_v2.0_Chr2g0164721' => 'rch', 'RcHm_v2.0_Chr3g0449911' => 'rch', 'RcHm_v2.0_Chr3g0450211' => 'rch', 'RcHm_v2.0_Chr3g0457271' => 'rch', 'RcHm_v2.0_Chr5g0018111' => 'rch', 'RcHm_v2.0_Chr5g0021011' => 'rch', 'RcHm_v2.0_Chr5g0081171' => 'rch', 'RcHm_v2.0_Chr5g0081211' => 'rch', 'RcHm_v2.0_Chr6g0275871' => 'rch', 'RcHm_v2.0_Chr6g0276071' => 'rch', 'RcHm_v2.0_Chr6g0285591' => 'rch', 'RcHm_v2.0_Chr6g0291931' => 'rch', 'RcHm_v2.0_Chr6g0292091' => 'rch', 'RcHm_v2.0_Chr6g0292271' => 'rch', 'RcHm_v2.0_Chr7g0221261' => 'rch', 'Rhsim08G0219900' => 'rsi', 'Rhsim08G0220200' => 'rsi', 'Rhsim08G0237800' => 'rsi', 'Rhsim08G0238800' => 'rsi', 'Sabra09G0102700' => 'sbr', 'Sabra09G0127200' => 'sbr', 'Sabra11G0003700' => 'sbr', 'Sabra15G0014700' => 'sbr', 'Sc19g0000590' => 'sci', 'Sc19g0001870' => 'sci', 'SGA_v2.0_scaffold1G00346' => 'sas', 'SGA_v2.0_scaffold1G00575' => 'sas', 'SGA_v2.0_scaffold1G00761' => 'sas', 'SGA_v2.0_scaffold232G43501' => 'sas', 'TAR625G1137' => 'tar', 'Thecc.03G222100' => 'tca', 'TPR.G12691' => 'tpr', 'TWI34G0727' => 'twi', 'TWI36G0117' => 'twi', 'VMungo1309G0868' => 'vmu' ), 'gf_id' => 'HOM05D001729', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001729' ), 'data_identifier' => 'HOM05D001729', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001729', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '375', 'num_species' => '42' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'Ah.07g204710' => 'amhyb', 'AUR62006001' => 'cqu', 'AUR62006002' => 'cqu', 'AUR62006003' => 'cqu', 'AUR62015641' => 'cqu', 'AUR62027174' => 'cqu', 'AUR62035623' => 'cqu', 'AUR62035624' => 'cqu', 'AUR62035625' => 'cqu', 'AUR62035626' => 'cqu', 'CAN.G1110.53' => 'can', 'CANSAT80G0415' => 'cansat', 'Ca_21364_v3' => 'car', 'COL.COLO4_30693' => 'col', 'COL.COLO4_30694' => 'col', 'COL.COLO4_30695' => 'col', 'COL.COLO4_30696' => 'col', 'COL.COLO4_34020' => 'col', 'DCAR_004585' => 'dca', 'Dinv04029' => 'din', 'Dinv34857' => 'din', 'Duzib147G0011' => 'dzi', 'Duzib170G0599' => 'dzi', 'Duzib192G1051' => 'dzi', 'FAN01G0708' => 'fan', 'FAN01G0742' => 'fan', 'FAN02G0048' => 'fan', 'FAN02G0583' => 'fan', 'FAN02G0688' => 'fan', 'FAN02G1588' => 'fan', 'FAN02G2194' => 'fan', 'FAN02G2750' => 'fan', 'FAN02G3094' => 'fan', 'FAN02G3887' => 'fan', 'FAN02G3911' => 'fan', 'FAN02G3994' => 'fan', 'FAN02G4432' => 'fan', 'FAN02G4556' => 'fan', 'FAN03G1977' => 'fan', 'FAN03G2781' => 'fan', 'FAN03G2850' => 'fan', 'FAN03G3155' => 'fan', 'FAN04G2487' => 'fan', 'FAN05G0208' => 'fan', 'FAN05G0656' => 'fan', 'FAN05G0696' => 'fan', 'FAN05G0810' => 'fan', 'FAN05G1447' => 'fan', 'FAN05G2640' => 'fan', 'FAN05G2911' => 'fan', 'FAN05G3901' => 'fan', 'FAN05G4859' => 'fan', 'FAN05G4861' => 'fan', 'FAN05G4988' => 'fan', 'FAN05G5187' => 'fan', 'FAN05G5452' => 'fan', 'FAN05G5500' => 'fan', 'FAN05G5688' => 'fan', 'FAN06G0177' => 'fan', 'FAN06G0675' => 'fan', 'FAN06G1290' => 'fan', 'FAN06G2191' => 'fan', 'FAN06G2405' => 'fan', 'FAN06G3231' => 'fan', 'FAN06G3932' => 'fan', 'FAN07G0163' => 'fan', 'FAN07G0471' => 'fan', 'FAN07G1354' => 'fan', 'FAN08G0338' => 'fan', 'FAN08G1373' => 'fan', 'FAN08G2539' => 'fan', 'FAN08G2728' => 'fan', 'FAN09G0608' => 'fan', 'FAN09G1136' => 'fan', 'FAN09G1958' => 'fan', 'FAN09G2508' => 'fan', 'FAN09G2597' => 'fan', 'FAN09G2658' => 'fan', 'FAN09G2757' => 'fan', 'FAN09G2983' => 'fan', 'FAN09G3130' => 'fan', 'FAN09G3565' => 'fan', 'FAN09G3613' => 'fan', 'FAN09G4011' => 'fan', 'FAN09G4239' => 'fan', 'FAN09G4277' => 'fan', 'FAN09G4720' => 'fan', 'FAN11G0139' => 'fan', 'FAN11G1727' => 'fan', 'FAN11G2672' => 'fan', 'FAN11G2795' => 'fan', 'FAN11G3238' => 'fan', 'FAN11G3734' => 'fan', 'FAN12G0631' => 'fan', 'FAN12G2239' => 'fan', 'FAN12G2308' => 'fan', 'FAN12G2569' => 'fan', 'FAN12G2623' => 'fan', 'FAN13G3182' => 'fan', 'FAN14G0053' => 'fan', 'FAN14G0370' => 'fan', 'FAN14G0382' => 'fan', 'FAN14G0421' => 'fan', 'FAN14G0866' => 'fan', 'FAN14G1187' => 'fan', 'FAN14G1727' => 'fan', 'FAN14G1791' => 'fan', 'FAN14G2361' => 'fan', 'FAN14G2668' => 'fan', 'FAN14G2770' => 'fan', 'FAN14G2874' => 'fan', 'FAN14G3193' => 'fan', 'FAN14G3624' => 'fan', 'FAN14G3676' => 'fan', 'FAN14G3807' => 'fan', 'FAN14G4082' => 'fan', 'FAN14G4342' => 'fan', 'FAN14G4985' => 'fan', 'FAN14G5126' => 'fan', 'FAN14G5781' => 'fan', 'FAN14G5808' => 'fan', 'FAN14G5949' => 'fan', 'FAN15G0828' => 'fan', 'FAN15G1054' => 'fan', 'FAN15G2023' => 'fan', 'FAN15G2506' => 'fan', 'FAN16G0128' => 'fan', 'FAN16G0249' => 'fan', 'FAN16G0429' => 'fan', 'FAN16G1493' => 'fan', 'FAN16G2210' => 'fan', 'FAN16G2506' => 'fan', 'FAN18G1542' => 'fan', 'FAN18G4057' => 'fan', 'FAN19G0745' => 'fan', 'FAN19G1216' => 'fan', 'FAN19G1733' => 'fan', 'FAN20G0258' => 'fan', 'FAN20G1095' => 'fan', 'FAN20G1557' => 'fan', 'FAN21G0302' => 'fan', 'FAN21G0519' => 'fan', 'FAN21G0970' => 'fan', 'FAN21G1159' => 'fan', 'FAN21G1312' => 'fan', 'FAN21G1440' => 'fan', 'FAN21G1715' => 'fan', 'FAN23G1584' => 'fan', 'FAN24G0045' => 'fan', 'FAN24G0053' => 'fan', 'FAN24G1500' => 'fan', 'FAN24G1817' => 'fan', 'FAN24G2147' => 'fan', 'FAN24G2236' => 'fan', 'FAN24G2446' => 'fan', 'FAN24G2684' => 'fan', 'FAN25G0187' => 'fan', 'FAN25G0505' => 'fan', 'FAN25G0589' => 'fan', 'FAN25G3663' => 'fan', 'FAN26G1025' => 'fan', 'FAN26G2860' => 'fan', 'FAN27G1329' => 'fan', 'FAN27G3392' => 'fan', 'FvH4_1g02011' => 'fve', 'FvH4_1g06511' => 'fve', 'FvH4_2g19900' => 'fve', 'FvH4_2g19920' => 'fve', 'FvH4_2g24261' => 'fve', 'FvH4_2g24270' => 'fve', 'FvH4_2g24631' => 'fve', 'FvH4_2g30622' => 'fve', 'FvH4_3g12920' => 'fve', 'FvH4_3g30171' => 'fve', 'FvH4_3g35490' => 'fve', 'FvH4_3g43682' => 'fve', 'FvH4_3g43730' => 'fve', 'FvH4_3g43732' => 'fve', 'FvH4_3g43751' => 'fve', 'FvH4_3g43752' => 'fve', 'FvH4_3g43770' => 'fve', 'FvH4_3g44471' => 'fve', 'FvH4_3g44510' => 'fve', 'FvH4_3g44582' => 'fve', 'FvH4_4g16921' => 'fve', 'FvH4_4g17121' => 'fve', 'FvH4_4g17782' => 'fve', 'FvH4_4g17783' => 'fve', 'FvH4_4g18120' => 'fve', 'FvH4_4g31310' => 'fve', 'FvH4_4g35052' => 'fve', 'FvH4_5g30862' => 'fve', 'FvH4_6g01541' => 'fve', 'FvH4_6g02021' => 'fve', 'FvH4_6g02041' => 'fve', 'FvH4_6g02071' => 'fve', 'FvH4_6g02171' => 'fve', 'FvH4_6g03181' => 'fve', 'FvH4_6g03182' => 'fve', 'FvH4_6g03221' => 'fve', 'FvH4_6g03380' => 'fve', 'FvH4_6g05201' => 'fve', 'FvH4_6g05203' => 'fve', 'FvH4_6g20231' => 'fve', 'FvH4_6g31981' => 'fve', 'FvH4_6g32061' => 'fve', 'FvH4_6g37041' => 'fve', 'FvH4_6g37932' => 'fve', 'FvH4_6g38731' => 'fve', 'FvH4_6g39370' => 'fve', 'FvH4_6g39371' => 'fve', 'FvH4_6g40891' => 'fve', 'FvH4_6g40892' => 'fve', 'FvH4_6g43143' => 'fve', 'FvH4_6g45251' => 'fve', 'FvH4_6g45260' => 'fve', 'FvH4_6g45291' => 'fve', 'FvH4_6g45890' => 'fve', 'FvH4_6g46240' => 'fve', 'FvH4_6g46241' => 'fve', 'FvH4_6g46242' => 'fve', 'FvH4_6g46260' => 'fve', 'FvH4_6g46280' => 'fve', 'FvH4_6g46380' => 'fve', 'FvH4_7g12841' => 'fve', 'FvH4_7g31431' => 'fve', 'Glyma.09G075900' => 'gma', 'Gohir.A09G096401' => 'ghi', 'Gohir.D09G096101' => 'ghi', 'Gorai.006G112800' => 'gra', 'HanXRQChr04g0121411' => 'han', 'Hund15878' => 'sun', 'Lj2A1107G68' => 'lonja', 'Lj2A630G63' => 'lonja', 'Lj2A946T25' => 'lonja', 'Lj2C714T1' => 'lonja', 'Lj2C966T3' => 'lonja', 'Lj2C966T4' => 'lonja', 'Lj4g0002979' => 'lja', 'Lsat_1_v5_gn_5_30901' => 'lsa', 'Lsat_1_v5_gn_5_31100' => 'lsa', 'Lsat_1_v5_gn_5_38600' => 'lsa', 'Lsat_1_v5_gn_6_92061' => 'lsa', 'Manes.05G071301' => 'mes', 'MD02G1008700' => 'mdo', 'MD02G1008900' => 'mdo', 'MD03G1256400' => 'mdo', 'MD04G1180900' => 'mdo', 'MD04G1181000' => 'mdo', 'MD04G1181200' => 'mdo', 'MD05G1244200' => 'mdo', 'MD05G1324200' => 'mdo', 'MD09G1201600' => 'mdo', 'MD10G1000600' => 'mdo', 'MD14G1026900' => 'mdo', 'MD14G1187900' => 'mdo', 'MD15G1017800' => 'mdo', 'MD15G1018100' => 'mdo', 'Medtr4g124160' => 'mtr', 'Migut.L01260' => 'egut', 'Nitab4.5_0000008g0440' => 'nta', 'Nitab4.5_0000207g0170' => 'nta', 'Nitab4.5_0007671g0030' => 'nta', 'Nitab4.5_0010853g0020' => 'nta', 'Oeu057656.1' => 'oeu', 'PGSC0003DMG400005638' => 'stu', 'PGSC0003DMG400005639' => 'stu', 'Phvul.009G222800' => 'pvu', 'Potri.009G132400' => 'ptr', 'Potri.009G163001' => 'ptr', 'Potri.011G000700' => 'ptr', 'Potri.011G004800' => 'ptr', 'Prupe.1G509300' => 'ppe', 'Prupe.1G509700' => 'ppe', 'Prupe.1G510400' => 'ppe', 'Prupe.1G510700' => 'ppe', 'Prupe.1G512600' => 'ppe', 'Prupe.2G073200' => 'ppe', 'Prupe.3G059500' => 'ppe', 'Prupe.3G059600' => 'ppe', 'Prupe.3G246100' => 'ppe', 'Prupe.3G265100' => 'ppe', 'Prupe.4G034700' => 'ppe', 'Prupe.4G052100' => 'ppe', 'Prupe.4G053600' => 'ppe', 'Prupe.5G068800' => 'ppe', 'Prupe.5G070600' => 'ppe', 'Prupe.6G075400' => 'ppe', 'Prupe.6G075500' => 'ppe', 'Prupe.6G076400' => 'ppe', 'Prupe.8G110700' => 'ppe', 'Psat4g020960' => 'psa', 'PSO135G0788' => 'pso', 'PSO210G6463' => 'pso', 'PSO384G0370' => 'pso', 'PSO386G0056' => 'pso', 'QL01p006048' => 'qlo', 'QL02p054283' => 'qlo', 'QL05p008000' => 'qlo', 'QL05p008212' => 'qlo', 'QL05p008950' => 'qlo', 'QL05p009042' => 'qlo', 'QL05p009518' => 'qlo', 'QL05p012589' => 'qlo', 'QL05p012608' => 'qlo', 'QL05p012650' => 'qlo', 'QL05p012667' => 'qlo', 'QL05p014501' => 'qlo', 'QL05p052800' => 'qlo', 'QL05p065010' => 'qlo', 'QL05p074156' => 'qlo', 'QL05p074160' => 'qlo', 'QL05p074174' => 'qlo', 'QL05p074178' => 'qlo', 'QL05p074214' => 'qlo', 'QL06p001050' => 'qlo', 'QL06p001056' => 'qlo', 'QL06p006093' => 'qlo', 'QL06p006111' => 'qlo', 'QL07p019784' => 'qlo', 'QL07p019801' => 'qlo', 'QL07p036110' => 'qlo', 'QL07p036134' => 'qlo', 'QL07p036147' => 'qlo', 'QL07p036156' => 'qlo', 'QL07p036300' => 'qlo', 'QL07p036320' => 'qlo', 'QL08p014547' => 'qlo', 'QL08p014551' => 'qlo', 'QL08p043319' => 'qlo', 'QL08p043324' => 'qlo', 'QL11p009094' => 'qlo', 'RcHm_v2.0_Chr1g0380481' => 'rch', 'RcHm_v2.0_Chr2g0089331' => 'rch', 'RcHm_v2.0_Chr2g0123691' => 'rch', 'RcHm_v2.0_Chr2g0151111' => 'rch', 'RcHm_v2.0_Chr2g0163011' => 'rch', 'RcHm_v2.0_Chr2g0163051' => 'rch', 'RcHm_v2.0_Chr2g0164671' => 'rch', 'RcHm_v2.0_Chr2g0164681' => 'rch', 'RcHm_v2.0_Chr2g0164721' => 'rch', 'RcHm_v2.0_Chr3g0449911' => 'rch', 'RcHm_v2.0_Chr3g0450211' => 'rch', 'RcHm_v2.0_Chr3g0457271' => 'rch', 'RcHm_v2.0_Chr5g0018111' => 'rch', 'RcHm_v2.0_Chr5g0021011' => 'rch', 'RcHm_v2.0_Chr5g0081171' => 'rch', 'RcHm_v2.0_Chr5g0081211' => 'rch', 'RcHm_v2.0_Chr6g0275871' => 'rch', 'RcHm_v2.0_Chr6g0276071' => 'rch', 'RcHm_v2.0_Chr6g0285591' => 'rch', 'RcHm_v2.0_Chr6g0291931' => 'rch', 'RcHm_v2.0_Chr6g0292091' => 'rch', 'RcHm_v2.0_Chr6g0292271' => 'rch', 'RcHm_v2.0_Chr7g0221261' => 'rch', 'Rhsim08G0219900' => 'rsi', 'Rhsim08G0220200' => 'rsi', 'Rhsim08G0237800' => 'rsi', 'Rhsim08G0238800' => 'rsi', 'Sabra09G0102700' => 'sbr', 'Sabra09G0127200' => 'sbr', 'Sabra11G0003700' => 'sbr', 'Sabra15G0014700' => 'sbr', 'Sc19g0000590' => 'sci', 'Sc19g0001870' => 'sci', 'SGA_v2.0_scaffold1G00346' => 'sas', 'SGA_v2.0_scaffold1G00575' => 'sas', 'SGA_v2.0_scaffold1G00761' => 'sas', 'SGA_v2.0_scaffold232G43501' => 'sas', 'TAR625G1137' => 'tar', 'Thecc.03G222100' => 'tca', 'TPR.G12691' => 'tpr', 'TWI34G0727' => 'twi', 'TWI36G0117' => 'twi', 'VMungo1309G0868' => 'vmu' ) $gf_id = 'HOM05D001729' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001729' ) $data_identifier = 'HOM05D001729' $data_type = 'gf_id' $species_gene_counts = array( 'amhyb' => (int) 1, 'cqu' => (int) 9, 'can' => (int) 1, 'cansat' => (int) 1, 'car' => (int) 1, 'col' => (int) 5, 'dca' => (int) 1, 'din' => (int) 2, 'dzi' => (int) 3, 'fan' => (int) 140, 'fve' => (int) 62, 'gma' => (int) 1, 'ghi' => (int) 2, 'gra' => (int) 1, 'han' => (int) 1, 'sun' => (int) 1, 'lonja' => (int) 6, 'lja' => (int) 1, 'lsa' => (int) 4, 'mes' => (int) 1, 'mdo' => (int) 14, 'mtr' => (int) 1, 'egut' => (int) 1, 'nta' => (int) 4, 'oeu' => (int) 1, 'stu' => (int) 2, 'pvu' => (int) 1, 'ptr' => (int) 4, 'ppe' => (int) 19, 'psa' => (int) 1, 'pso' => (int) 4, 'qlo' => (int) 36, 'rch' => (int) 23, 'rsi' => (int) 4, 'sbr' => (int) 4, 'sci' => (int) 2, 'sas' => (int) 4, 'tar' => (int) 1, 'tca' => (int) 1, 'tpr' => (int) 1, 'twi' => (int) 2, 'vmu' => (int) 1 ) $gf_gene_species = 'vmu' $gf_gene_id = 'VMungo1309G0868' $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' => 'HOM05D001729', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '375', 'num_species' => '42' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'Ah.07g204710' => 'amhyb', 'AUR62006001' => 'cqu', 'AUR62006002' => 'cqu', 'AUR62006003' => 'cqu', 'AUR62015641' => 'cqu', 'AUR62027174' => 'cqu', 'AUR62035623' => 'cqu', 'AUR62035624' => 'cqu', 'AUR62035625' => 'cqu', 'AUR62035626' => 'cqu', 'CAN.G1110.53' => 'can', 'CANSAT80G0415' => 'cansat', 'Ca_21364_v3' => 'car', 'COL.COLO4_30693' => 'col', 'COL.COLO4_30694' => 'col', 'COL.COLO4_30695' => 'col', 'COL.COLO4_30696' => 'col', 'COL.COLO4_34020' => 'col', 'DCAR_004585' => 'dca', 'Dinv04029' => 'din', 'Dinv34857' => 'din', 'Duzib147G0011' => 'dzi', 'Duzib170G0599' => 'dzi', 'Duzib192G1051' => 'dzi', 'FAN01G0708' => 'fan', 'FAN01G0742' => 'fan', 'FAN02G0048' => 'fan', 'FAN02G0583' => 'fan', 'FAN02G0688' => 'fan', 'FAN02G1588' => 'fan', 'FAN02G2194' => 'fan', 'FAN02G2750' => 'fan', 'FAN02G3094' => 'fan', 'FAN02G3887' => 'fan', 'FAN02G3911' => 'fan', 'FAN02G3994' => 'fan', 'FAN02G4432' => 'fan', 'FAN02G4556' => 'fan', 'FAN03G1977' => 'fan', 'FAN03G2781' => 'fan', 'FAN03G2850' => 'fan', 'FAN03G3155' => 'fan', 'FAN04G2487' => 'fan', 'FAN05G0208' => 'fan', 'FAN05G0656' => 'fan', 'FAN05G0696' => 'fan', 'FAN05G0810' => 'fan', 'FAN05G1447' => 'fan', 'FAN05G2640' => 'fan', 'FAN05G2911' => 'fan', 'FAN05G3901' => 'fan', 'FAN05G4859' => 'fan', 'FAN05G4861' => 'fan', 'FAN05G4988' => 'fan', 'FAN05G5187' => 'fan', 'FAN05G5452' => 'fan', 'FAN05G5500' => 'fan', 'FAN05G5688' => 'fan', 'FAN06G0177' => 'fan', 'FAN06G0675' => 'fan', 'FAN06G1290' => 'fan', 'FAN06G2191' => 'fan', 'FAN06G2405' => 'fan', 'FAN06G3231' => 'fan', 'FAN06G3932' => 'fan', 'FAN07G0163' => 'fan', 'FAN07G0471' => 'fan', 'FAN07G1354' => 'fan', 'FAN08G0338' => 'fan', 'FAN08G1373' => 'fan', 'FAN08G2539' => 'fan', 'FAN08G2728' => 'fan', 'FAN09G0608' => 'fan', 'FAN09G1136' => 'fan', 'FAN09G1958' => 'fan', 'FAN09G2508' => 'fan', 'FAN09G2597' => 'fan', 'FAN09G2658' => 'fan', 'FAN09G2757' => 'fan', 'FAN09G2983' => 'fan', 'FAN09G3130' => 'fan', 'FAN09G3565' => 'fan', 'FAN09G3613' => 'fan', 'FAN09G4011' => 'fan', 'FAN09G4239' => 'fan', 'FAN09G4277' => 'fan', 'FAN09G4720' => 'fan', 'FAN11G0139' => 'fan', 'FAN11G1727' => 'fan', 'FAN11G2672' => 'fan', 'FAN11G2795' => 'fan', 'FAN11G3238' => 'fan', 'FAN11G3734' => 'fan', 'FAN12G0631' => 'fan', 'FAN12G2239' => 'fan', 'FAN12G2308' => 'fan', 'FAN12G2569' => 'fan', 'FAN12G2623' => 'fan', 'FAN13G3182' => 'fan', 'FAN14G0053' => 'fan', 'FAN14G0370' => 'fan', 'FAN14G0382' => 'fan', 'FAN14G0421' => 'fan', 'FAN14G0866' => 'fan', 'FAN14G1187' => 'fan', 'FAN14G1727' => 'fan', 'FAN14G1791' => 'fan', 'FAN14G2361' => 'fan', 'FAN14G2668' => 'fan', 'FAN14G2770' => 'fan', 'FAN14G2874' => 'fan', 'FAN14G3193' => 'fan', 'FAN14G3624' => 'fan', 'FAN14G3676' => 'fan', 'FAN14G3807' => 'fan', 'FAN14G4082' => 'fan', 'FAN14G4342' => 'fan', 'FAN14G4985' => 'fan', 'FAN14G5126' => 'fan', 'FAN14G5781' => 'fan', 'FAN14G5808' => 'fan', 'FAN14G5949' => 'fan', 'FAN15G0828' => 'fan', 'FAN15G1054' => 'fan', 'FAN15G2023' => 'fan', 'FAN15G2506' => 'fan', 'FAN16G0128' => 'fan', 'FAN16G0249' => 'fan', 'FAN16G0429' => 'fan', 'FAN16G1493' => 'fan', 'FAN16G2210' => 'fan', 'FAN16G2506' => 'fan', 'FAN18G1542' => 'fan', 'FAN18G4057' => 'fan', 'FAN19G0745' => 'fan', 'FAN19G1216' => 'fan', 'FAN19G1733' => 'fan', 'FAN20G0258' => 'fan', 'FAN20G1095' => 'fan', 'FAN20G1557' => 'fan', 'FAN21G0302' => 'fan', 'FAN21G0519' => 'fan', 'FAN21G0970' => 'fan', 'FAN21G1159' => 'fan', 'FAN21G1312' => 'fan', 'FAN21G1440' => 'fan', 'FAN21G1715' => 'fan', 'FAN23G1584' => 'fan', 'FAN24G0045' => 'fan', 'FAN24G0053' => 'fan', 'FAN24G1500' => 'fan', 'FAN24G1817' => 'fan', 'FAN24G2147' => 'fan', 'FAN24G2236' => 'fan', 'FAN24G2446' => 'fan', 'FAN24G2684' => 'fan', 'FAN25G0187' => 'fan', 'FAN25G0505' => 'fan', 'FAN25G0589' => 'fan', 'FAN25G3663' => 'fan', 'FAN26G1025' => 'fan', 'FAN26G2860' => 'fan', 'FAN27G1329' => 'fan', 'FAN27G3392' => 'fan', 'FvH4_1g02011' => 'fve', 'FvH4_1g06511' => 'fve', 'FvH4_2g19900' => 'fve', 'FvH4_2g19920' => 'fve', 'FvH4_2g24261' => 'fve', 'FvH4_2g24270' => 'fve', 'FvH4_2g24631' => 'fve', 'FvH4_2g30622' => 'fve', 'FvH4_3g12920' => 'fve', 'FvH4_3g30171' => 'fve', 'FvH4_3g35490' => 'fve', 'FvH4_3g43682' => 'fve', 'FvH4_3g43730' => 'fve', 'FvH4_3g43732' => 'fve', 'FvH4_3g43751' => 'fve', 'FvH4_3g43752' => 'fve', 'FvH4_3g43770' => 'fve', 'FvH4_3g44471' => 'fve', 'FvH4_3g44510' => 'fve', 'FvH4_3g44582' => 'fve', 'FvH4_4g16921' => 'fve', 'FvH4_4g17121' => 'fve', 'FvH4_4g17782' => 'fve', 'FvH4_4g17783' => 'fve', 'FvH4_4g18120' => 'fve', 'FvH4_4g31310' => 'fve', 'FvH4_4g35052' => 'fve', 'FvH4_5g30862' => 'fve', 'FvH4_6g01541' => 'fve', 'FvH4_6g02021' => 'fve', 'FvH4_6g02041' => 'fve', 'FvH4_6g02071' => 'fve', 'FvH4_6g02171' => 'fve', 'FvH4_6g03181' => 'fve', 'FvH4_6g03182' => 'fve', 'FvH4_6g03221' => 'fve', 'FvH4_6g03380' => 'fve', 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'ppe', 'Prupe.1G512600' => 'ppe', 'Prupe.2G073200' => 'ppe', 'Prupe.3G059500' => 'ppe', 'Prupe.3G059600' => 'ppe', 'Prupe.3G246100' => 'ppe', 'Prupe.3G265100' => 'ppe', 'Prupe.4G034700' => 'ppe', 'Prupe.4G052100' => 'ppe', 'Prupe.4G053600' => 'ppe', 'Prupe.5G068800' => 'ppe', 'Prupe.5G070600' => 'ppe', 'Prupe.6G075400' => 'ppe', 'Prupe.6G075500' => 'ppe', 'Prupe.6G076400' => 'ppe', 'Prupe.8G110700' => 'ppe', 'Psat4g020960' => 'psa', 'PSO135G0788' => 'pso', 'PSO210G6463' => 'pso', 'PSO384G0370' => 'pso', 'PSO386G0056' => 'pso', 'QL01p006048' => 'qlo', 'QL02p054283' => 'qlo', 'QL05p008000' => 'qlo', 'QL05p008212' => 'qlo', 'QL05p008950' => 'qlo', 'QL05p009042' => 'qlo', 'QL05p009518' => 'qlo', 'QL05p012589' => 'qlo', 'QL05p012608' => 'qlo', 'QL05p012650' => 'qlo', 'QL05p012667' => 'qlo', 'QL05p014501' => 'qlo', 'QL05p052800' => 'qlo', 'QL05p065010' => 'qlo', 'QL05p074156' => 'qlo', 'QL05p074160' => 'qlo', 'QL05p074174' => 'qlo', 'QL05p074178' => 'qlo', 'QL05p074214' => 'qlo', 'QL06p001050' => 'qlo', 'QL06p001056' => 'qlo', 'QL06p006093' => 'qlo', 'QL06p006111' => 'qlo', 'QL07p019784' => 'qlo', 'QL07p019801' => 'qlo', 'QL07p036110' => 'qlo', 'QL07p036134' => 'qlo', 'QL07p036147' => 'qlo', 'QL07p036156' => 'qlo', 'QL07p036300' => 'qlo', 'QL07p036320' => 'qlo', 'QL08p014547' => 'qlo', 'QL08p014551' => 'qlo', 'QL08p043319' => 'qlo', 'QL08p043324' => 'qlo', 'QL11p009094' => 'qlo', 'RcHm_v2.0_Chr1g0380481' => 'rch', 'RcHm_v2.0_Chr2g0089331' => 'rch', 'RcHm_v2.0_Chr2g0123691' => 'rch', 'RcHm_v2.0_Chr2g0151111' => 'rch', 'RcHm_v2.0_Chr2g0163011' => 'rch', 'RcHm_v2.0_Chr2g0163051' => 'rch', 'RcHm_v2.0_Chr2g0164671' => 'rch', 'RcHm_v2.0_Chr2g0164681' => 'rch', 'RcHm_v2.0_Chr2g0164721' => 'rch', 'RcHm_v2.0_Chr3g0449911' => 'rch', 'RcHm_v2.0_Chr3g0450211' => 'rch', 'RcHm_v2.0_Chr3g0457271' => 'rch', 'RcHm_v2.0_Chr5g0018111' => 'rch', 'RcHm_v2.0_Chr5g0021011' => 'rch', 'RcHm_v2.0_Chr5g0081171' => 'rch', 'RcHm_v2.0_Chr5g0081211' => 'rch', 'RcHm_v2.0_Chr6g0275871' => 'rch', 'RcHm_v2.0_Chr6g0276071' => 'rch', 'RcHm_v2.0_Chr6g0285591' => 'rch', 'RcHm_v2.0_Chr6g0291931' => 'rch', 'RcHm_v2.0_Chr6g0292091' => 'rch', 'RcHm_v2.0_Chr6g0292271' => 'rch', 'RcHm_v2.0_Chr7g0221261' => 'rch', 'Rhsim08G0219900' => 'rsi', 'Rhsim08G0220200' => 'rsi', 'Rhsim08G0237800' => 'rsi', 'Rhsim08G0238800' => 'rsi', 'Sabra09G0102700' => 'sbr', 'Sabra09G0127200' => 'sbr', 'Sabra11G0003700' => 'sbr', 'Sabra15G0014700' => 'sbr', 'Sc19g0000590' => 'sci', 'Sc19g0001870' => 'sci', 'SGA_v2.0_scaffold1G00346' => 'sas', 'SGA_v2.0_scaffold1G00575' => 'sas', 'SGA_v2.0_scaffold1G00761' => 'sas', 'SGA_v2.0_scaffold232G43501' => 'sas', 'TAR625G1137' => 'tar', 'Thecc.03G222100' => 'tca', 'TPR.G12691' => 'tpr', 'TWI34G0727' => 'twi', 'TWI36G0117' => 'twi', 'VMungo1309G0868' => 'vmu' ), 'gf_id' => 'HOM05D001729', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001729' ), 'data_identifier' => 'HOM05D001729', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001729', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '375', 'num_species' => '42' ) 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'AUR62035624' => 'cqu', 'AUR62035625' => 'cqu', 'AUR62035626' => 'cqu', 'CAN.G1110.53' => 'can', 'CANSAT80G0415' => 'cansat', 'Ca_21364_v3' => 'car', 'COL.COLO4_30693' => 'col', 'COL.COLO4_30694' => 'col', 'COL.COLO4_30695' => 'col', 'COL.COLO4_30696' => 'col', 'COL.COLO4_34020' => 'col', 'DCAR_004585' => 'dca', 'Dinv04029' => 'din', 'Dinv34857' => 'din', 'Duzib147G0011' => 'dzi', 'Duzib170G0599' => 'dzi', 'Duzib192G1051' => 'dzi', 'FAN01G0708' => 'fan', 'FAN01G0742' => 'fan', 'FAN02G0048' => 'fan', 'FAN02G0583' => 'fan', 'FAN02G0688' => 'fan', 'FAN02G1588' => 'fan', 'FAN02G2194' => 'fan', 'FAN02G2750' => 'fan', 'FAN02G3094' => 'fan', 'FAN02G3887' => 'fan', 'FAN02G3911' => 'fan', 'FAN02G3994' => 'fan', 'FAN02G4432' => 'fan', 'FAN02G4556' => 'fan', 'FAN03G1977' => 'fan', 'FAN03G2781' => 'fan', 'FAN03G2850' => 'fan', 'FAN03G3155' => 'fan', 'FAN04G2487' => 'fan', 'FAN05G0208' => 'fan', 'FAN05G0656' => 'fan', 'FAN05G0696' => 'fan', 'FAN05G0810' => 'fan', 'FAN05G1447' => 'fan', 'FAN05G2640' => 'fan', 'FAN05G2911' => 'fan', 'FAN05G3901' => 'fan', 'FAN05G4859' => 'fan', 'FAN05G4861' => 'fan', 'FAN05G4988' => 'fan', 'FAN05G5187' => 'fan', 'FAN05G5452' => 'fan', 'FAN05G5500' => 'fan', 'FAN05G5688' => 'fan', 'FAN06G0177' => 'fan', 'FAN06G0675' => 'fan', 'FAN06G1290' => 'fan', 'FAN06G2191' => 'fan', 'FAN06G2405' => 'fan', 'FAN06G3231' => 'fan', 'FAN06G3932' => 'fan', 'FAN07G0163' => 'fan', 'FAN07G0471' => 'fan', 'FAN07G1354' => 'fan', 'FAN08G0338' => 'fan', 'FAN08G1373' => 'fan', 'FAN08G2539' => 'fan', 'FAN08G2728' => 'fan', 'FAN09G0608' => 'fan', 'FAN09G1136' => 'fan', 'FAN09G1958' => 'fan', 'FAN09G2508' => 'fan', 'FAN09G2597' => 'fan', 'FAN09G2658' => 'fan', 'FAN09G2757' => 'fan', 'FAN09G2983' => 'fan', 'FAN09G3130' => 'fan', 'FAN09G3565' => 'fan', 'FAN09G3613' => 'fan', 'FAN09G4011' => 'fan', 'FAN09G4239' => 'fan', 'FAN09G4277' => 'fan', 'FAN09G4720' => 'fan', 'FAN11G0139' => 'fan', 'FAN11G1727' => 'fan', 'FAN11G2672' => 'fan', 'FAN11G2795' => 'fan', 'FAN11G3238' => 'fan', 'FAN11G3734' => 'fan', 'FAN12G0631' => 'fan', 'FAN12G2239' => 'fan', 'FAN12G2308' => 'fan', 'FAN12G2569' => 'fan', 'FAN12G2623' => 'fan', 'FAN13G3182' => 'fan', 'FAN14G0053' => 'fan', 'FAN14G0370' => 'fan', 'FAN14G0382' => 'fan', 'FAN14G0421' => 'fan', 'FAN14G0866' => 'fan', 'FAN14G1187' => 'fan', 'FAN14G1727' => 'fan', 'FAN14G1791' => 'fan', 'FAN14G2361' => 'fan', 'FAN14G2668' => 'fan', 'FAN14G2770' => 'fan', 'FAN14G2874' => 'fan', 'FAN14G3193' => 'fan', 'FAN14G3624' => 'fan', 'FAN14G3676' => 'fan', 'FAN14G3807' => 'fan', 'FAN14G4082' => 'fan', 'FAN14G4342' => 'fan', 'FAN14G4985' => 'fan', 'FAN14G5126' => 'fan', 'FAN14G5781' => 'fan', 'FAN14G5808' => 'fan', 'FAN14G5949' => 'fan', 'FAN15G0828' => 'fan', 'FAN15G1054' => 'fan', 'FAN15G2023' => 'fan', 'FAN15G2506' => 'fan', 'FAN16G0128' => 'fan', 'FAN16G0249' => 'fan', 'FAN16G0429' => 'fan', 'FAN16G1493' => 'fan', 'FAN16G2210' => 'fan', 'FAN16G2506' => 'fan', 'FAN18G1542' => 'fan', 'FAN18G4057' => 'fan', 'FAN19G0745' => 'fan', 'FAN19G1216' => 'fan', 'FAN19G1733' => 'fan', 'FAN20G0258' => 'fan', 'FAN20G1095' => 'fan', 'FAN20G1557' => 'fan', 'FAN21G0302' => 'fan', 'FAN21G0519' => 'fan', 'FAN21G0970' => 'fan', 'FAN21G1159' => 'fan', 'FAN21G1312' => 'fan', 'FAN21G1440' => 'fan', 'FAN21G1715' => 'fan', 'FAN23G1584' => 'fan', 'FAN24G0045' => 'fan', 'FAN24G0053' => 'fan', 'FAN24G1500' => 'fan', 'FAN24G1817' => 'fan', 'FAN24G2147' => 'fan', 'FAN24G2236' => 'fan', 'FAN24G2446' => 'fan', 'FAN24G2684' => 'fan', 'FAN25G0187' => 'fan', 'FAN25G0505' => 'fan', 'FAN25G0589' => 'fan', 'FAN25G3663' => 'fan', 'FAN26G1025' => 'fan', 'FAN26G2860' => 'fan', 'FAN27G1329' => 'fan', 'FAN27G3392' => 'fan', 'FvH4_1g02011' => 'fve', 'FvH4_1g06511' => 'fve', 'FvH4_2g19900' => 'fve', 'FvH4_2g19920' => 'fve', 'FvH4_2g24261' => 'fve', 'FvH4_2g24270' => 'fve', 'FvH4_2g24631' => 'fve', 'FvH4_2g30622' => 'fve', 'FvH4_3g12920' => 'fve', 'FvH4_3g30171' => 'fve', 'FvH4_3g35490' => 'fve', 'FvH4_3g43682' => 'fve', 'FvH4_3g43730' => 'fve', 'FvH4_3g43732' => 'fve', 'FvH4_3g43751' => 'fve', 'FvH4_3g43752' => 'fve', 'FvH4_3g43770' => 'fve', 'FvH4_3g44471' => 'fve', 'FvH4_3g44510' => 'fve', 'FvH4_3g44582' => 'fve', 'FvH4_4g16921' => 'fve', 'FvH4_4g17121' => 'fve', 'FvH4_4g17782' => 'fve', 'FvH4_4g17783' => 'fve', 'FvH4_4g18120' => 'fve', 'FvH4_4g31310' => 'fve', 'FvH4_4g35052' => 'fve', 'FvH4_5g30862' => 'fve', 'FvH4_6g01541' => 'fve', 'FvH4_6g02021' => 'fve', 'FvH4_6g02041' => 'fve', 'FvH4_6g02071' => 'fve', 'FvH4_6g02171' => 'fve', 'FvH4_6g03181' => 'fve', 'FvH4_6g03182' => 'fve', 'FvH4_6g03221' => 'fve', 'FvH4_6g03380' => 'fve', 'FvH4_6g05201' => 'fve', 'FvH4_6g05203' => 'fve', 'FvH4_6g20231' => 'fve', 'FvH4_6g31981' => 'fve', 'FvH4_6g32061' => 'fve', 'FvH4_6g37041' => 'fve', 'FvH4_6g37932' => 'fve', 'FvH4_6g38731' => 'fve', 'FvH4_6g39370' => 'fve', 'FvH4_6g39371' => 'fve', 'FvH4_6g40891' => 'fve', 'FvH4_6g40892' => 'fve', 'FvH4_6g43143' => 'fve', 'FvH4_6g45251' => 'fve', 'FvH4_6g45260' => 'fve', 'FvH4_6g45291' => 'fve', 'FvH4_6g45890' => 'fve', 'FvH4_6g46240' => 'fve', 'FvH4_6g46241' => 'fve', 'FvH4_6g46242' => 'fve', 'FvH4_6g46260' => 'fve', 'FvH4_6g46280' => 'fve', 'FvH4_6g46380' => 'fve', 'FvH4_7g12841' => 'fve', 'FvH4_7g31431' => 'fve', 'Glyma.09G075900' => 'gma', 'Gohir.A09G096401' => 'ghi', 'Gohir.D09G096101' => 'ghi', 'Gorai.006G112800' => 'gra', 'HanXRQChr04g0121411' => 'han', 'Hund15878' => 'sun', 'Lj2A1107G68' => 'lonja', 'Lj2A630G63' => 'lonja', 'Lj2A946T25' => 'lonja', 'Lj2C714T1' => 'lonja', 'Lj2C966T3' => 'lonja', 'Lj2C966T4' => 'lonja', 'Lj4g0002979' => 'lja', 'Lsat_1_v5_gn_5_30901' => 'lsa', 'Lsat_1_v5_gn_5_31100' => 'lsa', 'Lsat_1_v5_gn_5_38600' => 'lsa', 'Lsat_1_v5_gn_6_92061' => 'lsa', 'Manes.05G071301' => 'mes', 'MD02G1008700' => 'mdo', 'MD02G1008900' => 'mdo', 'MD03G1256400' => 'mdo', 'MD04G1180900' => 'mdo', 'MD04G1181000' => 'mdo', 'MD04G1181200' => 'mdo', 'MD05G1244200' => 'mdo', 'MD05G1324200' => 'mdo', 'MD09G1201600' => 'mdo', 'MD10G1000600' => 'mdo', 'MD14G1026900' => 'mdo', 'MD14G1187900' => 'mdo', 'MD15G1017800' => 'mdo', 'MD15G1018100' => 'mdo', 'Medtr4g124160' => 'mtr', 'Migut.L01260' => 'egut', 'Nitab4.5_0000008g0440' => 'nta', 'Nitab4.5_0000207g0170' => 'nta', 'Nitab4.5_0007671g0030' => 'nta', 'Nitab4.5_0010853g0020' => 'nta', 'Oeu057656.1' => 'oeu', 'PGSC0003DMG400005638' => 'stu', 'PGSC0003DMG400005639' => 'stu', 'Phvul.009G222800' => 'pvu', 'Potri.009G132400' => 'ptr', 'Potri.009G163001' => 'ptr', 'Potri.011G000700' => 'ptr', 'Potri.011G004800' => 'ptr', 'Prupe.1G509300' => 'ppe', 'Prupe.1G509700' => 'ppe', 'Prupe.1G510400' => 'ppe', 'Prupe.1G510700' => 'ppe', 'Prupe.1G512600' => 'ppe', 'Prupe.2G073200' => 'ppe', 'Prupe.3G059500' => 'ppe', 'Prupe.3G059600' => 'ppe', 'Prupe.3G246100' => 'ppe', 'Prupe.3G265100' => 'ppe', 'Prupe.4G034700' => 'ppe', 'Prupe.4G052100' => 'ppe', 'Prupe.4G053600' => 'ppe', 'Prupe.5G068800' => 'ppe', 'Prupe.5G070600' => 'ppe', 'Prupe.6G075400' => 'ppe', 'Prupe.6G075500' => 'ppe', 'Prupe.6G076400' => 'ppe', 'Prupe.8G110700' => 'ppe', 'Psat4g020960' => 'psa', 'PSO135G0788' => 'pso', 'PSO210G6463' => 'pso', 'PSO384G0370' => 'pso', 'PSO386G0056' => 'pso', 'QL01p006048' => 'qlo', 'QL02p054283' => 'qlo', 'QL05p008000' => 'qlo', 'QL05p008212' => 'qlo', 'QL05p008950' => 'qlo', 'QL05p009042' => 'qlo', 'QL05p009518' => 'qlo', 'QL05p012589' => 'qlo', 'QL05p012608' => 'qlo', 'QL05p012650' => 'qlo', 'QL05p012667' => 'qlo', 'QL05p014501' => 'qlo', 'QL05p052800' => 'qlo', 'QL05p065010' => 'qlo', 'QL05p074156' => 'qlo', 'QL05p074160' => 'qlo', 'QL05p074174' => 'qlo', 'QL05p074178' => 'qlo', 'QL05p074214' => 'qlo', 'QL06p001050' => 'qlo', 'QL06p001056' => 'qlo', 'QL06p006093' => 'qlo', 'QL06p006111' => 'qlo', 'QL07p019784' => 'qlo', 'QL07p019801' => 'qlo', 'QL07p036110' => 'qlo', 'QL07p036134' => 'qlo', 'QL07p036147' => 'qlo', 'QL07p036156' => 'qlo', 'QL07p036300' => 'qlo', 'QL07p036320' => 'qlo', 'QL08p014547' => 'qlo', 'QL08p014551' => 'qlo', 'QL08p043319' => 'qlo', 'QL08p043324' => 'qlo', 'QL11p009094' => 'qlo', 'RcHm_v2.0_Chr1g0380481' => 'rch', 'RcHm_v2.0_Chr2g0089331' => 'rch', 'RcHm_v2.0_Chr2g0123691' => 'rch', 'RcHm_v2.0_Chr2g0151111' => 'rch', 'RcHm_v2.0_Chr2g0163011' => 'rch', 'RcHm_v2.0_Chr2g0163051' => 'rch', 'RcHm_v2.0_Chr2g0164671' => 'rch', 'RcHm_v2.0_Chr2g0164681' => 'rch', 'RcHm_v2.0_Chr2g0164721' => 'rch', 'RcHm_v2.0_Chr3g0449911' => 'rch', 'RcHm_v2.0_Chr3g0450211' => 'rch', 'RcHm_v2.0_Chr3g0457271' => 'rch', 'RcHm_v2.0_Chr5g0018111' => 'rch', 'RcHm_v2.0_Chr5g0021011' => 'rch', 'RcHm_v2.0_Chr5g0081171' => 'rch', 'RcHm_v2.0_Chr5g0081211' => 'rch', 'RcHm_v2.0_Chr6g0275871' => 'rch', 'RcHm_v2.0_Chr6g0276071' => 'rch', 'RcHm_v2.0_Chr6g0285591' => 'rch', 'RcHm_v2.0_Chr6g0291931' => 'rch', 'RcHm_v2.0_Chr6g0292091' => 'rch', 'RcHm_v2.0_Chr6g0292271' => 'rch', 'RcHm_v2.0_Chr7g0221261' => 'rch', 'Rhsim08G0219900' => 'rsi', 'Rhsim08G0220200' => 'rsi', 'Rhsim08G0237800' => 'rsi', 'Rhsim08G0238800' => 'rsi', 'Sabra09G0102700' => 'sbr', 'Sabra09G0127200' => 'sbr', 'Sabra11G0003700' => 'sbr', 'Sabra15G0014700' => 'sbr', 'Sc19g0000590' => 'sci', 'Sc19g0001870' => 'sci', 'SGA_v2.0_scaffold1G00346' => 'sas', 'SGA_v2.0_scaffold1G00575' => 'sas', 'SGA_v2.0_scaffold1G00761' => 'sas', 'SGA_v2.0_scaffold232G43501' => 'sas', 'TAR625G1137' => 'tar', 'Thecc.03G222100' => 'tca', 'TPR.G12691' => 'tpr', 'TWI34G0727' => 'twi', 'TWI36G0117' => 'twi', 'VMungo1309G0868' => 'vmu' ) $gf_id = 'HOM05D001729' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001729' ) $data_identifier = 'HOM05D001729' $data_type = 'gf_id' $species_gene_counts = array( 'amhyb' => (int) 1, 'cqu' => (int) 9, 'can' => (int) 1, 'cansat' => (int) 1, 'car' => (int) 1, 'col' => (int) 5, 'dca' => (int) 1, 'din' => (int) 2, 'dzi' => (int) 3, 'fan' => (int) 140, 'fve' => (int) 62, 'gma' => (int) 1, 'ghi' => (int) 2, 'gra' => (int) 1, 'han' => (int) 1, 'sun' => (int) 1, 'lonja' => (int) 6, 'lja' => (int) 1, 'lsa' => (int) 4, 'mes' => (int) 1, 'mdo' => (int) 14, 'mtr' => (int) 1, 'egut' => (int) 1, 'nta' => (int) 4, 'oeu' => (int) 1, 'stu' => (int) 2, 'pvu' => (int) 1, 'ptr' => (int) 4, 'ppe' => (int) 19, 'psa' => (int) 1, 'pso' => (int) 4, 'qlo' => (int) 36, 'rch' => (int) 23, 'rsi' => (int) 4, 'sbr' => (int) 4, 'sci' => (int) 2, 'sas' => (int) 4, 'tar' => (int) 1, 'tca' => (int) 1, 'tpr' => (int) 1, 'twi' => (int) 2, 'vmu' => (int) 1 ) $gf_gene_species = 'vmu' $gf_gene_id = 'VMungo1309G0868' $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' => 'HOM05D001729', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '375', 'num_species' => '42' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'Ah.07g204710' => 'amhyb', 'AUR62006001' => 'cqu', 'AUR62006002' => 'cqu', 'AUR62006003' => 'cqu', 'AUR62015641' => 'cqu', 'AUR62027174' => 'cqu', 'AUR62035623' => 'cqu', 'AUR62035624' => 'cqu', 'AUR62035625' => 'cqu', 'AUR62035626' => 'cqu', 'CAN.G1110.53' => 'can', 'CANSAT80G0415' => 'cansat', 'Ca_21364_v3' => 'car', 'COL.COLO4_30693' => 'col', 'COL.COLO4_30694' => 'col', 'COL.COLO4_30695' => 'col', 'COL.COLO4_30696' => 'col', 'COL.COLO4_34020' => 'col', 'DCAR_004585' => 'dca', 'Dinv04029' => 'din', 'Dinv34857' => 'din', 'Duzib147G0011' => 'dzi', 'Duzib170G0599' => 'dzi', 'Duzib192G1051' => 'dzi', 'FAN01G0708' => 'fan', 'FAN01G0742' => 'fan', 'FAN02G0048' => 'fan', 'FAN02G0583' => 'fan', 'FAN02G0688' => 'fan', 'FAN02G1588' => 'fan', 'FAN02G2194' => 'fan', 'FAN02G2750' => 'fan', 'FAN02G3094' => 'fan', 'FAN02G3887' => 'fan', 'FAN02G3911' => 'fan', 'FAN02G3994' => 'fan', 'FAN02G4432' => 'fan', 'FAN02G4556' => 'fan', 'FAN03G1977' => 'fan', 'FAN03G2781' => 'fan', 'FAN03G2850' => 'fan', 'FAN03G3155' => 'fan', 'FAN04G2487' => 'fan', 'FAN05G0208' => 'fan', 'FAN05G0656' => 'fan', 'FAN05G0696' => 'fan', 'FAN05G0810' => 'fan', 'FAN05G1447' => 'fan', 'FAN05G2640' => 'fan', 'FAN05G2911' => 'fan', 'FAN05G3901' => 'fan', 'FAN05G4859' => 'fan', 'FAN05G4861' => 'fan', 'FAN05G4988' => 'fan', 'FAN05G5187' => 'fan', 'FAN05G5452' => 'fan', 'FAN05G5500' => 'fan', 'FAN05G5688' => 'fan', 'FAN06G0177' => 'fan', 'FAN06G0675' => 'fan', 'FAN06G1290' => 'fan', 'FAN06G2191' => 'fan', 'FAN06G2405' => 'fan', 'FAN06G3231' => 'fan', 'FAN06G3932' => 'fan', 'FAN07G0163' => 'fan', 'FAN07G0471' => 'fan', 'FAN07G1354' => 'fan', 'FAN08G0338' => 'fan', 'FAN08G1373' => 'fan', 'FAN08G2539' => 'fan', 'FAN08G2728' => 'fan', 'FAN09G0608' => 'fan', 'FAN09G1136' => 'fan', 'FAN09G1958' => 'fan', 'FAN09G2508' => 'fan', 'FAN09G2597' => 'fan', 'FAN09G2658' => 'fan', 'FAN09G2757' => 'fan', 'FAN09G2983' => 'fan', 'FAN09G3130' => 'fan', 'FAN09G3565' => 'fan', 'FAN09G3613' => 'fan', 'FAN09G4011' => 'fan', 'FAN09G4239' => 'fan', 'FAN09G4277' => 'fan', 'FAN09G4720' => 'fan', 'FAN11G0139' => 'fan', 'FAN11G1727' => 'fan', 'FAN11G2672' => 'fan', 'FAN11G2795' => 'fan', 'FAN11G3238' => 'fan', 'FAN11G3734' => 'fan', 'FAN12G0631' => 'fan', 'FAN12G2239' => 'fan', 'FAN12G2308' => 'fan', 'FAN12G2569' => 'fan', 'FAN12G2623' => 'fan', 'FAN13G3182' => 'fan', 'FAN14G0053' => 'fan', 'FAN14G0370' => 'fan', 'FAN14G0382' => 'fan', 'FAN14G0421' => 'fan', 'FAN14G0866' => 'fan', 'FAN14G1187' => 'fan', 'FAN14G1727' => 'fan', 'FAN14G1791' => 'fan', 'FAN14G2361' => 'fan', 'FAN14G2668' => 'fan', 'FAN14G2770' => 'fan', 'FAN14G2874' => 'fan', 'FAN14G3193' => 'fan', 'FAN14G3624' => 'fan', 'FAN14G3676' => 'fan', 'FAN14G3807' => 'fan', 'FAN14G4082' => 'fan', 'FAN14G4342' => 'fan', 'FAN14G4985' => 'fan', 'FAN14G5126' => 'fan', 'FAN14G5781' => 'fan', 'FAN14G5808' => 'fan', 'FAN14G5949' => 'fan', 'FAN15G0828' => 'fan', 'FAN15G1054' => 'fan', 'FAN15G2023' => 'fan', 'FAN15G2506' => 'fan', 'FAN16G0128' => 'fan', 'FAN16G0249' => 'fan', 'FAN16G0429' => 'fan', 'FAN16G1493' => 'fan', 'FAN16G2210' => 'fan', 'FAN16G2506' => 'fan', 'FAN18G1542' => 'fan', 'FAN18G4057' => 'fan', 'FAN19G0745' => 'fan', 'FAN19G1216' => 'fan', 'FAN19G1733' => 'fan', 'FAN20G0258' => 'fan', 'FAN20G1095' => 'fan', 'FAN20G1557' => 'fan', 'FAN21G0302' => 'fan', 'FAN21G0519' => 'fan', 'FAN21G0970' => 'fan', 'FAN21G1159' => 'fan', 'FAN21G1312' => 'fan', 'FAN21G1440' => 'fan', 'FAN21G1715' => 'fan', 'FAN23G1584' => 'fan', 'FAN24G0045' => 'fan', 'FAN24G0053' => 'fan', 'FAN24G1500' => 'fan', 'FAN24G1817' => 'fan', 'FAN24G2147' => 'fan', 'FAN24G2236' => 'fan', 'FAN24G2446' => 'fan', 'FAN24G2684' => 'fan', 'FAN25G0187' => 'fan', 'FAN25G0505' => 'fan', 'FAN25G0589' => 'fan', 'FAN25G3663' => 'fan', 'FAN26G1025' => 'fan', 'FAN26G2860' => 'fan', 'FAN27G1329' => 'fan', 'FAN27G3392' => 'fan', 'FvH4_1g02011' => 'fve', 'FvH4_1g06511' => 'fve', 'FvH4_2g19900' => 'fve', 'FvH4_2g19920' => 'fve', 'FvH4_2g24261' => 'fve', 'FvH4_2g24270' => 'fve', 'FvH4_2g24631' => 'fve', 'FvH4_2g30622' => 'fve', 'FvH4_3g12920' => 'fve', 'FvH4_3g30171' => 'fve', 'FvH4_3g35490' => 'fve', 'FvH4_3g43682' => 'fve', 'FvH4_3g43730' => 'fve', 'FvH4_3g43732' => 'fve', 'FvH4_3g43751' => 'fve', 'FvH4_3g43752' => 'fve', 'FvH4_3g43770' => 'fve', 'FvH4_3g44471' => 'fve', 'FvH4_3g44510' => 'fve', 'FvH4_3g44582' => 'fve', 'FvH4_4g16921' => 'fve', 'FvH4_4g17121' => 'fve', 'FvH4_4g17782' => 'fve', 'FvH4_4g17783' => 'fve', 'FvH4_4g18120' => 'fve', 'FvH4_4g31310' => 'fve', 'FvH4_4g35052' => 'fve', 'FvH4_5g30862' => 'fve', 'FvH4_6g01541' => 'fve', 'FvH4_6g02021' => 'fve', 'FvH4_6g02041' => 'fve', 'FvH4_6g02071' => 'fve', 'FvH4_6g02171' => 'fve', 'FvH4_6g03181' => 'fve', 'FvH4_6g03182' => 'fve', 'FvH4_6g03221' => 'fve', 'FvH4_6g03380' => 'fve', 'FvH4_6g05201' => 'fve', 'FvH4_6g05203' => 'fve', 'FvH4_6g20231' => 'fve', 'FvH4_6g31981' => 'fve', 'FvH4_6g32061' => 'fve', 'FvH4_6g37041' => 'fve', 'FvH4_6g37932' => 'fve', 'FvH4_6g38731' => 'fve', 'FvH4_6g39370' => 'fve', 'FvH4_6g39371' => 'fve', 'FvH4_6g40891' => 'fve', 'FvH4_6g40892' => 'fve', 'FvH4_6g43143' => 'fve', 'FvH4_6g45251' => 'fve', 'FvH4_6g45260' => 'fve', 'FvH4_6g45291' => 'fve', 'FvH4_6g45890' => 'fve', 'FvH4_6g46240' => 'fve', 'FvH4_6g46241' => 'fve', 'FvH4_6g46242' => 'fve', 'FvH4_6g46260' => 'fve', 'FvH4_6g46280' => 'fve', 'FvH4_6g46380' => 'fve', 'FvH4_7g12841' => 'fve', 'FvH4_7g31431' => 'fve', 'Glyma.09G075900' => 'gma', 'Gohir.A09G096401' => 'ghi', 'Gohir.D09G096101' => 'ghi', 'Gorai.006G112800' => 'gra', 'HanXRQChr04g0121411' => 'han', 'Hund15878' => 'sun', 'Lj2A1107G68' => 'lonja', 'Lj2A630G63' => 'lonja', 'Lj2A946T25' => 'lonja', 'Lj2C714T1' => 'lonja', 'Lj2C966T3' => 'lonja', 'Lj2C966T4' => 'lonja', 'Lj4g0002979' => 'lja', 'Lsat_1_v5_gn_5_30901' => 'lsa', 'Lsat_1_v5_gn_5_31100' => 'lsa', 'Lsat_1_v5_gn_5_38600' => 'lsa', 'Lsat_1_v5_gn_6_92061' => 'lsa', 'Manes.05G071301' => 'mes', 'MD02G1008700' => 'mdo', 'MD02G1008900' => 'mdo', 'MD03G1256400' => 'mdo', 'MD04G1180900' => 'mdo', 'MD04G1181000' => 'mdo', 'MD04G1181200' => 'mdo', 'MD05G1244200' => 'mdo', 'MD05G1324200' => 'mdo', 'MD09G1201600' => 'mdo', 'MD10G1000600' => 'mdo', 'MD14G1026900' => 'mdo', 'MD14G1187900' => 'mdo', 'MD15G1017800' => 'mdo', 'MD15G1018100' => 'mdo', 'Medtr4g124160' => 'mtr', 'Migut.L01260' => 'egut', 'Nitab4.5_0000008g0440' => 'nta', 'Nitab4.5_0000207g0170' => 'nta', 'Nitab4.5_0007671g0030' => 'nta', 'Nitab4.5_0010853g0020' => 'nta', 'Oeu057656.1' => 'oeu', 'PGSC0003DMG400005638' => 'stu', 'PGSC0003DMG400005639' => 'stu', 'Phvul.009G222800' => 'pvu', 'Potri.009G132400' => 'ptr', 'Potri.009G163001' => 'ptr', 'Potri.011G000700' => 'ptr', 'Potri.011G004800' => 'ptr', 'Prupe.1G509300' => 'ppe', 'Prupe.1G509700' => 'ppe', 'Prupe.1G510400' => 'ppe', 'Prupe.1G510700' => 'ppe', 'Prupe.1G512600' => 'ppe', 'Prupe.2G073200' => 'ppe', 'Prupe.3G059500' => 'ppe', 'Prupe.3G059600' => 'ppe', 'Prupe.3G246100' => 'ppe', 'Prupe.3G265100' => 'ppe', 'Prupe.4G034700' => 'ppe', 'Prupe.4G052100' => 'ppe', 'Prupe.4G053600' => 'ppe', 'Prupe.5G068800' => 'ppe', 'Prupe.5G070600' => 'ppe', 'Prupe.6G075400' => 'ppe', 'Prupe.6G075500' => 'ppe', 'Prupe.6G076400' => 'ppe', 'Prupe.8G110700' => 'ppe', 'Psat4g020960' => 'psa', 'PSO135G0788' => 'pso', 'PSO210G6463' => 'pso', 'PSO384G0370' => 'pso', 'PSO386G0056' => 'pso', 'QL01p006048' => 'qlo', 'QL02p054283' => 'qlo', 'QL05p008000' => 'qlo', 'QL05p008212' => 'qlo', 'QL05p008950' => 'qlo', 'QL05p009042' => 'qlo', 'QL05p009518' => 'qlo', 'QL05p012589' => 'qlo', 'QL05p012608' => 'qlo', 'QL05p012650' => 'qlo', 'QL05p012667' => 'qlo', 'QL05p014501' => 'qlo', 'QL05p052800' => 'qlo', 'QL05p065010' => 'qlo', 'QL05p074156' => 'qlo', 'QL05p074160' => 'qlo', 'QL05p074174' => 'qlo', 'QL05p074178' => 'qlo', 'QL05p074214' => 'qlo', 'QL06p001050' => 'qlo', 'QL06p001056' => 'qlo', 'QL06p006093' => 'qlo', 'QL06p006111' => 'qlo', 'QL07p019784' => 'qlo', 'QL07p019801' => 'qlo', 'QL07p036110' => 'qlo', 'QL07p036134' => 'qlo', 'QL07p036147' => 'qlo', 'QL07p036156' => 'qlo', 'QL07p036300' => 'qlo', 'QL07p036320' => 'qlo', 'QL08p014547' => 'qlo', 'QL08p014551' => 'qlo', 'QL08p043319' => 'qlo', 'QL08p043324' => 'qlo', 'QL11p009094' => 'qlo', 'RcHm_v2.0_Chr1g0380481' => 'rch', 'RcHm_v2.0_Chr2g0089331' => 'rch', 'RcHm_v2.0_Chr2g0123691' => 'rch', 'RcHm_v2.0_Chr2g0151111' => 'rch', 'RcHm_v2.0_Chr2g0163011' => 'rch', 'RcHm_v2.0_Chr2g0163051' => 'rch', 'RcHm_v2.0_Chr2g0164671' => 'rch', 'RcHm_v2.0_Chr2g0164681' => 'rch', 'RcHm_v2.0_Chr2g0164721' => 'rch', 'RcHm_v2.0_Chr3g0449911' => 'rch', 'RcHm_v2.0_Chr3g0450211' => 'rch', 'RcHm_v2.0_Chr3g0457271' => 'rch', 'RcHm_v2.0_Chr5g0018111' => 'rch', 'RcHm_v2.0_Chr5g0021011' => 'rch', 'RcHm_v2.0_Chr5g0081171' => 'rch', 'RcHm_v2.0_Chr5g0081211' => 'rch', 'RcHm_v2.0_Chr6g0275871' => 'rch', 'RcHm_v2.0_Chr6g0276071' => 'rch', 'RcHm_v2.0_Chr6g0285591' => 'rch', 'RcHm_v2.0_Chr6g0291931' => 'rch', 'RcHm_v2.0_Chr6g0292091' => 'rch', 'RcHm_v2.0_Chr6g0292271' => 'rch', 'RcHm_v2.0_Chr7g0221261' => 'rch', 'Rhsim08G0219900' => 'rsi', 'Rhsim08G0220200' => 'rsi', 'Rhsim08G0237800' => 'rsi', 'Rhsim08G0238800' => 'rsi', 'Sabra09G0102700' => 'sbr', 'Sabra09G0127200' => 'sbr', 'Sabra11G0003700' => 'sbr', 'Sabra15G0014700' => 'sbr', 'Sc19g0000590' => 'sci', 'Sc19g0001870' => 'sci', 'SGA_v2.0_scaffold1G00346' => 'sas', 'SGA_v2.0_scaffold1G00575' => 'sas', 'SGA_v2.0_scaffold1G00761' => 'sas', 'SGA_v2.0_scaffold232G43501' => 'sas', 'TAR625G1137' => 'tar', 'Thecc.03G222100' => 'tca', 'TPR.G12691' => 'tpr', 'TWI34G0727' => 'twi', 'TWI36G0117' => 'twi', 'VMungo1309G0868' => 'vmu' ), 'gf_id' => 'HOM05D001729', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001729' ), 'data_identifier' => 'HOM05D001729', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001729', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '375', 'num_species' => '42' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'Ah.07g204710' => 'amhyb', 'AUR62006001' => 'cqu', 'AUR62006002' => 'cqu', 'AUR62006003' => 'cqu', 'AUR62015641' => 'cqu', 'AUR62027174' => 'cqu', 'AUR62035623' => 'cqu', 'AUR62035624' => 'cqu', 'AUR62035625' => 'cqu', 'AUR62035626' => 'cqu', 'CAN.G1110.53' => 'can', 'CANSAT80G0415' => 'cansat', 'Ca_21364_v3' => 'car', 'COL.COLO4_30693' => 'col', 'COL.COLO4_30694' => 'col', 'COL.COLO4_30695' => 'col', 'COL.COLO4_30696' => 'col', 'COL.COLO4_34020' => 'col', 'DCAR_004585' => 'dca', 'Dinv04029' => 'din', 'Dinv34857' => 'din', 'Duzib147G0011' => 'dzi', 'Duzib170G0599' => 'dzi', 'Duzib192G1051' => 'dzi', 'FAN01G0708' => 'fan', 'FAN01G0742' => 'fan', 'FAN02G0048' => 'fan', 'FAN02G0583' => 'fan', 'FAN02G0688' => 'fan', 'FAN02G1588' => 'fan', 'FAN02G2194' => 'fan', 'FAN02G2750' => 'fan', 'FAN02G3094' => 'fan', 'FAN02G3887' => 'fan', 'FAN02G3911' => 'fan', 'FAN02G3994' => 'fan', 'FAN02G4432' => 'fan', 'FAN02G4556' => 'fan', 'FAN03G1977' => 'fan', 'FAN03G2781' => 'fan', 'FAN03G2850' => 'fan', 'FAN03G3155' => 'fan', 'FAN04G2487' => 'fan', 'FAN05G0208' => 'fan', 'FAN05G0656' => 'fan', 'FAN05G0696' => 'fan', 'FAN05G0810' => 'fan', 'FAN05G1447' => 'fan', 'FAN05G2640' => 'fan', 'FAN05G2911' => 'fan', 'FAN05G3901' => 'fan', 'FAN05G4859' => 'fan', 'FAN05G4861' => 'fan', 'FAN05G4988' => 'fan', 'FAN05G5187' => 'fan', 'FAN05G5452' => 'fan', 'FAN05G5500' => 'fan', 'FAN05G5688' => 'fan', 'FAN06G0177' => 'fan', 'FAN06G0675' => 'fan', 'FAN06G1290' => 'fan', 'FAN06G2191' => 'fan', 'FAN06G2405' => 'fan', 'FAN06G3231' => 'fan', 'FAN06G3932' => 'fan', 'FAN07G0163' => 'fan', 'FAN07G0471' => 'fan', 'FAN07G1354' => 'fan', 'FAN08G0338' => 'fan', 'FAN08G1373' => 'fan', 'FAN08G2539' => 'fan', 'FAN08G2728' => 'fan', 'FAN09G0608' => 'fan', 'FAN09G1136' => 'fan', 'FAN09G1958' => 'fan', 'FAN09G2508' => 'fan', 'FAN09G2597' => 'fan', 'FAN09G2658' => 'fan', 'FAN09G2757' => 'fan', 'FAN09G2983' => 'fan', 'FAN09G3130' => 'fan', 'FAN09G3565' => 'fan', 'FAN09G3613' => 'fan', 'FAN09G4011' => 'fan', 'FAN09G4239' => 'fan', 'FAN09G4277' => 'fan', 'FAN09G4720' => 'fan', 'FAN11G0139' => 'fan', 'FAN11G1727' => 'fan', 'FAN11G2672' => 'fan', 'FAN11G2795' => 'fan', 'FAN11G3238' => 'fan', 'FAN11G3734' => 'fan', 'FAN12G0631' => 'fan', 'FAN12G2239' => 'fan', 'FAN12G2308' => 'fan', 'FAN12G2569' => 'fan', 'FAN12G2623' => 'fan', 'FAN13G3182' => 'fan', 'FAN14G0053' => 'fan', 'FAN14G0370' => 'fan', 'FAN14G0382' => 'fan', 'FAN14G0421' => 'fan', 'FAN14G0866' => 'fan', 'FAN14G1187' => 'fan', 'FAN14G1727' => 'fan', 'FAN14G1791' => 'fan', 'FAN14G2361' => 'fan', 'FAN14G2668' => 'fan', 'FAN14G2770' => 'fan', 'FAN14G2874' => 'fan', 'FAN14G3193' => 'fan', 'FAN14G3624' => 'fan', 'FAN14G3676' => 'fan', 'FAN14G3807' => 'fan', 'FAN14G4082' => 'fan', 'FAN14G4342' => 'fan', 'FAN14G4985' => 'fan', 'FAN14G5126' => 'fan', 'FAN14G5781' => 'fan', 'FAN14G5808' => 'fan', 'FAN14G5949' => 'fan', 'FAN15G0828' => 'fan', 'FAN15G1054' => 'fan', 'FAN15G2023' => 'fan', 'FAN15G2506' => 'fan', 'FAN16G0128' => 'fan', 'FAN16G0249' => 'fan', 'FAN16G0429' => 'fan', 'FAN16G1493' => 'fan', 'FAN16G2210' => 'fan', 'FAN16G2506' => 'fan', 'FAN18G1542' => 'fan', 'FAN18G4057' => 'fan', 'FAN19G0745' => 'fan', 'FAN19G1216' => 'fan', 'FAN19G1733' => 'fan', 'FAN20G0258' => 'fan', 'FAN20G1095' => 'fan', 'FAN20G1557' => 'fan', 'FAN21G0302' => 'fan', 'FAN21G0519' => 'fan', 'FAN21G0970' => 'fan', 'FAN21G1159' => 'fan', 'FAN21G1312' => 'fan', 'FAN21G1440' => 'fan', 'FAN21G1715' => 'fan', 'FAN23G1584' => 'fan', 'FAN24G0045' => 'fan', 'FAN24G0053' => 'fan', 'FAN24G1500' => 'fan', 'FAN24G1817' => 'fan', 'FAN24G2147' => 'fan', 'FAN24G2236' => 'fan', 'FAN24G2446' => 'fan', 'FAN24G2684' => 'fan', 'FAN25G0187' => 'fan', 'FAN25G0505' => 'fan', 'FAN25G0589' => 'fan', 'FAN25G3663' => 'fan', 'FAN26G1025' => 'fan', 'FAN26G2860' => 'fan', 'FAN27G1329' => 'fan', 'FAN27G3392' => 'fan', 'FvH4_1g02011' => 'fve', 'FvH4_1g06511' => 'fve', 'FvH4_2g19900' => 'fve', 'FvH4_2g19920' => 'fve', 'FvH4_2g24261' => 'fve', 'FvH4_2g24270' => 'fve', 'FvH4_2g24631' => 'fve', 'FvH4_2g30622' => 'fve', 'FvH4_3g12920' => 'fve', 'FvH4_3g30171' => 'fve', 'FvH4_3g35490' => 'fve', 'FvH4_3g43682' => 'fve', 'FvH4_3g43730' => 'fve', 'FvH4_3g43732' => 'fve', 'FvH4_3g43751' => 'fve', 'FvH4_3g43752' => 'fve', 'FvH4_3g43770' => 'fve', 'FvH4_3g44471' => 'fve', 'FvH4_3g44510' => 'fve', 'FvH4_3g44582' => 'fve', 'FvH4_4g16921' => 'fve', 'FvH4_4g17121' => 'fve', 'FvH4_4g17782' => 'fve', 'FvH4_4g17783' => 'fve', 'FvH4_4g18120' => 'fve', 'FvH4_4g31310' => 'fve', 'FvH4_4g35052' => 'fve', 'FvH4_5g30862' => 'fve', 'FvH4_6g01541' => 'fve', 'FvH4_6g02021' => 'fve', 'FvH4_6g02041' => 'fve', 'FvH4_6g02071' => 'fve', 'FvH4_6g02171' => 'fve', 'FvH4_6g03181' => 'fve', 'FvH4_6g03182' => 'fve', 'FvH4_6g03221' => 'fve', 'FvH4_6g03380' => 'fve', 'FvH4_6g05201' => 'fve', 'FvH4_6g05203' => 'fve', 'FvH4_6g20231' => 'fve', 'FvH4_6g31981' => 'fve', 'FvH4_6g32061' => 'fve', 'FvH4_6g37041' => 'fve', 'FvH4_6g37932' => 'fve', 'FvH4_6g38731' => 'fve', 'FvH4_6g39370' => 'fve', 'FvH4_6g39371' => 'fve', 'FvH4_6g40891' => 'fve', 'FvH4_6g40892' => 'fve', 'FvH4_6g43143' => 'fve', 'FvH4_6g45251' => 'fve', 'FvH4_6g45260' => 'fve', 'FvH4_6g45291' => 'fve', 'FvH4_6g45890' => 'fve', 'FvH4_6g46240' => 'fve', 'FvH4_6g46241' => 'fve', 'FvH4_6g46242' => 'fve', 'FvH4_6g46260' => 'fve', 'FvH4_6g46280' => 'fve', 'FvH4_6g46380' => 'fve', 'FvH4_7g12841' => 'fve', 'FvH4_7g31431' => 'fve', 'Glyma.09G075900' => 'gma', 'Gohir.A09G096401' => 'ghi', 'Gohir.D09G096101' => 'ghi', 'Gorai.006G112800' => 'gra', 'HanXRQChr04g0121411' => 'han', 'Hund15878' => 'sun', 'Lj2A1107G68' => 'lonja', 'Lj2A630G63' => 'lonja', 'Lj2A946T25' => 'lonja', 'Lj2C714T1' => 'lonja', 'Lj2C966T3' => 'lonja', 'Lj2C966T4' => 'lonja', 'Lj4g0002979' => 'lja', 'Lsat_1_v5_gn_5_30901' => 'lsa', 'Lsat_1_v5_gn_5_31100' => 'lsa', 'Lsat_1_v5_gn_5_38600' => 'lsa', 'Lsat_1_v5_gn_6_92061' => 'lsa', 'Manes.05G071301' => 'mes', 'MD02G1008700' => 'mdo', 'MD02G1008900' => 'mdo', 'MD03G1256400' => 'mdo', 'MD04G1180900' => 'mdo', 'MD04G1181000' => 'mdo', 'MD04G1181200' => 'mdo', 'MD05G1244200' => 'mdo', 'MD05G1324200' => 'mdo', 'MD09G1201600' => 'mdo', 'MD10G1000600' => 'mdo', 'MD14G1026900' => 'mdo', 'MD14G1187900' => 'mdo', 'MD15G1017800' => 'mdo', 'MD15G1018100' => 'mdo', 'Medtr4g124160' => 'mtr', 'Migut.L01260' => 'egut', 'Nitab4.5_0000008g0440' => 'nta', 'Nitab4.5_0000207g0170' => 'nta', 'Nitab4.5_0007671g0030' => 'nta', 'Nitab4.5_0010853g0020' => 'nta', 'Oeu057656.1' => 'oeu', 'PGSC0003DMG400005638' => 'stu', 'PGSC0003DMG400005639' => 'stu', 'Phvul.009G222800' => 'pvu', 'Potri.009G132400' => 'ptr', 'Potri.009G163001' => 'ptr', 'Potri.011G000700' => 'ptr', 'Potri.011G004800' => 'ptr', 'Prupe.1G509300' => 'ppe', 'Prupe.1G509700' => 'ppe', 'Prupe.1G510400' => 'ppe', 'Prupe.1G510700' => 'ppe', 'Prupe.1G512600' => 'ppe', 'Prupe.2G073200' => 'ppe', 'Prupe.3G059500' => 'ppe', 'Prupe.3G059600' => 'ppe', 'Prupe.3G246100' => 'ppe', 'Prupe.3G265100' => 'ppe', 'Prupe.4G034700' => 'ppe', 'Prupe.4G052100' => 'ppe', 'Prupe.4G053600' => 'ppe', 'Prupe.5G068800' => 'ppe', 'Prupe.5G070600' => 'ppe', 'Prupe.6G075400' => 'ppe', 'Prupe.6G075500' => 'ppe', 'Prupe.6G076400' => 'ppe', 'Prupe.8G110700' => 'ppe', 'Psat4g020960' => 'psa', 'PSO135G0788' => 'pso', 'PSO210G6463' => 'pso', 'PSO384G0370' => 'pso', 'PSO386G0056' => 'pso', 'QL01p006048' => 'qlo', 'QL02p054283' => 'qlo', 'QL05p008000' => 'qlo', 'QL05p008212' => 'qlo', 'QL05p008950' => 'qlo', 'QL05p009042' => 'qlo', 'QL05p009518' => 'qlo', 'QL05p012589' => 'qlo', 'QL05p012608' => 'qlo', 'QL05p012650' => 'qlo', 'QL05p012667' => 'qlo', 'QL05p014501' => 'qlo', 'QL05p052800' => 'qlo', 'QL05p065010' => 'qlo', 'QL05p074156' => 'qlo', 'QL05p074160' => 'qlo', 'QL05p074174' => 'qlo', 'QL05p074178' => 'qlo', 'QL05p074214' => 'qlo', 'QL06p001050' => 'qlo', 'QL06p001056' => 'qlo', 'QL06p006093' => 'qlo', 'QL06p006111' => 'qlo', 'QL07p019784' => 'qlo', 'QL07p019801' => 'qlo', 'QL07p036110' => 'qlo', 'QL07p036134' => 'qlo', 'QL07p036147' => 'qlo', 'QL07p036156' => 'qlo', 'QL07p036300' => 'qlo', 'QL07p036320' => 'qlo', 'QL08p014547' => 'qlo', 'QL08p014551' => 'qlo', 'QL08p043319' => 'qlo', 'QL08p043324' => 'qlo', 'QL11p009094' => 'qlo', 'RcHm_v2.0_Chr1g0380481' => 'rch', 'RcHm_v2.0_Chr2g0089331' => 'rch', 'RcHm_v2.0_Chr2g0123691' => 'rch', 'RcHm_v2.0_Chr2g0151111' => 'rch', 'RcHm_v2.0_Chr2g0163011' => 'rch', 'RcHm_v2.0_Chr2g0163051' => 'rch', 'RcHm_v2.0_Chr2g0164671' => 'rch', 'RcHm_v2.0_Chr2g0164681' => 'rch', 'RcHm_v2.0_Chr2g0164721' => 'rch', 'RcHm_v2.0_Chr3g0449911' => 'rch', 'RcHm_v2.0_Chr3g0450211' => 'rch', 'RcHm_v2.0_Chr3g0457271' => 'rch', 'RcHm_v2.0_Chr5g0018111' => 'rch', 'RcHm_v2.0_Chr5g0021011' => 'rch', 'RcHm_v2.0_Chr5g0081171' => 'rch', 'RcHm_v2.0_Chr5g0081211' => 'rch', 'RcHm_v2.0_Chr6g0275871' => 'rch', 'RcHm_v2.0_Chr6g0276071' => 'rch', 'RcHm_v2.0_Chr6g0285591' => 'rch', 'RcHm_v2.0_Chr6g0291931' => 'rch', 'RcHm_v2.0_Chr6g0292091' => 'rch', 'RcHm_v2.0_Chr6g0292271' => 'rch', 'RcHm_v2.0_Chr7g0221261' => 'rch', 'Rhsim08G0219900' => 'rsi', 'Rhsim08G0220200' => 'rsi', 'Rhsim08G0237800' => 'rsi', 'Rhsim08G0238800' => 'rsi', 'Sabra09G0102700' => 'sbr', 'Sabra09G0127200' => 'sbr', 'Sabra11G0003700' => 'sbr', 'Sabra15G0014700' => 'sbr', 'Sc19g0000590' => 'sci', 'Sc19g0001870' => 'sci', 'SGA_v2.0_scaffold1G00346' => 'sas', 'SGA_v2.0_scaffold1G00575' => 'sas', 'SGA_v2.0_scaffold1G00761' => 'sas', 'SGA_v2.0_scaffold232G43501' => 'sas', 'TAR625G1137' => 'tar', 'Thecc.03G222100' => 'tca', 'TPR.G12691' => 'tpr', 'TWI34G0727' => 'twi', 'TWI36G0117' => 'twi', 'VMungo1309G0868' => 'vmu' ) $gf_id = 'HOM05D001729' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001729' ) $data_identifier = 'HOM05D001729' $data_type = 'gf_id' $species_gene_counts = array( 'amhyb' => (int) 1, 'cqu' => (int) 9, 'can' => (int) 1, 'cansat' => (int) 1, 'car' => (int) 1, 'col' => (int) 5, 'dca' => (int) 1, 'din' => (int) 2, 'dzi' => (int) 3, 'fan' => (int) 140, 'fve' => (int) 62, 'gma' => (int) 1, 'ghi' => (int) 2, 'gra' => (int) 1, 'han' => (int) 1, 'sun' => (int) 1, 'lonja' => (int) 6, 'lja' => (int) 1, 'lsa' => (int) 4, 'mes' => (int) 1, 'mdo' => (int) 14, 'mtr' => (int) 1, 'egut' => (int) 1, 'nta' => (int) 4, 'oeu' => (int) 1, 'stu' => (int) 2, 'pvu' => (int) 1, 'ptr' => (int) 4, 'ppe' => (int) 19, 'psa' => (int) 1, 'pso' => (int) 4, 'qlo' => (int) 36, 'rch' => (int) 23, 'rsi' => (int) 4, 'sbr' => (int) 4, 'sci' => (int) 2, 'sas' => (int) 4, 'tar' => (int) 1, 'tca' => (int) 1, 'tpr' => (int) 1, 'twi' => (int) 2, 'vmu' => (int) 1 ) $gf_gene_species = 'vmu' $gf_gene_id = 'VMungo1309G0868' $species_info = array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ) $local_species = 'fve' $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' => 'HOM05D001729', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '375', 'num_species' => '42' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'Ah.07g204710' => 'amhyb', 'AUR62006001' => 'cqu', 'AUR62006002' => 'cqu', 'AUR62006003' => 'cqu', 'AUR62015641' => 'cqu', 'AUR62027174' => 'cqu', 'AUR62035623' => 'cqu', 'AUR62035624' => 'cqu', 'AUR62035625' => 'cqu', 'AUR62035626' => 'cqu', 'CAN.G1110.53' => 'can', 'CANSAT80G0415' => 'cansat', 'Ca_21364_v3' => 'car', 'COL.COLO4_30693' => 'col', 'COL.COLO4_30694' => 'col', 'COL.COLO4_30695' => 'col', 'COL.COLO4_30696' => 'col', 'COL.COLO4_34020' => 'col', 'DCAR_004585' => 'dca', 'Dinv04029' => 'din', 'Dinv34857' => 'din', 'Duzib147G0011' => 'dzi', 'Duzib170G0599' => 'dzi', 'Duzib192G1051' => 'dzi', 'FAN01G0708' => 'fan', 'FAN01G0742' => 'fan', 'FAN02G0048' => 'fan', 'FAN02G0583' => 'fan', 'FAN02G0688' => 'fan', 'FAN02G1588' => 'fan', 'FAN02G2194' => 'fan', 'FAN02G2750' => 'fan', 'FAN02G3094' => 'fan', 'FAN02G3887' => 'fan', 'FAN02G3911' => 'fan', 'FAN02G3994' => 'fan', 'FAN02G4432' => 'fan', 'FAN02G4556' => 'fan', 'FAN03G1977' => 'fan', 'FAN03G2781' => 'fan', 'FAN03G2850' => 'fan', 'FAN03G3155' => 'fan', 'FAN04G2487' => 'fan', 'FAN05G0208' => 'fan', 'FAN05G0656' => 'fan', 'FAN05G0696' => 'fan', 'FAN05G0810' => 'fan', 'FAN05G1447' => 'fan', 'FAN05G2640' => 'fan', 'FAN05G2911' => 'fan', 'FAN05G3901' => 'fan', 'FAN05G4859' => 'fan', 'FAN05G4861' => 'fan', 'FAN05G4988' => 'fan', 'FAN05G5187' => 'fan', 'FAN05G5452' => 'fan', 'FAN05G5500' => 'fan', 'FAN05G5688' => 'fan', 'FAN06G0177' => 'fan', 'FAN06G0675' => 'fan', 'FAN06G1290' => 'fan', 'FAN06G2191' => 'fan', 'FAN06G2405' => 'fan', 'FAN06G3231' => 'fan', 'FAN06G3932' => 'fan', 'FAN07G0163' => 'fan', 'FAN07G0471' => 'fan', 'FAN07G1354' => 'fan', 'FAN08G0338' => 'fan', 'FAN08G1373' => 'fan', 'FAN08G2539' => 'fan', 'FAN08G2728' => 'fan', 'FAN09G0608' => 'fan', 'FAN09G1136' => 'fan', 'FAN09G1958' => 'fan', 'FAN09G2508' => 'fan', 'FAN09G2597' => 'fan', 'FAN09G2658' => 'fan', 'FAN09G2757' => 'fan', 'FAN09G2983' => 'fan', 'FAN09G3130' => 'fan', 'FAN09G3565' => 'fan', 'FAN09G3613' => 'fan', 'FAN09G4011' => 'fan', 'FAN09G4239' => 'fan', 'FAN09G4277' => 'fan', 'FAN09G4720' => 'fan', 'FAN11G0139' => 'fan', 'FAN11G1727' => 'fan', 'FAN11G2672' => 'fan', 'FAN11G2795' => 'fan', 'FAN11G3238' => 'fan', 'FAN11G3734' => 'fan', 'FAN12G0631' => 'fan', 'FAN12G2239' => 'fan', 'FAN12G2308' => 'fan', 'FAN12G2569' => 'fan', 'FAN12G2623' => 'fan', 'FAN13G3182' => 'fan', 'FAN14G0053' => 'fan', 'FAN14G0370' => 'fan', 'FAN14G0382' => 'fan', 'FAN14G0421' => 'fan', 'FAN14G0866' => 'fan', 'FAN14G1187' => 'fan', 'FAN14G1727' => 'fan', 'FAN14G1791' => 'fan', 'FAN14G2361' => 'fan', 'FAN14G2668' => 'fan', 'FAN14G2770' => 'fan', 'FAN14G2874' => 'fan', 'FAN14G3193' => 'fan', 'FAN14G3624' => 'fan', 'FAN14G3676' => 'fan', 'FAN14G3807' => 'fan', 'FAN14G4082' => 'fan', 'FAN14G4342' => 'fan', 'FAN14G4985' => 'fan', 'FAN14G5126' => 'fan', 'FAN14G5781' => 'fan', 'FAN14G5808' => 'fan', 'FAN14G5949' => 'fan', 'FAN15G0828' => 'fan', 'FAN15G1054' => 'fan', 'FAN15G2023' => 'fan', 'FAN15G2506' => 'fan', 'FAN16G0128' => 'fan', 'FAN16G0249' => 'fan', 'FAN16G0429' => 'fan', 'FAN16G1493' => 'fan', 'FAN16G2210' => 'fan', 'FAN16G2506' => 'fan', 'FAN18G1542' => 'fan', 'FAN18G4057' => 'fan', 'FAN19G0745' => 'fan', 'FAN19G1216' => 'fan', 'FAN19G1733' => 'fan', 'FAN20G0258' => 'fan', 'FAN20G1095' => 'fan', 'FAN20G1557' => 'fan', 'FAN21G0302' => 'fan', 'FAN21G0519' => 'fan', 'FAN21G0970' => 'fan', 'FAN21G1159' => 'fan', 'FAN21G1312' => 'fan', 'FAN21G1440' => 'fan', 'FAN21G1715' => 'fan', 'FAN23G1584' => 'fan', 'FAN24G0045' => 'fan', 'FAN24G0053' => 'fan', 'FAN24G1500' => 'fan', 'FAN24G1817' => 'fan', 'FAN24G2147' => 'fan', 'FAN24G2236' => 'fan', 'FAN24G2446' => 'fan', 'FAN24G2684' => 'fan', 'FAN25G0187' => 'fan', 'FAN25G0505' => 'fan', 'FAN25G0589' => 'fan', 'FAN25G3663' => 'fan', 'FAN26G1025' => 'fan', 'FAN26G2860' => 'fan', 'FAN27G1329' => 'fan', 'FAN27G3392' => 'fan', 'FvH4_1g02011' => 'fve', 'FvH4_1g06511' => 'fve', 'FvH4_2g19900' => 'fve', 'FvH4_2g19920' => 'fve', 'FvH4_2g24261' => 'fve', 'FvH4_2g24270' => 'fve', 'FvH4_2g24631' => 'fve', 'FvH4_2g30622' => 'fve', 'FvH4_3g12920' => 'fve', 'FvH4_3g30171' => 'fve', 'FvH4_3g35490' => 'fve', 'FvH4_3g43682' => 'fve', 'FvH4_3g43730' => 'fve', 'FvH4_3g43732' => 'fve', 'FvH4_3g43751' => 'fve', 'FvH4_3g43752' => 'fve', 'FvH4_3g43770' => 'fve', 'FvH4_3g44471' => 'fve', 'FvH4_3g44510' => 'fve', 'FvH4_3g44582' => 'fve', 'FvH4_4g16921' => 'fve', 'FvH4_4g17121' => 'fve', 'FvH4_4g17782' => 'fve', 'FvH4_4g17783' => 'fve', 'FvH4_4g18120' => 'fve', 'FvH4_4g31310' => 'fve', 'FvH4_4g35052' => 'fve', 'FvH4_5g30862' => 'fve', 'FvH4_6g01541' => 'fve', 'FvH4_6g02021' => 'fve', 'FvH4_6g02041' => 'fve', 'FvH4_6g02071' => 'fve', 'FvH4_6g02171' => 'fve', 'FvH4_6g03181' => 'fve', 'FvH4_6g03182' => 'fve', 'FvH4_6g03221' => 'fve', 'FvH4_6g03380' => 'fve', 'FvH4_6g05201' => 'fve', 'FvH4_6g05203' => 'fve', 'FvH4_6g20231' => 'fve', 'FvH4_6g31981' => 'fve', 'FvH4_6g32061' => 'fve', 'FvH4_6g37041' => 'fve', 'FvH4_6g37932' => 'fve', 'FvH4_6g38731' => 'fve', 'FvH4_6g39370' => 'fve', 'FvH4_6g39371' => 'fve', 'FvH4_6g40891' => 'fve', 'FvH4_6g40892' => 'fve', 'FvH4_6g43143' => 'fve', 'FvH4_6g45251' => 'fve', 'FvH4_6g45260' => 'fve', 'FvH4_6g45291' => 'fve', 'FvH4_6g45890' => 'fve', 'FvH4_6g46240' => 'fve', 'FvH4_6g46241' => 'fve', 'FvH4_6g46242' => 'fve', 'FvH4_6g46260' => 'fve', 'FvH4_6g46280' => 'fve', 'FvH4_6g46380' => 'fve', 'FvH4_7g12841' => 'fve', 'FvH4_7g31431' => 'fve', 'Glyma.09G075900' => 'gma', 'Gohir.A09G096401' => 'ghi', 'Gohir.D09G096101' => 'ghi', 'Gorai.006G112800' => 'gra', 'HanXRQChr04g0121411' => 'han', 'Hund15878' => 'sun', 'Lj2A1107G68' => 'lonja', 'Lj2A630G63' => 'lonja', 'Lj2A946T25' => 'lonja', 'Lj2C714T1' => 'lonja', 'Lj2C966T3' => 'lonja', 'Lj2C966T4' => 'lonja', 'Lj4g0002979' => 'lja', 'Lsat_1_v5_gn_5_30901' => 'lsa', 'Lsat_1_v5_gn_5_31100' => 'lsa', 'Lsat_1_v5_gn_5_38600' => 'lsa', 'Lsat_1_v5_gn_6_92061' => 'lsa', 'Manes.05G071301' => 'mes', 'MD02G1008700' => 'mdo', 'MD02G1008900' => 'mdo', 'MD03G1256400' => 'mdo', 'MD04G1180900' => 'mdo', 'MD04G1181000' => 'mdo', 'MD04G1181200' => 'mdo', 'MD05G1244200' => 'mdo', 'MD05G1324200' => 'mdo', 'MD09G1201600' => 'mdo', 'MD10G1000600' => 'mdo', 'MD14G1026900' => 'mdo', 'MD14G1187900' => 'mdo', 'MD15G1017800' => 'mdo', 'MD15G1018100' => 'mdo', 'Medtr4g124160' => 'mtr', 'Migut.L01260' => 'egut', 'Nitab4.5_0000008g0440' => 'nta', 'Nitab4.5_0000207g0170' => 'nta', 'Nitab4.5_0007671g0030' => 'nta', 'Nitab4.5_0010853g0020' => 'nta', 'Oeu057656.1' => 'oeu', 'PGSC0003DMG400005638' => 'stu', 'PGSC0003DMG400005639' => 'stu', 'Phvul.009G222800' => 'pvu', 'Potri.009G132400' => 'ptr', 'Potri.009G163001' => 'ptr', 'Potri.011G000700' => 'ptr', 'Potri.011G004800' => 'ptr', 'Prupe.1G509300' => 'ppe', 'Prupe.1G509700' => 'ppe', 'Prupe.1G510400' => 'ppe', 'Prupe.1G510700' => 'ppe', 'Prupe.1G512600' => 'ppe', 'Prupe.2G073200' => 'ppe', 'Prupe.3G059500' => 'ppe', 'Prupe.3G059600' => 'ppe', 'Prupe.3G246100' => 'ppe', 'Prupe.3G265100' => 'ppe', 'Prupe.4G034700' => 'ppe', 'Prupe.4G052100' => 'ppe', 'Prupe.4G053600' => 'ppe', 'Prupe.5G068800' => 'ppe', 'Prupe.5G070600' => 'ppe', 'Prupe.6G075400' => 'ppe', 'Prupe.6G075500' => 'ppe', 'Prupe.6G076400' => 'ppe', 'Prupe.8G110700' => 'ppe', 'Psat4g020960' => 'psa', 'PSO135G0788' => 'pso', 'PSO210G6463' => 'pso', 'PSO384G0370' => 'pso', 'PSO386G0056' => 'pso', 'QL01p006048' => 'qlo', 'QL02p054283' => 'qlo', 'QL05p008000' => 'qlo', 'QL05p008212' => 'qlo', 'QL05p008950' => 'qlo', 'QL05p009042' => 'qlo', 'QL05p009518' => 'qlo', 'QL05p012589' => 'qlo', 'QL05p012608' => 'qlo', 'QL05p012650' => 'qlo', 'QL05p012667' => 'qlo', 'QL05p014501' => 'qlo', 'QL05p052800' => 'qlo', 'QL05p065010' => 'qlo', 'QL05p074156' => 'qlo', 'QL05p074160' => 'qlo', 'QL05p074174' => 'qlo', 'QL05p074178' => 'qlo', 'QL05p074214' => 'qlo', 'QL06p001050' => 'qlo', 'QL06p001056' => 'qlo', 'QL06p006093' => 'qlo', 'QL06p006111' => 'qlo', 'QL07p019784' => 'qlo', 'QL07p019801' => 'qlo', 'QL07p036110' => 'qlo', 'QL07p036134' => 'qlo', 'QL07p036147' => 'qlo', 'QL07p036156' => 'qlo', 'QL07p036300' => 'qlo', 'QL07p036320' => 'qlo', 'QL08p014547' => 'qlo', 'QL08p014551' => 'qlo', 'QL08p043319' => 'qlo', 'QL08p043324' => 'qlo', 'QL11p009094' => 'qlo', 'RcHm_v2.0_Chr1g0380481' => 'rch', 'RcHm_v2.0_Chr2g0089331' => 'rch', 'RcHm_v2.0_Chr2g0123691' => 'rch', 'RcHm_v2.0_Chr2g0151111' => 'rch', 'RcHm_v2.0_Chr2g0163011' => 'rch', 'RcHm_v2.0_Chr2g0163051' => 'rch', 'RcHm_v2.0_Chr2g0164671' => 'rch', 'RcHm_v2.0_Chr2g0164681' => 'rch', 'RcHm_v2.0_Chr2g0164721' => 'rch', 'RcHm_v2.0_Chr3g0449911' => 'rch', 'RcHm_v2.0_Chr3g0450211' => 'rch', 'RcHm_v2.0_Chr3g0457271' => 'rch', 'RcHm_v2.0_Chr5g0018111' => 'rch', 'RcHm_v2.0_Chr5g0021011' => 'rch', 'RcHm_v2.0_Chr5g0081171' => 'rch', 'RcHm_v2.0_Chr5g0081211' => 'rch', 'RcHm_v2.0_Chr6g0275871' => 'rch', 'RcHm_v2.0_Chr6g0276071' => 'rch', 'RcHm_v2.0_Chr6g0285591' => 'rch', 'RcHm_v2.0_Chr6g0291931' => 'rch', 'RcHm_v2.0_Chr6g0292091' => 'rch', 'RcHm_v2.0_Chr6g0292271' => 'rch', 'RcHm_v2.0_Chr7g0221261' => 'rch', 'Rhsim08G0219900' => 'rsi', 'Rhsim08G0220200' => 'rsi', 'Rhsim08G0237800' => 'rsi', 'Rhsim08G0238800' => 'rsi', 'Sabra09G0102700' => 'sbr', 'Sabra09G0127200' => 'sbr', 'Sabra11G0003700' => 'sbr', 'Sabra15G0014700' => 'sbr', 'Sc19g0000590' => 'sci', 'Sc19g0001870' => 'sci', 'SGA_v2.0_scaffold1G00346' => 'sas', 'SGA_v2.0_scaffold1G00575' => 'sas', 'SGA_v2.0_scaffold1G00761' => 'sas', 'SGA_v2.0_scaffold232G43501' => 'sas', 'TAR625G1137' => 'tar', 'Thecc.03G222100' => 'tca', 'TPR.G12691' => 'tpr', 'TWI34G0727' => 'twi', 'TWI36G0117' => 'twi', 'VMungo1309G0868' => 'vmu' ), 'gf_id' => 'HOM05D001729', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001729' ), 'data_identifier' => 'HOM05D001729', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001729', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '375', 'num_species' => '42' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'Ah.07g204710' => 'amhyb', 'AUR62006001' => 'cqu', 'AUR62006002' => 'cqu', 'AUR62006003' => 'cqu', 'AUR62015641' => 'cqu', 'AUR62027174' => 'cqu', 'AUR62035623' => 'cqu', 'AUR62035624' => 'cqu', 'AUR62035625' => 'cqu', 'AUR62035626' => 'cqu', 'CAN.G1110.53' => 'can', 'CANSAT80G0415' => 'cansat', 'Ca_21364_v3' => 'car', 'COL.COLO4_30693' => 'col', 'COL.COLO4_30694' => 'col', 'COL.COLO4_30695' => 'col', 'COL.COLO4_30696' => 'col', 'COL.COLO4_34020' => 'col', 'DCAR_004585' => 'dca', 'Dinv04029' => 'din', 'Dinv34857' => 'din', 'Duzib147G0011' => 'dzi', 'Duzib170G0599' => 'dzi', 'Duzib192G1051' => 'dzi', 'FAN01G0708' => 'fan', 'FAN01G0742' => 'fan', 'FAN02G0048' => 'fan', 'FAN02G0583' => 'fan', 'FAN02G0688' => 'fan', 'FAN02G1588' => 'fan', 'FAN02G2194' => 'fan', 'FAN02G2750' => 'fan', 'FAN02G3094' => 'fan', 'FAN02G3887' => 'fan', 'FAN02G3911' => 'fan', 'FAN02G3994' => 'fan', 'FAN02G4432' => 'fan', 'FAN02G4556' => 'fan', 'FAN03G1977' => 'fan', 'FAN03G2781' => 'fan', 'FAN03G2850' => 'fan', 'FAN03G3155' => 'fan', 'FAN04G2487' => 'fan', 'FAN05G0208' => 'fan', 'FAN05G0656' => 'fan', 'FAN05G0696' => 'fan', 'FAN05G0810' => 'fan', 'FAN05G1447' => 'fan', 'FAN05G2640' => 'fan', 'FAN05G2911' => 'fan', 'FAN05G3901' => 'fan', 'FAN05G4859' => 'fan', 'FAN05G4861' => 'fan', 'FAN05G4988' => 'fan', 'FAN05G5187' => 'fan', 'FAN05G5452' => 'fan', 'FAN05G5500' => 'fan', 'FAN05G5688' => 'fan', 'FAN06G0177' => 'fan', 'FAN06G0675' => 'fan', 'FAN06G1290' => 'fan', 'FAN06G2191' => 'fan', 'FAN06G2405' => 'fan', 'FAN06G3231' => 'fan', 'FAN06G3932' => 'fan', 'FAN07G0163' => 'fan', 'FAN07G0471' => 'fan', 'FAN07G1354' => 'fan', 'FAN08G0338' => 'fan', 'FAN08G1373' => 'fan', 'FAN08G2539' => 'fan', 'FAN08G2728' => 'fan', 'FAN09G0608' => 'fan', 'FAN09G1136' => 'fan', 'FAN09G1958' => 'fan', 'FAN09G2508' => 'fan', 'FAN09G2597' => 'fan', 'FAN09G2658' => 'fan', 'FAN09G2757' => 'fan', 'FAN09G2983' => 'fan', 'FAN09G3130' => 'fan', 'FAN09G3565' => 'fan', 'FAN09G3613' => 'fan', 'FAN09G4011' => 'fan', 'FAN09G4239' => 'fan', 'FAN09G4277' => 'fan', 'FAN09G4720' => 'fan', 'FAN11G0139' => 'fan', 'FAN11G1727' => 'fan', 'FAN11G2672' => 'fan', 'FAN11G2795' => 'fan', 'FAN11G3238' => 'fan', 'FAN11G3734' => 'fan', 'FAN12G0631' => 'fan', 'FAN12G2239' => 'fan', 'FAN12G2308' => 'fan', 'FAN12G2569' => 'fan', 'FAN12G2623' => 'fan', 'FAN13G3182' => 'fan', 'FAN14G0053' => 'fan', 'FAN14G0370' => 'fan', 'FAN14G0382' => 'fan', 'FAN14G0421' => 'fan', 'FAN14G0866' => 'fan', 'FAN14G1187' => 'fan', 'FAN14G1727' => 'fan', 'FAN14G1791' => 'fan', 'FAN14G2361' => 'fan', 'FAN14G2668' => 'fan', 'FAN14G2770' => 'fan', 'FAN14G2874' => 'fan', 'FAN14G3193' => 'fan', 'FAN14G3624' => 'fan', 'FAN14G3676' => 'fan', 'FAN14G3807' => 'fan', 'FAN14G4082' => 'fan', 'FAN14G4342' => 'fan', 'FAN14G4985' => 'fan', 'FAN14G5126' => 'fan', 'FAN14G5781' => 'fan', 'FAN14G5808' => 'fan', 'FAN14G5949' => 'fan', 'FAN15G0828' => 'fan', 'FAN15G1054' => 'fan', 'FAN15G2023' => 'fan', 'FAN15G2506' => 'fan', 'FAN16G0128' => 'fan', 'FAN16G0249' => 'fan', 'FAN16G0429' => 'fan', 'FAN16G1493' => 'fan', 'FAN16G2210' => 'fan', 'FAN16G2506' => 'fan', 'FAN18G1542' => 'fan', 'FAN18G4057' => 'fan', 'FAN19G0745' => 'fan', 'FAN19G1216' => 'fan', 'FAN19G1733' => 'fan', 'FAN20G0258' => 'fan', 'FAN20G1095' => 'fan', 'FAN20G1557' => 'fan', 'FAN21G0302' => 'fan', 'FAN21G0519' => 'fan', 'FAN21G0970' => 'fan', 'FAN21G1159' => 'fan', 'FAN21G1312' => 'fan', 'FAN21G1440' => 'fan', 'FAN21G1715' => 'fan', 'FAN23G1584' => 'fan', 'FAN24G0045' => 'fan', 'FAN24G0053' => 'fan', 'FAN24G1500' => 'fan', 'FAN24G1817' => 'fan', 'FAN24G2147' => 'fan', 'FAN24G2236' => 'fan', 'FAN24G2446' => 'fan', 'FAN24G2684' => 'fan', 'FAN25G0187' => 'fan', 'FAN25G0505' => 'fan', 'FAN25G0589' => 'fan', 'FAN25G3663' => 'fan', 'FAN26G1025' => 'fan', 'FAN26G2860' => 'fan', 'FAN27G1329' => 'fan', 'FAN27G3392' => 'fan', 'FvH4_1g02011' => 'fve', 'FvH4_1g06511' => 'fve', 'FvH4_2g19900' => 'fve', 'FvH4_2g19920' => 'fve', 'FvH4_2g24261' => 'fve', 'FvH4_2g24270' => 'fve', 'FvH4_2g24631' => 'fve', 'FvH4_2g30622' => 'fve', 'FvH4_3g12920' => 'fve', 'FvH4_3g30171' => 'fve', 'FvH4_3g35490' => 'fve', 'FvH4_3g43682' => 'fve', 'FvH4_3g43730' => 'fve', 'FvH4_3g43732' => 'fve', 'FvH4_3g43751' => 'fve', 'FvH4_3g43752' => 'fve', 'FvH4_3g43770' => 'fve', 'FvH4_3g44471' => 'fve', 'FvH4_3g44510' => 'fve', 'FvH4_3g44582' => 'fve', 'FvH4_4g16921' => 'fve', 'FvH4_4g17121' => 'fve', 'FvH4_4g17782' => 'fve', 'FvH4_4g17783' => 'fve', 'FvH4_4g18120' => 'fve', 'FvH4_4g31310' => 'fve', 'FvH4_4g35052' => 'fve', 'FvH4_5g30862' => 'fve', 'FvH4_6g01541' => 'fve', 'FvH4_6g02021' => 'fve', 'FvH4_6g02041' => 'fve', 'FvH4_6g02071' => 'fve', 'FvH4_6g02171' => 'fve', 'FvH4_6g03181' => 'fve', 'FvH4_6g03182' => 'fve', 'FvH4_6g03221' => 'fve', 'FvH4_6g03380' => 'fve', 'FvH4_6g05201' => 'fve', 'FvH4_6g05203' => 'fve', 'FvH4_6g20231' => 'fve', 'FvH4_6g31981' => 'fve', 'FvH4_6g32061' => 'fve', 'FvH4_6g37041' => 'fve', 'FvH4_6g37932' => 'fve', 'FvH4_6g38731' => 'fve', 'FvH4_6g39370' => 'fve', 'FvH4_6g39371' => 'fve', 'FvH4_6g40891' => 'fve', 'FvH4_6g40892' => 'fve', 'FvH4_6g43143' => 'fve', 'FvH4_6g45251' => 'fve', 'FvH4_6g45260' => 'fve', 'FvH4_6g45291' => 'fve', 'FvH4_6g45890' => 'fve', 'FvH4_6g46240' => 'fve', 'FvH4_6g46241' => 'fve', 'FvH4_6g46242' => 'fve', 'FvH4_6g46260' => 'fve', 'FvH4_6g46280' => 'fve', 'FvH4_6g46380' => 'fve', 'FvH4_7g12841' => 'fve', 'FvH4_7g31431' => 'fve', 'Glyma.09G075900' => 'gma', 'Gohir.A09G096401' => 'ghi', 'Gohir.D09G096101' => 'ghi', 'Gorai.006G112800' => 'gra', 'HanXRQChr04g0121411' => 'han', 'Hund15878' => 'sun', 'Lj2A1107G68' => 'lonja', 'Lj2A630G63' => 'lonja', 'Lj2A946T25' => 'lonja', 'Lj2C714T1' => 'lonja', 'Lj2C966T3' => 'lonja', 'Lj2C966T4' => 'lonja', 'Lj4g0002979' => 'lja', 'Lsat_1_v5_gn_5_30901' => 'lsa', 'Lsat_1_v5_gn_5_31100' => 'lsa', 'Lsat_1_v5_gn_5_38600' => 'lsa', 'Lsat_1_v5_gn_6_92061' => 'lsa', 'Manes.05G071301' => 'mes', 'MD02G1008700' => 'mdo', 'MD02G1008900' => 'mdo', 'MD03G1256400' => 'mdo', 'MD04G1180900' => 'mdo', 'MD04G1181000' => 'mdo', 'MD04G1181200' => 'mdo', 'MD05G1244200' => 'mdo', 'MD05G1324200' => 'mdo', 'MD09G1201600' => 'mdo', 'MD10G1000600' => 'mdo', 'MD14G1026900' => 'mdo', 'MD14G1187900' => 'mdo', 'MD15G1017800' => 'mdo', 'MD15G1018100' => 'mdo', 'Medtr4g124160' => 'mtr', 'Migut.L01260' => 'egut', 'Nitab4.5_0000008g0440' => 'nta', 'Nitab4.5_0000207g0170' => 'nta', 'Nitab4.5_0007671g0030' => 'nta', 'Nitab4.5_0010853g0020' => 'nta', 'Oeu057656.1' => 'oeu', 'PGSC0003DMG400005638' => 'stu', 'PGSC0003DMG400005639' => 'stu', 'Phvul.009G222800' => 'pvu', 'Potri.009G132400' => 'ptr', 'Potri.009G163001' => 'ptr', 'Potri.011G000700' => 'ptr', 'Potri.011G004800' => 'ptr', 'Prupe.1G509300' => 'ppe', 'Prupe.1G509700' => 'ppe', 'Prupe.1G510400' => 'ppe', 'Prupe.1G510700' => 'ppe', 'Prupe.1G512600' => 'ppe', 'Prupe.2G073200' => 'ppe', 'Prupe.3G059500' => 'ppe', 'Prupe.3G059600' => 'ppe', 'Prupe.3G246100' => 'ppe', 'Prupe.3G265100' => 'ppe', 'Prupe.4G034700' => 'ppe', 'Prupe.4G052100' => 'ppe', 'Prupe.4G053600' => 'ppe', 'Prupe.5G068800' => 'ppe', 'Prupe.5G070600' => 'ppe', 'Prupe.6G075400' => 'ppe', 'Prupe.6G075500' => 'ppe', 'Prupe.6G076400' => 'ppe', 'Prupe.8G110700' => 'ppe', 'Psat4g020960' => 'psa', 'PSO135G0788' => 'pso', 'PSO210G6463' => 'pso', 'PSO384G0370' => 'pso', 'PSO386G0056' => 'pso', 'QL01p006048' => 'qlo', 'QL02p054283' => 'qlo', 'QL05p008000' => 'qlo', 'QL05p008212' => 'qlo', 'QL05p008950' => 'qlo', 'QL05p009042' => 'qlo', 'QL05p009518' => 'qlo', 'QL05p012589' => 'qlo', 'QL05p012608' => 'qlo', 'QL05p012650' => 'qlo', 'QL05p012667' => 'qlo', 'QL05p014501' => 'qlo', 'QL05p052800' => 'qlo', 'QL05p065010' => 'qlo', 'QL05p074156' => 'qlo', 'QL05p074160' => 'qlo', 'QL05p074174' => 'qlo', 'QL05p074178' => 'qlo', 'QL05p074214' => 'qlo', 'QL06p001050' => 'qlo', 'QL06p001056' => 'qlo', 'QL06p006093' => 'qlo', 'QL06p006111' => 'qlo', 'QL07p019784' => 'qlo', 'QL07p019801' => 'qlo', 'QL07p036110' => 'qlo', 'QL07p036134' => 'qlo', 'QL07p036147' => 'qlo', 'QL07p036156' => 'qlo', 'QL07p036300' => 'qlo', 'QL07p036320' => 'qlo', 'QL08p014547' => 'qlo', 'QL08p014551' => 'qlo', 'QL08p043319' => 'qlo', 'QL08p043324' => 'qlo', 'QL11p009094' => 'qlo', 'RcHm_v2.0_Chr1g0380481' => 'rch', 'RcHm_v2.0_Chr2g0089331' => 'rch', 'RcHm_v2.0_Chr2g0123691' => 'rch', 'RcHm_v2.0_Chr2g0151111' => 'rch', 'RcHm_v2.0_Chr2g0163011' => 'rch', 'RcHm_v2.0_Chr2g0163051' => 'rch', 'RcHm_v2.0_Chr2g0164671' => 'rch', 'RcHm_v2.0_Chr2g0164681' => 'rch', 'RcHm_v2.0_Chr2g0164721' => 'rch', 'RcHm_v2.0_Chr3g0449911' => 'rch', 'RcHm_v2.0_Chr3g0450211' => 'rch', 'RcHm_v2.0_Chr3g0457271' => 'rch', 'RcHm_v2.0_Chr5g0018111' => 'rch', 'RcHm_v2.0_Chr5g0021011' => 'rch', 'RcHm_v2.0_Chr5g0081171' => 'rch', 'RcHm_v2.0_Chr5g0081211' => 'rch', 'RcHm_v2.0_Chr6g0275871' => 'rch', 'RcHm_v2.0_Chr6g0276071' => 'rch', 'RcHm_v2.0_Chr6g0285591' => 'rch', 'RcHm_v2.0_Chr6g0291931' => 'rch', 'RcHm_v2.0_Chr6g0292091' => 'rch', 'RcHm_v2.0_Chr6g0292271' => 'rch', 'RcHm_v2.0_Chr7g0221261' => 'rch', 'Rhsim08G0219900' => 'rsi', 'Rhsim08G0220200' => 'rsi', 'Rhsim08G0237800' => 'rsi', 'Rhsim08G0238800' => 'rsi', 'Sabra09G0102700' => 'sbr', 'Sabra09G0127200' => 'sbr', 'Sabra11G0003700' => 'sbr', 'Sabra15G0014700' => 'sbr', 'Sc19g0000590' => 'sci', 'Sc19g0001870' => 'sci', 'SGA_v2.0_scaffold1G00346' => 'sas', 'SGA_v2.0_scaffold1G00575' => 'sas', 'SGA_v2.0_scaffold1G00761' => 'sas', 'SGA_v2.0_scaffold232G43501' => 'sas', 'TAR625G1137' => 'tar', 'Thecc.03G222100' => 'tca', 'TPR.G12691' => 'tpr', 'TWI34G0727' => 'twi', 'TWI36G0117' => 'twi', 'VMungo1309G0868' => 'vmu' ) $gf_id = 'HOM05D001729' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001729' ) $data_identifier = 'HOM05D001729' $data_type = 'gf_id' $species_gene_counts = array( 'amhyb' => (int) 1, 'cqu' => (int) 9, 'can' => (int) 1, 'cansat' => (int) 1, 'car' => (int) 1, 'col' => (int) 5, 'dca' => (int) 1, 'din' => (int) 2, 'dzi' => (int) 3, 'fan' => (int) 140, 'fve' => (int) 62, 'gma' => (int) 1, 'ghi' => (int) 2, 'gra' => (int) 1, 'han' => (int) 1, 'sun' => (int) 1, 'lonja' => (int) 6, 'lja' => (int) 1, 'lsa' => (int) 4, 'mes' => (int) 1, 'mdo' => (int) 14, 'mtr' => (int) 1, 'egut' => (int) 1, 'nta' => (int) 4, 'oeu' => (int) 1, 'stu' => (int) 2, 'pvu' => (int) 1, 'ptr' => (int) 4, 'ppe' => (int) 19, 'psa' => (int) 1, 'pso' => (int) 4, 'qlo' => (int) 36, 'rch' => (int) 23, 'rsi' => (int) 4, 'sbr' => (int) 4, 'sci' => (int) 2, 'sas' => (int) 4, 'tar' => (int) 1, 'tca' => (int) 1, 'tpr' => (int) 1, 'twi' => (int) 2, 'vmu' => (int) 1 ) $gf_gene_species = 'vmu' $gf_gene_id = 'VMungo1309G0868' $species_info = array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ) $local_species = 'fve' $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' => 'HOM05D001729', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '375', 'num_species' => '42' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'Ah.07g204710' => 'amhyb', 'AUR62006001' => 'cqu', 'AUR62006002' => 'cqu', 'AUR62006003' => 'cqu', 'AUR62015641' => 'cqu', 'AUR62027174' => 'cqu', 'AUR62035623' => 'cqu', 'AUR62035624' => 'cqu', 'AUR62035625' => 'cqu', 'AUR62035626' => 'cqu', 'CAN.G1110.53' => 'can', 'CANSAT80G0415' => 'cansat', 'Ca_21364_v3' => 'car', 'COL.COLO4_30693' => 'col', 'COL.COLO4_30694' => 'col', 'COL.COLO4_30695' => 'col', 'COL.COLO4_30696' => 'col', 'COL.COLO4_34020' => 'col', 'DCAR_004585' => 'dca', 'Dinv04029' => 'din', 'Dinv34857' => 'din', 'Duzib147G0011' => 'dzi', 'Duzib170G0599' => 'dzi', 'Duzib192G1051' => 'dzi', 'FAN01G0708' => 'fan', 'FAN01G0742' => 'fan', 'FAN02G0048' => 'fan', 'FAN02G0583' => 'fan', 'FAN02G0688' => 'fan', 'FAN02G1588' => 'fan', 'FAN02G2194' => 'fan', 'FAN02G2750' => 'fan', 'FAN02G3094' => 'fan', 'FAN02G3887' => 'fan', 'FAN02G3911' => 'fan', 'FAN02G3994' => 'fan', 'FAN02G4432' => 'fan', 'FAN02G4556' => 'fan', 'FAN03G1977' => 'fan', 'FAN03G2781' => 'fan', 'FAN03G2850' => 'fan', 'FAN03G3155' => 'fan', 'FAN04G2487' => 'fan', 'FAN05G0208' => 'fan', 'FAN05G0656' => 'fan', 'FAN05G0696' => 'fan', 'FAN05G0810' => 'fan', 'FAN05G1447' => 'fan', 'FAN05G2640' => 'fan', 'FAN05G2911' => 'fan', 'FAN05G3901' => 'fan', 'FAN05G4859' => 'fan', 'FAN05G4861' => 'fan', 'FAN05G4988' => 'fan', 'FAN05G5187' => 'fan', 'FAN05G5452' => 'fan', 'FAN05G5500' => 'fan', 'FAN05G5688' => 'fan', 'FAN06G0177' => 'fan', 'FAN06G0675' => 'fan', 'FAN06G1290' => 'fan', 'FAN06G2191' => 'fan', 'FAN06G2405' => 'fan', 'FAN06G3231' => 'fan', 'FAN06G3932' => 'fan', 'FAN07G0163' => 'fan', 'FAN07G0471' => 'fan', 'FAN07G1354' => 'fan', 'FAN08G0338' => 'fan', 'FAN08G1373' => 'fan', 'FAN08G2539' => 'fan', 'FAN08G2728' => 'fan', 'FAN09G0608' => 'fan', 'FAN09G1136' => 'fan', 'FAN09G1958' => 'fan', 'FAN09G2508' => 'fan', 'FAN09G2597' => 'fan', 'FAN09G2658' => 'fan', 'FAN09G2757' => 'fan', 'FAN09G2983' => 'fan', 'FAN09G3130' => 'fan', 'FAN09G3565' => 'fan', 'FAN09G3613' => 'fan', 'FAN09G4011' => 'fan', 'FAN09G4239' => 'fan', 'FAN09G4277' => 'fan', 'FAN09G4720' => 'fan', 'FAN11G0139' => 'fan', 'FAN11G1727' => 'fan', 'FAN11G2672' => 'fan', 'FAN11G2795' => 'fan', 'FAN11G3238' => 'fan', 'FAN11G3734' => 'fan', 'FAN12G0631' => 'fan', 'FAN12G2239' => 'fan', 'FAN12G2308' => 'fan', 'FAN12G2569' => 'fan', 'FAN12G2623' => 'fan', 'FAN13G3182' => 'fan', 'FAN14G0053' => 'fan', 'FAN14G0370' => 'fan', 'FAN14G0382' => 'fan', 'FAN14G0421' => 'fan', 'FAN14G0866' => 'fan', 'FAN14G1187' => 'fan', 'FAN14G1727' => 'fan', 'FAN14G1791' => 'fan', 'FAN14G2361' => 'fan', 'FAN14G2668' => 'fan', 'FAN14G2770' => 'fan', 'FAN14G2874' => 'fan', 'FAN14G3193' => 'fan', 'FAN14G3624' => 'fan', 'FAN14G3676' => 'fan', 'FAN14G3807' => 'fan', 'FAN14G4082' => 'fan', 'FAN14G4342' => 'fan', 'FAN14G4985' => 'fan', 'FAN14G5126' => 'fan', 'FAN14G5781' => 'fan', 'FAN14G5808' => 'fan', 'FAN14G5949' => 'fan', 'FAN15G0828' => 'fan', 'FAN15G1054' => 'fan', 'FAN15G2023' => 'fan', 'FAN15G2506' => 'fan', 'FAN16G0128' => 'fan', 'FAN16G0249' => 'fan', 'FAN16G0429' => 'fan', 'FAN16G1493' => 'fan', 'FAN16G2210' => 'fan', 'FAN16G2506' => 'fan', 'FAN18G1542' => 'fan', 'FAN18G4057' => 'fan', 'FAN19G0745' => 'fan', 'FAN19G1216' => 'fan', 'FAN19G1733' => 'fan', 'FAN20G0258' => 'fan', 'FAN20G1095' => 'fan', 'FAN20G1557' => 'fan', 'FAN21G0302' => 'fan', 'FAN21G0519' => 'fan', 'FAN21G0970' => 'fan', 'FAN21G1159' => 'fan', 'FAN21G1312' => 'fan', 'FAN21G1440' => 'fan', 'FAN21G1715' => 'fan', 'FAN23G1584' => 'fan', 'FAN24G0045' => 'fan', 'FAN24G0053' => 'fan', 'FAN24G1500' => 'fan', 'FAN24G1817' => 'fan', 'FAN24G2147' => 'fan', 'FAN24G2236' => 'fan', 'FAN24G2446' => 'fan', 'FAN24G2684' => 'fan', 'FAN25G0187' => 'fan', 'FAN25G0505' => 'fan', 'FAN25G0589' => 'fan', 'FAN25G3663' => 'fan', 'FAN26G1025' => 'fan', 'FAN26G2860' => 'fan', 'FAN27G1329' => 'fan', 'FAN27G3392' => 'fan', 'FvH4_1g02011' => 'fve', 'FvH4_1g06511' => 'fve', 'FvH4_2g19900' => 'fve', 'FvH4_2g19920' => 'fve', 'FvH4_2g24261' => 'fve', 'FvH4_2g24270' => 'fve', 'FvH4_2g24631' => 'fve', 'FvH4_2g30622' => 'fve', 'FvH4_3g12920' => 'fve', 'FvH4_3g30171' => 'fve', 'FvH4_3g35490' => 'fve', 'FvH4_3g43682' => 'fve', 'FvH4_3g43730' => 'fve', 'FvH4_3g43732' => 'fve', 'FvH4_3g43751' => 'fve', 'FvH4_3g43752' => 'fve', 'FvH4_3g43770' => 'fve', 'FvH4_3g44471' => 'fve', 'FvH4_3g44510' => 'fve', 'FvH4_3g44582' => 'fve', 'FvH4_4g16921' => 'fve', 'FvH4_4g17121' => 'fve', 'FvH4_4g17782' => 'fve', 'FvH4_4g17783' => 'fve', 'FvH4_4g18120' => 'fve', 'FvH4_4g31310' => 'fve', 'FvH4_4g35052' => 'fve', 'FvH4_5g30862' => 'fve', 'FvH4_6g01541' => 'fve', 'FvH4_6g02021' => 'fve', 'FvH4_6g02041' => 'fve', 'FvH4_6g02071' => 'fve', 'FvH4_6g02171' => 'fve', 'FvH4_6g03181' => 'fve', 'FvH4_6g03182' => 'fve', 'FvH4_6g03221' => 'fve', 'FvH4_6g03380' => 'fve', 'FvH4_6g05201' => 'fve', 'FvH4_6g05203' => 'fve', 'FvH4_6g20231' => 'fve', 'FvH4_6g31981' => 'fve', 'FvH4_6g32061' => 'fve', 'FvH4_6g37041' => 'fve', 'FvH4_6g37932' => 'fve', 'FvH4_6g38731' => 'fve', 'FvH4_6g39370' => 'fve', 'FvH4_6g39371' => 'fve', 'FvH4_6g40891' => 'fve', 'FvH4_6g40892' => 'fve', 'FvH4_6g43143' => 'fve', 'FvH4_6g45251' => 'fve', 'FvH4_6g45260' => 'fve', 'FvH4_6g45291' => 'fve', 'FvH4_6g45890' => 'fve', 'FvH4_6g46240' => 'fve', 'FvH4_6g46241' => 'fve', 'FvH4_6g46242' => 'fve', 'FvH4_6g46260' => 'fve', 'FvH4_6g46280' => 'fve', 'FvH4_6g46380' => 'fve', 'FvH4_7g12841' => 'fve', 'FvH4_7g31431' => 'fve', 'Glyma.09G075900' => 'gma', 'Gohir.A09G096401' => 'ghi', 'Gohir.D09G096101' => 'ghi', 'Gorai.006G112800' => 'gra', 'HanXRQChr04g0121411' => 'han', 'Hund15878' => 'sun', 'Lj2A1107G68' => 'lonja', 'Lj2A630G63' => 'lonja', 'Lj2A946T25' => 'lonja', 'Lj2C714T1' => 'lonja', 'Lj2C966T3' => 'lonja', 'Lj2C966T4' => 'lonja', 'Lj4g0002979' => 'lja', 'Lsat_1_v5_gn_5_30901' => 'lsa', 'Lsat_1_v5_gn_5_31100' => 'lsa', 'Lsat_1_v5_gn_5_38600' => 'lsa', 'Lsat_1_v5_gn_6_92061' => 'lsa', 'Manes.05G071301' => 'mes', 'MD02G1008700' => 'mdo', 'MD02G1008900' => 'mdo', 'MD03G1256400' => 'mdo', 'MD04G1180900' => 'mdo', 'MD04G1181000' => 'mdo', 'MD04G1181200' => 'mdo', 'MD05G1244200' => 'mdo', 'MD05G1324200' => 'mdo', 'MD09G1201600' => 'mdo', 'MD10G1000600' => 'mdo', 'MD14G1026900' => 'mdo', 'MD14G1187900' => 'mdo', 'MD15G1017800' => 'mdo', 'MD15G1018100' => 'mdo', 'Medtr4g124160' => 'mtr', 'Migut.L01260' => 'egut', 'Nitab4.5_0000008g0440' => 'nta', 'Nitab4.5_0000207g0170' => 'nta', 'Nitab4.5_0007671g0030' => 'nta', 'Nitab4.5_0010853g0020' => 'nta', 'Oeu057656.1' => 'oeu', 'PGSC0003DMG400005638' => 'stu', 'PGSC0003DMG400005639' => 'stu', 'Phvul.009G222800' => 'pvu', 'Potri.009G132400' => 'ptr', 'Potri.009G163001' => 'ptr', 'Potri.011G000700' => 'ptr', 'Potri.011G004800' => 'ptr', 'Prupe.1G509300' => 'ppe', 'Prupe.1G509700' => 'ppe', 'Prupe.1G510400' => 'ppe', 'Prupe.1G510700' => 'ppe', 'Prupe.1G512600' => 'ppe', 'Prupe.2G073200' => 'ppe', 'Prupe.3G059500' => 'ppe', 'Prupe.3G059600' => 'ppe', 'Prupe.3G246100' => 'ppe', 'Prupe.3G265100' => 'ppe', 'Prupe.4G034700' => 'ppe', 'Prupe.4G052100' => 'ppe', 'Prupe.4G053600' => 'ppe', 'Prupe.5G068800' => 'ppe', 'Prupe.5G070600' => 'ppe', 'Prupe.6G075400' => 'ppe', 'Prupe.6G075500' => 'ppe', 'Prupe.6G076400' => 'ppe', 'Prupe.8G110700' => 'ppe', 'Psat4g020960' => 'psa', 'PSO135G0788' => 'pso', 'PSO210G6463' => 'pso', 'PSO384G0370' => 'pso', 'PSO386G0056' => 'pso', 'QL01p006048' => 'qlo', 'QL02p054283' => 'qlo', 'QL05p008000' => 'qlo', 'QL05p008212' => 'qlo', 'QL05p008950' => 'qlo', 'QL05p009042' => 'qlo', 'QL05p009518' => 'qlo', 'QL05p012589' => 'qlo', 'QL05p012608' => 'qlo', 'QL05p012650' => 'qlo', 'QL05p012667' => 'qlo', 'QL05p014501' => 'qlo', 'QL05p052800' => 'qlo', 'QL05p065010' => 'qlo', 'QL05p074156' => 'qlo', 'QL05p074160' => 'qlo', 'QL05p074174' => 'qlo', 'QL05p074178' => 'qlo', 'QL05p074214' => 'qlo', 'QL06p001050' => 'qlo', 'QL06p001056' => 'qlo', 'QL06p006093' => 'qlo', 'QL06p006111' => 'qlo', 'QL07p019784' => 'qlo', 'QL07p019801' => 'qlo', 'QL07p036110' => 'qlo', 'QL07p036134' => 'qlo', 'QL07p036147' => 'qlo', 'QL07p036156' => 'qlo', 'QL07p036300' => 'qlo', 'QL07p036320' => 'qlo', 'QL08p014547' => 'qlo', 'QL08p014551' => 'qlo', 'QL08p043319' => 'qlo', 'QL08p043324' => 'qlo', 'QL11p009094' => 'qlo', 'RcHm_v2.0_Chr1g0380481' => 'rch', 'RcHm_v2.0_Chr2g0089331' => 'rch', 'RcHm_v2.0_Chr2g0123691' => 'rch', 'RcHm_v2.0_Chr2g0151111' => 'rch', 'RcHm_v2.0_Chr2g0163011' => 'rch', 'RcHm_v2.0_Chr2g0163051' => 'rch', 'RcHm_v2.0_Chr2g0164671' => 'rch', 'RcHm_v2.0_Chr2g0164681' => 'rch', 'RcHm_v2.0_Chr2g0164721' => 'rch', 'RcHm_v2.0_Chr3g0449911' => 'rch', 'RcHm_v2.0_Chr3g0450211' => 'rch', 'RcHm_v2.0_Chr3g0457271' => 'rch', 'RcHm_v2.0_Chr5g0018111' => 'rch', 'RcHm_v2.0_Chr5g0021011' => 'rch', 'RcHm_v2.0_Chr5g0081171' => 'rch', 'RcHm_v2.0_Chr5g0081211' => 'rch', 'RcHm_v2.0_Chr6g0275871' => 'rch', 'RcHm_v2.0_Chr6g0276071' => 'rch', 'RcHm_v2.0_Chr6g0285591' => 'rch', 'RcHm_v2.0_Chr6g0291931' => 'rch', 'RcHm_v2.0_Chr6g0292091' => 'rch', 'RcHm_v2.0_Chr6g0292271' => 'rch', 'RcHm_v2.0_Chr7g0221261' => 'rch', 'Rhsim08G0219900' => 'rsi', 'Rhsim08G0220200' => 'rsi', 'Rhsim08G0237800' => 'rsi', 'Rhsim08G0238800' => 'rsi', 'Sabra09G0102700' => 'sbr', 'Sabra09G0127200' => 'sbr', 'Sabra11G0003700' => 'sbr', 'Sabra15G0014700' => 'sbr', 'Sc19g0000590' => 'sci', 'Sc19g0001870' => 'sci', 'SGA_v2.0_scaffold1G00346' => 'sas', 'SGA_v2.0_scaffold1G00575' => 'sas', 'SGA_v2.0_scaffold1G00761' => 'sas', 'SGA_v2.0_scaffold232G43501' => 'sas', 'TAR625G1137' => 'tar', 'Thecc.03G222100' => 'tca', 'TPR.G12691' => 'tpr', 'TWI34G0727' => 'twi', 'TWI36G0117' => 'twi', 'VMungo1309G0868' => 'vmu' ), 'gf_id' => 'HOM05D001729', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001729' ), 'data_identifier' => 'HOM05D001729', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001729', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '375', 'num_species' => '42' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'Ah.07g204710' => 'amhyb', 'AUR62006001' => 'cqu', 'AUR62006002' => 'cqu', 'AUR62006003' => 'cqu', 'AUR62015641' => 'cqu', 'AUR62027174' => 'cqu', 'AUR62035623' => 'cqu', 'AUR62035624' => 'cqu', 'AUR62035625' => 'cqu', 'AUR62035626' => 'cqu', 'CAN.G1110.53' => 'can', 'CANSAT80G0415' => 'cansat', 'Ca_21364_v3' => 'car', 'COL.COLO4_30693' => 'col', 'COL.COLO4_30694' => 'col', 'COL.COLO4_30695' => 'col', 'COL.COLO4_30696' => 'col', 'COL.COLO4_34020' => 'col', 'DCAR_004585' => 'dca', 'Dinv04029' => 'din', 'Dinv34857' => 'din', 'Duzib147G0011' => 'dzi', 'Duzib170G0599' => 'dzi', 'Duzib192G1051' => 'dzi', 'FAN01G0708' => 'fan', 'FAN01G0742' => 'fan', 'FAN02G0048' => 'fan', 'FAN02G0583' => 'fan', 'FAN02G0688' => 'fan', 'FAN02G1588' => 'fan', 'FAN02G2194' => 'fan', 'FAN02G2750' => 'fan', 'FAN02G3094' => 'fan', 'FAN02G3887' => 'fan', 'FAN02G3911' => 'fan', 'FAN02G3994' => 'fan', 'FAN02G4432' => 'fan', 'FAN02G4556' => 'fan', 'FAN03G1977' => 'fan', 'FAN03G2781' => 'fan', 'FAN03G2850' => 'fan', 'FAN03G3155' => 'fan', 'FAN04G2487' => 'fan', 'FAN05G0208' => 'fan', 'FAN05G0656' => 'fan', 'FAN05G0696' => 'fan', 'FAN05G0810' => 'fan', 'FAN05G1447' => 'fan', 'FAN05G2640' => 'fan', 'FAN05G2911' => 'fan', 'FAN05G3901' => 'fan', 'FAN05G4859' => 'fan', 'FAN05G4861' => 'fan', 'FAN05G4988' => 'fan', 'FAN05G5187' => 'fan', 'FAN05G5452' => 'fan', 'FAN05G5500' => 'fan', 'FAN05G5688' => 'fan', 'FAN06G0177' => 'fan', 'FAN06G0675' => 'fan', 'FAN06G1290' => 'fan', 'FAN06G2191' => 'fan', 'FAN06G2405' => 'fan', 'FAN06G3231' => 'fan', 'FAN06G3932' => 'fan', 'FAN07G0163' => 'fan', 'FAN07G0471' => 'fan', 'FAN07G1354' => 'fan', 'FAN08G0338' => 'fan', 'FAN08G1373' => 'fan', 'FAN08G2539' => 'fan', 'FAN08G2728' => 'fan', 'FAN09G0608' => 'fan', 'FAN09G1136' => 'fan', 'FAN09G1958' => 'fan', 'FAN09G2508' => 'fan', 'FAN09G2597' => 'fan', 'FAN09G2658' => 'fan', 'FAN09G2757' => 'fan', 'FAN09G2983' => 'fan', 'FAN09G3130' => 'fan', 'FAN09G3565' => 'fan', 'FAN09G3613' => 'fan', 'FAN09G4011' => 'fan', 'FAN09G4239' => 'fan', 'FAN09G4277' => 'fan', 'FAN09G4720' => 'fan', 'FAN11G0139' => 'fan', 'FAN11G1727' => 'fan', 'FAN11G2672' => 'fan', 'FAN11G2795' => 'fan', 'FAN11G3238' => 'fan', 'FAN11G3734' => 'fan', 'FAN12G0631' => 'fan', 'FAN12G2239' => 'fan', 'FAN12G2308' => 'fan', 'FAN12G2569' => 'fan', 'FAN12G2623' => 'fan', 'FAN13G3182' => 'fan', 'FAN14G0053' => 'fan', 'FAN14G0370' => 'fan', 'FAN14G0382' => 'fan', 'FAN14G0421' => 'fan', 'FAN14G0866' => 'fan', 'FAN14G1187' => 'fan', 'FAN14G1727' => 'fan', 'FAN14G1791' => 'fan', 'FAN14G2361' => 'fan', 'FAN14G2668' => 'fan', 'FAN14G2770' => 'fan', 'FAN14G2874' => 'fan', 'FAN14G3193' => 'fan', 'FAN14G3624' => 'fan', 'FAN14G3676' => 'fan', 'FAN14G3807' => 'fan', 'FAN14G4082' => 'fan', 'FAN14G4342' => 'fan', 'FAN14G4985' => 'fan', 'FAN14G5126' => 'fan', 'FAN14G5781' => 'fan', 'FAN14G5808' => 'fan', 'FAN14G5949' => 'fan', 'FAN15G0828' => 'fan', 'FAN15G1054' => 'fan', 'FAN15G2023' => 'fan', 'FAN15G2506' => 'fan', 'FAN16G0128' => 'fan', 'FAN16G0249' => 'fan', 'FAN16G0429' => 'fan', 'FAN16G1493' => 'fan', 'FAN16G2210' => 'fan', 'FAN16G2506' => 'fan', 'FAN18G1542' => 'fan', 'FAN18G4057' => 'fan', 'FAN19G0745' => 'fan', 'FAN19G1216' => 'fan', 'FAN19G1733' => 'fan', 'FAN20G0258' => 'fan', 'FAN20G1095' => 'fan', 'FAN20G1557' => 'fan', 'FAN21G0302' => 'fan', 'FAN21G0519' => 'fan', 'FAN21G0970' => 'fan', 'FAN21G1159' => 'fan', 'FAN21G1312' => 'fan', 'FAN21G1440' => 'fan', 'FAN21G1715' => 'fan', 'FAN23G1584' => 'fan', 'FAN24G0045' => 'fan', 'FAN24G0053' => 'fan', 'FAN24G1500' => 'fan', 'FAN24G1817' => 'fan', 'FAN24G2147' => 'fan', 'FAN24G2236' => 'fan', 'FAN24G2446' => 'fan', 'FAN24G2684' => 'fan', 'FAN25G0187' => 'fan', 'FAN25G0505' => 'fan', 'FAN25G0589' => 'fan', 'FAN25G3663' => 'fan', 'FAN26G1025' => 'fan', 'FAN26G2860' => 'fan', 'FAN27G1329' => 'fan', 'FAN27G3392' => 'fan', 'FvH4_1g02011' => 'fve', 'FvH4_1g06511' => 'fve', 'FvH4_2g19900' => 'fve', 'FvH4_2g19920' => 'fve', 'FvH4_2g24261' => 'fve', 'FvH4_2g24270' => 'fve', 'FvH4_2g24631' => 'fve', 'FvH4_2g30622' => 'fve', 'FvH4_3g12920' => 'fve', 'FvH4_3g30171' => 'fve', 'FvH4_3g35490' => 'fve', 'FvH4_3g43682' => 'fve', 'FvH4_3g43730' => 'fve', 'FvH4_3g43732' => 'fve', 'FvH4_3g43751' => 'fve', 'FvH4_3g43752' => 'fve', 'FvH4_3g43770' => 'fve', 'FvH4_3g44471' => 'fve', 'FvH4_3g44510' => 'fve', 'FvH4_3g44582' => 'fve', 'FvH4_4g16921' => 'fve', 'FvH4_4g17121' => 'fve', 'FvH4_4g17782' => 'fve', 'FvH4_4g17783' => 'fve', 'FvH4_4g18120' => 'fve', 'FvH4_4g31310' => 'fve', 'FvH4_4g35052' => 'fve', 'FvH4_5g30862' => 'fve', 'FvH4_6g01541' => 'fve', 'FvH4_6g02021' => 'fve', 'FvH4_6g02041' => 'fve', 'FvH4_6g02071' => 'fve', 'FvH4_6g02171' => 'fve', 'FvH4_6g03181' => 'fve', 'FvH4_6g03182' => 'fve', 'FvH4_6g03221' => 'fve', 'FvH4_6g03380' => 'fve', 'FvH4_6g05201' => 'fve', 'FvH4_6g05203' => 'fve', 'FvH4_6g20231' => 'fve', 'FvH4_6g31981' => 'fve', 'FvH4_6g32061' => 'fve', 'FvH4_6g37041' => 'fve', 'FvH4_6g37932' => 'fve', 'FvH4_6g38731' => 'fve', 'FvH4_6g39370' => 'fve', 'FvH4_6g39371' => 'fve', 'FvH4_6g40891' => 'fve', 'FvH4_6g40892' => 'fve', 'FvH4_6g43143' => 'fve', 'FvH4_6g45251' => 'fve', 'FvH4_6g45260' => 'fve', 'FvH4_6g45291' => 'fve', 'FvH4_6g45890' => 'fve', 'FvH4_6g46240' => 'fve', 'FvH4_6g46241' => 'fve', 'FvH4_6g46242' => 'fve', 'FvH4_6g46260' => 'fve', 'FvH4_6g46280' => 'fve', 'FvH4_6g46380' => 'fve', 'FvH4_7g12841' => 'fve', 'FvH4_7g31431' => 'fve', 'Glyma.09G075900' => 'gma', 'Gohir.A09G096401' => 'ghi', 'Gohir.D09G096101' => 'ghi', 'Gorai.006G112800' => 'gra', 'HanXRQChr04g0121411' => 'han', 'Hund15878' => 'sun', 'Lj2A1107G68' => 'lonja', 'Lj2A630G63' => 'lonja', 'Lj2A946T25' => 'lonja', 'Lj2C714T1' => 'lonja', 'Lj2C966T3' => 'lonja', 'Lj2C966T4' => 'lonja', 'Lj4g0002979' => 'lja', 'Lsat_1_v5_gn_5_30901' => 'lsa', 'Lsat_1_v5_gn_5_31100' => 'lsa', 'Lsat_1_v5_gn_5_38600' => 'lsa', 'Lsat_1_v5_gn_6_92061' => 'lsa', 'Manes.05G071301' => 'mes', 'MD02G1008700' => 'mdo', 'MD02G1008900' => 'mdo', 'MD03G1256400' => 'mdo', 'MD04G1180900' => 'mdo', 'MD04G1181000' => 'mdo', 'MD04G1181200' => 'mdo', 'MD05G1244200' => 'mdo', 'MD05G1324200' => 'mdo', 'MD09G1201600' => 'mdo', 'MD10G1000600' => 'mdo', 'MD14G1026900' => 'mdo', 'MD14G1187900' => 'mdo', 'MD15G1017800' => 'mdo', 'MD15G1018100' => 'mdo', 'Medtr4g124160' => 'mtr', 'Migut.L01260' => 'egut', 'Nitab4.5_0000008g0440' => 'nta', 'Nitab4.5_0000207g0170' => 'nta', 'Nitab4.5_0007671g0030' => 'nta', 'Nitab4.5_0010853g0020' => 'nta', 'Oeu057656.1' => 'oeu', 'PGSC0003DMG400005638' => 'stu', 'PGSC0003DMG400005639' => 'stu', 'Phvul.009G222800' => 'pvu', 'Potri.009G132400' => 'ptr', 'Potri.009G163001' => 'ptr', 'Potri.011G000700' => 'ptr', 'Potri.011G004800' => 'ptr', 'Prupe.1G509300' => 'ppe', 'Prupe.1G509700' => 'ppe', 'Prupe.1G510400' => 'ppe', 'Prupe.1G510700' => 'ppe', 'Prupe.1G512600' => 'ppe', 'Prupe.2G073200' => 'ppe', 'Prupe.3G059500' => 'ppe', 'Prupe.3G059600' => 'ppe', 'Prupe.3G246100' => 'ppe', 'Prupe.3G265100' => 'ppe', 'Prupe.4G034700' => 'ppe', 'Prupe.4G052100' => 'ppe', 'Prupe.4G053600' => 'ppe', 'Prupe.5G068800' => 'ppe', 'Prupe.5G070600' => 'ppe', 'Prupe.6G075400' => 'ppe', 'Prupe.6G075500' => 'ppe', 'Prupe.6G076400' => 'ppe', 'Prupe.8G110700' => 'ppe', 'Psat4g020960' => 'psa', 'PSO135G0788' => 'pso', 'PSO210G6463' => 'pso', 'PSO384G0370' => 'pso', 'PSO386G0056' => 'pso', 'QL01p006048' => 'qlo', 'QL02p054283' => 'qlo', 'QL05p008000' => 'qlo', 'QL05p008212' => 'qlo', 'QL05p008950' => 'qlo', 'QL05p009042' => 'qlo', 'QL05p009518' => 'qlo', 'QL05p012589' => 'qlo', 'QL05p012608' => 'qlo', 'QL05p012650' => 'qlo', 'QL05p012667' => 'qlo', 'QL05p014501' => 'qlo', 'QL05p052800' => 'qlo', 'QL05p065010' => 'qlo', 'QL05p074156' => 'qlo', 'QL05p074160' => 'qlo', 'QL05p074174' => 'qlo', 'QL05p074178' => 'qlo', 'QL05p074214' => 'qlo', 'QL06p001050' => 'qlo', 'QL06p001056' => 'qlo', 'QL06p006093' => 'qlo', 'QL06p006111' => 'qlo', 'QL07p019784' => 'qlo', 'QL07p019801' => 'qlo', 'QL07p036110' => 'qlo', 'QL07p036134' => 'qlo', 'QL07p036147' => 'qlo', 'QL07p036156' => 'qlo', 'QL07p036300' => 'qlo', 'QL07p036320' => 'qlo', 'QL08p014547' => 'qlo', 'QL08p014551' => 'qlo', 'QL08p043319' => 'qlo', 'QL08p043324' => 'qlo', 'QL11p009094' => 'qlo', 'RcHm_v2.0_Chr1g0380481' => 'rch', 'RcHm_v2.0_Chr2g0089331' => 'rch', 'RcHm_v2.0_Chr2g0123691' => 'rch', 'RcHm_v2.0_Chr2g0151111' => 'rch', 'RcHm_v2.0_Chr2g0163011' => 'rch', 'RcHm_v2.0_Chr2g0163051' => 'rch', 'RcHm_v2.0_Chr2g0164671' => 'rch', 'RcHm_v2.0_Chr2g0164681' => 'rch', 'RcHm_v2.0_Chr2g0164721' => 'rch', 'RcHm_v2.0_Chr3g0449911' => 'rch', 'RcHm_v2.0_Chr3g0450211' => 'rch', 'RcHm_v2.0_Chr3g0457271' => 'rch', 'RcHm_v2.0_Chr5g0018111' => 'rch', 'RcHm_v2.0_Chr5g0021011' => 'rch', 'RcHm_v2.0_Chr5g0081171' => 'rch', 'RcHm_v2.0_Chr5g0081211' => 'rch', 'RcHm_v2.0_Chr6g0275871' => 'rch', 'RcHm_v2.0_Chr6g0276071' => 'rch', 'RcHm_v2.0_Chr6g0285591' => 'rch', 'RcHm_v2.0_Chr6g0291931' => 'rch', 'RcHm_v2.0_Chr6g0292091' => 'rch', 'RcHm_v2.0_Chr6g0292271' => 'rch', 'RcHm_v2.0_Chr7g0221261' => 'rch', 'Rhsim08G0219900' => 'rsi', 'Rhsim08G0220200' => 'rsi', 'Rhsim08G0237800' => 'rsi', 'Rhsim08G0238800' => 'rsi', 'Sabra09G0102700' => 'sbr', 'Sabra09G0127200' => 'sbr', 'Sabra11G0003700' => 'sbr', 'Sabra15G0014700' => 'sbr', 'Sc19g0000590' => 'sci', 'Sc19g0001870' => 'sci', 'SGA_v2.0_scaffold1G00346' => 'sas', 'SGA_v2.0_scaffold1G00575' => 'sas', 'SGA_v2.0_scaffold1G00761' => 'sas', 'SGA_v2.0_scaffold232G43501' => 'sas', 'TAR625G1137' => 'tar', 'Thecc.03G222100' => 'tca', 'TPR.G12691' => 'tpr', 'TWI34G0727' => 'twi', 'TWI36G0117' => 'twi', 'VMungo1309G0868' => 'vmu' ) $gf_id = 'HOM05D001729' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001729' ) $data_identifier = 'HOM05D001729' $data_type = 'gf_id' $species_gene_counts = array( 'amhyb' => (int) 1, 'cqu' => (int) 9, 'can' => (int) 1, 'cansat' => (int) 1, 'car' => (int) 1, 'col' => (int) 5, 'dca' => (int) 1, 'din' => (int) 2, 'dzi' => (int) 3, 'fan' => (int) 140, 'fve' => (int) 62, 'gma' => (int) 1, 'ghi' => (int) 2, 'gra' => (int) 1, 'han' => (int) 1, 'sun' => (int) 1, 'lonja' => (int) 6, 'lja' => (int) 1, 'lsa' => (int) 4, 'mes' => (int) 1, 'mdo' => (int) 14, 'mtr' => (int) 1, 'egut' => (int) 1, 'nta' => (int) 4, 'oeu' => (int) 1, 'stu' => (int) 2, 'pvu' => (int) 1, 'ptr' => (int) 4, 'ppe' => (int) 19, 'psa' => (int) 1, 'pso' => (int) 4, 'qlo' => (int) 36, 'rch' => (int) 23, 'rsi' => (int) 4, 'sbr' => (int) 4, 'sci' => (int) 2, 'sas' => (int) 4, 'tar' => (int) 1, 'tca' => (int) 1, 'tpr' => (int) 1, 'twi' => (int) 2, 'vmu' => (int) 1 ) $gf_gene_species = 'vmu' $gf_gene_id = 'VMungo1309G0868' $species_info = array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ) $local_species = 'fan' $disabled = '' $selected = '' $num_hits = (int) 1include - APP/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp, line 33 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933 View::_renderElement() - CORE/Cake/View/View.php, line 1224 View::element() - CORE/Cake/View/View.php, line 418 include - APP/View/Elements/analysis/phylogenetics_module/gf_data_settings.ctp, line 37 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933 View::_renderElement() - CORE/Cake/View/View.php, line 1224 View::element() - CORE/Cake/View/View.php, line 418 include - APP/View/Elements/analysis/phylogenetics_module/parameter_selection.ctp, line 64 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933 View::_renderElement() - CORE/Cake/View/View.php, line 1224 View::element() - CORE/Cake/View/View.php, line 418 include - APP/View/Analysis/custom_tree_creation.ctp, line 27 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933
$viewFile = '/www/bioinformatics01_ro/plaza/_dev_instances/feedback/app/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp' $dataForView = array( 'sidebar_info' => array( 'gf_id' => 'HOM05D001729', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '375', 'num_species' => '42' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'Ah.07g204710' => 'amhyb', 'AUR62006001' => 'cqu', 'AUR62006002' => 'cqu', 'AUR62006003' => 'cqu', 'AUR62015641' => 'cqu', 'AUR62027174' => 'cqu', 'AUR62035623' => 'cqu', 'AUR62035624' => 'cqu', 'AUR62035625' => 'cqu', 'AUR62035626' => 'cqu', 'CAN.G1110.53' => 'can', 'CANSAT80G0415' => 'cansat', 'Ca_21364_v3' => 'car', 'COL.COLO4_30693' => 'col', 'COL.COLO4_30694' => 'col', 'COL.COLO4_30695' => 'col', 'COL.COLO4_30696' => 'col', 'COL.COLO4_34020' => 'col', 'DCAR_004585' => 'dca', 'Dinv04029' => 'din', 'Dinv34857' => 'din', 'Duzib147G0011' => 'dzi', 'Duzib170G0599' => 'dzi', 'Duzib192G1051' => 'dzi', 'FAN01G0708' => 'fan', 'FAN01G0742' => 'fan', 'FAN02G0048' => 'fan', 'FAN02G0583' => 'fan', 'FAN02G0688' => 'fan', 'FAN02G1588' => 'fan', 'FAN02G2194' => 'fan', 'FAN02G2750' => 'fan', 'FAN02G3094' => 'fan', 'FAN02G3887' => 'fan', 'FAN02G3911' => 'fan', 'FAN02G3994' => 'fan', 'FAN02G4432' => 'fan', 'FAN02G4556' => 'fan', 'FAN03G1977' => 'fan', 'FAN03G2781' => 'fan', 'FAN03G2850' => 'fan', 'FAN03G3155' => 'fan', 'FAN04G2487' => 'fan', 'FAN05G0208' => 'fan', 'FAN05G0656' => 'fan', 'FAN05G0696' => 'fan', 'FAN05G0810' => 'fan', 'FAN05G1447' => 'fan', 'FAN05G2640' => 'fan', 'FAN05G2911' => 'fan', 'FAN05G3901' => 'fan', 'FAN05G4859' => 'fan', 'FAN05G4861' => 'fan', 'FAN05G4988' => 'fan', 'FAN05G5187' => 'fan', 'FAN05G5452' => 'fan', 'FAN05G5500' => 'fan', 'FAN05G5688' => 'fan', 'FAN06G0177' => 'fan', 'FAN06G0675' => 'fan', 'FAN06G1290' => 'fan', 'FAN06G2191' => 'fan', 'FAN06G2405' => 'fan', 'FAN06G3231' => 'fan', 'FAN06G3932' => 'fan', 'FAN07G0163' => 'fan', 'FAN07G0471' => 'fan', 'FAN07G1354' => 'fan', 'FAN08G0338' => 'fan', 'FAN08G1373' => 'fan', 'FAN08G2539' => 'fan', 'FAN08G2728' => 'fan', 'FAN09G0608' => 'fan', 'FAN09G1136' => 'fan', 'FAN09G1958' => 'fan', 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'FAN14G5126' => 'fan', 'FAN14G5781' => 'fan', 'FAN14G5808' => 'fan', 'FAN14G5949' => 'fan', 'FAN15G0828' => 'fan', 'FAN15G1054' => 'fan', 'FAN15G2023' => 'fan', 'FAN15G2506' => 'fan', 'FAN16G0128' => 'fan', 'FAN16G0249' => 'fan', 'FAN16G0429' => 'fan', 'FAN16G1493' => 'fan', 'FAN16G2210' => 'fan', 'FAN16G2506' => 'fan', 'FAN18G1542' => 'fan', 'FAN18G4057' => 'fan', 'FAN19G0745' => 'fan', 'FAN19G1216' => 'fan', 'FAN19G1733' => 'fan', 'FAN20G0258' => 'fan', 'FAN20G1095' => 'fan', 'FAN20G1557' => 'fan', 'FAN21G0302' => 'fan', 'FAN21G0519' => 'fan', 'FAN21G0970' => 'fan', 'FAN21G1159' => 'fan', 'FAN21G1312' => 'fan', 'FAN21G1440' => 'fan', 'FAN21G1715' => 'fan', 'FAN23G1584' => 'fan', 'FAN24G0045' => 'fan', 'FAN24G0053' => 'fan', 'FAN24G1500' => 'fan', 'FAN24G1817' => 'fan', 'FAN24G2147' => 'fan', 'FAN24G2236' => 'fan', 'FAN24G2446' => 'fan', 'FAN24G2684' => 'fan', 'FAN25G0187' => 'fan', 'FAN25G0505' => 'fan', 'FAN25G0589' => 'fan', 'FAN25G3663' => 'fan', 'FAN26G1025' => 'fan', 'FAN26G2860' => 'fan', 'FAN27G1329' => 'fan', 'FAN27G3392' => 'fan', 'FvH4_1g02011' => 'fve', 'FvH4_1g06511' => 'fve', 'FvH4_2g19900' => 'fve', 'FvH4_2g19920' => 'fve', 'FvH4_2g24261' => 'fve', 'FvH4_2g24270' => 'fve', 'FvH4_2g24631' => 'fve', 'FvH4_2g30622' => 'fve', 'FvH4_3g12920' => 'fve', 'FvH4_3g30171' => 'fve', 'FvH4_3g35490' => 'fve', 'FvH4_3g43682' => 'fve', 'FvH4_3g43730' => 'fve', 'FvH4_3g43732' => 'fve', 'FvH4_3g43751' => 'fve', 'FvH4_3g43752' => 'fve', 'FvH4_3g43770' => 'fve', 'FvH4_3g44471' => 'fve', 'FvH4_3g44510' => 'fve', 'FvH4_3g44582' => 'fve', 'FvH4_4g16921' => 'fve', 'FvH4_4g17121' => 'fve', 'FvH4_4g17782' => 'fve', 'FvH4_4g17783' => 'fve', 'FvH4_4g18120' => 'fve', 'FvH4_4g31310' => 'fve', 'FvH4_4g35052' => 'fve', 'FvH4_5g30862' => 'fve', 'FvH4_6g01541' => 'fve', 'FvH4_6g02021' => 'fve', 'FvH4_6g02041' => 'fve', 'FvH4_6g02071' => 'fve', 'FvH4_6g02171' => 'fve', 'FvH4_6g03181' => 'fve', 'FvH4_6g03182' => 'fve', 'FvH4_6g03221' => 'fve', 'FvH4_6g03380' => 'fve', 'FvH4_6g05201' => 'fve', 'FvH4_6g05203' => 'fve', 'FvH4_6g20231' => 'fve', 'FvH4_6g31981' => 'fve', 'FvH4_6g32061' => 'fve', 'FvH4_6g37041' => 'fve', 'FvH4_6g37932' => 'fve', 'FvH4_6g38731' => 'fve', 'FvH4_6g39370' => 'fve', 'FvH4_6g39371' => 'fve', 'FvH4_6g40891' => 'fve', 'FvH4_6g40892' => 'fve', 'FvH4_6g43143' => 'fve', 'FvH4_6g45251' => 'fve', 'FvH4_6g45260' => 'fve', 'FvH4_6g45291' => 'fve', 'FvH4_6g45890' => 'fve', 'FvH4_6g46240' => 'fve', 'FvH4_6g46241' => 'fve', 'FvH4_6g46242' => 'fve', 'FvH4_6g46260' => 'fve', 'FvH4_6g46280' => 'fve', 'FvH4_6g46380' => 'fve', 'FvH4_7g12841' => 'fve', 'FvH4_7g31431' => 'fve', 'Glyma.09G075900' => 'gma', 'Gohir.A09G096401' => 'ghi', 'Gohir.D09G096101' => 'ghi', 'Gorai.006G112800' => 'gra', 'HanXRQChr04g0121411' => 'han', 'Hund15878' => 'sun', 'Lj2A1107G68' => 'lonja', 'Lj2A630G63' => 'lonja', 'Lj2A946T25' => 'lonja', 'Lj2C714T1' => 'lonja', 'Lj2C966T3' => 'lonja', 'Lj2C966T4' => 'lonja', 'Lj4g0002979' => 'lja', 'Lsat_1_v5_gn_5_30901' => 'lsa', 'Lsat_1_v5_gn_5_31100' => 'lsa', 'Lsat_1_v5_gn_5_38600' => 'lsa', 'Lsat_1_v5_gn_6_92061' => 'lsa', 'Manes.05G071301' => 'mes', 'MD02G1008700' => 'mdo', 'MD02G1008900' => 'mdo', 'MD03G1256400' => 'mdo', 'MD04G1180900' => 'mdo', 'MD04G1181000' => 'mdo', 'MD04G1181200' => 'mdo', 'MD05G1244200' => 'mdo', 'MD05G1324200' => 'mdo', 'MD09G1201600' => 'mdo', 'MD10G1000600' => 'mdo', 'MD14G1026900' => 'mdo', 'MD14G1187900' => 'mdo', 'MD15G1017800' => 'mdo', 'MD15G1018100' => 'mdo', 'Medtr4g124160' => 'mtr', 'Migut.L01260' => 'egut', 'Nitab4.5_0000008g0440' => 'nta', 'Nitab4.5_0000207g0170' => 'nta', 'Nitab4.5_0007671g0030' => 'nta', 'Nitab4.5_0010853g0020' => 'nta', 'Oeu057656.1' => 'oeu', 'PGSC0003DMG400005638' => 'stu', 'PGSC0003DMG400005639' => 'stu', 'Phvul.009G222800' => 'pvu', 'Potri.009G132400' => 'ptr', 'Potri.009G163001' => 'ptr', 'Potri.011G000700' => 'ptr', 'Potri.011G004800' => 'ptr', 'Prupe.1G509300' => 'ppe', 'Prupe.1G509700' => 'ppe', 'Prupe.1G510400' => 'ppe', 'Prupe.1G510700' => 'ppe', 'Prupe.1G512600' => 'ppe', 'Prupe.2G073200' => 'ppe', 'Prupe.3G059500' => 'ppe', 'Prupe.3G059600' => 'ppe', 'Prupe.3G246100' => 'ppe', 'Prupe.3G265100' => 'ppe', 'Prupe.4G034700' => 'ppe', 'Prupe.4G052100' => 'ppe', 'Prupe.4G053600' => 'ppe', 'Prupe.5G068800' => 'ppe', 'Prupe.5G070600' => 'ppe', 'Prupe.6G075400' => 'ppe', 'Prupe.6G075500' => 'ppe', 'Prupe.6G076400' => 'ppe', 'Prupe.8G110700' => 'ppe', 'Psat4g020960' => 'psa', 'PSO135G0788' => 'pso', 'PSO210G6463' => 'pso', 'PSO384G0370' => 'pso', 'PSO386G0056' => 'pso', 'QL01p006048' => 'qlo', 'QL02p054283' => 'qlo', 'QL05p008000' => 'qlo', 'QL05p008212' => 'qlo', 'QL05p008950' => 'qlo', 'QL05p009042' => 'qlo', 'QL05p009518' => 'qlo', 'QL05p012589' => 'qlo', 'QL05p012608' => 'qlo', 'QL05p012650' => 'qlo', 'QL05p012667' => 'qlo', 'QL05p014501' => 'qlo', 'QL05p052800' => 'qlo', 'QL05p065010' => 'qlo', 'QL05p074156' => 'qlo', 'QL05p074160' => 'qlo', 'QL05p074174' => 'qlo', 'QL05p074178' => 'qlo', 'QL05p074214' => 'qlo', 'QL06p001050' => 'qlo', 'QL06p001056' => 'qlo', 'QL06p006093' => 'qlo', 'QL06p006111' => 'qlo', 'QL07p019784' => 'qlo', 'QL07p019801' => 'qlo', 'QL07p036110' => 'qlo', 'QL07p036134' => 'qlo', 'QL07p036147' => 'qlo', 'QL07p036156' => 'qlo', 'QL07p036300' => 'qlo', 'QL07p036320' => 'qlo', 'QL08p014547' => 'qlo', 'QL08p014551' => 'qlo', 'QL08p043319' => 'qlo', 'QL08p043324' => 'qlo', 'QL11p009094' => 'qlo', 'RcHm_v2.0_Chr1g0380481' => 'rch', 'RcHm_v2.0_Chr2g0089331' => 'rch', 'RcHm_v2.0_Chr2g0123691' => 'rch', 'RcHm_v2.0_Chr2g0151111' => 'rch', 'RcHm_v2.0_Chr2g0163011' => 'rch', 'RcHm_v2.0_Chr2g0163051' => 'rch', 'RcHm_v2.0_Chr2g0164671' => 'rch', 'RcHm_v2.0_Chr2g0164681' => 'rch', 'RcHm_v2.0_Chr2g0164721' => 'rch', 'RcHm_v2.0_Chr3g0449911' => 'rch', 'RcHm_v2.0_Chr3g0450211' => 'rch', 'RcHm_v2.0_Chr3g0457271' => 'rch', 'RcHm_v2.0_Chr5g0018111' => 'rch', 'RcHm_v2.0_Chr5g0021011' => 'rch', 'RcHm_v2.0_Chr5g0081171' => 'rch', 'RcHm_v2.0_Chr5g0081211' => 'rch', 'RcHm_v2.0_Chr6g0275871' => 'rch', 'RcHm_v2.0_Chr6g0276071' => 'rch', 'RcHm_v2.0_Chr6g0285591' => 'rch', 'RcHm_v2.0_Chr6g0291931' => 'rch', 'RcHm_v2.0_Chr6g0292091' => 'rch', 'RcHm_v2.0_Chr6g0292271' => 'rch', 'RcHm_v2.0_Chr7g0221261' => 'rch', 'Rhsim08G0219900' => 'rsi', 'Rhsim08G0220200' => 'rsi', 'Rhsim08G0237800' => 'rsi', 'Rhsim08G0238800' => 'rsi', 'Sabra09G0102700' => 'sbr', 'Sabra09G0127200' => 'sbr', 'Sabra11G0003700' => 'sbr', 'Sabra15G0014700' => 'sbr', 'Sc19g0000590' => 'sci', 'Sc19g0001870' => 'sci', 'SGA_v2.0_scaffold1G00346' => 'sas', 'SGA_v2.0_scaffold1G00575' => 'sas', 'SGA_v2.0_scaffold1G00761' => 'sas', 'SGA_v2.0_scaffold232G43501' => 'sas', 'TAR625G1137' => 'tar', 'Thecc.03G222100' => 'tca', 'TPR.G12691' => 'tpr', 'TWI34G0727' => 'twi', 'TWI36G0117' => 'twi', 'VMungo1309G0868' => 'vmu' ), 'gf_id' => 'HOM05D001729', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001729' ), 'data_identifier' => 'HOM05D001729', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001729', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '375', 'num_species' => '42' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'Ah.07g204710' => 'amhyb', 'AUR62006001' => 'cqu', 'AUR62006002' => 'cqu', 'AUR62006003' => 'cqu', 'AUR62015641' => 'cqu', 'AUR62027174' => 'cqu', 'AUR62035623' => 'cqu', 'AUR62035624' => 'cqu', 'AUR62035625' => 'cqu', 'AUR62035626' => 'cqu', 'CAN.G1110.53' => 'can', 'CANSAT80G0415' => 'cansat', 'Ca_21364_v3' => 'car', 'COL.COLO4_30693' => 'col', 'COL.COLO4_30694' => 'col', 'COL.COLO4_30695' => 'col', 'COL.COLO4_30696' => 'col', 'COL.COLO4_34020' => 'col', 'DCAR_004585' => 'dca', 'Dinv04029' => 'din', 'Dinv34857' => 'din', 'Duzib147G0011' => 'dzi', 'Duzib170G0599' => 'dzi', 'Duzib192G1051' => 'dzi', 'FAN01G0708' => 'fan', 'FAN01G0742' => 'fan', 'FAN02G0048' => 'fan', 'FAN02G0583' => 'fan', 'FAN02G0688' => 'fan', 'FAN02G1588' => 'fan', 'FAN02G2194' => 'fan', 'FAN02G2750' => 'fan', 'FAN02G3094' => 'fan', 'FAN02G3887' => 'fan', 'FAN02G3911' => 'fan', 'FAN02G3994' => 'fan', 'FAN02G4432' => 'fan', 'FAN02G4556' => 'fan', 'FAN03G1977' => 'fan', 'FAN03G2781' => 'fan', 'FAN03G2850' => 'fan', 'FAN03G3155' => 'fan', 'FAN04G2487' => 'fan', 'FAN05G0208' => 'fan', 'FAN05G0656' => 'fan', 'FAN05G0696' => 'fan', 'FAN05G0810' => 'fan', 'FAN05G1447' => 'fan', 'FAN05G2640' => 'fan', 'FAN05G2911' => 'fan', 'FAN05G3901' => 'fan', 'FAN05G4859' => 'fan', 'FAN05G4861' => 'fan', 'FAN05G4988' => 'fan', 'FAN05G5187' => 'fan', 'FAN05G5452' => 'fan', 'FAN05G5500' => 'fan', 'FAN05G5688' => 'fan', 'FAN06G0177' => 'fan', 'FAN06G0675' => 'fan', 'FAN06G1290' => 'fan', 'FAN06G2191' => 'fan', 'FAN06G2405' => 'fan', 'FAN06G3231' => 'fan', 'FAN06G3932' => 'fan', 'FAN07G0163' => 'fan', 'FAN07G0471' => 'fan', 'FAN07G1354' => 'fan', 'FAN08G0338' => 'fan', 'FAN08G1373' => 'fan', 'FAN08G2539' => 'fan', 'FAN08G2728' => 'fan', 'FAN09G0608' => 'fan', 'FAN09G1136' => 'fan', 'FAN09G1958' => 'fan', 'FAN09G2508' => 'fan', 'FAN09G2597' => 'fan', 'FAN09G2658' => 'fan', 'FAN09G2757' => 'fan', 'FAN09G2983' => 'fan', 'FAN09G3130' => 'fan', 'FAN09G3565' => 'fan', 'FAN09G3613' => 'fan', 'FAN09G4011' => 'fan', 'FAN09G4239' => 'fan', 'FAN09G4277' => 'fan', 'FAN09G4720' => 'fan', 'FAN11G0139' => 'fan', 'FAN11G1727' => 'fan', 'FAN11G2672' => 'fan', 'FAN11G2795' => 'fan', 'FAN11G3238' => 'fan', 'FAN11G3734' => 'fan', 'FAN12G0631' => 'fan', 'FAN12G2239' => 'fan', 'FAN12G2308' => 'fan', 'FAN12G2569' => 'fan', 'FAN12G2623' => 'fan', 'FAN13G3182' => 'fan', 'FAN14G0053' => 'fan', 'FAN14G0370' => 'fan', 'FAN14G0382' => 'fan', 'FAN14G0421' => 'fan', 'FAN14G0866' => 'fan', 'FAN14G1187' => 'fan', 'FAN14G1727' => 'fan', 'FAN14G1791' => 'fan', 'FAN14G2361' => 'fan', 'FAN14G2668' => 'fan', 'FAN14G2770' => 'fan', 'FAN14G2874' => 'fan', 'FAN14G3193' => 'fan', 'FAN14G3624' => 'fan', 'FAN14G3676' => 'fan', 'FAN14G3807' => 'fan', 'FAN14G4082' => 'fan', 'FAN14G4342' => 'fan', 'FAN14G4985' => 'fan', 'FAN14G5126' => 'fan', 'FAN14G5781' => 'fan', 'FAN14G5808' => 'fan', 'FAN14G5949' => 'fan', 'FAN15G0828' => 'fan', 'FAN15G1054' => 'fan', 'FAN15G2023' => 'fan', 'FAN15G2506' => 'fan', 'FAN16G0128' => 'fan', 'FAN16G0249' => 'fan', 'FAN16G0429' => 'fan', 'FAN16G1493' => 'fan', 'FAN16G2210' => 'fan', 'FAN16G2506' => 'fan', 'FAN18G1542' => 'fan', 'FAN18G4057' => 'fan', 'FAN19G0745' => 'fan', 'FAN19G1216' => 'fan', 'FAN19G1733' => 'fan', 'FAN20G0258' => 'fan', 'FAN20G1095' => 'fan', 'FAN20G1557' => 'fan', 'FAN21G0302' => 'fan', 'FAN21G0519' => 'fan', 'FAN21G0970' => 'fan', 'FAN21G1159' => 'fan', 'FAN21G1312' => 'fan', 'FAN21G1440' => 'fan', 'FAN21G1715' => 'fan', 'FAN23G1584' => 'fan', 'FAN24G0045' => 'fan', 'FAN24G0053' => 'fan', 'FAN24G1500' => 'fan', 'FAN24G1817' => 'fan', 'FAN24G2147' => 'fan', 'FAN24G2236' => 'fan', 'FAN24G2446' => 'fan', 'FAN24G2684' => 'fan', 'FAN25G0187' => 'fan', 'FAN25G0505' => 'fan', 'FAN25G0589' => 'fan', 'FAN25G3663' => 'fan', 'FAN26G1025' => 'fan', 'FAN26G2860' => 'fan', 'FAN27G1329' => 'fan', 'FAN27G3392' => 'fan', 'FvH4_1g02011' => 'fve', 'FvH4_1g06511' => 'fve', 'FvH4_2g19900' => 'fve', 'FvH4_2g19920' => 'fve', 'FvH4_2g24261' => 'fve', 'FvH4_2g24270' => 'fve', 'FvH4_2g24631' => 'fve', 'FvH4_2g30622' => 'fve', 'FvH4_3g12920' => 'fve', 'FvH4_3g30171' => 'fve', 'FvH4_3g35490' => 'fve', 'FvH4_3g43682' => 'fve', 'FvH4_3g43730' => 'fve', 'FvH4_3g43732' => 'fve', 'FvH4_3g43751' => 'fve', 'FvH4_3g43752' => 'fve', 'FvH4_3g43770' => 'fve', 'FvH4_3g44471' => 'fve', 'FvH4_3g44510' => 'fve', 'FvH4_3g44582' => 'fve', 'FvH4_4g16921' => 'fve', 'FvH4_4g17121' => 'fve', 'FvH4_4g17782' => 'fve', 'FvH4_4g17783' => 'fve', 'FvH4_4g18120' => 'fve', 'FvH4_4g31310' => 'fve', 'FvH4_4g35052' => 'fve', 'FvH4_5g30862' => 'fve', 'FvH4_6g01541' => 'fve', 'FvH4_6g02021' => 'fve', 'FvH4_6g02041' => 'fve', 'FvH4_6g02071' => 'fve', 'FvH4_6g02171' => 'fve', 'FvH4_6g03181' => 'fve', 'FvH4_6g03182' => 'fve', 'FvH4_6g03221' => 'fve', 'FvH4_6g03380' => 'fve', 'FvH4_6g05201' => 'fve', 'FvH4_6g05203' => 'fve', 'FvH4_6g20231' => 'fve', 'FvH4_6g31981' => 'fve', 'FvH4_6g32061' => 'fve', 'FvH4_6g37041' => 'fve', 'FvH4_6g37932' => 'fve', 'FvH4_6g38731' => 'fve', 'FvH4_6g39370' => 'fve', 'FvH4_6g39371' => 'fve', 'FvH4_6g40891' => 'fve', 'FvH4_6g40892' => 'fve', 'FvH4_6g43143' => 'fve', 'FvH4_6g45251' => 'fve', 'FvH4_6g45260' => 'fve', 'FvH4_6g45291' => 'fve', 'FvH4_6g45890' => 'fve', 'FvH4_6g46240' => 'fve', 'FvH4_6g46241' => 'fve', 'FvH4_6g46242' => 'fve', 'FvH4_6g46260' => 'fve', 'FvH4_6g46280' => 'fve', 'FvH4_6g46380' => 'fve', 'FvH4_7g12841' => 'fve', 'FvH4_7g31431' => 'fve', 'Glyma.09G075900' => 'gma', 'Gohir.A09G096401' => 'ghi', 'Gohir.D09G096101' => 'ghi', 'Gorai.006G112800' => 'gra', 'HanXRQChr04g0121411' => 'han', 'Hund15878' => 'sun', 'Lj2A1107G68' => 'lonja', 'Lj2A630G63' => 'lonja', 'Lj2A946T25' => 'lonja', 'Lj2C714T1' => 'lonja', 'Lj2C966T3' => 'lonja', 'Lj2C966T4' => 'lonja', 'Lj4g0002979' => 'lja', 'Lsat_1_v5_gn_5_30901' => 'lsa', 'Lsat_1_v5_gn_5_31100' => 'lsa', 'Lsat_1_v5_gn_5_38600' => 'lsa', 'Lsat_1_v5_gn_6_92061' => 'lsa', 'Manes.05G071301' => 'mes', 'MD02G1008700' => 'mdo', 'MD02G1008900' => 'mdo', 'MD03G1256400' => 'mdo', 'MD04G1180900' => 'mdo', 'MD04G1181000' => 'mdo', 'MD04G1181200' => 'mdo', 'MD05G1244200' => 'mdo', 'MD05G1324200' => 'mdo', 'MD09G1201600' => 'mdo', 'MD10G1000600' => 'mdo', 'MD14G1026900' => 'mdo', 'MD14G1187900' => 'mdo', 'MD15G1017800' => 'mdo', 'MD15G1018100' => 'mdo', 'Medtr4g124160' => 'mtr', 'Migut.L01260' => 'egut', 'Nitab4.5_0000008g0440' => 'nta', 'Nitab4.5_0000207g0170' => 'nta', 'Nitab4.5_0007671g0030' => 'nta', 'Nitab4.5_0010853g0020' => 'nta', 'Oeu057656.1' => 'oeu', 'PGSC0003DMG400005638' => 'stu', 'PGSC0003DMG400005639' => 'stu', 'Phvul.009G222800' => 'pvu', 'Potri.009G132400' => 'ptr', 'Potri.009G163001' => 'ptr', 'Potri.011G000700' => 'ptr', 'Potri.011G004800' => 'ptr', 'Prupe.1G509300' => 'ppe', 'Prupe.1G509700' => 'ppe', 'Prupe.1G510400' => 'ppe', 'Prupe.1G510700' => 'ppe', 'Prupe.1G512600' => 'ppe', 'Prupe.2G073200' => 'ppe', 'Prupe.3G059500' => 'ppe', 'Prupe.3G059600' => 'ppe', 'Prupe.3G246100' => 'ppe', 'Prupe.3G265100' => 'ppe', 'Prupe.4G034700' => 'ppe', 'Prupe.4G052100' => 'ppe', 'Prupe.4G053600' => 'ppe', 'Prupe.5G068800' => 'ppe', 'Prupe.5G070600' => 'ppe', 'Prupe.6G075400' => 'ppe', 'Prupe.6G075500' => 'ppe', 'Prupe.6G076400' => 'ppe', 'Prupe.8G110700' => 'ppe', 'Psat4g020960' => 'psa', 'PSO135G0788' => 'pso', 'PSO210G6463' => 'pso', 'PSO384G0370' => 'pso', 'PSO386G0056' => 'pso', 'QL01p006048' => 'qlo', 'QL02p054283' => 'qlo', 'QL05p008000' => 'qlo', 'QL05p008212' => 'qlo', 'QL05p008950' => 'qlo', 'QL05p009042' => 'qlo', 'QL05p009518' => 'qlo', 'QL05p012589' => 'qlo', 'QL05p012608' => 'qlo', 'QL05p012650' => 'qlo', 'QL05p012667' => 'qlo', 'QL05p014501' => 'qlo', 'QL05p052800' => 'qlo', 'QL05p065010' => 'qlo', 'QL05p074156' => 'qlo', 'QL05p074160' => 'qlo', 'QL05p074174' => 'qlo', 'QL05p074178' => 'qlo', 'QL05p074214' => 'qlo', 'QL06p001050' => 'qlo', 'QL06p001056' => 'qlo', 'QL06p006093' => 'qlo', 'QL06p006111' => 'qlo', 'QL07p019784' => 'qlo', 'QL07p019801' => 'qlo', 'QL07p036110' => 'qlo', 'QL07p036134' => 'qlo', 'QL07p036147' => 'qlo', 'QL07p036156' => 'qlo', 'QL07p036300' => 'qlo', 'QL07p036320' => 'qlo', 'QL08p014547' => 'qlo', 'QL08p014551' => 'qlo', 'QL08p043319' => 'qlo', 'QL08p043324' => 'qlo', 'QL11p009094' => 'qlo', 'RcHm_v2.0_Chr1g0380481' => 'rch', 'RcHm_v2.0_Chr2g0089331' => 'rch', 'RcHm_v2.0_Chr2g0123691' => 'rch', 'RcHm_v2.0_Chr2g0151111' => 'rch', 'RcHm_v2.0_Chr2g0163011' => 'rch', 'RcHm_v2.0_Chr2g0163051' => 'rch', 'RcHm_v2.0_Chr2g0164671' => 'rch', 'RcHm_v2.0_Chr2g0164681' => 'rch', 'RcHm_v2.0_Chr2g0164721' => 'rch', 'RcHm_v2.0_Chr3g0449911' => 'rch', 'RcHm_v2.0_Chr3g0450211' => 'rch', 'RcHm_v2.0_Chr3g0457271' => 'rch', 'RcHm_v2.0_Chr5g0018111' => 'rch', 'RcHm_v2.0_Chr5g0021011' => 'rch', 'RcHm_v2.0_Chr5g0081171' => 'rch', 'RcHm_v2.0_Chr5g0081211' => 'rch', 'RcHm_v2.0_Chr6g0275871' => 'rch', 'RcHm_v2.0_Chr6g0276071' => 'rch', 'RcHm_v2.0_Chr6g0285591' => 'rch', 'RcHm_v2.0_Chr6g0291931' => 'rch', 'RcHm_v2.0_Chr6g0292091' => 'rch', 'RcHm_v2.0_Chr6g0292271' => 'rch', 'RcHm_v2.0_Chr7g0221261' => 'rch', 'Rhsim08G0219900' => 'rsi', 'Rhsim08G0220200' => 'rsi', 'Rhsim08G0237800' => 'rsi', 'Rhsim08G0238800' => 'rsi', 'Sabra09G0102700' => 'sbr', 'Sabra09G0127200' => 'sbr', 'Sabra11G0003700' => 'sbr', 'Sabra15G0014700' => 'sbr', 'Sc19g0000590' => 'sci', 'Sc19g0001870' => 'sci', 'SGA_v2.0_scaffold1G00346' => 'sas', 'SGA_v2.0_scaffold1G00575' => 'sas', 'SGA_v2.0_scaffold1G00761' => 'sas', 'SGA_v2.0_scaffold232G43501' => 'sas', 'TAR625G1137' => 'tar', 'Thecc.03G222100' => 'tca', 'TPR.G12691' => 'tpr', 'TWI34G0727' => 'twi', 'TWI36G0117' => 'twi', 'VMungo1309G0868' => 'vmu' ) $gf_id = 'HOM05D001729' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001729' ) $data_identifier = 'HOM05D001729' $data_type = 'gf_id' $species_gene_counts = array( 'amhyb' => (int) 1, 'cqu' => (int) 9, 'can' => (int) 1, 'cansat' => (int) 1, 'car' => (int) 1, 'col' => (int) 5, 'dca' => (int) 1, 'din' => (int) 2, 'dzi' => (int) 3, 'fan' => (int) 140, 'fve' => (int) 62, 'gma' => (int) 1, 'ghi' => (int) 2, 'gra' => (int) 1, 'han' => (int) 1, 'sun' => (int) 1, 'lonja' => (int) 6, 'lja' => (int) 1, 'lsa' => (int) 4, 'mes' => (int) 1, 'mdo' => (int) 14, 'mtr' => (int) 1, 'egut' => (int) 1, 'nta' => (int) 4, 'oeu' => (int) 1, 'stu' => (int) 2, 'pvu' => (int) 1, 'ptr' => (int) 4, 'ppe' => (int) 19, 'psa' => (int) 1, 'pso' => (int) 4, 'qlo' => (int) 36, 'rch' => (int) 23, 'rsi' => (int) 4, 'sbr' => (int) 4, 'sci' => (int) 2, 'sas' => (int) 4, 'tar' => (int) 1, 'tca' => (int) 1, 'tpr' => (int) 1, 'twi' => (int) 2, 'vmu' => (int) 1 ) $gf_gene_species = 'vmu' $gf_gene_id = 'VMungo1309G0868' $species_info = array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ) $local_species = 'fan' $disabled = '' $selected = '' $num_hits = (int) 1
Warning (2): count(): Parameter must be an array or an object that implements Countable [APP/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp, line 33]Code Context $disabled = (!array_key_exists($local_species,$species_gene_counts))?"disabled":""; $selected = (isset($selected_species) && array_key_exists($local_species,$selected_species))?"checked='checked'":""; $num_hits = (array_key_exists($local_species,$species_gene_counts))?count($species_gene_counts[$local_species]):0; $viewFile = '/www/bioinformatics01_ro/plaza/_dev_instances/feedback/app/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp' $dataForView = array( 'sidebar_info' => array( 'gf_id' => 'HOM05D001729', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '375', 'num_species' => '42' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'Ah.07g204710' => 'amhyb', 'AUR62006001' => 'cqu', 'AUR62006002' => 'cqu', 'AUR62006003' => 'cqu', 'AUR62015641' => 'cqu', 'AUR62027174' => 'cqu', 'AUR62035623' => 'cqu', 'AUR62035624' => 'cqu', 'AUR62035625' => 'cqu', 'AUR62035626' => 'cqu', 'CAN.G1110.53' => 'can', 'CANSAT80G0415' => 'cansat', 'Ca_21364_v3' => 'car', 'COL.COLO4_30693' => 'col', 'COL.COLO4_30694' => 'col', 'COL.COLO4_30695' => 'col', 'COL.COLO4_30696' => 'col', 'COL.COLO4_34020' => 'col', 'DCAR_004585' => 'dca', 'Dinv04029' => 'din', 'Dinv34857' => 'din', 'Duzib147G0011' => 'dzi', 'Duzib170G0599' => 'dzi', 'Duzib192G1051' => 'dzi', 'FAN01G0708' => 'fan', 'FAN01G0742' => 'fan', 'FAN02G0048' => 'fan', 'FAN02G0583' => 'fan', 'FAN02G0688' => 'fan', 'FAN02G1588' => 'fan', 'FAN02G2194' => 'fan', 'FAN02G2750' => 'fan', 'FAN02G3094' => 'fan', 'FAN02G3887' => 'fan', 'FAN02G3911' => 'fan', 'FAN02G3994' => 'fan', 'FAN02G4432' => 'fan', 'FAN02G4556' => 'fan', 'FAN03G1977' => 'fan', 'FAN03G2781' => 'fan', 'FAN03G2850' => 'fan', 'FAN03G3155' => 'fan', 'FAN04G2487' => 'fan', 'FAN05G0208' => 'fan', 'FAN05G0656' => 'fan', 'FAN05G0696' => 'fan', 'FAN05G0810' => 'fan', 'FAN05G1447' => 'fan', 'FAN05G2640' => 'fan', 'FAN05G2911' => 'fan', 'FAN05G3901' => 'fan', 'FAN05G4859' => 'fan', 'FAN05G4861' => 'fan', 'FAN05G4988' => 'fan', 'FAN05G5187' => 'fan', 'FAN05G5452' => 'fan', 'FAN05G5500' => 'fan', 'FAN05G5688' => 'fan', 'FAN06G0177' => 'fan', 'FAN06G0675' => 'fan', 'FAN06G1290' => 'fan', 'FAN06G2191' => 'fan', 'FAN06G2405' => 'fan', 'FAN06G3231' => 'fan', 'FAN06G3932' => 'fan', 'FAN07G0163' => 'fan', 'FAN07G0471' => 'fan', 'FAN07G1354' => 'fan', 'FAN08G0338' => 'fan', 'FAN08G1373' => 'fan', 'FAN08G2539' => 'fan', 'FAN08G2728' => 'fan', 'FAN09G0608' => 'fan', 'FAN09G1136' => 'fan', 'FAN09G1958' => 'fan', 'FAN09G2508' => 'fan', 'FAN09G2597' => 'fan', 'FAN09G2658' => 'fan', 'FAN09G2757' => 'fan', 'FAN09G2983' => 'fan', 'FAN09G3130' => 'fan', 'FAN09G3565' => 'fan', 'FAN09G3613' => 'fan', 'FAN09G4011' => 'fan', 'FAN09G4239' => 'fan', 'FAN09G4277' => 'fan', 'FAN09G4720' => 'fan', 'FAN11G0139' => 'fan', 'FAN11G1727' => 'fan', 'FAN11G2672' => 'fan', 'FAN11G2795' => 'fan', 'FAN11G3238' => 'fan', 'FAN11G3734' => 'fan', 'FAN12G0631' => 'fan', 'FAN12G2239' => 'fan', 'FAN12G2308' => 'fan', 'FAN12G2569' => 'fan', 'FAN12G2623' => 'fan', 'FAN13G3182' => 'fan', 'FAN14G0053' => 'fan', 'FAN14G0370' => 'fan', 'FAN14G0382' => 'fan', 'FAN14G0421' => 'fan', 'FAN14G0866' => 'fan', 'FAN14G1187' => 'fan', 'FAN14G1727' => 'fan', 'FAN14G1791' => 'fan', 'FAN14G2361' => 'fan', 'FAN14G2668' => 'fan', 'FAN14G2770' => 'fan', 'FAN14G2874' => 'fan', 'FAN14G3193' => 'fan', 'FAN14G3624' => 'fan', 'FAN14G3676' => 'fan', 'FAN14G3807' => 'fan', 'FAN14G4082' => 'fan', 'FAN14G4342' => 'fan', 'FAN14G4985' => 'fan', 'FAN14G5126' => 'fan', 'FAN14G5781' => 'fan', 'FAN14G5808' => 'fan', 'FAN14G5949' => 'fan', 'FAN15G0828' => 'fan', 'FAN15G1054' => 'fan', 'FAN15G2023' => 'fan', 'FAN15G2506' => 'fan', 'FAN16G0128' => 'fan', 'FAN16G0249' => 'fan', 'FAN16G0429' => 'fan', 'FAN16G1493' => 'fan', 'FAN16G2210' => 'fan', 'FAN16G2506' => 'fan', 'FAN18G1542' => 'fan', 'FAN18G4057' => 'fan', 'FAN19G0745' => 'fan', 'FAN19G1216' => 'fan', 'FAN19G1733' => 'fan', 'FAN20G0258' => 'fan', 'FAN20G1095' => 'fan', 'FAN20G1557' => 'fan', 'FAN21G0302' => 'fan', 'FAN21G0519' => 'fan', 'FAN21G0970' => 'fan', 'FAN21G1159' => 'fan', 'FAN21G1312' => 'fan', 'FAN21G1440' => 'fan', 'FAN21G1715' => 'fan', 'FAN23G1584' => 'fan', 'FAN24G0045' => 'fan', 'FAN24G0053' => 'fan', 'FAN24G1500' => 'fan', 'FAN24G1817' => 'fan', 'FAN24G2147' => 'fan', 'FAN24G2236' => 'fan', 'FAN24G2446' => 'fan', 'FAN24G2684' => 'fan', 'FAN25G0187' => 'fan', 'FAN25G0505' => 'fan', 'FAN25G0589' => 'fan', 'FAN25G3663' => 'fan', 'FAN26G1025' => 'fan', 'FAN26G2860' => 'fan', 'FAN27G1329' => 'fan', 'FAN27G3392' => 'fan', 'FvH4_1g02011' => 'fve', 'FvH4_1g06511' => 'fve', 'FvH4_2g19900' => 'fve', 'FvH4_2g19920' => 'fve', 'FvH4_2g24261' => 'fve', 'FvH4_2g24270' => 'fve', 'FvH4_2g24631' => 'fve', 'FvH4_2g30622' => 'fve', 'FvH4_3g12920' => 'fve', 'FvH4_3g30171' => 'fve', 'FvH4_3g35490' => 'fve', 'FvH4_3g43682' => 'fve', 'FvH4_3g43730' => 'fve', 'FvH4_3g43732' => 'fve', 'FvH4_3g43751' => 'fve', 'FvH4_3g43752' => 'fve', 'FvH4_3g43770' => 'fve', 'FvH4_3g44471' => 'fve', 'FvH4_3g44510' => 'fve', 'FvH4_3g44582' => 'fve', 'FvH4_4g16921' => 'fve', 'FvH4_4g17121' => 'fve', 'FvH4_4g17782' => 'fve', 'FvH4_4g17783' => 'fve', 'FvH4_4g18120' => 'fve', 'FvH4_4g31310' => 'fve', 'FvH4_4g35052' => 'fve', 'FvH4_5g30862' => 'fve', 'FvH4_6g01541' => 'fve', 'FvH4_6g02021' => 'fve', 'FvH4_6g02041' => 'fve', 'FvH4_6g02071' => 'fve', 'FvH4_6g02171' => 'fve', 'FvH4_6g03181' => 'fve', 'FvH4_6g03182' => 'fve', 'FvH4_6g03221' => 'fve', 'FvH4_6g03380' => 'fve', 'FvH4_6g05201' => 'fve', 'FvH4_6g05203' => 'fve', 'FvH4_6g20231' => 'fve', 'FvH4_6g31981' => 'fve', 'FvH4_6g32061' => 'fve', 'FvH4_6g37041' => 'fve', 'FvH4_6g37932' => 'fve', 'FvH4_6g38731' => 'fve', 'FvH4_6g39370' => 'fve', 'FvH4_6g39371' => 'fve', 'FvH4_6g40891' => 'fve', 'FvH4_6g40892' => 'fve', 'FvH4_6g43143' => 'fve', 'FvH4_6g45251' => 'fve', 'FvH4_6g45260' => 'fve', 'FvH4_6g45291' => 'fve', 'FvH4_6g45890' => 'fve', 'FvH4_6g46240' => 'fve', 'FvH4_6g46241' => 'fve', 'FvH4_6g46242' => 'fve', 'FvH4_6g46260' => 'fve', 'FvH4_6g46280' => 'fve', 'FvH4_6g46380' => 'fve', 'FvH4_7g12841' => 'fve', 'FvH4_7g31431' => 'fve', 'Glyma.09G075900' => 'gma', 'Gohir.A09G096401' => 'ghi', 'Gohir.D09G096101' => 'ghi', 'Gorai.006G112800' => 'gra', 'HanXRQChr04g0121411' => 'han', 'Hund15878' => 'sun', 'Lj2A1107G68' => 'lonja', 'Lj2A630G63' => 'lonja', 'Lj2A946T25' => 'lonja', 'Lj2C714T1' => 'lonja', 'Lj2C966T3' => 'lonja', 'Lj2C966T4' => 'lonja', 'Lj4g0002979' => 'lja', 'Lsat_1_v5_gn_5_30901' => 'lsa', 'Lsat_1_v5_gn_5_31100' => 'lsa', 'Lsat_1_v5_gn_5_38600' => 'lsa', 'Lsat_1_v5_gn_6_92061' => 'lsa', 'Manes.05G071301' => 'mes', 'MD02G1008700' => 'mdo', 'MD02G1008900' => 'mdo', 'MD03G1256400' => 'mdo', 'MD04G1180900' => 'mdo', 'MD04G1181000' => 'mdo', 'MD04G1181200' => 'mdo', 'MD05G1244200' => 'mdo', 'MD05G1324200' => 'mdo', 'MD09G1201600' => 'mdo', 'MD10G1000600' => 'mdo', 'MD14G1026900' => 'mdo', 'MD14G1187900' => 'mdo', 'MD15G1017800' => 'mdo', 'MD15G1018100' => 'mdo', 'Medtr4g124160' => 'mtr', 'Migut.L01260' => 'egut', 'Nitab4.5_0000008g0440' => 'nta', 'Nitab4.5_0000207g0170' => 'nta', 'Nitab4.5_0007671g0030' => 'nta', 'Nitab4.5_0010853g0020' => 'nta', 'Oeu057656.1' => 'oeu', 'PGSC0003DMG400005638' => 'stu', 'PGSC0003DMG400005639' => 'stu', 'Phvul.009G222800' => 'pvu', 'Potri.009G132400' => 'ptr', 'Potri.009G163001' => 'ptr', 'Potri.011G000700' => 'ptr', 'Potri.011G004800' => 'ptr', 'Prupe.1G509300' => 'ppe', 'Prupe.1G509700' => 'ppe', 'Prupe.1G510400' => 'ppe', 'Prupe.1G510700' => 'ppe', 'Prupe.1G512600' => 'ppe', 'Prupe.2G073200' => 'ppe', 'Prupe.3G059500' => 'ppe', 'Prupe.3G059600' => 'ppe', 'Prupe.3G246100' => 'ppe', 'Prupe.3G265100' => 'ppe', 'Prupe.4G034700' => 'ppe', 'Prupe.4G052100' => 'ppe', 'Prupe.4G053600' => 'ppe', 'Prupe.5G068800' => 'ppe', 'Prupe.5G070600' => 'ppe', 'Prupe.6G075400' => 'ppe', 'Prupe.6G075500' => 'ppe', 'Prupe.6G076400' => 'ppe', 'Prupe.8G110700' => 'ppe', 'Psat4g020960' => 'psa', 'PSO135G0788' => 'pso', 'PSO210G6463' => 'pso', 'PSO384G0370' => 'pso', 'PSO386G0056' => 'pso', 'QL01p006048' => 'qlo', 'QL02p054283' => 'qlo', 'QL05p008000' => 'qlo', 'QL05p008212' => 'qlo', 'QL05p008950' => 'qlo', 'QL05p009042' => 'qlo', 'QL05p009518' => 'qlo', 'QL05p012589' => 'qlo', 'QL05p012608' => 'qlo', 'QL05p012650' => 'qlo', 'QL05p012667' => 'qlo', 'QL05p014501' => 'qlo', 'QL05p052800' => 'qlo', 'QL05p065010' => 'qlo', 'QL05p074156' => 'qlo', 'QL05p074160' => 'qlo', 'QL05p074174' => 'qlo', 'QL05p074178' => 'qlo', 'QL05p074214' => 'qlo', 'QL06p001050' => 'qlo', 'QL06p001056' => 'qlo', 'QL06p006093' => 'qlo', 'QL06p006111' => 'qlo', 'QL07p019784' => 'qlo', 'QL07p019801' => 'qlo', 'QL07p036110' => 'qlo', 'QL07p036134' => 'qlo', 'QL07p036147' => 'qlo', 'QL07p036156' => 'qlo', 'QL07p036300' => 'qlo', 'QL07p036320' => 'qlo', 'QL08p014547' => 'qlo', 'QL08p014551' => 'qlo', 'QL08p043319' => 'qlo', 'QL08p043324' => 'qlo', 'QL11p009094' => 'qlo', 'RcHm_v2.0_Chr1g0380481' => 'rch', 'RcHm_v2.0_Chr2g0089331' => 'rch', 'RcHm_v2.0_Chr2g0123691' => 'rch', 'RcHm_v2.0_Chr2g0151111' => 'rch', 'RcHm_v2.0_Chr2g0163011' => 'rch', 'RcHm_v2.0_Chr2g0163051' => 'rch', 'RcHm_v2.0_Chr2g0164671' => 'rch', 'RcHm_v2.0_Chr2g0164681' => 'rch', 'RcHm_v2.0_Chr2g0164721' => 'rch', 'RcHm_v2.0_Chr3g0449911' => 'rch', 'RcHm_v2.0_Chr3g0450211' => 'rch', 'RcHm_v2.0_Chr3g0457271' => 'rch', 'RcHm_v2.0_Chr5g0018111' => 'rch', 'RcHm_v2.0_Chr5g0021011' => 'rch', 'RcHm_v2.0_Chr5g0081171' => 'rch', 'RcHm_v2.0_Chr5g0081211' => 'rch', 'RcHm_v2.0_Chr6g0275871' => 'rch', 'RcHm_v2.0_Chr6g0276071' => 'rch', 'RcHm_v2.0_Chr6g0285591' => 'rch', 'RcHm_v2.0_Chr6g0291931' => 'rch', 'RcHm_v2.0_Chr6g0292091' => 'rch', 'RcHm_v2.0_Chr6g0292271' => 'rch', 'RcHm_v2.0_Chr7g0221261' => 'rch', 'Rhsim08G0219900' => 'rsi', 'Rhsim08G0220200' => 'rsi', 'Rhsim08G0237800' => 'rsi', 'Rhsim08G0238800' => 'rsi', 'Sabra09G0102700' => 'sbr', 'Sabra09G0127200' => 'sbr', 'Sabra11G0003700' => 'sbr', 'Sabra15G0014700' => 'sbr', 'Sc19g0000590' => 'sci', 'Sc19g0001870' => 'sci', 'SGA_v2.0_scaffold1G00346' => 'sas', 'SGA_v2.0_scaffold1G00575' => 'sas', 'SGA_v2.0_scaffold1G00761' => 'sas', 'SGA_v2.0_scaffold232G43501' => 'sas', 'TAR625G1137' => 'tar', 'Thecc.03G222100' => 'tca', 'TPR.G12691' => 'tpr', 'TWI34G0727' => 'twi', 'TWI36G0117' => 'twi', 'VMungo1309G0868' => 'vmu' ), 'gf_id' => 'HOM05D001729', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001729' ), 'data_identifier' => 'HOM05D001729', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001729', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '375', 'num_species' => '42' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'Ah.07g204710' => 'amhyb', 'AUR62006001' => 'cqu', 'AUR62006002' => 'cqu', 'AUR62006003' => 'cqu', 'AUR62015641' => 'cqu', 'AUR62027174' => 'cqu', 'AUR62035623' => 'cqu', 'AUR62035624' => 'cqu', 'AUR62035625' => 'cqu', 'AUR62035626' => 'cqu', 'CAN.G1110.53' => 'can', 'CANSAT80G0415' => 'cansat', 'Ca_21364_v3' => 'car', 'COL.COLO4_30693' => 'col', 'COL.COLO4_30694' => 'col', 'COL.COLO4_30695' => 'col', 'COL.COLO4_30696' => 'col', 'COL.COLO4_34020' => 'col', 'DCAR_004585' => 'dca', 'Dinv04029' => 'din', 'Dinv34857' => 'din', 'Duzib147G0011' => 'dzi', 'Duzib170G0599' => 'dzi', 'Duzib192G1051' => 'dzi', 'FAN01G0708' => 'fan', 'FAN01G0742' => 'fan', 'FAN02G0048' => 'fan', 'FAN02G0583' => 'fan', 'FAN02G0688' => 'fan', 'FAN02G1588' => 'fan', 'FAN02G2194' => 'fan', 'FAN02G2750' => 'fan', 'FAN02G3094' => 'fan', 'FAN02G3887' => 'fan', 'FAN02G3911' => 'fan', 'FAN02G3994' => 'fan', 'FAN02G4432' => 'fan', 'FAN02G4556' => 'fan', 'FAN03G1977' => 'fan', 'FAN03G2781' => 'fan', 'FAN03G2850' => 'fan', 'FAN03G3155' => 'fan', 'FAN04G2487' => 'fan', 'FAN05G0208' => 'fan', 'FAN05G0656' => 'fan', 'FAN05G0696' => 'fan', 'FAN05G0810' => 'fan', 'FAN05G1447' => 'fan', 'FAN05G2640' => 'fan', 'FAN05G2911' => 'fan', 'FAN05G3901' => 'fan', 'FAN05G4859' => 'fan', 'FAN05G4861' => 'fan', 'FAN05G4988' => 'fan', 'FAN05G5187' => 'fan', 'FAN05G5452' => 'fan', 'FAN05G5500' => 'fan', 'FAN05G5688' => 'fan', 'FAN06G0177' => 'fan', 'FAN06G0675' => 'fan', 'FAN06G1290' => 'fan', 'FAN06G2191' => 'fan', 'FAN06G2405' => 'fan', 'FAN06G3231' => 'fan', 'FAN06G3932' => 'fan', 'FAN07G0163' => 'fan', 'FAN07G0471' => 'fan', 'FAN07G1354' => 'fan', 'FAN08G0338' => 'fan', 'FAN08G1373' => 'fan', 'FAN08G2539' => 'fan', 'FAN08G2728' => 'fan', 'FAN09G0608' => 'fan', 'FAN09G1136' => 'fan', 'FAN09G1958' => 'fan', 'FAN09G2508' => 'fan', 'FAN09G2597' => 'fan', 'FAN09G2658' => 'fan', 'FAN09G2757' => 'fan', 'FAN09G2983' => 'fan', 'FAN09G3130' => 'fan', 'FAN09G3565' => 'fan', 'FAN09G3613' => 'fan', 'FAN09G4011' => 'fan', 'FAN09G4239' => 'fan', 'FAN09G4277' => 'fan', 'FAN09G4720' => 'fan', 'FAN11G0139' => 'fan', 'FAN11G1727' => 'fan', 'FAN11G2672' => 'fan', 'FAN11G2795' => 'fan', 'FAN11G3238' => 'fan', 'FAN11G3734' => 'fan', 'FAN12G0631' => 'fan', 'FAN12G2239' => 'fan', 'FAN12G2308' => 'fan', 'FAN12G2569' => 'fan', 'FAN12G2623' => 'fan', 'FAN13G3182' => 'fan', 'FAN14G0053' => 'fan', 'FAN14G0370' => 'fan', 'FAN14G0382' => 'fan', 'FAN14G0421' => 'fan', 'FAN14G0866' => 'fan', 'FAN14G1187' => 'fan', 'FAN14G1727' => 'fan', 'FAN14G1791' => 'fan', 'FAN14G2361' => 'fan', 'FAN14G2668' => 'fan', 'FAN14G2770' => 'fan', 'FAN14G2874' => 'fan', 'FAN14G3193' => 'fan', 'FAN14G3624' => 'fan', 'FAN14G3676' => 'fan', 'FAN14G3807' => 'fan', 'FAN14G4082' => 'fan', 'FAN14G4342' => 'fan', 'FAN14G4985' => 'fan', 'FAN14G5126' => 'fan', 'FAN14G5781' => 'fan', 'FAN14G5808' => 'fan', 'FAN14G5949' => 'fan', 'FAN15G0828' => 'fan', 'FAN15G1054' => 'fan', 'FAN15G2023' => 'fan', 'FAN15G2506' => 'fan', 'FAN16G0128' => 'fan', 'FAN16G0249' => 'fan', 'FAN16G0429' => 'fan', 'FAN16G1493' => 'fan', 'FAN16G2210' => 'fan', 'FAN16G2506' => 'fan', 'FAN18G1542' => 'fan', 'FAN18G4057' => 'fan', 'FAN19G0745' => 'fan', 'FAN19G1216' => 'fan', 'FAN19G1733' => 'fan', 'FAN20G0258' => 'fan', 'FAN20G1095' => 'fan', 'FAN20G1557' => 'fan', 'FAN21G0302' => 'fan', 'FAN21G0519' => 'fan', 'FAN21G0970' => 'fan', 'FAN21G1159' => 'fan', 'FAN21G1312' => 'fan', 'FAN21G1440' => 'fan', 'FAN21G1715' => 'fan', 'FAN23G1584' => 'fan', 'FAN24G0045' => 'fan', 'FAN24G0053' => 'fan', 'FAN24G1500' => 'fan', 'FAN24G1817' => 'fan', 'FAN24G2147' => 'fan', 'FAN24G2236' => 'fan', 'FAN24G2446' => 'fan', 'FAN24G2684' => 'fan', 'FAN25G0187' => 'fan', 'FAN25G0505' => 'fan', 'FAN25G0589' => 'fan', 'FAN25G3663' => 'fan', 'FAN26G1025' => 'fan', 'FAN26G2860' => 'fan', 'FAN27G1329' => 'fan', 'FAN27G3392' => 'fan', 'FvH4_1g02011' => 'fve', 'FvH4_1g06511' => 'fve', 'FvH4_2g19900' => 'fve', 'FvH4_2g19920' => 'fve', 'FvH4_2g24261' => 'fve', 'FvH4_2g24270' => 'fve', 'FvH4_2g24631' => 'fve', 'FvH4_2g30622' => 'fve', 'FvH4_3g12920' => 'fve', 'FvH4_3g30171' => 'fve', 'FvH4_3g35490' => 'fve', 'FvH4_3g43682' => 'fve', 'FvH4_3g43730' => 'fve', 'FvH4_3g43732' => 'fve', 'FvH4_3g43751' => 'fve', 'FvH4_3g43752' => 'fve', 'FvH4_3g43770' => 'fve', 'FvH4_3g44471' => 'fve', 'FvH4_3g44510' => 'fve', 'FvH4_3g44582' => 'fve', 'FvH4_4g16921' => 'fve', 'FvH4_4g17121' => 'fve', 'FvH4_4g17782' => 'fve', 'FvH4_4g17783' => 'fve', 'FvH4_4g18120' => 'fve', 'FvH4_4g31310' => 'fve', 'FvH4_4g35052' => 'fve', 'FvH4_5g30862' => 'fve', 'FvH4_6g01541' => 'fve', 'FvH4_6g02021' => 'fve', 'FvH4_6g02041' => 'fve', 'FvH4_6g02071' => 'fve', 'FvH4_6g02171' => 'fve', 'FvH4_6g03181' => 'fve', 'FvH4_6g03182' => 'fve', 'FvH4_6g03221' => 'fve', 'FvH4_6g03380' => 'fve', 'FvH4_6g05201' => 'fve', 'FvH4_6g05203' => 'fve', 'FvH4_6g20231' => 'fve', 'FvH4_6g31981' => 'fve', 'FvH4_6g32061' => 'fve', 'FvH4_6g37041' => 'fve', 'FvH4_6g37932' => 'fve', 'FvH4_6g38731' => 'fve', 'FvH4_6g39370' => 'fve', 'FvH4_6g39371' => 'fve', 'FvH4_6g40891' => 'fve', 'FvH4_6g40892' => 'fve', 'FvH4_6g43143' => 'fve', 'FvH4_6g45251' => 'fve', 'FvH4_6g45260' => 'fve', 'FvH4_6g45291' => 'fve', 'FvH4_6g45890' => 'fve', 'FvH4_6g46240' => 'fve', 'FvH4_6g46241' => 'fve', 'FvH4_6g46242' => 'fve', 'FvH4_6g46260' => 'fve', 'FvH4_6g46280' => 'fve', 'FvH4_6g46380' => 'fve', 'FvH4_7g12841' => 'fve', 'FvH4_7g31431' => 'fve', 'Glyma.09G075900' => 'gma', 'Gohir.A09G096401' => 'ghi', 'Gohir.D09G096101' => 'ghi', 'Gorai.006G112800' => 'gra', 'HanXRQChr04g0121411' => 'han', 'Hund15878' => 'sun', 'Lj2A1107G68' => 'lonja', 'Lj2A630G63' => 'lonja', 'Lj2A946T25' => 'lonja', 'Lj2C714T1' => 'lonja', 'Lj2C966T3' => 'lonja', 'Lj2C966T4' => 'lonja', 'Lj4g0002979' => 'lja', 'Lsat_1_v5_gn_5_30901' => 'lsa', 'Lsat_1_v5_gn_5_31100' => 'lsa', 'Lsat_1_v5_gn_5_38600' => 'lsa', 'Lsat_1_v5_gn_6_92061' => 'lsa', 'Manes.05G071301' => 'mes', 'MD02G1008700' => 'mdo', 'MD02G1008900' => 'mdo', 'MD03G1256400' => 'mdo', 'MD04G1180900' => 'mdo', 'MD04G1181000' => 'mdo', 'MD04G1181200' => 'mdo', 'MD05G1244200' => 'mdo', 'MD05G1324200' => 'mdo', 'MD09G1201600' => 'mdo', 'MD10G1000600' => 'mdo', 'MD14G1026900' => 'mdo', 'MD14G1187900' => 'mdo', 'MD15G1017800' => 'mdo', 'MD15G1018100' => 'mdo', 'Medtr4g124160' => 'mtr', 'Migut.L01260' => 'egut', 'Nitab4.5_0000008g0440' => 'nta', 'Nitab4.5_0000207g0170' => 'nta', 'Nitab4.5_0007671g0030' => 'nta', 'Nitab4.5_0010853g0020' => 'nta', 'Oeu057656.1' => 'oeu', 'PGSC0003DMG400005638' => 'stu', 'PGSC0003DMG400005639' => 'stu', 'Phvul.009G222800' => 'pvu', 'Potri.009G132400' => 'ptr', 'Potri.009G163001' => 'ptr', 'Potri.011G000700' => 'ptr', 'Potri.011G004800' => 'ptr', 'Prupe.1G509300' => 'ppe', 'Prupe.1G509700' => 'ppe', 'Prupe.1G510400' => 'ppe', 'Prupe.1G510700' => 'ppe', 'Prupe.1G512600' => 'ppe', 'Prupe.2G073200' => 'ppe', 'Prupe.3G059500' => 'ppe', 'Prupe.3G059600' => 'ppe', 'Prupe.3G246100' => 'ppe', 'Prupe.3G265100' => 'ppe', 'Prupe.4G034700' => 'ppe', 'Prupe.4G052100' => 'ppe', 'Prupe.4G053600' => 'ppe', 'Prupe.5G068800' => 'ppe', 'Prupe.5G070600' => 'ppe', 'Prupe.6G075400' => 'ppe', 'Prupe.6G075500' => 'ppe', 'Prupe.6G076400' => 'ppe', 'Prupe.8G110700' => 'ppe', 'Psat4g020960' => 'psa', 'PSO135G0788' => 'pso', 'PSO210G6463' => 'pso', 'PSO384G0370' => 'pso', 'PSO386G0056' => 'pso', 'QL01p006048' => 'qlo', 'QL02p054283' => 'qlo', 'QL05p008000' => 'qlo', 'QL05p008212' => 'qlo', 'QL05p008950' => 'qlo', 'QL05p009042' => 'qlo', 'QL05p009518' => 'qlo', 'QL05p012589' => 'qlo', 'QL05p012608' => 'qlo', 'QL05p012650' => 'qlo', 'QL05p012667' => 'qlo', 'QL05p014501' => 'qlo', 'QL05p052800' => 'qlo', 'QL05p065010' => 'qlo', 'QL05p074156' => 'qlo', 'QL05p074160' => 'qlo', 'QL05p074174' => 'qlo', 'QL05p074178' => 'qlo', 'QL05p074214' => 'qlo', 'QL06p001050' => 'qlo', 'QL06p001056' => 'qlo', 'QL06p006093' => 'qlo', 'QL06p006111' => 'qlo', 'QL07p019784' => 'qlo', 'QL07p019801' => 'qlo', 'QL07p036110' => 'qlo', 'QL07p036134' => 'qlo', 'QL07p036147' => 'qlo', 'QL07p036156' => 'qlo', 'QL07p036300' => 'qlo', 'QL07p036320' => 'qlo', 'QL08p014547' => 'qlo', 'QL08p014551' => 'qlo', 'QL08p043319' => 'qlo', 'QL08p043324' => 'qlo', 'QL11p009094' => 'qlo', 'RcHm_v2.0_Chr1g0380481' => 'rch', 'RcHm_v2.0_Chr2g0089331' => 'rch', 'RcHm_v2.0_Chr2g0123691' => 'rch', 'RcHm_v2.0_Chr2g0151111' => 'rch', 'RcHm_v2.0_Chr2g0163011' => 'rch', 'RcHm_v2.0_Chr2g0163051' => 'rch', 'RcHm_v2.0_Chr2g0164671' => 'rch', 'RcHm_v2.0_Chr2g0164681' => 'rch', 'RcHm_v2.0_Chr2g0164721' => 'rch', 'RcHm_v2.0_Chr3g0449911' => 'rch', 'RcHm_v2.0_Chr3g0450211' => 'rch', 'RcHm_v2.0_Chr3g0457271' => 'rch', 'RcHm_v2.0_Chr5g0018111' => 'rch', 'RcHm_v2.0_Chr5g0021011' => 'rch', 'RcHm_v2.0_Chr5g0081171' => 'rch', 'RcHm_v2.0_Chr5g0081211' => 'rch', 'RcHm_v2.0_Chr6g0275871' => 'rch', 'RcHm_v2.0_Chr6g0276071' => 'rch', 'RcHm_v2.0_Chr6g0285591' => 'rch', 'RcHm_v2.0_Chr6g0291931' => 'rch', 'RcHm_v2.0_Chr6g0292091' => 'rch', 'RcHm_v2.0_Chr6g0292271' => 'rch', 'RcHm_v2.0_Chr7g0221261' => 'rch', 'Rhsim08G0219900' => 'rsi', 'Rhsim08G0220200' => 'rsi', 'Rhsim08G0237800' => 'rsi', 'Rhsim08G0238800' => 'rsi', 'Sabra09G0102700' => 'sbr', 'Sabra09G0127200' => 'sbr', 'Sabra11G0003700' => 'sbr', 'Sabra15G0014700' => 'sbr', 'Sc19g0000590' => 'sci', 'Sc19g0001870' => 'sci', 'SGA_v2.0_scaffold1G00346' => 'sas', 'SGA_v2.0_scaffold1G00575' => 'sas', 'SGA_v2.0_scaffold1G00761' => 'sas', 'SGA_v2.0_scaffold232G43501' => 'sas', 'TAR625G1137' => 'tar', 'Thecc.03G222100' => 'tca', 'TPR.G12691' => 'tpr', 'TWI34G0727' => 'twi', 'TWI36G0117' => 'twi', 'VMungo1309G0868' => 'vmu' ) $gf_id = 'HOM05D001729' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001729' ) $data_identifier = 'HOM05D001729' $data_type = 'gf_id' $species_gene_counts = array( 'amhyb' => (int) 1, 'cqu' => (int) 9, 'can' => (int) 1, 'cansat' => (int) 1, 'car' => (int) 1, 'col' => (int) 5, 'dca' => (int) 1, 'din' => (int) 2, 'dzi' => (int) 3, 'fan' => (int) 140, 'fve' => (int) 62, 'gma' => (int) 1, 'ghi' => (int) 2, 'gra' => (int) 1, 'han' => (int) 1, 'sun' => (int) 1, 'lonja' => (int) 6, 'lja' => (int) 1, 'lsa' => (int) 4, 'mes' => (int) 1, 'mdo' => (int) 14, 'mtr' => (int) 1, 'egut' => (int) 1, 'nta' => (int) 4, 'oeu' => (int) 1, 'stu' => (int) 2, 'pvu' => (int) 1, 'ptr' => (int) 4, 'ppe' => (int) 19, 'psa' => (int) 1, 'pso' => (int) 4, 'qlo' => (int) 36, 'rch' => (int) 23, 'rsi' => (int) 4, 'sbr' => (int) 4, 'sci' => (int) 2, 'sas' => (int) 4, 'tar' => (int) 1, 'tca' => (int) 1, 'tpr' => (int) 1, 'twi' => (int) 2, 'vmu' => (int) 1 ) $gf_gene_species = 'vmu' $gf_gene_id = 'VMungo1309G0868' $species_info = array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ) $local_species = 'gma' $disabled = '' $selected = '' $num_hits = (int) 1include - APP/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp, line 33 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933 View::_renderElement() - CORE/Cake/View/View.php, line 1224 View::element() - CORE/Cake/View/View.php, line 418 include - APP/View/Elements/analysis/phylogenetics_module/gf_data_settings.ctp, line 37 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933 View::_renderElement() - CORE/Cake/View/View.php, line 1224 View::element() - CORE/Cake/View/View.php, line 418 include - APP/View/Elements/analysis/phylogenetics_module/parameter_selection.ctp, line 64 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933 View::_renderElement() - CORE/Cake/View/View.php, line 1224 View::element() - CORE/Cake/View/View.php, line 418 include - APP/View/Analysis/custom_tree_creation.ctp, line 27 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933
$viewFile = '/www/bioinformatics01_ro/plaza/_dev_instances/feedback/app/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp' $dataForView = array( 'sidebar_info' => array( 'gf_id' => 'HOM05D001729', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '375', 'num_species' => '42' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'Ah.07g204710' => 'amhyb', 'AUR62006001' => 'cqu', 'AUR62006002' => 'cqu', 'AUR62006003' => 'cqu', 'AUR62015641' => 'cqu', 'AUR62027174' => 'cqu', 'AUR62035623' => 'cqu', 'AUR62035624' => 'cqu', 'AUR62035625' => 'cqu', 'AUR62035626' => 'cqu', 'CAN.G1110.53' => 'can', 'CANSAT80G0415' => 'cansat', 'Ca_21364_v3' => 'car', 'COL.COLO4_30693' => 'col', 'COL.COLO4_30694' => 'col', 'COL.COLO4_30695' => 'col', 'COL.COLO4_30696' => 'col', 'COL.COLO4_34020' => 'col', 'DCAR_004585' => 'dca', 'Dinv04029' => 'din', 'Dinv34857' => 'din', 'Duzib147G0011' => 'dzi', 'Duzib170G0599' => 'dzi', 'Duzib192G1051' => 'dzi', 'FAN01G0708' => 'fan', 'FAN01G0742' => 'fan', 'FAN02G0048' => 'fan', 'FAN02G0583' => 'fan', 'FAN02G0688' => 'fan', 'FAN02G1588' => 'fan', 'FAN02G2194' => 'fan', 'FAN02G2750' => 'fan', 'FAN02G3094' => 'fan', 'FAN02G3887' => 'fan', 'FAN02G3911' => 'fan', 'FAN02G3994' => 'fan', 'FAN02G4432' => 'fan', 'FAN02G4556' => 'fan', 'FAN03G1977' => 'fan', 'FAN03G2781' => 'fan', 'FAN03G2850' => 'fan', 'FAN03G3155' => 'fan', 'FAN04G2487' => 'fan', 'FAN05G0208' => 'fan', 'FAN05G0656' => 'fan', 'FAN05G0696' => 'fan', 'FAN05G0810' => 'fan', 'FAN05G1447' => 'fan', 'FAN05G2640' => 'fan', 'FAN05G2911' => 'fan', 'FAN05G3901' => 'fan', 'FAN05G4859' => 'fan', 'FAN05G4861' => 'fan', 'FAN05G4988' => 'fan', 'FAN05G5187' => 'fan', 'FAN05G5452' => 'fan', 'FAN05G5500' => 'fan', 'FAN05G5688' => 'fan', 'FAN06G0177' => 'fan', 'FAN06G0675' => 'fan', 'FAN06G1290' => 'fan', 'FAN06G2191' => 'fan', 'FAN06G2405' => 'fan', 'FAN06G3231' => 'fan', 'FAN06G3932' => 'fan', 'FAN07G0163' => 'fan', 'FAN07G0471' => 'fan', 'FAN07G1354' => 'fan', 'FAN08G0338' => 'fan', 'FAN08G1373' => 'fan', 'FAN08G2539' => 'fan', 'FAN08G2728' => 'fan', 'FAN09G0608' => 'fan', 'FAN09G1136' => 'fan', 'FAN09G1958' => 'fan', 'FAN09G2508' => 'fan', 'FAN09G2597' => 'fan', 'FAN09G2658' => 'fan', 'FAN09G2757' => 'fan', 'FAN09G2983' => 'fan', 'FAN09G3130' => 'fan', 'FAN09G3565' => 'fan', 'FAN09G3613' => 'fan', 'FAN09G4011' => 'fan', 'FAN09G4239' => 'fan', 'FAN09G4277' => 'fan', 'FAN09G4720' => 'fan', 'FAN11G0139' => 'fan', 'FAN11G1727' => 'fan', 'FAN11G2672' => 'fan', 'FAN11G2795' => 'fan', 'FAN11G3238' => 'fan', 'FAN11G3734' => 'fan', 'FAN12G0631' => 'fan', 'FAN12G2239' => 'fan', 'FAN12G2308' => 'fan', 'FAN12G2569' => 'fan', 'FAN12G2623' => 'fan', 'FAN13G3182' => 'fan', 'FAN14G0053' => 'fan', 'FAN14G0370' => 'fan', 'FAN14G0382' => 'fan', 'FAN14G0421' => 'fan', 'FAN14G0866' => 'fan', 'FAN14G1187' => 'fan', 'FAN14G1727' => 'fan', 'FAN14G1791' => 'fan', 'FAN14G2361' => 'fan', 'FAN14G2668' => 'fan', 'FAN14G2770' => 'fan', 'FAN14G2874' => 'fan', 'FAN14G3193' => 'fan', 'FAN14G3624' => 'fan', 'FAN14G3676' => 'fan', 'FAN14G3807' => 'fan', 'FAN14G4082' => 'fan', 'FAN14G4342' => 'fan', 'FAN14G4985' => 'fan', 'FAN14G5126' => 'fan', 'FAN14G5781' => 'fan', 'FAN14G5808' => 'fan', 'FAN14G5949' => 'fan', 'FAN15G0828' => 'fan', 'FAN15G1054' => 'fan', 'FAN15G2023' => 'fan', 'FAN15G2506' => 'fan', 'FAN16G0128' => 'fan', 'FAN16G0249' => 'fan', 'FAN16G0429' => 'fan', 'FAN16G1493' => 'fan', 'FAN16G2210' => 'fan', 'FAN16G2506' => 'fan', 'FAN18G1542' => 'fan', 'FAN18G4057' => 'fan', 'FAN19G0745' => 'fan', 'FAN19G1216' => 'fan', 'FAN19G1733' => 'fan', 'FAN20G0258' => 'fan', 'FAN20G1095' => 'fan', 'FAN20G1557' => 'fan', 'FAN21G0302' => 'fan', 'FAN21G0519' => 'fan', 'FAN21G0970' => 'fan', 'FAN21G1159' => 'fan', 'FAN21G1312' => 'fan', 'FAN21G1440' => 'fan', 'FAN21G1715' => 'fan', 'FAN23G1584' => 'fan', 'FAN24G0045' => 'fan', 'FAN24G0053' => 'fan', 'FAN24G1500' => 'fan', 'FAN24G1817' => 'fan', 'FAN24G2147' => 'fan', 'FAN24G2236' => 'fan', 'FAN24G2446' => 'fan', 'FAN24G2684' => 'fan', 'FAN25G0187' => 'fan', 'FAN25G0505' => 'fan', 'FAN25G0589' => 'fan', 'FAN25G3663' => 'fan', 'FAN26G1025' => 'fan', 'FAN26G2860' => 'fan', 'FAN27G1329' => 'fan', 'FAN27G3392' => 'fan', 'FvH4_1g02011' => 'fve', 'FvH4_1g06511' => 'fve', 'FvH4_2g19900' => 'fve', 'FvH4_2g19920' => 'fve', 'FvH4_2g24261' => 'fve', 'FvH4_2g24270' => 'fve', 'FvH4_2g24631' => 'fve', 'FvH4_2g30622' => 'fve', 'FvH4_3g12920' => 'fve', 'FvH4_3g30171' => 'fve', 'FvH4_3g35490' => 'fve', 'FvH4_3g43682' => 'fve', 'FvH4_3g43730' => 'fve', 'FvH4_3g43732' => 'fve', 'FvH4_3g43751' => 'fve', 'FvH4_3g43752' => 'fve', 'FvH4_3g43770' => 'fve', 'FvH4_3g44471' => 'fve', 'FvH4_3g44510' => 'fve', 'FvH4_3g44582' => 'fve', 'FvH4_4g16921' => 'fve', 'FvH4_4g17121' => 'fve', 'FvH4_4g17782' => 'fve', 'FvH4_4g17783' => 'fve', 'FvH4_4g18120' => 'fve', 'FvH4_4g31310' => 'fve', 'FvH4_4g35052' => 'fve', 'FvH4_5g30862' => 'fve', 'FvH4_6g01541' => 'fve', 'FvH4_6g02021' => 'fve', 'FvH4_6g02041' => 'fve', 'FvH4_6g02071' => 'fve', 'FvH4_6g02171' => 'fve', 'FvH4_6g03181' => 'fve', 'FvH4_6g03182' => 'fve', 'FvH4_6g03221' => 'fve', 'FvH4_6g03380' => 'fve', 'FvH4_6g05201' => 'fve', 'FvH4_6g05203' => 'fve', 'FvH4_6g20231' => 'fve', 'FvH4_6g31981' => 'fve', 'FvH4_6g32061' => 'fve', 'FvH4_6g37041' => 'fve', 'FvH4_6g37932' => 'fve', 'FvH4_6g38731' => 'fve', 'FvH4_6g39370' => 'fve', 'FvH4_6g39371' => 'fve', 'FvH4_6g40891' => 'fve', 'FvH4_6g40892' => 'fve', 'FvH4_6g43143' => 'fve', 'FvH4_6g45251' => 'fve', 'FvH4_6g45260' => 'fve', 'FvH4_6g45291' => 'fve', 'FvH4_6g45890' => 'fve', 'FvH4_6g46240' => 'fve', 'FvH4_6g46241' => 'fve', 'FvH4_6g46242' => 'fve', 'FvH4_6g46260' => 'fve', 'FvH4_6g46280' => 'fve', 'FvH4_6g46380' => 'fve', 'FvH4_7g12841' => 'fve', 'FvH4_7g31431' => 'fve', 'Glyma.09G075900' => 'gma', 'Gohir.A09G096401' => 'ghi', 'Gohir.D09G096101' => 'ghi', 'Gorai.006G112800' => 'gra', 'HanXRQChr04g0121411' => 'han', 'Hund15878' => 'sun', 'Lj2A1107G68' => 'lonja', 'Lj2A630G63' => 'lonja', 'Lj2A946T25' => 'lonja', 'Lj2C714T1' => 'lonja', 'Lj2C966T3' => 'lonja', 'Lj2C966T4' => 'lonja', 'Lj4g0002979' => 'lja', 'Lsat_1_v5_gn_5_30901' => 'lsa', 'Lsat_1_v5_gn_5_31100' => 'lsa', 'Lsat_1_v5_gn_5_38600' => 'lsa', 'Lsat_1_v5_gn_6_92061' => 'lsa', 'Manes.05G071301' => 'mes', 'MD02G1008700' => 'mdo', 'MD02G1008900' => 'mdo', 'MD03G1256400' => 'mdo', 'MD04G1180900' => 'mdo', 'MD04G1181000' => 'mdo', 'MD04G1181200' => 'mdo', 'MD05G1244200' => 'mdo', 'MD05G1324200' => 'mdo', 'MD09G1201600' => 'mdo', 'MD10G1000600' => 'mdo', 'MD14G1026900' => 'mdo', 'MD14G1187900' => 'mdo', 'MD15G1017800' => 'mdo', 'MD15G1018100' => 'mdo', 'Medtr4g124160' => 'mtr', 'Migut.L01260' => 'egut', 'Nitab4.5_0000008g0440' => 'nta', 'Nitab4.5_0000207g0170' => 'nta', 'Nitab4.5_0007671g0030' => 'nta', 'Nitab4.5_0010853g0020' => 'nta', 'Oeu057656.1' => 'oeu', 'PGSC0003DMG400005638' => 'stu', 'PGSC0003DMG400005639' => 'stu', 'Phvul.009G222800' => 'pvu', 'Potri.009G132400' => 'ptr', 'Potri.009G163001' => 'ptr', 'Potri.011G000700' => 'ptr', 'Potri.011G004800' => 'ptr', 'Prupe.1G509300' => 'ppe', 'Prupe.1G509700' => 'ppe', 'Prupe.1G510400' => 'ppe', 'Prupe.1G510700' => 'ppe', 'Prupe.1G512600' => 'ppe', 'Prupe.2G073200' => 'ppe', 'Prupe.3G059500' => 'ppe', 'Prupe.3G059600' => 'ppe', 'Prupe.3G246100' => 'ppe', 'Prupe.3G265100' => 'ppe', 'Prupe.4G034700' => 'ppe', 'Prupe.4G052100' => 'ppe', 'Prupe.4G053600' => 'ppe', 'Prupe.5G068800' => 'ppe', 'Prupe.5G070600' => 'ppe', 'Prupe.6G075400' => 'ppe', 'Prupe.6G075500' => 'ppe', 'Prupe.6G076400' => 'ppe', 'Prupe.8G110700' => 'ppe', 'Psat4g020960' => 'psa', 'PSO135G0788' => 'pso', 'PSO210G6463' => 'pso', 'PSO384G0370' => 'pso', 'PSO386G0056' => 'pso', 'QL01p006048' => 'qlo', 'QL02p054283' => 'qlo', 'QL05p008000' => 'qlo', 'QL05p008212' => 'qlo', 'QL05p008950' => 'qlo', 'QL05p009042' => 'qlo', 'QL05p009518' => 'qlo', 'QL05p012589' => 'qlo', 'QL05p012608' => 'qlo', 'QL05p012650' => 'qlo', 'QL05p012667' => 'qlo', 'QL05p014501' => 'qlo', 'QL05p052800' => 'qlo', 'QL05p065010' => 'qlo', 'QL05p074156' => 'qlo', 'QL05p074160' => 'qlo', 'QL05p074174' => 'qlo', 'QL05p074178' => 'qlo', 'QL05p074214' => 'qlo', 'QL06p001050' => 'qlo', 'QL06p001056' => 'qlo', 'QL06p006093' => 'qlo', 'QL06p006111' => 'qlo', 'QL07p019784' => 'qlo', 'QL07p019801' => 'qlo', 'QL07p036110' => 'qlo', 'QL07p036134' => 'qlo', 'QL07p036147' => 'qlo', 'QL07p036156' => 'qlo', 'QL07p036300' => 'qlo', 'QL07p036320' => 'qlo', 'QL08p014547' => 'qlo', 'QL08p014551' => 'qlo', 'QL08p043319' => 'qlo', 'QL08p043324' => 'qlo', 'QL11p009094' => 'qlo', 'RcHm_v2.0_Chr1g0380481' => 'rch', 'RcHm_v2.0_Chr2g0089331' => 'rch', 'RcHm_v2.0_Chr2g0123691' => 'rch', 'RcHm_v2.0_Chr2g0151111' => 'rch', 'RcHm_v2.0_Chr2g0163011' => 'rch', 'RcHm_v2.0_Chr2g0163051' => 'rch', 'RcHm_v2.0_Chr2g0164671' => 'rch', 'RcHm_v2.0_Chr2g0164681' => 'rch', 'RcHm_v2.0_Chr2g0164721' => 'rch', 'RcHm_v2.0_Chr3g0449911' => 'rch', 'RcHm_v2.0_Chr3g0450211' => 'rch', 'RcHm_v2.0_Chr3g0457271' => 'rch', 'RcHm_v2.0_Chr5g0018111' => 'rch', 'RcHm_v2.0_Chr5g0021011' => 'rch', 'RcHm_v2.0_Chr5g0081171' => 'rch', 'RcHm_v2.0_Chr5g0081211' => 'rch', 'RcHm_v2.0_Chr6g0275871' => 'rch', 'RcHm_v2.0_Chr6g0276071' => 'rch', 'RcHm_v2.0_Chr6g0285591' => 'rch', 'RcHm_v2.0_Chr6g0291931' => 'rch', 'RcHm_v2.0_Chr6g0292091' => 'rch', 'RcHm_v2.0_Chr6g0292271' => 'rch', 'RcHm_v2.0_Chr7g0221261' => 'rch', 'Rhsim08G0219900' => 'rsi', 'Rhsim08G0220200' => 'rsi', 'Rhsim08G0237800' => 'rsi', 'Rhsim08G0238800' => 'rsi', 'Sabra09G0102700' => 'sbr', 'Sabra09G0127200' => 'sbr', 'Sabra11G0003700' => 'sbr', 'Sabra15G0014700' => 'sbr', 'Sc19g0000590' => 'sci', 'Sc19g0001870' => 'sci', 'SGA_v2.0_scaffold1G00346' => 'sas', 'SGA_v2.0_scaffold1G00575' => 'sas', 'SGA_v2.0_scaffold1G00761' => 'sas', 'SGA_v2.0_scaffold232G43501' => 'sas', 'TAR625G1137' => 'tar', 'Thecc.03G222100' => 'tca', 'TPR.G12691' => 'tpr', 'TWI34G0727' => 'twi', 'TWI36G0117' => 'twi', 'VMungo1309G0868' => 'vmu' ), 'gf_id' => 'HOM05D001729', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001729' ), 'data_identifier' => 'HOM05D001729', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001729', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '375', 'num_species' => '42' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'Ah.07g204710' => 'amhyb', 'AUR62006001' => 'cqu', 'AUR62006002' => 'cqu', 'AUR62006003' => 'cqu', 'AUR62015641' => 'cqu', 'AUR62027174' => 'cqu', 'AUR62035623' => 'cqu', 'AUR62035624' => 'cqu', 'AUR62035625' => 'cqu', 'AUR62035626' => 'cqu', 'CAN.G1110.53' => 'can', 'CANSAT80G0415' => 'cansat', 'Ca_21364_v3' => 'car', 'COL.COLO4_30693' => 'col', 'COL.COLO4_30694' => 'col', 'COL.COLO4_30695' => 'col', 'COL.COLO4_30696' => 'col', 'COL.COLO4_34020' => 'col', 'DCAR_004585' => 'dca', 'Dinv04029' => 'din', 'Dinv34857' => 'din', 'Duzib147G0011' => 'dzi', 'Duzib170G0599' => 'dzi', 'Duzib192G1051' => 'dzi', 'FAN01G0708' => 'fan', 'FAN01G0742' => 'fan', 'FAN02G0048' => 'fan', 'FAN02G0583' => 'fan', 'FAN02G0688' => 'fan', 'FAN02G1588' => 'fan', 'FAN02G2194' => 'fan', 'FAN02G2750' => 'fan', 'FAN02G3094' => 'fan', 'FAN02G3887' => 'fan', 'FAN02G3911' => 'fan', 'FAN02G3994' => 'fan', 'FAN02G4432' => 'fan', 'FAN02G4556' => 'fan', 'FAN03G1977' => 'fan', 'FAN03G2781' => 'fan', 'FAN03G2850' => 'fan', 'FAN03G3155' => 'fan', 'FAN04G2487' => 'fan', 'FAN05G0208' => 'fan', 'FAN05G0656' => 'fan', 'FAN05G0696' => 'fan', 'FAN05G0810' => 'fan', 'FAN05G1447' => 'fan', 'FAN05G2640' => 'fan', 'FAN05G2911' => 'fan', 'FAN05G3901' => 'fan', 'FAN05G4859' => 'fan', 'FAN05G4861' => 'fan', 'FAN05G4988' => 'fan', 'FAN05G5187' => 'fan', 'FAN05G5452' => 'fan', 'FAN05G5500' => 'fan', 'FAN05G5688' => 'fan', 'FAN06G0177' => 'fan', 'FAN06G0675' => 'fan', 'FAN06G1290' => 'fan', 'FAN06G2191' => 'fan', 'FAN06G2405' => 'fan', 'FAN06G3231' => 'fan', 'FAN06G3932' => 'fan', 'FAN07G0163' => 'fan', 'FAN07G0471' => 'fan', 'FAN07G1354' => 'fan', 'FAN08G0338' => 'fan', 'FAN08G1373' => 'fan', 'FAN08G2539' => 'fan', 'FAN08G2728' => 'fan', 'FAN09G0608' => 'fan', 'FAN09G1136' => 'fan', 'FAN09G1958' => 'fan', 'FAN09G2508' => 'fan', 'FAN09G2597' => 'fan', 'FAN09G2658' => 'fan', 'FAN09G2757' => 'fan', 'FAN09G2983' => 'fan', 'FAN09G3130' => 'fan', 'FAN09G3565' => 'fan', 'FAN09G3613' => 'fan', 'FAN09G4011' => 'fan', 'FAN09G4239' => 'fan', 'FAN09G4277' => 'fan', 'FAN09G4720' => 'fan', 'FAN11G0139' => 'fan', 'FAN11G1727' => 'fan', 'FAN11G2672' => 'fan', 'FAN11G2795' => 'fan', 'FAN11G3238' => 'fan', 'FAN11G3734' => 'fan', 'FAN12G0631' => 'fan', 'FAN12G2239' => 'fan', 'FAN12G2308' => 'fan', 'FAN12G2569' => 'fan', 'FAN12G2623' => 'fan', 'FAN13G3182' => 'fan', 'FAN14G0053' => 'fan', 'FAN14G0370' => 'fan', 'FAN14G0382' => 'fan', 'FAN14G0421' => 'fan', 'FAN14G0866' => 'fan', 'FAN14G1187' => 'fan', 'FAN14G1727' => 'fan', 'FAN14G1791' => 'fan', 'FAN14G2361' => 'fan', 'FAN14G2668' => 'fan', 'FAN14G2770' => 'fan', 'FAN14G2874' => 'fan', 'FAN14G3193' => 'fan', 'FAN14G3624' => 'fan', 'FAN14G3676' => 'fan', 'FAN14G3807' => 'fan', 'FAN14G4082' => 'fan', 'FAN14G4342' => 'fan', 'FAN14G4985' => 'fan', 'FAN14G5126' => 'fan', 'FAN14G5781' => 'fan', 'FAN14G5808' => 'fan', 'FAN14G5949' => 'fan', 'FAN15G0828' => 'fan', 'FAN15G1054' => 'fan', 'FAN15G2023' => 'fan', 'FAN15G2506' => 'fan', 'FAN16G0128' => 'fan', 'FAN16G0249' => 'fan', 'FAN16G0429' => 'fan', 'FAN16G1493' => 'fan', 'FAN16G2210' => 'fan', 'FAN16G2506' => 'fan', 'FAN18G1542' => 'fan', 'FAN18G4057' => 'fan', 'FAN19G0745' => 'fan', 'FAN19G1216' => 'fan', 'FAN19G1733' => 'fan', 'FAN20G0258' => 'fan', 'FAN20G1095' => 'fan', 'FAN20G1557' => 'fan', 'FAN21G0302' => 'fan', 'FAN21G0519' => 'fan', 'FAN21G0970' => 'fan', 'FAN21G1159' => 'fan', 'FAN21G1312' => 'fan', 'FAN21G1440' => 'fan', 'FAN21G1715' => 'fan', 'FAN23G1584' => 'fan', 'FAN24G0045' => 'fan', 'FAN24G0053' => 'fan', 'FAN24G1500' => 'fan', 'FAN24G1817' => 'fan', 'FAN24G2147' => 'fan', 'FAN24G2236' => 'fan', 'FAN24G2446' => 'fan', 'FAN24G2684' => 'fan', 'FAN25G0187' => 'fan', 'FAN25G0505' => 'fan', 'FAN25G0589' => 'fan', 'FAN25G3663' => 'fan', 'FAN26G1025' => 'fan', 'FAN26G2860' => 'fan', 'FAN27G1329' => 'fan', 'FAN27G3392' => 'fan', 'FvH4_1g02011' => 'fve', 'FvH4_1g06511' => 'fve', 'FvH4_2g19900' => 'fve', 'FvH4_2g19920' => 'fve', 'FvH4_2g24261' => 'fve', 'FvH4_2g24270' => 'fve', 'FvH4_2g24631' => 'fve', 'FvH4_2g30622' => 'fve', 'FvH4_3g12920' => 'fve', 'FvH4_3g30171' => 'fve', 'FvH4_3g35490' => 'fve', 'FvH4_3g43682' => 'fve', 'FvH4_3g43730' => 'fve', 'FvH4_3g43732' => 'fve', 'FvH4_3g43751' => 'fve', 'FvH4_3g43752' => 'fve', 'FvH4_3g43770' => 'fve', 'FvH4_3g44471' => 'fve', 'FvH4_3g44510' => 'fve', 'FvH4_3g44582' => 'fve', 'FvH4_4g16921' => 'fve', 'FvH4_4g17121' => 'fve', 'FvH4_4g17782' => 'fve', 'FvH4_4g17783' => 'fve', 'FvH4_4g18120' => 'fve', 'FvH4_4g31310' => 'fve', 'FvH4_4g35052' => 'fve', 'FvH4_5g30862' => 'fve', 'FvH4_6g01541' => 'fve', 'FvH4_6g02021' => 'fve', 'FvH4_6g02041' => 'fve', 'FvH4_6g02071' => 'fve', 'FvH4_6g02171' => 'fve', 'FvH4_6g03181' => 'fve', 'FvH4_6g03182' => 'fve', 'FvH4_6g03221' => 'fve', 'FvH4_6g03380' => 'fve', 'FvH4_6g05201' => 'fve', 'FvH4_6g05203' => 'fve', 'FvH4_6g20231' => 'fve', 'FvH4_6g31981' => 'fve', 'FvH4_6g32061' => 'fve', 'FvH4_6g37041' => 'fve', 'FvH4_6g37932' => 'fve', 'FvH4_6g38731' => 'fve', 'FvH4_6g39370' => 'fve', 'FvH4_6g39371' => 'fve', 'FvH4_6g40891' => 'fve', 'FvH4_6g40892' => 'fve', 'FvH4_6g43143' => 'fve', 'FvH4_6g45251' => 'fve', 'FvH4_6g45260' => 'fve', 'FvH4_6g45291' => 'fve', 'FvH4_6g45890' => 'fve', 'FvH4_6g46240' => 'fve', 'FvH4_6g46241' => 'fve', 'FvH4_6g46242' => 'fve', 'FvH4_6g46260' => 'fve', 'FvH4_6g46280' => 'fve', 'FvH4_6g46380' => 'fve', 'FvH4_7g12841' => 'fve', 'FvH4_7g31431' => 'fve', 'Glyma.09G075900' => 'gma', 'Gohir.A09G096401' => 'ghi', 'Gohir.D09G096101' => 'ghi', 'Gorai.006G112800' => 'gra', 'HanXRQChr04g0121411' => 'han', 'Hund15878' => 'sun', 'Lj2A1107G68' => 'lonja', 'Lj2A630G63' => 'lonja', 'Lj2A946T25' => 'lonja', 'Lj2C714T1' => 'lonja', 'Lj2C966T3' => 'lonja', 'Lj2C966T4' => 'lonja', 'Lj4g0002979' => 'lja', 'Lsat_1_v5_gn_5_30901' => 'lsa', 'Lsat_1_v5_gn_5_31100' => 'lsa', 'Lsat_1_v5_gn_5_38600' => 'lsa', 'Lsat_1_v5_gn_6_92061' => 'lsa', 'Manes.05G071301' => 'mes', 'MD02G1008700' => 'mdo', 'MD02G1008900' => 'mdo', 'MD03G1256400' => 'mdo', 'MD04G1180900' => 'mdo', 'MD04G1181000' => 'mdo', 'MD04G1181200' => 'mdo', 'MD05G1244200' => 'mdo', 'MD05G1324200' => 'mdo', 'MD09G1201600' => 'mdo', 'MD10G1000600' => 'mdo', 'MD14G1026900' => 'mdo', 'MD14G1187900' => 'mdo', 'MD15G1017800' => 'mdo', 'MD15G1018100' => 'mdo', 'Medtr4g124160' => 'mtr', 'Migut.L01260' => 'egut', 'Nitab4.5_0000008g0440' => 'nta', 'Nitab4.5_0000207g0170' => 'nta', 'Nitab4.5_0007671g0030' => 'nta', 'Nitab4.5_0010853g0020' => 'nta', 'Oeu057656.1' => 'oeu', 'PGSC0003DMG400005638' => 'stu', 'PGSC0003DMG400005639' => 'stu', 'Phvul.009G222800' => 'pvu', 'Potri.009G132400' => 'ptr', 'Potri.009G163001' => 'ptr', 'Potri.011G000700' => 'ptr', 'Potri.011G004800' => 'ptr', 'Prupe.1G509300' => 'ppe', 'Prupe.1G509700' => 'ppe', 'Prupe.1G510400' => 'ppe', 'Prupe.1G510700' => 'ppe', 'Prupe.1G512600' => 'ppe', 'Prupe.2G073200' => 'ppe', 'Prupe.3G059500' => 'ppe', 'Prupe.3G059600' => 'ppe', 'Prupe.3G246100' => 'ppe', 'Prupe.3G265100' => 'ppe', 'Prupe.4G034700' => 'ppe', 'Prupe.4G052100' => 'ppe', 'Prupe.4G053600' => 'ppe', 'Prupe.5G068800' => 'ppe', 'Prupe.5G070600' => 'ppe', 'Prupe.6G075400' => 'ppe', 'Prupe.6G075500' => 'ppe', 'Prupe.6G076400' => 'ppe', 'Prupe.8G110700' => 'ppe', 'Psat4g020960' => 'psa', 'PSO135G0788' => 'pso', 'PSO210G6463' => 'pso', 'PSO384G0370' => 'pso', 'PSO386G0056' => 'pso', 'QL01p006048' => 'qlo', 'QL02p054283' => 'qlo', 'QL05p008000' => 'qlo', 'QL05p008212' => 'qlo', 'QL05p008950' => 'qlo', 'QL05p009042' => 'qlo', 'QL05p009518' => 'qlo', 'QL05p012589' => 'qlo', 'QL05p012608' => 'qlo', 'QL05p012650' => 'qlo', 'QL05p012667' => 'qlo', 'QL05p014501' => 'qlo', 'QL05p052800' => 'qlo', 'QL05p065010' => 'qlo', 'QL05p074156' => 'qlo', 'QL05p074160' => 'qlo', 'QL05p074174' => 'qlo', 'QL05p074178' => 'qlo', 'QL05p074214' => 'qlo', 'QL06p001050' => 'qlo', 'QL06p001056' => 'qlo', 'QL06p006093' => 'qlo', 'QL06p006111' => 'qlo', 'QL07p019784' => 'qlo', 'QL07p019801' => 'qlo', 'QL07p036110' => 'qlo', 'QL07p036134' => 'qlo', 'QL07p036147' => 'qlo', 'QL07p036156' => 'qlo', 'QL07p036300' => 'qlo', 'QL07p036320' => 'qlo', 'QL08p014547' => 'qlo', 'QL08p014551' => 'qlo', 'QL08p043319' => 'qlo', 'QL08p043324' => 'qlo', 'QL11p009094' => 'qlo', 'RcHm_v2.0_Chr1g0380481' => 'rch', 'RcHm_v2.0_Chr2g0089331' => 'rch', 'RcHm_v2.0_Chr2g0123691' => 'rch', 'RcHm_v2.0_Chr2g0151111' => 'rch', 'RcHm_v2.0_Chr2g0163011' => 'rch', 'RcHm_v2.0_Chr2g0163051' => 'rch', 'RcHm_v2.0_Chr2g0164671' => 'rch', 'RcHm_v2.0_Chr2g0164681' => 'rch', 'RcHm_v2.0_Chr2g0164721' => 'rch', 'RcHm_v2.0_Chr3g0449911' => 'rch', 'RcHm_v2.0_Chr3g0450211' => 'rch', 'RcHm_v2.0_Chr3g0457271' => 'rch', 'RcHm_v2.0_Chr5g0018111' => 'rch', 'RcHm_v2.0_Chr5g0021011' => 'rch', 'RcHm_v2.0_Chr5g0081171' => 'rch', 'RcHm_v2.0_Chr5g0081211' => 'rch', 'RcHm_v2.0_Chr6g0275871' => 'rch', 'RcHm_v2.0_Chr6g0276071' => 'rch', 'RcHm_v2.0_Chr6g0285591' => 'rch', 'RcHm_v2.0_Chr6g0291931' => 'rch', 'RcHm_v2.0_Chr6g0292091' => 'rch', 'RcHm_v2.0_Chr6g0292271' => 'rch', 'RcHm_v2.0_Chr7g0221261' => 'rch', 'Rhsim08G0219900' => 'rsi', 'Rhsim08G0220200' => 'rsi', 'Rhsim08G0237800' => 'rsi', 'Rhsim08G0238800' => 'rsi', 'Sabra09G0102700' => 'sbr', 'Sabra09G0127200' => 'sbr', 'Sabra11G0003700' => 'sbr', 'Sabra15G0014700' => 'sbr', 'Sc19g0000590' => 'sci', 'Sc19g0001870' => 'sci', 'SGA_v2.0_scaffold1G00346' => 'sas', 'SGA_v2.0_scaffold1G00575' => 'sas', 'SGA_v2.0_scaffold1G00761' => 'sas', 'SGA_v2.0_scaffold232G43501' => 'sas', 'TAR625G1137' => 'tar', 'Thecc.03G222100' => 'tca', 'TPR.G12691' => 'tpr', 'TWI34G0727' => 'twi', 'TWI36G0117' => 'twi', 'VMungo1309G0868' => 'vmu' ) $gf_id = 'HOM05D001729' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001729' ) $data_identifier = 'HOM05D001729' $data_type = 'gf_id' $species_gene_counts = array( 'amhyb' => (int) 1, 'cqu' => (int) 9, 'can' => (int) 1, 'cansat' => (int) 1, 'car' => (int) 1, 'col' => (int) 5, 'dca' => (int) 1, 'din' => (int) 2, 'dzi' => (int) 3, 'fan' => (int) 140, 'fve' => (int) 62, 'gma' => (int) 1, 'ghi' => (int) 2, 'gra' => (int) 1, 'han' => (int) 1, 'sun' => (int) 1, 'lonja' => (int) 6, 'lja' => (int) 1, 'lsa' => (int) 4, 'mes' => (int) 1, 'mdo' => (int) 14, 'mtr' => (int) 1, 'egut' => (int) 1, 'nta' => (int) 4, 'oeu' => (int) 1, 'stu' => (int) 2, 'pvu' => (int) 1, 'ptr' => (int) 4, 'ppe' => (int) 19, 'psa' => (int) 1, 'pso' => (int) 4, 'qlo' => (int) 36, 'rch' => (int) 23, 'rsi' => (int) 4, 'sbr' => (int) 4, 'sci' => (int) 2, 'sas' => (int) 4, 'tar' => (int) 1, 'tca' => (int) 1, 'tpr' => (int) 1, 'twi' => (int) 2, 'vmu' => (int) 1 ) $gf_gene_species = 'vmu' $gf_gene_id = 'VMungo1309G0868' $species_info = array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ) $local_species = 'gma' $disabled = '' $selected = '' $num_hits = (int) 1
Warning (2): count(): Parameter must be an array or an object that implements Countable [APP/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp, line 33]Code Context $disabled = (!array_key_exists($local_species,$species_gene_counts))?"disabled":""; $selected = (isset($selected_species) && array_key_exists($local_species,$selected_species))?"checked='checked'":""; $num_hits = (array_key_exists($local_species,$species_gene_counts))?count($species_gene_counts[$local_species]):0; $viewFile = '/www/bioinformatics01_ro/plaza/_dev_instances/feedback/app/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp' $dataForView = array( 'sidebar_info' => array( 'gf_id' => 'HOM05D001729', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '375', 'num_species' => '42' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'Ah.07g204710' => 'amhyb', 'AUR62006001' => 'cqu', 'AUR62006002' => 'cqu', 'AUR62006003' => 'cqu', 'AUR62015641' => 'cqu', 'AUR62027174' => 'cqu', 'AUR62035623' => 'cqu', 'AUR62035624' => 'cqu', 'AUR62035625' => 'cqu', 'AUR62035626' => 'cqu', 'CAN.G1110.53' => 'can', 'CANSAT80G0415' => 'cansat', 'Ca_21364_v3' => 'car', 'COL.COLO4_30693' => 'col', 'COL.COLO4_30694' => 'col', 'COL.COLO4_30695' => 'col', 'COL.COLO4_30696' => 'col', 'COL.COLO4_34020' => 'col', 'DCAR_004585' => 'dca', 'Dinv04029' => 'din', 'Dinv34857' => 'din', 'Duzib147G0011' => 'dzi', 'Duzib170G0599' => 'dzi', 'Duzib192G1051' => 'dzi', 'FAN01G0708' => 'fan', 'FAN01G0742' => 'fan', 'FAN02G0048' => 'fan', 'FAN02G0583' => 'fan', 'FAN02G0688' => 'fan', 'FAN02G1588' => 'fan', 'FAN02G2194' => 'fan', 'FAN02G2750' => 'fan', 'FAN02G3094' => 'fan', 'FAN02G3887' => 'fan', 'FAN02G3911' => 'fan', 'FAN02G3994' => 'fan', 'FAN02G4432' => 'fan', 'FAN02G4556' => 'fan', 'FAN03G1977' => 'fan', 'FAN03G2781' => 'fan', 'FAN03G2850' => 'fan', 'FAN03G3155' => 'fan', 'FAN04G2487' => 'fan', 'FAN05G0208' => 'fan', 'FAN05G0656' => 'fan', 'FAN05G0696' => 'fan', 'FAN05G0810' => 'fan', 'FAN05G1447' => 'fan', 'FAN05G2640' => 'fan', 'FAN05G2911' => 'fan', 'FAN05G3901' => 'fan', 'FAN05G4859' => 'fan', 'FAN05G4861' => 'fan', 'FAN05G4988' => 'fan', 'FAN05G5187' => 'fan', 'FAN05G5452' => 'fan', 'FAN05G5500' => 'fan', 'FAN05G5688' => 'fan', 'FAN06G0177' => 'fan', 'FAN06G0675' => 'fan', 'FAN06G1290' => 'fan', 'FAN06G2191' => 'fan', 'FAN06G2405' => 'fan', 'FAN06G3231' => 'fan', 'FAN06G3932' => 'fan', 'FAN07G0163' => 'fan', 'FAN07G0471' => 'fan', 'FAN07G1354' => 'fan', 'FAN08G0338' => 'fan', 'FAN08G1373' => 'fan', 'FAN08G2539' => 'fan', 'FAN08G2728' => 'fan', 'FAN09G0608' => 'fan', 'FAN09G1136' => 'fan', 'FAN09G1958' => 'fan', 'FAN09G2508' => 'fan', 'FAN09G2597' => 'fan', 'FAN09G2658' => 'fan', 'FAN09G2757' => 'fan', 'FAN09G2983' => 'fan', 'FAN09G3130' => 'fan', 'FAN09G3565' => 'fan', 'FAN09G3613' => 'fan', 'FAN09G4011' => 'fan', 'FAN09G4239' => 'fan', 'FAN09G4277' => 'fan', 'FAN09G4720' => 'fan', 'FAN11G0139' => 'fan', 'FAN11G1727' => 'fan', 'FAN11G2672' => 'fan', 'FAN11G2795' => 'fan', 'FAN11G3238' => 'fan', 'FAN11G3734' => 'fan', 'FAN12G0631' => 'fan', 'FAN12G2239' => 'fan', 'FAN12G2308' => 'fan', 'FAN12G2569' => 'fan', 'FAN12G2623' => 'fan', 'FAN13G3182' => 'fan', 'FAN14G0053' => 'fan', 'FAN14G0370' => 'fan', 'FAN14G0382' => 'fan', 'FAN14G0421' => 'fan', 'FAN14G0866' => 'fan', 'FAN14G1187' => 'fan', 'FAN14G1727' => 'fan', 'FAN14G1791' => 'fan', 'FAN14G2361' => 'fan', 'FAN14G2668' => 'fan', 'FAN14G2770' => 'fan', 'FAN14G2874' => 'fan', 'FAN14G3193' => 'fan', 'FAN14G3624' => 'fan', 'FAN14G3676' => 'fan', 'FAN14G3807' => 'fan', 'FAN14G4082' => 'fan', 'FAN14G4342' => 'fan', 'FAN14G4985' => 'fan', 'FAN14G5126' => 'fan', 'FAN14G5781' => 'fan', 'FAN14G5808' => 'fan', 'FAN14G5949' => 'fan', 'FAN15G0828' => 'fan', 'FAN15G1054' => 'fan', 'FAN15G2023' => 'fan', 'FAN15G2506' => 'fan', 'FAN16G0128' => 'fan', 'FAN16G0249' => 'fan', 'FAN16G0429' => 'fan', 'FAN16G1493' => 'fan', 'FAN16G2210' => 'fan', 'FAN16G2506' => 'fan', 'FAN18G1542' => 'fan', 'FAN18G4057' => 'fan', 'FAN19G0745' => 'fan', 'FAN19G1216' => 'fan', 'FAN19G1733' => 'fan', 'FAN20G0258' => 'fan', 'FAN20G1095' => 'fan', 'FAN20G1557' => 'fan', 'FAN21G0302' => 'fan', 'FAN21G0519' => 'fan', 'FAN21G0970' => 'fan', 'FAN21G1159' => 'fan', 'FAN21G1312' => 'fan', 'FAN21G1440' => 'fan', 'FAN21G1715' => 'fan', 'FAN23G1584' => 'fan', 'FAN24G0045' => 'fan', 'FAN24G0053' => 'fan', 'FAN24G1500' => 'fan', 'FAN24G1817' => 'fan', 'FAN24G2147' => 'fan', 'FAN24G2236' => 'fan', 'FAN24G2446' => 'fan', 'FAN24G2684' => 'fan', 'FAN25G0187' => 'fan', 'FAN25G0505' => 'fan', 'FAN25G0589' => 'fan', 'FAN25G3663' => 'fan', 'FAN26G1025' => 'fan', 'FAN26G2860' => 'fan', 'FAN27G1329' => 'fan', 'FAN27G3392' => 'fan', 'FvH4_1g02011' => 'fve', 'FvH4_1g06511' => 'fve', 'FvH4_2g19900' => 'fve', 'FvH4_2g19920' => 'fve', 'FvH4_2g24261' => 'fve', 'FvH4_2g24270' => 'fve', 'FvH4_2g24631' => 'fve', 'FvH4_2g30622' => 'fve', 'FvH4_3g12920' => 'fve', 'FvH4_3g30171' => 'fve', 'FvH4_3g35490' => 'fve', 'FvH4_3g43682' => 'fve', 'FvH4_3g43730' => 'fve', 'FvH4_3g43732' => 'fve', 'FvH4_3g43751' => 'fve', 'FvH4_3g43752' => 'fve', 'FvH4_3g43770' => 'fve', 'FvH4_3g44471' => 'fve', 'FvH4_3g44510' => 'fve', 'FvH4_3g44582' => 'fve', 'FvH4_4g16921' => 'fve', 'FvH4_4g17121' => 'fve', 'FvH4_4g17782' => 'fve', 'FvH4_4g17783' => 'fve', 'FvH4_4g18120' => 'fve', 'FvH4_4g31310' => 'fve', 'FvH4_4g35052' => 'fve', 'FvH4_5g30862' => 'fve', 'FvH4_6g01541' => 'fve', 'FvH4_6g02021' => 'fve', 'FvH4_6g02041' => 'fve', 'FvH4_6g02071' => 'fve', 'FvH4_6g02171' => 'fve', 'FvH4_6g03181' => 'fve', 'FvH4_6g03182' => 'fve', 'FvH4_6g03221' => 'fve', 'FvH4_6g03380' => 'fve', 'FvH4_6g05201' => 'fve', 'FvH4_6g05203' => 'fve', 'FvH4_6g20231' => 'fve', 'FvH4_6g31981' => 'fve', 'FvH4_6g32061' => 'fve', 'FvH4_6g37041' => 'fve', 'FvH4_6g37932' => 'fve', 'FvH4_6g38731' => 'fve', 'FvH4_6g39370' => 'fve', 'FvH4_6g39371' => 'fve', 'FvH4_6g40891' => 'fve', 'FvH4_6g40892' => 'fve', 'FvH4_6g43143' => 'fve', 'FvH4_6g45251' => 'fve', 'FvH4_6g45260' => 'fve', 'FvH4_6g45291' => 'fve', 'FvH4_6g45890' => 'fve', 'FvH4_6g46240' => 'fve', 'FvH4_6g46241' => 'fve', 'FvH4_6g46242' => 'fve', 'FvH4_6g46260' => 'fve', 'FvH4_6g46280' => 'fve', 'FvH4_6g46380' => 'fve', 'FvH4_7g12841' => 'fve', 'FvH4_7g31431' => 'fve', 'Glyma.09G075900' => 'gma', 'Gohir.A09G096401' => 'ghi', 'Gohir.D09G096101' => 'ghi', 'Gorai.006G112800' => 'gra', 'HanXRQChr04g0121411' => 'han', 'Hund15878' => 'sun', 'Lj2A1107G68' => 'lonja', 'Lj2A630G63' => 'lonja', 'Lj2A946T25' => 'lonja', 'Lj2C714T1' => 'lonja', 'Lj2C966T3' => 'lonja', 'Lj2C966T4' => 'lonja', 'Lj4g0002979' => 'lja', 'Lsat_1_v5_gn_5_30901' => 'lsa', 'Lsat_1_v5_gn_5_31100' => 'lsa', 'Lsat_1_v5_gn_5_38600' => 'lsa', 'Lsat_1_v5_gn_6_92061' => 'lsa', 'Manes.05G071301' => 'mes', 'MD02G1008700' => 'mdo', 'MD02G1008900' => 'mdo', 'MD03G1256400' => 'mdo', 'MD04G1180900' => 'mdo', 'MD04G1181000' => 'mdo', 'MD04G1181200' => 'mdo', 'MD05G1244200' => 'mdo', 'MD05G1324200' => 'mdo', 'MD09G1201600' => 'mdo', 'MD10G1000600' => 'mdo', 'MD14G1026900' => 'mdo', 'MD14G1187900' => 'mdo', 'MD15G1017800' => 'mdo', 'MD15G1018100' => 'mdo', 'Medtr4g124160' => 'mtr', 'Migut.L01260' => 'egut', 'Nitab4.5_0000008g0440' => 'nta', 'Nitab4.5_0000207g0170' => 'nta', 'Nitab4.5_0007671g0030' => 'nta', 'Nitab4.5_0010853g0020' => 'nta', 'Oeu057656.1' => 'oeu', 'PGSC0003DMG400005638' => 'stu', 'PGSC0003DMG400005639' => 'stu', 'Phvul.009G222800' => 'pvu', 'Potri.009G132400' => 'ptr', 'Potri.009G163001' => 'ptr', 'Potri.011G000700' => 'ptr', 'Potri.011G004800' => 'ptr', 'Prupe.1G509300' => 'ppe', 'Prupe.1G509700' => 'ppe', 'Prupe.1G510400' => 'ppe', 'Prupe.1G510700' => 'ppe', 'Prupe.1G512600' => 'ppe', 'Prupe.2G073200' => 'ppe', 'Prupe.3G059500' => 'ppe', 'Prupe.3G059600' => 'ppe', 'Prupe.3G246100' => 'ppe', 'Prupe.3G265100' => 'ppe', 'Prupe.4G034700' => 'ppe', 'Prupe.4G052100' => 'ppe', 'Prupe.4G053600' => 'ppe', 'Prupe.5G068800' => 'ppe', 'Prupe.5G070600' => 'ppe', 'Prupe.6G075400' => 'ppe', 'Prupe.6G075500' => 'ppe', 'Prupe.6G076400' => 'ppe', 'Prupe.8G110700' => 'ppe', 'Psat4g020960' => 'psa', 'PSO135G0788' => 'pso', 'PSO210G6463' => 'pso', 'PSO384G0370' => 'pso', 'PSO386G0056' => 'pso', 'QL01p006048' => 'qlo', 'QL02p054283' => 'qlo', 'QL05p008000' => 'qlo', 'QL05p008212' => 'qlo', 'QL05p008950' => 'qlo', 'QL05p009042' => 'qlo', 'QL05p009518' => 'qlo', 'QL05p012589' => 'qlo', 'QL05p012608' => 'qlo', 'QL05p012650' => 'qlo', 'QL05p012667' => 'qlo', 'QL05p014501' => 'qlo', 'QL05p052800' => 'qlo', 'QL05p065010' => 'qlo', 'QL05p074156' => 'qlo', 'QL05p074160' => 'qlo', 'QL05p074174' => 'qlo', 'QL05p074178' => 'qlo', 'QL05p074214' => 'qlo', 'QL06p001050' => 'qlo', 'QL06p001056' => 'qlo', 'QL06p006093' => 'qlo', 'QL06p006111' => 'qlo', 'QL07p019784' => 'qlo', 'QL07p019801' => 'qlo', 'QL07p036110' => 'qlo', 'QL07p036134' => 'qlo', 'QL07p036147' => 'qlo', 'QL07p036156' => 'qlo', 'QL07p036300' => 'qlo', 'QL07p036320' => 'qlo', 'QL08p014547' => 'qlo', 'QL08p014551' => 'qlo', 'QL08p043319' => 'qlo', 'QL08p043324' => 'qlo', 'QL11p009094' => 'qlo', 'RcHm_v2.0_Chr1g0380481' => 'rch', 'RcHm_v2.0_Chr2g0089331' => 'rch', 'RcHm_v2.0_Chr2g0123691' => 'rch', 'RcHm_v2.0_Chr2g0151111' => 'rch', 'RcHm_v2.0_Chr2g0163011' => 'rch', 'RcHm_v2.0_Chr2g0163051' => 'rch', 'RcHm_v2.0_Chr2g0164671' => 'rch', 'RcHm_v2.0_Chr2g0164681' => 'rch', 'RcHm_v2.0_Chr2g0164721' => 'rch', 'RcHm_v2.0_Chr3g0449911' => 'rch', 'RcHm_v2.0_Chr3g0450211' => 'rch', 'RcHm_v2.0_Chr3g0457271' => 'rch', 'RcHm_v2.0_Chr5g0018111' => 'rch', 'RcHm_v2.0_Chr5g0021011' => 'rch', 'RcHm_v2.0_Chr5g0081171' => 'rch', 'RcHm_v2.0_Chr5g0081211' => 'rch', 'RcHm_v2.0_Chr6g0275871' => 'rch', 'RcHm_v2.0_Chr6g0276071' => 'rch', 'RcHm_v2.0_Chr6g0285591' => 'rch', 'RcHm_v2.0_Chr6g0291931' => 'rch', 'RcHm_v2.0_Chr6g0292091' => 'rch', 'RcHm_v2.0_Chr6g0292271' => 'rch', 'RcHm_v2.0_Chr7g0221261' => 'rch', 'Rhsim08G0219900' => 'rsi', 'Rhsim08G0220200' => 'rsi', 'Rhsim08G0237800' => 'rsi', 'Rhsim08G0238800' => 'rsi', 'Sabra09G0102700' => 'sbr', 'Sabra09G0127200' => 'sbr', 'Sabra11G0003700' => 'sbr', 'Sabra15G0014700' => 'sbr', 'Sc19g0000590' => 'sci', 'Sc19g0001870' => 'sci', 'SGA_v2.0_scaffold1G00346' => 'sas', 'SGA_v2.0_scaffold1G00575' => 'sas', 'SGA_v2.0_scaffold1G00761' => 'sas', 'SGA_v2.0_scaffold232G43501' => 'sas', 'TAR625G1137' => 'tar', 'Thecc.03G222100' => 'tca', 'TPR.G12691' => 'tpr', 'TWI34G0727' => 'twi', 'TWI36G0117' => 'twi', 'VMungo1309G0868' => 'vmu' ), 'gf_id' => 'HOM05D001729', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001729' ), 'data_identifier' => 'HOM05D001729', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001729', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '375', 'num_species' => '42' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'Ah.07g204710' => 'amhyb', 'AUR62006001' => 'cqu', 'AUR62006002' => 'cqu', 'AUR62006003' => 'cqu', 'AUR62015641' => 'cqu', 'AUR62027174' => 'cqu', 'AUR62035623' => 'cqu', 'AUR62035624' => 'cqu', 'AUR62035625' => 'cqu', 'AUR62035626' => 'cqu', 'CAN.G1110.53' => 'can', 'CANSAT80G0415' => 'cansat', 'Ca_21364_v3' => 'car', 'COL.COLO4_30693' => 'col', 'COL.COLO4_30694' => 'col', 'COL.COLO4_30695' => 'col', 'COL.COLO4_30696' => 'col', 'COL.COLO4_34020' => 'col', 'DCAR_004585' => 'dca', 'Dinv04029' => 'din', 'Dinv34857' => 'din', 'Duzib147G0011' => 'dzi', 'Duzib170G0599' => 'dzi', 'Duzib192G1051' => 'dzi', 'FAN01G0708' => 'fan', 'FAN01G0742' => 'fan', 'FAN02G0048' => 'fan', 'FAN02G0583' => 'fan', 'FAN02G0688' => 'fan', 'FAN02G1588' => 'fan', 'FAN02G2194' => 'fan', 'FAN02G2750' => 'fan', 'FAN02G3094' => 'fan', 'FAN02G3887' => 'fan', 'FAN02G3911' => 'fan', 'FAN02G3994' => 'fan', 'FAN02G4432' => 'fan', 'FAN02G4556' => 'fan', 'FAN03G1977' => 'fan', 'FAN03G2781' => 'fan', 'FAN03G2850' => 'fan', 'FAN03G3155' => 'fan', 'FAN04G2487' => 'fan', 'FAN05G0208' => 'fan', 'FAN05G0656' => 'fan', 'FAN05G0696' => 'fan', 'FAN05G0810' => 'fan', 'FAN05G1447' => 'fan', 'FAN05G2640' => 'fan', 'FAN05G2911' => 'fan', 'FAN05G3901' => 'fan', 'FAN05G4859' => 'fan', 'FAN05G4861' => 'fan', 'FAN05G4988' => 'fan', 'FAN05G5187' => 'fan', 'FAN05G5452' => 'fan', 'FAN05G5500' => 'fan', 'FAN05G5688' => 'fan', 'FAN06G0177' => 'fan', 'FAN06G0675' => 'fan', 'FAN06G1290' => 'fan', 'FAN06G2191' => 'fan', 'FAN06G2405' => 'fan', 'FAN06G3231' => 'fan', 'FAN06G3932' => 'fan', 'FAN07G0163' => 'fan', 'FAN07G0471' => 'fan', 'FAN07G1354' => 'fan', 'FAN08G0338' => 'fan', 'FAN08G1373' => 'fan', 'FAN08G2539' => 'fan', 'FAN08G2728' => 'fan', 'FAN09G0608' => 'fan', 'FAN09G1136' => 'fan', 'FAN09G1958' => 'fan', 'FAN09G2508' => 'fan', 'FAN09G2597' => 'fan', 'FAN09G2658' => 'fan', 'FAN09G2757' => 'fan', 'FAN09G2983' => 'fan', 'FAN09G3130' => 'fan', 'FAN09G3565' => 'fan', 'FAN09G3613' => 'fan', 'FAN09G4011' => 'fan', 'FAN09G4239' => 'fan', 'FAN09G4277' => 'fan', 'FAN09G4720' => 'fan', 'FAN11G0139' => 'fan', 'FAN11G1727' => 'fan', 'FAN11G2672' => 'fan', 'FAN11G2795' => 'fan', 'FAN11G3238' => 'fan', 'FAN11G3734' => 'fan', 'FAN12G0631' => 'fan', 'FAN12G2239' => 'fan', 'FAN12G2308' => 'fan', 'FAN12G2569' => 'fan', 'FAN12G2623' => 'fan', 'FAN13G3182' => 'fan', 'FAN14G0053' => 'fan', 'FAN14G0370' => 'fan', 'FAN14G0382' => 'fan', 'FAN14G0421' => 'fan', 'FAN14G0866' => 'fan', 'FAN14G1187' => 'fan', 'FAN14G1727' => 'fan', 'FAN14G1791' => 'fan', 'FAN14G2361' => 'fan', 'FAN14G2668' => 'fan', 'FAN14G2770' => 'fan', 'FAN14G2874' => 'fan', 'FAN14G3193' => 'fan', 'FAN14G3624' => 'fan', 'FAN14G3676' => 'fan', 'FAN14G3807' => 'fan', 'FAN14G4082' => 'fan', 'FAN14G4342' => 'fan', 'FAN14G4985' => 'fan', 'FAN14G5126' => 'fan', 'FAN14G5781' => 'fan', 'FAN14G5808' => 'fan', 'FAN14G5949' => 'fan', 'FAN15G0828' => 'fan', 'FAN15G1054' => 'fan', 'FAN15G2023' => 'fan', 'FAN15G2506' => 'fan', 'FAN16G0128' => 'fan', 'FAN16G0249' => 'fan', 'FAN16G0429' => 'fan', 'FAN16G1493' => 'fan', 'FAN16G2210' => 'fan', 'FAN16G2506' => 'fan', 'FAN18G1542' => 'fan', 'FAN18G4057' => 'fan', 'FAN19G0745' => 'fan', 'FAN19G1216' => 'fan', 'FAN19G1733' => 'fan', 'FAN20G0258' => 'fan', 'FAN20G1095' => 'fan', 'FAN20G1557' => 'fan', 'FAN21G0302' => 'fan', 'FAN21G0519' => 'fan', 'FAN21G0970' => 'fan', 'FAN21G1159' => 'fan', 'FAN21G1312' => 'fan', 'FAN21G1440' => 'fan', 'FAN21G1715' => 'fan', 'FAN23G1584' => 'fan', 'FAN24G0045' => 'fan', 'FAN24G0053' => 'fan', 'FAN24G1500' => 'fan', 'FAN24G1817' => 'fan', 'FAN24G2147' => 'fan', 'FAN24G2236' => 'fan', 'FAN24G2446' => 'fan', 'FAN24G2684' => 'fan', 'FAN25G0187' => 'fan', 'FAN25G0505' => 'fan', 'FAN25G0589' => 'fan', 'FAN25G3663' => 'fan', 'FAN26G1025' => 'fan', 'FAN26G2860' => 'fan', 'FAN27G1329' => 'fan', 'FAN27G3392' => 'fan', 'FvH4_1g02011' => 'fve', 'FvH4_1g06511' => 'fve', 'FvH4_2g19900' => 'fve', 'FvH4_2g19920' => 'fve', 'FvH4_2g24261' => 'fve', 'FvH4_2g24270' => 'fve', 'FvH4_2g24631' => 'fve', 'FvH4_2g30622' => 'fve', 'FvH4_3g12920' => 'fve', 'FvH4_3g30171' => 'fve', 'FvH4_3g35490' => 'fve', 'FvH4_3g43682' => 'fve', 'FvH4_3g43730' => 'fve', 'FvH4_3g43732' => 'fve', 'FvH4_3g43751' => 'fve', 'FvH4_3g43752' => 'fve', 'FvH4_3g43770' => 'fve', 'FvH4_3g44471' => 'fve', 'FvH4_3g44510' => 'fve', 'FvH4_3g44582' => 'fve', 'FvH4_4g16921' => 'fve', 'FvH4_4g17121' => 'fve', 'FvH4_4g17782' => 'fve', 'FvH4_4g17783' => 'fve', 'FvH4_4g18120' => 'fve', 'FvH4_4g31310' => 'fve', 'FvH4_4g35052' => 'fve', 'FvH4_5g30862' => 'fve', 'FvH4_6g01541' => 'fve', 'FvH4_6g02021' => 'fve', 'FvH4_6g02041' => 'fve', 'FvH4_6g02071' => 'fve', 'FvH4_6g02171' => 'fve', 'FvH4_6g03181' => 'fve', 'FvH4_6g03182' => 'fve', 'FvH4_6g03221' => 'fve', 'FvH4_6g03380' => 'fve', 'FvH4_6g05201' => 'fve', 'FvH4_6g05203' => 'fve', 'FvH4_6g20231' => 'fve', 'FvH4_6g31981' => 'fve', 'FvH4_6g32061' => 'fve', 'FvH4_6g37041' => 'fve', 'FvH4_6g37932' => 'fve', 'FvH4_6g38731' => 'fve', 'FvH4_6g39370' => 'fve', 'FvH4_6g39371' => 'fve', 'FvH4_6g40891' => 'fve', 'FvH4_6g40892' => 'fve', 'FvH4_6g43143' => 'fve', 'FvH4_6g45251' => 'fve', 'FvH4_6g45260' => 'fve', 'FvH4_6g45291' => 'fve', 'FvH4_6g45890' => 'fve', 'FvH4_6g46240' => 'fve', 'FvH4_6g46241' => 'fve', 'FvH4_6g46242' => 'fve', 'FvH4_6g46260' => 'fve', 'FvH4_6g46280' => 'fve', 'FvH4_6g46380' => 'fve', 'FvH4_7g12841' => 'fve', 'FvH4_7g31431' => 'fve', 'Glyma.09G075900' => 'gma', 'Gohir.A09G096401' => 'ghi', 'Gohir.D09G096101' => 'ghi', 'Gorai.006G112800' => 'gra', 'HanXRQChr04g0121411' => 'han', 'Hund15878' => 'sun', 'Lj2A1107G68' => 'lonja', 'Lj2A630G63' => 'lonja', 'Lj2A946T25' => 'lonja', 'Lj2C714T1' => 'lonja', 'Lj2C966T3' => 'lonja', 'Lj2C966T4' => 'lonja', 'Lj4g0002979' => 'lja', 'Lsat_1_v5_gn_5_30901' => 'lsa', 'Lsat_1_v5_gn_5_31100' => 'lsa', 'Lsat_1_v5_gn_5_38600' => 'lsa', 'Lsat_1_v5_gn_6_92061' => 'lsa', 'Manes.05G071301' => 'mes', 'MD02G1008700' => 'mdo', 'MD02G1008900' => 'mdo', 'MD03G1256400' => 'mdo', 'MD04G1180900' => 'mdo', 'MD04G1181000' => 'mdo', 'MD04G1181200' => 'mdo', 'MD05G1244200' => 'mdo', 'MD05G1324200' => 'mdo', 'MD09G1201600' => 'mdo', 'MD10G1000600' => 'mdo', 'MD14G1026900' => 'mdo', 'MD14G1187900' => 'mdo', 'MD15G1017800' => 'mdo', 'MD15G1018100' => 'mdo', 'Medtr4g124160' => 'mtr', 'Migut.L01260' => 'egut', 'Nitab4.5_0000008g0440' => 'nta', 'Nitab4.5_0000207g0170' => 'nta', 'Nitab4.5_0007671g0030' => 'nta', 'Nitab4.5_0010853g0020' => 'nta', 'Oeu057656.1' => 'oeu', 'PGSC0003DMG400005638' => 'stu', 'PGSC0003DMG400005639' => 'stu', 'Phvul.009G222800' => 'pvu', 'Potri.009G132400' => 'ptr', 'Potri.009G163001' => 'ptr', 'Potri.011G000700' => 'ptr', 'Potri.011G004800' => 'ptr', 'Prupe.1G509300' => 'ppe', 'Prupe.1G509700' => 'ppe', 'Prupe.1G510400' => 'ppe', 'Prupe.1G510700' => 'ppe', 'Prupe.1G512600' => 'ppe', 'Prupe.2G073200' => 'ppe', 'Prupe.3G059500' => 'ppe', 'Prupe.3G059600' => 'ppe', 'Prupe.3G246100' => 'ppe', 'Prupe.3G265100' => 'ppe', 'Prupe.4G034700' => 'ppe', 'Prupe.4G052100' => 'ppe', 'Prupe.4G053600' => 'ppe', 'Prupe.5G068800' => 'ppe', 'Prupe.5G070600' => 'ppe', 'Prupe.6G075400' => 'ppe', 'Prupe.6G075500' => 'ppe', 'Prupe.6G076400' => 'ppe', 'Prupe.8G110700' => 'ppe', 'Psat4g020960' => 'psa', 'PSO135G0788' => 'pso', 'PSO210G6463' => 'pso', 'PSO384G0370' => 'pso', 'PSO386G0056' => 'pso', 'QL01p006048' => 'qlo', 'QL02p054283' => 'qlo', 'QL05p008000' => 'qlo', 'QL05p008212' => 'qlo', 'QL05p008950' => 'qlo', 'QL05p009042' => 'qlo', 'QL05p009518' => 'qlo', 'QL05p012589' => 'qlo', 'QL05p012608' => 'qlo', 'QL05p012650' => 'qlo', 'QL05p012667' => 'qlo', 'QL05p014501' => 'qlo', 'QL05p052800' => 'qlo', 'QL05p065010' => 'qlo', 'QL05p074156' => 'qlo', 'QL05p074160' => 'qlo', 'QL05p074174' => 'qlo', 'QL05p074178' => 'qlo', 'QL05p074214' => 'qlo', 'QL06p001050' => 'qlo', 'QL06p001056' => 'qlo', 'QL06p006093' => 'qlo', 'QL06p006111' => 'qlo', 'QL07p019784' => 'qlo', 'QL07p019801' => 'qlo', 'QL07p036110' => 'qlo', 'QL07p036134' => 'qlo', 'QL07p036147' => 'qlo', 'QL07p036156' => 'qlo', 'QL07p036300' => 'qlo', 'QL07p036320' => 'qlo', 'QL08p014547' => 'qlo', 'QL08p014551' => 'qlo', 'QL08p043319' => 'qlo', 'QL08p043324' => 'qlo', 'QL11p009094' => 'qlo', 'RcHm_v2.0_Chr1g0380481' => 'rch', 'RcHm_v2.0_Chr2g0089331' => 'rch', 'RcHm_v2.0_Chr2g0123691' => 'rch', 'RcHm_v2.0_Chr2g0151111' => 'rch', 'RcHm_v2.0_Chr2g0163011' => 'rch', 'RcHm_v2.0_Chr2g0163051' => 'rch', 'RcHm_v2.0_Chr2g0164671' => 'rch', 'RcHm_v2.0_Chr2g0164681' => 'rch', 'RcHm_v2.0_Chr2g0164721' => 'rch', 'RcHm_v2.0_Chr3g0449911' => 'rch', 'RcHm_v2.0_Chr3g0450211' => 'rch', 'RcHm_v2.0_Chr3g0457271' => 'rch', 'RcHm_v2.0_Chr5g0018111' => 'rch', 'RcHm_v2.0_Chr5g0021011' => 'rch', 'RcHm_v2.0_Chr5g0081171' => 'rch', 'RcHm_v2.0_Chr5g0081211' => 'rch', 'RcHm_v2.0_Chr6g0275871' => 'rch', 'RcHm_v2.0_Chr6g0276071' => 'rch', 'RcHm_v2.0_Chr6g0285591' => 'rch', 'RcHm_v2.0_Chr6g0291931' => 'rch', 'RcHm_v2.0_Chr6g0292091' => 'rch', 'RcHm_v2.0_Chr6g0292271' => 'rch', 'RcHm_v2.0_Chr7g0221261' => 'rch', 'Rhsim08G0219900' => 'rsi', 'Rhsim08G0220200' => 'rsi', 'Rhsim08G0237800' => 'rsi', 'Rhsim08G0238800' => 'rsi', 'Sabra09G0102700' => 'sbr', 'Sabra09G0127200' => 'sbr', 'Sabra11G0003700' => 'sbr', 'Sabra15G0014700' => 'sbr', 'Sc19g0000590' => 'sci', 'Sc19g0001870' => 'sci', 'SGA_v2.0_scaffold1G00346' => 'sas', 'SGA_v2.0_scaffold1G00575' => 'sas', 'SGA_v2.0_scaffold1G00761' => 'sas', 'SGA_v2.0_scaffold232G43501' => 'sas', 'TAR625G1137' => 'tar', 'Thecc.03G222100' => 'tca', 'TPR.G12691' => 'tpr', 'TWI34G0727' => 'twi', 'TWI36G0117' => 'twi', 'VMungo1309G0868' => 'vmu' ) $gf_id = 'HOM05D001729' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001729' ) $data_identifier = 'HOM05D001729' $data_type = 'gf_id' $species_gene_counts = array( 'amhyb' => (int) 1, 'cqu' => (int) 9, 'can' => (int) 1, 'cansat' => (int) 1, 'car' => (int) 1, 'col' => (int) 5, 'dca' => (int) 1, 'din' => (int) 2, 'dzi' => (int) 3, 'fan' => (int) 140, 'fve' => (int) 62, 'gma' => (int) 1, 'ghi' => (int) 2, 'gra' => (int) 1, 'han' => (int) 1, 'sun' => (int) 1, 'lonja' => (int) 6, 'lja' => (int) 1, 'lsa' => (int) 4, 'mes' => (int) 1, 'mdo' => (int) 14, 'mtr' => (int) 1, 'egut' => (int) 1, 'nta' => (int) 4, 'oeu' => (int) 1, 'stu' => (int) 2, 'pvu' => (int) 1, 'ptr' => (int) 4, 'ppe' => (int) 19, 'psa' => (int) 1, 'pso' => (int) 4, 'qlo' => (int) 36, 'rch' => (int) 23, 'rsi' => (int) 4, 'sbr' => (int) 4, 'sci' => (int) 2, 'sas' => (int) 4, 'tar' => (int) 1, 'tca' => (int) 1, 'tpr' => (int) 1, 'twi' => (int) 2, 'vmu' => (int) 1 ) $gf_gene_species = 'vmu' $gf_gene_id = 'VMungo1309G0868' $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' => 'HOM05D001729', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '375', 'num_species' => '42' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'Ah.07g204710' => 'amhyb', 'AUR62006001' => 'cqu', 'AUR62006002' => 'cqu', 'AUR62006003' => 'cqu', 'AUR62015641' => 'cqu', 'AUR62027174' => 'cqu', 'AUR62035623' => 'cqu', 'AUR62035624' => 'cqu', 'AUR62035625' => 'cqu', 'AUR62035626' => 'cqu', 'CAN.G1110.53' => 'can', 'CANSAT80G0415' => 'cansat', 'Ca_21364_v3' => 'car', 'COL.COLO4_30693' => 'col', 'COL.COLO4_30694' => 'col', 'COL.COLO4_30695' => 'col', 'COL.COLO4_30696' => 'col', 'COL.COLO4_34020' => 'col', 'DCAR_004585' => 'dca', 'Dinv04029' => 'din', 'Dinv34857' => 'din', 'Duzib147G0011' => 'dzi', 'Duzib170G0599' => 'dzi', 'Duzib192G1051' => 'dzi', 'FAN01G0708' => 'fan', 'FAN01G0742' => 'fan', 'FAN02G0048' => 'fan', 'FAN02G0583' => 'fan', 'FAN02G0688' => 'fan', 'FAN02G1588' => 'fan', 'FAN02G2194' => 'fan', 'FAN02G2750' => 'fan', 'FAN02G3094' => 'fan', 'FAN02G3887' => 'fan', 'FAN02G3911' => 'fan', 'FAN02G3994' => 'fan', 'FAN02G4432' => 'fan', 'FAN02G4556' => 'fan', 'FAN03G1977' => 'fan', 'FAN03G2781' => 'fan', 'FAN03G2850' => 'fan', 'FAN03G3155' => 'fan', 'FAN04G2487' => 'fan', 'FAN05G0208' => 'fan', 'FAN05G0656' => 'fan', 'FAN05G0696' => 'fan', 'FAN05G0810' => 'fan', 'FAN05G1447' => 'fan', 'FAN05G2640' => 'fan', 'FAN05G2911' => 'fan', 'FAN05G3901' => 'fan', 'FAN05G4859' => 'fan', 'FAN05G4861' => 'fan', 'FAN05G4988' => 'fan', 'FAN05G5187' => 'fan', 'FAN05G5452' => 'fan', 'FAN05G5500' => 'fan', 'FAN05G5688' => 'fan', 'FAN06G0177' => 'fan', 'FAN06G0675' => 'fan', 'FAN06G1290' => 'fan', 'FAN06G2191' => 'fan', 'FAN06G2405' => 'fan', 'FAN06G3231' => 'fan', 'FAN06G3932' => 'fan', 'FAN07G0163' => 'fan', 'FAN07G0471' => 'fan', 'FAN07G1354' => 'fan', 'FAN08G0338' => 'fan', 'FAN08G1373' => 'fan', 'FAN08G2539' => 'fan', 'FAN08G2728' => 'fan', 'FAN09G0608' => 'fan', 'FAN09G1136' => 'fan', 'FAN09G1958' => 'fan', 'FAN09G2508' => 'fan', 'FAN09G2597' => 'fan', 'FAN09G2658' => 'fan', 'FAN09G2757' => 'fan', 'FAN09G2983' => 'fan', 'FAN09G3130' => 'fan', 'FAN09G3565' => 'fan', 'FAN09G3613' => 'fan', 'FAN09G4011' => 'fan', 'FAN09G4239' => 'fan', 'FAN09G4277' => 'fan', 'FAN09G4720' => 'fan', 'FAN11G0139' => 'fan', 'FAN11G1727' => 'fan', 'FAN11G2672' => 'fan', 'FAN11G2795' => 'fan', 'FAN11G3238' => 'fan', 'FAN11G3734' => 'fan', 'FAN12G0631' => 'fan', 'FAN12G2239' => 'fan', 'FAN12G2308' => 'fan', 'FAN12G2569' => 'fan', 'FAN12G2623' => 'fan', 'FAN13G3182' => 'fan', 'FAN14G0053' => 'fan', 'FAN14G0370' => 'fan', 'FAN14G0382' => 'fan', 'FAN14G0421' => 'fan', 'FAN14G0866' => 'fan', 'FAN14G1187' => 'fan', 'FAN14G1727' => 'fan', 'FAN14G1791' => 'fan', 'FAN14G2361' => 'fan', 'FAN14G2668' => 'fan', 'FAN14G2770' => 'fan', 'FAN14G2874' => 'fan', 'FAN14G3193' => 'fan', 'FAN14G3624' => 'fan', 'FAN14G3676' => 'fan', 'FAN14G3807' => 'fan', 'FAN14G4082' => 'fan', 'FAN14G4342' => 'fan', 'FAN14G4985' => 'fan', 'FAN14G5126' => 'fan', 'FAN14G5781' => 'fan', 'FAN14G5808' => 'fan', 'FAN14G5949' => 'fan', 'FAN15G0828' => 'fan', 'FAN15G1054' => 'fan', 'FAN15G2023' => 'fan', 'FAN15G2506' => 'fan', 'FAN16G0128' => 'fan', 'FAN16G0249' => 'fan', 'FAN16G0429' => 'fan', 'FAN16G1493' => 'fan', 'FAN16G2210' => 'fan', 'FAN16G2506' => 'fan', 'FAN18G1542' => 'fan', 'FAN18G4057' => 'fan', 'FAN19G0745' => 'fan', 'FAN19G1216' => 'fan', 'FAN19G1733' => 'fan', 'FAN20G0258' => 'fan', 'FAN20G1095' => 'fan', 'FAN20G1557' => 'fan', 'FAN21G0302' => 'fan', 'FAN21G0519' => 'fan', 'FAN21G0970' => 'fan', 'FAN21G1159' => 'fan', 'FAN21G1312' => 'fan', 'FAN21G1440' => 'fan', 'FAN21G1715' => 'fan', 'FAN23G1584' => 'fan', 'FAN24G0045' => 'fan', 'FAN24G0053' => 'fan', 'FAN24G1500' => 'fan', 'FAN24G1817' => 'fan', 'FAN24G2147' => 'fan', 'FAN24G2236' => 'fan', 'FAN24G2446' => 'fan', 'FAN24G2684' => 'fan', 'FAN25G0187' => 'fan', 'FAN25G0505' => 'fan', 'FAN25G0589' => 'fan', 'FAN25G3663' => 'fan', 'FAN26G1025' => 'fan', 'FAN26G2860' => 'fan', 'FAN27G1329' => 'fan', 'FAN27G3392' => 'fan', 'FvH4_1g02011' => 'fve', 'FvH4_1g06511' => 'fve', 'FvH4_2g19900' => 'fve', 'FvH4_2g19920' => 'fve', 'FvH4_2g24261' => 'fve', 'FvH4_2g24270' => 'fve', 'FvH4_2g24631' => 'fve', 'FvH4_2g30622' => 'fve', 'FvH4_3g12920' => 'fve', 'FvH4_3g30171' => 'fve', 'FvH4_3g35490' => 'fve', 'FvH4_3g43682' => 'fve', 'FvH4_3g43730' => 'fve', 'FvH4_3g43732' => 'fve', 'FvH4_3g43751' => 'fve', 'FvH4_3g43752' => 'fve', 'FvH4_3g43770' => 'fve', 'FvH4_3g44471' => 'fve', 'FvH4_3g44510' => 'fve', 'FvH4_3g44582' => 'fve', 'FvH4_4g16921' => 'fve', 'FvH4_4g17121' => 'fve', 'FvH4_4g17782' => 'fve', 'FvH4_4g17783' => 'fve', 'FvH4_4g18120' => 'fve', 'FvH4_4g31310' => 'fve', 'FvH4_4g35052' => 'fve', 'FvH4_5g30862' => 'fve', 'FvH4_6g01541' => 'fve', 'FvH4_6g02021' => 'fve', 'FvH4_6g02041' => 'fve', 'FvH4_6g02071' => 'fve', 'FvH4_6g02171' => 'fve', 'FvH4_6g03181' => 'fve', 'FvH4_6g03182' => 'fve', 'FvH4_6g03221' => 'fve', 'FvH4_6g03380' => 'fve', 'FvH4_6g05201' => 'fve', 'FvH4_6g05203' => 'fve', 'FvH4_6g20231' => 'fve', 'FvH4_6g31981' => 'fve', 'FvH4_6g32061' => 'fve', 'FvH4_6g37041' => 'fve', 'FvH4_6g37932' => 'fve', 'FvH4_6g38731' => 'fve', 'FvH4_6g39370' => 'fve', 'FvH4_6g39371' => 'fve', 'FvH4_6g40891' => 'fve', 'FvH4_6g40892' => 'fve', 'FvH4_6g43143' => 'fve', 'FvH4_6g45251' => 'fve', 'FvH4_6g45260' => 'fve', 'FvH4_6g45291' => 'fve', 'FvH4_6g45890' => 'fve', 'FvH4_6g46240' => 'fve', 'FvH4_6g46241' => 'fve', 'FvH4_6g46242' => 'fve', 'FvH4_6g46260' => 'fve', 'FvH4_6g46280' => 'fve', 'FvH4_6g46380' => 'fve', 'FvH4_7g12841' => 'fve', 'FvH4_7g31431' => 'fve', 'Glyma.09G075900' => 'gma', 'Gohir.A09G096401' => 'ghi', 'Gohir.D09G096101' => 'ghi', 'Gorai.006G112800' => 'gra', 'HanXRQChr04g0121411' => 'han', 'Hund15878' => 'sun', 'Lj2A1107G68' => 'lonja', 'Lj2A630G63' => 'lonja', 'Lj2A946T25' => 'lonja', 'Lj2C714T1' => 'lonja', 'Lj2C966T3' => 'lonja', 'Lj2C966T4' => 'lonja', 'Lj4g0002979' => 'lja', 'Lsat_1_v5_gn_5_30901' => 'lsa', 'Lsat_1_v5_gn_5_31100' => 'lsa', 'Lsat_1_v5_gn_5_38600' => 'lsa', 'Lsat_1_v5_gn_6_92061' => 'lsa', 'Manes.05G071301' => 'mes', 'MD02G1008700' => 'mdo', 'MD02G1008900' => 'mdo', 'MD03G1256400' => 'mdo', 'MD04G1180900' => 'mdo', 'MD04G1181000' => 'mdo', 'MD04G1181200' => 'mdo', 'MD05G1244200' => 'mdo', 'MD05G1324200' => 'mdo', 'MD09G1201600' => 'mdo', 'MD10G1000600' => 'mdo', 'MD14G1026900' => 'mdo', 'MD14G1187900' => 'mdo', 'MD15G1017800' => 'mdo', 'MD15G1018100' => 'mdo', 'Medtr4g124160' => 'mtr', 'Migut.L01260' => 'egut', 'Nitab4.5_0000008g0440' => 'nta', 'Nitab4.5_0000207g0170' => 'nta', 'Nitab4.5_0007671g0030' => 'nta', 'Nitab4.5_0010853g0020' => 'nta', 'Oeu057656.1' => 'oeu', 'PGSC0003DMG400005638' => 'stu', 'PGSC0003DMG400005639' => 'stu', 'Phvul.009G222800' => 'pvu', 'Potri.009G132400' => 'ptr', 'Potri.009G163001' => 'ptr', 'Potri.011G000700' => 'ptr', 'Potri.011G004800' => 'ptr', 'Prupe.1G509300' => 'ppe', 'Prupe.1G509700' => 'ppe', 'Prupe.1G510400' => 'ppe', 'Prupe.1G510700' => 'ppe', 'Prupe.1G512600' => 'ppe', 'Prupe.2G073200' => 'ppe', 'Prupe.3G059500' => 'ppe', 'Prupe.3G059600' => 'ppe', 'Prupe.3G246100' => 'ppe', 'Prupe.3G265100' => 'ppe', 'Prupe.4G034700' => 'ppe', 'Prupe.4G052100' => 'ppe', 'Prupe.4G053600' => 'ppe', 'Prupe.5G068800' => 'ppe', 'Prupe.5G070600' => 'ppe', 'Prupe.6G075400' => 'ppe', 'Prupe.6G075500' => 'ppe', 'Prupe.6G076400' => 'ppe', 'Prupe.8G110700' => 'ppe', 'Psat4g020960' => 'psa', 'PSO135G0788' => 'pso', 'PSO210G6463' => 'pso', 'PSO384G0370' => 'pso', 'PSO386G0056' => 'pso', 'QL01p006048' => 'qlo', 'QL02p054283' => 'qlo', 'QL05p008000' => 'qlo', 'QL05p008212' => 'qlo', 'QL05p008950' => 'qlo', 'QL05p009042' => 'qlo', 'QL05p009518' => 'qlo', 'QL05p012589' => 'qlo', 'QL05p012608' => 'qlo', 'QL05p012650' => 'qlo', 'QL05p012667' => 'qlo', 'QL05p014501' => 'qlo', 'QL05p052800' => 'qlo', 'QL05p065010' => 'qlo', 'QL05p074156' => 'qlo', 'QL05p074160' => 'qlo', 'QL05p074174' => 'qlo', 'QL05p074178' => 'qlo', 'QL05p074214' => 'qlo', 'QL06p001050' => 'qlo', 'QL06p001056' => 'qlo', 'QL06p006093' => 'qlo', 'QL06p006111' => 'qlo', 'QL07p019784' => 'qlo', 'QL07p019801' => 'qlo', 'QL07p036110' => 'qlo', 'QL07p036134' => 'qlo', 'QL07p036147' => 'qlo', 'QL07p036156' => 'qlo', 'QL07p036300' => 'qlo', 'QL07p036320' => 'qlo', 'QL08p014547' => 'qlo', 'QL08p014551' => 'qlo', 'QL08p043319' => 'qlo', 'QL08p043324' => 'qlo', 'QL11p009094' => 'qlo', 'RcHm_v2.0_Chr1g0380481' => 'rch', 'RcHm_v2.0_Chr2g0089331' => 'rch', 'RcHm_v2.0_Chr2g0123691' => 'rch', 'RcHm_v2.0_Chr2g0151111' => 'rch', 'RcHm_v2.0_Chr2g0163011' => 'rch', 'RcHm_v2.0_Chr2g0163051' => 'rch', 'RcHm_v2.0_Chr2g0164671' => 'rch', 'RcHm_v2.0_Chr2g0164681' => 'rch', 'RcHm_v2.0_Chr2g0164721' => 'rch', 'RcHm_v2.0_Chr3g0449911' => 'rch', 'RcHm_v2.0_Chr3g0450211' => 'rch', 'RcHm_v2.0_Chr3g0457271' => 'rch', 'RcHm_v2.0_Chr5g0018111' => 'rch', 'RcHm_v2.0_Chr5g0021011' => 'rch', 'RcHm_v2.0_Chr5g0081171' => 'rch', 'RcHm_v2.0_Chr5g0081211' => 'rch', 'RcHm_v2.0_Chr6g0275871' => 'rch', 'RcHm_v2.0_Chr6g0276071' => 'rch', 'RcHm_v2.0_Chr6g0285591' => 'rch', 'RcHm_v2.0_Chr6g0291931' => 'rch', 'RcHm_v2.0_Chr6g0292091' => 'rch', 'RcHm_v2.0_Chr6g0292271' => 'rch', 'RcHm_v2.0_Chr7g0221261' => 'rch', 'Rhsim08G0219900' => 'rsi', 'Rhsim08G0220200' => 'rsi', 'Rhsim08G0237800' => 'rsi', 'Rhsim08G0238800' => 'rsi', 'Sabra09G0102700' => 'sbr', 'Sabra09G0127200' => 'sbr', 'Sabra11G0003700' => 'sbr', 'Sabra15G0014700' => 'sbr', 'Sc19g0000590' => 'sci', 'Sc19g0001870' => 'sci', 'SGA_v2.0_scaffold1G00346' => 'sas', 'SGA_v2.0_scaffold1G00575' => 'sas', 'SGA_v2.0_scaffold1G00761' => 'sas', 'SGA_v2.0_scaffold232G43501' => 'sas', 'TAR625G1137' => 'tar', 'Thecc.03G222100' => 'tca', 'TPR.G12691' => 'tpr', 'TWI34G0727' => 'twi', 'TWI36G0117' => 'twi', 'VMungo1309G0868' => 'vmu' ), 'gf_id' => 'HOM05D001729', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001729' ), 'data_identifier' => 'HOM05D001729', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001729', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '375', 'num_species' => '42' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'Ah.07g204710' => 'amhyb', 'AUR62006001' => 'cqu', 'AUR62006002' => 'cqu', 'AUR62006003' => 'cqu', 'AUR62015641' => 'cqu', 'AUR62027174' => 'cqu', 'AUR62035623' => 'cqu', 'AUR62035624' => 'cqu', 'AUR62035625' => 'cqu', 'AUR62035626' => 'cqu', 'CAN.G1110.53' => 'can', 'CANSAT80G0415' => 'cansat', 'Ca_21364_v3' => 'car', 'COL.COLO4_30693' => 'col', 'COL.COLO4_30694' => 'col', 'COL.COLO4_30695' => 'col', 'COL.COLO4_30696' => 'col', 'COL.COLO4_34020' => 'col', 'DCAR_004585' => 'dca', 'Dinv04029' => 'din', 'Dinv34857' => 'din', 'Duzib147G0011' => 'dzi', 'Duzib170G0599' => 'dzi', 'Duzib192G1051' => 'dzi', 'FAN01G0708' => 'fan', 'FAN01G0742' => 'fan', 'FAN02G0048' => 'fan', 'FAN02G0583' => 'fan', 'FAN02G0688' => 'fan', 'FAN02G1588' => 'fan', 'FAN02G2194' => 'fan', 'FAN02G2750' => 'fan', 'FAN02G3094' => 'fan', 'FAN02G3887' => 'fan', 'FAN02G3911' => 'fan', 'FAN02G3994' => 'fan', 'FAN02G4432' => 'fan', 'FAN02G4556' => 'fan', 'FAN03G1977' => 'fan', 'FAN03G2781' => 'fan', 'FAN03G2850' => 'fan', 'FAN03G3155' => 'fan', 'FAN04G2487' => 'fan', 'FAN05G0208' => 'fan', 'FAN05G0656' => 'fan', 'FAN05G0696' => 'fan', 'FAN05G0810' => 'fan', 'FAN05G1447' => 'fan', 'FAN05G2640' => 'fan', 'FAN05G2911' => 'fan', 'FAN05G3901' => 'fan', 'FAN05G4859' => 'fan', 'FAN05G4861' => 'fan', 'FAN05G4988' => 'fan', 'FAN05G5187' => 'fan', 'FAN05G5452' => 'fan', 'FAN05G5500' => 'fan', 'FAN05G5688' => 'fan', 'FAN06G0177' => 'fan', 'FAN06G0675' => 'fan', 'FAN06G1290' => 'fan', 'FAN06G2191' => 'fan', 'FAN06G2405' => 'fan', 'FAN06G3231' => 'fan', 'FAN06G3932' => 'fan', 'FAN07G0163' => 'fan', 'FAN07G0471' => 'fan', 'FAN07G1354' => 'fan', 'FAN08G0338' => 'fan', 'FAN08G1373' => 'fan', 'FAN08G2539' => 'fan', 'FAN08G2728' => 'fan', 'FAN09G0608' => 'fan', 'FAN09G1136' => 'fan', 'FAN09G1958' => 'fan', 'FAN09G2508' => 'fan', 'FAN09G2597' => 'fan', 'FAN09G2658' => 'fan', 'FAN09G2757' => 'fan', 'FAN09G2983' => 'fan', 'FAN09G3130' => 'fan', 'FAN09G3565' => 'fan', 'FAN09G3613' => 'fan', 'FAN09G4011' => 'fan', 'FAN09G4239' => 'fan', 'FAN09G4277' => 'fan', 'FAN09G4720' => 'fan', 'FAN11G0139' => 'fan', 'FAN11G1727' => 'fan', 'FAN11G2672' => 'fan', 'FAN11G2795' => 'fan', 'FAN11G3238' => 'fan', 'FAN11G3734' => 'fan', 'FAN12G0631' => 'fan', 'FAN12G2239' => 'fan', 'FAN12G2308' => 'fan', 'FAN12G2569' => 'fan', 'FAN12G2623' => 'fan', 'FAN13G3182' => 'fan', 'FAN14G0053' => 'fan', 'FAN14G0370' => 'fan', 'FAN14G0382' => 'fan', 'FAN14G0421' => 'fan', 'FAN14G0866' => 'fan', 'FAN14G1187' => 'fan', 'FAN14G1727' => 'fan', 'FAN14G1791' => 'fan', 'FAN14G2361' => 'fan', 'FAN14G2668' => 'fan', 'FAN14G2770' => 'fan', 'FAN14G2874' => 'fan', 'FAN14G3193' => 'fan', 'FAN14G3624' => 'fan', 'FAN14G3676' => 'fan', 'FAN14G3807' => 'fan', 'FAN14G4082' => 'fan', 'FAN14G4342' => 'fan', 'FAN14G4985' => 'fan', 'FAN14G5126' => 'fan', 'FAN14G5781' => 'fan', 'FAN14G5808' => 'fan', 'FAN14G5949' => 'fan', 'FAN15G0828' => 'fan', 'FAN15G1054' => 'fan', 'FAN15G2023' => 'fan', 'FAN15G2506' => 'fan', 'FAN16G0128' => 'fan', 'FAN16G0249' => 'fan', 'FAN16G0429' => 'fan', 'FAN16G1493' => 'fan', 'FAN16G2210' => 'fan', 'FAN16G2506' => 'fan', 'FAN18G1542' => 'fan', 'FAN18G4057' => 'fan', 'FAN19G0745' => 'fan', 'FAN19G1216' => 'fan', 'FAN19G1733' => 'fan', 'FAN20G0258' => 'fan', 'FAN20G1095' => 'fan', 'FAN20G1557' => 'fan', 'FAN21G0302' => 'fan', 'FAN21G0519' => 'fan', 'FAN21G0970' => 'fan', 'FAN21G1159' => 'fan', 'FAN21G1312' => 'fan', 'FAN21G1440' => 'fan', 'FAN21G1715' => 'fan', 'FAN23G1584' => 'fan', 'FAN24G0045' => 'fan', 'FAN24G0053' => 'fan', 'FAN24G1500' => 'fan', 'FAN24G1817' => 'fan', 'FAN24G2147' => 'fan', 'FAN24G2236' => 'fan', 'FAN24G2446' => 'fan', 'FAN24G2684' => 'fan', 'FAN25G0187' => 'fan', 'FAN25G0505' => 'fan', 'FAN25G0589' => 'fan', 'FAN25G3663' => 'fan', 'FAN26G1025' => 'fan', 'FAN26G2860' => 'fan', 'FAN27G1329' => 'fan', 'FAN27G3392' => 'fan', 'FvH4_1g02011' => 'fve', 'FvH4_1g06511' => 'fve', 'FvH4_2g19900' => 'fve', 'FvH4_2g19920' => 'fve', 'FvH4_2g24261' => 'fve', 'FvH4_2g24270' => 'fve', 'FvH4_2g24631' => 'fve', 'FvH4_2g30622' => 'fve', 'FvH4_3g12920' => 'fve', 'FvH4_3g30171' => 'fve', 'FvH4_3g35490' => 'fve', 'FvH4_3g43682' => 'fve', 'FvH4_3g43730' => 'fve', 'FvH4_3g43732' => 'fve', 'FvH4_3g43751' => 'fve', 'FvH4_3g43752' => 'fve', 'FvH4_3g43770' => 'fve', 'FvH4_3g44471' => 'fve', 'FvH4_3g44510' => 'fve', 'FvH4_3g44582' => 'fve', 'FvH4_4g16921' => 'fve', 'FvH4_4g17121' => 'fve', 'FvH4_4g17782' => 'fve', 'FvH4_4g17783' => 'fve', 'FvH4_4g18120' => 'fve', 'FvH4_4g31310' => 'fve', 'FvH4_4g35052' => 'fve', 'FvH4_5g30862' => 'fve', 'FvH4_6g01541' => 'fve', 'FvH4_6g02021' => 'fve', 'FvH4_6g02041' => 'fve', 'FvH4_6g02071' => 'fve', 'FvH4_6g02171' => 'fve', 'FvH4_6g03181' => 'fve', 'FvH4_6g03182' => 'fve', 'FvH4_6g03221' => 'fve', 'FvH4_6g03380' => 'fve', 'FvH4_6g05201' => 'fve', 'FvH4_6g05203' => 'fve', 'FvH4_6g20231' => 'fve', 'FvH4_6g31981' => 'fve', 'FvH4_6g32061' => 'fve', 'FvH4_6g37041' => 'fve', 'FvH4_6g37932' => 'fve', 'FvH4_6g38731' => 'fve', 'FvH4_6g39370' => 'fve', 'FvH4_6g39371' => 'fve', 'FvH4_6g40891' => 'fve', 'FvH4_6g40892' => 'fve', 'FvH4_6g43143' => 'fve', 'FvH4_6g45251' => 'fve', 'FvH4_6g45260' => 'fve', 'FvH4_6g45291' => 'fve', 'FvH4_6g45890' => 'fve', 'FvH4_6g46240' => 'fve', 'FvH4_6g46241' => 'fve', 'FvH4_6g46242' => 'fve', 'FvH4_6g46260' => 'fve', 'FvH4_6g46280' => 'fve', 'FvH4_6g46380' => 'fve', 'FvH4_7g12841' => 'fve', 'FvH4_7g31431' => 'fve', 'Glyma.09G075900' => 'gma', 'Gohir.A09G096401' => 'ghi', 'Gohir.D09G096101' => 'ghi', 'Gorai.006G112800' => 'gra', 'HanXRQChr04g0121411' => 'han', 'Hund15878' => 'sun', 'Lj2A1107G68' => 'lonja', 'Lj2A630G63' => 'lonja', 'Lj2A946T25' => 'lonja', 'Lj2C714T1' => 'lonja', 'Lj2C966T3' => 'lonja', 'Lj2C966T4' => 'lonja', 'Lj4g0002979' => 'lja', 'Lsat_1_v5_gn_5_30901' => 'lsa', 'Lsat_1_v5_gn_5_31100' => 'lsa', 'Lsat_1_v5_gn_5_38600' => 'lsa', 'Lsat_1_v5_gn_6_92061' => 'lsa', 'Manes.05G071301' => 'mes', 'MD02G1008700' => 'mdo', 'MD02G1008900' => 'mdo', 'MD03G1256400' => 'mdo', 'MD04G1180900' => 'mdo', 'MD04G1181000' => 'mdo', 'MD04G1181200' => 'mdo', 'MD05G1244200' => 'mdo', 'MD05G1324200' => 'mdo', 'MD09G1201600' => 'mdo', 'MD10G1000600' => 'mdo', 'MD14G1026900' => 'mdo', 'MD14G1187900' => 'mdo', 'MD15G1017800' => 'mdo', 'MD15G1018100' => 'mdo', 'Medtr4g124160' => 'mtr', 'Migut.L01260' => 'egut', 'Nitab4.5_0000008g0440' => 'nta', 'Nitab4.5_0000207g0170' => 'nta', 'Nitab4.5_0007671g0030' => 'nta', 'Nitab4.5_0010853g0020' => 'nta', 'Oeu057656.1' => 'oeu', 'PGSC0003DMG400005638' => 'stu', 'PGSC0003DMG400005639' => 'stu', 'Phvul.009G222800' => 'pvu', 'Potri.009G132400' => 'ptr', 'Potri.009G163001' => 'ptr', 'Potri.011G000700' => 'ptr', 'Potri.011G004800' => 'ptr', 'Prupe.1G509300' => 'ppe', 'Prupe.1G509700' => 'ppe', 'Prupe.1G510400' => 'ppe', 'Prupe.1G510700' => 'ppe', 'Prupe.1G512600' => 'ppe', 'Prupe.2G073200' => 'ppe', 'Prupe.3G059500' => 'ppe', 'Prupe.3G059600' => 'ppe', 'Prupe.3G246100' => 'ppe', 'Prupe.3G265100' => 'ppe', 'Prupe.4G034700' => 'ppe', 'Prupe.4G052100' => 'ppe', 'Prupe.4G053600' => 'ppe', 'Prupe.5G068800' => 'ppe', 'Prupe.5G070600' => 'ppe', 'Prupe.6G075400' => 'ppe', 'Prupe.6G075500' => 'ppe', 'Prupe.6G076400' => 'ppe', 'Prupe.8G110700' => 'ppe', 'Psat4g020960' => 'psa', 'PSO135G0788' => 'pso', 'PSO210G6463' => 'pso', 'PSO384G0370' => 'pso', 'PSO386G0056' => 'pso', 'QL01p006048' => 'qlo', 'QL02p054283' => 'qlo', 'QL05p008000' => 'qlo', 'QL05p008212' => 'qlo', 'QL05p008950' => 'qlo', 'QL05p009042' => 'qlo', 'QL05p009518' => 'qlo', 'QL05p012589' => 'qlo', 'QL05p012608' => 'qlo', 'QL05p012650' => 'qlo', 'QL05p012667' => 'qlo', 'QL05p014501' => 'qlo', 'QL05p052800' => 'qlo', 'QL05p065010' => 'qlo', 'QL05p074156' => 'qlo', 'QL05p074160' => 'qlo', 'QL05p074174' => 'qlo', 'QL05p074178' => 'qlo', 'QL05p074214' => 'qlo', 'QL06p001050' => 'qlo', 'QL06p001056' => 'qlo', 'QL06p006093' => 'qlo', 'QL06p006111' => 'qlo', 'QL07p019784' => 'qlo', 'QL07p019801' => 'qlo', 'QL07p036110' => 'qlo', 'QL07p036134' => 'qlo', 'QL07p036147' => 'qlo', 'QL07p036156' => 'qlo', 'QL07p036300' => 'qlo', 'QL07p036320' => 'qlo', 'QL08p014547' => 'qlo', 'QL08p014551' => 'qlo', 'QL08p043319' => 'qlo', 'QL08p043324' => 'qlo', 'QL11p009094' => 'qlo', 'RcHm_v2.0_Chr1g0380481' => 'rch', 'RcHm_v2.0_Chr2g0089331' => 'rch', 'RcHm_v2.0_Chr2g0123691' => 'rch', 'RcHm_v2.0_Chr2g0151111' => 'rch', 'RcHm_v2.0_Chr2g0163011' => 'rch', 'RcHm_v2.0_Chr2g0163051' => 'rch', 'RcHm_v2.0_Chr2g0164671' => 'rch', 'RcHm_v2.0_Chr2g0164681' => 'rch', 'RcHm_v2.0_Chr2g0164721' => 'rch', 'RcHm_v2.0_Chr3g0449911' => 'rch', 'RcHm_v2.0_Chr3g0450211' => 'rch', 'RcHm_v2.0_Chr3g0457271' => 'rch', 'RcHm_v2.0_Chr5g0018111' => 'rch', 'RcHm_v2.0_Chr5g0021011' => 'rch', 'RcHm_v2.0_Chr5g0081171' => 'rch', 'RcHm_v2.0_Chr5g0081211' => 'rch', 'RcHm_v2.0_Chr6g0275871' => 'rch', 'RcHm_v2.0_Chr6g0276071' => 'rch', 'RcHm_v2.0_Chr6g0285591' => 'rch', 'RcHm_v2.0_Chr6g0291931' => 'rch', 'RcHm_v2.0_Chr6g0292091' => 'rch', 'RcHm_v2.0_Chr6g0292271' => 'rch', 'RcHm_v2.0_Chr7g0221261' => 'rch', 'Rhsim08G0219900' => 'rsi', 'Rhsim08G0220200' => 'rsi', 'Rhsim08G0237800' => 'rsi', 'Rhsim08G0238800' => 'rsi', 'Sabra09G0102700' => 'sbr', 'Sabra09G0127200' => 'sbr', 'Sabra11G0003700' => 'sbr', 'Sabra15G0014700' => 'sbr', 'Sc19g0000590' => 'sci', 'Sc19g0001870' => 'sci', 'SGA_v2.0_scaffold1G00346' => 'sas', 'SGA_v2.0_scaffold1G00575' => 'sas', 'SGA_v2.0_scaffold1G00761' => 'sas', 'SGA_v2.0_scaffold232G43501' => 'sas', 'TAR625G1137' => 'tar', 'Thecc.03G222100' => 'tca', 'TPR.G12691' => 'tpr', 'TWI34G0727' => 'twi', 'TWI36G0117' => 'twi', 'VMungo1309G0868' => 'vmu' ) $gf_id = 'HOM05D001729' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001729' ) $data_identifier = 'HOM05D001729' $data_type = 'gf_id' $species_gene_counts = array( 'amhyb' => (int) 1, 'cqu' => (int) 9, 'can' => (int) 1, 'cansat' => (int) 1, 'car' => (int) 1, 'col' => (int) 5, 'dca' => (int) 1, 'din' => (int) 2, 'dzi' => (int) 3, 'fan' => (int) 140, 'fve' => (int) 62, 'gma' => (int) 1, 'ghi' => (int) 2, 'gra' => (int) 1, 'han' => (int) 1, 'sun' => (int) 1, 'lonja' => (int) 6, 'lja' => (int) 1, 'lsa' => (int) 4, 'mes' => (int) 1, 'mdo' => (int) 14, 'mtr' => (int) 1, 'egut' => (int) 1, 'nta' => (int) 4, 'oeu' => (int) 1, 'stu' => (int) 2, 'pvu' => (int) 1, 'ptr' => (int) 4, 'ppe' => (int) 19, 'psa' => (int) 1, 'pso' => (int) 4, 'qlo' => (int) 36, 'rch' => (int) 23, 'rsi' => (int) 4, 'sbr' => (int) 4, 'sci' => (int) 2, 'sas' => (int) 4, 'tar' => (int) 1, 'tca' => (int) 1, 'tpr' => (int) 1, 'twi' => (int) 2, 'vmu' => (int) 1 ) $gf_gene_species = 'vmu' $gf_gene_id = 'VMungo1309G0868' $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' => 'HOM05D001729', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '375', 'num_species' => '42' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'Ah.07g204710' => 'amhyb', 'AUR62006001' => 'cqu', 'AUR62006002' => 'cqu', 'AUR62006003' => 'cqu', 'AUR62015641' => 'cqu', 'AUR62027174' => 'cqu', 'AUR62035623' => 'cqu', 'AUR62035624' => 'cqu', 'AUR62035625' => 'cqu', 'AUR62035626' => 'cqu', 'CAN.G1110.53' => 'can', 'CANSAT80G0415' => 'cansat', 'Ca_21364_v3' => 'car', 'COL.COLO4_30693' => 'col', 'COL.COLO4_30694' => 'col', 'COL.COLO4_30695' => 'col', 'COL.COLO4_30696' => 'col', 'COL.COLO4_34020' => 'col', 'DCAR_004585' => 'dca', 'Dinv04029' => 'din', 'Dinv34857' => 'din', 'Duzib147G0011' => 'dzi', 'Duzib170G0599' => 'dzi', 'Duzib192G1051' => 'dzi', 'FAN01G0708' => 'fan', 'FAN01G0742' => 'fan', 'FAN02G0048' => 'fan', 'FAN02G0583' => 'fan', 'FAN02G0688' => 'fan', 'FAN02G1588' => 'fan', 'FAN02G2194' => 'fan', 'FAN02G2750' => 'fan', 'FAN02G3094' => 'fan', 'FAN02G3887' => 'fan', 'FAN02G3911' => 'fan', 'FAN02G3994' => 'fan', 'FAN02G4432' => 'fan', 'FAN02G4556' => 'fan', 'FAN03G1977' => 'fan', 'FAN03G2781' => 'fan', 'FAN03G2850' => 'fan', 'FAN03G3155' => 'fan', 'FAN04G2487' => 'fan', 'FAN05G0208' => 'fan', 'FAN05G0656' => 'fan', 'FAN05G0696' => 'fan', 'FAN05G0810' => 'fan', 'FAN05G1447' => 'fan', 'FAN05G2640' => 'fan', 'FAN05G2911' => 'fan', 'FAN05G3901' => 'fan', 'FAN05G4859' => 'fan', 'FAN05G4861' => 'fan', 'FAN05G4988' => 'fan', 'FAN05G5187' => 'fan', 'FAN05G5452' => 'fan', 'FAN05G5500' => 'fan', 'FAN05G5688' => 'fan', 'FAN06G0177' => 'fan', 'FAN06G0675' => 'fan', 'FAN06G1290' => 'fan', 'FAN06G2191' => 'fan', 'FAN06G2405' => 'fan', 'FAN06G3231' => 'fan', 'FAN06G3932' => 'fan', 'FAN07G0163' => 'fan', 'FAN07G0471' => 'fan', 'FAN07G1354' => 'fan', 'FAN08G0338' => 'fan', 'FAN08G1373' => 'fan', 'FAN08G2539' => 'fan', 'FAN08G2728' => 'fan', 'FAN09G0608' => 'fan', 'FAN09G1136' => 'fan', 'FAN09G1958' => 'fan', 'FAN09G2508' => 'fan', 'FAN09G2597' => 'fan', 'FAN09G2658' => 'fan', 'FAN09G2757' => 'fan', 'FAN09G2983' => 'fan', 'FAN09G3130' => 'fan', 'FAN09G3565' => 'fan', 'FAN09G3613' => 'fan', 'FAN09G4011' => 'fan', 'FAN09G4239' => 'fan', 'FAN09G4277' => 'fan', 'FAN09G4720' => 'fan', 'FAN11G0139' => 'fan', 'FAN11G1727' => 'fan', 'FAN11G2672' => 'fan', 'FAN11G2795' => 'fan', 'FAN11G3238' => 'fan', 'FAN11G3734' => 'fan', 'FAN12G0631' => 'fan', 'FAN12G2239' => 'fan', 'FAN12G2308' => 'fan', 'FAN12G2569' => 'fan', 'FAN12G2623' => 'fan', 'FAN13G3182' => 'fan', 'FAN14G0053' => 'fan', 'FAN14G0370' => 'fan', 'FAN14G0382' => 'fan', 'FAN14G0421' => 'fan', 'FAN14G0866' => 'fan', 'FAN14G1187' => 'fan', 'FAN14G1727' => 'fan', 'FAN14G1791' => 'fan', 'FAN14G2361' => 'fan', 'FAN14G2668' => 'fan', 'FAN14G2770' => 'fan', 'FAN14G2874' => 'fan', 'FAN14G3193' => 'fan', 'FAN14G3624' => 'fan', 'FAN14G3676' => 'fan', 'FAN14G3807' => 'fan', 'FAN14G4082' => 'fan', 'FAN14G4342' => 'fan', 'FAN14G4985' => 'fan', 'FAN14G5126' => 'fan', 'FAN14G5781' => 'fan', 'FAN14G5808' => 'fan', 'FAN14G5949' => 'fan', 'FAN15G0828' => 'fan', 'FAN15G1054' => 'fan', 'FAN15G2023' => 'fan', 'FAN15G2506' => 'fan', 'FAN16G0128' => 'fan', 'FAN16G0249' => 'fan', 'FAN16G0429' => 'fan', 'FAN16G1493' => 'fan', 'FAN16G2210' => 'fan', 'FAN16G2506' => 'fan', 'FAN18G1542' => 'fan', 'FAN18G4057' => 'fan', 'FAN19G0745' => 'fan', 'FAN19G1216' => 'fan', 'FAN19G1733' => 'fan', 'FAN20G0258' => 'fan', 'FAN20G1095' => 'fan', 'FAN20G1557' => 'fan', 'FAN21G0302' => 'fan', 'FAN21G0519' => 'fan', 'FAN21G0970' => 'fan', 'FAN21G1159' => 'fan', 'FAN21G1312' => 'fan', 'FAN21G1440' => 'fan', 'FAN21G1715' => 'fan', 'FAN23G1584' => 'fan', 'FAN24G0045' => 'fan', 'FAN24G0053' => 'fan', 'FAN24G1500' => 'fan', 'FAN24G1817' => 'fan', 'FAN24G2147' => 'fan', 'FAN24G2236' => 'fan', 'FAN24G2446' => 'fan', 'FAN24G2684' => 'fan', 'FAN25G0187' => 'fan', 'FAN25G0505' => 'fan', 'FAN25G0589' => 'fan', 'FAN25G3663' => 'fan', 'FAN26G1025' => 'fan', 'FAN26G2860' => 'fan', 'FAN27G1329' => 'fan', 'FAN27G3392' => 'fan', 'FvH4_1g02011' => 'fve', 'FvH4_1g06511' => 'fve', 'FvH4_2g19900' => 'fve', 'FvH4_2g19920' => 'fve', 'FvH4_2g24261' => 'fve', 'FvH4_2g24270' => 'fve', 'FvH4_2g24631' => 'fve', 'FvH4_2g30622' => 'fve', 'FvH4_3g12920' => 'fve', 'FvH4_3g30171' => 'fve', 'FvH4_3g35490' => 'fve', 'FvH4_3g43682' => 'fve', 'FvH4_3g43730' => 'fve', 'FvH4_3g43732' => 'fve', 'FvH4_3g43751' => 'fve', 'FvH4_3g43752' => 'fve', 'FvH4_3g43770' => 'fve', 'FvH4_3g44471' => 'fve', 'FvH4_3g44510' => 'fve', 'FvH4_3g44582' => 'fve', 'FvH4_4g16921' => 'fve', 'FvH4_4g17121' => 'fve', 'FvH4_4g17782' => 'fve', 'FvH4_4g17783' => 'fve', 'FvH4_4g18120' => 'fve', 'FvH4_4g31310' => 'fve', 'FvH4_4g35052' => 'fve', 'FvH4_5g30862' => 'fve', 'FvH4_6g01541' => 'fve', 'FvH4_6g02021' => 'fve', 'FvH4_6g02041' => 'fve', 'FvH4_6g02071' => 'fve', 'FvH4_6g02171' => 'fve', 'FvH4_6g03181' => 'fve', 'FvH4_6g03182' => 'fve', 'FvH4_6g03221' => 'fve', 'FvH4_6g03380' => 'fve', 'FvH4_6g05201' => 'fve', 'FvH4_6g05203' => 'fve', 'FvH4_6g20231' => 'fve', 'FvH4_6g31981' => 'fve', 'FvH4_6g32061' => 'fve', 'FvH4_6g37041' => 'fve', 'FvH4_6g37932' => 'fve', 'FvH4_6g38731' => 'fve', 'FvH4_6g39370' => 'fve', 'FvH4_6g39371' => 'fve', 'FvH4_6g40891' => 'fve', 'FvH4_6g40892' => 'fve', 'FvH4_6g43143' => 'fve', 'FvH4_6g45251' => 'fve', 'FvH4_6g45260' => 'fve', 'FvH4_6g45291' => 'fve', 'FvH4_6g45890' => 'fve', 'FvH4_6g46240' => 'fve', 'FvH4_6g46241' => 'fve', 'FvH4_6g46242' => 'fve', 'FvH4_6g46260' => 'fve', 'FvH4_6g46280' => 'fve', 'FvH4_6g46380' => 'fve', 'FvH4_7g12841' => 'fve', 'FvH4_7g31431' => 'fve', 'Glyma.09G075900' => 'gma', 'Gohir.A09G096401' => 'ghi', 'Gohir.D09G096101' => 'ghi', 'Gorai.006G112800' => 'gra', 'HanXRQChr04g0121411' => 'han', 'Hund15878' => 'sun', 'Lj2A1107G68' => 'lonja', 'Lj2A630G63' => 'lonja', 'Lj2A946T25' => 'lonja', 'Lj2C714T1' => 'lonja', 'Lj2C966T3' => 'lonja', 'Lj2C966T4' => 'lonja', 'Lj4g0002979' => 'lja', 'Lsat_1_v5_gn_5_30901' => 'lsa', 'Lsat_1_v5_gn_5_31100' => 'lsa', 'Lsat_1_v5_gn_5_38600' => 'lsa', 'Lsat_1_v5_gn_6_92061' => 'lsa', 'Manes.05G071301' => 'mes', 'MD02G1008700' => 'mdo', 'MD02G1008900' => 'mdo', 'MD03G1256400' => 'mdo', 'MD04G1180900' => 'mdo', 'MD04G1181000' => 'mdo', 'MD04G1181200' => 'mdo', 'MD05G1244200' => 'mdo', 'MD05G1324200' => 'mdo', 'MD09G1201600' => 'mdo', 'MD10G1000600' => 'mdo', 'MD14G1026900' => 'mdo', 'MD14G1187900' => 'mdo', 'MD15G1017800' => 'mdo', 'MD15G1018100' => 'mdo', 'Medtr4g124160' => 'mtr', 'Migut.L01260' => 'egut', 'Nitab4.5_0000008g0440' => 'nta', 'Nitab4.5_0000207g0170' => 'nta', 'Nitab4.5_0007671g0030' => 'nta', 'Nitab4.5_0010853g0020' => 'nta', 'Oeu057656.1' => 'oeu', 'PGSC0003DMG400005638' => 'stu', 'PGSC0003DMG400005639' => 'stu', 'Phvul.009G222800' => 'pvu', 'Potri.009G132400' => 'ptr', 'Potri.009G163001' => 'ptr', 'Potri.011G000700' => 'ptr', 'Potri.011G004800' => 'ptr', 'Prupe.1G509300' => 'ppe', 'Prupe.1G509700' => 'ppe', 'Prupe.1G510400' => 'ppe', 'Prupe.1G510700' => 'ppe', 'Prupe.1G512600' => 'ppe', 'Prupe.2G073200' => 'ppe', 'Prupe.3G059500' => 'ppe', 'Prupe.3G059600' => 'ppe', 'Prupe.3G246100' => 'ppe', 'Prupe.3G265100' => 'ppe', 'Prupe.4G034700' => 'ppe', 'Prupe.4G052100' => 'ppe', 'Prupe.4G053600' => 'ppe', 'Prupe.5G068800' => 'ppe', 'Prupe.5G070600' => 'ppe', 'Prupe.6G075400' => 'ppe', 'Prupe.6G075500' => 'ppe', 'Prupe.6G076400' => 'ppe', 'Prupe.8G110700' => 'ppe', 'Psat4g020960' => 'psa', 'PSO135G0788' => 'pso', 'PSO210G6463' => 'pso', 'PSO384G0370' => 'pso', 'PSO386G0056' => 'pso', 'QL01p006048' => 'qlo', 'QL02p054283' => 'qlo', 'QL05p008000' => 'qlo', 'QL05p008212' => 'qlo', 'QL05p008950' => 'qlo', 'QL05p009042' => 'qlo', 'QL05p009518' => 'qlo', 'QL05p012589' => 'qlo', 'QL05p012608' => 'qlo', 'QL05p012650' => 'qlo', 'QL05p012667' => 'qlo', 'QL05p014501' => 'qlo', 'QL05p052800' => 'qlo', 'QL05p065010' => 'qlo', 'QL05p074156' => 'qlo', 'QL05p074160' => 'qlo', 'QL05p074174' => 'qlo', 'QL05p074178' => 'qlo', 'QL05p074214' => 'qlo', 'QL06p001050' => 'qlo', 'QL06p001056' => 'qlo', 'QL06p006093' => 'qlo', 'QL06p006111' => 'qlo', 'QL07p019784' => 'qlo', 'QL07p019801' => 'qlo', 'QL07p036110' => 'qlo', 'QL07p036134' => 'qlo', 'QL07p036147' => 'qlo', 'QL07p036156' => 'qlo', 'QL07p036300' => 'qlo', 'QL07p036320' => 'qlo', 'QL08p014547' => 'qlo', 'QL08p014551' => 'qlo', 'QL08p043319' => 'qlo', 'QL08p043324' => 'qlo', 'QL11p009094' => 'qlo', 'RcHm_v2.0_Chr1g0380481' => 'rch', 'RcHm_v2.0_Chr2g0089331' => 'rch', 'RcHm_v2.0_Chr2g0123691' => 'rch', 'RcHm_v2.0_Chr2g0151111' => 'rch', 'RcHm_v2.0_Chr2g0163011' => 'rch', 'RcHm_v2.0_Chr2g0163051' => 'rch', 'RcHm_v2.0_Chr2g0164671' => 'rch', 'RcHm_v2.0_Chr2g0164681' => 'rch', 'RcHm_v2.0_Chr2g0164721' => 'rch', 'RcHm_v2.0_Chr3g0449911' => 'rch', 'RcHm_v2.0_Chr3g0450211' => 'rch', 'RcHm_v2.0_Chr3g0457271' => 'rch', 'RcHm_v2.0_Chr5g0018111' => 'rch', 'RcHm_v2.0_Chr5g0021011' => 'rch', 'RcHm_v2.0_Chr5g0081171' => 'rch', 'RcHm_v2.0_Chr5g0081211' => 'rch', 'RcHm_v2.0_Chr6g0275871' => 'rch', 'RcHm_v2.0_Chr6g0276071' => 'rch', 'RcHm_v2.0_Chr6g0285591' => 'rch', 'RcHm_v2.0_Chr6g0291931' => 'rch', 'RcHm_v2.0_Chr6g0292091' => 'rch', 'RcHm_v2.0_Chr6g0292271' => 'rch', 'RcHm_v2.0_Chr7g0221261' => 'rch', 'Rhsim08G0219900' => 'rsi', 'Rhsim08G0220200' => 'rsi', 'Rhsim08G0237800' => 'rsi', 'Rhsim08G0238800' => 'rsi', 'Sabra09G0102700' => 'sbr', 'Sabra09G0127200' => 'sbr', 'Sabra11G0003700' => 'sbr', 'Sabra15G0014700' => 'sbr', 'Sc19g0000590' => 'sci', 'Sc19g0001870' => 'sci', 'SGA_v2.0_scaffold1G00346' => 'sas', 'SGA_v2.0_scaffold1G00575' => 'sas', 'SGA_v2.0_scaffold1G00761' => 'sas', 'SGA_v2.0_scaffold232G43501' => 'sas', 'TAR625G1137' => 'tar', 'Thecc.03G222100' => 'tca', 'TPR.G12691' => 'tpr', 'TWI34G0727' => 'twi', 'TWI36G0117' => 'twi', 'VMungo1309G0868' => 'vmu' ), 'gf_id' => 'HOM05D001729', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001729' ), 'data_identifier' => 'HOM05D001729', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001729', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '375', 'num_species' => '42' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'Ah.07g204710' => 'amhyb', 'AUR62006001' => 'cqu', 'AUR62006002' => 'cqu', 'AUR62006003' => 'cqu', 'AUR62015641' => 'cqu', 'AUR62027174' => 'cqu', 'AUR62035623' => 'cqu', 'AUR62035624' => 'cqu', 'AUR62035625' => 'cqu', 'AUR62035626' => 'cqu', 'CAN.G1110.53' => 'can', 'CANSAT80G0415' => 'cansat', 'Ca_21364_v3' => 'car', 'COL.COLO4_30693' => 'col', 'COL.COLO4_30694' => 'col', 'COL.COLO4_30695' => 'col', 'COL.COLO4_30696' => 'col', 'COL.COLO4_34020' => 'col', 'DCAR_004585' => 'dca', 'Dinv04029' => 'din', 'Dinv34857' => 'din', 'Duzib147G0011' => 'dzi', 'Duzib170G0599' => 'dzi', 'Duzib192G1051' => 'dzi', 'FAN01G0708' => 'fan', 'FAN01G0742' => 'fan', 'FAN02G0048' => 'fan', 'FAN02G0583' => 'fan', 'FAN02G0688' => 'fan', 'FAN02G1588' => 'fan', 'FAN02G2194' => 'fan', 'FAN02G2750' => 'fan', 'FAN02G3094' => 'fan', 'FAN02G3887' => 'fan', 'FAN02G3911' => 'fan', 'FAN02G3994' => 'fan', 'FAN02G4432' => 'fan', 'FAN02G4556' => 'fan', 'FAN03G1977' => 'fan', 'FAN03G2781' => 'fan', 'FAN03G2850' => 'fan', 'FAN03G3155' => 'fan', 'FAN04G2487' => 'fan', 'FAN05G0208' => 'fan', 'FAN05G0656' => 'fan', 'FAN05G0696' => 'fan', 'FAN05G0810' => 'fan', 'FAN05G1447' => 'fan', 'FAN05G2640' => 'fan', 'FAN05G2911' => 'fan', 'FAN05G3901' => 'fan', 'FAN05G4859' => 'fan', 'FAN05G4861' => 'fan', 'FAN05G4988' => 'fan', 'FAN05G5187' => 'fan', 'FAN05G5452' => 'fan', 'FAN05G5500' => 'fan', 'FAN05G5688' => 'fan', 'FAN06G0177' => 'fan', 'FAN06G0675' => 'fan', 'FAN06G1290' => 'fan', 'FAN06G2191' => 'fan', 'FAN06G2405' => 'fan', 'FAN06G3231' => 'fan', 'FAN06G3932' => 'fan', 'FAN07G0163' => 'fan', 'FAN07G0471' => 'fan', 'FAN07G1354' => 'fan', 'FAN08G0338' => 'fan', 'FAN08G1373' => 'fan', 'FAN08G2539' => 'fan', 'FAN08G2728' => 'fan', 'FAN09G0608' => 'fan', 'FAN09G1136' => 'fan', 'FAN09G1958' => 'fan', 'FAN09G2508' => 'fan', 'FAN09G2597' => 'fan', 'FAN09G2658' => 'fan', 'FAN09G2757' => 'fan', 'FAN09G2983' => 'fan', 'FAN09G3130' => 'fan', 'FAN09G3565' => 'fan', 'FAN09G3613' => 'fan', 'FAN09G4011' => 'fan', 'FAN09G4239' => 'fan', 'FAN09G4277' => 'fan', 'FAN09G4720' => 'fan', 'FAN11G0139' => 'fan', 'FAN11G1727' => 'fan', 'FAN11G2672' => 'fan', 'FAN11G2795' => 'fan', 'FAN11G3238' => 'fan', 'FAN11G3734' => 'fan', 'FAN12G0631' => 'fan', 'FAN12G2239' => 'fan', 'FAN12G2308' => 'fan', 'FAN12G2569' => 'fan', 'FAN12G2623' => 'fan', 'FAN13G3182' => 'fan', 'FAN14G0053' => 'fan', 'FAN14G0370' => 'fan', 'FAN14G0382' => 'fan', 'FAN14G0421' => 'fan', 'FAN14G0866' => 'fan', 'FAN14G1187' => 'fan', 'FAN14G1727' => 'fan', 'FAN14G1791' => 'fan', 'FAN14G2361' => 'fan', 'FAN14G2668' => 'fan', 'FAN14G2770' => 'fan', 'FAN14G2874' => 'fan', 'FAN14G3193' => 'fan', 'FAN14G3624' => 'fan', 'FAN14G3676' => 'fan', 'FAN14G3807' => 'fan', 'FAN14G4082' => 'fan', 'FAN14G4342' => 'fan', 'FAN14G4985' => 'fan', 'FAN14G5126' => 'fan', 'FAN14G5781' => 'fan', 'FAN14G5808' => 'fan', 'FAN14G5949' => 'fan', 'FAN15G0828' => 'fan', 'FAN15G1054' => 'fan', 'FAN15G2023' => 'fan', 'FAN15G2506' => 'fan', 'FAN16G0128' => 'fan', 'FAN16G0249' => 'fan', 'FAN16G0429' => 'fan', 'FAN16G1493' => 'fan', 'FAN16G2210' => 'fan', 'FAN16G2506' => 'fan', 'FAN18G1542' => 'fan', 'FAN18G4057' => 'fan', 'FAN19G0745' => 'fan', 'FAN19G1216' => 'fan', 'FAN19G1733' => 'fan', 'FAN20G0258' => 'fan', 'FAN20G1095' => 'fan', 'FAN20G1557' => 'fan', 'FAN21G0302' => 'fan', 'FAN21G0519' => 'fan', 'FAN21G0970' => 'fan', 'FAN21G1159' => 'fan', 'FAN21G1312' => 'fan', 'FAN21G1440' => 'fan', 'FAN21G1715' => 'fan', 'FAN23G1584' => 'fan', 'FAN24G0045' => 'fan', 'FAN24G0053' => 'fan', 'FAN24G1500' => 'fan', 'FAN24G1817' => 'fan', 'FAN24G2147' => 'fan', 'FAN24G2236' => 'fan', 'FAN24G2446' => 'fan', 'FAN24G2684' => 'fan', 'FAN25G0187' => 'fan', 'FAN25G0505' => 'fan', 'FAN25G0589' => 'fan', 'FAN25G3663' => 'fan', 'FAN26G1025' => 'fan', 'FAN26G2860' => 'fan', 'FAN27G1329' => 'fan', 'FAN27G3392' => 'fan', 'FvH4_1g02011' => 'fve', 'FvH4_1g06511' => 'fve', 'FvH4_2g19900' => 'fve', 'FvH4_2g19920' => 'fve', 'FvH4_2g24261' => 'fve', 'FvH4_2g24270' => 'fve', 'FvH4_2g24631' => 'fve', 'FvH4_2g30622' => 'fve', 'FvH4_3g12920' => 'fve', 'FvH4_3g30171' => 'fve', 'FvH4_3g35490' => 'fve', 'FvH4_3g43682' => 'fve', 'FvH4_3g43730' => 'fve', 'FvH4_3g43732' => 'fve', 'FvH4_3g43751' => 'fve', 'FvH4_3g43752' => 'fve', 'FvH4_3g43770' => 'fve', 'FvH4_3g44471' => 'fve', 'FvH4_3g44510' => 'fve', 'FvH4_3g44582' => 'fve', 'FvH4_4g16921' => 'fve', 'FvH4_4g17121' => 'fve', 'FvH4_4g17782' => 'fve', 'FvH4_4g17783' => 'fve', 'FvH4_4g18120' => 'fve', 'FvH4_4g31310' => 'fve', 'FvH4_4g35052' => 'fve', 'FvH4_5g30862' => 'fve', 'FvH4_6g01541' => 'fve', 'FvH4_6g02021' => 'fve', 'FvH4_6g02041' => 'fve', 'FvH4_6g02071' => 'fve', 'FvH4_6g02171' => 'fve', 'FvH4_6g03181' => 'fve', 'FvH4_6g03182' => 'fve', 'FvH4_6g03221' => 'fve', 'FvH4_6g03380' => 'fve', 'FvH4_6g05201' => 'fve', 'FvH4_6g05203' => 'fve', 'FvH4_6g20231' => 'fve', 'FvH4_6g31981' => 'fve', 'FvH4_6g32061' => 'fve', 'FvH4_6g37041' => 'fve', 'FvH4_6g37932' => 'fve', 'FvH4_6g38731' => 'fve', 'FvH4_6g39370' => 'fve', 'FvH4_6g39371' => 'fve', 'FvH4_6g40891' => 'fve', 'FvH4_6g40892' => 'fve', 'FvH4_6g43143' => 'fve', 'FvH4_6g45251' => 'fve', 'FvH4_6g45260' => 'fve', 'FvH4_6g45291' => 'fve', 'FvH4_6g45890' => 'fve', 'FvH4_6g46240' => 'fve', 'FvH4_6g46241' => 'fve', 'FvH4_6g46242' => 'fve', 'FvH4_6g46260' => 'fve', 'FvH4_6g46280' => 'fve', 'FvH4_6g46380' => 'fve', 'FvH4_7g12841' => 'fve', 'FvH4_7g31431' => 'fve', 'Glyma.09G075900' => 'gma', 'Gohir.A09G096401' => 'ghi', 'Gohir.D09G096101' => 'ghi', 'Gorai.006G112800' => 'gra', 'HanXRQChr04g0121411' => 'han', 'Hund15878' => 'sun', 'Lj2A1107G68' => 'lonja', 'Lj2A630G63' => 'lonja', 'Lj2A946T25' => 'lonja', 'Lj2C714T1' => 'lonja', 'Lj2C966T3' => 'lonja', 'Lj2C966T4' => 'lonja', 'Lj4g0002979' => 'lja', 'Lsat_1_v5_gn_5_30901' => 'lsa', 'Lsat_1_v5_gn_5_31100' => 'lsa', 'Lsat_1_v5_gn_5_38600' => 'lsa', 'Lsat_1_v5_gn_6_92061' => 'lsa', 'Manes.05G071301' => 'mes', 'MD02G1008700' => 'mdo', 'MD02G1008900' => 'mdo', 'MD03G1256400' => 'mdo', 'MD04G1180900' => 'mdo', 'MD04G1181000' => 'mdo', 'MD04G1181200' => 'mdo', 'MD05G1244200' => 'mdo', 'MD05G1324200' => 'mdo', 'MD09G1201600' => 'mdo', 'MD10G1000600' => 'mdo', 'MD14G1026900' => 'mdo', 'MD14G1187900' => 'mdo', 'MD15G1017800' => 'mdo', 'MD15G1018100' => 'mdo', 'Medtr4g124160' => 'mtr', 'Migut.L01260' => 'egut', 'Nitab4.5_0000008g0440' => 'nta', 'Nitab4.5_0000207g0170' => 'nta', 'Nitab4.5_0007671g0030' => 'nta', 'Nitab4.5_0010853g0020' => 'nta', 'Oeu057656.1' => 'oeu', 'PGSC0003DMG400005638' => 'stu', 'PGSC0003DMG400005639' => 'stu', 'Phvul.009G222800' => 'pvu', 'Potri.009G132400' => 'ptr', 'Potri.009G163001' => 'ptr', 'Potri.011G000700' => 'ptr', 'Potri.011G004800' => 'ptr', 'Prupe.1G509300' => 'ppe', 'Prupe.1G509700' => 'ppe', 'Prupe.1G510400' => 'ppe', 'Prupe.1G510700' => 'ppe', 'Prupe.1G512600' => 'ppe', 'Prupe.2G073200' => 'ppe', 'Prupe.3G059500' => 'ppe', 'Prupe.3G059600' => 'ppe', 'Prupe.3G246100' => 'ppe', 'Prupe.3G265100' => 'ppe', 'Prupe.4G034700' => 'ppe', 'Prupe.4G052100' => 'ppe', 'Prupe.4G053600' => 'ppe', 'Prupe.5G068800' => 'ppe', 'Prupe.5G070600' => 'ppe', 'Prupe.6G075400' => 'ppe', 'Prupe.6G075500' => 'ppe', 'Prupe.6G076400' => 'ppe', 'Prupe.8G110700' => 'ppe', 'Psat4g020960' => 'psa', 'PSO135G0788' => 'pso', 'PSO210G6463' => 'pso', 'PSO384G0370' => 'pso', 'PSO386G0056' => 'pso', 'QL01p006048' => 'qlo', 'QL02p054283' => 'qlo', 'QL05p008000' => 'qlo', 'QL05p008212' => 'qlo', 'QL05p008950' => 'qlo', 'QL05p009042' => 'qlo', 'QL05p009518' => 'qlo', 'QL05p012589' => 'qlo', 'QL05p012608' => 'qlo', 'QL05p012650' => 'qlo', 'QL05p012667' => 'qlo', 'QL05p014501' => 'qlo', 'QL05p052800' => 'qlo', 'QL05p065010' => 'qlo', 'QL05p074156' => 'qlo', 'QL05p074160' => 'qlo', 'QL05p074174' => 'qlo', 'QL05p074178' => 'qlo', 'QL05p074214' => 'qlo', 'QL06p001050' => 'qlo', 'QL06p001056' => 'qlo', 'QL06p006093' => 'qlo', 'QL06p006111' => 'qlo', 'QL07p019784' => 'qlo', 'QL07p019801' => 'qlo', 'QL07p036110' => 'qlo', 'QL07p036134' => 'qlo', 'QL07p036147' => 'qlo', 'QL07p036156' => 'qlo', 'QL07p036300' => 'qlo', 'QL07p036320' => 'qlo', 'QL08p014547' => 'qlo', 'QL08p014551' => 'qlo', 'QL08p043319' => 'qlo', 'QL08p043324' => 'qlo', 'QL11p009094' => 'qlo', 'RcHm_v2.0_Chr1g0380481' => 'rch', 'RcHm_v2.0_Chr2g0089331' => 'rch', 'RcHm_v2.0_Chr2g0123691' => 'rch', 'RcHm_v2.0_Chr2g0151111' => 'rch', 'RcHm_v2.0_Chr2g0163011' => 'rch', 'RcHm_v2.0_Chr2g0163051' => 'rch', 'RcHm_v2.0_Chr2g0164671' => 'rch', 'RcHm_v2.0_Chr2g0164681' => 'rch', 'RcHm_v2.0_Chr2g0164721' => 'rch', 'RcHm_v2.0_Chr3g0449911' => 'rch', 'RcHm_v2.0_Chr3g0450211' => 'rch', 'RcHm_v2.0_Chr3g0457271' => 'rch', 'RcHm_v2.0_Chr5g0018111' => 'rch', 'RcHm_v2.0_Chr5g0021011' => 'rch', 'RcHm_v2.0_Chr5g0081171' => 'rch', 'RcHm_v2.0_Chr5g0081211' => 'rch', 'RcHm_v2.0_Chr6g0275871' => 'rch', 'RcHm_v2.0_Chr6g0276071' => 'rch', 'RcHm_v2.0_Chr6g0285591' => 'rch', 'RcHm_v2.0_Chr6g0291931' => 'rch', 'RcHm_v2.0_Chr6g0292091' => 'rch', 'RcHm_v2.0_Chr6g0292271' => 'rch', 'RcHm_v2.0_Chr7g0221261' => 'rch', 'Rhsim08G0219900' => 'rsi', 'Rhsim08G0220200' => 'rsi', 'Rhsim08G0237800' => 'rsi', 'Rhsim08G0238800' => 'rsi', 'Sabra09G0102700' => 'sbr', 'Sabra09G0127200' => 'sbr', 'Sabra11G0003700' => 'sbr', 'Sabra15G0014700' => 'sbr', 'Sc19g0000590' => 'sci', 'Sc19g0001870' => 'sci', 'SGA_v2.0_scaffold1G00346' => 'sas', 'SGA_v2.0_scaffold1G00575' => 'sas', 'SGA_v2.0_scaffold1G00761' => 'sas', 'SGA_v2.0_scaffold232G43501' => 'sas', 'TAR625G1137' => 'tar', 'Thecc.03G222100' => 'tca', 'TPR.G12691' => 'tpr', 'TWI34G0727' => 'twi', 'TWI36G0117' => 'twi', 'VMungo1309G0868' => 'vmu' ) $gf_id = 'HOM05D001729' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001729' ) $data_identifier = 'HOM05D001729' $data_type = 'gf_id' $species_gene_counts = array( 'amhyb' => (int) 1, 'cqu' => (int) 9, 'can' => (int) 1, 'cansat' => (int) 1, 'car' => (int) 1, 'col' => (int) 5, 'dca' => (int) 1, 'din' => (int) 2, 'dzi' => (int) 3, 'fan' => (int) 140, 'fve' => (int) 62, 'gma' => (int) 1, 'ghi' => (int) 2, 'gra' => (int) 1, 'han' => (int) 1, 'sun' => (int) 1, 'lonja' => (int) 6, 'lja' => (int) 1, 'lsa' => (int) 4, 'mes' => (int) 1, 'mdo' => (int) 14, 'mtr' => (int) 1, 'egut' => (int) 1, 'nta' => (int) 4, 'oeu' => (int) 1, 'stu' => (int) 2, 'pvu' => (int) 1, 'ptr' => (int) 4, 'ppe' => (int) 19, 'psa' => (int) 1, 'pso' => (int) 4, 'qlo' => (int) 36, 'rch' => (int) 23, 'rsi' => (int) 4, 'sbr' => (int) 4, 'sci' => (int) 2, 'sas' => (int) 4, 'tar' => (int) 1, 'tca' => (int) 1, 'tpr' => (int) 1, 'twi' => (int) 2, 'vmu' => (int) 1 ) $gf_gene_species = 'vmu' $gf_gene_id = 'VMungo1309G0868' $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' => 'HOM05D001729', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '375', 'num_species' => '42' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'Ah.07g204710' => 'amhyb', 'AUR62006001' => 'cqu', 'AUR62006002' => 'cqu', 'AUR62006003' => 'cqu', 'AUR62015641' => 'cqu', 'AUR62027174' => 'cqu', 'AUR62035623' => 'cqu', 'AUR62035624' => 'cqu', 'AUR62035625' => 'cqu', 'AUR62035626' => 'cqu', 'CAN.G1110.53' => 'can', 'CANSAT80G0415' => 'cansat', 'Ca_21364_v3' => 'car', 'COL.COLO4_30693' => 'col', 'COL.COLO4_30694' => 'col', 'COL.COLO4_30695' => 'col', 'COL.COLO4_30696' => 'col', 'COL.COLO4_34020' => 'col', 'DCAR_004585' => 'dca', 'Dinv04029' => 'din', 'Dinv34857' => 'din', 'Duzib147G0011' => 'dzi', 'Duzib170G0599' => 'dzi', 'Duzib192G1051' => 'dzi', 'FAN01G0708' => 'fan', 'FAN01G0742' => 'fan', 'FAN02G0048' => 'fan', 'FAN02G0583' => 'fan', 'FAN02G0688' => 'fan', 'FAN02G1588' => 'fan', 'FAN02G2194' => 'fan', 'FAN02G2750' => 'fan', 'FAN02G3094' => 'fan', 'FAN02G3887' => 'fan', 'FAN02G3911' => 'fan', 'FAN02G3994' => 'fan', 'FAN02G4432' => 'fan', 'FAN02G4556' => 'fan', 'FAN03G1977' => 'fan', 'FAN03G2781' => 'fan', 'FAN03G2850' => 'fan', 'FAN03G3155' => 'fan', 'FAN04G2487' => 'fan', 'FAN05G0208' => 'fan', 'FAN05G0656' => 'fan', 'FAN05G0696' => 'fan', 'FAN05G0810' => 'fan', 'FAN05G1447' => 'fan', 'FAN05G2640' => 'fan', 'FAN05G2911' => 'fan', 'FAN05G3901' => 'fan', 'FAN05G4859' => 'fan', 'FAN05G4861' => 'fan', 'FAN05G4988' => 'fan', 'FAN05G5187' => 'fan', 'FAN05G5452' => 'fan', 'FAN05G5500' => 'fan', 'FAN05G5688' => 'fan', 'FAN06G0177' => 'fan', 'FAN06G0675' => 'fan', 'FAN06G1290' => 'fan', 'FAN06G2191' => 'fan', 'FAN06G2405' => 'fan', 'FAN06G3231' => 'fan', 'FAN06G3932' => 'fan', 'FAN07G0163' => 'fan', 'FAN07G0471' => 'fan', 'FAN07G1354' => 'fan', 'FAN08G0338' => 'fan', 'FAN08G1373' => 'fan', 'FAN08G2539' => 'fan', 'FAN08G2728' => 'fan', 'FAN09G0608' => 'fan', 'FAN09G1136' => 'fan', 'FAN09G1958' => 'fan', 'FAN09G2508' => 'fan', 'FAN09G2597' => 'fan', 'FAN09G2658' => 'fan', 'FAN09G2757' => 'fan', 'FAN09G2983' => 'fan', 'FAN09G3130' => 'fan', 'FAN09G3565' => 'fan', 'FAN09G3613' => 'fan', 'FAN09G4011' => 'fan', 'FAN09G4239' => 'fan', 'FAN09G4277' => 'fan', 'FAN09G4720' => 'fan', 'FAN11G0139' => 'fan', 'FAN11G1727' => 'fan', 'FAN11G2672' => 'fan', 'FAN11G2795' => 'fan', 'FAN11G3238' => 'fan', 'FAN11G3734' => 'fan', 'FAN12G0631' => 'fan', 'FAN12G2239' => 'fan', 'FAN12G2308' => 'fan', 'FAN12G2569' => 'fan', 'FAN12G2623' => 'fan', 'FAN13G3182' => 'fan', 'FAN14G0053' => 'fan', 'FAN14G0370' => 'fan', 'FAN14G0382' => 'fan', 'FAN14G0421' => 'fan', 'FAN14G0866' => 'fan', 'FAN14G1187' => 'fan', 'FAN14G1727' => 'fan', 'FAN14G1791' => 'fan', 'FAN14G2361' => 'fan', 'FAN14G2668' => 'fan', 'FAN14G2770' => 'fan', 'FAN14G2874' => 'fan', 'FAN14G3193' => 'fan', 'FAN14G3624' => 'fan', 'FAN14G3676' => 'fan', 'FAN14G3807' => 'fan', 'FAN14G4082' => 'fan', 'FAN14G4342' => 'fan', 'FAN14G4985' => 'fan', 'FAN14G5126' => 'fan', 'FAN14G5781' => 'fan', 'FAN14G5808' => 'fan', 'FAN14G5949' => 'fan', 'FAN15G0828' => 'fan', 'FAN15G1054' => 'fan', 'FAN15G2023' => 'fan', 'FAN15G2506' => 'fan', 'FAN16G0128' => 'fan', 'FAN16G0249' => 'fan', 'FAN16G0429' => 'fan', 'FAN16G1493' => 'fan', 'FAN16G2210' => 'fan', 'FAN16G2506' => 'fan', 'FAN18G1542' => 'fan', 'FAN18G4057' => 'fan', 'FAN19G0745' => 'fan', 'FAN19G1216' => 'fan', 'FAN19G1733' => 'fan', 'FAN20G0258' => 'fan', 'FAN20G1095' => 'fan', 'FAN20G1557' => 'fan', 'FAN21G0302' => 'fan', 'FAN21G0519' => 'fan', 'FAN21G0970' => 'fan', 'FAN21G1159' => 'fan', 'FAN21G1312' => 'fan', 'FAN21G1440' => 'fan', 'FAN21G1715' => 'fan', 'FAN23G1584' => 'fan', 'FAN24G0045' => 'fan', 'FAN24G0053' => 'fan', 'FAN24G1500' => 'fan', 'FAN24G1817' => 'fan', 'FAN24G2147' => 'fan', 'FAN24G2236' => 'fan', 'FAN24G2446' => 'fan', 'FAN24G2684' => 'fan', 'FAN25G0187' => 'fan', 'FAN25G0505' => 'fan', 'FAN25G0589' => 'fan', 'FAN25G3663' => 'fan', 'FAN26G1025' => 'fan', 'FAN26G2860' => 'fan', 'FAN27G1329' => 'fan', 'FAN27G3392' => 'fan', 'FvH4_1g02011' => 'fve', 'FvH4_1g06511' => 'fve', 'FvH4_2g19900' => 'fve', 'FvH4_2g19920' => 'fve', 'FvH4_2g24261' => 'fve', 'FvH4_2g24270' => 'fve', 'FvH4_2g24631' => 'fve', 'FvH4_2g30622' => 'fve', 'FvH4_3g12920' => 'fve', 'FvH4_3g30171' => 'fve', 'FvH4_3g35490' => 'fve', 'FvH4_3g43682' => 'fve', 'FvH4_3g43730' => 'fve', 'FvH4_3g43732' => 'fve', 'FvH4_3g43751' => 'fve', 'FvH4_3g43752' => 'fve', 'FvH4_3g43770' => 'fve', 'FvH4_3g44471' => 'fve', 'FvH4_3g44510' => 'fve', 'FvH4_3g44582' => 'fve', 'FvH4_4g16921' => 'fve', 'FvH4_4g17121' => 'fve', 'FvH4_4g17782' => 'fve', 'FvH4_4g17783' => 'fve', 'FvH4_4g18120' => 'fve', 'FvH4_4g31310' => 'fve', 'FvH4_4g35052' => 'fve', 'FvH4_5g30862' => 'fve', 'FvH4_6g01541' => 'fve', 'FvH4_6g02021' => 'fve', 'FvH4_6g02041' => 'fve', 'FvH4_6g02071' => 'fve', 'FvH4_6g02171' => 'fve', 'FvH4_6g03181' => 'fve', 'FvH4_6g03182' => 'fve', 'FvH4_6g03221' => 'fve', 'FvH4_6g03380' => 'fve', 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'ppe', 'Prupe.1G512600' => 'ppe', 'Prupe.2G073200' => 'ppe', 'Prupe.3G059500' => 'ppe', 'Prupe.3G059600' => 'ppe', 'Prupe.3G246100' => 'ppe', 'Prupe.3G265100' => 'ppe', 'Prupe.4G034700' => 'ppe', 'Prupe.4G052100' => 'ppe', 'Prupe.4G053600' => 'ppe', 'Prupe.5G068800' => 'ppe', 'Prupe.5G070600' => 'ppe', 'Prupe.6G075400' => 'ppe', 'Prupe.6G075500' => 'ppe', 'Prupe.6G076400' => 'ppe', 'Prupe.8G110700' => 'ppe', 'Psat4g020960' => 'psa', 'PSO135G0788' => 'pso', 'PSO210G6463' => 'pso', 'PSO384G0370' => 'pso', 'PSO386G0056' => 'pso', 'QL01p006048' => 'qlo', 'QL02p054283' => 'qlo', 'QL05p008000' => 'qlo', 'QL05p008212' => 'qlo', 'QL05p008950' => 'qlo', 'QL05p009042' => 'qlo', 'QL05p009518' => 'qlo', 'QL05p012589' => 'qlo', 'QL05p012608' => 'qlo', 'QL05p012650' => 'qlo', 'QL05p012667' => 'qlo', 'QL05p014501' => 'qlo', 'QL05p052800' => 'qlo', 'QL05p065010' => 'qlo', 'QL05p074156' => 'qlo', 'QL05p074160' => 'qlo', 'QL05p074174' => 'qlo', 'QL05p074178' => 'qlo', 'QL05p074214' => 'qlo', 'QL06p001050' => 'qlo', 'QL06p001056' => 'qlo', 'QL06p006093' => 'qlo', 'QL06p006111' => 'qlo', 'QL07p019784' => 'qlo', 'QL07p019801' => 'qlo', 'QL07p036110' => 'qlo', 'QL07p036134' => 'qlo', 'QL07p036147' => 'qlo', 'QL07p036156' => 'qlo', 'QL07p036300' => 'qlo', 'QL07p036320' => 'qlo', 'QL08p014547' => 'qlo', 'QL08p014551' => 'qlo', 'QL08p043319' => 'qlo', 'QL08p043324' => 'qlo', 'QL11p009094' => 'qlo', 'RcHm_v2.0_Chr1g0380481' => 'rch', 'RcHm_v2.0_Chr2g0089331' => 'rch', 'RcHm_v2.0_Chr2g0123691' => 'rch', 'RcHm_v2.0_Chr2g0151111' => 'rch', 'RcHm_v2.0_Chr2g0163011' => 'rch', 'RcHm_v2.0_Chr2g0163051' => 'rch', 'RcHm_v2.0_Chr2g0164671' => 'rch', 'RcHm_v2.0_Chr2g0164681' => 'rch', 'RcHm_v2.0_Chr2g0164721' => 'rch', 'RcHm_v2.0_Chr3g0449911' => 'rch', 'RcHm_v2.0_Chr3g0450211' => 'rch', 'RcHm_v2.0_Chr3g0457271' => 'rch', 'RcHm_v2.0_Chr5g0018111' => 'rch', 'RcHm_v2.0_Chr5g0021011' => 'rch', 'RcHm_v2.0_Chr5g0081171' => 'rch', 'RcHm_v2.0_Chr5g0081211' => 'rch', 'RcHm_v2.0_Chr6g0275871' => 'rch', 'RcHm_v2.0_Chr6g0276071' => 'rch', 'RcHm_v2.0_Chr6g0285591' => 'rch', 'RcHm_v2.0_Chr6g0291931' => 'rch', 'RcHm_v2.0_Chr6g0292091' => 'rch', 'RcHm_v2.0_Chr6g0292271' => 'rch', 'RcHm_v2.0_Chr7g0221261' => 'rch', 'Rhsim08G0219900' => 'rsi', 'Rhsim08G0220200' => 'rsi', 'Rhsim08G0237800' => 'rsi', 'Rhsim08G0238800' => 'rsi', 'Sabra09G0102700' => 'sbr', 'Sabra09G0127200' => 'sbr', 'Sabra11G0003700' => 'sbr', 'Sabra15G0014700' => 'sbr', 'Sc19g0000590' => 'sci', 'Sc19g0001870' => 'sci', 'SGA_v2.0_scaffold1G00346' => 'sas', 'SGA_v2.0_scaffold1G00575' => 'sas', 'SGA_v2.0_scaffold1G00761' => 'sas', 'SGA_v2.0_scaffold232G43501' => 'sas', 'TAR625G1137' => 'tar', 'Thecc.03G222100' => 'tca', 'TPR.G12691' => 'tpr', 'TWI34G0727' => 'twi', 'TWI36G0117' => 'twi', 'VMungo1309G0868' => 'vmu' ), 'gf_id' => 'HOM05D001729', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001729' ), 'data_identifier' => 'HOM05D001729', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001729', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '375', 'num_species' => '42' ) 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'AUR62035624' => 'cqu', 'AUR62035625' => 'cqu', 'AUR62035626' => 'cqu', 'CAN.G1110.53' => 'can', 'CANSAT80G0415' => 'cansat', 'Ca_21364_v3' => 'car', 'COL.COLO4_30693' => 'col', 'COL.COLO4_30694' => 'col', 'COL.COLO4_30695' => 'col', 'COL.COLO4_30696' => 'col', 'COL.COLO4_34020' => 'col', 'DCAR_004585' => 'dca', 'Dinv04029' => 'din', 'Dinv34857' => 'din', 'Duzib147G0011' => 'dzi', 'Duzib170G0599' => 'dzi', 'Duzib192G1051' => 'dzi', 'FAN01G0708' => 'fan', 'FAN01G0742' => 'fan', 'FAN02G0048' => 'fan', 'FAN02G0583' => 'fan', 'FAN02G0688' => 'fan', 'FAN02G1588' => 'fan', 'FAN02G2194' => 'fan', 'FAN02G2750' => 'fan', 'FAN02G3094' => 'fan', 'FAN02G3887' => 'fan', 'FAN02G3911' => 'fan', 'FAN02G3994' => 'fan', 'FAN02G4432' => 'fan', 'FAN02G4556' => 'fan', 'FAN03G1977' => 'fan', 'FAN03G2781' => 'fan', 'FAN03G2850' => 'fan', 'FAN03G3155' => 'fan', 'FAN04G2487' => 'fan', 'FAN05G0208' => 'fan', 'FAN05G0656' => 'fan', 'FAN05G0696' => 'fan', 'FAN05G0810' => 'fan', 'FAN05G1447' => 'fan', 'FAN05G2640' => 'fan', 'FAN05G2911' => 'fan', 'FAN05G3901' => 'fan', 'FAN05G4859' => 'fan', 'FAN05G4861' => 'fan', 'FAN05G4988' => 'fan', 'FAN05G5187' => 'fan', 'FAN05G5452' => 'fan', 'FAN05G5500' => 'fan', 'FAN05G5688' => 'fan', 'FAN06G0177' => 'fan', 'FAN06G0675' => 'fan', 'FAN06G1290' => 'fan', 'FAN06G2191' => 'fan', 'FAN06G2405' => 'fan', 'FAN06G3231' => 'fan', 'FAN06G3932' => 'fan', 'FAN07G0163' => 'fan', 'FAN07G0471' => 'fan', 'FAN07G1354' => 'fan', 'FAN08G0338' => 'fan', 'FAN08G1373' => 'fan', 'FAN08G2539' => 'fan', 'FAN08G2728' => 'fan', 'FAN09G0608' => 'fan', 'FAN09G1136' => 'fan', 'FAN09G1958' => 'fan', 'FAN09G2508' => 'fan', 'FAN09G2597' => 'fan', 'FAN09G2658' => 'fan', 'FAN09G2757' => 'fan', 'FAN09G2983' => 'fan', 'FAN09G3130' => 'fan', 'FAN09G3565' => 'fan', 'FAN09G3613' => 'fan', 'FAN09G4011' => 'fan', 'FAN09G4239' => 'fan', 'FAN09G4277' => 'fan', 'FAN09G4720' => 'fan', 'FAN11G0139' => 'fan', 'FAN11G1727' => 'fan', 'FAN11G2672' => 'fan', 'FAN11G2795' => 'fan', 'FAN11G3238' => 'fan', 'FAN11G3734' => 'fan', 'FAN12G0631' => 'fan', 'FAN12G2239' => 'fan', 'FAN12G2308' => 'fan', 'FAN12G2569' => 'fan', 'FAN12G2623' => 'fan', 'FAN13G3182' => 'fan', 'FAN14G0053' => 'fan', 'FAN14G0370' => 'fan', 'FAN14G0382' => 'fan', 'FAN14G0421' => 'fan', 'FAN14G0866' => 'fan', 'FAN14G1187' => 'fan', 'FAN14G1727' => 'fan', 'FAN14G1791' => 'fan', 'FAN14G2361' => 'fan', 'FAN14G2668' => 'fan', 'FAN14G2770' => 'fan', 'FAN14G2874' => 'fan', 'FAN14G3193' => 'fan', 'FAN14G3624' => 'fan', 'FAN14G3676' => 'fan', 'FAN14G3807' => 'fan', 'FAN14G4082' => 'fan', 'FAN14G4342' => 'fan', 'FAN14G4985' => 'fan', 'FAN14G5126' => 'fan', 'FAN14G5781' => 'fan', 'FAN14G5808' => 'fan', 'FAN14G5949' => 'fan', 'FAN15G0828' => 'fan', 'FAN15G1054' => 'fan', 'FAN15G2023' => 'fan', 'FAN15G2506' => 'fan', 'FAN16G0128' => 'fan', 'FAN16G0249' => 'fan', 'FAN16G0429' => 'fan', 'FAN16G1493' => 'fan', 'FAN16G2210' => 'fan', 'FAN16G2506' => 'fan', 'FAN18G1542' => 'fan', 'FAN18G4057' => 'fan', 'FAN19G0745' => 'fan', 'FAN19G1216' => 'fan', 'FAN19G1733' => 'fan', 'FAN20G0258' => 'fan', 'FAN20G1095' => 'fan', 'FAN20G1557' => 'fan', 'FAN21G0302' => 'fan', 'FAN21G0519' => 'fan', 'FAN21G0970' => 'fan', 'FAN21G1159' => 'fan', 'FAN21G1312' => 'fan', 'FAN21G1440' => 'fan', 'FAN21G1715' => 'fan', 'FAN23G1584' => 'fan', 'FAN24G0045' => 'fan', 'FAN24G0053' => 'fan', 'FAN24G1500' => 'fan', 'FAN24G1817' => 'fan', 'FAN24G2147' => 'fan', 'FAN24G2236' => 'fan', 'FAN24G2446' => 'fan', 'FAN24G2684' => 'fan', 'FAN25G0187' => 'fan', 'FAN25G0505' => 'fan', 'FAN25G0589' => 'fan', 'FAN25G3663' => 'fan', 'FAN26G1025' => 'fan', 'FAN26G2860' => 'fan', 'FAN27G1329' => 'fan', 'FAN27G3392' => 'fan', 'FvH4_1g02011' => 'fve', 'FvH4_1g06511' => 'fve', 'FvH4_2g19900' => 'fve', 'FvH4_2g19920' => 'fve', 'FvH4_2g24261' => 'fve', 'FvH4_2g24270' => 'fve', 'FvH4_2g24631' => 'fve', 'FvH4_2g30622' => 'fve', 'FvH4_3g12920' => 'fve', 'FvH4_3g30171' => 'fve', 'FvH4_3g35490' => 'fve', 'FvH4_3g43682' => 'fve', 'FvH4_3g43730' => 'fve', 'FvH4_3g43732' => 'fve', 'FvH4_3g43751' => 'fve', 'FvH4_3g43752' => 'fve', 'FvH4_3g43770' => 'fve', 'FvH4_3g44471' => 'fve', 'FvH4_3g44510' => 'fve', 'FvH4_3g44582' => 'fve', 'FvH4_4g16921' => 'fve', 'FvH4_4g17121' => 'fve', 'FvH4_4g17782' => 'fve', 'FvH4_4g17783' => 'fve', 'FvH4_4g18120' => 'fve', 'FvH4_4g31310' => 'fve', 'FvH4_4g35052' => 'fve', 'FvH4_5g30862' => 'fve', 'FvH4_6g01541' => 'fve', 'FvH4_6g02021' => 'fve', 'FvH4_6g02041' => 'fve', 'FvH4_6g02071' => 'fve', 'FvH4_6g02171' => 'fve', 'FvH4_6g03181' => 'fve', 'FvH4_6g03182' => 'fve', 'FvH4_6g03221' => 'fve', 'FvH4_6g03380' => 'fve', 'FvH4_6g05201' => 'fve', 'FvH4_6g05203' => 'fve', 'FvH4_6g20231' => 'fve', 'FvH4_6g31981' => 'fve', 'FvH4_6g32061' => 'fve', 'FvH4_6g37041' => 'fve', 'FvH4_6g37932' => 'fve', 'FvH4_6g38731' => 'fve', 'FvH4_6g39370' => 'fve', 'FvH4_6g39371' => 'fve', 'FvH4_6g40891' => 'fve', 'FvH4_6g40892' => 'fve', 'FvH4_6g43143' => 'fve', 'FvH4_6g45251' => 'fve', 'FvH4_6g45260' => 'fve', 'FvH4_6g45291' => 'fve', 'FvH4_6g45890' => 'fve', 'FvH4_6g46240' => 'fve', 'FvH4_6g46241' => 'fve', 'FvH4_6g46242' => 'fve', 'FvH4_6g46260' => 'fve', 'FvH4_6g46280' => 'fve', 'FvH4_6g46380' => 'fve', 'FvH4_7g12841' => 'fve', 'FvH4_7g31431' => 'fve', 'Glyma.09G075900' => 'gma', 'Gohir.A09G096401' => 'ghi', 'Gohir.D09G096101' => 'ghi', 'Gorai.006G112800' => 'gra', 'HanXRQChr04g0121411' => 'han', 'Hund15878' => 'sun', 'Lj2A1107G68' => 'lonja', 'Lj2A630G63' => 'lonja', 'Lj2A946T25' => 'lonja', 'Lj2C714T1' => 'lonja', 'Lj2C966T3' => 'lonja', 'Lj2C966T4' => 'lonja', 'Lj4g0002979' => 'lja', 'Lsat_1_v5_gn_5_30901' => 'lsa', 'Lsat_1_v5_gn_5_31100' => 'lsa', 'Lsat_1_v5_gn_5_38600' => 'lsa', 'Lsat_1_v5_gn_6_92061' => 'lsa', 'Manes.05G071301' => 'mes', 'MD02G1008700' => 'mdo', 'MD02G1008900' => 'mdo', 'MD03G1256400' => 'mdo', 'MD04G1180900' => 'mdo', 'MD04G1181000' => 'mdo', 'MD04G1181200' => 'mdo', 'MD05G1244200' => 'mdo', 'MD05G1324200' => 'mdo', 'MD09G1201600' => 'mdo', 'MD10G1000600' => 'mdo', 'MD14G1026900' => 'mdo', 'MD14G1187900' => 'mdo', 'MD15G1017800' => 'mdo', 'MD15G1018100' => 'mdo', 'Medtr4g124160' => 'mtr', 'Migut.L01260' => 'egut', 'Nitab4.5_0000008g0440' => 'nta', 'Nitab4.5_0000207g0170' => 'nta', 'Nitab4.5_0007671g0030' => 'nta', 'Nitab4.5_0010853g0020' => 'nta', 'Oeu057656.1' => 'oeu', 'PGSC0003DMG400005638' => 'stu', 'PGSC0003DMG400005639' => 'stu', 'Phvul.009G222800' => 'pvu', 'Potri.009G132400' => 'ptr', 'Potri.009G163001' => 'ptr', 'Potri.011G000700' => 'ptr', 'Potri.011G004800' => 'ptr', 'Prupe.1G509300' => 'ppe', 'Prupe.1G509700' => 'ppe', 'Prupe.1G510400' => 'ppe', 'Prupe.1G510700' => 'ppe', 'Prupe.1G512600' => 'ppe', 'Prupe.2G073200' => 'ppe', 'Prupe.3G059500' => 'ppe', 'Prupe.3G059600' => 'ppe', 'Prupe.3G246100' => 'ppe', 'Prupe.3G265100' => 'ppe', 'Prupe.4G034700' => 'ppe', 'Prupe.4G052100' => 'ppe', 'Prupe.4G053600' => 'ppe', 'Prupe.5G068800' => 'ppe', 'Prupe.5G070600' => 'ppe', 'Prupe.6G075400' => 'ppe', 'Prupe.6G075500' => 'ppe', 'Prupe.6G076400' => 'ppe', 'Prupe.8G110700' => 'ppe', 'Psat4g020960' => 'psa', 'PSO135G0788' => 'pso', 'PSO210G6463' => 'pso', 'PSO384G0370' => 'pso', 'PSO386G0056' => 'pso', 'QL01p006048' => 'qlo', 'QL02p054283' => 'qlo', 'QL05p008000' => 'qlo', 'QL05p008212' => 'qlo', 'QL05p008950' => 'qlo', 'QL05p009042' => 'qlo', 'QL05p009518' => 'qlo', 'QL05p012589' => 'qlo', 'QL05p012608' => 'qlo', 'QL05p012650' => 'qlo', 'QL05p012667' => 'qlo', 'QL05p014501' => 'qlo', 'QL05p052800' => 'qlo', 'QL05p065010' => 'qlo', 'QL05p074156' => 'qlo', 'QL05p074160' => 'qlo', 'QL05p074174' => 'qlo', 'QL05p074178' => 'qlo', 'QL05p074214' => 'qlo', 'QL06p001050' => 'qlo', 'QL06p001056' => 'qlo', 'QL06p006093' => 'qlo', 'QL06p006111' => 'qlo', 'QL07p019784' => 'qlo', 'QL07p019801' => 'qlo', 'QL07p036110' => 'qlo', 'QL07p036134' => 'qlo', 'QL07p036147' => 'qlo', 'QL07p036156' => 'qlo', 'QL07p036300' => 'qlo', 'QL07p036320' => 'qlo', 'QL08p014547' => 'qlo', 'QL08p014551' => 'qlo', 'QL08p043319' => 'qlo', 'QL08p043324' => 'qlo', 'QL11p009094' => 'qlo', 'RcHm_v2.0_Chr1g0380481' => 'rch', 'RcHm_v2.0_Chr2g0089331' => 'rch', 'RcHm_v2.0_Chr2g0123691' => 'rch', 'RcHm_v2.0_Chr2g0151111' => 'rch', 'RcHm_v2.0_Chr2g0163011' => 'rch', 'RcHm_v2.0_Chr2g0163051' => 'rch', 'RcHm_v2.0_Chr2g0164671' => 'rch', 'RcHm_v2.0_Chr2g0164681' => 'rch', 'RcHm_v2.0_Chr2g0164721' => 'rch', 'RcHm_v2.0_Chr3g0449911' => 'rch', 'RcHm_v2.0_Chr3g0450211' => 'rch', 'RcHm_v2.0_Chr3g0457271' => 'rch', 'RcHm_v2.0_Chr5g0018111' => 'rch', 'RcHm_v2.0_Chr5g0021011' => 'rch', 'RcHm_v2.0_Chr5g0081171' => 'rch', 'RcHm_v2.0_Chr5g0081211' => 'rch', 'RcHm_v2.0_Chr6g0275871' => 'rch', 'RcHm_v2.0_Chr6g0276071' => 'rch', 'RcHm_v2.0_Chr6g0285591' => 'rch', 'RcHm_v2.0_Chr6g0291931' => 'rch', 'RcHm_v2.0_Chr6g0292091' => 'rch', 'RcHm_v2.0_Chr6g0292271' => 'rch', 'RcHm_v2.0_Chr7g0221261' => 'rch', 'Rhsim08G0219900' => 'rsi', 'Rhsim08G0220200' => 'rsi', 'Rhsim08G0237800' => 'rsi', 'Rhsim08G0238800' => 'rsi', 'Sabra09G0102700' => 'sbr', 'Sabra09G0127200' => 'sbr', 'Sabra11G0003700' => 'sbr', 'Sabra15G0014700' => 'sbr', 'Sc19g0000590' => 'sci', 'Sc19g0001870' => 'sci', 'SGA_v2.0_scaffold1G00346' => 'sas', 'SGA_v2.0_scaffold1G00575' => 'sas', 'SGA_v2.0_scaffold1G00761' => 'sas', 'SGA_v2.0_scaffold232G43501' => 'sas', 'TAR625G1137' => 'tar', 'Thecc.03G222100' => 'tca', 'TPR.G12691' => 'tpr', 'TWI34G0727' => 'twi', 'TWI36G0117' => 'twi', 'VMungo1309G0868' => 'vmu' ) $gf_id = 'HOM05D001729' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001729' ) $data_identifier = 'HOM05D001729' $data_type = 'gf_id' $species_gene_counts = array( 'amhyb' => (int) 1, 'cqu' => (int) 9, 'can' => (int) 1, 'cansat' => (int) 1, 'car' => (int) 1, 'col' => (int) 5, 'dca' => (int) 1, 'din' => (int) 2, 'dzi' => (int) 3, 'fan' => (int) 140, 'fve' => (int) 62, 'gma' => (int) 1, 'ghi' => (int) 2, 'gra' => (int) 1, 'han' => (int) 1, 'sun' => (int) 1, 'lonja' => (int) 6, 'lja' => (int) 1, 'lsa' => (int) 4, 'mes' => (int) 1, 'mdo' => (int) 14, 'mtr' => (int) 1, 'egut' => (int) 1, 'nta' => (int) 4, 'oeu' => (int) 1, 'stu' => (int) 2, 'pvu' => (int) 1, 'ptr' => (int) 4, 'ppe' => (int) 19, 'psa' => (int) 1, 'pso' => (int) 4, 'qlo' => (int) 36, 'rch' => (int) 23, 'rsi' => (int) 4, 'sbr' => (int) 4, 'sci' => (int) 2, 'sas' => (int) 4, 'tar' => (int) 1, 'tca' => (int) 1, 'tpr' => (int) 1, 'twi' => (int) 2, 'vmu' => (int) 1 ) $gf_gene_species = 'vmu' $gf_gene_id = 'VMungo1309G0868' $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' => 'HOM05D001729', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '375', 'num_species' => '42' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'Ah.07g204710' => 'amhyb', 'AUR62006001' => 'cqu', 'AUR62006002' => 'cqu', 'AUR62006003' => 'cqu', 'AUR62015641' => 'cqu', 'AUR62027174' => 'cqu', 'AUR62035623' => 'cqu', 'AUR62035624' => 'cqu', 'AUR62035625' => 'cqu', 'AUR62035626' => 'cqu', 'CAN.G1110.53' => 'can', 'CANSAT80G0415' => 'cansat', 'Ca_21364_v3' => 'car', 'COL.COLO4_30693' => 'col', 'COL.COLO4_30694' => 'col', 'COL.COLO4_30695' => 'col', 'COL.COLO4_30696' => 'col', 'COL.COLO4_34020' => 'col', 'DCAR_004585' => 'dca', 'Dinv04029' => 'din', 'Dinv34857' => 'din', 'Duzib147G0011' => 'dzi', 'Duzib170G0599' => 'dzi', 'Duzib192G1051' => 'dzi', 'FAN01G0708' => 'fan', 'FAN01G0742' => 'fan', 'FAN02G0048' => 'fan', 'FAN02G0583' => 'fan', 'FAN02G0688' => 'fan', 'FAN02G1588' => 'fan', 'FAN02G2194' => 'fan', 'FAN02G2750' => 'fan', 'FAN02G3094' => 'fan', 'FAN02G3887' => 'fan', 'FAN02G3911' => 'fan', 'FAN02G3994' => 'fan', 'FAN02G4432' => 'fan', 'FAN02G4556' => 'fan', 'FAN03G1977' => 'fan', 'FAN03G2781' => 'fan', 'FAN03G2850' => 'fan', 'FAN03G3155' => 'fan', 'FAN04G2487' => 'fan', 'FAN05G0208' => 'fan', 'FAN05G0656' => 'fan', 'FAN05G0696' => 'fan', 'FAN05G0810' => 'fan', 'FAN05G1447' => 'fan', 'FAN05G2640' => 'fan', 'FAN05G2911' => 'fan', 'FAN05G3901' => 'fan', 'FAN05G4859' => 'fan', 'FAN05G4861' => 'fan', 'FAN05G4988' => 'fan', 'FAN05G5187' => 'fan', 'FAN05G5452' => 'fan', 'FAN05G5500' => 'fan', 'FAN05G5688' => 'fan', 'FAN06G0177' => 'fan', 'FAN06G0675' => 'fan', 'FAN06G1290' => 'fan', 'FAN06G2191' => 'fan', 'FAN06G2405' => 'fan', 'FAN06G3231' => 'fan', 'FAN06G3932' => 'fan', 'FAN07G0163' => 'fan', 'FAN07G0471' => 'fan', 'FAN07G1354' => 'fan', 'FAN08G0338' => 'fan', 'FAN08G1373' => 'fan', 'FAN08G2539' => 'fan', 'FAN08G2728' => 'fan', 'FAN09G0608' => 'fan', 'FAN09G1136' => 'fan', 'FAN09G1958' => 'fan', 'FAN09G2508' => 'fan', 'FAN09G2597' => 'fan', 'FAN09G2658' => 'fan', 'FAN09G2757' => 'fan', 'FAN09G2983' => 'fan', 'FAN09G3130' => 'fan', 'FAN09G3565' => 'fan', 'FAN09G3613' => 'fan', 'FAN09G4011' => 'fan', 'FAN09G4239' => 'fan', 'FAN09G4277' => 'fan', 'FAN09G4720' => 'fan', 'FAN11G0139' => 'fan', 'FAN11G1727' => 'fan', 'FAN11G2672' => 'fan', 'FAN11G2795' => 'fan', 'FAN11G3238' => 'fan', 'FAN11G3734' => 'fan', 'FAN12G0631' => 'fan', 'FAN12G2239' => 'fan', 'FAN12G2308' => 'fan', 'FAN12G2569' => 'fan', 'FAN12G2623' => 'fan', 'FAN13G3182' => 'fan', 'FAN14G0053' => 'fan', 'FAN14G0370' => 'fan', 'FAN14G0382' => 'fan', 'FAN14G0421' => 'fan', 'FAN14G0866' => 'fan', 'FAN14G1187' => 'fan', 'FAN14G1727' => 'fan', 'FAN14G1791' => 'fan', 'FAN14G2361' => 'fan', 'FAN14G2668' => 'fan', 'FAN14G2770' => 'fan', 'FAN14G2874' => 'fan', 'FAN14G3193' => 'fan', 'FAN14G3624' => 'fan', 'FAN14G3676' => 'fan', 'FAN14G3807' => 'fan', 'FAN14G4082' => 'fan', 'FAN14G4342' => 'fan', 'FAN14G4985' => 'fan', 'FAN14G5126' => 'fan', 'FAN14G5781' => 'fan', 'FAN14G5808' => 'fan', 'FAN14G5949' => 'fan', 'FAN15G0828' => 'fan', 'FAN15G1054' => 'fan', 'FAN15G2023' => 'fan', 'FAN15G2506' => 'fan', 'FAN16G0128' => 'fan', 'FAN16G0249' => 'fan', 'FAN16G0429' => 'fan', 'FAN16G1493' => 'fan', 'FAN16G2210' => 'fan', 'FAN16G2506' => 'fan', 'FAN18G1542' => 'fan', 'FAN18G4057' => 'fan', 'FAN19G0745' => 'fan', 'FAN19G1216' => 'fan', 'FAN19G1733' => 'fan', 'FAN20G0258' => 'fan', 'FAN20G1095' => 'fan', 'FAN20G1557' => 'fan', 'FAN21G0302' => 'fan', 'FAN21G0519' => 'fan', 'FAN21G0970' => 'fan', 'FAN21G1159' => 'fan', 'FAN21G1312' => 'fan', 'FAN21G1440' => 'fan', 'FAN21G1715' => 'fan', 'FAN23G1584' => 'fan', 'FAN24G0045' => 'fan', 'FAN24G0053' => 'fan', 'FAN24G1500' => 'fan', 'FAN24G1817' => 'fan', 'FAN24G2147' => 'fan', 'FAN24G2236' => 'fan', 'FAN24G2446' => 'fan', 'FAN24G2684' => 'fan', 'FAN25G0187' => 'fan', 'FAN25G0505' => 'fan', 'FAN25G0589' => 'fan', 'FAN25G3663' => 'fan', 'FAN26G1025' => 'fan', 'FAN26G2860' => 'fan', 'FAN27G1329' => 'fan', 'FAN27G3392' => 'fan', 'FvH4_1g02011' => 'fve', 'FvH4_1g06511' => 'fve', 'FvH4_2g19900' => 'fve', 'FvH4_2g19920' => 'fve', 'FvH4_2g24261' => 'fve', 'FvH4_2g24270' => 'fve', 'FvH4_2g24631' => 'fve', 'FvH4_2g30622' => 'fve', 'FvH4_3g12920' => 'fve', 'FvH4_3g30171' => 'fve', 'FvH4_3g35490' => 'fve', 'FvH4_3g43682' => 'fve', 'FvH4_3g43730' => 'fve', 'FvH4_3g43732' => 'fve', 'FvH4_3g43751' => 'fve', 'FvH4_3g43752' => 'fve', 'FvH4_3g43770' => 'fve', 'FvH4_3g44471' => 'fve', 'FvH4_3g44510' => 'fve', 'FvH4_3g44582' => 'fve', 'FvH4_4g16921' => 'fve', 'FvH4_4g17121' => 'fve', 'FvH4_4g17782' => 'fve', 'FvH4_4g17783' => 'fve', 'FvH4_4g18120' => 'fve', 'FvH4_4g31310' => 'fve', 'FvH4_4g35052' => 'fve', 'FvH4_5g30862' => 'fve', 'FvH4_6g01541' => 'fve', 'FvH4_6g02021' => 'fve', 'FvH4_6g02041' => 'fve', 'FvH4_6g02071' => 'fve', 'FvH4_6g02171' => 'fve', 'FvH4_6g03181' => 'fve', 'FvH4_6g03182' => 'fve', 'FvH4_6g03221' => 'fve', 'FvH4_6g03380' => 'fve', 'FvH4_6g05201' => 'fve', 'FvH4_6g05203' => 'fve', 'FvH4_6g20231' => 'fve', 'FvH4_6g31981' => 'fve', 'FvH4_6g32061' => 'fve', 'FvH4_6g37041' => 'fve', 'FvH4_6g37932' => 'fve', 'FvH4_6g38731' => 'fve', 'FvH4_6g39370' => 'fve', 'FvH4_6g39371' => 'fve', 'FvH4_6g40891' => 'fve', 'FvH4_6g40892' => 'fve', 'FvH4_6g43143' => 'fve', 'FvH4_6g45251' => 'fve', 'FvH4_6g45260' => 'fve', 'FvH4_6g45291' => 'fve', 'FvH4_6g45890' => 'fve', 'FvH4_6g46240' => 'fve', 'FvH4_6g46241' => 'fve', 'FvH4_6g46242' => 'fve', 'FvH4_6g46260' => 'fve', 'FvH4_6g46280' => 'fve', 'FvH4_6g46380' => 'fve', 'FvH4_7g12841' => 'fve', 'FvH4_7g31431' => 'fve', 'Glyma.09G075900' => 'gma', 'Gohir.A09G096401' => 'ghi', 'Gohir.D09G096101' => 'ghi', 'Gorai.006G112800' => 'gra', 'HanXRQChr04g0121411' => 'han', 'Hund15878' => 'sun', 'Lj2A1107G68' => 'lonja', 'Lj2A630G63' => 'lonja', 'Lj2A946T25' => 'lonja', 'Lj2C714T1' => 'lonja', 'Lj2C966T3' => 'lonja', 'Lj2C966T4' => 'lonja', 'Lj4g0002979' => 'lja', 'Lsat_1_v5_gn_5_30901' => 'lsa', 'Lsat_1_v5_gn_5_31100' => 'lsa', 'Lsat_1_v5_gn_5_38600' => 'lsa', 'Lsat_1_v5_gn_6_92061' => 'lsa', 'Manes.05G071301' => 'mes', 'MD02G1008700' => 'mdo', 'MD02G1008900' => 'mdo', 'MD03G1256400' => 'mdo', 'MD04G1180900' => 'mdo', 'MD04G1181000' => 'mdo', 'MD04G1181200' => 'mdo', 'MD05G1244200' => 'mdo', 'MD05G1324200' => 'mdo', 'MD09G1201600' => 'mdo', 'MD10G1000600' => 'mdo', 'MD14G1026900' => 'mdo', 'MD14G1187900' => 'mdo', 'MD15G1017800' => 'mdo', 'MD15G1018100' => 'mdo', 'Medtr4g124160' => 'mtr', 'Migut.L01260' => 'egut', 'Nitab4.5_0000008g0440' => 'nta', 'Nitab4.5_0000207g0170' => 'nta', 'Nitab4.5_0007671g0030' => 'nta', 'Nitab4.5_0010853g0020' => 'nta', 'Oeu057656.1' => 'oeu', 'PGSC0003DMG400005638' => 'stu', 'PGSC0003DMG400005639' => 'stu', 'Phvul.009G222800' => 'pvu', 'Potri.009G132400' => 'ptr', 'Potri.009G163001' => 'ptr', 'Potri.011G000700' => 'ptr', 'Potri.011G004800' => 'ptr', 'Prupe.1G509300' => 'ppe', 'Prupe.1G509700' => 'ppe', 'Prupe.1G510400' => 'ppe', 'Prupe.1G510700' => 'ppe', 'Prupe.1G512600' => 'ppe', 'Prupe.2G073200' => 'ppe', 'Prupe.3G059500' => 'ppe', 'Prupe.3G059600' => 'ppe', 'Prupe.3G246100' => 'ppe', 'Prupe.3G265100' => 'ppe', 'Prupe.4G034700' => 'ppe', 'Prupe.4G052100' => 'ppe', 'Prupe.4G053600' => 'ppe', 'Prupe.5G068800' => 'ppe', 'Prupe.5G070600' => 'ppe', 'Prupe.6G075400' => 'ppe', 'Prupe.6G075500' => 'ppe', 'Prupe.6G076400' => 'ppe', 'Prupe.8G110700' => 'ppe', 'Psat4g020960' => 'psa', 'PSO135G0788' => 'pso', 'PSO210G6463' => 'pso', 'PSO384G0370' => 'pso', 'PSO386G0056' => 'pso', 'QL01p006048' => 'qlo', 'QL02p054283' => 'qlo', 'QL05p008000' => 'qlo', 'QL05p008212' => 'qlo', 'QL05p008950' => 'qlo', 'QL05p009042' => 'qlo', 'QL05p009518' => 'qlo', 'QL05p012589' => 'qlo', 'QL05p012608' => 'qlo', 'QL05p012650' => 'qlo', 'QL05p012667' => 'qlo', 'QL05p014501' => 'qlo', 'QL05p052800' => 'qlo', 'QL05p065010' => 'qlo', 'QL05p074156' => 'qlo', 'QL05p074160' => 'qlo', 'QL05p074174' => 'qlo', 'QL05p074178' => 'qlo', 'QL05p074214' => 'qlo', 'QL06p001050' => 'qlo', 'QL06p001056' => 'qlo', 'QL06p006093' => 'qlo', 'QL06p006111' => 'qlo', 'QL07p019784' => 'qlo', 'QL07p019801' => 'qlo', 'QL07p036110' => 'qlo', 'QL07p036134' => 'qlo', 'QL07p036147' => 'qlo', 'QL07p036156' => 'qlo', 'QL07p036300' => 'qlo', 'QL07p036320' => 'qlo', 'QL08p014547' => 'qlo', 'QL08p014551' => 'qlo', 'QL08p043319' => 'qlo', 'QL08p043324' => 'qlo', 'QL11p009094' => 'qlo', 'RcHm_v2.0_Chr1g0380481' => 'rch', 'RcHm_v2.0_Chr2g0089331' => 'rch', 'RcHm_v2.0_Chr2g0123691' => 'rch', 'RcHm_v2.0_Chr2g0151111' => 'rch', 'RcHm_v2.0_Chr2g0163011' => 'rch', 'RcHm_v2.0_Chr2g0163051' => 'rch', 'RcHm_v2.0_Chr2g0164671' => 'rch', 'RcHm_v2.0_Chr2g0164681' => 'rch', 'RcHm_v2.0_Chr2g0164721' => 'rch', 'RcHm_v2.0_Chr3g0449911' => 'rch', 'RcHm_v2.0_Chr3g0450211' => 'rch', 'RcHm_v2.0_Chr3g0457271' => 'rch', 'RcHm_v2.0_Chr5g0018111' => 'rch', 'RcHm_v2.0_Chr5g0021011' => 'rch', 'RcHm_v2.0_Chr5g0081171' => 'rch', 'RcHm_v2.0_Chr5g0081211' => 'rch', 'RcHm_v2.0_Chr6g0275871' => 'rch', 'RcHm_v2.0_Chr6g0276071' => 'rch', 'RcHm_v2.0_Chr6g0285591' => 'rch', 'RcHm_v2.0_Chr6g0291931' => 'rch', 'RcHm_v2.0_Chr6g0292091' => 'rch', 'RcHm_v2.0_Chr6g0292271' => 'rch', 'RcHm_v2.0_Chr7g0221261' => 'rch', 'Rhsim08G0219900' => 'rsi', 'Rhsim08G0220200' => 'rsi', 'Rhsim08G0237800' => 'rsi', 'Rhsim08G0238800' => 'rsi', 'Sabra09G0102700' => 'sbr', 'Sabra09G0127200' => 'sbr', 'Sabra11G0003700' => 'sbr', 'Sabra15G0014700' => 'sbr', 'Sc19g0000590' => 'sci', 'Sc19g0001870' => 'sci', 'SGA_v2.0_scaffold1G00346' => 'sas', 'SGA_v2.0_scaffold1G00575' => 'sas', 'SGA_v2.0_scaffold1G00761' => 'sas', 'SGA_v2.0_scaffold232G43501' => 'sas', 'TAR625G1137' => 'tar', 'Thecc.03G222100' => 'tca', 'TPR.G12691' => 'tpr', 'TWI34G0727' => 'twi', 'TWI36G0117' => 'twi', 'VMungo1309G0868' => 'vmu' ), 'gf_id' => 'HOM05D001729', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001729' ), 'data_identifier' => 'HOM05D001729', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001729', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '375', 'num_species' => '42' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'Ah.07g204710' => 'amhyb', 'AUR62006001' => 'cqu', 'AUR62006002' => 'cqu', 'AUR62006003' => 'cqu', 'AUR62015641' => 'cqu', 'AUR62027174' => 'cqu', 'AUR62035623' => 'cqu', 'AUR62035624' => 'cqu', 'AUR62035625' => 'cqu', 'AUR62035626' => 'cqu', 'CAN.G1110.53' => 'can', 'CANSAT80G0415' => 'cansat', 'Ca_21364_v3' => 'car', 'COL.COLO4_30693' => 'col', 'COL.COLO4_30694' => 'col', 'COL.COLO4_30695' => 'col', 'COL.COLO4_30696' => 'col', 'COL.COLO4_34020' => 'col', 'DCAR_004585' => 'dca', 'Dinv04029' => 'din', 'Dinv34857' => 'din', 'Duzib147G0011' => 'dzi', 'Duzib170G0599' => 'dzi', 'Duzib192G1051' => 'dzi', 'FAN01G0708' => 'fan', 'FAN01G0742' => 'fan', 'FAN02G0048' => 'fan', 'FAN02G0583' => 'fan', 'FAN02G0688' => 'fan', 'FAN02G1588' => 'fan', 'FAN02G2194' => 'fan', 'FAN02G2750' => 'fan', 'FAN02G3094' => 'fan', 'FAN02G3887' => 'fan', 'FAN02G3911' => 'fan', 'FAN02G3994' => 'fan', 'FAN02G4432' => 'fan', 'FAN02G4556' => 'fan', 'FAN03G1977' => 'fan', 'FAN03G2781' => 'fan', 'FAN03G2850' => 'fan', 'FAN03G3155' => 'fan', 'FAN04G2487' => 'fan', 'FAN05G0208' => 'fan', 'FAN05G0656' => 'fan', 'FAN05G0696' => 'fan', 'FAN05G0810' => 'fan', 'FAN05G1447' => 'fan', 'FAN05G2640' => 'fan', 'FAN05G2911' => 'fan', 'FAN05G3901' => 'fan', 'FAN05G4859' => 'fan', 'FAN05G4861' => 'fan', 'FAN05G4988' => 'fan', 'FAN05G5187' => 'fan', 'FAN05G5452' => 'fan', 'FAN05G5500' => 'fan', 'FAN05G5688' => 'fan', 'FAN06G0177' => 'fan', 'FAN06G0675' => 'fan', 'FAN06G1290' => 'fan', 'FAN06G2191' => 'fan', 'FAN06G2405' => 'fan', 'FAN06G3231' => 'fan', 'FAN06G3932' => 'fan', 'FAN07G0163' => 'fan', 'FAN07G0471' => 'fan', 'FAN07G1354' => 'fan', 'FAN08G0338' => 'fan', 'FAN08G1373' => 'fan', 'FAN08G2539' => 'fan', 'FAN08G2728' => 'fan', 'FAN09G0608' => 'fan', 'FAN09G1136' => 'fan', 'FAN09G1958' => 'fan', 'FAN09G2508' => 'fan', 'FAN09G2597' => 'fan', 'FAN09G2658' => 'fan', 'FAN09G2757' => 'fan', 'FAN09G2983' => 'fan', 'FAN09G3130' => 'fan', 'FAN09G3565' => 'fan', 'FAN09G3613' => 'fan', 'FAN09G4011' => 'fan', 'FAN09G4239' => 'fan', 'FAN09G4277' => 'fan', 'FAN09G4720' => 'fan', 'FAN11G0139' => 'fan', 'FAN11G1727' => 'fan', 'FAN11G2672' => 'fan', 'FAN11G2795' => 'fan', 'FAN11G3238' => 'fan', 'FAN11G3734' => 'fan', 'FAN12G0631' => 'fan', 'FAN12G2239' => 'fan', 'FAN12G2308' => 'fan', 'FAN12G2569' => 'fan', 'FAN12G2623' => 'fan', 'FAN13G3182' => 'fan', 'FAN14G0053' => 'fan', 'FAN14G0370' => 'fan', 'FAN14G0382' => 'fan', 'FAN14G0421' => 'fan', 'FAN14G0866' => 'fan', 'FAN14G1187' => 'fan', 'FAN14G1727' => 'fan', 'FAN14G1791' => 'fan', 'FAN14G2361' => 'fan', 'FAN14G2668' => 'fan', 'FAN14G2770' => 'fan', 'FAN14G2874' => 'fan', 'FAN14G3193' => 'fan', 'FAN14G3624' => 'fan', 'FAN14G3676' => 'fan', 'FAN14G3807' => 'fan', 'FAN14G4082' => 'fan', 'FAN14G4342' => 'fan', 'FAN14G4985' => 'fan', 'FAN14G5126' => 'fan', 'FAN14G5781' => 'fan', 'FAN14G5808' => 'fan', 'FAN14G5949' => 'fan', 'FAN15G0828' => 'fan', 'FAN15G1054' => 'fan', 'FAN15G2023' => 'fan', 'FAN15G2506' => 'fan', 'FAN16G0128' => 'fan', 'FAN16G0249' => 'fan', 'FAN16G0429' => 'fan', 'FAN16G1493' => 'fan', 'FAN16G2210' => 'fan', 'FAN16G2506' => 'fan', 'FAN18G1542' => 'fan', 'FAN18G4057' => 'fan', 'FAN19G0745' => 'fan', 'FAN19G1216' => 'fan', 'FAN19G1733' => 'fan', 'FAN20G0258' => 'fan', 'FAN20G1095' => 'fan', 'FAN20G1557' => 'fan', 'FAN21G0302' => 'fan', 'FAN21G0519' => 'fan', 'FAN21G0970' => 'fan', 'FAN21G1159' => 'fan', 'FAN21G1312' => 'fan', 'FAN21G1440' => 'fan', 'FAN21G1715' => 'fan', 'FAN23G1584' => 'fan', 'FAN24G0045' => 'fan', 'FAN24G0053' => 'fan', 'FAN24G1500' => 'fan', 'FAN24G1817' => 'fan', 'FAN24G2147' => 'fan', 'FAN24G2236' => 'fan', 'FAN24G2446' => 'fan', 'FAN24G2684' => 'fan', 'FAN25G0187' => 'fan', 'FAN25G0505' => 'fan', 'FAN25G0589' => 'fan', 'FAN25G3663' => 'fan', 'FAN26G1025' => 'fan', 'FAN26G2860' => 'fan', 'FAN27G1329' => 'fan', 'FAN27G3392' => 'fan', 'FvH4_1g02011' => 'fve', 'FvH4_1g06511' => 'fve', 'FvH4_2g19900' => 'fve', 'FvH4_2g19920' => 'fve', 'FvH4_2g24261' => 'fve', 'FvH4_2g24270' => 'fve', 'FvH4_2g24631' => 'fve', 'FvH4_2g30622' => 'fve', 'FvH4_3g12920' => 'fve', 'FvH4_3g30171' => 'fve', 'FvH4_3g35490' => 'fve', 'FvH4_3g43682' => 'fve', 'FvH4_3g43730' => 'fve', 'FvH4_3g43732' => 'fve', 'FvH4_3g43751' => 'fve', 'FvH4_3g43752' => 'fve', 'FvH4_3g43770' => 'fve', 'FvH4_3g44471' => 'fve', 'FvH4_3g44510' => 'fve', 'FvH4_3g44582' => 'fve', 'FvH4_4g16921' => 'fve', 'FvH4_4g17121' => 'fve', 'FvH4_4g17782' => 'fve', 'FvH4_4g17783' => 'fve', 'FvH4_4g18120' => 'fve', 'FvH4_4g31310' => 'fve', 'FvH4_4g35052' => 'fve', 'FvH4_5g30862' => 'fve', 'FvH4_6g01541' => 'fve', 'FvH4_6g02021' => 'fve', 'FvH4_6g02041' => 'fve', 'FvH4_6g02071' => 'fve', 'FvH4_6g02171' => 'fve', 'FvH4_6g03181' => 'fve', 'FvH4_6g03182' => 'fve', 'FvH4_6g03221' => 'fve', 'FvH4_6g03380' => 'fve', 'FvH4_6g05201' => 'fve', 'FvH4_6g05203' => 'fve', 'FvH4_6g20231' => 'fve', 'FvH4_6g31981' => 'fve', 'FvH4_6g32061' => 'fve', 'FvH4_6g37041' => 'fve', 'FvH4_6g37932' => 'fve', 'FvH4_6g38731' => 'fve', 'FvH4_6g39370' => 'fve', 'FvH4_6g39371' => 'fve', 'FvH4_6g40891' => 'fve', 'FvH4_6g40892' => 'fve', 'FvH4_6g43143' => 'fve', 'FvH4_6g45251' => 'fve', 'FvH4_6g45260' => 'fve', 'FvH4_6g45291' => 'fve', 'FvH4_6g45890' => 'fve', 'FvH4_6g46240' => 'fve', 'FvH4_6g46241' => 'fve', 'FvH4_6g46242' => 'fve', 'FvH4_6g46260' => 'fve', 'FvH4_6g46280' => 'fve', 'FvH4_6g46380' => 'fve', 'FvH4_7g12841' => 'fve', 'FvH4_7g31431' => 'fve', 'Glyma.09G075900' => 'gma', 'Gohir.A09G096401' => 'ghi', 'Gohir.D09G096101' => 'ghi', 'Gorai.006G112800' => 'gra', 'HanXRQChr04g0121411' => 'han', 'Hund15878' => 'sun', 'Lj2A1107G68' => 'lonja', 'Lj2A630G63' => 'lonja', 'Lj2A946T25' => 'lonja', 'Lj2C714T1' => 'lonja', 'Lj2C966T3' => 'lonja', 'Lj2C966T4' => 'lonja', 'Lj4g0002979' => 'lja', 'Lsat_1_v5_gn_5_30901' => 'lsa', 'Lsat_1_v5_gn_5_31100' => 'lsa', 'Lsat_1_v5_gn_5_38600' => 'lsa', 'Lsat_1_v5_gn_6_92061' => 'lsa', 'Manes.05G071301' => 'mes', 'MD02G1008700' => 'mdo', 'MD02G1008900' => 'mdo', 'MD03G1256400' => 'mdo', 'MD04G1180900' => 'mdo', 'MD04G1181000' => 'mdo', 'MD04G1181200' => 'mdo', 'MD05G1244200' => 'mdo', 'MD05G1324200' => 'mdo', 'MD09G1201600' => 'mdo', 'MD10G1000600' => 'mdo', 'MD14G1026900' => 'mdo', 'MD14G1187900' => 'mdo', 'MD15G1017800' => 'mdo', 'MD15G1018100' => 'mdo', 'Medtr4g124160' => 'mtr', 'Migut.L01260' => 'egut', 'Nitab4.5_0000008g0440' => 'nta', 'Nitab4.5_0000207g0170' => 'nta', 'Nitab4.5_0007671g0030' => 'nta', 'Nitab4.5_0010853g0020' => 'nta', 'Oeu057656.1' => 'oeu', 'PGSC0003DMG400005638' => 'stu', 'PGSC0003DMG400005639' => 'stu', 'Phvul.009G222800' => 'pvu', 'Potri.009G132400' => 'ptr', 'Potri.009G163001' => 'ptr', 'Potri.011G000700' => 'ptr', 'Potri.011G004800' => 'ptr', 'Prupe.1G509300' => 'ppe', 'Prupe.1G509700' => 'ppe', 'Prupe.1G510400' => 'ppe', 'Prupe.1G510700' => 'ppe', 'Prupe.1G512600' => 'ppe', 'Prupe.2G073200' => 'ppe', 'Prupe.3G059500' => 'ppe', 'Prupe.3G059600' => 'ppe', 'Prupe.3G246100' => 'ppe', 'Prupe.3G265100' => 'ppe', 'Prupe.4G034700' => 'ppe', 'Prupe.4G052100' => 'ppe', 'Prupe.4G053600' => 'ppe', 'Prupe.5G068800' => 'ppe', 'Prupe.5G070600' => 'ppe', 'Prupe.6G075400' => 'ppe', 'Prupe.6G075500' => 'ppe', 'Prupe.6G076400' => 'ppe', 'Prupe.8G110700' => 'ppe', 'Psat4g020960' => 'psa', 'PSO135G0788' => 'pso', 'PSO210G6463' => 'pso', 'PSO384G0370' => 'pso', 'PSO386G0056' => 'pso', 'QL01p006048' => 'qlo', 'QL02p054283' => 'qlo', 'QL05p008000' => 'qlo', 'QL05p008212' => 'qlo', 'QL05p008950' => 'qlo', 'QL05p009042' => 'qlo', 'QL05p009518' => 'qlo', 'QL05p012589' => 'qlo', 'QL05p012608' => 'qlo', 'QL05p012650' => 'qlo', 'QL05p012667' => 'qlo', 'QL05p014501' => 'qlo', 'QL05p052800' => 'qlo', 'QL05p065010' => 'qlo', 'QL05p074156' => 'qlo', 'QL05p074160' => 'qlo', 'QL05p074174' => 'qlo', 'QL05p074178' => 'qlo', 'QL05p074214' => 'qlo', 'QL06p001050' => 'qlo', 'QL06p001056' => 'qlo', 'QL06p006093' => 'qlo', 'QL06p006111' => 'qlo', 'QL07p019784' => 'qlo', 'QL07p019801' => 'qlo', 'QL07p036110' => 'qlo', 'QL07p036134' => 'qlo', 'QL07p036147' => 'qlo', 'QL07p036156' => 'qlo', 'QL07p036300' => 'qlo', 'QL07p036320' => 'qlo', 'QL08p014547' => 'qlo', 'QL08p014551' => 'qlo', 'QL08p043319' => 'qlo', 'QL08p043324' => 'qlo', 'QL11p009094' => 'qlo', 'RcHm_v2.0_Chr1g0380481' => 'rch', 'RcHm_v2.0_Chr2g0089331' => 'rch', 'RcHm_v2.0_Chr2g0123691' => 'rch', 'RcHm_v2.0_Chr2g0151111' => 'rch', 'RcHm_v2.0_Chr2g0163011' => 'rch', 'RcHm_v2.0_Chr2g0163051' => 'rch', 'RcHm_v2.0_Chr2g0164671' => 'rch', 'RcHm_v2.0_Chr2g0164681' => 'rch', 'RcHm_v2.0_Chr2g0164721' => 'rch', 'RcHm_v2.0_Chr3g0449911' => 'rch', 'RcHm_v2.0_Chr3g0450211' => 'rch', 'RcHm_v2.0_Chr3g0457271' => 'rch', 'RcHm_v2.0_Chr5g0018111' => 'rch', 'RcHm_v2.0_Chr5g0021011' => 'rch', 'RcHm_v2.0_Chr5g0081171' => 'rch', 'RcHm_v2.0_Chr5g0081211' => 'rch', 'RcHm_v2.0_Chr6g0275871' => 'rch', 'RcHm_v2.0_Chr6g0276071' => 'rch', 'RcHm_v2.0_Chr6g0285591' => 'rch', 'RcHm_v2.0_Chr6g0291931' => 'rch', 'RcHm_v2.0_Chr6g0292091' => 'rch', 'RcHm_v2.0_Chr6g0292271' => 'rch', 'RcHm_v2.0_Chr7g0221261' => 'rch', 'Rhsim08G0219900' => 'rsi', 'Rhsim08G0220200' => 'rsi', 'Rhsim08G0237800' => 'rsi', 'Rhsim08G0238800' => 'rsi', 'Sabra09G0102700' => 'sbr', 'Sabra09G0127200' => 'sbr', 'Sabra11G0003700' => 'sbr', 'Sabra15G0014700' => 'sbr', 'Sc19g0000590' => 'sci', 'Sc19g0001870' => 'sci', 'SGA_v2.0_scaffold1G00346' => 'sas', 'SGA_v2.0_scaffold1G00575' => 'sas', 'SGA_v2.0_scaffold1G00761' => 'sas', 'SGA_v2.0_scaffold232G43501' => 'sas', 'TAR625G1137' => 'tar', 'Thecc.03G222100' => 'tca', 'TPR.G12691' => 'tpr', 'TWI34G0727' => 'twi', 'TWI36G0117' => 'twi', 'VMungo1309G0868' => 'vmu' ) $gf_id = 'HOM05D001729' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001729' ) $data_identifier = 'HOM05D001729' $data_type = 'gf_id' $species_gene_counts = array( 'amhyb' => (int) 1, 'cqu' => (int) 9, 'can' => (int) 1, 'cansat' => (int) 1, 'car' => (int) 1, 'col' => (int) 5, 'dca' => (int) 1, 'din' => (int) 2, 'dzi' => (int) 3, 'fan' => (int) 140, 'fve' => (int) 62, 'gma' => (int) 1, 'ghi' => (int) 2, 'gra' => (int) 1, 'han' => (int) 1, 'sun' => (int) 1, 'lonja' => (int) 6, 'lja' => (int) 1, 'lsa' => (int) 4, 'mes' => (int) 1, 'mdo' => (int) 14, 'mtr' => (int) 1, 'egut' => (int) 1, 'nta' => (int) 4, 'oeu' => (int) 1, 'stu' => (int) 2, 'pvu' => (int) 1, 'ptr' => (int) 4, 'ppe' => (int) 19, 'psa' => (int) 1, 'pso' => (int) 4, 'qlo' => (int) 36, 'rch' => (int) 23, 'rsi' => (int) 4, 'sbr' => (int) 4, 'sci' => (int) 2, 'sas' => (int) 4, 'tar' => (int) 1, 'tca' => (int) 1, 'tpr' => (int) 1, 'twi' => (int) 2, 'vmu' => (int) 1 ) $gf_gene_species = 'vmu' $gf_gene_id = 'VMungo1309G0868' $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' => 'HOM05D001729', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '375', 'num_species' => '42' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'Ah.07g204710' => 'amhyb', 'AUR62006001' => 'cqu', 'AUR62006002' => 'cqu', 'AUR62006003' => 'cqu', 'AUR62015641' => 'cqu', 'AUR62027174' => 'cqu', 'AUR62035623' => 'cqu', 'AUR62035624' => 'cqu', 'AUR62035625' => 'cqu', 'AUR62035626' => 'cqu', 'CAN.G1110.53' => 'can', 'CANSAT80G0415' => 'cansat', 'Ca_21364_v3' => 'car', 'COL.COLO4_30693' => 'col', 'COL.COLO4_30694' => 'col', 'COL.COLO4_30695' => 'col', 'COL.COLO4_30696' => 'col', 'COL.COLO4_34020' => 'col', 'DCAR_004585' => 'dca', 'Dinv04029' => 'din', 'Dinv34857' => 'din', 'Duzib147G0011' => 'dzi', 'Duzib170G0599' => 'dzi', 'Duzib192G1051' => 'dzi', 'FAN01G0708' => 'fan', 'FAN01G0742' => 'fan', 'FAN02G0048' => 'fan', 'FAN02G0583' => 'fan', 'FAN02G0688' => 'fan', 'FAN02G1588' => 'fan', 'FAN02G2194' => 'fan', 'FAN02G2750' => 'fan', 'FAN02G3094' => 'fan', 'FAN02G3887' => 'fan', 'FAN02G3911' => 'fan', 'FAN02G3994' => 'fan', 'FAN02G4432' => 'fan', 'FAN02G4556' => 'fan', 'FAN03G1977' => 'fan', 'FAN03G2781' => 'fan', 'FAN03G2850' => 'fan', 'FAN03G3155' => 'fan', 'FAN04G2487' => 'fan', 'FAN05G0208' => 'fan', 'FAN05G0656' => 'fan', 'FAN05G0696' => 'fan', 'FAN05G0810' => 'fan', 'FAN05G1447' => 'fan', 'FAN05G2640' => 'fan', 'FAN05G2911' => 'fan', 'FAN05G3901' => 'fan', 'FAN05G4859' => 'fan', 'FAN05G4861' => 'fan', 'FAN05G4988' => 'fan', 'FAN05G5187' => 'fan', 'FAN05G5452' => 'fan', 'FAN05G5500' => 'fan', 'FAN05G5688' => 'fan', 'FAN06G0177' => 'fan', 'FAN06G0675' => 'fan', 'FAN06G1290' => 'fan', 'FAN06G2191' => 'fan', 'FAN06G2405' => 'fan', 'FAN06G3231' => 'fan', 'FAN06G3932' => 'fan', 'FAN07G0163' => 'fan', 'FAN07G0471' => 'fan', 'FAN07G1354' => 'fan', 'FAN08G0338' => 'fan', 'FAN08G1373' => 'fan', 'FAN08G2539' => 'fan', 'FAN08G2728' => 'fan', 'FAN09G0608' => 'fan', 'FAN09G1136' => 'fan', 'FAN09G1958' => 'fan', 'FAN09G2508' => 'fan', 'FAN09G2597' => 'fan', 'FAN09G2658' => 'fan', 'FAN09G2757' => 'fan', 'FAN09G2983' => 'fan', 'FAN09G3130' => 'fan', 'FAN09G3565' => 'fan', 'FAN09G3613' => 'fan', 'FAN09G4011' => 'fan', 'FAN09G4239' => 'fan', 'FAN09G4277' => 'fan', 'FAN09G4720' => 'fan', 'FAN11G0139' => 'fan', 'FAN11G1727' => 'fan', 'FAN11G2672' => 'fan', 'FAN11G2795' => 'fan', 'FAN11G3238' => 'fan', 'FAN11G3734' => 'fan', 'FAN12G0631' => 'fan', 'FAN12G2239' => 'fan', 'FAN12G2308' => 'fan', 'FAN12G2569' => 'fan', 'FAN12G2623' => 'fan', 'FAN13G3182' => 'fan', 'FAN14G0053' => 'fan', 'FAN14G0370' => 'fan', 'FAN14G0382' => 'fan', 'FAN14G0421' => 'fan', 'FAN14G0866' => 'fan', 'FAN14G1187' => 'fan', 'FAN14G1727' => 'fan', 'FAN14G1791' => 'fan', 'FAN14G2361' => 'fan', 'FAN14G2668' => 'fan', 'FAN14G2770' => 'fan', 'FAN14G2874' => 'fan', 'FAN14G3193' => 'fan', 'FAN14G3624' => 'fan', 'FAN14G3676' => 'fan', 'FAN14G3807' => 'fan', 'FAN14G4082' => 'fan', 'FAN14G4342' => 'fan', 'FAN14G4985' => 'fan', 'FAN14G5126' => 'fan', 'FAN14G5781' => 'fan', 'FAN14G5808' => 'fan', 'FAN14G5949' => 'fan', 'FAN15G0828' => 'fan', 'FAN15G1054' => 'fan', 'FAN15G2023' => 'fan', 'FAN15G2506' => 'fan', 'FAN16G0128' => 'fan', 'FAN16G0249' => 'fan', 'FAN16G0429' => 'fan', 'FAN16G1493' => 'fan', 'FAN16G2210' => 'fan', 'FAN16G2506' => 'fan', 'FAN18G1542' => 'fan', 'FAN18G4057' => 'fan', 'FAN19G0745' => 'fan', 'FAN19G1216' => 'fan', 'FAN19G1733' => 'fan', 'FAN20G0258' => 'fan', 'FAN20G1095' => 'fan', 'FAN20G1557' => 'fan', 'FAN21G0302' => 'fan', 'FAN21G0519' => 'fan', 'FAN21G0970' => 'fan', 'FAN21G1159' => 'fan', 'FAN21G1312' => 'fan', 'FAN21G1440' => 'fan', 'FAN21G1715' => 'fan', 'FAN23G1584' => 'fan', 'FAN24G0045' => 'fan', 'FAN24G0053' => 'fan', 'FAN24G1500' => 'fan', 'FAN24G1817' => 'fan', 'FAN24G2147' => 'fan', 'FAN24G2236' => 'fan', 'FAN24G2446' => 'fan', 'FAN24G2684' => 'fan', 'FAN25G0187' => 'fan', 'FAN25G0505' => 'fan', 'FAN25G0589' => 'fan', 'FAN25G3663' => 'fan', 'FAN26G1025' => 'fan', 'FAN26G2860' => 'fan', 'FAN27G1329' => 'fan', 'FAN27G3392' => 'fan', 'FvH4_1g02011' => 'fve', 'FvH4_1g06511' => 'fve', 'FvH4_2g19900' => 'fve', 'FvH4_2g19920' => 'fve', 'FvH4_2g24261' => 'fve', 'FvH4_2g24270' => 'fve', 'FvH4_2g24631' => 'fve', 'FvH4_2g30622' => 'fve', 'FvH4_3g12920' => 'fve', 'FvH4_3g30171' => 'fve', 'FvH4_3g35490' => 'fve', 'FvH4_3g43682' => 'fve', 'FvH4_3g43730' => 'fve', 'FvH4_3g43732' => 'fve', 'FvH4_3g43751' => 'fve', 'FvH4_3g43752' => 'fve', 'FvH4_3g43770' => 'fve', 'FvH4_3g44471' => 'fve', 'FvH4_3g44510' => 'fve', 'FvH4_3g44582' => 'fve', 'FvH4_4g16921' => 'fve', 'FvH4_4g17121' => 'fve', 'FvH4_4g17782' => 'fve', 'FvH4_4g17783' => 'fve', 'FvH4_4g18120' => 'fve', 'FvH4_4g31310' => 'fve', 'FvH4_4g35052' => 'fve', 'FvH4_5g30862' => 'fve', 'FvH4_6g01541' => 'fve', 'FvH4_6g02021' => 'fve', 'FvH4_6g02041' => 'fve', 'FvH4_6g02071' => 'fve', 'FvH4_6g02171' => 'fve', 'FvH4_6g03181' => 'fve', 'FvH4_6g03182' => 'fve', 'FvH4_6g03221' => 'fve', 'FvH4_6g03380' => 'fve', 'FvH4_6g05201' => 'fve', 'FvH4_6g05203' => 'fve', 'FvH4_6g20231' => 'fve', 'FvH4_6g31981' => 'fve', 'FvH4_6g32061' => 'fve', 'FvH4_6g37041' => 'fve', 'FvH4_6g37932' => 'fve', 'FvH4_6g38731' => 'fve', 'FvH4_6g39370' => 'fve', 'FvH4_6g39371' => 'fve', 'FvH4_6g40891' => 'fve', 'FvH4_6g40892' => 'fve', 'FvH4_6g43143' => 'fve', 'FvH4_6g45251' => 'fve', 'FvH4_6g45260' => 'fve', 'FvH4_6g45291' => 'fve', 'FvH4_6g45890' => 'fve', 'FvH4_6g46240' => 'fve', 'FvH4_6g46241' => 'fve', 'FvH4_6g46242' => 'fve', 'FvH4_6g46260' => 'fve', 'FvH4_6g46280' => 'fve', 'FvH4_6g46380' => 'fve', 'FvH4_7g12841' => 'fve', 'FvH4_7g31431' => 'fve', 'Glyma.09G075900' => 'gma', 'Gohir.A09G096401' => 'ghi', 'Gohir.D09G096101' => 'ghi', 'Gorai.006G112800' => 'gra', 'HanXRQChr04g0121411' => 'han', 'Hund15878' => 'sun', 'Lj2A1107G68' => 'lonja', 'Lj2A630G63' => 'lonja', 'Lj2A946T25' => 'lonja', 'Lj2C714T1' => 'lonja', 'Lj2C966T3' => 'lonja', 'Lj2C966T4' => 'lonja', 'Lj4g0002979' => 'lja', 'Lsat_1_v5_gn_5_30901' => 'lsa', 'Lsat_1_v5_gn_5_31100' => 'lsa', 'Lsat_1_v5_gn_5_38600' => 'lsa', 'Lsat_1_v5_gn_6_92061' => 'lsa', 'Manes.05G071301' => 'mes', 'MD02G1008700' => 'mdo', 'MD02G1008900' => 'mdo', 'MD03G1256400' => 'mdo', 'MD04G1180900' => 'mdo', 'MD04G1181000' => 'mdo', 'MD04G1181200' => 'mdo', 'MD05G1244200' => 'mdo', 'MD05G1324200' => 'mdo', 'MD09G1201600' => 'mdo', 'MD10G1000600' => 'mdo', 'MD14G1026900' => 'mdo', 'MD14G1187900' => 'mdo', 'MD15G1017800' => 'mdo', 'MD15G1018100' => 'mdo', 'Medtr4g124160' => 'mtr', 'Migut.L01260' => 'egut', 'Nitab4.5_0000008g0440' => 'nta', 'Nitab4.5_0000207g0170' => 'nta', 'Nitab4.5_0007671g0030' => 'nta', 'Nitab4.5_0010853g0020' => 'nta', 'Oeu057656.1' => 'oeu', 'PGSC0003DMG400005638' => 'stu', 'PGSC0003DMG400005639' => 'stu', 'Phvul.009G222800' => 'pvu', 'Potri.009G132400' => 'ptr', 'Potri.009G163001' => 'ptr', 'Potri.011G000700' => 'ptr', 'Potri.011G004800' => 'ptr', 'Prupe.1G509300' => 'ppe', 'Prupe.1G509700' => 'ppe', 'Prupe.1G510400' => 'ppe', 'Prupe.1G510700' => 'ppe', 'Prupe.1G512600' => 'ppe', 'Prupe.2G073200' => 'ppe', 'Prupe.3G059500' => 'ppe', 'Prupe.3G059600' => 'ppe', 'Prupe.3G246100' => 'ppe', 'Prupe.3G265100' => 'ppe', 'Prupe.4G034700' => 'ppe', 'Prupe.4G052100' => 'ppe', 'Prupe.4G053600' => 'ppe', 'Prupe.5G068800' => 'ppe', 'Prupe.5G070600' => 'ppe', 'Prupe.6G075400' => 'ppe', 'Prupe.6G075500' => 'ppe', 'Prupe.6G076400' => 'ppe', 'Prupe.8G110700' => 'ppe', 'Psat4g020960' => 'psa', 'PSO135G0788' => 'pso', 'PSO210G6463' => 'pso', 'PSO384G0370' => 'pso', 'PSO386G0056' => 'pso', 'QL01p006048' => 'qlo', 'QL02p054283' => 'qlo', 'QL05p008000' => 'qlo', 'QL05p008212' => 'qlo', 'QL05p008950' => 'qlo', 'QL05p009042' => 'qlo', 'QL05p009518' => 'qlo', 'QL05p012589' => 'qlo', 'QL05p012608' => 'qlo', 'QL05p012650' => 'qlo', 'QL05p012667' => 'qlo', 'QL05p014501' => 'qlo', 'QL05p052800' => 'qlo', 'QL05p065010' => 'qlo', 'QL05p074156' => 'qlo', 'QL05p074160' => 'qlo', 'QL05p074174' => 'qlo', 'QL05p074178' => 'qlo', 'QL05p074214' => 'qlo', 'QL06p001050' => 'qlo', 'QL06p001056' => 'qlo', 'QL06p006093' => 'qlo', 'QL06p006111' => 'qlo', 'QL07p019784' => 'qlo', 'QL07p019801' => 'qlo', 'QL07p036110' => 'qlo', 'QL07p036134' => 'qlo', 'QL07p036147' => 'qlo', 'QL07p036156' => 'qlo', 'QL07p036300' => 'qlo', 'QL07p036320' => 'qlo', 'QL08p014547' => 'qlo', 'QL08p014551' => 'qlo', 'QL08p043319' => 'qlo', 'QL08p043324' => 'qlo', 'QL11p009094' => 'qlo', 'RcHm_v2.0_Chr1g0380481' => 'rch', 'RcHm_v2.0_Chr2g0089331' => 'rch', 'RcHm_v2.0_Chr2g0123691' => 'rch', 'RcHm_v2.0_Chr2g0151111' => 'rch', 'RcHm_v2.0_Chr2g0163011' => 'rch', 'RcHm_v2.0_Chr2g0163051' => 'rch', 'RcHm_v2.0_Chr2g0164671' => 'rch', 'RcHm_v2.0_Chr2g0164681' => 'rch', 'RcHm_v2.0_Chr2g0164721' => 'rch', 'RcHm_v2.0_Chr3g0449911' => 'rch', 'RcHm_v2.0_Chr3g0450211' => 'rch', 'RcHm_v2.0_Chr3g0457271' => 'rch', 'RcHm_v2.0_Chr5g0018111' => 'rch', 'RcHm_v2.0_Chr5g0021011' => 'rch', 'RcHm_v2.0_Chr5g0081171' => 'rch', 'RcHm_v2.0_Chr5g0081211' => 'rch', 'RcHm_v2.0_Chr6g0275871' => 'rch', 'RcHm_v2.0_Chr6g0276071' => 'rch', 'RcHm_v2.0_Chr6g0285591' => 'rch', 'RcHm_v2.0_Chr6g0291931' => 'rch', 'RcHm_v2.0_Chr6g0292091' => 'rch', 'RcHm_v2.0_Chr6g0292271' => 'rch', 'RcHm_v2.0_Chr7g0221261' => 'rch', 'Rhsim08G0219900' => 'rsi', 'Rhsim08G0220200' => 'rsi', 'Rhsim08G0237800' => 'rsi', 'Rhsim08G0238800' => 'rsi', 'Sabra09G0102700' => 'sbr', 'Sabra09G0127200' => 'sbr', 'Sabra11G0003700' => 'sbr', 'Sabra15G0014700' => 'sbr', 'Sc19g0000590' => 'sci', 'Sc19g0001870' => 'sci', 'SGA_v2.0_scaffold1G00346' => 'sas', 'SGA_v2.0_scaffold1G00575' => 'sas', 'SGA_v2.0_scaffold1G00761' => 'sas', 'SGA_v2.0_scaffold232G43501' => 'sas', 'TAR625G1137' => 'tar', 'Thecc.03G222100' => 'tca', 'TPR.G12691' => 'tpr', 'TWI34G0727' => 'twi', 'TWI36G0117' => 'twi', 'VMungo1309G0868' => 'vmu' ), 'gf_id' => 'HOM05D001729', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001729' ), 'data_identifier' => 'HOM05D001729', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001729', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '375', 'num_species' => '42' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'Ah.07g204710' => 'amhyb', 'AUR62006001' => 'cqu', 'AUR62006002' => 'cqu', 'AUR62006003' => 'cqu', 'AUR62015641' => 'cqu', 'AUR62027174' => 'cqu', 'AUR62035623' => 'cqu', 'AUR62035624' => 'cqu', 'AUR62035625' => 'cqu', 'AUR62035626' => 'cqu', 'CAN.G1110.53' => 'can', 'CANSAT80G0415' => 'cansat', 'Ca_21364_v3' => 'car', 'COL.COLO4_30693' => 'col', 'COL.COLO4_30694' => 'col', 'COL.COLO4_30695' => 'col', 'COL.COLO4_30696' => 'col', 'COL.COLO4_34020' => 'col', 'DCAR_004585' => 'dca', 'Dinv04029' => 'din', 'Dinv34857' => 'din', 'Duzib147G0011' => 'dzi', 'Duzib170G0599' => 'dzi', 'Duzib192G1051' => 'dzi', 'FAN01G0708' => 'fan', 'FAN01G0742' => 'fan', 'FAN02G0048' => 'fan', 'FAN02G0583' => 'fan', 'FAN02G0688' => 'fan', 'FAN02G1588' => 'fan', 'FAN02G2194' => 'fan', 'FAN02G2750' => 'fan', 'FAN02G3094' => 'fan', 'FAN02G3887' => 'fan', 'FAN02G3911' => 'fan', 'FAN02G3994' => 'fan', 'FAN02G4432' => 'fan', 'FAN02G4556' => 'fan', 'FAN03G1977' => 'fan', 'FAN03G2781' => 'fan', 'FAN03G2850' => 'fan', 'FAN03G3155' => 'fan', 'FAN04G2487' => 'fan', 'FAN05G0208' => 'fan', 'FAN05G0656' => 'fan', 'FAN05G0696' => 'fan', 'FAN05G0810' => 'fan', 'FAN05G1447' => 'fan', 'FAN05G2640' => 'fan', 'FAN05G2911' => 'fan', 'FAN05G3901' => 'fan', 'FAN05G4859' => 'fan', 'FAN05G4861' => 'fan', 'FAN05G4988' => 'fan', 'FAN05G5187' => 'fan', 'FAN05G5452' => 'fan', 'FAN05G5500' => 'fan', 'FAN05G5688' => 'fan', 'FAN06G0177' => 'fan', 'FAN06G0675' => 'fan', 'FAN06G1290' => 'fan', 'FAN06G2191' => 'fan', 'FAN06G2405' => 'fan', 'FAN06G3231' => 'fan', 'FAN06G3932' => 'fan', 'FAN07G0163' => 'fan', 'FAN07G0471' => 'fan', 'FAN07G1354' => 'fan', 'FAN08G0338' => 'fan', 'FAN08G1373' => 'fan', 'FAN08G2539' => 'fan', 'FAN08G2728' => 'fan', 'FAN09G0608' => 'fan', 'FAN09G1136' => 'fan', 'FAN09G1958' => 'fan', 'FAN09G2508' => 'fan', 'FAN09G2597' => 'fan', 'FAN09G2658' => 'fan', 'FAN09G2757' => 'fan', 'FAN09G2983' => 'fan', 'FAN09G3130' => 'fan', 'FAN09G3565' => 'fan', 'FAN09G3613' => 'fan', 'FAN09G4011' => 'fan', 'FAN09G4239' => 'fan', 'FAN09G4277' => 'fan', 'FAN09G4720' => 'fan', 'FAN11G0139' => 'fan', 'FAN11G1727' => 'fan', 'FAN11G2672' => 'fan', 'FAN11G2795' => 'fan', 'FAN11G3238' => 'fan', 'FAN11G3734' => 'fan', 'FAN12G0631' => 'fan', 'FAN12G2239' => 'fan', 'FAN12G2308' => 'fan', 'FAN12G2569' => 'fan', 'FAN12G2623' => 'fan', 'FAN13G3182' => 'fan', 'FAN14G0053' => 'fan', 'FAN14G0370' => 'fan', 'FAN14G0382' => 'fan', 'FAN14G0421' => 'fan', 'FAN14G0866' => 'fan', 'FAN14G1187' => 'fan', 'FAN14G1727' => 'fan', 'FAN14G1791' => 'fan', 'FAN14G2361' => 'fan', 'FAN14G2668' => 'fan', 'FAN14G2770' => 'fan', 'FAN14G2874' => 'fan', 'FAN14G3193' => 'fan', 'FAN14G3624' => 'fan', 'FAN14G3676' => 'fan', 'FAN14G3807' => 'fan', 'FAN14G4082' => 'fan', 'FAN14G4342' => 'fan', 'FAN14G4985' => 'fan', 'FAN14G5126' => 'fan', 'FAN14G5781' => 'fan', 'FAN14G5808' => 'fan', 'FAN14G5949' => 'fan', 'FAN15G0828' => 'fan', 'FAN15G1054' => 'fan', 'FAN15G2023' => 'fan', 'FAN15G2506' => 'fan', 'FAN16G0128' => 'fan', 'FAN16G0249' => 'fan', 'FAN16G0429' => 'fan', 'FAN16G1493' => 'fan', 'FAN16G2210' => 'fan', 'FAN16G2506' => 'fan', 'FAN18G1542' => 'fan', 'FAN18G4057' => 'fan', 'FAN19G0745' => 'fan', 'FAN19G1216' => 'fan', 'FAN19G1733' => 'fan', 'FAN20G0258' => 'fan', 'FAN20G1095' => 'fan', 'FAN20G1557' => 'fan', 'FAN21G0302' => 'fan', 'FAN21G0519' => 'fan', 'FAN21G0970' => 'fan', 'FAN21G1159' => 'fan', 'FAN21G1312' => 'fan', 'FAN21G1440' => 'fan', 'FAN21G1715' => 'fan', 'FAN23G1584' => 'fan', 'FAN24G0045' => 'fan', 'FAN24G0053' => 'fan', 'FAN24G1500' => 'fan', 'FAN24G1817' => 'fan', 'FAN24G2147' => 'fan', 'FAN24G2236' => 'fan', 'FAN24G2446' => 'fan', 'FAN24G2684' => 'fan', 'FAN25G0187' => 'fan', 'FAN25G0505' => 'fan', 'FAN25G0589' => 'fan', 'FAN25G3663' => 'fan', 'FAN26G1025' => 'fan', 'FAN26G2860' => 'fan', 'FAN27G1329' => 'fan', 'FAN27G3392' => 'fan', 'FvH4_1g02011' => 'fve', 'FvH4_1g06511' => 'fve', 'FvH4_2g19900' => 'fve', 'FvH4_2g19920' => 'fve', 'FvH4_2g24261' => 'fve', 'FvH4_2g24270' => 'fve', 'FvH4_2g24631' => 'fve', 'FvH4_2g30622' => 'fve', 'FvH4_3g12920' => 'fve', 'FvH4_3g30171' => 'fve', 'FvH4_3g35490' => 'fve', 'FvH4_3g43682' => 'fve', 'FvH4_3g43730' => 'fve', 'FvH4_3g43732' => 'fve', 'FvH4_3g43751' => 'fve', 'FvH4_3g43752' => 'fve', 'FvH4_3g43770' => 'fve', 'FvH4_3g44471' => 'fve', 'FvH4_3g44510' => 'fve', 'FvH4_3g44582' => 'fve', 'FvH4_4g16921' => 'fve', 'FvH4_4g17121' => 'fve', 'FvH4_4g17782' => 'fve', 'FvH4_4g17783' => 'fve', 'FvH4_4g18120' => 'fve', 'FvH4_4g31310' => 'fve', 'FvH4_4g35052' => 'fve', 'FvH4_5g30862' => 'fve', 'FvH4_6g01541' => 'fve', 'FvH4_6g02021' => 'fve', 'FvH4_6g02041' => 'fve', 'FvH4_6g02071' => 'fve', 'FvH4_6g02171' => 'fve', 'FvH4_6g03181' => 'fve', 'FvH4_6g03182' => 'fve', 'FvH4_6g03221' => 'fve', 'FvH4_6g03380' => 'fve', 'FvH4_6g05201' => 'fve', 'FvH4_6g05203' => 'fve', 'FvH4_6g20231' => 'fve', 'FvH4_6g31981' => 'fve', 'FvH4_6g32061' => 'fve', 'FvH4_6g37041' => 'fve', 'FvH4_6g37932' => 'fve', 'FvH4_6g38731' => 'fve', 'FvH4_6g39370' => 'fve', 'FvH4_6g39371' => 'fve', 'FvH4_6g40891' => 'fve', 'FvH4_6g40892' => 'fve', 'FvH4_6g43143' => 'fve', 'FvH4_6g45251' => 'fve', 'FvH4_6g45260' => 'fve', 'FvH4_6g45291' => 'fve', 'FvH4_6g45890' => 'fve', 'FvH4_6g46240' => 'fve', 'FvH4_6g46241' => 'fve', 'FvH4_6g46242' => 'fve', 'FvH4_6g46260' => 'fve', 'FvH4_6g46280' => 'fve', 'FvH4_6g46380' => 'fve', 'FvH4_7g12841' => 'fve', 'FvH4_7g31431' => 'fve', 'Glyma.09G075900' => 'gma', 'Gohir.A09G096401' => 'ghi', 'Gohir.D09G096101' => 'ghi', 'Gorai.006G112800' => 'gra', 'HanXRQChr04g0121411' => 'han', 'Hund15878' => 'sun', 'Lj2A1107G68' => 'lonja', 'Lj2A630G63' => 'lonja', 'Lj2A946T25' => 'lonja', 'Lj2C714T1' => 'lonja', 'Lj2C966T3' => 'lonja', 'Lj2C966T4' => 'lonja', 'Lj4g0002979' => 'lja', 'Lsat_1_v5_gn_5_30901' => 'lsa', 'Lsat_1_v5_gn_5_31100' => 'lsa', 'Lsat_1_v5_gn_5_38600' => 'lsa', 'Lsat_1_v5_gn_6_92061' => 'lsa', 'Manes.05G071301' => 'mes', 'MD02G1008700' => 'mdo', 'MD02G1008900' => 'mdo', 'MD03G1256400' => 'mdo', 'MD04G1180900' => 'mdo', 'MD04G1181000' => 'mdo', 'MD04G1181200' => 'mdo', 'MD05G1244200' => 'mdo', 'MD05G1324200' => 'mdo', 'MD09G1201600' => 'mdo', 'MD10G1000600' => 'mdo', 'MD14G1026900' => 'mdo', 'MD14G1187900' => 'mdo', 'MD15G1017800' => 'mdo', 'MD15G1018100' => 'mdo', 'Medtr4g124160' => 'mtr', 'Migut.L01260' => 'egut', 'Nitab4.5_0000008g0440' => 'nta', 'Nitab4.5_0000207g0170' => 'nta', 'Nitab4.5_0007671g0030' => 'nta', 'Nitab4.5_0010853g0020' => 'nta', 'Oeu057656.1' => 'oeu', 'PGSC0003DMG400005638' => 'stu', 'PGSC0003DMG400005639' => 'stu', 'Phvul.009G222800' => 'pvu', 'Potri.009G132400' => 'ptr', 'Potri.009G163001' => 'ptr', 'Potri.011G000700' => 'ptr', 'Potri.011G004800' => 'ptr', 'Prupe.1G509300' => 'ppe', 'Prupe.1G509700' => 'ppe', 'Prupe.1G510400' => 'ppe', 'Prupe.1G510700' => 'ppe', 'Prupe.1G512600' => 'ppe', 'Prupe.2G073200' => 'ppe', 'Prupe.3G059500' => 'ppe', 'Prupe.3G059600' => 'ppe', 'Prupe.3G246100' => 'ppe', 'Prupe.3G265100' => 'ppe', 'Prupe.4G034700' => 'ppe', 'Prupe.4G052100' => 'ppe', 'Prupe.4G053600' => 'ppe', 'Prupe.5G068800' => 'ppe', 'Prupe.5G070600' => 'ppe', 'Prupe.6G075400' => 'ppe', 'Prupe.6G075500' => 'ppe', 'Prupe.6G076400' => 'ppe', 'Prupe.8G110700' => 'ppe', 'Psat4g020960' => 'psa', 'PSO135G0788' => 'pso', 'PSO210G6463' => 'pso', 'PSO384G0370' => 'pso', 'PSO386G0056' => 'pso', 'QL01p006048' => 'qlo', 'QL02p054283' => 'qlo', 'QL05p008000' => 'qlo', 'QL05p008212' => 'qlo', 'QL05p008950' => 'qlo', 'QL05p009042' => 'qlo', 'QL05p009518' => 'qlo', 'QL05p012589' => 'qlo', 'QL05p012608' => 'qlo', 'QL05p012650' => 'qlo', 'QL05p012667' => 'qlo', 'QL05p014501' => 'qlo', 'QL05p052800' => 'qlo', 'QL05p065010' => 'qlo', 'QL05p074156' => 'qlo', 'QL05p074160' => 'qlo', 'QL05p074174' => 'qlo', 'QL05p074178' => 'qlo', 'QL05p074214' => 'qlo', 'QL06p001050' => 'qlo', 'QL06p001056' => 'qlo', 'QL06p006093' => 'qlo', 'QL06p006111' => 'qlo', 'QL07p019784' => 'qlo', 'QL07p019801' => 'qlo', 'QL07p036110' => 'qlo', 'QL07p036134' => 'qlo', 'QL07p036147' => 'qlo', 'QL07p036156' => 'qlo', 'QL07p036300' => 'qlo', 'QL07p036320' => 'qlo', 'QL08p014547' => 'qlo', 'QL08p014551' => 'qlo', 'QL08p043319' => 'qlo', 'QL08p043324' => 'qlo', 'QL11p009094' => 'qlo', 'RcHm_v2.0_Chr1g0380481' => 'rch', 'RcHm_v2.0_Chr2g0089331' => 'rch', 'RcHm_v2.0_Chr2g0123691' => 'rch', 'RcHm_v2.0_Chr2g0151111' => 'rch', 'RcHm_v2.0_Chr2g0163011' => 'rch', 'RcHm_v2.0_Chr2g0163051' => 'rch', 'RcHm_v2.0_Chr2g0164671' => 'rch', 'RcHm_v2.0_Chr2g0164681' => 'rch', 'RcHm_v2.0_Chr2g0164721' => 'rch', 'RcHm_v2.0_Chr3g0449911' => 'rch', 'RcHm_v2.0_Chr3g0450211' => 'rch', 'RcHm_v2.0_Chr3g0457271' => 'rch', 'RcHm_v2.0_Chr5g0018111' => 'rch', 'RcHm_v2.0_Chr5g0021011' => 'rch', 'RcHm_v2.0_Chr5g0081171' => 'rch', 'RcHm_v2.0_Chr5g0081211' => 'rch', 'RcHm_v2.0_Chr6g0275871' => 'rch', 'RcHm_v2.0_Chr6g0276071' => 'rch', 'RcHm_v2.0_Chr6g0285591' => 'rch', 'RcHm_v2.0_Chr6g0291931' => 'rch', 'RcHm_v2.0_Chr6g0292091' => 'rch', 'RcHm_v2.0_Chr6g0292271' => 'rch', 'RcHm_v2.0_Chr7g0221261' => 'rch', 'Rhsim08G0219900' => 'rsi', 'Rhsim08G0220200' => 'rsi', 'Rhsim08G0237800' => 'rsi', 'Rhsim08G0238800' => 'rsi', 'Sabra09G0102700' => 'sbr', 'Sabra09G0127200' => 'sbr', 'Sabra11G0003700' => 'sbr', 'Sabra15G0014700' => 'sbr', 'Sc19g0000590' => 'sci', 'Sc19g0001870' => 'sci', 'SGA_v2.0_scaffold1G00346' => 'sas', 'SGA_v2.0_scaffold1G00575' => 'sas', 'SGA_v2.0_scaffold1G00761' => 'sas', 'SGA_v2.0_scaffold232G43501' => 'sas', 'TAR625G1137' => 'tar', 'Thecc.03G222100' => 'tca', 'TPR.G12691' => 'tpr', 'TWI34G0727' => 'twi', 'TWI36G0117' => 'twi', 'VMungo1309G0868' => 'vmu' ) $gf_id = 'HOM05D001729' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001729' ) $data_identifier = 'HOM05D001729' $data_type = 'gf_id' $species_gene_counts = array( 'amhyb' => (int) 1, 'cqu' => (int) 9, 'can' => (int) 1, 'cansat' => (int) 1, 'car' => (int) 1, 'col' => (int) 5, 'dca' => (int) 1, 'din' => (int) 2, 'dzi' => (int) 3, 'fan' => (int) 140, 'fve' => (int) 62, 'gma' => (int) 1, 'ghi' => (int) 2, 'gra' => (int) 1, 'han' => (int) 1, 'sun' => (int) 1, 'lonja' => (int) 6, 'lja' => (int) 1, 'lsa' => (int) 4, 'mes' => (int) 1, 'mdo' => (int) 14, 'mtr' => (int) 1, 'egut' => (int) 1, 'nta' => (int) 4, 'oeu' => (int) 1, 'stu' => (int) 2, 'pvu' => (int) 1, 'ptr' => (int) 4, 'ppe' => (int) 19, 'psa' => (int) 1, 'pso' => (int) 4, 'qlo' => (int) 36, 'rch' => (int) 23, 'rsi' => (int) 4, 'sbr' => (int) 4, 'sci' => (int) 2, 'sas' => (int) 4, 'tar' => (int) 1, 'tca' => (int) 1, 'tpr' => (int) 1, 'twi' => (int) 2, 'vmu' => (int) 1 ) $gf_gene_species = 'vmu' $gf_gene_id = 'VMungo1309G0868' $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' => 'HOM05D001729', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '375', 'num_species' => '42' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'Ah.07g204710' => 'amhyb', 'AUR62006001' => 'cqu', 'AUR62006002' => 'cqu', 'AUR62006003' => 'cqu', 'AUR62015641' => 'cqu', 'AUR62027174' => 'cqu', 'AUR62035623' => 'cqu', 'AUR62035624' => 'cqu', 'AUR62035625' => 'cqu', 'AUR62035626' => 'cqu', 'CAN.G1110.53' => 'can', 'CANSAT80G0415' => 'cansat', 'Ca_21364_v3' => 'car', 'COL.COLO4_30693' => 'col', 'COL.COLO4_30694' => 'col', 'COL.COLO4_30695' => 'col', 'COL.COLO4_30696' => 'col', 'COL.COLO4_34020' => 'col', 'DCAR_004585' => 'dca', 'Dinv04029' => 'din', 'Dinv34857' => 'din', 'Duzib147G0011' => 'dzi', 'Duzib170G0599' => 'dzi', 'Duzib192G1051' => 'dzi', 'FAN01G0708' => 'fan', 'FAN01G0742' => 'fan', 'FAN02G0048' => 'fan', 'FAN02G0583' => 'fan', 'FAN02G0688' => 'fan', 'FAN02G1588' => 'fan', 'FAN02G2194' => 'fan', 'FAN02G2750' => 'fan', 'FAN02G3094' => 'fan', 'FAN02G3887' => 'fan', 'FAN02G3911' => 'fan', 'FAN02G3994' => 'fan', 'FAN02G4432' => 'fan', 'FAN02G4556' => 'fan', 'FAN03G1977' => 'fan', 'FAN03G2781' => 'fan', 'FAN03G2850' => 'fan', 'FAN03G3155' => 'fan', 'FAN04G2487' => 'fan', 'FAN05G0208' => 'fan', 'FAN05G0656' => 'fan', 'FAN05G0696' => 'fan', 'FAN05G0810' => 'fan', 'FAN05G1447' => 'fan', 'FAN05G2640' => 'fan', 'FAN05G2911' => 'fan', 'FAN05G3901' => 'fan', 'FAN05G4859' => 'fan', 'FAN05G4861' => 'fan', 'FAN05G4988' => 'fan', 'FAN05G5187' => 'fan', 'FAN05G5452' => 'fan', 'FAN05G5500' => 'fan', 'FAN05G5688' => 'fan', 'FAN06G0177' => 'fan', 'FAN06G0675' => 'fan', 'FAN06G1290' => 'fan', 'FAN06G2191' => 'fan', 'FAN06G2405' => 'fan', 'FAN06G3231' => 'fan', 'FAN06G3932' => 'fan', 'FAN07G0163' => 'fan', 'FAN07G0471' => 'fan', 'FAN07G1354' => 'fan', 'FAN08G0338' => 'fan', 'FAN08G1373' => 'fan', 'FAN08G2539' => 'fan', 'FAN08G2728' => 'fan', 'FAN09G0608' => 'fan', 'FAN09G1136' => 'fan', 'FAN09G1958' => 'fan', 'FAN09G2508' => 'fan', 'FAN09G2597' => 'fan', 'FAN09G2658' => 'fan', 'FAN09G2757' => 'fan', 'FAN09G2983' => 'fan', 'FAN09G3130' => 'fan', 'FAN09G3565' => 'fan', 'FAN09G3613' => 'fan', 'FAN09G4011' => 'fan', 'FAN09G4239' => 'fan', 'FAN09G4277' => 'fan', 'FAN09G4720' => 'fan', 'FAN11G0139' => 'fan', 'FAN11G1727' => 'fan', 'FAN11G2672' => 'fan', 'FAN11G2795' => 'fan', 'FAN11G3238' => 'fan', 'FAN11G3734' => 'fan', 'FAN12G0631' => 'fan', 'FAN12G2239' => 'fan', 'FAN12G2308' => 'fan', 'FAN12G2569' => 'fan', 'FAN12G2623' => 'fan', 'FAN13G3182' => 'fan', 'FAN14G0053' => 'fan', 'FAN14G0370' => 'fan', 'FAN14G0382' => 'fan', 'FAN14G0421' => 'fan', 'FAN14G0866' => 'fan', 'FAN14G1187' => 'fan', 'FAN14G1727' => 'fan', 'FAN14G1791' => 'fan', 'FAN14G2361' => 'fan', 'FAN14G2668' => 'fan', 'FAN14G2770' => 'fan', 'FAN14G2874' => 'fan', 'FAN14G3193' => 'fan', 'FAN14G3624' => 'fan', 'FAN14G3676' => 'fan', 'FAN14G3807' => 'fan', 'FAN14G4082' => 'fan', 'FAN14G4342' => 'fan', 'FAN14G4985' => 'fan', 'FAN14G5126' => 'fan', 'FAN14G5781' => 'fan', 'FAN14G5808' => 'fan', 'FAN14G5949' => 'fan', 'FAN15G0828' => 'fan', 'FAN15G1054' => 'fan', 'FAN15G2023' => 'fan', 'FAN15G2506' => 'fan', 'FAN16G0128' => 'fan', 'FAN16G0249' => 'fan', 'FAN16G0429' => 'fan', 'FAN16G1493' => 'fan', 'FAN16G2210' => 'fan', 'FAN16G2506' => 'fan', 'FAN18G1542' => 'fan', 'FAN18G4057' => 'fan', 'FAN19G0745' => 'fan', 'FAN19G1216' => 'fan', 'FAN19G1733' => 'fan', 'FAN20G0258' => 'fan', 'FAN20G1095' => 'fan', 'FAN20G1557' => 'fan', 'FAN21G0302' => 'fan', 'FAN21G0519' => 'fan', 'FAN21G0970' => 'fan', 'FAN21G1159' => 'fan', 'FAN21G1312' => 'fan', 'FAN21G1440' => 'fan', 'FAN21G1715' => 'fan', 'FAN23G1584' => 'fan', 'FAN24G0045' => 'fan', 'FAN24G0053' => 'fan', 'FAN24G1500' => 'fan', 'FAN24G1817' => 'fan', 'FAN24G2147' => 'fan', 'FAN24G2236' => 'fan', 'FAN24G2446' => 'fan', 'FAN24G2684' => 'fan', 'FAN25G0187' => 'fan', 'FAN25G0505' => 'fan', 'FAN25G0589' => 'fan', 'FAN25G3663' => 'fan', 'FAN26G1025' => 'fan', 'FAN26G2860' => 'fan', 'FAN27G1329' => 'fan', 'FAN27G3392' => 'fan', 'FvH4_1g02011' => 'fve', 'FvH4_1g06511' => 'fve', 'FvH4_2g19900' => 'fve', 'FvH4_2g19920' => 'fve', 'FvH4_2g24261' => 'fve', 'FvH4_2g24270' => 'fve', 'FvH4_2g24631' => 'fve', 'FvH4_2g30622' => 'fve', 'FvH4_3g12920' => 'fve', 'FvH4_3g30171' => 'fve', 'FvH4_3g35490' => 'fve', 'FvH4_3g43682' => 'fve', 'FvH4_3g43730' => 'fve', 'FvH4_3g43732' => 'fve', 'FvH4_3g43751' => 'fve', 'FvH4_3g43752' => 'fve', 'FvH4_3g43770' => 'fve', 'FvH4_3g44471' => 'fve', 'FvH4_3g44510' => 'fve', 'FvH4_3g44582' => 'fve', 'FvH4_4g16921' => 'fve', 'FvH4_4g17121' => 'fve', 'FvH4_4g17782' => 'fve', 'FvH4_4g17783' => 'fve', 'FvH4_4g18120' => 'fve', 'FvH4_4g31310' => 'fve', 'FvH4_4g35052' => 'fve', 'FvH4_5g30862' => 'fve', 'FvH4_6g01541' => 'fve', 'FvH4_6g02021' => 'fve', 'FvH4_6g02041' => 'fve', 'FvH4_6g02071' => 'fve', 'FvH4_6g02171' => 'fve', 'FvH4_6g03181' => 'fve', 'FvH4_6g03182' => 'fve', 'FvH4_6g03221' => 'fve', 'FvH4_6g03380' => 'fve', 'FvH4_6g05201' => 'fve', 'FvH4_6g05203' => 'fve', 'FvH4_6g20231' => 'fve', 'FvH4_6g31981' => 'fve', 'FvH4_6g32061' => 'fve', 'FvH4_6g37041' => 'fve', 'FvH4_6g37932' => 'fve', 'FvH4_6g38731' => 'fve', 'FvH4_6g39370' => 'fve', 'FvH4_6g39371' => 'fve', 'FvH4_6g40891' => 'fve', 'FvH4_6g40892' => 'fve', 'FvH4_6g43143' => 'fve', 'FvH4_6g45251' => 'fve', 'FvH4_6g45260' => 'fve', 'FvH4_6g45291' => 'fve', 'FvH4_6g45890' => 'fve', 'FvH4_6g46240' => 'fve', 'FvH4_6g46241' => 'fve', 'FvH4_6g46242' => 'fve', 'FvH4_6g46260' => 'fve', 'FvH4_6g46280' => 'fve', 'FvH4_6g46380' => 'fve', 'FvH4_7g12841' => 'fve', 'FvH4_7g31431' => 'fve', 'Glyma.09G075900' => 'gma', 'Gohir.A09G096401' => 'ghi', 'Gohir.D09G096101' => 'ghi', 'Gorai.006G112800' => 'gra', 'HanXRQChr04g0121411' => 'han', 'Hund15878' => 'sun', 'Lj2A1107G68' => 'lonja', 'Lj2A630G63' => 'lonja', 'Lj2A946T25' => 'lonja', 'Lj2C714T1' => 'lonja', 'Lj2C966T3' => 'lonja', 'Lj2C966T4' => 'lonja', 'Lj4g0002979' => 'lja', 'Lsat_1_v5_gn_5_30901' => 'lsa', 'Lsat_1_v5_gn_5_31100' => 'lsa', 'Lsat_1_v5_gn_5_38600' => 'lsa', 'Lsat_1_v5_gn_6_92061' => 'lsa', 'Manes.05G071301' => 'mes', 'MD02G1008700' => 'mdo', 'MD02G1008900' => 'mdo', 'MD03G1256400' => 'mdo', 'MD04G1180900' => 'mdo', 'MD04G1181000' => 'mdo', 'MD04G1181200' => 'mdo', 'MD05G1244200' => 'mdo', 'MD05G1324200' => 'mdo', 'MD09G1201600' => 'mdo', 'MD10G1000600' => 'mdo', 'MD14G1026900' => 'mdo', 'MD14G1187900' => 'mdo', 'MD15G1017800' => 'mdo', 'MD15G1018100' => 'mdo', 'Medtr4g124160' => 'mtr', 'Migut.L01260' => 'egut', 'Nitab4.5_0000008g0440' => 'nta', 'Nitab4.5_0000207g0170' => 'nta', 'Nitab4.5_0007671g0030' => 'nta', 'Nitab4.5_0010853g0020' => 'nta', 'Oeu057656.1' => 'oeu', 'PGSC0003DMG400005638' => 'stu', 'PGSC0003DMG400005639' => 'stu', 'Phvul.009G222800' => 'pvu', 'Potri.009G132400' => 'ptr', 'Potri.009G163001' => 'ptr', 'Potri.011G000700' => 'ptr', 'Potri.011G004800' => 'ptr', 'Prupe.1G509300' => 'ppe', 'Prupe.1G509700' => 'ppe', 'Prupe.1G510400' => 'ppe', 'Prupe.1G510700' => 'ppe', 'Prupe.1G512600' => 'ppe', 'Prupe.2G073200' => 'ppe', 'Prupe.3G059500' => 'ppe', 'Prupe.3G059600' => 'ppe', 'Prupe.3G246100' => 'ppe', 'Prupe.3G265100' => 'ppe', 'Prupe.4G034700' => 'ppe', 'Prupe.4G052100' => 'ppe', 'Prupe.4G053600' => 'ppe', 'Prupe.5G068800' => 'ppe', 'Prupe.5G070600' => 'ppe', 'Prupe.6G075400' => 'ppe', 'Prupe.6G075500' => 'ppe', 'Prupe.6G076400' => 'ppe', 'Prupe.8G110700' => 'ppe', 'Psat4g020960' => 'psa', 'PSO135G0788' => 'pso', 'PSO210G6463' => 'pso', 'PSO384G0370' => 'pso', 'PSO386G0056' => 'pso', 'QL01p006048' => 'qlo', 'QL02p054283' => 'qlo', 'QL05p008000' => 'qlo', 'QL05p008212' => 'qlo', 'QL05p008950' => 'qlo', 'QL05p009042' => 'qlo', 'QL05p009518' => 'qlo', 'QL05p012589' => 'qlo', 'QL05p012608' => 'qlo', 'QL05p012650' => 'qlo', 'QL05p012667' => 'qlo', 'QL05p014501' => 'qlo', 'QL05p052800' => 'qlo', 'QL05p065010' => 'qlo', 'QL05p074156' => 'qlo', 'QL05p074160' => 'qlo', 'QL05p074174' => 'qlo', 'QL05p074178' => 'qlo', 'QL05p074214' => 'qlo', 'QL06p001050' => 'qlo', 'QL06p001056' => 'qlo', 'QL06p006093' => 'qlo', 'QL06p006111' => 'qlo', 'QL07p019784' => 'qlo', 'QL07p019801' => 'qlo', 'QL07p036110' => 'qlo', 'QL07p036134' => 'qlo', 'QL07p036147' => 'qlo', 'QL07p036156' => 'qlo', 'QL07p036300' => 'qlo', 'QL07p036320' => 'qlo', 'QL08p014547' => 'qlo', 'QL08p014551' => 'qlo', 'QL08p043319' => 'qlo', 'QL08p043324' => 'qlo', 'QL11p009094' => 'qlo', 'RcHm_v2.0_Chr1g0380481' => 'rch', 'RcHm_v2.0_Chr2g0089331' => 'rch', 'RcHm_v2.0_Chr2g0123691' => 'rch', 'RcHm_v2.0_Chr2g0151111' => 'rch', 'RcHm_v2.0_Chr2g0163011' => 'rch', 'RcHm_v2.0_Chr2g0163051' => 'rch', 'RcHm_v2.0_Chr2g0164671' => 'rch', 'RcHm_v2.0_Chr2g0164681' => 'rch', 'RcHm_v2.0_Chr2g0164721' => 'rch', 'RcHm_v2.0_Chr3g0449911' => 'rch', 'RcHm_v2.0_Chr3g0450211' => 'rch', 'RcHm_v2.0_Chr3g0457271' => 'rch', 'RcHm_v2.0_Chr5g0018111' => 'rch', 'RcHm_v2.0_Chr5g0021011' => 'rch', 'RcHm_v2.0_Chr5g0081171' => 'rch', 'RcHm_v2.0_Chr5g0081211' => 'rch', 'RcHm_v2.0_Chr6g0275871' => 'rch', 'RcHm_v2.0_Chr6g0276071' => 'rch', 'RcHm_v2.0_Chr6g0285591' => 'rch', 'RcHm_v2.0_Chr6g0291931' => 'rch', 'RcHm_v2.0_Chr6g0292091' => 'rch', 'RcHm_v2.0_Chr6g0292271' => 'rch', 'RcHm_v2.0_Chr7g0221261' => 'rch', 'Rhsim08G0219900' => 'rsi', 'Rhsim08G0220200' => 'rsi', 'Rhsim08G0237800' => 'rsi', 'Rhsim08G0238800' => 'rsi', 'Sabra09G0102700' => 'sbr', 'Sabra09G0127200' => 'sbr', 'Sabra11G0003700' => 'sbr', 'Sabra15G0014700' => 'sbr', 'Sc19g0000590' => 'sci', 'Sc19g0001870' => 'sci', 'SGA_v2.0_scaffold1G00346' => 'sas', 'SGA_v2.0_scaffold1G00575' => 'sas', 'SGA_v2.0_scaffold1G00761' => 'sas', 'SGA_v2.0_scaffold232G43501' => 'sas', 'TAR625G1137' => 'tar', 'Thecc.03G222100' => 'tca', 'TPR.G12691' => 'tpr', 'TWI34G0727' => 'twi', 'TWI36G0117' => 'twi', 'VMungo1309G0868' => 'vmu' ), 'gf_id' => 'HOM05D001729', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001729' ), 'data_identifier' => 'HOM05D001729', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001729', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '375', 'num_species' => '42' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'Ah.07g204710' => 'amhyb', 'AUR62006001' => 'cqu', 'AUR62006002' => 'cqu', 'AUR62006003' => 'cqu', 'AUR62015641' => 'cqu', 'AUR62027174' => 'cqu', 'AUR62035623' => 'cqu', 'AUR62035624' => 'cqu', 'AUR62035625' => 'cqu', 'AUR62035626' => 'cqu', 'CAN.G1110.53' => 'can', 'CANSAT80G0415' => 'cansat', 'Ca_21364_v3' => 'car', 'COL.COLO4_30693' => 'col', 'COL.COLO4_30694' => 'col', 'COL.COLO4_30695' => 'col', 'COL.COLO4_30696' => 'col', 'COL.COLO4_34020' => 'col', 'DCAR_004585' => 'dca', 'Dinv04029' => 'din', 'Dinv34857' => 'din', 'Duzib147G0011' => 'dzi', 'Duzib170G0599' => 'dzi', 'Duzib192G1051' => 'dzi', 'FAN01G0708' => 'fan', 'FAN01G0742' => 'fan', 'FAN02G0048' => 'fan', 'FAN02G0583' => 'fan', 'FAN02G0688' => 'fan', 'FAN02G1588' => 'fan', 'FAN02G2194' => 'fan', 'FAN02G2750' => 'fan', 'FAN02G3094' => 'fan', 'FAN02G3887' => 'fan', 'FAN02G3911' => 'fan', 'FAN02G3994' => 'fan', 'FAN02G4432' => 'fan', 'FAN02G4556' => 'fan', 'FAN03G1977' => 'fan', 'FAN03G2781' => 'fan', 'FAN03G2850' => 'fan', 'FAN03G3155' => 'fan', 'FAN04G2487' => 'fan', 'FAN05G0208' => 'fan', 'FAN05G0656' => 'fan', 'FAN05G0696' => 'fan', 'FAN05G0810' => 'fan', 'FAN05G1447' => 'fan', 'FAN05G2640' => 'fan', 'FAN05G2911' => 'fan', 'FAN05G3901' => 'fan', 'FAN05G4859' => 'fan', 'FAN05G4861' => 'fan', 'FAN05G4988' => 'fan', 'FAN05G5187' => 'fan', 'FAN05G5452' => 'fan', 'FAN05G5500' => 'fan', 'FAN05G5688' => 'fan', 'FAN06G0177' => 'fan', 'FAN06G0675' => 'fan', 'FAN06G1290' => 'fan', 'FAN06G2191' => 'fan', 'FAN06G2405' => 'fan', 'FAN06G3231' => 'fan', 'FAN06G3932' => 'fan', 'FAN07G0163' => 'fan', 'FAN07G0471' => 'fan', 'FAN07G1354' => 'fan', 'FAN08G0338' => 'fan', 'FAN08G1373' => 'fan', 'FAN08G2539' => 'fan', 'FAN08G2728' => 'fan', 'FAN09G0608' => 'fan', 'FAN09G1136' => 'fan', 'FAN09G1958' => 'fan', 'FAN09G2508' => 'fan', 'FAN09G2597' => 'fan', 'FAN09G2658' => 'fan', 'FAN09G2757' => 'fan', 'FAN09G2983' => 'fan', 'FAN09G3130' => 'fan', 'FAN09G3565' => 'fan', 'FAN09G3613' => 'fan', 'FAN09G4011' => 'fan', 'FAN09G4239' => 'fan', 'FAN09G4277' => 'fan', 'FAN09G4720' => 'fan', 'FAN11G0139' => 'fan', 'FAN11G1727' => 'fan', 'FAN11G2672' => 'fan', 'FAN11G2795' => 'fan', 'FAN11G3238' => 'fan', 'FAN11G3734' => 'fan', 'FAN12G0631' => 'fan', 'FAN12G2239' => 'fan', 'FAN12G2308' => 'fan', 'FAN12G2569' => 'fan', 'FAN12G2623' => 'fan', 'FAN13G3182' => 'fan', 'FAN14G0053' => 'fan', 'FAN14G0370' => 'fan', 'FAN14G0382' => 'fan', 'FAN14G0421' => 'fan', 'FAN14G0866' => 'fan', 'FAN14G1187' => 'fan', 'FAN14G1727' => 'fan', 'FAN14G1791' => 'fan', 'FAN14G2361' => 'fan', 'FAN14G2668' => 'fan', 'FAN14G2770' => 'fan', 'FAN14G2874' => 'fan', 'FAN14G3193' => 'fan', 'FAN14G3624' => 'fan', 'FAN14G3676' => 'fan', 'FAN14G3807' => 'fan', 'FAN14G4082' => 'fan', 'FAN14G4342' => 'fan', 'FAN14G4985' => 'fan', 'FAN14G5126' => 'fan', 'FAN14G5781' => 'fan', 'FAN14G5808' => 'fan', 'FAN14G5949' => 'fan', 'FAN15G0828' => 'fan', 'FAN15G1054' => 'fan', 'FAN15G2023' => 'fan', 'FAN15G2506' => 'fan', 'FAN16G0128' => 'fan', 'FAN16G0249' => 'fan', 'FAN16G0429' => 'fan', 'FAN16G1493' => 'fan', 'FAN16G2210' => 'fan', 'FAN16G2506' => 'fan', 'FAN18G1542' => 'fan', 'FAN18G4057' => 'fan', 'FAN19G0745' => 'fan', 'FAN19G1216' => 'fan', 'FAN19G1733' => 'fan', 'FAN20G0258' => 'fan', 'FAN20G1095' => 'fan', 'FAN20G1557' => 'fan', 'FAN21G0302' => 'fan', 'FAN21G0519' => 'fan', 'FAN21G0970' => 'fan', 'FAN21G1159' => 'fan', 'FAN21G1312' => 'fan', 'FAN21G1440' => 'fan', 'FAN21G1715' => 'fan', 'FAN23G1584' => 'fan', 'FAN24G0045' => 'fan', 'FAN24G0053' => 'fan', 'FAN24G1500' => 'fan', 'FAN24G1817' => 'fan', 'FAN24G2147' => 'fan', 'FAN24G2236' => 'fan', 'FAN24G2446' => 'fan', 'FAN24G2684' => 'fan', 'FAN25G0187' => 'fan', 'FAN25G0505' => 'fan', 'FAN25G0589' => 'fan', 'FAN25G3663' => 'fan', 'FAN26G1025' => 'fan', 'FAN26G2860' => 'fan', 'FAN27G1329' => 'fan', 'FAN27G3392' => 'fan', 'FvH4_1g02011' => 'fve', 'FvH4_1g06511' => 'fve', 'FvH4_2g19900' => 'fve', 'FvH4_2g19920' => 'fve', 'FvH4_2g24261' => 'fve', 'FvH4_2g24270' => 'fve', 'FvH4_2g24631' => 'fve', 'FvH4_2g30622' => 'fve', 'FvH4_3g12920' => 'fve', 'FvH4_3g30171' => 'fve', 'FvH4_3g35490' => 'fve', 'FvH4_3g43682' => 'fve', 'FvH4_3g43730' => 'fve', 'FvH4_3g43732' => 'fve', 'FvH4_3g43751' => 'fve', 'FvH4_3g43752' => 'fve', 'FvH4_3g43770' => 'fve', 'FvH4_3g44471' => 'fve', 'FvH4_3g44510' => 'fve', 'FvH4_3g44582' => 'fve', 'FvH4_4g16921' => 'fve', 'FvH4_4g17121' => 'fve', 'FvH4_4g17782' => 'fve', 'FvH4_4g17783' => 'fve', 'FvH4_4g18120' => 'fve', 'FvH4_4g31310' => 'fve', 'FvH4_4g35052' => 'fve', 'FvH4_5g30862' => 'fve', 'FvH4_6g01541' => 'fve', 'FvH4_6g02021' => 'fve', 'FvH4_6g02041' => 'fve', 'FvH4_6g02071' => 'fve', 'FvH4_6g02171' => 'fve', 'FvH4_6g03181' => 'fve', 'FvH4_6g03182' => 'fve', 'FvH4_6g03221' => 'fve', 'FvH4_6g03380' => 'fve', 'FvH4_6g05201' => 'fve', 'FvH4_6g05203' => 'fve', 'FvH4_6g20231' => 'fve', 'FvH4_6g31981' => 'fve', 'FvH4_6g32061' => 'fve', 'FvH4_6g37041' => 'fve', 'FvH4_6g37932' => 'fve', 'FvH4_6g38731' => 'fve', 'FvH4_6g39370' => 'fve', 'FvH4_6g39371' => 'fve', 'FvH4_6g40891' => 'fve', 'FvH4_6g40892' => 'fve', 'FvH4_6g43143' => 'fve', 'FvH4_6g45251' => 'fve', 'FvH4_6g45260' => 'fve', 'FvH4_6g45291' => 'fve', 'FvH4_6g45890' => 'fve', 'FvH4_6g46240' => 'fve', 'FvH4_6g46241' => 'fve', 'FvH4_6g46242' => 'fve', 'FvH4_6g46260' => 'fve', 'FvH4_6g46280' => 'fve', 'FvH4_6g46380' => 'fve', 'FvH4_7g12841' => 'fve', 'FvH4_7g31431' => 'fve', 'Glyma.09G075900' => 'gma', 'Gohir.A09G096401' => 'ghi', 'Gohir.D09G096101' => 'ghi', 'Gorai.006G112800' => 'gra', 'HanXRQChr04g0121411' => 'han', 'Hund15878' => 'sun', 'Lj2A1107G68' => 'lonja', 'Lj2A630G63' => 'lonja', 'Lj2A946T25' => 'lonja', 'Lj2C714T1' => 'lonja', 'Lj2C966T3' => 'lonja', 'Lj2C966T4' => 'lonja', 'Lj4g0002979' => 'lja', 'Lsat_1_v5_gn_5_30901' => 'lsa', 'Lsat_1_v5_gn_5_31100' => 'lsa', 'Lsat_1_v5_gn_5_38600' => 'lsa', 'Lsat_1_v5_gn_6_92061' => 'lsa', 'Manes.05G071301' => 'mes', 'MD02G1008700' => 'mdo', 'MD02G1008900' => 'mdo', 'MD03G1256400' => 'mdo', 'MD04G1180900' => 'mdo', 'MD04G1181000' => 'mdo', 'MD04G1181200' => 'mdo', 'MD05G1244200' => 'mdo', 'MD05G1324200' => 'mdo', 'MD09G1201600' => 'mdo', 'MD10G1000600' => 'mdo', 'MD14G1026900' => 'mdo', 'MD14G1187900' => 'mdo', 'MD15G1017800' => 'mdo', 'MD15G1018100' => 'mdo', 'Medtr4g124160' => 'mtr', 'Migut.L01260' => 'egut', 'Nitab4.5_0000008g0440' => 'nta', 'Nitab4.5_0000207g0170' => 'nta', 'Nitab4.5_0007671g0030' => 'nta', 'Nitab4.5_0010853g0020' => 'nta', 'Oeu057656.1' => 'oeu', 'PGSC0003DMG400005638' => 'stu', 'PGSC0003DMG400005639' => 'stu', 'Phvul.009G222800' => 'pvu', 'Potri.009G132400' => 'ptr', 'Potri.009G163001' => 'ptr', 'Potri.011G000700' => 'ptr', 'Potri.011G004800' => 'ptr', 'Prupe.1G509300' => 'ppe', 'Prupe.1G509700' => 'ppe', 'Prupe.1G510400' => 'ppe', 'Prupe.1G510700' => 'ppe', 'Prupe.1G512600' => 'ppe', 'Prupe.2G073200' => 'ppe', 'Prupe.3G059500' => 'ppe', 'Prupe.3G059600' => 'ppe', 'Prupe.3G246100' => 'ppe', 'Prupe.3G265100' => 'ppe', 'Prupe.4G034700' => 'ppe', 'Prupe.4G052100' => 'ppe', 'Prupe.4G053600' => 'ppe', 'Prupe.5G068800' => 'ppe', 'Prupe.5G070600' => 'ppe', 'Prupe.6G075400' => 'ppe', 'Prupe.6G075500' => 'ppe', 'Prupe.6G076400' => 'ppe', 'Prupe.8G110700' => 'ppe', 'Psat4g020960' => 'psa', 'PSO135G0788' => 'pso', 'PSO210G6463' => 'pso', 'PSO384G0370' => 'pso', 'PSO386G0056' => 'pso', 'QL01p006048' => 'qlo', 'QL02p054283' => 'qlo', 'QL05p008000' => 'qlo', 'QL05p008212' => 'qlo', 'QL05p008950' => 'qlo', 'QL05p009042' => 'qlo', 'QL05p009518' => 'qlo', 'QL05p012589' => 'qlo', 'QL05p012608' => 'qlo', 'QL05p012650' => 'qlo', 'QL05p012667' => 'qlo', 'QL05p014501' => 'qlo', 'QL05p052800' => 'qlo', 'QL05p065010' => 'qlo', 'QL05p074156' => 'qlo', 'QL05p074160' => 'qlo', 'QL05p074174' => 'qlo', 'QL05p074178' => 'qlo', 'QL05p074214' => 'qlo', 'QL06p001050' => 'qlo', 'QL06p001056' => 'qlo', 'QL06p006093' => 'qlo', 'QL06p006111' => 'qlo', 'QL07p019784' => 'qlo', 'QL07p019801' => 'qlo', 'QL07p036110' => 'qlo', 'QL07p036134' => 'qlo', 'QL07p036147' => 'qlo', 'QL07p036156' => 'qlo', 'QL07p036300' => 'qlo', 'QL07p036320' => 'qlo', 'QL08p014547' => 'qlo', 'QL08p014551' => 'qlo', 'QL08p043319' => 'qlo', 'QL08p043324' => 'qlo', 'QL11p009094' => 'qlo', 'RcHm_v2.0_Chr1g0380481' => 'rch', 'RcHm_v2.0_Chr2g0089331' => 'rch', 'RcHm_v2.0_Chr2g0123691' => 'rch', 'RcHm_v2.0_Chr2g0151111' => 'rch', 'RcHm_v2.0_Chr2g0163011' => 'rch', 'RcHm_v2.0_Chr2g0163051' => 'rch', 'RcHm_v2.0_Chr2g0164671' => 'rch', 'RcHm_v2.0_Chr2g0164681' => 'rch', 'RcHm_v2.0_Chr2g0164721' => 'rch', 'RcHm_v2.0_Chr3g0449911' => 'rch', 'RcHm_v2.0_Chr3g0450211' => 'rch', 'RcHm_v2.0_Chr3g0457271' => 'rch', 'RcHm_v2.0_Chr5g0018111' => 'rch', 'RcHm_v2.0_Chr5g0021011' => 'rch', 'RcHm_v2.0_Chr5g0081171' => 'rch', 'RcHm_v2.0_Chr5g0081211' => 'rch', 'RcHm_v2.0_Chr6g0275871' => 'rch', 'RcHm_v2.0_Chr6g0276071' => 'rch', 'RcHm_v2.0_Chr6g0285591' => 'rch', 'RcHm_v2.0_Chr6g0291931' => 'rch', 'RcHm_v2.0_Chr6g0292091' => 'rch', 'RcHm_v2.0_Chr6g0292271' => 'rch', 'RcHm_v2.0_Chr7g0221261' => 'rch', 'Rhsim08G0219900' => 'rsi', 'Rhsim08G0220200' => 'rsi', 'Rhsim08G0237800' => 'rsi', 'Rhsim08G0238800' => 'rsi', 'Sabra09G0102700' => 'sbr', 'Sabra09G0127200' => 'sbr', 'Sabra11G0003700' => 'sbr', 'Sabra15G0014700' => 'sbr', 'Sc19g0000590' => 'sci', 'Sc19g0001870' => 'sci', 'SGA_v2.0_scaffold1G00346' => 'sas', 'SGA_v2.0_scaffold1G00575' => 'sas', 'SGA_v2.0_scaffold1G00761' => 'sas', 'SGA_v2.0_scaffold232G43501' => 'sas', 'TAR625G1137' => 'tar', 'Thecc.03G222100' => 'tca', 'TPR.G12691' => 'tpr', 'TWI34G0727' => 'twi', 'TWI36G0117' => 'twi', 'VMungo1309G0868' => 'vmu' ) $gf_id = 'HOM05D001729' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001729' ) $data_identifier = 'HOM05D001729' $data_type = 'gf_id' $species_gene_counts = array( 'amhyb' => (int) 1, 'cqu' => (int) 9, 'can' => (int) 1, 'cansat' => (int) 1, 'car' => (int) 1, 'col' => (int) 5, 'dca' => (int) 1, 'din' => (int) 2, 'dzi' => (int) 3, 'fan' => (int) 140, 'fve' => (int) 62, 'gma' => (int) 1, 'ghi' => (int) 2, 'gra' => (int) 1, 'han' => (int) 1, 'sun' => (int) 1, 'lonja' => (int) 6, 'lja' => (int) 1, 'lsa' => (int) 4, 'mes' => (int) 1, 'mdo' => (int) 14, 'mtr' => (int) 1, 'egut' => (int) 1, 'nta' => (int) 4, 'oeu' => (int) 1, 'stu' => (int) 2, 'pvu' => (int) 1, 'ptr' => (int) 4, 'ppe' => (int) 19, 'psa' => (int) 1, 'pso' => (int) 4, 'qlo' => (int) 36, 'rch' => (int) 23, 'rsi' => (int) 4, 'sbr' => (int) 4, 'sci' => (int) 2, 'sas' => (int) 4, 'tar' => (int) 1, 'tca' => (int) 1, 'tpr' => (int) 1, 'twi' => (int) 2, 'vmu' => (int) 1 ) $gf_gene_species = 'vmu' $gf_gene_id = 'VMungo1309G0868' $species_info = array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ) $local_species = 'lsa' $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' => 'HOM05D001729', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '375', 'num_species' => '42' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'Ah.07g204710' => 'amhyb', 'AUR62006001' => 'cqu', 'AUR62006002' => 'cqu', 'AUR62006003' => 'cqu', 'AUR62015641' => 'cqu', 'AUR62027174' => 'cqu', 'AUR62035623' => 'cqu', 'AUR62035624' => 'cqu', 'AUR62035625' => 'cqu', 'AUR62035626' => 'cqu', 'CAN.G1110.53' => 'can', 'CANSAT80G0415' => 'cansat', 'Ca_21364_v3' => 'car', 'COL.COLO4_30693' => 'col', 'COL.COLO4_30694' => 'col', 'COL.COLO4_30695' => 'col', 'COL.COLO4_30696' => 'col', 'COL.COLO4_34020' => 'col', 'DCAR_004585' => 'dca', 'Dinv04029' => 'din', 'Dinv34857' => 'din', 'Duzib147G0011' => 'dzi', 'Duzib170G0599' => 'dzi', 'Duzib192G1051' => 'dzi', 'FAN01G0708' => 'fan', 'FAN01G0742' => 'fan', 'FAN02G0048' => 'fan', 'FAN02G0583' => 'fan', 'FAN02G0688' => 'fan', 'FAN02G1588' => 'fan', 'FAN02G2194' => 'fan', 'FAN02G2750' => 'fan', 'FAN02G3094' => 'fan', 'FAN02G3887' => 'fan', 'FAN02G3911' => 'fan', 'FAN02G3994' => 'fan', 'FAN02G4432' => 'fan', 'FAN02G4556' => 'fan', 'FAN03G1977' => 'fan', 'FAN03G2781' => 'fan', 'FAN03G2850' => 'fan', 'FAN03G3155' => 'fan', 'FAN04G2487' => 'fan', 'FAN05G0208' => 'fan', 'FAN05G0656' => 'fan', 'FAN05G0696' => 'fan', 'FAN05G0810' => 'fan', 'FAN05G1447' => 'fan', 'FAN05G2640' => 'fan', 'FAN05G2911' => 'fan', 'FAN05G3901' => 'fan', 'FAN05G4859' => 'fan', 'FAN05G4861' => 'fan', 'FAN05G4988' => 'fan', 'FAN05G5187' => 'fan', 'FAN05G5452' => 'fan', 'FAN05G5500' => 'fan', 'FAN05G5688' => 'fan', 'FAN06G0177' => 'fan', 'FAN06G0675' => 'fan', 'FAN06G1290' => 'fan', 'FAN06G2191' => 'fan', 'FAN06G2405' => 'fan', 'FAN06G3231' => 'fan', 'FAN06G3932' => 'fan', 'FAN07G0163' => 'fan', 'FAN07G0471' => 'fan', 'FAN07G1354' => 'fan', 'FAN08G0338' => 'fan', 'FAN08G1373' => 'fan', 'FAN08G2539' => 'fan', 'FAN08G2728' => 'fan', 'FAN09G0608' => 'fan', 'FAN09G1136' => 'fan', 'FAN09G1958' => 'fan', 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'FAN14G5126' => 'fan', 'FAN14G5781' => 'fan', 'FAN14G5808' => 'fan', 'FAN14G5949' => 'fan', 'FAN15G0828' => 'fan', 'FAN15G1054' => 'fan', 'FAN15G2023' => 'fan', 'FAN15G2506' => 'fan', 'FAN16G0128' => 'fan', 'FAN16G0249' => 'fan', 'FAN16G0429' => 'fan', 'FAN16G1493' => 'fan', 'FAN16G2210' => 'fan', 'FAN16G2506' => 'fan', 'FAN18G1542' => 'fan', 'FAN18G4057' => 'fan', 'FAN19G0745' => 'fan', 'FAN19G1216' => 'fan', 'FAN19G1733' => 'fan', 'FAN20G0258' => 'fan', 'FAN20G1095' => 'fan', 'FAN20G1557' => 'fan', 'FAN21G0302' => 'fan', 'FAN21G0519' => 'fan', 'FAN21G0970' => 'fan', 'FAN21G1159' => 'fan', 'FAN21G1312' => 'fan', 'FAN21G1440' => 'fan', 'FAN21G1715' => 'fan', 'FAN23G1584' => 'fan', 'FAN24G0045' => 'fan', 'FAN24G0053' => 'fan', 'FAN24G1500' => 'fan', 'FAN24G1817' => 'fan', 'FAN24G2147' => 'fan', 'FAN24G2236' => 'fan', 'FAN24G2446' => 'fan', 'FAN24G2684' => 'fan', 'FAN25G0187' => 'fan', 'FAN25G0505' => 'fan', 'FAN25G0589' => 'fan', 'FAN25G3663' => 'fan', 'FAN26G1025' => 'fan', 'FAN26G2860' => 'fan', 'FAN27G1329' => 'fan', 'FAN27G3392' => 'fan', 'FvH4_1g02011' => 'fve', 'FvH4_1g06511' => 'fve', 'FvH4_2g19900' => 'fve', 'FvH4_2g19920' => 'fve', 'FvH4_2g24261' => 'fve', 'FvH4_2g24270' => 'fve', 'FvH4_2g24631' => 'fve', 'FvH4_2g30622' => 'fve', 'FvH4_3g12920' => 'fve', 'FvH4_3g30171' => 'fve', 'FvH4_3g35490' => 'fve', 'FvH4_3g43682' => 'fve', 'FvH4_3g43730' => 'fve', 'FvH4_3g43732' => 'fve', 'FvH4_3g43751' => 'fve', 'FvH4_3g43752' => 'fve', 'FvH4_3g43770' => 'fve', 'FvH4_3g44471' => 'fve', 'FvH4_3g44510' => 'fve', 'FvH4_3g44582' => 'fve', 'FvH4_4g16921' => 'fve', 'FvH4_4g17121' => 'fve', 'FvH4_4g17782' => 'fve', 'FvH4_4g17783' => 'fve', 'FvH4_4g18120' => 'fve', 'FvH4_4g31310' => 'fve', 'FvH4_4g35052' => 'fve', 'FvH4_5g30862' => 'fve', 'FvH4_6g01541' => 'fve', 'FvH4_6g02021' => 'fve', 'FvH4_6g02041' => 'fve', 'FvH4_6g02071' => 'fve', 'FvH4_6g02171' => 'fve', 'FvH4_6g03181' => 'fve', 'FvH4_6g03182' => 'fve', 'FvH4_6g03221' => 'fve', 'FvH4_6g03380' => 'fve', 'FvH4_6g05201' => 'fve', 'FvH4_6g05203' => 'fve', 'FvH4_6g20231' => 'fve', 'FvH4_6g31981' => 'fve', 'FvH4_6g32061' => 'fve', 'FvH4_6g37041' => 'fve', 'FvH4_6g37932' => 'fve', 'FvH4_6g38731' => 'fve', 'FvH4_6g39370' => 'fve', 'FvH4_6g39371' => 'fve', 'FvH4_6g40891' => 'fve', 'FvH4_6g40892' => 'fve', 'FvH4_6g43143' => 'fve', 'FvH4_6g45251' => 'fve', 'FvH4_6g45260' => 'fve', 'FvH4_6g45291' => 'fve', 'FvH4_6g45890' => 'fve', 'FvH4_6g46240' => 'fve', 'FvH4_6g46241' => 'fve', 'FvH4_6g46242' => 'fve', 'FvH4_6g46260' => 'fve', 'FvH4_6g46280' => 'fve', 'FvH4_6g46380' => 'fve', 'FvH4_7g12841' => 'fve', 'FvH4_7g31431' => 'fve', 'Glyma.09G075900' => 'gma', 'Gohir.A09G096401' => 'ghi', 'Gohir.D09G096101' => 'ghi', 'Gorai.006G112800' => 'gra', 'HanXRQChr04g0121411' => 'han', 'Hund15878' => 'sun', 'Lj2A1107G68' => 'lonja', 'Lj2A630G63' => 'lonja', 'Lj2A946T25' => 'lonja', 'Lj2C714T1' => 'lonja', 'Lj2C966T3' => 'lonja', 'Lj2C966T4' => 'lonja', 'Lj4g0002979' => 'lja', 'Lsat_1_v5_gn_5_30901' => 'lsa', 'Lsat_1_v5_gn_5_31100' => 'lsa', 'Lsat_1_v5_gn_5_38600' => 'lsa', 'Lsat_1_v5_gn_6_92061' => 'lsa', 'Manes.05G071301' => 'mes', 'MD02G1008700' => 'mdo', 'MD02G1008900' => 'mdo', 'MD03G1256400' => 'mdo', 'MD04G1180900' => 'mdo', 'MD04G1181000' => 'mdo', 'MD04G1181200' => 'mdo', 'MD05G1244200' => 'mdo', 'MD05G1324200' => 'mdo', 'MD09G1201600' => 'mdo', 'MD10G1000600' => 'mdo', 'MD14G1026900' => 'mdo', 'MD14G1187900' => 'mdo', 'MD15G1017800' => 'mdo', 'MD15G1018100' => 'mdo', 'Medtr4g124160' => 'mtr', 'Migut.L01260' => 'egut', 'Nitab4.5_0000008g0440' => 'nta', 'Nitab4.5_0000207g0170' => 'nta', 'Nitab4.5_0007671g0030' => 'nta', 'Nitab4.5_0010853g0020' => 'nta', 'Oeu057656.1' => 'oeu', 'PGSC0003DMG400005638' => 'stu', 'PGSC0003DMG400005639' => 'stu', 'Phvul.009G222800' => 'pvu', 'Potri.009G132400' => 'ptr', 'Potri.009G163001' => 'ptr', 'Potri.011G000700' => 'ptr', 'Potri.011G004800' => 'ptr', 'Prupe.1G509300' => 'ppe', 'Prupe.1G509700' => 'ppe', 'Prupe.1G510400' => 'ppe', 'Prupe.1G510700' => 'ppe', 'Prupe.1G512600' => 'ppe', 'Prupe.2G073200' => 'ppe', 'Prupe.3G059500' => 'ppe', 'Prupe.3G059600' => 'ppe', 'Prupe.3G246100' => 'ppe', 'Prupe.3G265100' => 'ppe', 'Prupe.4G034700' => 'ppe', 'Prupe.4G052100' => 'ppe', 'Prupe.4G053600' => 'ppe', 'Prupe.5G068800' => 'ppe', 'Prupe.5G070600' => 'ppe', 'Prupe.6G075400' => 'ppe', 'Prupe.6G075500' => 'ppe', 'Prupe.6G076400' => 'ppe', 'Prupe.8G110700' => 'ppe', 'Psat4g020960' => 'psa', 'PSO135G0788' => 'pso', 'PSO210G6463' => 'pso', 'PSO384G0370' => 'pso', 'PSO386G0056' => 'pso', 'QL01p006048' => 'qlo', 'QL02p054283' => 'qlo', 'QL05p008000' => 'qlo', 'QL05p008212' => 'qlo', 'QL05p008950' => 'qlo', 'QL05p009042' => 'qlo', 'QL05p009518' => 'qlo', 'QL05p012589' => 'qlo', 'QL05p012608' => 'qlo', 'QL05p012650' => 'qlo', 'QL05p012667' => 'qlo', 'QL05p014501' => 'qlo', 'QL05p052800' => 'qlo', 'QL05p065010' => 'qlo', 'QL05p074156' => 'qlo', 'QL05p074160' => 'qlo', 'QL05p074174' => 'qlo', 'QL05p074178' => 'qlo', 'QL05p074214' => 'qlo', 'QL06p001050' => 'qlo', 'QL06p001056' => 'qlo', 'QL06p006093' => 'qlo', 'QL06p006111' => 'qlo', 'QL07p019784' => 'qlo', 'QL07p019801' => 'qlo', 'QL07p036110' => 'qlo', 'QL07p036134' => 'qlo', 'QL07p036147' => 'qlo', 'QL07p036156' => 'qlo', 'QL07p036300' => 'qlo', 'QL07p036320' => 'qlo', 'QL08p014547' => 'qlo', 'QL08p014551' => 'qlo', 'QL08p043319' => 'qlo', 'QL08p043324' => 'qlo', 'QL11p009094' => 'qlo', 'RcHm_v2.0_Chr1g0380481' => 'rch', 'RcHm_v2.0_Chr2g0089331' => 'rch', 'RcHm_v2.0_Chr2g0123691' => 'rch', 'RcHm_v2.0_Chr2g0151111' => 'rch', 'RcHm_v2.0_Chr2g0163011' => 'rch', 'RcHm_v2.0_Chr2g0163051' => 'rch', 'RcHm_v2.0_Chr2g0164671' => 'rch', 'RcHm_v2.0_Chr2g0164681' => 'rch', 'RcHm_v2.0_Chr2g0164721' => 'rch', 'RcHm_v2.0_Chr3g0449911' => 'rch', 'RcHm_v2.0_Chr3g0450211' => 'rch', 'RcHm_v2.0_Chr3g0457271' => 'rch', 'RcHm_v2.0_Chr5g0018111' => 'rch', 'RcHm_v2.0_Chr5g0021011' => 'rch', 'RcHm_v2.0_Chr5g0081171' => 'rch', 'RcHm_v2.0_Chr5g0081211' => 'rch', 'RcHm_v2.0_Chr6g0275871' => 'rch', 'RcHm_v2.0_Chr6g0276071' => 'rch', 'RcHm_v2.0_Chr6g0285591' => 'rch', 'RcHm_v2.0_Chr6g0291931' => 'rch', 'RcHm_v2.0_Chr6g0292091' => 'rch', 'RcHm_v2.0_Chr6g0292271' => 'rch', 'RcHm_v2.0_Chr7g0221261' => 'rch', 'Rhsim08G0219900' => 'rsi', 'Rhsim08G0220200' => 'rsi', 'Rhsim08G0237800' => 'rsi', 'Rhsim08G0238800' => 'rsi', 'Sabra09G0102700' => 'sbr', 'Sabra09G0127200' => 'sbr', 'Sabra11G0003700' => 'sbr', 'Sabra15G0014700' => 'sbr', 'Sc19g0000590' => 'sci', 'Sc19g0001870' => 'sci', 'SGA_v2.0_scaffold1G00346' => 'sas', 'SGA_v2.0_scaffold1G00575' => 'sas', 'SGA_v2.0_scaffold1G00761' => 'sas', 'SGA_v2.0_scaffold232G43501' => 'sas', 'TAR625G1137' => 'tar', 'Thecc.03G222100' => 'tca', 'TPR.G12691' => 'tpr', 'TWI34G0727' => 'twi', 'TWI36G0117' => 'twi', 'VMungo1309G0868' => 'vmu' ), 'gf_id' => 'HOM05D001729', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001729' ), 'data_identifier' => 'HOM05D001729', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001729', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '375', 'num_species' => '42' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'Ah.07g204710' => 'amhyb', 'AUR62006001' => 'cqu', 'AUR62006002' => 'cqu', 'AUR62006003' => 'cqu', 'AUR62015641' => 'cqu', 'AUR62027174' => 'cqu', 'AUR62035623' => 'cqu', 'AUR62035624' => 'cqu', 'AUR62035625' => 'cqu', 'AUR62035626' => 'cqu', 'CAN.G1110.53' => 'can', 'CANSAT80G0415' => 'cansat', 'Ca_21364_v3' => 'car', 'COL.COLO4_30693' => 'col', 'COL.COLO4_30694' => 'col', 'COL.COLO4_30695' => 'col', 'COL.COLO4_30696' => 'col', 'COL.COLO4_34020' => 'col', 'DCAR_004585' => 'dca', 'Dinv04029' => 'din', 'Dinv34857' => 'din', 'Duzib147G0011' => 'dzi', 'Duzib170G0599' => 'dzi', 'Duzib192G1051' => 'dzi', 'FAN01G0708' => 'fan', 'FAN01G0742' => 'fan', 'FAN02G0048' => 'fan', 'FAN02G0583' => 'fan', 'FAN02G0688' => 'fan', 'FAN02G1588' => 'fan', 'FAN02G2194' => 'fan', 'FAN02G2750' => 'fan', 'FAN02G3094' => 'fan', 'FAN02G3887' => 'fan', 'FAN02G3911' => 'fan', 'FAN02G3994' => 'fan', 'FAN02G4432' => 'fan', 'FAN02G4556' => 'fan', 'FAN03G1977' => 'fan', 'FAN03G2781' => 'fan', 'FAN03G2850' => 'fan', 'FAN03G3155' => 'fan', 'FAN04G2487' => 'fan', 'FAN05G0208' => 'fan', 'FAN05G0656' => 'fan', 'FAN05G0696' => 'fan', 'FAN05G0810' => 'fan', 'FAN05G1447' => 'fan', 'FAN05G2640' => 'fan', 'FAN05G2911' => 'fan', 'FAN05G3901' => 'fan', 'FAN05G4859' => 'fan', 'FAN05G4861' => 'fan', 'FAN05G4988' => 'fan', 'FAN05G5187' => 'fan', 'FAN05G5452' => 'fan', 'FAN05G5500' => 'fan', 'FAN05G5688' => 'fan', 'FAN06G0177' => 'fan', 'FAN06G0675' => 'fan', 'FAN06G1290' => 'fan', 'FAN06G2191' => 'fan', 'FAN06G2405' => 'fan', 'FAN06G3231' => 'fan', 'FAN06G3932' => 'fan', 'FAN07G0163' => 'fan', 'FAN07G0471' => 'fan', 'FAN07G1354' => 'fan', 'FAN08G0338' => 'fan', 'FAN08G1373' => 'fan', 'FAN08G2539' => 'fan', 'FAN08G2728' => 'fan', 'FAN09G0608' => 'fan', 'FAN09G1136' => 'fan', 'FAN09G1958' => 'fan', 'FAN09G2508' => 'fan', 'FAN09G2597' => 'fan', 'FAN09G2658' => 'fan', 'FAN09G2757' => 'fan', 'FAN09G2983' => 'fan', 'FAN09G3130' => 'fan', 'FAN09G3565' => 'fan', 'FAN09G3613' => 'fan', 'FAN09G4011' => 'fan', 'FAN09G4239' => 'fan', 'FAN09G4277' => 'fan', 'FAN09G4720' => 'fan', 'FAN11G0139' => 'fan', 'FAN11G1727' => 'fan', 'FAN11G2672' => 'fan', 'FAN11G2795' => 'fan', 'FAN11G3238' => 'fan', 'FAN11G3734' => 'fan', 'FAN12G0631' => 'fan', 'FAN12G2239' => 'fan', 'FAN12G2308' => 'fan', 'FAN12G2569' => 'fan', 'FAN12G2623' => 'fan', 'FAN13G3182' => 'fan', 'FAN14G0053' => 'fan', 'FAN14G0370' => 'fan', 'FAN14G0382' => 'fan', 'FAN14G0421' => 'fan', 'FAN14G0866' => 'fan', 'FAN14G1187' => 'fan', 'FAN14G1727' => 'fan', 'FAN14G1791' => 'fan', 'FAN14G2361' => 'fan', 'FAN14G2668' => 'fan', 'FAN14G2770' => 'fan', 'FAN14G2874' => 'fan', 'FAN14G3193' => 'fan', 'FAN14G3624' => 'fan', 'FAN14G3676' => 'fan', 'FAN14G3807' => 'fan', 'FAN14G4082' => 'fan', 'FAN14G4342' => 'fan', 'FAN14G4985' => 'fan', 'FAN14G5126' => 'fan', 'FAN14G5781' => 'fan', 'FAN14G5808' => 'fan', 'FAN14G5949' => 'fan', 'FAN15G0828' => 'fan', 'FAN15G1054' => 'fan', 'FAN15G2023' => 'fan', 'FAN15G2506' => 'fan', 'FAN16G0128' => 'fan', 'FAN16G0249' => 'fan', 'FAN16G0429' => 'fan', 'FAN16G1493' => 'fan', 'FAN16G2210' => 'fan', 'FAN16G2506' => 'fan', 'FAN18G1542' => 'fan', 'FAN18G4057' => 'fan', 'FAN19G0745' => 'fan', 'FAN19G1216' => 'fan', 'FAN19G1733' => 'fan', 'FAN20G0258' => 'fan', 'FAN20G1095' => 'fan', 'FAN20G1557' => 'fan', 'FAN21G0302' => 'fan', 'FAN21G0519' => 'fan', 'FAN21G0970' => 'fan', 'FAN21G1159' => 'fan', 'FAN21G1312' => 'fan', 'FAN21G1440' => 'fan', 'FAN21G1715' => 'fan', 'FAN23G1584' => 'fan', 'FAN24G0045' => 'fan', 'FAN24G0053' => 'fan', 'FAN24G1500' => 'fan', 'FAN24G1817' => 'fan', 'FAN24G2147' => 'fan', 'FAN24G2236' => 'fan', 'FAN24G2446' => 'fan', 'FAN24G2684' => 'fan', 'FAN25G0187' => 'fan', 'FAN25G0505' => 'fan', 'FAN25G0589' => 'fan', 'FAN25G3663' => 'fan', 'FAN26G1025' => 'fan', 'FAN26G2860' => 'fan', 'FAN27G1329' => 'fan', 'FAN27G3392' => 'fan', 'FvH4_1g02011' => 'fve', 'FvH4_1g06511' => 'fve', 'FvH4_2g19900' => 'fve', 'FvH4_2g19920' => 'fve', 'FvH4_2g24261' => 'fve', 'FvH4_2g24270' => 'fve', 'FvH4_2g24631' => 'fve', 'FvH4_2g30622' => 'fve', 'FvH4_3g12920' => 'fve', 'FvH4_3g30171' => 'fve', 'FvH4_3g35490' => 'fve', 'FvH4_3g43682' => 'fve', 'FvH4_3g43730' => 'fve', 'FvH4_3g43732' => 'fve', 'FvH4_3g43751' => 'fve', 'FvH4_3g43752' => 'fve', 'FvH4_3g43770' => 'fve', 'FvH4_3g44471' => 'fve', 'FvH4_3g44510' => 'fve', 'FvH4_3g44582' => 'fve', 'FvH4_4g16921' => 'fve', 'FvH4_4g17121' => 'fve', 'FvH4_4g17782' => 'fve', 'FvH4_4g17783' => 'fve', 'FvH4_4g18120' => 'fve', 'FvH4_4g31310' => 'fve', 'FvH4_4g35052' => 'fve', 'FvH4_5g30862' => 'fve', 'FvH4_6g01541' => 'fve', 'FvH4_6g02021' => 'fve', 'FvH4_6g02041' => 'fve', 'FvH4_6g02071' => 'fve', 'FvH4_6g02171' => 'fve', 'FvH4_6g03181' => 'fve', 'FvH4_6g03182' => 'fve', 'FvH4_6g03221' => 'fve', 'FvH4_6g03380' => 'fve', 'FvH4_6g05201' => 'fve', 'FvH4_6g05203' => 'fve', 'FvH4_6g20231' => 'fve', 'FvH4_6g31981' => 'fve', 'FvH4_6g32061' => 'fve', 'FvH4_6g37041' => 'fve', 'FvH4_6g37932' => 'fve', 'FvH4_6g38731' => 'fve', 'FvH4_6g39370' => 'fve', 'FvH4_6g39371' => 'fve', 'FvH4_6g40891' => 'fve', 'FvH4_6g40892' => 'fve', 'FvH4_6g43143' => 'fve', 'FvH4_6g45251' => 'fve', 'FvH4_6g45260' => 'fve', 'FvH4_6g45291' => 'fve', 'FvH4_6g45890' => 'fve', 'FvH4_6g46240' => 'fve', 'FvH4_6g46241' => 'fve', 'FvH4_6g46242' => 'fve', 'FvH4_6g46260' => 'fve', 'FvH4_6g46280' => 'fve', 'FvH4_6g46380' => 'fve', 'FvH4_7g12841' => 'fve', 'FvH4_7g31431' => 'fve', 'Glyma.09G075900' => 'gma', 'Gohir.A09G096401' => 'ghi', 'Gohir.D09G096101' => 'ghi', 'Gorai.006G112800' => 'gra', 'HanXRQChr04g0121411' => 'han', 'Hund15878' => 'sun', 'Lj2A1107G68' => 'lonja', 'Lj2A630G63' => 'lonja', 'Lj2A946T25' => 'lonja', 'Lj2C714T1' => 'lonja', 'Lj2C966T3' => 'lonja', 'Lj2C966T4' => 'lonja', 'Lj4g0002979' => 'lja', 'Lsat_1_v5_gn_5_30901' => 'lsa', 'Lsat_1_v5_gn_5_31100' => 'lsa', 'Lsat_1_v5_gn_5_38600' => 'lsa', 'Lsat_1_v5_gn_6_92061' => 'lsa', 'Manes.05G071301' => 'mes', 'MD02G1008700' => 'mdo', 'MD02G1008900' => 'mdo', 'MD03G1256400' => 'mdo', 'MD04G1180900' => 'mdo', 'MD04G1181000' => 'mdo', 'MD04G1181200' => 'mdo', 'MD05G1244200' => 'mdo', 'MD05G1324200' => 'mdo', 'MD09G1201600' => 'mdo', 'MD10G1000600' => 'mdo', 'MD14G1026900' => 'mdo', 'MD14G1187900' => 'mdo', 'MD15G1017800' => 'mdo', 'MD15G1018100' => 'mdo', 'Medtr4g124160' => 'mtr', 'Migut.L01260' => 'egut', 'Nitab4.5_0000008g0440' => 'nta', 'Nitab4.5_0000207g0170' => 'nta', 'Nitab4.5_0007671g0030' => 'nta', 'Nitab4.5_0010853g0020' => 'nta', 'Oeu057656.1' => 'oeu', 'PGSC0003DMG400005638' => 'stu', 'PGSC0003DMG400005639' => 'stu', 'Phvul.009G222800' => 'pvu', 'Potri.009G132400' => 'ptr', 'Potri.009G163001' => 'ptr', 'Potri.011G000700' => 'ptr', 'Potri.011G004800' => 'ptr', 'Prupe.1G509300' => 'ppe', 'Prupe.1G509700' => 'ppe', 'Prupe.1G510400' => 'ppe', 'Prupe.1G510700' => 'ppe', 'Prupe.1G512600' => 'ppe', 'Prupe.2G073200' => 'ppe', 'Prupe.3G059500' => 'ppe', 'Prupe.3G059600' => 'ppe', 'Prupe.3G246100' => 'ppe', 'Prupe.3G265100' => 'ppe', 'Prupe.4G034700' => 'ppe', 'Prupe.4G052100' => 'ppe', 'Prupe.4G053600' => 'ppe', 'Prupe.5G068800' => 'ppe', 'Prupe.5G070600' => 'ppe', 'Prupe.6G075400' => 'ppe', 'Prupe.6G075500' => 'ppe', 'Prupe.6G076400' => 'ppe', 'Prupe.8G110700' => 'ppe', 'Psat4g020960' => 'psa', 'PSO135G0788' => 'pso', 'PSO210G6463' => 'pso', 'PSO384G0370' => 'pso', 'PSO386G0056' => 'pso', 'QL01p006048' => 'qlo', 'QL02p054283' => 'qlo', 'QL05p008000' => 'qlo', 'QL05p008212' => 'qlo', 'QL05p008950' => 'qlo', 'QL05p009042' => 'qlo', 'QL05p009518' => 'qlo', 'QL05p012589' => 'qlo', 'QL05p012608' => 'qlo', 'QL05p012650' => 'qlo', 'QL05p012667' => 'qlo', 'QL05p014501' => 'qlo', 'QL05p052800' => 'qlo', 'QL05p065010' => 'qlo', 'QL05p074156' => 'qlo', 'QL05p074160' => 'qlo', 'QL05p074174' => 'qlo', 'QL05p074178' => 'qlo', 'QL05p074214' => 'qlo', 'QL06p001050' => 'qlo', 'QL06p001056' => 'qlo', 'QL06p006093' => 'qlo', 'QL06p006111' => 'qlo', 'QL07p019784' => 'qlo', 'QL07p019801' => 'qlo', 'QL07p036110' => 'qlo', 'QL07p036134' => 'qlo', 'QL07p036147' => 'qlo', 'QL07p036156' => 'qlo', 'QL07p036300' => 'qlo', 'QL07p036320' => 'qlo', 'QL08p014547' => 'qlo', 'QL08p014551' => 'qlo', 'QL08p043319' => 'qlo', 'QL08p043324' => 'qlo', 'QL11p009094' => 'qlo', 'RcHm_v2.0_Chr1g0380481' => 'rch', 'RcHm_v2.0_Chr2g0089331' => 'rch', 'RcHm_v2.0_Chr2g0123691' => 'rch', 'RcHm_v2.0_Chr2g0151111' => 'rch', 'RcHm_v2.0_Chr2g0163011' => 'rch', 'RcHm_v2.0_Chr2g0163051' => 'rch', 'RcHm_v2.0_Chr2g0164671' => 'rch', 'RcHm_v2.0_Chr2g0164681' => 'rch', 'RcHm_v2.0_Chr2g0164721' => 'rch', 'RcHm_v2.0_Chr3g0449911' => 'rch', 'RcHm_v2.0_Chr3g0450211' => 'rch', 'RcHm_v2.0_Chr3g0457271' => 'rch', 'RcHm_v2.0_Chr5g0018111' => 'rch', 'RcHm_v2.0_Chr5g0021011' => 'rch', 'RcHm_v2.0_Chr5g0081171' => 'rch', 'RcHm_v2.0_Chr5g0081211' => 'rch', 'RcHm_v2.0_Chr6g0275871' => 'rch', 'RcHm_v2.0_Chr6g0276071' => 'rch', 'RcHm_v2.0_Chr6g0285591' => 'rch', 'RcHm_v2.0_Chr6g0291931' => 'rch', 'RcHm_v2.0_Chr6g0292091' => 'rch', 'RcHm_v2.0_Chr6g0292271' => 'rch', 'RcHm_v2.0_Chr7g0221261' => 'rch', 'Rhsim08G0219900' => 'rsi', 'Rhsim08G0220200' => 'rsi', 'Rhsim08G0237800' => 'rsi', 'Rhsim08G0238800' => 'rsi', 'Sabra09G0102700' => 'sbr', 'Sabra09G0127200' => 'sbr', 'Sabra11G0003700' => 'sbr', 'Sabra15G0014700' => 'sbr', 'Sc19g0000590' => 'sci', 'Sc19g0001870' => 'sci', 'SGA_v2.0_scaffold1G00346' => 'sas', 'SGA_v2.0_scaffold1G00575' => 'sas', 'SGA_v2.0_scaffold1G00761' => 'sas', 'SGA_v2.0_scaffold232G43501' => 'sas', 'TAR625G1137' => 'tar', 'Thecc.03G222100' => 'tca', 'TPR.G12691' => 'tpr', 'TWI34G0727' => 'twi', 'TWI36G0117' => 'twi', 'VMungo1309G0868' => 'vmu' ) $gf_id = 'HOM05D001729' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001729' ) $data_identifier = 'HOM05D001729' $data_type = 'gf_id' $species_gene_counts = array( 'amhyb' => (int) 1, 'cqu' => (int) 9, 'can' => (int) 1, 'cansat' => (int) 1, 'car' => (int) 1, 'col' => (int) 5, 'dca' => (int) 1, 'din' => (int) 2, 'dzi' => (int) 3, 'fan' => (int) 140, 'fve' => (int) 62, 'gma' => (int) 1, 'ghi' => (int) 2, 'gra' => (int) 1, 'han' => (int) 1, 'sun' => (int) 1, 'lonja' => (int) 6, 'lja' => (int) 1, 'lsa' => (int) 4, 'mes' => (int) 1, 'mdo' => (int) 14, 'mtr' => (int) 1, 'egut' => (int) 1, 'nta' => (int) 4, 'oeu' => (int) 1, 'stu' => (int) 2, 'pvu' => (int) 1, 'ptr' => (int) 4, 'ppe' => (int) 19, 'psa' => (int) 1, 'pso' => (int) 4, 'qlo' => (int) 36, 'rch' => (int) 23, 'rsi' => (int) 4, 'sbr' => (int) 4, 'sci' => (int) 2, 'sas' => (int) 4, 'tar' => (int) 1, 'tca' => (int) 1, 'tpr' => (int) 1, 'twi' => (int) 2, 'vmu' => (int) 1 ) $gf_gene_species = 'vmu' $gf_gene_id = 'VMungo1309G0868' $species_info = array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ) $local_species = 'lsa' $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' => 'HOM05D001729', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '375', 'num_species' => '42' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'Ah.07g204710' => 'amhyb', 'AUR62006001' => 'cqu', 'AUR62006002' => 'cqu', 'AUR62006003' => 'cqu', 'AUR62015641' => 'cqu', 'AUR62027174' => 'cqu', 'AUR62035623' => 'cqu', 'AUR62035624' => 'cqu', 'AUR62035625' => 'cqu', 'AUR62035626' => 'cqu', 'CAN.G1110.53' => 'can', 'CANSAT80G0415' => 'cansat', 'Ca_21364_v3' => 'car', 'COL.COLO4_30693' => 'col', 'COL.COLO4_30694' => 'col', 'COL.COLO4_30695' => 'col', 'COL.COLO4_30696' => 'col', 'COL.COLO4_34020' => 'col', 'DCAR_004585' => 'dca', 'Dinv04029' => 'din', 'Dinv34857' => 'din', 'Duzib147G0011' => 'dzi', 'Duzib170G0599' => 'dzi', 'Duzib192G1051' => 'dzi', 'FAN01G0708' => 'fan', 'FAN01G0742' => 'fan', 'FAN02G0048' => 'fan', 'FAN02G0583' => 'fan', 'FAN02G0688' => 'fan', 'FAN02G1588' => 'fan', 'FAN02G2194' => 'fan', 'FAN02G2750' => 'fan', 'FAN02G3094' => 'fan', 'FAN02G3887' => 'fan', 'FAN02G3911' => 'fan', 'FAN02G3994' => 'fan', 'FAN02G4432' => 'fan', 'FAN02G4556' => 'fan', 'FAN03G1977' => 'fan', 'FAN03G2781' => 'fan', 'FAN03G2850' => 'fan', 'FAN03G3155' => 'fan', 'FAN04G2487' => 'fan', 'FAN05G0208' => 'fan', 'FAN05G0656' => 'fan', 'FAN05G0696' => 'fan', 'FAN05G0810' => 'fan', 'FAN05G1447' => 'fan', 'FAN05G2640' => 'fan', 'FAN05G2911' => 'fan', 'FAN05G3901' => 'fan', 'FAN05G4859' => 'fan', 'FAN05G4861' => 'fan', 'FAN05G4988' => 'fan', 'FAN05G5187' => 'fan', 'FAN05G5452' => 'fan', 'FAN05G5500' => 'fan', 'FAN05G5688' => 'fan', 'FAN06G0177' => 'fan', 'FAN06G0675' => 'fan', 'FAN06G1290' => 'fan', 'FAN06G2191' => 'fan', 'FAN06G2405' => 'fan', 'FAN06G3231' => 'fan', 'FAN06G3932' => 'fan', 'FAN07G0163' => 'fan', 'FAN07G0471' => 'fan', 'FAN07G1354' => 'fan', 'FAN08G0338' => 'fan', 'FAN08G1373' => 'fan', 'FAN08G2539' => 'fan', 'FAN08G2728' => 'fan', 'FAN09G0608' => 'fan', 'FAN09G1136' => 'fan', 'FAN09G1958' => 'fan', 'FAN09G2508' => 'fan', 'FAN09G2597' => 'fan', 'FAN09G2658' => 'fan', 'FAN09G2757' => 'fan', 'FAN09G2983' => 'fan', 'FAN09G3130' => 'fan', 'FAN09G3565' => 'fan', 'FAN09G3613' => 'fan', 'FAN09G4011' => 'fan', 'FAN09G4239' => 'fan', 'FAN09G4277' => 'fan', 'FAN09G4720' => 'fan', 'FAN11G0139' => 'fan', 'FAN11G1727' => 'fan', 'FAN11G2672' => 'fan', 'FAN11G2795' => 'fan', 'FAN11G3238' => 'fan', 'FAN11G3734' => 'fan', 'FAN12G0631' => 'fan', 'FAN12G2239' => 'fan', 'FAN12G2308' => 'fan', 'FAN12G2569' => 'fan', 'FAN12G2623' => 'fan', 'FAN13G3182' => 'fan', 'FAN14G0053' => 'fan', 'FAN14G0370' => 'fan', 'FAN14G0382' => 'fan', 'FAN14G0421' => 'fan', 'FAN14G0866' => 'fan', 'FAN14G1187' => 'fan', 'FAN14G1727' => 'fan', 'FAN14G1791' => 'fan', 'FAN14G2361' => 'fan', 'FAN14G2668' => 'fan', 'FAN14G2770' => 'fan', 'FAN14G2874' => 'fan', 'FAN14G3193' => 'fan', 'FAN14G3624' => 'fan', 'FAN14G3676' => 'fan', 'FAN14G3807' => 'fan', 'FAN14G4082' => 'fan', 'FAN14G4342' => 'fan', 'FAN14G4985' => 'fan', 'FAN14G5126' => 'fan', 'FAN14G5781' => 'fan', 'FAN14G5808' => 'fan', 'FAN14G5949' => 'fan', 'FAN15G0828' => 'fan', 'FAN15G1054' => 'fan', 'FAN15G2023' => 'fan', 'FAN15G2506' => 'fan', 'FAN16G0128' => 'fan', 'FAN16G0249' => 'fan', 'FAN16G0429' => 'fan', 'FAN16G1493' => 'fan', 'FAN16G2210' => 'fan', 'FAN16G2506' => 'fan', 'FAN18G1542' => 'fan', 'FAN18G4057' => 'fan', 'FAN19G0745' => 'fan', 'FAN19G1216' => 'fan', 'FAN19G1733' => 'fan', 'FAN20G0258' => 'fan', 'FAN20G1095' => 'fan', 'FAN20G1557' => 'fan', 'FAN21G0302' => 'fan', 'FAN21G0519' => 'fan', 'FAN21G0970' => 'fan', 'FAN21G1159' => 'fan', 'FAN21G1312' => 'fan', 'FAN21G1440' => 'fan', 'FAN21G1715' => 'fan', 'FAN23G1584' => 'fan', 'FAN24G0045' => 'fan', 'FAN24G0053' => 'fan', 'FAN24G1500' => 'fan', 'FAN24G1817' => 'fan', 'FAN24G2147' => 'fan', 'FAN24G2236' => 'fan', 'FAN24G2446' => 'fan', 'FAN24G2684' => 'fan', 'FAN25G0187' => 'fan', 'FAN25G0505' => 'fan', 'FAN25G0589' => 'fan', 'FAN25G3663' => 'fan', 'FAN26G1025' => 'fan', 'FAN26G2860' => 'fan', 'FAN27G1329' => 'fan', 'FAN27G3392' => 'fan', 'FvH4_1g02011' => 'fve', 'FvH4_1g06511' => 'fve', 'FvH4_2g19900' => 'fve', 'FvH4_2g19920' => 'fve', 'FvH4_2g24261' => 'fve', 'FvH4_2g24270' => 'fve', 'FvH4_2g24631' => 'fve', 'FvH4_2g30622' => 'fve', 'FvH4_3g12920' => 'fve', 'FvH4_3g30171' => 'fve', 'FvH4_3g35490' => 'fve', 'FvH4_3g43682' => 'fve', 'FvH4_3g43730' => 'fve', 'FvH4_3g43732' => 'fve', 'FvH4_3g43751' => 'fve', 'FvH4_3g43752' => 'fve', 'FvH4_3g43770' => 'fve', 'FvH4_3g44471' => 'fve', 'FvH4_3g44510' => 'fve', 'FvH4_3g44582' => 'fve', 'FvH4_4g16921' => 'fve', 'FvH4_4g17121' => 'fve', 'FvH4_4g17782' => 'fve', 'FvH4_4g17783' => 'fve', 'FvH4_4g18120' => 'fve', 'FvH4_4g31310' => 'fve', 'FvH4_4g35052' => 'fve', 'FvH4_5g30862' => 'fve', 'FvH4_6g01541' => 'fve', 'FvH4_6g02021' => 'fve', 'FvH4_6g02041' => 'fve', 'FvH4_6g02071' => 'fve', 'FvH4_6g02171' => 'fve', 'FvH4_6g03181' => 'fve', 'FvH4_6g03182' => 'fve', 'FvH4_6g03221' => 'fve', 'FvH4_6g03380' => 'fve', 'FvH4_6g05201' => 'fve', 'FvH4_6g05203' => 'fve', 'FvH4_6g20231' => 'fve', 'FvH4_6g31981' => 'fve', 'FvH4_6g32061' => 'fve', 'FvH4_6g37041' => 'fve', 'FvH4_6g37932' => 'fve', 'FvH4_6g38731' => 'fve', 'FvH4_6g39370' => 'fve', 'FvH4_6g39371' => 'fve', 'FvH4_6g40891' => 'fve', 'FvH4_6g40892' => 'fve', 'FvH4_6g43143' => 'fve', 'FvH4_6g45251' => 'fve', 'FvH4_6g45260' => 'fve', 'FvH4_6g45291' => 'fve', 'FvH4_6g45890' => 'fve', 'FvH4_6g46240' => 'fve', 'FvH4_6g46241' => 'fve', 'FvH4_6g46242' => 'fve', 'FvH4_6g46260' => 'fve', 'FvH4_6g46280' => 'fve', 'FvH4_6g46380' => 'fve', 'FvH4_7g12841' => 'fve', 'FvH4_7g31431' => 'fve', 'Glyma.09G075900' => 'gma', 'Gohir.A09G096401' => 'ghi', 'Gohir.D09G096101' => 'ghi', 'Gorai.006G112800' => 'gra', 'HanXRQChr04g0121411' => 'han', 'Hund15878' => 'sun', 'Lj2A1107G68' => 'lonja', 'Lj2A630G63' => 'lonja', 'Lj2A946T25' => 'lonja', 'Lj2C714T1' => 'lonja', 'Lj2C966T3' => 'lonja', 'Lj2C966T4' => 'lonja', 'Lj4g0002979' => 'lja', 'Lsat_1_v5_gn_5_30901' => 'lsa', 'Lsat_1_v5_gn_5_31100' => 'lsa', 'Lsat_1_v5_gn_5_38600' => 'lsa', 'Lsat_1_v5_gn_6_92061' => 'lsa', 'Manes.05G071301' => 'mes', 'MD02G1008700' => 'mdo', 'MD02G1008900' => 'mdo', 'MD03G1256400' => 'mdo', 'MD04G1180900' => 'mdo', 'MD04G1181000' => 'mdo', 'MD04G1181200' => 'mdo', 'MD05G1244200' => 'mdo', 'MD05G1324200' => 'mdo', 'MD09G1201600' => 'mdo', 'MD10G1000600' => 'mdo', 'MD14G1026900' => 'mdo', 'MD14G1187900' => 'mdo', 'MD15G1017800' => 'mdo', 'MD15G1018100' => 'mdo', 'Medtr4g124160' => 'mtr', 'Migut.L01260' => 'egut', 'Nitab4.5_0000008g0440' => 'nta', 'Nitab4.5_0000207g0170' => 'nta', 'Nitab4.5_0007671g0030' => 'nta', 'Nitab4.5_0010853g0020' => 'nta', 'Oeu057656.1' => 'oeu', 'PGSC0003DMG400005638' => 'stu', 'PGSC0003DMG400005639' => 'stu', 'Phvul.009G222800' => 'pvu', 'Potri.009G132400' => 'ptr', 'Potri.009G163001' => 'ptr', 'Potri.011G000700' => 'ptr', 'Potri.011G004800' => 'ptr', 'Prupe.1G509300' => 'ppe', 'Prupe.1G509700' => 'ppe', 'Prupe.1G510400' => 'ppe', 'Prupe.1G510700' => 'ppe', 'Prupe.1G512600' => 'ppe', 'Prupe.2G073200' => 'ppe', 'Prupe.3G059500' => 'ppe', 'Prupe.3G059600' => 'ppe', 'Prupe.3G246100' => 'ppe', 'Prupe.3G265100' => 'ppe', 'Prupe.4G034700' => 'ppe', 'Prupe.4G052100' => 'ppe', 'Prupe.4G053600' => 'ppe', 'Prupe.5G068800' => 'ppe', 'Prupe.5G070600' => 'ppe', 'Prupe.6G075400' => 'ppe', 'Prupe.6G075500' => 'ppe', 'Prupe.6G076400' => 'ppe', 'Prupe.8G110700' => 'ppe', 'Psat4g020960' => 'psa', 'PSO135G0788' => 'pso', 'PSO210G6463' => 'pso', 'PSO384G0370' => 'pso', 'PSO386G0056' => 'pso', 'QL01p006048' => 'qlo', 'QL02p054283' => 'qlo', 'QL05p008000' => 'qlo', 'QL05p008212' => 'qlo', 'QL05p008950' => 'qlo', 'QL05p009042' => 'qlo', 'QL05p009518' => 'qlo', 'QL05p012589' => 'qlo', 'QL05p012608' => 'qlo', 'QL05p012650' => 'qlo', 'QL05p012667' => 'qlo', 'QL05p014501' => 'qlo', 'QL05p052800' => 'qlo', 'QL05p065010' => 'qlo', 'QL05p074156' => 'qlo', 'QL05p074160' => 'qlo', 'QL05p074174' => 'qlo', 'QL05p074178' => 'qlo', 'QL05p074214' => 'qlo', 'QL06p001050' => 'qlo', 'QL06p001056' => 'qlo', 'QL06p006093' => 'qlo', 'QL06p006111' => 'qlo', 'QL07p019784' => 'qlo', 'QL07p019801' => 'qlo', 'QL07p036110' => 'qlo', 'QL07p036134' => 'qlo', 'QL07p036147' => 'qlo', 'QL07p036156' => 'qlo', 'QL07p036300' => 'qlo', 'QL07p036320' => 'qlo', 'QL08p014547' => 'qlo', 'QL08p014551' => 'qlo', 'QL08p043319' => 'qlo', 'QL08p043324' => 'qlo', 'QL11p009094' => 'qlo', 'RcHm_v2.0_Chr1g0380481' => 'rch', 'RcHm_v2.0_Chr2g0089331' => 'rch', 'RcHm_v2.0_Chr2g0123691' => 'rch', 'RcHm_v2.0_Chr2g0151111' => 'rch', 'RcHm_v2.0_Chr2g0163011' => 'rch', 'RcHm_v2.0_Chr2g0163051' => 'rch', 'RcHm_v2.0_Chr2g0164671' => 'rch', 'RcHm_v2.0_Chr2g0164681' => 'rch', 'RcHm_v2.0_Chr2g0164721' => 'rch', 'RcHm_v2.0_Chr3g0449911' => 'rch', 'RcHm_v2.0_Chr3g0450211' => 'rch', 'RcHm_v2.0_Chr3g0457271' => 'rch', 'RcHm_v2.0_Chr5g0018111' => 'rch', 'RcHm_v2.0_Chr5g0021011' => 'rch', 'RcHm_v2.0_Chr5g0081171' => 'rch', 'RcHm_v2.0_Chr5g0081211' => 'rch', 'RcHm_v2.0_Chr6g0275871' => 'rch', 'RcHm_v2.0_Chr6g0276071' => 'rch', 'RcHm_v2.0_Chr6g0285591' => 'rch', 'RcHm_v2.0_Chr6g0291931' => 'rch', 'RcHm_v2.0_Chr6g0292091' => 'rch', 'RcHm_v2.0_Chr6g0292271' => 'rch', 'RcHm_v2.0_Chr7g0221261' => 'rch', 'Rhsim08G0219900' => 'rsi', 'Rhsim08G0220200' => 'rsi', 'Rhsim08G0237800' => 'rsi', 'Rhsim08G0238800' => 'rsi', 'Sabra09G0102700' => 'sbr', 'Sabra09G0127200' => 'sbr', 'Sabra11G0003700' => 'sbr', 'Sabra15G0014700' => 'sbr', 'Sc19g0000590' => 'sci', 'Sc19g0001870' => 'sci', 'SGA_v2.0_scaffold1G00346' => 'sas', 'SGA_v2.0_scaffold1G00575' => 'sas', 'SGA_v2.0_scaffold1G00761' => 'sas', 'SGA_v2.0_scaffold232G43501' => 'sas', 'TAR625G1137' => 'tar', 'Thecc.03G222100' => 'tca', 'TPR.G12691' => 'tpr', 'TWI34G0727' => 'twi', 'TWI36G0117' => 'twi', 'VMungo1309G0868' => 'vmu' ), 'gf_id' => 'HOM05D001729', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001729' ), 'data_identifier' => 'HOM05D001729', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001729', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '375', 'num_species' => '42' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'Ah.07g204710' => 'amhyb', 'AUR62006001' => 'cqu', 'AUR62006002' => 'cqu', 'AUR62006003' => 'cqu', 'AUR62015641' => 'cqu', 'AUR62027174' => 'cqu', 'AUR62035623' => 'cqu', 'AUR62035624' => 'cqu', 'AUR62035625' => 'cqu', 'AUR62035626' => 'cqu', 'CAN.G1110.53' => 'can', 'CANSAT80G0415' => 'cansat', 'Ca_21364_v3' => 'car', 'COL.COLO4_30693' => 'col', 'COL.COLO4_30694' => 'col', 'COL.COLO4_30695' => 'col', 'COL.COLO4_30696' => 'col', 'COL.COLO4_34020' => 'col', 'DCAR_004585' => 'dca', 'Dinv04029' => 'din', 'Dinv34857' => 'din', 'Duzib147G0011' => 'dzi', 'Duzib170G0599' => 'dzi', 'Duzib192G1051' => 'dzi', 'FAN01G0708' => 'fan', 'FAN01G0742' => 'fan', 'FAN02G0048' => 'fan', 'FAN02G0583' => 'fan', 'FAN02G0688' => 'fan', 'FAN02G1588' => 'fan', 'FAN02G2194' => 'fan', 'FAN02G2750' => 'fan', 'FAN02G3094' => 'fan', 'FAN02G3887' => 'fan', 'FAN02G3911' => 'fan', 'FAN02G3994' => 'fan', 'FAN02G4432' => 'fan', 'FAN02G4556' => 'fan', 'FAN03G1977' => 'fan', 'FAN03G2781' => 'fan', 'FAN03G2850' => 'fan', 'FAN03G3155' => 'fan', 'FAN04G2487' => 'fan', 'FAN05G0208' => 'fan', 'FAN05G0656' => 'fan', 'FAN05G0696' => 'fan', 'FAN05G0810' => 'fan', 'FAN05G1447' => 'fan', 'FAN05G2640' => 'fan', 'FAN05G2911' => 'fan', 'FAN05G3901' => 'fan', 'FAN05G4859' => 'fan', 'FAN05G4861' => 'fan', 'FAN05G4988' => 'fan', 'FAN05G5187' => 'fan', 'FAN05G5452' => 'fan', 'FAN05G5500' => 'fan', 'FAN05G5688' => 'fan', 'FAN06G0177' => 'fan', 'FAN06G0675' => 'fan', 'FAN06G1290' => 'fan', 'FAN06G2191' => 'fan', 'FAN06G2405' => 'fan', 'FAN06G3231' => 'fan', 'FAN06G3932' => 'fan', 'FAN07G0163' => 'fan', 'FAN07G0471' => 'fan', 'FAN07G1354' => 'fan', 'FAN08G0338' => 'fan', 'FAN08G1373' => 'fan', 'FAN08G2539' => 'fan', 'FAN08G2728' => 'fan', 'FAN09G0608' => 'fan', 'FAN09G1136' => 'fan', 'FAN09G1958' => 'fan', 'FAN09G2508' => 'fan', 'FAN09G2597' => 'fan', 'FAN09G2658' => 'fan', 'FAN09G2757' => 'fan', 'FAN09G2983' => 'fan', 'FAN09G3130' => 'fan', 'FAN09G3565' => 'fan', 'FAN09G3613' => 'fan', 'FAN09G4011' => 'fan', 'FAN09G4239' => 'fan', 'FAN09G4277' => 'fan', 'FAN09G4720' => 'fan', 'FAN11G0139' => 'fan', 'FAN11G1727' => 'fan', 'FAN11G2672' => 'fan', 'FAN11G2795' => 'fan', 'FAN11G3238' => 'fan', 'FAN11G3734' => 'fan', 'FAN12G0631' => 'fan', 'FAN12G2239' => 'fan', 'FAN12G2308' => 'fan', 'FAN12G2569' => 'fan', 'FAN12G2623' => 'fan', 'FAN13G3182' => 'fan', 'FAN14G0053' => 'fan', 'FAN14G0370' => 'fan', 'FAN14G0382' => 'fan', 'FAN14G0421' => 'fan', 'FAN14G0866' => 'fan', 'FAN14G1187' => 'fan', 'FAN14G1727' => 'fan', 'FAN14G1791' => 'fan', 'FAN14G2361' => 'fan', 'FAN14G2668' => 'fan', 'FAN14G2770' => 'fan', 'FAN14G2874' => 'fan', 'FAN14G3193' => 'fan', 'FAN14G3624' => 'fan', 'FAN14G3676' => 'fan', 'FAN14G3807' => 'fan', 'FAN14G4082' => 'fan', 'FAN14G4342' => 'fan', 'FAN14G4985' => 'fan', 'FAN14G5126' => 'fan', 'FAN14G5781' => 'fan', 'FAN14G5808' => 'fan', 'FAN14G5949' => 'fan', 'FAN15G0828' => 'fan', 'FAN15G1054' => 'fan', 'FAN15G2023' => 'fan', 'FAN15G2506' => 'fan', 'FAN16G0128' => 'fan', 'FAN16G0249' => 'fan', 'FAN16G0429' => 'fan', 'FAN16G1493' => 'fan', 'FAN16G2210' => 'fan', 'FAN16G2506' => 'fan', 'FAN18G1542' => 'fan', 'FAN18G4057' => 'fan', 'FAN19G0745' => 'fan', 'FAN19G1216' => 'fan', 'FAN19G1733' => 'fan', 'FAN20G0258' => 'fan', 'FAN20G1095' => 'fan', 'FAN20G1557' => 'fan', 'FAN21G0302' => 'fan', 'FAN21G0519' => 'fan', 'FAN21G0970' => 'fan', 'FAN21G1159' => 'fan', 'FAN21G1312' => 'fan', 'FAN21G1440' => 'fan', 'FAN21G1715' => 'fan', 'FAN23G1584' => 'fan', 'FAN24G0045' => 'fan', 'FAN24G0053' => 'fan', 'FAN24G1500' => 'fan', 'FAN24G1817' => 'fan', 'FAN24G2147' => 'fan', 'FAN24G2236' => 'fan', 'FAN24G2446' => 'fan', 'FAN24G2684' => 'fan', 'FAN25G0187' => 'fan', 'FAN25G0505' => 'fan', 'FAN25G0589' => 'fan', 'FAN25G3663' => 'fan', 'FAN26G1025' => 'fan', 'FAN26G2860' => 'fan', 'FAN27G1329' => 'fan', 'FAN27G3392' => 'fan', 'FvH4_1g02011' => 'fve', 'FvH4_1g06511' => 'fve', 'FvH4_2g19900' => 'fve', 'FvH4_2g19920' => 'fve', 'FvH4_2g24261' => 'fve', 'FvH4_2g24270' => 'fve', 'FvH4_2g24631' => 'fve', 'FvH4_2g30622' => 'fve', 'FvH4_3g12920' => 'fve', 'FvH4_3g30171' => 'fve', 'FvH4_3g35490' => 'fve', 'FvH4_3g43682' => 'fve', 'FvH4_3g43730' => 'fve', 'FvH4_3g43732' => 'fve', 'FvH4_3g43751' => 'fve', 'FvH4_3g43752' => 'fve', 'FvH4_3g43770' => 'fve', 'FvH4_3g44471' => 'fve', 'FvH4_3g44510' => 'fve', 'FvH4_3g44582' => 'fve', 'FvH4_4g16921' => 'fve', 'FvH4_4g17121' => 'fve', 'FvH4_4g17782' => 'fve', 'FvH4_4g17783' => 'fve', 'FvH4_4g18120' => 'fve', 'FvH4_4g31310' => 'fve', 'FvH4_4g35052' => 'fve', 'FvH4_5g30862' => 'fve', 'FvH4_6g01541' => 'fve', 'FvH4_6g02021' => 'fve', 'FvH4_6g02041' => 'fve', 'FvH4_6g02071' => 'fve', 'FvH4_6g02171' => 'fve', 'FvH4_6g03181' => 'fve', 'FvH4_6g03182' => 'fve', 'FvH4_6g03221' => 'fve', 'FvH4_6g03380' => 'fve', 'FvH4_6g05201' => 'fve', 'FvH4_6g05203' => 'fve', 'FvH4_6g20231' => 'fve', 'FvH4_6g31981' => 'fve', 'FvH4_6g32061' => 'fve', 'FvH4_6g37041' => 'fve', 'FvH4_6g37932' => 'fve', 'FvH4_6g38731' => 'fve', 'FvH4_6g39370' => 'fve', 'FvH4_6g39371' => 'fve', 'FvH4_6g40891' => 'fve', 'FvH4_6g40892' => 'fve', 'FvH4_6g43143' => 'fve', 'FvH4_6g45251' => 'fve', 'FvH4_6g45260' => 'fve', 'FvH4_6g45291' => 'fve', 'FvH4_6g45890' => 'fve', 'FvH4_6g46240' => 'fve', 'FvH4_6g46241' => 'fve', 'FvH4_6g46242' => 'fve', 'FvH4_6g46260' => 'fve', 'FvH4_6g46280' => 'fve', 'FvH4_6g46380' => 'fve', 'FvH4_7g12841' => 'fve', 'FvH4_7g31431' => 'fve', 'Glyma.09G075900' => 'gma', 'Gohir.A09G096401' => 'ghi', 'Gohir.D09G096101' => 'ghi', 'Gorai.006G112800' => 'gra', 'HanXRQChr04g0121411' => 'han', 'Hund15878' => 'sun', 'Lj2A1107G68' => 'lonja', 'Lj2A630G63' => 'lonja', 'Lj2A946T25' => 'lonja', 'Lj2C714T1' => 'lonja', 'Lj2C966T3' => 'lonja', 'Lj2C966T4' => 'lonja', 'Lj4g0002979' => 'lja', 'Lsat_1_v5_gn_5_30901' => 'lsa', 'Lsat_1_v5_gn_5_31100' => 'lsa', 'Lsat_1_v5_gn_5_38600' => 'lsa', 'Lsat_1_v5_gn_6_92061' => 'lsa', 'Manes.05G071301' => 'mes', 'MD02G1008700' => 'mdo', 'MD02G1008900' => 'mdo', 'MD03G1256400' => 'mdo', 'MD04G1180900' => 'mdo', 'MD04G1181000' => 'mdo', 'MD04G1181200' => 'mdo', 'MD05G1244200' => 'mdo', 'MD05G1324200' => 'mdo', 'MD09G1201600' => 'mdo', 'MD10G1000600' => 'mdo', 'MD14G1026900' => 'mdo', 'MD14G1187900' => 'mdo', 'MD15G1017800' => 'mdo', 'MD15G1018100' => 'mdo', 'Medtr4g124160' => 'mtr', 'Migut.L01260' => 'egut', 'Nitab4.5_0000008g0440' => 'nta', 'Nitab4.5_0000207g0170' => 'nta', 'Nitab4.5_0007671g0030' => 'nta', 'Nitab4.5_0010853g0020' => 'nta', 'Oeu057656.1' => 'oeu', 'PGSC0003DMG400005638' => 'stu', 'PGSC0003DMG400005639' => 'stu', 'Phvul.009G222800' => 'pvu', 'Potri.009G132400' => 'ptr', 'Potri.009G163001' => 'ptr', 'Potri.011G000700' => 'ptr', 'Potri.011G004800' => 'ptr', 'Prupe.1G509300' => 'ppe', 'Prupe.1G509700' => 'ppe', 'Prupe.1G510400' => 'ppe', 'Prupe.1G510700' => 'ppe', 'Prupe.1G512600' => 'ppe', 'Prupe.2G073200' => 'ppe', 'Prupe.3G059500' => 'ppe', 'Prupe.3G059600' => 'ppe', 'Prupe.3G246100' => 'ppe', 'Prupe.3G265100' => 'ppe', 'Prupe.4G034700' => 'ppe', 'Prupe.4G052100' => 'ppe', 'Prupe.4G053600' => 'ppe', 'Prupe.5G068800' => 'ppe', 'Prupe.5G070600' => 'ppe', 'Prupe.6G075400' => 'ppe', 'Prupe.6G075500' => 'ppe', 'Prupe.6G076400' => 'ppe', 'Prupe.8G110700' => 'ppe', 'Psat4g020960' => 'psa', 'PSO135G0788' => 'pso', 'PSO210G6463' => 'pso', 'PSO384G0370' => 'pso', 'PSO386G0056' => 'pso', 'QL01p006048' => 'qlo', 'QL02p054283' => 'qlo', 'QL05p008000' => 'qlo', 'QL05p008212' => 'qlo', 'QL05p008950' => 'qlo', 'QL05p009042' => 'qlo', 'QL05p009518' => 'qlo', 'QL05p012589' => 'qlo', 'QL05p012608' => 'qlo', 'QL05p012650' => 'qlo', 'QL05p012667' => 'qlo', 'QL05p014501' => 'qlo', 'QL05p052800' => 'qlo', 'QL05p065010' => 'qlo', 'QL05p074156' => 'qlo', 'QL05p074160' => 'qlo', 'QL05p074174' => 'qlo', 'QL05p074178' => 'qlo', 'QL05p074214' => 'qlo', 'QL06p001050' => 'qlo', 'QL06p001056' => 'qlo', 'QL06p006093' => 'qlo', 'QL06p006111' => 'qlo', 'QL07p019784' => 'qlo', 'QL07p019801' => 'qlo', 'QL07p036110' => 'qlo', 'QL07p036134' => 'qlo', 'QL07p036147' => 'qlo', 'QL07p036156' => 'qlo', 'QL07p036300' => 'qlo', 'QL07p036320' => 'qlo', 'QL08p014547' => 'qlo', 'QL08p014551' => 'qlo', 'QL08p043319' => 'qlo', 'QL08p043324' => 'qlo', 'QL11p009094' => 'qlo', 'RcHm_v2.0_Chr1g0380481' => 'rch', 'RcHm_v2.0_Chr2g0089331' => 'rch', 'RcHm_v2.0_Chr2g0123691' => 'rch', 'RcHm_v2.0_Chr2g0151111' => 'rch', 'RcHm_v2.0_Chr2g0163011' => 'rch', 'RcHm_v2.0_Chr2g0163051' => 'rch', 'RcHm_v2.0_Chr2g0164671' => 'rch', 'RcHm_v2.0_Chr2g0164681' => 'rch', 'RcHm_v2.0_Chr2g0164721' => 'rch', 'RcHm_v2.0_Chr3g0449911' => 'rch', 'RcHm_v2.0_Chr3g0450211' => 'rch', 'RcHm_v2.0_Chr3g0457271' => 'rch', 'RcHm_v2.0_Chr5g0018111' => 'rch', 'RcHm_v2.0_Chr5g0021011' => 'rch', 'RcHm_v2.0_Chr5g0081171' => 'rch', 'RcHm_v2.0_Chr5g0081211' => 'rch', 'RcHm_v2.0_Chr6g0275871' => 'rch', 'RcHm_v2.0_Chr6g0276071' => 'rch', 'RcHm_v2.0_Chr6g0285591' => 'rch', 'RcHm_v2.0_Chr6g0291931' => 'rch', 'RcHm_v2.0_Chr6g0292091' => 'rch', 'RcHm_v2.0_Chr6g0292271' => 'rch', 'RcHm_v2.0_Chr7g0221261' => 'rch', 'Rhsim08G0219900' => 'rsi', 'Rhsim08G0220200' => 'rsi', 'Rhsim08G0237800' => 'rsi', 'Rhsim08G0238800' => 'rsi', 'Sabra09G0102700' => 'sbr', 'Sabra09G0127200' => 'sbr', 'Sabra11G0003700' => 'sbr', 'Sabra15G0014700' => 'sbr', 'Sc19g0000590' => 'sci', 'Sc19g0001870' => 'sci', 'SGA_v2.0_scaffold1G00346' => 'sas', 'SGA_v2.0_scaffold1G00575' => 'sas', 'SGA_v2.0_scaffold1G00761' => 'sas', 'SGA_v2.0_scaffold232G43501' => 'sas', 'TAR625G1137' => 'tar', 'Thecc.03G222100' => 'tca', 'TPR.G12691' => 'tpr', 'TWI34G0727' => 'twi', 'TWI36G0117' => 'twi', 'VMungo1309G0868' => 'vmu' ) $gf_id = 'HOM05D001729' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001729' ) $data_identifier = 'HOM05D001729' $data_type = 'gf_id' $species_gene_counts = array( 'amhyb' => (int) 1, 'cqu' => (int) 9, 'can' => (int) 1, 'cansat' => (int) 1, 'car' => (int) 1, 'col' => (int) 5, 'dca' => (int) 1, 'din' => (int) 2, 'dzi' => (int) 3, 'fan' => (int) 140, 'fve' => (int) 62, 'gma' => (int) 1, 'ghi' => (int) 2, 'gra' => (int) 1, 'han' => (int) 1, 'sun' => (int) 1, 'lonja' => (int) 6, 'lja' => (int) 1, 'lsa' => (int) 4, 'mes' => (int) 1, 'mdo' => (int) 14, 'mtr' => (int) 1, 'egut' => (int) 1, 'nta' => (int) 4, 'oeu' => (int) 1, 'stu' => (int) 2, 'pvu' => (int) 1, 'ptr' => (int) 4, 'ppe' => (int) 19, 'psa' => (int) 1, 'pso' => (int) 4, 'qlo' => (int) 36, 'rch' => (int) 23, 'rsi' => (int) 4, 'sbr' => (int) 4, 'sci' => (int) 2, 'sas' => (int) 4, 'tar' => (int) 1, 'tca' => (int) 1, 'tpr' => (int) 1, 'twi' => (int) 2, 'vmu' => (int) 1 ) $gf_gene_species = 'vmu' $gf_gene_id = 'VMungo1309G0868' $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' => 'HOM05D001729', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '375', 'num_species' => '42' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'Ah.07g204710' => 'amhyb', 'AUR62006001' => 'cqu', 'AUR62006002' => 'cqu', 'AUR62006003' => 'cqu', 'AUR62015641' => 'cqu', 'AUR62027174' => 'cqu', 'AUR62035623' => 'cqu', 'AUR62035624' => 'cqu', 'AUR62035625' => 'cqu', 'AUR62035626' => 'cqu', 'CAN.G1110.53' => 'can', 'CANSAT80G0415' => 'cansat', 'Ca_21364_v3' => 'car', 'COL.COLO4_30693' => 'col', 'COL.COLO4_30694' => 'col', 'COL.COLO4_30695' => 'col', 'COL.COLO4_30696' => 'col', 'COL.COLO4_34020' => 'col', 'DCAR_004585' => 'dca', 'Dinv04029' => 'din', 'Dinv34857' => 'din', 'Duzib147G0011' => 'dzi', 'Duzib170G0599' => 'dzi', 'Duzib192G1051' => 'dzi', 'FAN01G0708' => 'fan', 'FAN01G0742' => 'fan', 'FAN02G0048' => 'fan', 'FAN02G0583' => 'fan', 'FAN02G0688' => 'fan', 'FAN02G1588' => 'fan', 'FAN02G2194' => 'fan', 'FAN02G2750' => 'fan', 'FAN02G3094' => 'fan', 'FAN02G3887' => 'fan', 'FAN02G3911' => 'fan', 'FAN02G3994' => 'fan', 'FAN02G4432' => 'fan', 'FAN02G4556' => 'fan', 'FAN03G1977' => 'fan', 'FAN03G2781' => 'fan', 'FAN03G2850' => 'fan', 'FAN03G3155' => 'fan', 'FAN04G2487' => 'fan', 'FAN05G0208' => 'fan', 'FAN05G0656' => 'fan', 'FAN05G0696' => 'fan', 'FAN05G0810' => 'fan', 'FAN05G1447' => 'fan', 'FAN05G2640' => 'fan', 'FAN05G2911' => 'fan', 'FAN05G3901' => 'fan', 'FAN05G4859' => 'fan', 'FAN05G4861' => 'fan', 'FAN05G4988' => 'fan', 'FAN05G5187' => 'fan', 'FAN05G5452' => 'fan', 'FAN05G5500' => 'fan', 'FAN05G5688' => 'fan', 'FAN06G0177' => 'fan', 'FAN06G0675' => 'fan', 'FAN06G1290' => 'fan', 'FAN06G2191' => 'fan', 'FAN06G2405' => 'fan', 'FAN06G3231' => 'fan', 'FAN06G3932' => 'fan', 'FAN07G0163' => 'fan', 'FAN07G0471' => 'fan', 'FAN07G1354' => 'fan', 'FAN08G0338' => 'fan', 'FAN08G1373' => 'fan', 'FAN08G2539' => 'fan', 'FAN08G2728' => 'fan', 'FAN09G0608' => 'fan', 'FAN09G1136' => 'fan', 'FAN09G1958' => 'fan', 'FAN09G2508' => 'fan', 'FAN09G2597' => 'fan', 'FAN09G2658' => 'fan', 'FAN09G2757' => 'fan', 'FAN09G2983' => 'fan', 'FAN09G3130' => 'fan', 'FAN09G3565' => 'fan', 'FAN09G3613' => 'fan', 'FAN09G4011' => 'fan', 'FAN09G4239' => 'fan', 'FAN09G4277' => 'fan', 'FAN09G4720' => 'fan', 'FAN11G0139' => 'fan', 'FAN11G1727' => 'fan', 'FAN11G2672' => 'fan', 'FAN11G2795' => 'fan', 'FAN11G3238' => 'fan', 'FAN11G3734' => 'fan', 'FAN12G0631' => 'fan', 'FAN12G2239' => 'fan', 'FAN12G2308' => 'fan', 'FAN12G2569' => 'fan', 'FAN12G2623' => 'fan', 'FAN13G3182' => 'fan', 'FAN14G0053' => 'fan', 'FAN14G0370' => 'fan', 'FAN14G0382' => 'fan', 'FAN14G0421' => 'fan', 'FAN14G0866' => 'fan', 'FAN14G1187' => 'fan', 'FAN14G1727' => 'fan', 'FAN14G1791' => 'fan', 'FAN14G2361' => 'fan', 'FAN14G2668' => 'fan', 'FAN14G2770' => 'fan', 'FAN14G2874' => 'fan', 'FAN14G3193' => 'fan', 'FAN14G3624' => 'fan', 'FAN14G3676' => 'fan', 'FAN14G3807' => 'fan', 'FAN14G4082' => 'fan', 'FAN14G4342' => 'fan', 'FAN14G4985' => 'fan', 'FAN14G5126' => 'fan', 'FAN14G5781' => 'fan', 'FAN14G5808' => 'fan', 'FAN14G5949' => 'fan', 'FAN15G0828' => 'fan', 'FAN15G1054' => 'fan', 'FAN15G2023' => 'fan', 'FAN15G2506' => 'fan', 'FAN16G0128' => 'fan', 'FAN16G0249' => 'fan', 'FAN16G0429' => 'fan', 'FAN16G1493' => 'fan', 'FAN16G2210' => 'fan', 'FAN16G2506' => 'fan', 'FAN18G1542' => 'fan', 'FAN18G4057' => 'fan', 'FAN19G0745' => 'fan', 'FAN19G1216' => 'fan', 'FAN19G1733' => 'fan', 'FAN20G0258' => 'fan', 'FAN20G1095' => 'fan', 'FAN20G1557' => 'fan', 'FAN21G0302' => 'fan', 'FAN21G0519' => 'fan', 'FAN21G0970' => 'fan', 'FAN21G1159' => 'fan', 'FAN21G1312' => 'fan', 'FAN21G1440' => 'fan', 'FAN21G1715' => 'fan', 'FAN23G1584' => 'fan', 'FAN24G0045' => 'fan', 'FAN24G0053' => 'fan', 'FAN24G1500' => 'fan', 'FAN24G1817' => 'fan', 'FAN24G2147' => 'fan', 'FAN24G2236' => 'fan', 'FAN24G2446' => 'fan', 'FAN24G2684' => 'fan', 'FAN25G0187' => 'fan', 'FAN25G0505' => 'fan', 'FAN25G0589' => 'fan', 'FAN25G3663' => 'fan', 'FAN26G1025' => 'fan', 'FAN26G2860' => 'fan', 'FAN27G1329' => 'fan', 'FAN27G3392' => 'fan', 'FvH4_1g02011' => 'fve', 'FvH4_1g06511' => 'fve', 'FvH4_2g19900' => 'fve', 'FvH4_2g19920' => 'fve', 'FvH4_2g24261' => 'fve', 'FvH4_2g24270' => 'fve', 'FvH4_2g24631' => 'fve', 'FvH4_2g30622' => 'fve', 'FvH4_3g12920' => 'fve', 'FvH4_3g30171' => 'fve', 'FvH4_3g35490' => 'fve', 'FvH4_3g43682' => 'fve', 'FvH4_3g43730' => 'fve', 'FvH4_3g43732' => 'fve', 'FvH4_3g43751' => 'fve', 'FvH4_3g43752' => 'fve', 'FvH4_3g43770' => 'fve', 'FvH4_3g44471' => 'fve', 'FvH4_3g44510' => 'fve', 'FvH4_3g44582' => 'fve', 'FvH4_4g16921' => 'fve', 'FvH4_4g17121' => 'fve', 'FvH4_4g17782' => 'fve', 'FvH4_4g17783' => 'fve', 'FvH4_4g18120' => 'fve', 'FvH4_4g31310' => 'fve', 'FvH4_4g35052' => 'fve', 'FvH4_5g30862' => 'fve', 'FvH4_6g01541' => 'fve', 'FvH4_6g02021' => 'fve', 'FvH4_6g02041' => 'fve', 'FvH4_6g02071' => 'fve', 'FvH4_6g02171' => 'fve', 'FvH4_6g03181' => 'fve', 'FvH4_6g03182' => 'fve', 'FvH4_6g03221' => 'fve', 'FvH4_6g03380' => 'fve', 'FvH4_6g05201' => 'fve', 'FvH4_6g05203' => 'fve', 'FvH4_6g20231' => 'fve', 'FvH4_6g31981' => 'fve', 'FvH4_6g32061' => 'fve', 'FvH4_6g37041' => 'fve', 'FvH4_6g37932' => 'fve', 'FvH4_6g38731' => 'fve', 'FvH4_6g39370' => 'fve', 'FvH4_6g39371' => 'fve', 'FvH4_6g40891' => 'fve', 'FvH4_6g40892' => 'fve', 'FvH4_6g43143' => 'fve', 'FvH4_6g45251' => 'fve', 'FvH4_6g45260' => 'fve', 'FvH4_6g45291' => 'fve', 'FvH4_6g45890' => 'fve', 'FvH4_6g46240' => 'fve', 'FvH4_6g46241' => 'fve', 'FvH4_6g46242' => 'fve', 'FvH4_6g46260' => 'fve', 'FvH4_6g46280' => 'fve', 'FvH4_6g46380' => 'fve', 'FvH4_7g12841' => 'fve', 'FvH4_7g31431' => 'fve', 'Glyma.09G075900' => 'gma', 'Gohir.A09G096401' => 'ghi', 'Gohir.D09G096101' => 'ghi', 'Gorai.006G112800' => 'gra', 'HanXRQChr04g0121411' => 'han', 'Hund15878' => 'sun', 'Lj2A1107G68' => 'lonja', 'Lj2A630G63' => 'lonja', 'Lj2A946T25' => 'lonja', 'Lj2C714T1' => 'lonja', 'Lj2C966T3' => 'lonja', 'Lj2C966T4' => 'lonja', 'Lj4g0002979' => 'lja', 'Lsat_1_v5_gn_5_30901' => 'lsa', 'Lsat_1_v5_gn_5_31100' => 'lsa', 'Lsat_1_v5_gn_5_38600' => 'lsa', 'Lsat_1_v5_gn_6_92061' => 'lsa', 'Manes.05G071301' => 'mes', 'MD02G1008700' => 'mdo', 'MD02G1008900' => 'mdo', 'MD03G1256400' => 'mdo', 'MD04G1180900' => 'mdo', 'MD04G1181000' => 'mdo', 'MD04G1181200' => 'mdo', 'MD05G1244200' => 'mdo', 'MD05G1324200' => 'mdo', 'MD09G1201600' => 'mdo', 'MD10G1000600' => 'mdo', 'MD14G1026900' => 'mdo', 'MD14G1187900' => 'mdo', 'MD15G1017800' => 'mdo', 'MD15G1018100' => 'mdo', 'Medtr4g124160' => 'mtr', 'Migut.L01260' => 'egut', 'Nitab4.5_0000008g0440' => 'nta', 'Nitab4.5_0000207g0170' => 'nta', 'Nitab4.5_0007671g0030' => 'nta', 'Nitab4.5_0010853g0020' => 'nta', 'Oeu057656.1' => 'oeu', 'PGSC0003DMG400005638' => 'stu', 'PGSC0003DMG400005639' => 'stu', 'Phvul.009G222800' => 'pvu', 'Potri.009G132400' => 'ptr', 'Potri.009G163001' => 'ptr', 'Potri.011G000700' => 'ptr', 'Potri.011G004800' => 'ptr', 'Prupe.1G509300' => 'ppe', 'Prupe.1G509700' => 'ppe', 'Prupe.1G510400' => 'ppe', 'Prupe.1G510700' => 'ppe', 'Prupe.1G512600' => 'ppe', 'Prupe.2G073200' => 'ppe', 'Prupe.3G059500' => 'ppe', 'Prupe.3G059600' => 'ppe', 'Prupe.3G246100' => 'ppe', 'Prupe.3G265100' => 'ppe', 'Prupe.4G034700' => 'ppe', 'Prupe.4G052100' => 'ppe', 'Prupe.4G053600' => 'ppe', 'Prupe.5G068800' => 'ppe', 'Prupe.5G070600' => 'ppe', 'Prupe.6G075400' => 'ppe', 'Prupe.6G075500' => 'ppe', 'Prupe.6G076400' => 'ppe', 'Prupe.8G110700' => 'ppe', 'Psat4g020960' => 'psa', 'PSO135G0788' => 'pso', 'PSO210G6463' => 'pso', 'PSO384G0370' => 'pso', 'PSO386G0056' => 'pso', 'QL01p006048' => 'qlo', 'QL02p054283' => 'qlo', 'QL05p008000' => 'qlo', 'QL05p008212' => 'qlo', 'QL05p008950' => 'qlo', 'QL05p009042' => 'qlo', 'QL05p009518' => 'qlo', 'QL05p012589' => 'qlo', 'QL05p012608' => 'qlo', 'QL05p012650' => 'qlo', 'QL05p012667' => 'qlo', 'QL05p014501' => 'qlo', 'QL05p052800' => 'qlo', 'QL05p065010' => 'qlo', 'QL05p074156' => 'qlo', 'QL05p074160' => 'qlo', 'QL05p074174' => 'qlo', 'QL05p074178' => 'qlo', 'QL05p074214' => 'qlo', 'QL06p001050' => 'qlo', 'QL06p001056' => 'qlo', 'QL06p006093' => 'qlo', 'QL06p006111' => 'qlo', 'QL07p019784' => 'qlo', 'QL07p019801' => 'qlo', 'QL07p036110' => 'qlo', 'QL07p036134' => 'qlo', 'QL07p036147' => 'qlo', 'QL07p036156' => 'qlo', 'QL07p036300' => 'qlo', 'QL07p036320' => 'qlo', 'QL08p014547' => 'qlo', 'QL08p014551' => 'qlo', 'QL08p043319' => 'qlo', 'QL08p043324' => 'qlo', 'QL11p009094' => 'qlo', 'RcHm_v2.0_Chr1g0380481' => 'rch', 'RcHm_v2.0_Chr2g0089331' => 'rch', 'RcHm_v2.0_Chr2g0123691' => 'rch', 'RcHm_v2.0_Chr2g0151111' => 'rch', 'RcHm_v2.0_Chr2g0163011' => 'rch', 'RcHm_v2.0_Chr2g0163051' => 'rch', 'RcHm_v2.0_Chr2g0164671' => 'rch', 'RcHm_v2.0_Chr2g0164681' => 'rch', 'RcHm_v2.0_Chr2g0164721' => 'rch', 'RcHm_v2.0_Chr3g0449911' => 'rch', 'RcHm_v2.0_Chr3g0450211' => 'rch', 'RcHm_v2.0_Chr3g0457271' => 'rch', 'RcHm_v2.0_Chr5g0018111' => 'rch', 'RcHm_v2.0_Chr5g0021011' => 'rch', 'RcHm_v2.0_Chr5g0081171' => 'rch', 'RcHm_v2.0_Chr5g0081211' => 'rch', 'RcHm_v2.0_Chr6g0275871' => 'rch', 'RcHm_v2.0_Chr6g0276071' => 'rch', 'RcHm_v2.0_Chr6g0285591' => 'rch', 'RcHm_v2.0_Chr6g0291931' => 'rch', 'RcHm_v2.0_Chr6g0292091' => 'rch', 'RcHm_v2.0_Chr6g0292271' => 'rch', 'RcHm_v2.0_Chr7g0221261' => 'rch', 'Rhsim08G0219900' => 'rsi', 'Rhsim08G0220200' => 'rsi', 'Rhsim08G0237800' => 'rsi', 'Rhsim08G0238800' => 'rsi', 'Sabra09G0102700' => 'sbr', 'Sabra09G0127200' => 'sbr', 'Sabra11G0003700' => 'sbr', 'Sabra15G0014700' => 'sbr', 'Sc19g0000590' => 'sci', 'Sc19g0001870' => 'sci', 'SGA_v2.0_scaffold1G00346' => 'sas', 'SGA_v2.0_scaffold1G00575' => 'sas', 'SGA_v2.0_scaffold1G00761' => 'sas', 'SGA_v2.0_scaffold232G43501' => 'sas', 'TAR625G1137' => 'tar', 'Thecc.03G222100' => 'tca', 'TPR.G12691' => 'tpr', 'TWI34G0727' => 'twi', 'TWI36G0117' => 'twi', 'VMungo1309G0868' => 'vmu' ), 'gf_id' => 'HOM05D001729', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001729' ), 'data_identifier' => 'HOM05D001729', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001729', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '375', 'num_species' => '42' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'Ah.07g204710' => 'amhyb', 'AUR62006001' => 'cqu', 'AUR62006002' => 'cqu', 'AUR62006003' => 'cqu', 'AUR62015641' => 'cqu', 'AUR62027174' => 'cqu', 'AUR62035623' => 'cqu', 'AUR62035624' => 'cqu', 'AUR62035625' => 'cqu', 'AUR62035626' => 'cqu', 'CAN.G1110.53' => 'can', 'CANSAT80G0415' => 'cansat', 'Ca_21364_v3' => 'car', 'COL.COLO4_30693' => 'col', 'COL.COLO4_30694' => 'col', 'COL.COLO4_30695' => 'col', 'COL.COLO4_30696' => 'col', 'COL.COLO4_34020' => 'col', 'DCAR_004585' => 'dca', 'Dinv04029' => 'din', 'Dinv34857' => 'din', 'Duzib147G0011' => 'dzi', 'Duzib170G0599' => 'dzi', 'Duzib192G1051' => 'dzi', 'FAN01G0708' => 'fan', 'FAN01G0742' => 'fan', 'FAN02G0048' => 'fan', 'FAN02G0583' => 'fan', 'FAN02G0688' => 'fan', 'FAN02G1588' => 'fan', 'FAN02G2194' => 'fan', 'FAN02G2750' => 'fan', 'FAN02G3094' => 'fan', 'FAN02G3887' => 'fan', 'FAN02G3911' => 'fan', 'FAN02G3994' => 'fan', 'FAN02G4432' => 'fan', 'FAN02G4556' => 'fan', 'FAN03G1977' => 'fan', 'FAN03G2781' => 'fan', 'FAN03G2850' => 'fan', 'FAN03G3155' => 'fan', 'FAN04G2487' => 'fan', 'FAN05G0208' => 'fan', 'FAN05G0656' => 'fan', 'FAN05G0696' => 'fan', 'FAN05G0810' => 'fan', 'FAN05G1447' => 'fan', 'FAN05G2640' => 'fan', 'FAN05G2911' => 'fan', 'FAN05G3901' => 'fan', 'FAN05G4859' => 'fan', 'FAN05G4861' => 'fan', 'FAN05G4988' => 'fan', 'FAN05G5187' => 'fan', 'FAN05G5452' => 'fan', 'FAN05G5500' => 'fan', 'FAN05G5688' => 'fan', 'FAN06G0177' => 'fan', 'FAN06G0675' => 'fan', 'FAN06G1290' => 'fan', 'FAN06G2191' => 'fan', 'FAN06G2405' => 'fan', 'FAN06G3231' => 'fan', 'FAN06G3932' => 'fan', 'FAN07G0163' => 'fan', 'FAN07G0471' => 'fan', 'FAN07G1354' => 'fan', 'FAN08G0338' => 'fan', 'FAN08G1373' => 'fan', 'FAN08G2539' => 'fan', 'FAN08G2728' => 'fan', 'FAN09G0608' => 'fan', 'FAN09G1136' => 'fan', 'FAN09G1958' => 'fan', 'FAN09G2508' => 'fan', 'FAN09G2597' => 'fan', 'FAN09G2658' => 'fan', 'FAN09G2757' => 'fan', 'FAN09G2983' => 'fan', 'FAN09G3130' => 'fan', 'FAN09G3565' => 'fan', 'FAN09G3613' => 'fan', 'FAN09G4011' => 'fan', 'FAN09G4239' => 'fan', 'FAN09G4277' => 'fan', 'FAN09G4720' => 'fan', 'FAN11G0139' => 'fan', 'FAN11G1727' => 'fan', 'FAN11G2672' => 'fan', 'FAN11G2795' => 'fan', 'FAN11G3238' => 'fan', 'FAN11G3734' => 'fan', 'FAN12G0631' => 'fan', 'FAN12G2239' => 'fan', 'FAN12G2308' => 'fan', 'FAN12G2569' => 'fan', 'FAN12G2623' => 'fan', 'FAN13G3182' => 'fan', 'FAN14G0053' => 'fan', 'FAN14G0370' => 'fan', 'FAN14G0382' => 'fan', 'FAN14G0421' => 'fan', 'FAN14G0866' => 'fan', 'FAN14G1187' => 'fan', 'FAN14G1727' => 'fan', 'FAN14G1791' => 'fan', 'FAN14G2361' => 'fan', 'FAN14G2668' => 'fan', 'FAN14G2770' => 'fan', 'FAN14G2874' => 'fan', 'FAN14G3193' => 'fan', 'FAN14G3624' => 'fan', 'FAN14G3676' => 'fan', 'FAN14G3807' => 'fan', 'FAN14G4082' => 'fan', 'FAN14G4342' => 'fan', 'FAN14G4985' => 'fan', 'FAN14G5126' => 'fan', 'FAN14G5781' => 'fan', 'FAN14G5808' => 'fan', 'FAN14G5949' => 'fan', 'FAN15G0828' => 'fan', 'FAN15G1054' => 'fan', 'FAN15G2023' => 'fan', 'FAN15G2506' => 'fan', 'FAN16G0128' => 'fan', 'FAN16G0249' => 'fan', 'FAN16G0429' => 'fan', 'FAN16G1493' => 'fan', 'FAN16G2210' => 'fan', 'FAN16G2506' => 'fan', 'FAN18G1542' => 'fan', 'FAN18G4057' => 'fan', 'FAN19G0745' => 'fan', 'FAN19G1216' => 'fan', 'FAN19G1733' => 'fan', 'FAN20G0258' => 'fan', 'FAN20G1095' => 'fan', 'FAN20G1557' => 'fan', 'FAN21G0302' => 'fan', 'FAN21G0519' => 'fan', 'FAN21G0970' => 'fan', 'FAN21G1159' => 'fan', 'FAN21G1312' => 'fan', 'FAN21G1440' => 'fan', 'FAN21G1715' => 'fan', 'FAN23G1584' => 'fan', 'FAN24G0045' => 'fan', 'FAN24G0053' => 'fan', 'FAN24G1500' => 'fan', 'FAN24G1817' => 'fan', 'FAN24G2147' => 'fan', 'FAN24G2236' => 'fan', 'FAN24G2446' => 'fan', 'FAN24G2684' => 'fan', 'FAN25G0187' => 'fan', 'FAN25G0505' => 'fan', 'FAN25G0589' => 'fan', 'FAN25G3663' => 'fan', 'FAN26G1025' => 'fan', 'FAN26G2860' => 'fan', 'FAN27G1329' => 'fan', 'FAN27G3392' => 'fan', 'FvH4_1g02011' => 'fve', 'FvH4_1g06511' => 'fve', 'FvH4_2g19900' => 'fve', 'FvH4_2g19920' => 'fve', 'FvH4_2g24261' => 'fve', 'FvH4_2g24270' => 'fve', 'FvH4_2g24631' => 'fve', 'FvH4_2g30622' => 'fve', 'FvH4_3g12920' => 'fve', 'FvH4_3g30171' => 'fve', 'FvH4_3g35490' => 'fve', 'FvH4_3g43682' => 'fve', 'FvH4_3g43730' => 'fve', 'FvH4_3g43732' => 'fve', 'FvH4_3g43751' => 'fve', 'FvH4_3g43752' => 'fve', 'FvH4_3g43770' => 'fve', 'FvH4_3g44471' => 'fve', 'FvH4_3g44510' => 'fve', 'FvH4_3g44582' => 'fve', 'FvH4_4g16921' => 'fve', 'FvH4_4g17121' => 'fve', 'FvH4_4g17782' => 'fve', 'FvH4_4g17783' => 'fve', 'FvH4_4g18120' => 'fve', 'FvH4_4g31310' => 'fve', 'FvH4_4g35052' => 'fve', 'FvH4_5g30862' => 'fve', 'FvH4_6g01541' => 'fve', 'FvH4_6g02021' => 'fve', 'FvH4_6g02041' => 'fve', 'FvH4_6g02071' => 'fve', 'FvH4_6g02171' => 'fve', 'FvH4_6g03181' => 'fve', 'FvH4_6g03182' => 'fve', 'FvH4_6g03221' => 'fve', 'FvH4_6g03380' => 'fve', 'FvH4_6g05201' => 'fve', 'FvH4_6g05203' => 'fve', 'FvH4_6g20231' => 'fve', 'FvH4_6g31981' => 'fve', 'FvH4_6g32061' => 'fve', 'FvH4_6g37041' => 'fve', 'FvH4_6g37932' => 'fve', 'FvH4_6g38731' => 'fve', 'FvH4_6g39370' => 'fve', 'FvH4_6g39371' => 'fve', 'FvH4_6g40891' => 'fve', 'FvH4_6g40892' => 'fve', 'FvH4_6g43143' => 'fve', 'FvH4_6g45251' => 'fve', 'FvH4_6g45260' => 'fve', 'FvH4_6g45291' => 'fve', 'FvH4_6g45890' => 'fve', 'FvH4_6g46240' => 'fve', 'FvH4_6g46241' => 'fve', 'FvH4_6g46242' => 'fve', 'FvH4_6g46260' => 'fve', 'FvH4_6g46280' => 'fve', 'FvH4_6g46380' => 'fve', 'FvH4_7g12841' => 'fve', 'FvH4_7g31431' => 'fve', 'Glyma.09G075900' => 'gma', 'Gohir.A09G096401' => 'ghi', 'Gohir.D09G096101' => 'ghi', 'Gorai.006G112800' => 'gra', 'HanXRQChr04g0121411' => 'han', 'Hund15878' => 'sun', 'Lj2A1107G68' => 'lonja', 'Lj2A630G63' => 'lonja', 'Lj2A946T25' => 'lonja', 'Lj2C714T1' => 'lonja', 'Lj2C966T3' => 'lonja', 'Lj2C966T4' => 'lonja', 'Lj4g0002979' => 'lja', 'Lsat_1_v5_gn_5_30901' => 'lsa', 'Lsat_1_v5_gn_5_31100' => 'lsa', 'Lsat_1_v5_gn_5_38600' => 'lsa', 'Lsat_1_v5_gn_6_92061' => 'lsa', 'Manes.05G071301' => 'mes', 'MD02G1008700' => 'mdo', 'MD02G1008900' => 'mdo', 'MD03G1256400' => 'mdo', 'MD04G1180900' => 'mdo', 'MD04G1181000' => 'mdo', 'MD04G1181200' => 'mdo', 'MD05G1244200' => 'mdo', 'MD05G1324200' => 'mdo', 'MD09G1201600' => 'mdo', 'MD10G1000600' => 'mdo', 'MD14G1026900' => 'mdo', 'MD14G1187900' => 'mdo', 'MD15G1017800' => 'mdo', 'MD15G1018100' => 'mdo', 'Medtr4g124160' => 'mtr', 'Migut.L01260' => 'egut', 'Nitab4.5_0000008g0440' => 'nta', 'Nitab4.5_0000207g0170' => 'nta', 'Nitab4.5_0007671g0030' => 'nta', 'Nitab4.5_0010853g0020' => 'nta', 'Oeu057656.1' => 'oeu', 'PGSC0003DMG400005638' => 'stu', 'PGSC0003DMG400005639' => 'stu', 'Phvul.009G222800' => 'pvu', 'Potri.009G132400' => 'ptr', 'Potri.009G163001' => 'ptr', 'Potri.011G000700' => 'ptr', 'Potri.011G004800' => 'ptr', 'Prupe.1G509300' => 'ppe', 'Prupe.1G509700' => 'ppe', 'Prupe.1G510400' => 'ppe', 'Prupe.1G510700' => 'ppe', 'Prupe.1G512600' => 'ppe', 'Prupe.2G073200' => 'ppe', 'Prupe.3G059500' => 'ppe', 'Prupe.3G059600' => 'ppe', 'Prupe.3G246100' => 'ppe', 'Prupe.3G265100' => 'ppe', 'Prupe.4G034700' => 'ppe', 'Prupe.4G052100' => 'ppe', 'Prupe.4G053600' => 'ppe', 'Prupe.5G068800' => 'ppe', 'Prupe.5G070600' => 'ppe', 'Prupe.6G075400' => 'ppe', 'Prupe.6G075500' => 'ppe', 'Prupe.6G076400' => 'ppe', 'Prupe.8G110700' => 'ppe', 'Psat4g020960' => 'psa', 'PSO135G0788' => 'pso', 'PSO210G6463' => 'pso', 'PSO384G0370' => 'pso', 'PSO386G0056' => 'pso', 'QL01p006048' => 'qlo', 'QL02p054283' => 'qlo', 'QL05p008000' => 'qlo', 'QL05p008212' => 'qlo', 'QL05p008950' => 'qlo', 'QL05p009042' => 'qlo', 'QL05p009518' => 'qlo', 'QL05p012589' => 'qlo', 'QL05p012608' => 'qlo', 'QL05p012650' => 'qlo', 'QL05p012667' => 'qlo', 'QL05p014501' => 'qlo', 'QL05p052800' => 'qlo', 'QL05p065010' => 'qlo', 'QL05p074156' => 'qlo', 'QL05p074160' => 'qlo', 'QL05p074174' => 'qlo', 'QL05p074178' => 'qlo', 'QL05p074214' => 'qlo', 'QL06p001050' => 'qlo', 'QL06p001056' => 'qlo', 'QL06p006093' => 'qlo', 'QL06p006111' => 'qlo', 'QL07p019784' => 'qlo', 'QL07p019801' => 'qlo', 'QL07p036110' => 'qlo', 'QL07p036134' => 'qlo', 'QL07p036147' => 'qlo', 'QL07p036156' => 'qlo', 'QL07p036300' => 'qlo', 'QL07p036320' => 'qlo', 'QL08p014547' => 'qlo', 'QL08p014551' => 'qlo', 'QL08p043319' => 'qlo', 'QL08p043324' => 'qlo', 'QL11p009094' => 'qlo', 'RcHm_v2.0_Chr1g0380481' => 'rch', 'RcHm_v2.0_Chr2g0089331' => 'rch', 'RcHm_v2.0_Chr2g0123691' => 'rch', 'RcHm_v2.0_Chr2g0151111' => 'rch', 'RcHm_v2.0_Chr2g0163011' => 'rch', 'RcHm_v2.0_Chr2g0163051' => 'rch', 'RcHm_v2.0_Chr2g0164671' => 'rch', 'RcHm_v2.0_Chr2g0164681' => 'rch', 'RcHm_v2.0_Chr2g0164721' => 'rch', 'RcHm_v2.0_Chr3g0449911' => 'rch', 'RcHm_v2.0_Chr3g0450211' => 'rch', 'RcHm_v2.0_Chr3g0457271' => 'rch', 'RcHm_v2.0_Chr5g0018111' => 'rch', 'RcHm_v2.0_Chr5g0021011' => 'rch', 'RcHm_v2.0_Chr5g0081171' => 'rch', 'RcHm_v2.0_Chr5g0081211' => 'rch', 'RcHm_v2.0_Chr6g0275871' => 'rch', 'RcHm_v2.0_Chr6g0276071' => 'rch', 'RcHm_v2.0_Chr6g0285591' => 'rch', 'RcHm_v2.0_Chr6g0291931' => 'rch', 'RcHm_v2.0_Chr6g0292091' => 'rch', 'RcHm_v2.0_Chr6g0292271' => 'rch', 'RcHm_v2.0_Chr7g0221261' => 'rch', 'Rhsim08G0219900' => 'rsi', 'Rhsim08G0220200' => 'rsi', 'Rhsim08G0237800' => 'rsi', 'Rhsim08G0238800' => 'rsi', 'Sabra09G0102700' => 'sbr', 'Sabra09G0127200' => 'sbr', 'Sabra11G0003700' => 'sbr', 'Sabra15G0014700' => 'sbr', 'Sc19g0000590' => 'sci', 'Sc19g0001870' => 'sci', 'SGA_v2.0_scaffold1G00346' => 'sas', 'SGA_v2.0_scaffold1G00575' => 'sas', 'SGA_v2.0_scaffold1G00761' => 'sas', 'SGA_v2.0_scaffold232G43501' => 'sas', 'TAR625G1137' => 'tar', 'Thecc.03G222100' => 'tca', 'TPR.G12691' => 'tpr', 'TWI34G0727' => 'twi', 'TWI36G0117' => 'twi', 'VMungo1309G0868' => 'vmu' ) $gf_id = 'HOM05D001729' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001729' ) $data_identifier = 'HOM05D001729' $data_type = 'gf_id' $species_gene_counts = array( 'amhyb' => (int) 1, 'cqu' => (int) 9, 'can' => (int) 1, 'cansat' => (int) 1, 'car' => (int) 1, 'col' => (int) 5, 'dca' => (int) 1, 'din' => (int) 2, 'dzi' => (int) 3, 'fan' => (int) 140, 'fve' => (int) 62, 'gma' => (int) 1, 'ghi' => (int) 2, 'gra' => (int) 1, 'han' => (int) 1, 'sun' => (int) 1, 'lonja' => (int) 6, 'lja' => (int) 1, 'lsa' => (int) 4, 'mes' => (int) 1, 'mdo' => (int) 14, 'mtr' => (int) 1, 'egut' => (int) 1, 'nta' => (int) 4, 'oeu' => (int) 1, 'stu' => (int) 2, 'pvu' => (int) 1, 'ptr' => (int) 4, 'ppe' => (int) 19, 'psa' => (int) 1, 'pso' => (int) 4, 'qlo' => (int) 36, 'rch' => (int) 23, 'rsi' => (int) 4, 'sbr' => (int) 4, 'sci' => (int) 2, 'sas' => (int) 4, 'tar' => (int) 1, 'tca' => (int) 1, 'tpr' => (int) 1, 'twi' => (int) 2, 'vmu' => (int) 1 ) $gf_gene_species = 'vmu' $gf_gene_id = 'VMungo1309G0868' $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' => 'HOM05D001729', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '375', 'num_species' => '42' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'Ah.07g204710' => 'amhyb', 'AUR62006001' => 'cqu', 'AUR62006002' => 'cqu', 'AUR62006003' => 'cqu', 'AUR62015641' => 'cqu', 'AUR62027174' => 'cqu', 'AUR62035623' => 'cqu', 'AUR62035624' => 'cqu', 'AUR62035625' => 'cqu', 'AUR62035626' => 'cqu', 'CAN.G1110.53' => 'can', 'CANSAT80G0415' => 'cansat', 'Ca_21364_v3' => 'car', 'COL.COLO4_30693' => 'col', 'COL.COLO4_30694' => 'col', 'COL.COLO4_30695' => 'col', 'COL.COLO4_30696' => 'col', 'COL.COLO4_34020' => 'col', 'DCAR_004585' => 'dca', 'Dinv04029' => 'din', 'Dinv34857' => 'din', 'Duzib147G0011' => 'dzi', 'Duzib170G0599' => 'dzi', 'Duzib192G1051' => 'dzi', 'FAN01G0708' => 'fan', 'FAN01G0742' => 'fan', 'FAN02G0048' => 'fan', 'FAN02G0583' => 'fan', 'FAN02G0688' => 'fan', 'FAN02G1588' => 'fan', 'FAN02G2194' => 'fan', 'FAN02G2750' => 'fan', 'FAN02G3094' => 'fan', 'FAN02G3887' => 'fan', 'FAN02G3911' => 'fan', 'FAN02G3994' => 'fan', 'FAN02G4432' => 'fan', 'FAN02G4556' => 'fan', 'FAN03G1977' => 'fan', 'FAN03G2781' => 'fan', 'FAN03G2850' => 'fan', 'FAN03G3155' => 'fan', 'FAN04G2487' => 'fan', 'FAN05G0208' => 'fan', 'FAN05G0656' => 'fan', 'FAN05G0696' => 'fan', 'FAN05G0810' => 'fan', 'FAN05G1447' => 'fan', 'FAN05G2640' => 'fan', 'FAN05G2911' => 'fan', 'FAN05G3901' => 'fan', 'FAN05G4859' => 'fan', 'FAN05G4861' => 'fan', 'FAN05G4988' => 'fan', 'FAN05G5187' => 'fan', 'FAN05G5452' => 'fan', 'FAN05G5500' => 'fan', 'FAN05G5688' => 'fan', 'FAN06G0177' => 'fan', 'FAN06G0675' => 'fan', 'FAN06G1290' => 'fan', 'FAN06G2191' => 'fan', 'FAN06G2405' => 'fan', 'FAN06G3231' => 'fan', 'FAN06G3932' => 'fan', 'FAN07G0163' => 'fan', 'FAN07G0471' => 'fan', 'FAN07G1354' => 'fan', 'FAN08G0338' => 'fan', 'FAN08G1373' => 'fan', 'FAN08G2539' => 'fan', 'FAN08G2728' => 'fan', 'FAN09G0608' => 'fan', 'FAN09G1136' => 'fan', 'FAN09G1958' => 'fan', 'FAN09G2508' => 'fan', 'FAN09G2597' => 'fan', 'FAN09G2658' => 'fan', 'FAN09G2757' => 'fan', 'FAN09G2983' => 'fan', 'FAN09G3130' => 'fan', 'FAN09G3565' => 'fan', 'FAN09G3613' => 'fan', 'FAN09G4011' => 'fan', 'FAN09G4239' => 'fan', 'FAN09G4277' => 'fan', 'FAN09G4720' => 'fan', 'FAN11G0139' => 'fan', 'FAN11G1727' => 'fan', 'FAN11G2672' => 'fan', 'FAN11G2795' => 'fan', 'FAN11G3238' => 'fan', 'FAN11G3734' => 'fan', 'FAN12G0631' => 'fan', 'FAN12G2239' => 'fan', 'FAN12G2308' => 'fan', 'FAN12G2569' => 'fan', 'FAN12G2623' => 'fan', 'FAN13G3182' => 'fan', 'FAN14G0053' => 'fan', 'FAN14G0370' => 'fan', 'FAN14G0382' => 'fan', 'FAN14G0421' => 'fan', 'FAN14G0866' => 'fan', 'FAN14G1187' => 'fan', 'FAN14G1727' => 'fan', 'FAN14G1791' => 'fan', 'FAN14G2361' => 'fan', 'FAN14G2668' => 'fan', 'FAN14G2770' => 'fan', 'FAN14G2874' => 'fan', 'FAN14G3193' => 'fan', 'FAN14G3624' => 'fan', 'FAN14G3676' => 'fan', 'FAN14G3807' => 'fan', 'FAN14G4082' => 'fan', 'FAN14G4342' => 'fan', 'FAN14G4985' => 'fan', 'FAN14G5126' => 'fan', 'FAN14G5781' => 'fan', 'FAN14G5808' => 'fan', 'FAN14G5949' => 'fan', 'FAN15G0828' => 'fan', 'FAN15G1054' => 'fan', 'FAN15G2023' => 'fan', 'FAN15G2506' => 'fan', 'FAN16G0128' => 'fan', 'FAN16G0249' => 'fan', 'FAN16G0429' => 'fan', 'FAN16G1493' => 'fan', 'FAN16G2210' => 'fan', 'FAN16G2506' => 'fan', 'FAN18G1542' => 'fan', 'FAN18G4057' => 'fan', 'FAN19G0745' => 'fan', 'FAN19G1216' => 'fan', 'FAN19G1733' => 'fan', 'FAN20G0258' => 'fan', 'FAN20G1095' => 'fan', 'FAN20G1557' => 'fan', 'FAN21G0302' => 'fan', 'FAN21G0519' => 'fan', 'FAN21G0970' => 'fan', 'FAN21G1159' => 'fan', 'FAN21G1312' => 'fan', 'FAN21G1440' => 'fan', 'FAN21G1715' => 'fan', 'FAN23G1584' => 'fan', 'FAN24G0045' => 'fan', 'FAN24G0053' => 'fan', 'FAN24G1500' => 'fan', 'FAN24G1817' => 'fan', 'FAN24G2147' => 'fan', 'FAN24G2236' => 'fan', 'FAN24G2446' => 'fan', 'FAN24G2684' => 'fan', 'FAN25G0187' => 'fan', 'FAN25G0505' => 'fan', 'FAN25G0589' => 'fan', 'FAN25G3663' => 'fan', 'FAN26G1025' => 'fan', 'FAN26G2860' => 'fan', 'FAN27G1329' => 'fan', 'FAN27G3392' => 'fan', 'FvH4_1g02011' => 'fve', 'FvH4_1g06511' => 'fve', 'FvH4_2g19900' => 'fve', 'FvH4_2g19920' => 'fve', 'FvH4_2g24261' => 'fve', 'FvH4_2g24270' => 'fve', 'FvH4_2g24631' => 'fve', 'FvH4_2g30622' => 'fve', 'FvH4_3g12920' => 'fve', 'FvH4_3g30171' => 'fve', 'FvH4_3g35490' => 'fve', 'FvH4_3g43682' => 'fve', 'FvH4_3g43730' => 'fve', 'FvH4_3g43732' => 'fve', 'FvH4_3g43751' => 'fve', 'FvH4_3g43752' => 'fve', 'FvH4_3g43770' => 'fve', 'FvH4_3g44471' => 'fve', 'FvH4_3g44510' => 'fve', 'FvH4_3g44582' => 'fve', 'FvH4_4g16921' => 'fve', 'FvH4_4g17121' => 'fve', 'FvH4_4g17782' => 'fve', 'FvH4_4g17783' => 'fve', 'FvH4_4g18120' => 'fve', 'FvH4_4g31310' => 'fve', 'FvH4_4g35052' => 'fve', 'FvH4_5g30862' => 'fve', 'FvH4_6g01541' => 'fve', 'FvH4_6g02021' => 'fve', 'FvH4_6g02041' => 'fve', 'FvH4_6g02071' => 'fve', 'FvH4_6g02171' => 'fve', 'FvH4_6g03181' => 'fve', 'FvH4_6g03182' => 'fve', 'FvH4_6g03221' => 'fve', 'FvH4_6g03380' => 'fve', 'FvH4_6g05201' => 'fve', 'FvH4_6g05203' => 'fve', 'FvH4_6g20231' => 'fve', 'FvH4_6g31981' => 'fve', 'FvH4_6g32061' => 'fve', 'FvH4_6g37041' => 'fve', 'FvH4_6g37932' => 'fve', 'FvH4_6g38731' => 'fve', 'FvH4_6g39370' => 'fve', 'FvH4_6g39371' => 'fve', 'FvH4_6g40891' => 'fve', 'FvH4_6g40892' => 'fve', 'FvH4_6g43143' => 'fve', 'FvH4_6g45251' => 'fve', 'FvH4_6g45260' => 'fve', 'FvH4_6g45291' => 'fve', 'FvH4_6g45890' => 'fve', 'FvH4_6g46240' => 'fve', 'FvH4_6g46241' => 'fve', 'FvH4_6g46242' => 'fve', 'FvH4_6g46260' => 'fve', 'FvH4_6g46280' => 'fve', 'FvH4_6g46380' => 'fve', 'FvH4_7g12841' => 'fve', 'FvH4_7g31431' => 'fve', 'Glyma.09G075900' => 'gma', 'Gohir.A09G096401' => 'ghi', 'Gohir.D09G096101' => 'ghi', 'Gorai.006G112800' => 'gra', 'HanXRQChr04g0121411' => 'han', 'Hund15878' => 'sun', 'Lj2A1107G68' => 'lonja', 'Lj2A630G63' => 'lonja', 'Lj2A946T25' => 'lonja', 'Lj2C714T1' => 'lonja', 'Lj2C966T3' => 'lonja', 'Lj2C966T4' => 'lonja', 'Lj4g0002979' => 'lja', 'Lsat_1_v5_gn_5_30901' => 'lsa', 'Lsat_1_v5_gn_5_31100' => 'lsa', 'Lsat_1_v5_gn_5_38600' => 'lsa', 'Lsat_1_v5_gn_6_92061' => 'lsa', 'Manes.05G071301' => 'mes', 'MD02G1008700' => 'mdo', 'MD02G1008900' => 'mdo', 'MD03G1256400' => 'mdo', 'MD04G1180900' => 'mdo', 'MD04G1181000' => 'mdo', 'MD04G1181200' => 'mdo', 'MD05G1244200' => 'mdo', 'MD05G1324200' => 'mdo', 'MD09G1201600' => 'mdo', 'MD10G1000600' => 'mdo', 'MD14G1026900' => 'mdo', 'MD14G1187900' => 'mdo', 'MD15G1017800' => 'mdo', 'MD15G1018100' => 'mdo', 'Medtr4g124160' => 'mtr', 'Migut.L01260' => 'egut', 'Nitab4.5_0000008g0440' => 'nta', 'Nitab4.5_0000207g0170' => 'nta', 'Nitab4.5_0007671g0030' => 'nta', 'Nitab4.5_0010853g0020' => 'nta', 'Oeu057656.1' => 'oeu', 'PGSC0003DMG400005638' => 'stu', 'PGSC0003DMG400005639' => 'stu', 'Phvul.009G222800' => 'pvu', 'Potri.009G132400' => 'ptr', 'Potri.009G163001' => 'ptr', 'Potri.011G000700' => 'ptr', 'Potri.011G004800' => 'ptr', 'Prupe.1G509300' => 'ppe', 'Prupe.1G509700' => 'ppe', 'Prupe.1G510400' => 'ppe', 'Prupe.1G510700' => 'ppe', 'Prupe.1G512600' => 'ppe', 'Prupe.2G073200' => 'ppe', 'Prupe.3G059500' => 'ppe', 'Prupe.3G059600' => 'ppe', 'Prupe.3G246100' => 'ppe', 'Prupe.3G265100' => 'ppe', 'Prupe.4G034700' => 'ppe', 'Prupe.4G052100' => 'ppe', 'Prupe.4G053600' => 'ppe', 'Prupe.5G068800' => 'ppe', 'Prupe.5G070600' => 'ppe', 'Prupe.6G075400' => 'ppe', 'Prupe.6G075500' => 'ppe', 'Prupe.6G076400' => 'ppe', 'Prupe.8G110700' => 'ppe', 'Psat4g020960' => 'psa', 'PSO135G0788' => 'pso', 'PSO210G6463' => 'pso', 'PSO384G0370' => 'pso', 'PSO386G0056' => 'pso', 'QL01p006048' => 'qlo', 'QL02p054283' => 'qlo', 'QL05p008000' => 'qlo', 'QL05p008212' => 'qlo', 'QL05p008950' => 'qlo', 'QL05p009042' => 'qlo', 'QL05p009518' => 'qlo', 'QL05p012589' => 'qlo', 'QL05p012608' => 'qlo', 'QL05p012650' => 'qlo', 'QL05p012667' => 'qlo', 'QL05p014501' => 'qlo', 'QL05p052800' => 'qlo', 'QL05p065010' => 'qlo', 'QL05p074156' => 'qlo', 'QL05p074160' => 'qlo', 'QL05p074174' => 'qlo', 'QL05p074178' => 'qlo', 'QL05p074214' => 'qlo', 'QL06p001050' => 'qlo', 'QL06p001056' => 'qlo', 'QL06p006093' => 'qlo', 'QL06p006111' => 'qlo', 'QL07p019784' => 'qlo', 'QL07p019801' => 'qlo', 'QL07p036110' => 'qlo', 'QL07p036134' => 'qlo', 'QL07p036147' => 'qlo', 'QL07p036156' => 'qlo', 'QL07p036300' => 'qlo', 'QL07p036320' => 'qlo', 'QL08p014547' => 'qlo', 'QL08p014551' => 'qlo', 'QL08p043319' => 'qlo', 'QL08p043324' => 'qlo', 'QL11p009094' => 'qlo', 'RcHm_v2.0_Chr1g0380481' => 'rch', 'RcHm_v2.0_Chr2g0089331' => 'rch', 'RcHm_v2.0_Chr2g0123691' => 'rch', 'RcHm_v2.0_Chr2g0151111' => 'rch', 'RcHm_v2.0_Chr2g0163011' => 'rch', 'RcHm_v2.0_Chr2g0163051' => 'rch', 'RcHm_v2.0_Chr2g0164671' => 'rch', 'RcHm_v2.0_Chr2g0164681' => 'rch', 'RcHm_v2.0_Chr2g0164721' => 'rch', 'RcHm_v2.0_Chr3g0449911' => 'rch', 'RcHm_v2.0_Chr3g0450211' => 'rch', 'RcHm_v2.0_Chr3g0457271' => 'rch', 'RcHm_v2.0_Chr5g0018111' => 'rch', 'RcHm_v2.0_Chr5g0021011' => 'rch', 'RcHm_v2.0_Chr5g0081171' => 'rch', 'RcHm_v2.0_Chr5g0081211' => 'rch', 'RcHm_v2.0_Chr6g0275871' => 'rch', 'RcHm_v2.0_Chr6g0276071' => 'rch', 'RcHm_v2.0_Chr6g0285591' => 'rch', 'RcHm_v2.0_Chr6g0291931' => 'rch', 'RcHm_v2.0_Chr6g0292091' => 'rch', 'RcHm_v2.0_Chr6g0292271' => 'rch', 'RcHm_v2.0_Chr7g0221261' => 'rch', 'Rhsim08G0219900' => 'rsi', 'Rhsim08G0220200' => 'rsi', 'Rhsim08G0237800' => 'rsi', 'Rhsim08G0238800' => 'rsi', 'Sabra09G0102700' => 'sbr', 'Sabra09G0127200' => 'sbr', 'Sabra11G0003700' => 'sbr', 'Sabra15G0014700' => 'sbr', 'Sc19g0000590' => 'sci', 'Sc19g0001870' => 'sci', 'SGA_v2.0_scaffold1G00346' => 'sas', 'SGA_v2.0_scaffold1G00575' => 'sas', 'SGA_v2.0_scaffold1G00761' => 'sas', 'SGA_v2.0_scaffold232G43501' => 'sas', 'TAR625G1137' => 'tar', 'Thecc.03G222100' => 'tca', 'TPR.G12691' => 'tpr', 'TWI34G0727' => 'twi', 'TWI36G0117' => 'twi', 'VMungo1309G0868' => 'vmu' ), 'gf_id' => 'HOM05D001729', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001729' ), 'data_identifier' => 'HOM05D001729', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001729', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '375', 'num_species' => '42' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'Ah.07g204710' => 'amhyb', 'AUR62006001' => 'cqu', 'AUR62006002' => 'cqu', 'AUR62006003' => 'cqu', 'AUR62015641' => 'cqu', 'AUR62027174' => 'cqu', 'AUR62035623' => 'cqu', 'AUR62035624' => 'cqu', 'AUR62035625' => 'cqu', 'AUR62035626' => 'cqu', 'CAN.G1110.53' => 'can', 'CANSAT80G0415' => 'cansat', 'Ca_21364_v3' => 'car', 'COL.COLO4_30693' => 'col', 'COL.COLO4_30694' => 'col', 'COL.COLO4_30695' => 'col', 'COL.COLO4_30696' => 'col', 'COL.COLO4_34020' => 'col', 'DCAR_004585' => 'dca', 'Dinv04029' => 'din', 'Dinv34857' => 'din', 'Duzib147G0011' => 'dzi', 'Duzib170G0599' => 'dzi', 'Duzib192G1051' => 'dzi', 'FAN01G0708' => 'fan', 'FAN01G0742' => 'fan', 'FAN02G0048' => 'fan', 'FAN02G0583' => 'fan', 'FAN02G0688' => 'fan', 'FAN02G1588' => 'fan', 'FAN02G2194' => 'fan', 'FAN02G2750' => 'fan', 'FAN02G3094' => 'fan', 'FAN02G3887' => 'fan', 'FAN02G3911' => 'fan', 'FAN02G3994' => 'fan', 'FAN02G4432' => 'fan', 'FAN02G4556' => 'fan', 'FAN03G1977' => 'fan', 'FAN03G2781' => 'fan', 'FAN03G2850' => 'fan', 'FAN03G3155' => 'fan', 'FAN04G2487' => 'fan', 'FAN05G0208' => 'fan', 'FAN05G0656' => 'fan', 'FAN05G0696' => 'fan', 'FAN05G0810' => 'fan', 'FAN05G1447' => 'fan', 'FAN05G2640' => 'fan', 'FAN05G2911' => 'fan', 'FAN05G3901' => 'fan', 'FAN05G4859' => 'fan', 'FAN05G4861' => 'fan', 'FAN05G4988' => 'fan', 'FAN05G5187' => 'fan', 'FAN05G5452' => 'fan', 'FAN05G5500' => 'fan', 'FAN05G5688' => 'fan', 'FAN06G0177' => 'fan', 'FAN06G0675' => 'fan', 'FAN06G1290' => 'fan', 'FAN06G2191' => 'fan', 'FAN06G2405' => 'fan', 'FAN06G3231' => 'fan', 'FAN06G3932' => 'fan', 'FAN07G0163' => 'fan', 'FAN07G0471' => 'fan', 'FAN07G1354' => 'fan', 'FAN08G0338' => 'fan', 'FAN08G1373' => 'fan', 'FAN08G2539' => 'fan', 'FAN08G2728' => 'fan', 'FAN09G0608' => 'fan', 'FAN09G1136' => 'fan', 'FAN09G1958' => 'fan', 'FAN09G2508' => 'fan', 'FAN09G2597' => 'fan', 'FAN09G2658' => 'fan', 'FAN09G2757' => 'fan', 'FAN09G2983' => 'fan', 'FAN09G3130' => 'fan', 'FAN09G3565' => 'fan', 'FAN09G3613' => 'fan', 'FAN09G4011' => 'fan', 'FAN09G4239' => 'fan', 'FAN09G4277' => 'fan', 'FAN09G4720' => 'fan', 'FAN11G0139' => 'fan', 'FAN11G1727' => 'fan', 'FAN11G2672' => 'fan', 'FAN11G2795' => 'fan', 'FAN11G3238' => 'fan', 'FAN11G3734' => 'fan', 'FAN12G0631' => 'fan', 'FAN12G2239' => 'fan', 'FAN12G2308' => 'fan', 'FAN12G2569' => 'fan', 'FAN12G2623' => 'fan', 'FAN13G3182' => 'fan', 'FAN14G0053' => 'fan', 'FAN14G0370' => 'fan', 'FAN14G0382' => 'fan', 'FAN14G0421' => 'fan', 'FAN14G0866' => 'fan', 'FAN14G1187' => 'fan', 'FAN14G1727' => 'fan', 'FAN14G1791' => 'fan', 'FAN14G2361' => 'fan', 'FAN14G2668' => 'fan', 'FAN14G2770' => 'fan', 'FAN14G2874' => 'fan', 'FAN14G3193' => 'fan', 'FAN14G3624' => 'fan', 'FAN14G3676' => 'fan', 'FAN14G3807' => 'fan', 'FAN14G4082' => 'fan', 'FAN14G4342' => 'fan', 'FAN14G4985' => 'fan', 'FAN14G5126' => 'fan', 'FAN14G5781' => 'fan', 'FAN14G5808' => 'fan', 'FAN14G5949' => 'fan', 'FAN15G0828' => 'fan', 'FAN15G1054' => 'fan', 'FAN15G2023' => 'fan', 'FAN15G2506' => 'fan', 'FAN16G0128' => 'fan', 'FAN16G0249' => 'fan', 'FAN16G0429' => 'fan', 'FAN16G1493' => 'fan', 'FAN16G2210' => 'fan', 'FAN16G2506' => 'fan', 'FAN18G1542' => 'fan', 'FAN18G4057' => 'fan', 'FAN19G0745' => 'fan', 'FAN19G1216' => 'fan', 'FAN19G1733' => 'fan', 'FAN20G0258' => 'fan', 'FAN20G1095' => 'fan', 'FAN20G1557' => 'fan', 'FAN21G0302' => 'fan', 'FAN21G0519' => 'fan', 'FAN21G0970' => 'fan', 'FAN21G1159' => 'fan', 'FAN21G1312' => 'fan', 'FAN21G1440' => 'fan', 'FAN21G1715' => 'fan', 'FAN23G1584' => 'fan', 'FAN24G0045' => 'fan', 'FAN24G0053' => 'fan', 'FAN24G1500' => 'fan', 'FAN24G1817' => 'fan', 'FAN24G2147' => 'fan', 'FAN24G2236' => 'fan', 'FAN24G2446' => 'fan', 'FAN24G2684' => 'fan', 'FAN25G0187' => 'fan', 'FAN25G0505' => 'fan', 'FAN25G0589' => 'fan', 'FAN25G3663' => 'fan', 'FAN26G1025' => 'fan', 'FAN26G2860' => 'fan', 'FAN27G1329' => 'fan', 'FAN27G3392' => 'fan', 'FvH4_1g02011' => 'fve', 'FvH4_1g06511' => 'fve', 'FvH4_2g19900' => 'fve', 'FvH4_2g19920' => 'fve', 'FvH4_2g24261' => 'fve', 'FvH4_2g24270' => 'fve', 'FvH4_2g24631' => 'fve', 'FvH4_2g30622' => 'fve', 'FvH4_3g12920' => 'fve', 'FvH4_3g30171' => 'fve', 'FvH4_3g35490' => 'fve', 'FvH4_3g43682' => 'fve', 'FvH4_3g43730' => 'fve', 'FvH4_3g43732' => 'fve', 'FvH4_3g43751' => 'fve', 'FvH4_3g43752' => 'fve', 'FvH4_3g43770' => 'fve', 'FvH4_3g44471' => 'fve', 'FvH4_3g44510' => 'fve', 'FvH4_3g44582' => 'fve', 'FvH4_4g16921' => 'fve', 'FvH4_4g17121' => 'fve', 'FvH4_4g17782' => 'fve', 'FvH4_4g17783' => 'fve', 'FvH4_4g18120' => 'fve', 'FvH4_4g31310' => 'fve', 'FvH4_4g35052' => 'fve', 'FvH4_5g30862' => 'fve', 'FvH4_6g01541' => 'fve', 'FvH4_6g02021' => 'fve', 'FvH4_6g02041' => 'fve', 'FvH4_6g02071' => 'fve', 'FvH4_6g02171' => 'fve', 'FvH4_6g03181' => 'fve', 'FvH4_6g03182' => 'fve', 'FvH4_6g03221' => 'fve', 'FvH4_6g03380' => 'fve', 'FvH4_6g05201' => 'fve', 'FvH4_6g05203' => 'fve', 'FvH4_6g20231' => 'fve', 'FvH4_6g31981' => 'fve', 'FvH4_6g32061' => 'fve', 'FvH4_6g37041' => 'fve', 'FvH4_6g37932' => 'fve', 'FvH4_6g38731' => 'fve', 'FvH4_6g39370' => 'fve', 'FvH4_6g39371' => 'fve', 'FvH4_6g40891' => 'fve', 'FvH4_6g40892' => 'fve', 'FvH4_6g43143' => 'fve', 'FvH4_6g45251' => 'fve', 'FvH4_6g45260' => 'fve', 'FvH4_6g45291' => 'fve', 'FvH4_6g45890' => 'fve', 'FvH4_6g46240' => 'fve', 'FvH4_6g46241' => 'fve', 'FvH4_6g46242' => 'fve', 'FvH4_6g46260' => 'fve', 'FvH4_6g46280' => 'fve', 'FvH4_6g46380' => 'fve', 'FvH4_7g12841' => 'fve', 'FvH4_7g31431' => 'fve', 'Glyma.09G075900' => 'gma', 'Gohir.A09G096401' => 'ghi', 'Gohir.D09G096101' => 'ghi', 'Gorai.006G112800' => 'gra', 'HanXRQChr04g0121411' => 'han', 'Hund15878' => 'sun', 'Lj2A1107G68' => 'lonja', 'Lj2A630G63' => 'lonja', 'Lj2A946T25' => 'lonja', 'Lj2C714T1' => 'lonja', 'Lj2C966T3' => 'lonja', 'Lj2C966T4' => 'lonja', 'Lj4g0002979' => 'lja', 'Lsat_1_v5_gn_5_30901' => 'lsa', 'Lsat_1_v5_gn_5_31100' => 'lsa', 'Lsat_1_v5_gn_5_38600' => 'lsa', 'Lsat_1_v5_gn_6_92061' => 'lsa', 'Manes.05G071301' => 'mes', 'MD02G1008700' => 'mdo', 'MD02G1008900' => 'mdo', 'MD03G1256400' => 'mdo', 'MD04G1180900' => 'mdo', 'MD04G1181000' => 'mdo', 'MD04G1181200' => 'mdo', 'MD05G1244200' => 'mdo', 'MD05G1324200' => 'mdo', 'MD09G1201600' => 'mdo', 'MD10G1000600' => 'mdo', 'MD14G1026900' => 'mdo', 'MD14G1187900' => 'mdo', 'MD15G1017800' => 'mdo', 'MD15G1018100' => 'mdo', 'Medtr4g124160' => 'mtr', 'Migut.L01260' => 'egut', 'Nitab4.5_0000008g0440' => 'nta', 'Nitab4.5_0000207g0170' => 'nta', 'Nitab4.5_0007671g0030' => 'nta', 'Nitab4.5_0010853g0020' => 'nta', 'Oeu057656.1' => 'oeu', 'PGSC0003DMG400005638' => 'stu', 'PGSC0003DMG400005639' => 'stu', 'Phvul.009G222800' => 'pvu', 'Potri.009G132400' => 'ptr', 'Potri.009G163001' => 'ptr', 'Potri.011G000700' => 'ptr', 'Potri.011G004800' => 'ptr', 'Prupe.1G509300' => 'ppe', 'Prupe.1G509700' => 'ppe', 'Prupe.1G510400' => 'ppe', 'Prupe.1G510700' => 'ppe', 'Prupe.1G512600' => 'ppe', 'Prupe.2G073200' => 'ppe', 'Prupe.3G059500' => 'ppe', 'Prupe.3G059600' => 'ppe', 'Prupe.3G246100' => 'ppe', 'Prupe.3G265100' => 'ppe', 'Prupe.4G034700' => 'ppe', 'Prupe.4G052100' => 'ppe', 'Prupe.4G053600' => 'ppe', 'Prupe.5G068800' => 'ppe', 'Prupe.5G070600' => 'ppe', 'Prupe.6G075400' => 'ppe', 'Prupe.6G075500' => 'ppe', 'Prupe.6G076400' => 'ppe', 'Prupe.8G110700' => 'ppe', 'Psat4g020960' => 'psa', 'PSO135G0788' => 'pso', 'PSO210G6463' => 'pso', 'PSO384G0370' => 'pso', 'PSO386G0056' => 'pso', 'QL01p006048' => 'qlo', 'QL02p054283' => 'qlo', 'QL05p008000' => 'qlo', 'QL05p008212' => 'qlo', 'QL05p008950' => 'qlo', 'QL05p009042' => 'qlo', 'QL05p009518' => 'qlo', 'QL05p012589' => 'qlo', 'QL05p012608' => 'qlo', 'QL05p012650' => 'qlo', 'QL05p012667' => 'qlo', 'QL05p014501' => 'qlo', 'QL05p052800' => 'qlo', 'QL05p065010' => 'qlo', 'QL05p074156' => 'qlo', 'QL05p074160' => 'qlo', 'QL05p074174' => 'qlo', 'QL05p074178' => 'qlo', 'QL05p074214' => 'qlo', 'QL06p001050' => 'qlo', 'QL06p001056' => 'qlo', 'QL06p006093' => 'qlo', 'QL06p006111' => 'qlo', 'QL07p019784' => 'qlo', 'QL07p019801' => 'qlo', 'QL07p036110' => 'qlo', 'QL07p036134' => 'qlo', 'QL07p036147' => 'qlo', 'QL07p036156' => 'qlo', 'QL07p036300' => 'qlo', 'QL07p036320' => 'qlo', 'QL08p014547' => 'qlo', 'QL08p014551' => 'qlo', 'QL08p043319' => 'qlo', 'QL08p043324' => 'qlo', 'QL11p009094' => 'qlo', 'RcHm_v2.0_Chr1g0380481' => 'rch', 'RcHm_v2.0_Chr2g0089331' => 'rch', 'RcHm_v2.0_Chr2g0123691' => 'rch', 'RcHm_v2.0_Chr2g0151111' => 'rch', 'RcHm_v2.0_Chr2g0163011' => 'rch', 'RcHm_v2.0_Chr2g0163051' => 'rch', 'RcHm_v2.0_Chr2g0164671' => 'rch', 'RcHm_v2.0_Chr2g0164681' => 'rch', 'RcHm_v2.0_Chr2g0164721' => 'rch', 'RcHm_v2.0_Chr3g0449911' => 'rch', 'RcHm_v2.0_Chr3g0450211' => 'rch', 'RcHm_v2.0_Chr3g0457271' => 'rch', 'RcHm_v2.0_Chr5g0018111' => 'rch', 'RcHm_v2.0_Chr5g0021011' => 'rch', 'RcHm_v2.0_Chr5g0081171' => 'rch', 'RcHm_v2.0_Chr5g0081211' => 'rch', 'RcHm_v2.0_Chr6g0275871' => 'rch', 'RcHm_v2.0_Chr6g0276071' => 'rch', 'RcHm_v2.0_Chr6g0285591' => 'rch', 'RcHm_v2.0_Chr6g0291931' => 'rch', 'RcHm_v2.0_Chr6g0292091' => 'rch', 'RcHm_v2.0_Chr6g0292271' => 'rch', 'RcHm_v2.0_Chr7g0221261' => 'rch', 'Rhsim08G0219900' => 'rsi', 'Rhsim08G0220200' => 'rsi', 'Rhsim08G0237800' => 'rsi', 'Rhsim08G0238800' => 'rsi', 'Sabra09G0102700' => 'sbr', 'Sabra09G0127200' => 'sbr', 'Sabra11G0003700' => 'sbr', 'Sabra15G0014700' => 'sbr', 'Sc19g0000590' => 'sci', 'Sc19g0001870' => 'sci', 'SGA_v2.0_scaffold1G00346' => 'sas', 'SGA_v2.0_scaffold1G00575' => 'sas', 'SGA_v2.0_scaffold1G00761' => 'sas', 'SGA_v2.0_scaffold232G43501' => 'sas', 'TAR625G1137' => 'tar', 'Thecc.03G222100' => 'tca', 'TPR.G12691' => 'tpr', 'TWI34G0727' => 'twi', 'TWI36G0117' => 'twi', 'VMungo1309G0868' => 'vmu' ) $gf_id = 'HOM05D001729' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001729' ) $data_identifier = 'HOM05D001729' $data_type = 'gf_id' $species_gene_counts = array( 'amhyb' => (int) 1, 'cqu' => (int) 9, 'can' => (int) 1, 'cansat' => (int) 1, 'car' => (int) 1, 'col' => (int) 5, 'dca' => (int) 1, 'din' => (int) 2, 'dzi' => (int) 3, 'fan' => (int) 140, 'fve' => (int) 62, 'gma' => (int) 1, 'ghi' => (int) 2, 'gra' => (int) 1, 'han' => (int) 1, 'sun' => (int) 1, 'lonja' => (int) 6, 'lja' => (int) 1, 'lsa' => (int) 4, 'mes' => (int) 1, 'mdo' => (int) 14, 'mtr' => (int) 1, 'egut' => (int) 1, 'nta' => (int) 4, 'oeu' => (int) 1, 'stu' => (int) 2, 'pvu' => (int) 1, 'ptr' => (int) 4, 'ppe' => (int) 19, 'psa' => (int) 1, 'pso' => (int) 4, 'qlo' => (int) 36, 'rch' => (int) 23, 'rsi' => (int) 4, 'sbr' => (int) 4, 'sci' => (int) 2, 'sas' => (int) 4, 'tar' => (int) 1, 'tca' => (int) 1, 'tpr' => (int) 1, 'twi' => (int) 2, 'vmu' => (int) 1 ) $gf_gene_species = 'vmu' $gf_gene_id = 'VMungo1309G0868' $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' => 'HOM05D001729', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '375', 'num_species' => '42' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'Ah.07g204710' => 'amhyb', 'AUR62006001' => 'cqu', 'AUR62006002' => 'cqu', 'AUR62006003' => 'cqu', 'AUR62015641' => 'cqu', 'AUR62027174' => 'cqu', 'AUR62035623' => 'cqu', 'AUR62035624' => 'cqu', 'AUR62035625' => 'cqu', 'AUR62035626' => 'cqu', 'CAN.G1110.53' => 'can', 'CANSAT80G0415' => 'cansat', 'Ca_21364_v3' => 'car', 'COL.COLO4_30693' => 'col', 'COL.COLO4_30694' => 'col', 'COL.COLO4_30695' => 'col', 'COL.COLO4_30696' => 'col', 'COL.COLO4_34020' => 'col', 'DCAR_004585' => 'dca', 'Dinv04029' => 'din', 'Dinv34857' => 'din', 'Duzib147G0011' => 'dzi', 'Duzib170G0599' => 'dzi', 'Duzib192G1051' => 'dzi', 'FAN01G0708' => 'fan', 'FAN01G0742' => 'fan', 'FAN02G0048' => 'fan', 'FAN02G0583' => 'fan', 'FAN02G0688' => 'fan', 'FAN02G1588' => 'fan', 'FAN02G2194' => 'fan', 'FAN02G2750' => 'fan', 'FAN02G3094' => 'fan', 'FAN02G3887' => 'fan', 'FAN02G3911' => 'fan', 'FAN02G3994' => 'fan', 'FAN02G4432' => 'fan', 'FAN02G4556' => 'fan', 'FAN03G1977' => 'fan', 'FAN03G2781' => 'fan', 'FAN03G2850' => 'fan', 'FAN03G3155' => 'fan', 'FAN04G2487' => 'fan', 'FAN05G0208' => 'fan', 'FAN05G0656' => 'fan', 'FAN05G0696' => 'fan', 'FAN05G0810' => 'fan', 'FAN05G1447' => 'fan', 'FAN05G2640' => 'fan', 'FAN05G2911' => 'fan', 'FAN05G3901' => 'fan', 'FAN05G4859' => 'fan', 'FAN05G4861' => 'fan', 'FAN05G4988' => 'fan', 'FAN05G5187' => 'fan', 'FAN05G5452' => 'fan', 'FAN05G5500' => 'fan', 'FAN05G5688' => 'fan', 'FAN06G0177' => 'fan', 'FAN06G0675' => 'fan', 'FAN06G1290' => 'fan', 'FAN06G2191' => 'fan', 'FAN06G2405' => 'fan', 'FAN06G3231' => 'fan', 'FAN06G3932' => 'fan', 'FAN07G0163' => 'fan', 'FAN07G0471' => 'fan', 'FAN07G1354' => 'fan', 'FAN08G0338' => 'fan', 'FAN08G1373' => 'fan', 'FAN08G2539' => 'fan', 'FAN08G2728' => 'fan', 'FAN09G0608' => 'fan', 'FAN09G1136' => 'fan', 'FAN09G1958' => 'fan', 'FAN09G2508' => 'fan', 'FAN09G2597' => 'fan', 'FAN09G2658' => 'fan', 'FAN09G2757' => 'fan', 'FAN09G2983' => 'fan', 'FAN09G3130' => 'fan', 'FAN09G3565' => 'fan', 'FAN09G3613' => 'fan', 'FAN09G4011' => 'fan', 'FAN09G4239' => 'fan', 'FAN09G4277' => 'fan', 'FAN09G4720' => 'fan', 'FAN11G0139' => 'fan', 'FAN11G1727' => 'fan', 'FAN11G2672' => 'fan', 'FAN11G2795' => 'fan', 'FAN11G3238' => 'fan', 'FAN11G3734' => 'fan', 'FAN12G0631' => 'fan', 'FAN12G2239' => 'fan', 'FAN12G2308' => 'fan', 'FAN12G2569' => 'fan', 'FAN12G2623' => 'fan', 'FAN13G3182' => 'fan', 'FAN14G0053' => 'fan', 'FAN14G0370' => 'fan', 'FAN14G0382' => 'fan', 'FAN14G0421' => 'fan', 'FAN14G0866' => 'fan', 'FAN14G1187' => 'fan', 'FAN14G1727' => 'fan', 'FAN14G1791' => 'fan', 'FAN14G2361' => 'fan', 'FAN14G2668' => 'fan', 'FAN14G2770' => 'fan', 'FAN14G2874' => 'fan', 'FAN14G3193' => 'fan', 'FAN14G3624' => 'fan', 'FAN14G3676' => 'fan', 'FAN14G3807' => 'fan', 'FAN14G4082' => 'fan', 'FAN14G4342' => 'fan', 'FAN14G4985' => 'fan', 'FAN14G5126' => 'fan', 'FAN14G5781' => 'fan', 'FAN14G5808' => 'fan', 'FAN14G5949' => 'fan', 'FAN15G0828' => 'fan', 'FAN15G1054' => 'fan', 'FAN15G2023' => 'fan', 'FAN15G2506' => 'fan', 'FAN16G0128' => 'fan', 'FAN16G0249' => 'fan', 'FAN16G0429' => 'fan', 'FAN16G1493' => 'fan', 'FAN16G2210' => 'fan', 'FAN16G2506' => 'fan', 'FAN18G1542' => 'fan', 'FAN18G4057' => 'fan', 'FAN19G0745' => 'fan', 'FAN19G1216' => 'fan', 'FAN19G1733' => 'fan', 'FAN20G0258' => 'fan', 'FAN20G1095' => 'fan', 'FAN20G1557' => 'fan', 'FAN21G0302' => 'fan', 'FAN21G0519' => 'fan', 'FAN21G0970' => 'fan', 'FAN21G1159' => 'fan', 'FAN21G1312' => 'fan', 'FAN21G1440' => 'fan', 'FAN21G1715' => 'fan', 'FAN23G1584' => 'fan', 'FAN24G0045' => 'fan', 'FAN24G0053' => 'fan', 'FAN24G1500' => 'fan', 'FAN24G1817' => 'fan', 'FAN24G2147' => 'fan', 'FAN24G2236' => 'fan', 'FAN24G2446' => 'fan', 'FAN24G2684' => 'fan', 'FAN25G0187' => 'fan', 'FAN25G0505' => 'fan', 'FAN25G0589' => 'fan', 'FAN25G3663' => 'fan', 'FAN26G1025' => 'fan', 'FAN26G2860' => 'fan', 'FAN27G1329' => 'fan', 'FAN27G3392' => 'fan', 'FvH4_1g02011' => 'fve', 'FvH4_1g06511' => 'fve', 'FvH4_2g19900' => 'fve', 'FvH4_2g19920' => 'fve', 'FvH4_2g24261' => 'fve', 'FvH4_2g24270' => 'fve', 'FvH4_2g24631' => 'fve', 'FvH4_2g30622' => 'fve', 'FvH4_3g12920' => 'fve', 'FvH4_3g30171' => 'fve', 'FvH4_3g35490' => 'fve', 'FvH4_3g43682' => 'fve', 'FvH4_3g43730' => 'fve', 'FvH4_3g43732' => 'fve', 'FvH4_3g43751' => 'fve', 'FvH4_3g43752' => 'fve', 'FvH4_3g43770' => 'fve', 'FvH4_3g44471' => 'fve', 'FvH4_3g44510' => 'fve', 'FvH4_3g44582' => 'fve', 'FvH4_4g16921' => 'fve', 'FvH4_4g17121' => 'fve', 'FvH4_4g17782' => 'fve', 'FvH4_4g17783' => 'fve', 'FvH4_4g18120' => 'fve', 'FvH4_4g31310' => 'fve', 'FvH4_4g35052' => 'fve', 'FvH4_5g30862' => 'fve', 'FvH4_6g01541' => 'fve', 'FvH4_6g02021' => 'fve', 'FvH4_6g02041' => 'fve', 'FvH4_6g02071' => 'fve', 'FvH4_6g02171' => 'fve', 'FvH4_6g03181' => 'fve', 'FvH4_6g03182' => 'fve', 'FvH4_6g03221' => 'fve', 'FvH4_6g03380' => 'fve', 'FvH4_6g05201' => 'fve', 'FvH4_6g05203' => 'fve', 'FvH4_6g20231' => 'fve', 'FvH4_6g31981' => 'fve', 'FvH4_6g32061' => 'fve', 'FvH4_6g37041' => 'fve', 'FvH4_6g37932' => 'fve', 'FvH4_6g38731' => 'fve', 'FvH4_6g39370' => 'fve', 'FvH4_6g39371' => 'fve', 'FvH4_6g40891' => 'fve', 'FvH4_6g40892' => 'fve', 'FvH4_6g43143' => 'fve', 'FvH4_6g45251' => 'fve', 'FvH4_6g45260' => 'fve', 'FvH4_6g45291' => 'fve', 'FvH4_6g45890' => 'fve', 'FvH4_6g46240' => 'fve', 'FvH4_6g46241' => 'fve', 'FvH4_6g46242' => 'fve', 'FvH4_6g46260' => 'fve', 'FvH4_6g46280' => 'fve', 'FvH4_6g46380' => 'fve', 'FvH4_7g12841' => 'fve', 'FvH4_7g31431' => 'fve', 'Glyma.09G075900' => 'gma', 'Gohir.A09G096401' => 'ghi', 'Gohir.D09G096101' => 'ghi', 'Gorai.006G112800' => 'gra', 'HanXRQChr04g0121411' => 'han', 'Hund15878' => 'sun', 'Lj2A1107G68' => 'lonja', 'Lj2A630G63' => 'lonja', 'Lj2A946T25' => 'lonja', 'Lj2C714T1' => 'lonja', 'Lj2C966T3' => 'lonja', 'Lj2C966T4' => 'lonja', 'Lj4g0002979' => 'lja', 'Lsat_1_v5_gn_5_30901' => 'lsa', 'Lsat_1_v5_gn_5_31100' => 'lsa', 'Lsat_1_v5_gn_5_38600' => 'lsa', 'Lsat_1_v5_gn_6_92061' => 'lsa', 'Manes.05G071301' => 'mes', 'MD02G1008700' => 'mdo', 'MD02G1008900' => 'mdo', 'MD03G1256400' => 'mdo', 'MD04G1180900' => 'mdo', 'MD04G1181000' => 'mdo', 'MD04G1181200' => 'mdo', 'MD05G1244200' => 'mdo', 'MD05G1324200' => 'mdo', 'MD09G1201600' => 'mdo', 'MD10G1000600' => 'mdo', 'MD14G1026900' => 'mdo', 'MD14G1187900' => 'mdo', 'MD15G1017800' => 'mdo', 'MD15G1018100' => 'mdo', 'Medtr4g124160' => 'mtr', 'Migut.L01260' => 'egut', 'Nitab4.5_0000008g0440' => 'nta', 'Nitab4.5_0000207g0170' => 'nta', 'Nitab4.5_0007671g0030' => 'nta', 'Nitab4.5_0010853g0020' => 'nta', 'Oeu057656.1' => 'oeu', 'PGSC0003DMG400005638' => 'stu', 'PGSC0003DMG400005639' => 'stu', 'Phvul.009G222800' => 'pvu', 'Potri.009G132400' => 'ptr', 'Potri.009G163001' => 'ptr', 'Potri.011G000700' => 'ptr', 'Potri.011G004800' => 'ptr', 'Prupe.1G509300' => 'ppe', 'Prupe.1G509700' => 'ppe', 'Prupe.1G510400' => 'ppe', 'Prupe.1G510700' => 'ppe', 'Prupe.1G512600' => 'ppe', 'Prupe.2G073200' => 'ppe', 'Prupe.3G059500' => 'ppe', 'Prupe.3G059600' => 'ppe', 'Prupe.3G246100' => 'ppe', 'Prupe.3G265100' => 'ppe', 'Prupe.4G034700' => 'ppe', 'Prupe.4G052100' => 'ppe', 'Prupe.4G053600' => 'ppe', 'Prupe.5G068800' => 'ppe', 'Prupe.5G070600' => 'ppe', 'Prupe.6G075400' => 'ppe', 'Prupe.6G075500' => 'ppe', 'Prupe.6G076400' => 'ppe', 'Prupe.8G110700' => 'ppe', 'Psat4g020960' => 'psa', 'PSO135G0788' => 'pso', 'PSO210G6463' => 'pso', 'PSO384G0370' => 'pso', 'PSO386G0056' => 'pso', 'QL01p006048' => 'qlo', 'QL02p054283' => 'qlo', 'QL05p008000' => 'qlo', 'QL05p008212' => 'qlo', 'QL05p008950' => 'qlo', 'QL05p009042' => 'qlo', 'QL05p009518' => 'qlo', 'QL05p012589' => 'qlo', 'QL05p012608' => 'qlo', 'QL05p012650' => 'qlo', 'QL05p012667' => 'qlo', 'QL05p014501' => 'qlo', 'QL05p052800' => 'qlo', 'QL05p065010' => 'qlo', 'QL05p074156' => 'qlo', 'QL05p074160' => 'qlo', 'QL05p074174' => 'qlo', 'QL05p074178' => 'qlo', 'QL05p074214' => 'qlo', 'QL06p001050' => 'qlo', 'QL06p001056' => 'qlo', 'QL06p006093' => 'qlo', 'QL06p006111' => 'qlo', 'QL07p019784' => 'qlo', 'QL07p019801' => 'qlo', 'QL07p036110' => 'qlo', 'QL07p036134' => 'qlo', 'QL07p036147' => 'qlo', 'QL07p036156' => 'qlo', 'QL07p036300' => 'qlo', 'QL07p036320' => 'qlo', 'QL08p014547' => 'qlo', 'QL08p014551' => 'qlo', 'QL08p043319' => 'qlo', 'QL08p043324' => 'qlo', 'QL11p009094' => 'qlo', 'RcHm_v2.0_Chr1g0380481' => 'rch', 'RcHm_v2.0_Chr2g0089331' => 'rch', 'RcHm_v2.0_Chr2g0123691' => 'rch', 'RcHm_v2.0_Chr2g0151111' => 'rch', 'RcHm_v2.0_Chr2g0163011' => 'rch', 'RcHm_v2.0_Chr2g0163051' => 'rch', 'RcHm_v2.0_Chr2g0164671' => 'rch', 'RcHm_v2.0_Chr2g0164681' => 'rch', 'RcHm_v2.0_Chr2g0164721' => 'rch', 'RcHm_v2.0_Chr3g0449911' => 'rch', 'RcHm_v2.0_Chr3g0450211' => 'rch', 'RcHm_v2.0_Chr3g0457271' => 'rch', 'RcHm_v2.0_Chr5g0018111' => 'rch', 'RcHm_v2.0_Chr5g0021011' => 'rch', 'RcHm_v2.0_Chr5g0081171' => 'rch', 'RcHm_v2.0_Chr5g0081211' => 'rch', 'RcHm_v2.0_Chr6g0275871' => 'rch', 'RcHm_v2.0_Chr6g0276071' => 'rch', 'RcHm_v2.0_Chr6g0285591' => 'rch', 'RcHm_v2.0_Chr6g0291931' => 'rch', 'RcHm_v2.0_Chr6g0292091' => 'rch', 'RcHm_v2.0_Chr6g0292271' => 'rch', 'RcHm_v2.0_Chr7g0221261' => 'rch', 'Rhsim08G0219900' => 'rsi', 'Rhsim08G0220200' => 'rsi', 'Rhsim08G0237800' => 'rsi', 'Rhsim08G0238800' => 'rsi', 'Sabra09G0102700' => 'sbr', 'Sabra09G0127200' => 'sbr', 'Sabra11G0003700' => 'sbr', 'Sabra15G0014700' => 'sbr', 'Sc19g0000590' => 'sci', 'Sc19g0001870' => 'sci', 'SGA_v2.0_scaffold1G00346' => 'sas', 'SGA_v2.0_scaffold1G00575' => 'sas', 'SGA_v2.0_scaffold1G00761' => 'sas', 'SGA_v2.0_scaffold232G43501' => 'sas', 'TAR625G1137' => 'tar', 'Thecc.03G222100' => 'tca', 'TPR.G12691' => 'tpr', 'TWI34G0727' => 'twi', 'TWI36G0117' => 'twi', 'VMungo1309G0868' => 'vmu' ), 'gf_id' => 'HOM05D001729', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001729' ), 'data_identifier' => 'HOM05D001729', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001729', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '375', 'num_species' => '42' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'Ah.07g204710' => 'amhyb', 'AUR62006001' => 'cqu', 'AUR62006002' => 'cqu', 'AUR62006003' => 'cqu', 'AUR62015641' => 'cqu', 'AUR62027174' => 'cqu', 'AUR62035623' => 'cqu', 'AUR62035624' => 'cqu', 'AUR62035625' => 'cqu', 'AUR62035626' => 'cqu', 'CAN.G1110.53' => 'can', 'CANSAT80G0415' => 'cansat', 'Ca_21364_v3' => 'car', 'COL.COLO4_30693' => 'col', 'COL.COLO4_30694' => 'col', 'COL.COLO4_30695' => 'col', 'COL.COLO4_30696' => 'col', 'COL.COLO4_34020' => 'col', 'DCAR_004585' => 'dca', 'Dinv04029' => 'din', 'Dinv34857' => 'din', 'Duzib147G0011' => 'dzi', 'Duzib170G0599' => 'dzi', 'Duzib192G1051' => 'dzi', 'FAN01G0708' => 'fan', 'FAN01G0742' => 'fan', 'FAN02G0048' => 'fan', 'FAN02G0583' => 'fan', 'FAN02G0688' => 'fan', 'FAN02G1588' => 'fan', 'FAN02G2194' => 'fan', 'FAN02G2750' => 'fan', 'FAN02G3094' => 'fan', 'FAN02G3887' => 'fan', 'FAN02G3911' => 'fan', 'FAN02G3994' => 'fan', 'FAN02G4432' => 'fan', 'FAN02G4556' => 'fan', 'FAN03G1977' => 'fan', 'FAN03G2781' => 'fan', 'FAN03G2850' => 'fan', 'FAN03G3155' => 'fan', 'FAN04G2487' => 'fan', 'FAN05G0208' => 'fan', 'FAN05G0656' => 'fan', 'FAN05G0696' => 'fan', 'FAN05G0810' => 'fan', 'FAN05G1447' => 'fan', 'FAN05G2640' => 'fan', 'FAN05G2911' => 'fan', 'FAN05G3901' => 'fan', 'FAN05G4859' => 'fan', 'FAN05G4861' => 'fan', 'FAN05G4988' => 'fan', 'FAN05G5187' => 'fan', 'FAN05G5452' => 'fan', 'FAN05G5500' => 'fan', 'FAN05G5688' => 'fan', 'FAN06G0177' => 'fan', 'FAN06G0675' => 'fan', 'FAN06G1290' => 'fan', 'FAN06G2191' => 'fan', 'FAN06G2405' => 'fan', 'FAN06G3231' => 'fan', 'FAN06G3932' => 'fan', 'FAN07G0163' => 'fan', 'FAN07G0471' => 'fan', 'FAN07G1354' => 'fan', 'FAN08G0338' => 'fan', 'FAN08G1373' => 'fan', 'FAN08G2539' => 'fan', 'FAN08G2728' => 'fan', 'FAN09G0608' => 'fan', 'FAN09G1136' => 'fan', 'FAN09G1958' => 'fan', 'FAN09G2508' => 'fan', 'FAN09G2597' => 'fan', 'FAN09G2658' => 'fan', 'FAN09G2757' => 'fan', 'FAN09G2983' => 'fan', 'FAN09G3130' => 'fan', 'FAN09G3565' => 'fan', 'FAN09G3613' => 'fan', 'FAN09G4011' => 'fan', 'FAN09G4239' => 'fan', 'FAN09G4277' => 'fan', 'FAN09G4720' => 'fan', 'FAN11G0139' => 'fan', 'FAN11G1727' => 'fan', 'FAN11G2672' => 'fan', 'FAN11G2795' => 'fan', 'FAN11G3238' => 'fan', 'FAN11G3734' => 'fan', 'FAN12G0631' => 'fan', 'FAN12G2239' => 'fan', 'FAN12G2308' => 'fan', 'FAN12G2569' => 'fan', 'FAN12G2623' => 'fan', 'FAN13G3182' => 'fan', 'FAN14G0053' => 'fan', 'FAN14G0370' => 'fan', 'FAN14G0382' => 'fan', 'FAN14G0421' => 'fan', 'FAN14G0866' => 'fan', 'FAN14G1187' => 'fan', 'FAN14G1727' => 'fan', 'FAN14G1791' => 'fan', 'FAN14G2361' => 'fan', 'FAN14G2668' => 'fan', 'FAN14G2770' => 'fan', 'FAN14G2874' => 'fan', 'FAN14G3193' => 'fan', 'FAN14G3624' => 'fan', 'FAN14G3676' => 'fan', 'FAN14G3807' => 'fan', 'FAN14G4082' => 'fan', 'FAN14G4342' => 'fan', 'FAN14G4985' => 'fan', 'FAN14G5126' => 'fan', 'FAN14G5781' => 'fan', 'FAN14G5808' => 'fan', 'FAN14G5949' => 'fan', 'FAN15G0828' => 'fan', 'FAN15G1054' => 'fan', 'FAN15G2023' => 'fan', 'FAN15G2506' => 'fan', 'FAN16G0128' => 'fan', 'FAN16G0249' => 'fan', 'FAN16G0429' => 'fan', 'FAN16G1493' => 'fan', 'FAN16G2210' => 'fan', 'FAN16G2506' => 'fan', 'FAN18G1542' => 'fan', 'FAN18G4057' => 'fan', 'FAN19G0745' => 'fan', 'FAN19G1216' => 'fan', 'FAN19G1733' => 'fan', 'FAN20G0258' => 'fan', 'FAN20G1095' => 'fan', 'FAN20G1557' => 'fan', 'FAN21G0302' => 'fan', 'FAN21G0519' => 'fan', 'FAN21G0970' => 'fan', 'FAN21G1159' => 'fan', 'FAN21G1312' => 'fan', 'FAN21G1440' => 'fan', 'FAN21G1715' => 'fan', 'FAN23G1584' => 'fan', 'FAN24G0045' => 'fan', 'FAN24G0053' => 'fan', 'FAN24G1500' => 'fan', 'FAN24G1817' => 'fan', 'FAN24G2147' => 'fan', 'FAN24G2236' => 'fan', 'FAN24G2446' => 'fan', 'FAN24G2684' => 'fan', 'FAN25G0187' => 'fan', 'FAN25G0505' => 'fan', 'FAN25G0589' => 'fan', 'FAN25G3663' => 'fan', 'FAN26G1025' => 'fan', 'FAN26G2860' => 'fan', 'FAN27G1329' => 'fan', 'FAN27G3392' => 'fan', 'FvH4_1g02011' => 'fve', 'FvH4_1g06511' => 'fve', 'FvH4_2g19900' => 'fve', 'FvH4_2g19920' => 'fve', 'FvH4_2g24261' => 'fve', 'FvH4_2g24270' => 'fve', 'FvH4_2g24631' => 'fve', 'FvH4_2g30622' => 'fve', 'FvH4_3g12920' => 'fve', 'FvH4_3g30171' => 'fve', 'FvH4_3g35490' => 'fve', 'FvH4_3g43682' => 'fve', 'FvH4_3g43730' => 'fve', 'FvH4_3g43732' => 'fve', 'FvH4_3g43751' => 'fve', 'FvH4_3g43752' => 'fve', 'FvH4_3g43770' => 'fve', 'FvH4_3g44471' => 'fve', 'FvH4_3g44510' => 'fve', 'FvH4_3g44582' => 'fve', 'FvH4_4g16921' => 'fve', 'FvH4_4g17121' => 'fve', 'FvH4_4g17782' => 'fve', 'FvH4_4g17783' => 'fve', 'FvH4_4g18120' => 'fve', 'FvH4_4g31310' => 'fve', 'FvH4_4g35052' => 'fve', 'FvH4_5g30862' => 'fve', 'FvH4_6g01541' => 'fve', 'FvH4_6g02021' => 'fve', 'FvH4_6g02041' => 'fve', 'FvH4_6g02071' => 'fve', 'FvH4_6g02171' => 'fve', 'FvH4_6g03181' => 'fve', 'FvH4_6g03182' => 'fve', 'FvH4_6g03221' => 'fve', 'FvH4_6g03380' => 'fve', 'FvH4_6g05201' => 'fve', 'FvH4_6g05203' => 'fve', 'FvH4_6g20231' => 'fve', 'FvH4_6g31981' => 'fve', 'FvH4_6g32061' => 'fve', 'FvH4_6g37041' => 'fve', 'FvH4_6g37932' => 'fve', 'FvH4_6g38731' => 'fve', 'FvH4_6g39370' => 'fve', 'FvH4_6g39371' => 'fve', 'FvH4_6g40891' => 'fve', 'FvH4_6g40892' => 'fve', 'FvH4_6g43143' => 'fve', 'FvH4_6g45251' => 'fve', 'FvH4_6g45260' => 'fve', 'FvH4_6g45291' => 'fve', 'FvH4_6g45890' => 'fve', 'FvH4_6g46240' => 'fve', 'FvH4_6g46241' => 'fve', 'FvH4_6g46242' => 'fve', 'FvH4_6g46260' => 'fve', 'FvH4_6g46280' => 'fve', 'FvH4_6g46380' => 'fve', 'FvH4_7g12841' => 'fve', 'FvH4_7g31431' => 'fve', 'Glyma.09G075900' => 'gma', 'Gohir.A09G096401' => 'ghi', 'Gohir.D09G096101' => 'ghi', 'Gorai.006G112800' => 'gra', 'HanXRQChr04g0121411' => 'han', 'Hund15878' => 'sun', 'Lj2A1107G68' => 'lonja', 'Lj2A630G63' => 'lonja', 'Lj2A946T25' => 'lonja', 'Lj2C714T1' => 'lonja', 'Lj2C966T3' => 'lonja', 'Lj2C966T4' => 'lonja', 'Lj4g0002979' => 'lja', 'Lsat_1_v5_gn_5_30901' => 'lsa', 'Lsat_1_v5_gn_5_31100' => 'lsa', 'Lsat_1_v5_gn_5_38600' => 'lsa', 'Lsat_1_v5_gn_6_92061' => 'lsa', 'Manes.05G071301' => 'mes', 'MD02G1008700' => 'mdo', 'MD02G1008900' => 'mdo', 'MD03G1256400' => 'mdo', 'MD04G1180900' => 'mdo', 'MD04G1181000' => 'mdo', 'MD04G1181200' => 'mdo', 'MD05G1244200' => 'mdo', 'MD05G1324200' => 'mdo', 'MD09G1201600' => 'mdo', 'MD10G1000600' => 'mdo', 'MD14G1026900' => 'mdo', 'MD14G1187900' => 'mdo', 'MD15G1017800' => 'mdo', 'MD15G1018100' => 'mdo', 'Medtr4g124160' => 'mtr', 'Migut.L01260' => 'egut', 'Nitab4.5_0000008g0440' => 'nta', 'Nitab4.5_0000207g0170' => 'nta', 'Nitab4.5_0007671g0030' => 'nta', 'Nitab4.5_0010853g0020' => 'nta', 'Oeu057656.1' => 'oeu', 'PGSC0003DMG400005638' => 'stu', 'PGSC0003DMG400005639' => 'stu', 'Phvul.009G222800' => 'pvu', 'Potri.009G132400' => 'ptr', 'Potri.009G163001' => 'ptr', 'Potri.011G000700' => 'ptr', 'Potri.011G004800' => 'ptr', 'Prupe.1G509300' => 'ppe', 'Prupe.1G509700' => 'ppe', 'Prupe.1G510400' => 'ppe', 'Prupe.1G510700' => 'ppe', 'Prupe.1G512600' => 'ppe', 'Prupe.2G073200' => 'ppe', 'Prupe.3G059500' => 'ppe', 'Prupe.3G059600' => 'ppe', 'Prupe.3G246100' => 'ppe', 'Prupe.3G265100' => 'ppe', 'Prupe.4G034700' => 'ppe', 'Prupe.4G052100' => 'ppe', 'Prupe.4G053600' => 'ppe', 'Prupe.5G068800' => 'ppe', 'Prupe.5G070600' => 'ppe', 'Prupe.6G075400' => 'ppe', 'Prupe.6G075500' => 'ppe', 'Prupe.6G076400' => 'ppe', 'Prupe.8G110700' => 'ppe', 'Psat4g020960' => 'psa', 'PSO135G0788' => 'pso', 'PSO210G6463' => 'pso', 'PSO384G0370' => 'pso', 'PSO386G0056' => 'pso', 'QL01p006048' => 'qlo', 'QL02p054283' => 'qlo', 'QL05p008000' => 'qlo', 'QL05p008212' => 'qlo', 'QL05p008950' => 'qlo', 'QL05p009042' => 'qlo', 'QL05p009518' => 'qlo', 'QL05p012589' => 'qlo', 'QL05p012608' => 'qlo', 'QL05p012650' => 'qlo', 'QL05p012667' => 'qlo', 'QL05p014501' => 'qlo', 'QL05p052800' => 'qlo', 'QL05p065010' => 'qlo', 'QL05p074156' => 'qlo', 'QL05p074160' => 'qlo', 'QL05p074174' => 'qlo', 'QL05p074178' => 'qlo', 'QL05p074214' => 'qlo', 'QL06p001050' => 'qlo', 'QL06p001056' => 'qlo', 'QL06p006093' => 'qlo', 'QL06p006111' => 'qlo', 'QL07p019784' => 'qlo', 'QL07p019801' => 'qlo', 'QL07p036110' => 'qlo', 'QL07p036134' => 'qlo', 'QL07p036147' => 'qlo', 'QL07p036156' => 'qlo', 'QL07p036300' => 'qlo', 'QL07p036320' => 'qlo', 'QL08p014547' => 'qlo', 'QL08p014551' => 'qlo', 'QL08p043319' => 'qlo', 'QL08p043324' => 'qlo', 'QL11p009094' => 'qlo', 'RcHm_v2.0_Chr1g0380481' => 'rch', 'RcHm_v2.0_Chr2g0089331' => 'rch', 'RcHm_v2.0_Chr2g0123691' => 'rch', 'RcHm_v2.0_Chr2g0151111' => 'rch', 'RcHm_v2.0_Chr2g0163011' => 'rch', 'RcHm_v2.0_Chr2g0163051' => 'rch', 'RcHm_v2.0_Chr2g0164671' => 'rch', 'RcHm_v2.0_Chr2g0164681' => 'rch', 'RcHm_v2.0_Chr2g0164721' => 'rch', 'RcHm_v2.0_Chr3g0449911' => 'rch', 'RcHm_v2.0_Chr3g0450211' => 'rch', 'RcHm_v2.0_Chr3g0457271' => 'rch', 'RcHm_v2.0_Chr5g0018111' => 'rch', 'RcHm_v2.0_Chr5g0021011' => 'rch', 'RcHm_v2.0_Chr5g0081171' => 'rch', 'RcHm_v2.0_Chr5g0081211' => 'rch', 'RcHm_v2.0_Chr6g0275871' => 'rch', 'RcHm_v2.0_Chr6g0276071' => 'rch', 'RcHm_v2.0_Chr6g0285591' => 'rch', 'RcHm_v2.0_Chr6g0291931' => 'rch', 'RcHm_v2.0_Chr6g0292091' => 'rch', 'RcHm_v2.0_Chr6g0292271' => 'rch', 'RcHm_v2.0_Chr7g0221261' => 'rch', 'Rhsim08G0219900' => 'rsi', 'Rhsim08G0220200' => 'rsi', 'Rhsim08G0237800' => 'rsi', 'Rhsim08G0238800' => 'rsi', 'Sabra09G0102700' => 'sbr', 'Sabra09G0127200' => 'sbr', 'Sabra11G0003700' => 'sbr', 'Sabra15G0014700' => 'sbr', 'Sc19g0000590' => 'sci', 'Sc19g0001870' => 'sci', 'SGA_v2.0_scaffold1G00346' => 'sas', 'SGA_v2.0_scaffold1G00575' => 'sas', 'SGA_v2.0_scaffold1G00761' => 'sas', 'SGA_v2.0_scaffold232G43501' => 'sas', 'TAR625G1137' => 'tar', 'Thecc.03G222100' => 'tca', 'TPR.G12691' => 'tpr', 'TWI34G0727' => 'twi', 'TWI36G0117' => 'twi', 'VMungo1309G0868' => 'vmu' ) $gf_id = 'HOM05D001729' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001729' ) $data_identifier = 'HOM05D001729' $data_type = 'gf_id' $species_gene_counts = array( 'amhyb' => (int) 1, 'cqu' => (int) 9, 'can' => (int) 1, 'cansat' => (int) 1, 'car' => (int) 1, 'col' => (int) 5, 'dca' => (int) 1, 'din' => (int) 2, 'dzi' => (int) 3, 'fan' => (int) 140, 'fve' => (int) 62, 'gma' => (int) 1, 'ghi' => (int) 2, 'gra' => (int) 1, 'han' => (int) 1, 'sun' => (int) 1, 'lonja' => (int) 6, 'lja' => (int) 1, 'lsa' => (int) 4, 'mes' => (int) 1, 'mdo' => (int) 14, 'mtr' => (int) 1, 'egut' => (int) 1, 'nta' => (int) 4, 'oeu' => (int) 1, 'stu' => (int) 2, 'pvu' => (int) 1, 'ptr' => (int) 4, 'ppe' => (int) 19, 'psa' => (int) 1, 'pso' => (int) 4, 'qlo' => (int) 36, 'rch' => (int) 23, 'rsi' => (int) 4, 'sbr' => (int) 4, 'sci' => (int) 2, 'sas' => (int) 4, 'tar' => (int) 1, 'tca' => (int) 1, 'tpr' => (int) 1, 'twi' => (int) 2, 'vmu' => (int) 1 ) $gf_gene_species = 'vmu' $gf_gene_id = 'VMungo1309G0868' $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' => 'HOM05D001729', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '375', 'num_species' => '42' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'Ah.07g204710' => 'amhyb', 'AUR62006001' => 'cqu', 'AUR62006002' => 'cqu', 'AUR62006003' => 'cqu', 'AUR62015641' => 'cqu', 'AUR62027174' => 'cqu', 'AUR62035623' => 'cqu', 'AUR62035624' => 'cqu', 'AUR62035625' => 'cqu', 'AUR62035626' => 'cqu', 'CAN.G1110.53' => 'can', 'CANSAT80G0415' => 'cansat', 'Ca_21364_v3' => 'car', 'COL.COLO4_30693' => 'col', 'COL.COLO4_30694' => 'col', 'COL.COLO4_30695' => 'col', 'COL.COLO4_30696' => 'col', 'COL.COLO4_34020' => 'col', 'DCAR_004585' => 'dca', 'Dinv04029' => 'din', 'Dinv34857' => 'din', 'Duzib147G0011' => 'dzi', 'Duzib170G0599' => 'dzi', 'Duzib192G1051' => 'dzi', 'FAN01G0708' => 'fan', 'FAN01G0742' => 'fan', 'FAN02G0048' => 'fan', 'FAN02G0583' => 'fan', 'FAN02G0688' => 'fan', 'FAN02G1588' => 'fan', 'FAN02G2194' => 'fan', 'FAN02G2750' => 'fan', 'FAN02G3094' => 'fan', 'FAN02G3887' => 'fan', 'FAN02G3911' => 'fan', 'FAN02G3994' => 'fan', 'FAN02G4432' => 'fan', 'FAN02G4556' => 'fan', 'FAN03G1977' => 'fan', 'FAN03G2781' => 'fan', 'FAN03G2850' => 'fan', 'FAN03G3155' => 'fan', 'FAN04G2487' => 'fan', 'FAN05G0208' => 'fan', 'FAN05G0656' => 'fan', 'FAN05G0696' => 'fan', 'FAN05G0810' => 'fan', 'FAN05G1447' => 'fan', 'FAN05G2640' => 'fan', 'FAN05G2911' => 'fan', 'FAN05G3901' => 'fan', 'FAN05G4859' => 'fan', 'FAN05G4861' => 'fan', 'FAN05G4988' => 'fan', 'FAN05G5187' => 'fan', 'FAN05G5452' => 'fan', 'FAN05G5500' => 'fan', 'FAN05G5688' => 'fan', 'FAN06G0177' => 'fan', 'FAN06G0675' => 'fan', 'FAN06G1290' => 'fan', 'FAN06G2191' => 'fan', 'FAN06G2405' => 'fan', 'FAN06G3231' => 'fan', 'FAN06G3932' => 'fan', 'FAN07G0163' => 'fan', 'FAN07G0471' => 'fan', 'FAN07G1354' => 'fan', 'FAN08G0338' => 'fan', 'FAN08G1373' => 'fan', 'FAN08G2539' => 'fan', 'FAN08G2728' => 'fan', 'FAN09G0608' => 'fan', 'FAN09G1136' => 'fan', 'FAN09G1958' => 'fan', 'FAN09G2508' => 'fan', 'FAN09G2597' => 'fan', 'FAN09G2658' => 'fan', 'FAN09G2757' => 'fan', 'FAN09G2983' => 'fan', 'FAN09G3130' => 'fan', 'FAN09G3565' => 'fan', 'FAN09G3613' => 'fan', 'FAN09G4011' => 'fan', 'FAN09G4239' => 'fan', 'FAN09G4277' => 'fan', 'FAN09G4720' => 'fan', 'FAN11G0139' => 'fan', 'FAN11G1727' => 'fan', 'FAN11G2672' => 'fan', 'FAN11G2795' => 'fan', 'FAN11G3238' => 'fan', 'FAN11G3734' => 'fan', 'FAN12G0631' => 'fan', 'FAN12G2239' => 'fan', 'FAN12G2308' => 'fan', 'FAN12G2569' => 'fan', 'FAN12G2623' => 'fan', 'FAN13G3182' => 'fan', 'FAN14G0053' => 'fan', 'FAN14G0370' => 'fan', 'FAN14G0382' => 'fan', 'FAN14G0421' => 'fan', 'FAN14G0866' => 'fan', 'FAN14G1187' => 'fan', 'FAN14G1727' => 'fan', 'FAN14G1791' => 'fan', 'FAN14G2361' => 'fan', 'FAN14G2668' => 'fan', 'FAN14G2770' => 'fan', 'FAN14G2874' => 'fan', 'FAN14G3193' => 'fan', 'FAN14G3624' => 'fan', 'FAN14G3676' => 'fan', 'FAN14G3807' => 'fan', 'FAN14G4082' => 'fan', 'FAN14G4342' => 'fan', 'FAN14G4985' => 'fan', 'FAN14G5126' => 'fan', 'FAN14G5781' => 'fan', 'FAN14G5808' => 'fan', 'FAN14G5949' => 'fan', 'FAN15G0828' => 'fan', 'FAN15G1054' => 'fan', 'FAN15G2023' => 'fan', 'FAN15G2506' => 'fan', 'FAN16G0128' => 'fan', 'FAN16G0249' => 'fan', 'FAN16G0429' => 'fan', 'FAN16G1493' => 'fan', 'FAN16G2210' => 'fan', 'FAN16G2506' => 'fan', 'FAN18G1542' => 'fan', 'FAN18G4057' => 'fan', 'FAN19G0745' => 'fan', 'FAN19G1216' => 'fan', 'FAN19G1733' => 'fan', 'FAN20G0258' => 'fan', 'FAN20G1095' => 'fan', 'FAN20G1557' => 'fan', 'FAN21G0302' => 'fan', 'FAN21G0519' => 'fan', 'FAN21G0970' => 'fan', 'FAN21G1159' => 'fan', 'FAN21G1312' => 'fan', 'FAN21G1440' => 'fan', 'FAN21G1715' => 'fan', 'FAN23G1584' => 'fan', 'FAN24G0045' => 'fan', 'FAN24G0053' => 'fan', 'FAN24G1500' => 'fan', 'FAN24G1817' => 'fan', 'FAN24G2147' => 'fan', 'FAN24G2236' => 'fan', 'FAN24G2446' => 'fan', 'FAN24G2684' => 'fan', 'FAN25G0187' => 'fan', 'FAN25G0505' => 'fan', 'FAN25G0589' => 'fan', 'FAN25G3663' => 'fan', 'FAN26G1025' => 'fan', 'FAN26G2860' => 'fan', 'FAN27G1329' => 'fan', 'FAN27G3392' => 'fan', 'FvH4_1g02011' => 'fve', 'FvH4_1g06511' => 'fve', 'FvH4_2g19900' => 'fve', 'FvH4_2g19920' => 'fve', 'FvH4_2g24261' => 'fve', 'FvH4_2g24270' => 'fve', 'FvH4_2g24631' => 'fve', 'FvH4_2g30622' => 'fve', 'FvH4_3g12920' => 'fve', 'FvH4_3g30171' => 'fve', 'FvH4_3g35490' => 'fve', 'FvH4_3g43682' => 'fve', 'FvH4_3g43730' => 'fve', 'FvH4_3g43732' => 'fve', 'FvH4_3g43751' => 'fve', 'FvH4_3g43752' => 'fve', 'FvH4_3g43770' => 'fve', 'FvH4_3g44471' => 'fve', 'FvH4_3g44510' => 'fve', 'FvH4_3g44582' => 'fve', 'FvH4_4g16921' => 'fve', 'FvH4_4g17121' => 'fve', 'FvH4_4g17782' => 'fve', 'FvH4_4g17783' => 'fve', 'FvH4_4g18120' => 'fve', 'FvH4_4g31310' => 'fve', 'FvH4_4g35052' => 'fve', 'FvH4_5g30862' => 'fve', 'FvH4_6g01541' => 'fve', 'FvH4_6g02021' => 'fve', 'FvH4_6g02041' => 'fve', 'FvH4_6g02071' => 'fve', 'FvH4_6g02171' => 'fve', 'FvH4_6g03181' => 'fve', 'FvH4_6g03182' => 'fve', 'FvH4_6g03221' => 'fve', 'FvH4_6g03380' => 'fve', 'FvH4_6g05201' => 'fve', 'FvH4_6g05203' => 'fve', 'FvH4_6g20231' => 'fve', 'FvH4_6g31981' => 'fve', 'FvH4_6g32061' => 'fve', 'FvH4_6g37041' => 'fve', 'FvH4_6g37932' => 'fve', 'FvH4_6g38731' => 'fve', 'FvH4_6g39370' => 'fve', 'FvH4_6g39371' => 'fve', 'FvH4_6g40891' => 'fve', 'FvH4_6g40892' => 'fve', 'FvH4_6g43143' => 'fve', 'FvH4_6g45251' => 'fve', 'FvH4_6g45260' => 'fve', 'FvH4_6g45291' => 'fve', 'FvH4_6g45890' => 'fve', 'FvH4_6g46240' => 'fve', 'FvH4_6g46241' => 'fve', 'FvH4_6g46242' => 'fve', 'FvH4_6g46260' => 'fve', 'FvH4_6g46280' => 'fve', 'FvH4_6g46380' => 'fve', 'FvH4_7g12841' => 'fve', 'FvH4_7g31431' => 'fve', 'Glyma.09G075900' => 'gma', 'Gohir.A09G096401' => 'ghi', 'Gohir.D09G096101' => 'ghi', 'Gorai.006G112800' => 'gra', 'HanXRQChr04g0121411' => 'han', 'Hund15878' => 'sun', 'Lj2A1107G68' => 'lonja', 'Lj2A630G63' => 'lonja', 'Lj2A946T25' => 'lonja', 'Lj2C714T1' => 'lonja', 'Lj2C966T3' => 'lonja', 'Lj2C966T4' => 'lonja', 'Lj4g0002979' => 'lja', 'Lsat_1_v5_gn_5_30901' => 'lsa', 'Lsat_1_v5_gn_5_31100' => 'lsa', 'Lsat_1_v5_gn_5_38600' => 'lsa', 'Lsat_1_v5_gn_6_92061' => 'lsa', 'Manes.05G071301' => 'mes', 'MD02G1008700' => 'mdo', 'MD02G1008900' => 'mdo', 'MD03G1256400' => 'mdo', 'MD04G1180900' => 'mdo', 'MD04G1181000' => 'mdo', 'MD04G1181200' => 'mdo', 'MD05G1244200' => 'mdo', 'MD05G1324200' => 'mdo', 'MD09G1201600' => 'mdo', 'MD10G1000600' => 'mdo', 'MD14G1026900' => 'mdo', 'MD14G1187900' => 'mdo', 'MD15G1017800' => 'mdo', 'MD15G1018100' => 'mdo', 'Medtr4g124160' => 'mtr', 'Migut.L01260' => 'egut', 'Nitab4.5_0000008g0440' => 'nta', 'Nitab4.5_0000207g0170' => 'nta', 'Nitab4.5_0007671g0030' => 'nta', 'Nitab4.5_0010853g0020' => 'nta', 'Oeu057656.1' => 'oeu', 'PGSC0003DMG400005638' => 'stu', 'PGSC0003DMG400005639' => 'stu', 'Phvul.009G222800' => 'pvu', 'Potri.009G132400' => 'ptr', 'Potri.009G163001' => 'ptr', 'Potri.011G000700' => 'ptr', 'Potri.011G004800' => 'ptr', 'Prupe.1G509300' => 'ppe', 'Prupe.1G509700' => 'ppe', 'Prupe.1G510400' => 'ppe', 'Prupe.1G510700' => 'ppe', 'Prupe.1G512600' => 'ppe', 'Prupe.2G073200' => 'ppe', 'Prupe.3G059500' => 'ppe', 'Prupe.3G059600' => 'ppe', 'Prupe.3G246100' => 'ppe', 'Prupe.3G265100' => 'ppe', 'Prupe.4G034700' => 'ppe', 'Prupe.4G052100' => 'ppe', 'Prupe.4G053600' => 'ppe', 'Prupe.5G068800' => 'ppe', 'Prupe.5G070600' => 'ppe', 'Prupe.6G075400' => 'ppe', 'Prupe.6G075500' => 'ppe', 'Prupe.6G076400' => 'ppe', 'Prupe.8G110700' => 'ppe', 'Psat4g020960' => 'psa', 'PSO135G0788' => 'pso', 'PSO210G6463' => 'pso', 'PSO384G0370' => 'pso', 'PSO386G0056' => 'pso', 'QL01p006048' => 'qlo', 'QL02p054283' => 'qlo', 'QL05p008000' => 'qlo', 'QL05p008212' => 'qlo', 'QL05p008950' => 'qlo', 'QL05p009042' => 'qlo', 'QL05p009518' => 'qlo', 'QL05p012589' => 'qlo', 'QL05p012608' => 'qlo', 'QL05p012650' => 'qlo', 'QL05p012667' => 'qlo', 'QL05p014501' => 'qlo', 'QL05p052800' => 'qlo', 'QL05p065010' => 'qlo', 'QL05p074156' => 'qlo', 'QL05p074160' => 'qlo', 'QL05p074174' => 'qlo', 'QL05p074178' => 'qlo', 'QL05p074214' => 'qlo', 'QL06p001050' => 'qlo', 'QL06p001056' => 'qlo', 'QL06p006093' => 'qlo', 'QL06p006111' => 'qlo', 'QL07p019784' => 'qlo', 'QL07p019801' => 'qlo', 'QL07p036110' => 'qlo', 'QL07p036134' => 'qlo', 'QL07p036147' => 'qlo', 'QL07p036156' => 'qlo', 'QL07p036300' => 'qlo', 'QL07p036320' => 'qlo', 'QL08p014547' => 'qlo', 'QL08p014551' => 'qlo', 'QL08p043319' => 'qlo', 'QL08p043324' => 'qlo', 'QL11p009094' => 'qlo', 'RcHm_v2.0_Chr1g0380481' => 'rch', 'RcHm_v2.0_Chr2g0089331' => 'rch', 'RcHm_v2.0_Chr2g0123691' => 'rch', 'RcHm_v2.0_Chr2g0151111' => 'rch', 'RcHm_v2.0_Chr2g0163011' => 'rch', 'RcHm_v2.0_Chr2g0163051' => 'rch', 'RcHm_v2.0_Chr2g0164671' => 'rch', 'RcHm_v2.0_Chr2g0164681' => 'rch', 'RcHm_v2.0_Chr2g0164721' => 'rch', 'RcHm_v2.0_Chr3g0449911' => 'rch', 'RcHm_v2.0_Chr3g0450211' => 'rch', 'RcHm_v2.0_Chr3g0457271' => 'rch', 'RcHm_v2.0_Chr5g0018111' => 'rch', 'RcHm_v2.0_Chr5g0021011' => 'rch', 'RcHm_v2.0_Chr5g0081171' => 'rch', 'RcHm_v2.0_Chr5g0081211' => 'rch', 'RcHm_v2.0_Chr6g0275871' => 'rch', 'RcHm_v2.0_Chr6g0276071' => 'rch', 'RcHm_v2.0_Chr6g0285591' => 'rch', 'RcHm_v2.0_Chr6g0291931' => 'rch', 'RcHm_v2.0_Chr6g0292091' => 'rch', 'RcHm_v2.0_Chr6g0292271' => 'rch', 'RcHm_v2.0_Chr7g0221261' => 'rch', 'Rhsim08G0219900' => 'rsi', 'Rhsim08G0220200' => 'rsi', 'Rhsim08G0237800' => 'rsi', 'Rhsim08G0238800' => 'rsi', 'Sabra09G0102700' => 'sbr', 'Sabra09G0127200' => 'sbr', 'Sabra11G0003700' => 'sbr', 'Sabra15G0014700' => 'sbr', 'Sc19g0000590' => 'sci', 'Sc19g0001870' => 'sci', 'SGA_v2.0_scaffold1G00346' => 'sas', 'SGA_v2.0_scaffold1G00575' => 'sas', 'SGA_v2.0_scaffold1G00761' => 'sas', 'SGA_v2.0_scaffold232G43501' => 'sas', 'TAR625G1137' => 'tar', 'Thecc.03G222100' => 'tca', 'TPR.G12691' => 'tpr', 'TWI34G0727' => 'twi', 'TWI36G0117' => 'twi', 'VMungo1309G0868' => 'vmu' ), 'gf_id' => 'HOM05D001729', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001729' ), 'data_identifier' => 'HOM05D001729', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001729', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '375', 'num_species' => '42' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'Ah.07g204710' => 'amhyb', 'AUR62006001' => 'cqu', 'AUR62006002' => 'cqu', 'AUR62006003' => 'cqu', 'AUR62015641' => 'cqu', 'AUR62027174' => 'cqu', 'AUR62035623' => 'cqu', 'AUR62035624' => 'cqu', 'AUR62035625' => 'cqu', 'AUR62035626' => 'cqu', 'CAN.G1110.53' => 'can', 'CANSAT80G0415' => 'cansat', 'Ca_21364_v3' => 'car', 'COL.COLO4_30693' => 'col', 'COL.COLO4_30694' => 'col', 'COL.COLO4_30695' => 'col', 'COL.COLO4_30696' => 'col', 'COL.COLO4_34020' => 'col', 'DCAR_004585' => 'dca', 'Dinv04029' => 'din', 'Dinv34857' => 'din', 'Duzib147G0011' => 'dzi', 'Duzib170G0599' => 'dzi', 'Duzib192G1051' => 'dzi', 'FAN01G0708' => 'fan', 'FAN01G0742' => 'fan', 'FAN02G0048' => 'fan', 'FAN02G0583' => 'fan', 'FAN02G0688' => 'fan', 'FAN02G1588' => 'fan', 'FAN02G2194' => 'fan', 'FAN02G2750' => 'fan', 'FAN02G3094' => 'fan', 'FAN02G3887' => 'fan', 'FAN02G3911' => 'fan', 'FAN02G3994' => 'fan', 'FAN02G4432' => 'fan', 'FAN02G4556' => 'fan', 'FAN03G1977' => 'fan', 'FAN03G2781' => 'fan', 'FAN03G2850' => 'fan', 'FAN03G3155' => 'fan', 'FAN04G2487' => 'fan', 'FAN05G0208' => 'fan', 'FAN05G0656' => 'fan', 'FAN05G0696' => 'fan', 'FAN05G0810' => 'fan', 'FAN05G1447' => 'fan', 'FAN05G2640' => 'fan', 'FAN05G2911' => 'fan', 'FAN05G3901' => 'fan', 'FAN05G4859' => 'fan', 'FAN05G4861' => 'fan', 'FAN05G4988' => 'fan', 'FAN05G5187' => 'fan', 'FAN05G5452' => 'fan', 'FAN05G5500' => 'fan', 'FAN05G5688' => 'fan', 'FAN06G0177' => 'fan', 'FAN06G0675' => 'fan', 'FAN06G1290' => 'fan', 'FAN06G2191' => 'fan', 'FAN06G2405' => 'fan', 'FAN06G3231' => 'fan', 'FAN06G3932' => 'fan', 'FAN07G0163' => 'fan', 'FAN07G0471' => 'fan', 'FAN07G1354' => 'fan', 'FAN08G0338' => 'fan', 'FAN08G1373' => 'fan', 'FAN08G2539' => 'fan', 'FAN08G2728' => 'fan', 'FAN09G0608' => 'fan', 'FAN09G1136' => 'fan', 'FAN09G1958' => 'fan', 'FAN09G2508' => 'fan', 'FAN09G2597' => 'fan', 'FAN09G2658' => 'fan', 'FAN09G2757' => 'fan', 'FAN09G2983' => 'fan', 'FAN09G3130' => 'fan', 'FAN09G3565' => 'fan', 'FAN09G3613' => 'fan', 'FAN09G4011' => 'fan', 'FAN09G4239' => 'fan', 'FAN09G4277' => 'fan', 'FAN09G4720' => 'fan', 'FAN11G0139' => 'fan', 'FAN11G1727' => 'fan', 'FAN11G2672' => 'fan', 'FAN11G2795' => 'fan', 'FAN11G3238' => 'fan', 'FAN11G3734' => 'fan', 'FAN12G0631' => 'fan', 'FAN12G2239' => 'fan', 'FAN12G2308' => 'fan', 'FAN12G2569' => 'fan', 'FAN12G2623' => 'fan', 'FAN13G3182' => 'fan', 'FAN14G0053' => 'fan', 'FAN14G0370' => 'fan', 'FAN14G0382' => 'fan', 'FAN14G0421' => 'fan', 'FAN14G0866' => 'fan', 'FAN14G1187' => 'fan', 'FAN14G1727' => 'fan', 'FAN14G1791' => 'fan', 'FAN14G2361' => 'fan', 'FAN14G2668' => 'fan', 'FAN14G2770' => 'fan', 'FAN14G2874' => 'fan', 'FAN14G3193' => 'fan', 'FAN14G3624' => 'fan', 'FAN14G3676' => 'fan', 'FAN14G3807' => 'fan', 'FAN14G4082' => 'fan', 'FAN14G4342' => 'fan', 'FAN14G4985' => 'fan', 'FAN14G5126' => 'fan', 'FAN14G5781' => 'fan', 'FAN14G5808' => 'fan', 'FAN14G5949' => 'fan', 'FAN15G0828' => 'fan', 'FAN15G1054' => 'fan', 'FAN15G2023' => 'fan', 'FAN15G2506' => 'fan', 'FAN16G0128' => 'fan', 'FAN16G0249' => 'fan', 'FAN16G0429' => 'fan', 'FAN16G1493' => 'fan', 'FAN16G2210' => 'fan', 'FAN16G2506' => 'fan', 'FAN18G1542' => 'fan', 'FAN18G4057' => 'fan', 'FAN19G0745' => 'fan', 'FAN19G1216' => 'fan', 'FAN19G1733' => 'fan', 'FAN20G0258' => 'fan', 'FAN20G1095' => 'fan', 'FAN20G1557' => 'fan', 'FAN21G0302' => 'fan', 'FAN21G0519' => 'fan', 'FAN21G0970' => 'fan', 'FAN21G1159' => 'fan', 'FAN21G1312' => 'fan', 'FAN21G1440' => 'fan', 'FAN21G1715' => 'fan', 'FAN23G1584' => 'fan', 'FAN24G0045' => 'fan', 'FAN24G0053' => 'fan', 'FAN24G1500' => 'fan', 'FAN24G1817' => 'fan', 'FAN24G2147' => 'fan', 'FAN24G2236' => 'fan', 'FAN24G2446' => 'fan', 'FAN24G2684' => 'fan', 'FAN25G0187' => 'fan', 'FAN25G0505' => 'fan', 'FAN25G0589' => 'fan', 'FAN25G3663' => 'fan', 'FAN26G1025' => 'fan', 'FAN26G2860' => 'fan', 'FAN27G1329' => 'fan', 'FAN27G3392' => 'fan', 'FvH4_1g02011' => 'fve', 'FvH4_1g06511' => 'fve', 'FvH4_2g19900' => 'fve', 'FvH4_2g19920' => 'fve', 'FvH4_2g24261' => 'fve', 'FvH4_2g24270' => 'fve', 'FvH4_2g24631' => 'fve', 'FvH4_2g30622' => 'fve', 'FvH4_3g12920' => 'fve', 'FvH4_3g30171' => 'fve', 'FvH4_3g35490' => 'fve', 'FvH4_3g43682' => 'fve', 'FvH4_3g43730' => 'fve', 'FvH4_3g43732' => 'fve', 'FvH4_3g43751' => 'fve', 'FvH4_3g43752' => 'fve', 'FvH4_3g43770' => 'fve', 'FvH4_3g44471' => 'fve', 'FvH4_3g44510' => 'fve', 'FvH4_3g44582' => 'fve', 'FvH4_4g16921' => 'fve', 'FvH4_4g17121' => 'fve', 'FvH4_4g17782' => 'fve', 'FvH4_4g17783' => 'fve', 'FvH4_4g18120' => 'fve', 'FvH4_4g31310' => 'fve', 'FvH4_4g35052' => 'fve', 'FvH4_5g30862' => 'fve', 'FvH4_6g01541' => 'fve', 'FvH4_6g02021' => 'fve', 'FvH4_6g02041' => 'fve', 'FvH4_6g02071' => 'fve', 'FvH4_6g02171' => 'fve', 'FvH4_6g03181' => 'fve', 'FvH4_6g03182' => 'fve', 'FvH4_6g03221' => 'fve', 'FvH4_6g03380' => 'fve', 'FvH4_6g05201' => 'fve', 'FvH4_6g05203' => 'fve', 'FvH4_6g20231' => 'fve', 'FvH4_6g31981' => 'fve', 'FvH4_6g32061' => 'fve', 'FvH4_6g37041' => 'fve', 'FvH4_6g37932' => 'fve', 'FvH4_6g38731' => 'fve', 'FvH4_6g39370' => 'fve', 'FvH4_6g39371' => 'fve', 'FvH4_6g40891' => 'fve', 'FvH4_6g40892' => 'fve', 'FvH4_6g43143' => 'fve', 'FvH4_6g45251' => 'fve', 'FvH4_6g45260' => 'fve', 'FvH4_6g45291' => 'fve', 'FvH4_6g45890' => 'fve', 'FvH4_6g46240' => 'fve', 'FvH4_6g46241' => 'fve', 'FvH4_6g46242' => 'fve', 'FvH4_6g46260' => 'fve', 'FvH4_6g46280' => 'fve', 'FvH4_6g46380' => 'fve', 'FvH4_7g12841' => 'fve', 'FvH4_7g31431' => 'fve', 'Glyma.09G075900' => 'gma', 'Gohir.A09G096401' => 'ghi', 'Gohir.D09G096101' => 'ghi', 'Gorai.006G112800' => 'gra', 'HanXRQChr04g0121411' => 'han', 'Hund15878' => 'sun', 'Lj2A1107G68' => 'lonja', 'Lj2A630G63' => 'lonja', 'Lj2A946T25' => 'lonja', 'Lj2C714T1' => 'lonja', 'Lj2C966T3' => 'lonja', 'Lj2C966T4' => 'lonja', 'Lj4g0002979' => 'lja', 'Lsat_1_v5_gn_5_30901' => 'lsa', 'Lsat_1_v5_gn_5_31100' => 'lsa', 'Lsat_1_v5_gn_5_38600' => 'lsa', 'Lsat_1_v5_gn_6_92061' => 'lsa', 'Manes.05G071301' => 'mes', 'MD02G1008700' => 'mdo', 'MD02G1008900' => 'mdo', 'MD03G1256400' => 'mdo', 'MD04G1180900' => 'mdo', 'MD04G1181000' => 'mdo', 'MD04G1181200' => 'mdo', 'MD05G1244200' => 'mdo', 'MD05G1324200' => 'mdo', 'MD09G1201600' => 'mdo', 'MD10G1000600' => 'mdo', 'MD14G1026900' => 'mdo', 'MD14G1187900' => 'mdo', 'MD15G1017800' => 'mdo', 'MD15G1018100' => 'mdo', 'Medtr4g124160' => 'mtr', 'Migut.L01260' => 'egut', 'Nitab4.5_0000008g0440' => 'nta', 'Nitab4.5_0000207g0170' => 'nta', 'Nitab4.5_0007671g0030' => 'nta', 'Nitab4.5_0010853g0020' => 'nta', 'Oeu057656.1' => 'oeu', 'PGSC0003DMG400005638' => 'stu', 'PGSC0003DMG400005639' => 'stu', 'Phvul.009G222800' => 'pvu', 'Potri.009G132400' => 'ptr', 'Potri.009G163001' => 'ptr', 'Potri.011G000700' => 'ptr', 'Potri.011G004800' => 'ptr', 'Prupe.1G509300' => 'ppe', 'Prupe.1G509700' => 'ppe', 'Prupe.1G510400' => 'ppe', 'Prupe.1G510700' => 'ppe', 'Prupe.1G512600' => 'ppe', 'Prupe.2G073200' => 'ppe', 'Prupe.3G059500' => 'ppe', 'Prupe.3G059600' => 'ppe', 'Prupe.3G246100' => 'ppe', 'Prupe.3G265100' => 'ppe', 'Prupe.4G034700' => 'ppe', 'Prupe.4G052100' => 'ppe', 'Prupe.4G053600' => 'ppe', 'Prupe.5G068800' => 'ppe', 'Prupe.5G070600' => 'ppe', 'Prupe.6G075400' => 'ppe', 'Prupe.6G075500' => 'ppe', 'Prupe.6G076400' => 'ppe', 'Prupe.8G110700' => 'ppe', 'Psat4g020960' => 'psa', 'PSO135G0788' => 'pso', 'PSO210G6463' => 'pso', 'PSO384G0370' => 'pso', 'PSO386G0056' => 'pso', 'QL01p006048' => 'qlo', 'QL02p054283' => 'qlo', 'QL05p008000' => 'qlo', 'QL05p008212' => 'qlo', 'QL05p008950' => 'qlo', 'QL05p009042' => 'qlo', 'QL05p009518' => 'qlo', 'QL05p012589' => 'qlo', 'QL05p012608' => 'qlo', 'QL05p012650' => 'qlo', 'QL05p012667' => 'qlo', 'QL05p014501' => 'qlo', 'QL05p052800' => 'qlo', 'QL05p065010' => 'qlo', 'QL05p074156' => 'qlo', 'QL05p074160' => 'qlo', 'QL05p074174' => 'qlo', 'QL05p074178' => 'qlo', 'QL05p074214' => 'qlo', 'QL06p001050' => 'qlo', 'QL06p001056' => 'qlo', 'QL06p006093' => 'qlo', 'QL06p006111' => 'qlo', 'QL07p019784' => 'qlo', 'QL07p019801' => 'qlo', 'QL07p036110' => 'qlo', 'QL07p036134' => 'qlo', 'QL07p036147' => 'qlo', 'QL07p036156' => 'qlo', 'QL07p036300' => 'qlo', 'QL07p036320' => 'qlo', 'QL08p014547' => 'qlo', 'QL08p014551' => 'qlo', 'QL08p043319' => 'qlo', 'QL08p043324' => 'qlo', 'QL11p009094' => 'qlo', 'RcHm_v2.0_Chr1g0380481' => 'rch', 'RcHm_v2.0_Chr2g0089331' => 'rch', 'RcHm_v2.0_Chr2g0123691' => 'rch', 'RcHm_v2.0_Chr2g0151111' => 'rch', 'RcHm_v2.0_Chr2g0163011' => 'rch', 'RcHm_v2.0_Chr2g0163051' => 'rch', 'RcHm_v2.0_Chr2g0164671' => 'rch', 'RcHm_v2.0_Chr2g0164681' => 'rch', 'RcHm_v2.0_Chr2g0164721' => 'rch', 'RcHm_v2.0_Chr3g0449911' => 'rch', 'RcHm_v2.0_Chr3g0450211' => 'rch', 'RcHm_v2.0_Chr3g0457271' => 'rch', 'RcHm_v2.0_Chr5g0018111' => 'rch', 'RcHm_v2.0_Chr5g0021011' => 'rch', 'RcHm_v2.0_Chr5g0081171' => 'rch', 'RcHm_v2.0_Chr5g0081211' => 'rch', 'RcHm_v2.0_Chr6g0275871' => 'rch', 'RcHm_v2.0_Chr6g0276071' => 'rch', 'RcHm_v2.0_Chr6g0285591' => 'rch', 'RcHm_v2.0_Chr6g0291931' => 'rch', 'RcHm_v2.0_Chr6g0292091' => 'rch', 'RcHm_v2.0_Chr6g0292271' => 'rch', 'RcHm_v2.0_Chr7g0221261' => 'rch', 'Rhsim08G0219900' => 'rsi', 'Rhsim08G0220200' => 'rsi', 'Rhsim08G0237800' => 'rsi', 'Rhsim08G0238800' => 'rsi', 'Sabra09G0102700' => 'sbr', 'Sabra09G0127200' => 'sbr', 'Sabra11G0003700' => 'sbr', 'Sabra15G0014700' => 'sbr', 'Sc19g0000590' => 'sci', 'Sc19g0001870' => 'sci', 'SGA_v2.0_scaffold1G00346' => 'sas', 'SGA_v2.0_scaffold1G00575' => 'sas', 'SGA_v2.0_scaffold1G00761' => 'sas', 'SGA_v2.0_scaffold232G43501' => 'sas', 'TAR625G1137' => 'tar', 'Thecc.03G222100' => 'tca', 'TPR.G12691' => 'tpr', 'TWI34G0727' => 'twi', 'TWI36G0117' => 'twi', 'VMungo1309G0868' => 'vmu' ) $gf_id = 'HOM05D001729' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001729' ) $data_identifier = 'HOM05D001729' $data_type = 'gf_id' $species_gene_counts = array( 'amhyb' => (int) 1, 'cqu' => (int) 9, 'can' => (int) 1, 'cansat' => (int) 1, 'car' => (int) 1, 'col' => (int) 5, 'dca' => (int) 1, 'din' => (int) 2, 'dzi' => (int) 3, 'fan' => (int) 140, 'fve' => (int) 62, 'gma' => (int) 1, 'ghi' => (int) 2, 'gra' => (int) 1, 'han' => (int) 1, 'sun' => (int) 1, 'lonja' => (int) 6, 'lja' => (int) 1, 'lsa' => (int) 4, 'mes' => (int) 1, 'mdo' => (int) 14, 'mtr' => (int) 1, 'egut' => (int) 1, 'nta' => (int) 4, 'oeu' => (int) 1, 'stu' => (int) 2, 'pvu' => (int) 1, 'ptr' => (int) 4, 'ppe' => (int) 19, 'psa' => (int) 1, 'pso' => (int) 4, 'qlo' => (int) 36, 'rch' => (int) 23, 'rsi' => (int) 4, 'sbr' => (int) 4, 'sci' => (int) 2, 'sas' => (int) 4, 'tar' => (int) 1, 'tca' => (int) 1, 'tpr' => (int) 1, 'twi' => (int) 2, 'vmu' => (int) 1 ) $gf_gene_species = 'vmu' $gf_gene_id = 'VMungo1309G0868' $species_info = array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ) $local_species = 'mdo' $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' => 'HOM05D001729', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '375', 'num_species' => '42' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'Ah.07g204710' => 'amhyb', 'AUR62006001' => 'cqu', 'AUR62006002' => 'cqu', 'AUR62006003' => 'cqu', 'AUR62015641' => 'cqu', 'AUR62027174' => 'cqu', 'AUR62035623' => 'cqu', 'AUR62035624' => 'cqu', 'AUR62035625' => 'cqu', 'AUR62035626' => 'cqu', 'CAN.G1110.53' => 'can', 'CANSAT80G0415' => 'cansat', 'Ca_21364_v3' => 'car', 'COL.COLO4_30693' => 'col', 'COL.COLO4_30694' => 'col', 'COL.COLO4_30695' => 'col', 'COL.COLO4_30696' => 'col', 'COL.COLO4_34020' => 'col', 'DCAR_004585' => 'dca', 'Dinv04029' => 'din', 'Dinv34857' => 'din', 'Duzib147G0011' => 'dzi', 'Duzib170G0599' => 'dzi', 'Duzib192G1051' => 'dzi', 'FAN01G0708' => 'fan', 'FAN01G0742' => 'fan', 'FAN02G0048' => 'fan', 'FAN02G0583' => 'fan', 'FAN02G0688' => 'fan', 'FAN02G1588' => 'fan', 'FAN02G2194' => 'fan', 'FAN02G2750' => 'fan', 'FAN02G3094' => 'fan', 'FAN02G3887' => 'fan', 'FAN02G3911' => 'fan', 'FAN02G3994' => 'fan', 'FAN02G4432' => 'fan', 'FAN02G4556' => 'fan', 'FAN03G1977' => 'fan', 'FAN03G2781' => 'fan', 'FAN03G2850' => 'fan', 'FAN03G3155' => 'fan', 'FAN04G2487' => 'fan', 'FAN05G0208' => 'fan', 'FAN05G0656' => 'fan', 'FAN05G0696' => 'fan', 'FAN05G0810' => 'fan', 'FAN05G1447' => 'fan', 'FAN05G2640' => 'fan', 'FAN05G2911' => 'fan', 'FAN05G3901' => 'fan', 'FAN05G4859' => 'fan', 'FAN05G4861' => 'fan', 'FAN05G4988' => 'fan', 'FAN05G5187' => 'fan', 'FAN05G5452' => 'fan', 'FAN05G5500' => 'fan', 'FAN05G5688' => 'fan', 'FAN06G0177' => 'fan', 'FAN06G0675' => 'fan', 'FAN06G1290' => 'fan', 'FAN06G2191' => 'fan', 'FAN06G2405' => 'fan', 'FAN06G3231' => 'fan', 'FAN06G3932' => 'fan', 'FAN07G0163' => 'fan', 'FAN07G0471' => 'fan', 'FAN07G1354' => 'fan', 'FAN08G0338' => 'fan', 'FAN08G1373' => 'fan', 'FAN08G2539' => 'fan', 'FAN08G2728' => 'fan', 'FAN09G0608' => 'fan', 'FAN09G1136' => 'fan', 'FAN09G1958' => 'fan', 'FAN09G2508' => 'fan', 'FAN09G2597' => 'fan', 'FAN09G2658' => 'fan', 'FAN09G2757' => 'fan', 'FAN09G2983' => 'fan', 'FAN09G3130' => 'fan', 'FAN09G3565' => 'fan', 'FAN09G3613' => 'fan', 'FAN09G4011' => 'fan', 'FAN09G4239' => 'fan', 'FAN09G4277' => 'fan', 'FAN09G4720' => 'fan', 'FAN11G0139' => 'fan', 'FAN11G1727' => 'fan', 'FAN11G2672' => 'fan', 'FAN11G2795' => 'fan', 'FAN11G3238' => 'fan', 'FAN11G3734' => 'fan', 'FAN12G0631' => 'fan', 'FAN12G2239' => 'fan', 'FAN12G2308' => 'fan', 'FAN12G2569' => 'fan', 'FAN12G2623' => 'fan', 'FAN13G3182' => 'fan', 'FAN14G0053' => 'fan', 'FAN14G0370' => 'fan', 'FAN14G0382' => 'fan', 'FAN14G0421' => 'fan', 'FAN14G0866' => 'fan', 'FAN14G1187' => 'fan', 'FAN14G1727' => 'fan', 'FAN14G1791' => 'fan', 'FAN14G2361' => 'fan', 'FAN14G2668' => 'fan', 'FAN14G2770' => 'fan', 'FAN14G2874' => 'fan', 'FAN14G3193' => 'fan', 'FAN14G3624' => 'fan', 'FAN14G3676' => 'fan', 'FAN14G3807' => 'fan', 'FAN14G4082' => 'fan', 'FAN14G4342' => 'fan', 'FAN14G4985' => 'fan', 'FAN14G5126' => 'fan', 'FAN14G5781' => 'fan', 'FAN14G5808' => 'fan', 'FAN14G5949' => 'fan', 'FAN15G0828' => 'fan', 'FAN15G1054' => 'fan', 'FAN15G2023' => 'fan', 'FAN15G2506' => 'fan', 'FAN16G0128' => 'fan', 'FAN16G0249' => 'fan', 'FAN16G0429' => 'fan', 'FAN16G1493' => 'fan', 'FAN16G2210' => 'fan', 'FAN16G2506' => 'fan', 'FAN18G1542' => 'fan', 'FAN18G4057' => 'fan', 'FAN19G0745' => 'fan', 'FAN19G1216' => 'fan', 'FAN19G1733' => 'fan', 'FAN20G0258' => 'fan', 'FAN20G1095' => 'fan', 'FAN20G1557' => 'fan', 'FAN21G0302' => 'fan', 'FAN21G0519' => 'fan', 'FAN21G0970' => 'fan', 'FAN21G1159' => 'fan', 'FAN21G1312' => 'fan', 'FAN21G1440' => 'fan', 'FAN21G1715' => 'fan', 'FAN23G1584' => 'fan', 'FAN24G0045' => 'fan', 'FAN24G0053' => 'fan', 'FAN24G1500' => 'fan', 'FAN24G1817' => 'fan', 'FAN24G2147' => 'fan', 'FAN24G2236' => 'fan', 'FAN24G2446' => 'fan', 'FAN24G2684' => 'fan', 'FAN25G0187' => 'fan', 'FAN25G0505' => 'fan', 'FAN25G0589' => 'fan', 'FAN25G3663' => 'fan', 'FAN26G1025' => 'fan', 'FAN26G2860' => 'fan', 'FAN27G1329' => 'fan', 'FAN27G3392' => 'fan', 'FvH4_1g02011' => 'fve', 'FvH4_1g06511' => 'fve', 'FvH4_2g19900' => 'fve', 'FvH4_2g19920' => 'fve', 'FvH4_2g24261' => 'fve', 'FvH4_2g24270' => 'fve', 'FvH4_2g24631' => 'fve', 'FvH4_2g30622' => 'fve', 'FvH4_3g12920' => 'fve', 'FvH4_3g30171' => 'fve', 'FvH4_3g35490' => 'fve', 'FvH4_3g43682' => 'fve', 'FvH4_3g43730' => 'fve', 'FvH4_3g43732' => 'fve', 'FvH4_3g43751' => 'fve', 'FvH4_3g43752' => 'fve', 'FvH4_3g43770' => 'fve', 'FvH4_3g44471' => 'fve', 'FvH4_3g44510' => 'fve', 'FvH4_3g44582' => 'fve', 'FvH4_4g16921' => 'fve', 'FvH4_4g17121' => 'fve', 'FvH4_4g17782' => 'fve', 'FvH4_4g17783' => 'fve', 'FvH4_4g18120' => 'fve', 'FvH4_4g31310' => 'fve', 'FvH4_4g35052' => 'fve', 'FvH4_5g30862' => 'fve', 'FvH4_6g01541' => 'fve', 'FvH4_6g02021' => 'fve', 'FvH4_6g02041' => 'fve', 'FvH4_6g02071' => 'fve', 'FvH4_6g02171' => 'fve', 'FvH4_6g03181' => 'fve', 'FvH4_6g03182' => 'fve', 'FvH4_6g03221' => 'fve', 'FvH4_6g03380' => 'fve', 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'ppe', 'Prupe.1G512600' => 'ppe', 'Prupe.2G073200' => 'ppe', 'Prupe.3G059500' => 'ppe', 'Prupe.3G059600' => 'ppe', 'Prupe.3G246100' => 'ppe', 'Prupe.3G265100' => 'ppe', 'Prupe.4G034700' => 'ppe', 'Prupe.4G052100' => 'ppe', 'Prupe.4G053600' => 'ppe', 'Prupe.5G068800' => 'ppe', 'Prupe.5G070600' => 'ppe', 'Prupe.6G075400' => 'ppe', 'Prupe.6G075500' => 'ppe', 'Prupe.6G076400' => 'ppe', 'Prupe.8G110700' => 'ppe', 'Psat4g020960' => 'psa', 'PSO135G0788' => 'pso', 'PSO210G6463' => 'pso', 'PSO384G0370' => 'pso', 'PSO386G0056' => 'pso', 'QL01p006048' => 'qlo', 'QL02p054283' => 'qlo', 'QL05p008000' => 'qlo', 'QL05p008212' => 'qlo', 'QL05p008950' => 'qlo', 'QL05p009042' => 'qlo', 'QL05p009518' => 'qlo', 'QL05p012589' => 'qlo', 'QL05p012608' => 'qlo', 'QL05p012650' => 'qlo', 'QL05p012667' => 'qlo', 'QL05p014501' => 'qlo', 'QL05p052800' => 'qlo', 'QL05p065010' => 'qlo', 'QL05p074156' => 'qlo', 'QL05p074160' => 'qlo', 'QL05p074174' => 'qlo', 'QL05p074178' => 'qlo', 'QL05p074214' => 'qlo', 'QL06p001050' => 'qlo', 'QL06p001056' => 'qlo', 'QL06p006093' => 'qlo', 'QL06p006111' => 'qlo', 'QL07p019784' => 'qlo', 'QL07p019801' => 'qlo', 'QL07p036110' => 'qlo', 'QL07p036134' => 'qlo', 'QL07p036147' => 'qlo', 'QL07p036156' => 'qlo', 'QL07p036300' => 'qlo', 'QL07p036320' => 'qlo', 'QL08p014547' => 'qlo', 'QL08p014551' => 'qlo', 'QL08p043319' => 'qlo', 'QL08p043324' => 'qlo', 'QL11p009094' => 'qlo', 'RcHm_v2.0_Chr1g0380481' => 'rch', 'RcHm_v2.0_Chr2g0089331' => 'rch', 'RcHm_v2.0_Chr2g0123691' => 'rch', 'RcHm_v2.0_Chr2g0151111' => 'rch', 'RcHm_v2.0_Chr2g0163011' => 'rch', 'RcHm_v2.0_Chr2g0163051' => 'rch', 'RcHm_v2.0_Chr2g0164671' => 'rch', 'RcHm_v2.0_Chr2g0164681' => 'rch', 'RcHm_v2.0_Chr2g0164721' => 'rch', 'RcHm_v2.0_Chr3g0449911' => 'rch', 'RcHm_v2.0_Chr3g0450211' => 'rch', 'RcHm_v2.0_Chr3g0457271' => 'rch', 'RcHm_v2.0_Chr5g0018111' => 'rch', 'RcHm_v2.0_Chr5g0021011' => 'rch', 'RcHm_v2.0_Chr5g0081171' => 'rch', 'RcHm_v2.0_Chr5g0081211' => 'rch', 'RcHm_v2.0_Chr6g0275871' => 'rch', 'RcHm_v2.0_Chr6g0276071' => 'rch', 'RcHm_v2.0_Chr6g0285591' => 'rch', 'RcHm_v2.0_Chr6g0291931' => 'rch', 'RcHm_v2.0_Chr6g0292091' => 'rch', 'RcHm_v2.0_Chr6g0292271' => 'rch', 'RcHm_v2.0_Chr7g0221261' => 'rch', 'Rhsim08G0219900' => 'rsi', 'Rhsim08G0220200' => 'rsi', 'Rhsim08G0237800' => 'rsi', 'Rhsim08G0238800' => 'rsi', 'Sabra09G0102700' => 'sbr', 'Sabra09G0127200' => 'sbr', 'Sabra11G0003700' => 'sbr', 'Sabra15G0014700' => 'sbr', 'Sc19g0000590' => 'sci', 'Sc19g0001870' => 'sci', 'SGA_v2.0_scaffold1G00346' => 'sas', 'SGA_v2.0_scaffold1G00575' => 'sas', 'SGA_v2.0_scaffold1G00761' => 'sas', 'SGA_v2.0_scaffold232G43501' => 'sas', 'TAR625G1137' => 'tar', 'Thecc.03G222100' => 'tca', 'TPR.G12691' => 'tpr', 'TWI34G0727' => 'twi', 'TWI36G0117' => 'twi', 'VMungo1309G0868' => 'vmu' ), 'gf_id' => 'HOM05D001729', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001729' ), 'data_identifier' => 'HOM05D001729', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001729', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '375', 'num_species' => '42' ) 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'AUR62035624' => 'cqu', 'AUR62035625' => 'cqu', 'AUR62035626' => 'cqu', 'CAN.G1110.53' => 'can', 'CANSAT80G0415' => 'cansat', 'Ca_21364_v3' => 'car', 'COL.COLO4_30693' => 'col', 'COL.COLO4_30694' => 'col', 'COL.COLO4_30695' => 'col', 'COL.COLO4_30696' => 'col', 'COL.COLO4_34020' => 'col', 'DCAR_004585' => 'dca', 'Dinv04029' => 'din', 'Dinv34857' => 'din', 'Duzib147G0011' => 'dzi', 'Duzib170G0599' => 'dzi', 'Duzib192G1051' => 'dzi', 'FAN01G0708' => 'fan', 'FAN01G0742' => 'fan', 'FAN02G0048' => 'fan', 'FAN02G0583' => 'fan', 'FAN02G0688' => 'fan', 'FAN02G1588' => 'fan', 'FAN02G2194' => 'fan', 'FAN02G2750' => 'fan', 'FAN02G3094' => 'fan', 'FAN02G3887' => 'fan', 'FAN02G3911' => 'fan', 'FAN02G3994' => 'fan', 'FAN02G4432' => 'fan', 'FAN02G4556' => 'fan', 'FAN03G1977' => 'fan', 'FAN03G2781' => 'fan', 'FAN03G2850' => 'fan', 'FAN03G3155' => 'fan', 'FAN04G2487' => 'fan', 'FAN05G0208' => 'fan', 'FAN05G0656' => 'fan', 'FAN05G0696' => 'fan', 'FAN05G0810' => 'fan', 'FAN05G1447' => 'fan', 'FAN05G2640' => 'fan', 'FAN05G2911' => 'fan', 'FAN05G3901' => 'fan', 'FAN05G4859' => 'fan', 'FAN05G4861' => 'fan', 'FAN05G4988' => 'fan', 'FAN05G5187' => 'fan', 'FAN05G5452' => 'fan', 'FAN05G5500' => 'fan', 'FAN05G5688' => 'fan', 'FAN06G0177' => 'fan', 'FAN06G0675' => 'fan', 'FAN06G1290' => 'fan', 'FAN06G2191' => 'fan', 'FAN06G2405' => 'fan', 'FAN06G3231' => 'fan', 'FAN06G3932' => 'fan', 'FAN07G0163' => 'fan', 'FAN07G0471' => 'fan', 'FAN07G1354' => 'fan', 'FAN08G0338' => 'fan', 'FAN08G1373' => 'fan', 'FAN08G2539' => 'fan', 'FAN08G2728' => 'fan', 'FAN09G0608' => 'fan', 'FAN09G1136' => 'fan', 'FAN09G1958' => 'fan', 'FAN09G2508' => 'fan', 'FAN09G2597' => 'fan', 'FAN09G2658' => 'fan', 'FAN09G2757' => 'fan', 'FAN09G2983' => 'fan', 'FAN09G3130' => 'fan', 'FAN09G3565' => 'fan', 'FAN09G3613' => 'fan', 'FAN09G4011' => 'fan', 'FAN09G4239' => 'fan', 'FAN09G4277' => 'fan', 'FAN09G4720' => 'fan', 'FAN11G0139' => 'fan', 'FAN11G1727' => 'fan', 'FAN11G2672' => 'fan', 'FAN11G2795' => 'fan', 'FAN11G3238' => 'fan', 'FAN11G3734' => 'fan', 'FAN12G0631' => 'fan', 'FAN12G2239' => 'fan', 'FAN12G2308' => 'fan', 'FAN12G2569' => 'fan', 'FAN12G2623' => 'fan', 'FAN13G3182' => 'fan', 'FAN14G0053' => 'fan', 'FAN14G0370' => 'fan', 'FAN14G0382' => 'fan', 'FAN14G0421' => 'fan', 'FAN14G0866' => 'fan', 'FAN14G1187' => 'fan', 'FAN14G1727' => 'fan', 'FAN14G1791' => 'fan', 'FAN14G2361' => 'fan', 'FAN14G2668' => 'fan', 'FAN14G2770' => 'fan', 'FAN14G2874' => 'fan', 'FAN14G3193' => 'fan', 'FAN14G3624' => 'fan', 'FAN14G3676' => 'fan', 'FAN14G3807' => 'fan', 'FAN14G4082' => 'fan', 'FAN14G4342' => 'fan', 'FAN14G4985' => 'fan', 'FAN14G5126' => 'fan', 'FAN14G5781' => 'fan', 'FAN14G5808' => 'fan', 'FAN14G5949' => 'fan', 'FAN15G0828' => 'fan', 'FAN15G1054' => 'fan', 'FAN15G2023' => 'fan', 'FAN15G2506' => 'fan', 'FAN16G0128' => 'fan', 'FAN16G0249' => 'fan', 'FAN16G0429' => 'fan', 'FAN16G1493' => 'fan', 'FAN16G2210' => 'fan', 'FAN16G2506' => 'fan', 'FAN18G1542' => 'fan', 'FAN18G4057' => 'fan', 'FAN19G0745' => 'fan', 'FAN19G1216' => 'fan', 'FAN19G1733' => 'fan', 'FAN20G0258' => 'fan', 'FAN20G1095' => 'fan', 'FAN20G1557' => 'fan', 'FAN21G0302' => 'fan', 'FAN21G0519' => 'fan', 'FAN21G0970' => 'fan', 'FAN21G1159' => 'fan', 'FAN21G1312' => 'fan', 'FAN21G1440' => 'fan', 'FAN21G1715' => 'fan', 'FAN23G1584' => 'fan', 'FAN24G0045' => 'fan', 'FAN24G0053' => 'fan', 'FAN24G1500' => 'fan', 'FAN24G1817' => 'fan', 'FAN24G2147' => 'fan', 'FAN24G2236' => 'fan', 'FAN24G2446' => 'fan', 'FAN24G2684' => 'fan', 'FAN25G0187' => 'fan', 'FAN25G0505' => 'fan', 'FAN25G0589' => 'fan', 'FAN25G3663' => 'fan', 'FAN26G1025' => 'fan', 'FAN26G2860' => 'fan', 'FAN27G1329' => 'fan', 'FAN27G3392' => 'fan', 'FvH4_1g02011' => 'fve', 'FvH4_1g06511' => 'fve', 'FvH4_2g19900' => 'fve', 'FvH4_2g19920' => 'fve', 'FvH4_2g24261' => 'fve', 'FvH4_2g24270' => 'fve', 'FvH4_2g24631' => 'fve', 'FvH4_2g30622' => 'fve', 'FvH4_3g12920' => 'fve', 'FvH4_3g30171' => 'fve', 'FvH4_3g35490' => 'fve', 'FvH4_3g43682' => 'fve', 'FvH4_3g43730' => 'fve', 'FvH4_3g43732' => 'fve', 'FvH4_3g43751' => 'fve', 'FvH4_3g43752' => 'fve', 'FvH4_3g43770' => 'fve', 'FvH4_3g44471' => 'fve', 'FvH4_3g44510' => 'fve', 'FvH4_3g44582' => 'fve', 'FvH4_4g16921' => 'fve', 'FvH4_4g17121' => 'fve', 'FvH4_4g17782' => 'fve', 'FvH4_4g17783' => 'fve', 'FvH4_4g18120' => 'fve', 'FvH4_4g31310' => 'fve', 'FvH4_4g35052' => 'fve', 'FvH4_5g30862' => 'fve', 'FvH4_6g01541' => 'fve', 'FvH4_6g02021' => 'fve', 'FvH4_6g02041' => 'fve', 'FvH4_6g02071' => 'fve', 'FvH4_6g02171' => 'fve', 'FvH4_6g03181' => 'fve', 'FvH4_6g03182' => 'fve', 'FvH4_6g03221' => 'fve', 'FvH4_6g03380' => 'fve', 'FvH4_6g05201' => 'fve', 'FvH4_6g05203' => 'fve', 'FvH4_6g20231' => 'fve', 'FvH4_6g31981' => 'fve', 'FvH4_6g32061' => 'fve', 'FvH4_6g37041' => 'fve', 'FvH4_6g37932' => 'fve', 'FvH4_6g38731' => 'fve', 'FvH4_6g39370' => 'fve', 'FvH4_6g39371' => 'fve', 'FvH4_6g40891' => 'fve', 'FvH4_6g40892' => 'fve', 'FvH4_6g43143' => 'fve', 'FvH4_6g45251' => 'fve', 'FvH4_6g45260' => 'fve', 'FvH4_6g45291' => 'fve', 'FvH4_6g45890' => 'fve', 'FvH4_6g46240' => 'fve', 'FvH4_6g46241' => 'fve', 'FvH4_6g46242' => 'fve', 'FvH4_6g46260' => 'fve', 'FvH4_6g46280' => 'fve', 'FvH4_6g46380' => 'fve', 'FvH4_7g12841' => 'fve', 'FvH4_7g31431' => 'fve', 'Glyma.09G075900' => 'gma', 'Gohir.A09G096401' => 'ghi', 'Gohir.D09G096101' => 'ghi', 'Gorai.006G112800' => 'gra', 'HanXRQChr04g0121411' => 'han', 'Hund15878' => 'sun', 'Lj2A1107G68' => 'lonja', 'Lj2A630G63' => 'lonja', 'Lj2A946T25' => 'lonja', 'Lj2C714T1' => 'lonja', 'Lj2C966T3' => 'lonja', 'Lj2C966T4' => 'lonja', 'Lj4g0002979' => 'lja', 'Lsat_1_v5_gn_5_30901' => 'lsa', 'Lsat_1_v5_gn_5_31100' => 'lsa', 'Lsat_1_v5_gn_5_38600' => 'lsa', 'Lsat_1_v5_gn_6_92061' => 'lsa', 'Manes.05G071301' => 'mes', 'MD02G1008700' => 'mdo', 'MD02G1008900' => 'mdo', 'MD03G1256400' => 'mdo', 'MD04G1180900' => 'mdo', 'MD04G1181000' => 'mdo', 'MD04G1181200' => 'mdo', 'MD05G1244200' => 'mdo', 'MD05G1324200' => 'mdo', 'MD09G1201600' => 'mdo', 'MD10G1000600' => 'mdo', 'MD14G1026900' => 'mdo', 'MD14G1187900' => 'mdo', 'MD15G1017800' => 'mdo', 'MD15G1018100' => 'mdo', 'Medtr4g124160' => 'mtr', 'Migut.L01260' => 'egut', 'Nitab4.5_0000008g0440' => 'nta', 'Nitab4.5_0000207g0170' => 'nta', 'Nitab4.5_0007671g0030' => 'nta', 'Nitab4.5_0010853g0020' => 'nta', 'Oeu057656.1' => 'oeu', 'PGSC0003DMG400005638' => 'stu', 'PGSC0003DMG400005639' => 'stu', 'Phvul.009G222800' => 'pvu', 'Potri.009G132400' => 'ptr', 'Potri.009G163001' => 'ptr', 'Potri.011G000700' => 'ptr', 'Potri.011G004800' => 'ptr', 'Prupe.1G509300' => 'ppe', 'Prupe.1G509700' => 'ppe', 'Prupe.1G510400' => 'ppe', 'Prupe.1G510700' => 'ppe', 'Prupe.1G512600' => 'ppe', 'Prupe.2G073200' => 'ppe', 'Prupe.3G059500' => 'ppe', 'Prupe.3G059600' => 'ppe', 'Prupe.3G246100' => 'ppe', 'Prupe.3G265100' => 'ppe', 'Prupe.4G034700' => 'ppe', 'Prupe.4G052100' => 'ppe', 'Prupe.4G053600' => 'ppe', 'Prupe.5G068800' => 'ppe', 'Prupe.5G070600' => 'ppe', 'Prupe.6G075400' => 'ppe', 'Prupe.6G075500' => 'ppe', 'Prupe.6G076400' => 'ppe', 'Prupe.8G110700' => 'ppe', 'Psat4g020960' => 'psa', 'PSO135G0788' => 'pso', 'PSO210G6463' => 'pso', 'PSO384G0370' => 'pso', 'PSO386G0056' => 'pso', 'QL01p006048' => 'qlo', 'QL02p054283' => 'qlo', 'QL05p008000' => 'qlo', 'QL05p008212' => 'qlo', 'QL05p008950' => 'qlo', 'QL05p009042' => 'qlo', 'QL05p009518' => 'qlo', 'QL05p012589' => 'qlo', 'QL05p012608' => 'qlo', 'QL05p012650' => 'qlo', 'QL05p012667' => 'qlo', 'QL05p014501' => 'qlo', 'QL05p052800' => 'qlo', 'QL05p065010' => 'qlo', 'QL05p074156' => 'qlo', 'QL05p074160' => 'qlo', 'QL05p074174' => 'qlo', 'QL05p074178' => 'qlo', 'QL05p074214' => 'qlo', 'QL06p001050' => 'qlo', 'QL06p001056' => 'qlo', 'QL06p006093' => 'qlo', 'QL06p006111' => 'qlo', 'QL07p019784' => 'qlo', 'QL07p019801' => 'qlo', 'QL07p036110' => 'qlo', 'QL07p036134' => 'qlo', 'QL07p036147' => 'qlo', 'QL07p036156' => 'qlo', 'QL07p036300' => 'qlo', 'QL07p036320' => 'qlo', 'QL08p014547' => 'qlo', 'QL08p014551' => 'qlo', 'QL08p043319' => 'qlo', 'QL08p043324' => 'qlo', 'QL11p009094' => 'qlo', 'RcHm_v2.0_Chr1g0380481' => 'rch', 'RcHm_v2.0_Chr2g0089331' => 'rch', 'RcHm_v2.0_Chr2g0123691' => 'rch', 'RcHm_v2.0_Chr2g0151111' => 'rch', 'RcHm_v2.0_Chr2g0163011' => 'rch', 'RcHm_v2.0_Chr2g0163051' => 'rch', 'RcHm_v2.0_Chr2g0164671' => 'rch', 'RcHm_v2.0_Chr2g0164681' => 'rch', 'RcHm_v2.0_Chr2g0164721' => 'rch', 'RcHm_v2.0_Chr3g0449911' => 'rch', 'RcHm_v2.0_Chr3g0450211' => 'rch', 'RcHm_v2.0_Chr3g0457271' => 'rch', 'RcHm_v2.0_Chr5g0018111' => 'rch', 'RcHm_v2.0_Chr5g0021011' => 'rch', 'RcHm_v2.0_Chr5g0081171' => 'rch', 'RcHm_v2.0_Chr5g0081211' => 'rch', 'RcHm_v2.0_Chr6g0275871' => 'rch', 'RcHm_v2.0_Chr6g0276071' => 'rch', 'RcHm_v2.0_Chr6g0285591' => 'rch', 'RcHm_v2.0_Chr6g0291931' => 'rch', 'RcHm_v2.0_Chr6g0292091' => 'rch', 'RcHm_v2.0_Chr6g0292271' => 'rch', 'RcHm_v2.0_Chr7g0221261' => 'rch', 'Rhsim08G0219900' => 'rsi', 'Rhsim08G0220200' => 'rsi', 'Rhsim08G0237800' => 'rsi', 'Rhsim08G0238800' => 'rsi', 'Sabra09G0102700' => 'sbr', 'Sabra09G0127200' => 'sbr', 'Sabra11G0003700' => 'sbr', 'Sabra15G0014700' => 'sbr', 'Sc19g0000590' => 'sci', 'Sc19g0001870' => 'sci', 'SGA_v2.0_scaffold1G00346' => 'sas', 'SGA_v2.0_scaffold1G00575' => 'sas', 'SGA_v2.0_scaffold1G00761' => 'sas', 'SGA_v2.0_scaffold232G43501' => 'sas', 'TAR625G1137' => 'tar', 'Thecc.03G222100' => 'tca', 'TPR.G12691' => 'tpr', 'TWI34G0727' => 'twi', 'TWI36G0117' => 'twi', 'VMungo1309G0868' => 'vmu' ) $gf_id = 'HOM05D001729' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001729' ) $data_identifier = 'HOM05D001729' $data_type = 'gf_id' $species_gene_counts = array( 'amhyb' => (int) 1, 'cqu' => (int) 9, 'can' => (int) 1, 'cansat' => (int) 1, 'car' => (int) 1, 'col' => (int) 5, 'dca' => (int) 1, 'din' => (int) 2, 'dzi' => (int) 3, 'fan' => (int) 140, 'fve' => (int) 62, 'gma' => (int) 1, 'ghi' => (int) 2, 'gra' => (int) 1, 'han' => (int) 1, 'sun' => (int) 1, 'lonja' => (int) 6, 'lja' => (int) 1, 'lsa' => (int) 4, 'mes' => (int) 1, 'mdo' => (int) 14, 'mtr' => (int) 1, 'egut' => (int) 1, 'nta' => (int) 4, 'oeu' => (int) 1, 'stu' => (int) 2, 'pvu' => (int) 1, 'ptr' => (int) 4, 'ppe' => (int) 19, 'psa' => (int) 1, 'pso' => (int) 4, 'qlo' => (int) 36, 'rch' => (int) 23, 'rsi' => (int) 4, 'sbr' => (int) 4, 'sci' => (int) 2, 'sas' => (int) 4, 'tar' => (int) 1, 'tca' => (int) 1, 'tpr' => (int) 1, 'twi' => (int) 2, 'vmu' => (int) 1 ) $gf_gene_species = 'vmu' $gf_gene_id = 'VMungo1309G0868' $species_info = array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ) $local_species = 'mdo' $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' => 'HOM05D001729', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '375', 'num_species' => '42' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'Ah.07g204710' => 'amhyb', 'AUR62006001' => 'cqu', 'AUR62006002' => 'cqu', 'AUR62006003' => 'cqu', 'AUR62015641' => 'cqu', 'AUR62027174' => 'cqu', 'AUR62035623' => 'cqu', 'AUR62035624' => 'cqu', 'AUR62035625' => 'cqu', 'AUR62035626' => 'cqu', 'CAN.G1110.53' => 'can', 'CANSAT80G0415' => 'cansat', 'Ca_21364_v3' => 'car', 'COL.COLO4_30693' => 'col', 'COL.COLO4_30694' => 'col', 'COL.COLO4_30695' => 'col', 'COL.COLO4_30696' => 'col', 'COL.COLO4_34020' => 'col', 'DCAR_004585' => 'dca', 'Dinv04029' => 'din', 'Dinv34857' => 'din', 'Duzib147G0011' => 'dzi', 'Duzib170G0599' => 'dzi', 'Duzib192G1051' => 'dzi', 'FAN01G0708' => 'fan', 'FAN01G0742' => 'fan', 'FAN02G0048' => 'fan', 'FAN02G0583' => 'fan', 'FAN02G0688' => 'fan', 'FAN02G1588' => 'fan', 'FAN02G2194' => 'fan', 'FAN02G2750' => 'fan', 'FAN02G3094' => 'fan', 'FAN02G3887' => 'fan', 'FAN02G3911' => 'fan', 'FAN02G3994' => 'fan', 'FAN02G4432' => 'fan', 'FAN02G4556' => 'fan', 'FAN03G1977' => 'fan', 'FAN03G2781' => 'fan', 'FAN03G2850' => 'fan', 'FAN03G3155' => 'fan', 'FAN04G2487' => 'fan', 'FAN05G0208' => 'fan', 'FAN05G0656' => 'fan', 'FAN05G0696' => 'fan', 'FAN05G0810' => 'fan', 'FAN05G1447' => 'fan', 'FAN05G2640' => 'fan', 'FAN05G2911' => 'fan', 'FAN05G3901' => 'fan', 'FAN05G4859' => 'fan', 'FAN05G4861' => 'fan', 'FAN05G4988' => 'fan', 'FAN05G5187' => 'fan', 'FAN05G5452' => 'fan', 'FAN05G5500' => 'fan', 'FAN05G5688' => 'fan', 'FAN06G0177' => 'fan', 'FAN06G0675' => 'fan', 'FAN06G1290' => 'fan', 'FAN06G2191' => 'fan', 'FAN06G2405' => 'fan', 'FAN06G3231' => 'fan', 'FAN06G3932' => 'fan', 'FAN07G0163' => 'fan', 'FAN07G0471' => 'fan', 'FAN07G1354' => 'fan', 'FAN08G0338' => 'fan', 'FAN08G1373' => 'fan', 'FAN08G2539' => 'fan', 'FAN08G2728' => 'fan', 'FAN09G0608' => 'fan', 'FAN09G1136' => 'fan', 'FAN09G1958' => 'fan', 'FAN09G2508' => 'fan', 'FAN09G2597' => 'fan', 'FAN09G2658' => 'fan', 'FAN09G2757' => 'fan', 'FAN09G2983' => 'fan', 'FAN09G3130' => 'fan', 'FAN09G3565' => 'fan', 'FAN09G3613' => 'fan', 'FAN09G4011' => 'fan', 'FAN09G4239' => 'fan', 'FAN09G4277' => 'fan', 'FAN09G4720' => 'fan', 'FAN11G0139' => 'fan', 'FAN11G1727' => 'fan', 'FAN11G2672' => 'fan', 'FAN11G2795' => 'fan', 'FAN11G3238' => 'fan', 'FAN11G3734' => 'fan', 'FAN12G0631' => 'fan', 'FAN12G2239' => 'fan', 'FAN12G2308' => 'fan', 'FAN12G2569' => 'fan', 'FAN12G2623' => 'fan', 'FAN13G3182' => 'fan', 'FAN14G0053' => 'fan', 'FAN14G0370' => 'fan', 'FAN14G0382' => 'fan', 'FAN14G0421' => 'fan', 'FAN14G0866' => 'fan', 'FAN14G1187' => 'fan', 'FAN14G1727' => 'fan', 'FAN14G1791' => 'fan', 'FAN14G2361' => 'fan', 'FAN14G2668' => 'fan', 'FAN14G2770' => 'fan', 'FAN14G2874' => 'fan', 'FAN14G3193' => 'fan', 'FAN14G3624' => 'fan', 'FAN14G3676' => 'fan', 'FAN14G3807' => 'fan', 'FAN14G4082' => 'fan', 'FAN14G4342' => 'fan', 'FAN14G4985' => 'fan', 'FAN14G5126' => 'fan', 'FAN14G5781' => 'fan', 'FAN14G5808' => 'fan', 'FAN14G5949' => 'fan', 'FAN15G0828' => 'fan', 'FAN15G1054' => 'fan', 'FAN15G2023' => 'fan', 'FAN15G2506' => 'fan', 'FAN16G0128' => 'fan', 'FAN16G0249' => 'fan', 'FAN16G0429' => 'fan', 'FAN16G1493' => 'fan', 'FAN16G2210' => 'fan', 'FAN16G2506' => 'fan', 'FAN18G1542' => 'fan', 'FAN18G4057' => 'fan', 'FAN19G0745' => 'fan', 'FAN19G1216' => 'fan', 'FAN19G1733' => 'fan', 'FAN20G0258' => 'fan', 'FAN20G1095' => 'fan', 'FAN20G1557' => 'fan', 'FAN21G0302' => 'fan', 'FAN21G0519' => 'fan', 'FAN21G0970' => 'fan', 'FAN21G1159' => 'fan', 'FAN21G1312' => 'fan', 'FAN21G1440' => 'fan', 'FAN21G1715' => 'fan', 'FAN23G1584' => 'fan', 'FAN24G0045' => 'fan', 'FAN24G0053' => 'fan', 'FAN24G1500' => 'fan', 'FAN24G1817' => 'fan', 'FAN24G2147' => 'fan', 'FAN24G2236' => 'fan', 'FAN24G2446' => 'fan', 'FAN24G2684' => 'fan', 'FAN25G0187' => 'fan', 'FAN25G0505' => 'fan', 'FAN25G0589' => 'fan', 'FAN25G3663' => 'fan', 'FAN26G1025' => 'fan', 'FAN26G2860' => 'fan', 'FAN27G1329' => 'fan', 'FAN27G3392' => 'fan', 'FvH4_1g02011' => 'fve', 'FvH4_1g06511' => 'fve', 'FvH4_2g19900' => 'fve', 'FvH4_2g19920' => 'fve', 'FvH4_2g24261' => 'fve', 'FvH4_2g24270' => 'fve', 'FvH4_2g24631' => 'fve', 'FvH4_2g30622' => 'fve', 'FvH4_3g12920' => 'fve', 'FvH4_3g30171' => 'fve', 'FvH4_3g35490' => 'fve', 'FvH4_3g43682' => 'fve', 'FvH4_3g43730' => 'fve', 'FvH4_3g43732' => 'fve', 'FvH4_3g43751' => 'fve', 'FvH4_3g43752' => 'fve', 'FvH4_3g43770' => 'fve', 'FvH4_3g44471' => 'fve', 'FvH4_3g44510' => 'fve', 'FvH4_3g44582' => 'fve', 'FvH4_4g16921' => 'fve', 'FvH4_4g17121' => 'fve', 'FvH4_4g17782' => 'fve', 'FvH4_4g17783' => 'fve', 'FvH4_4g18120' => 'fve', 'FvH4_4g31310' => 'fve', 'FvH4_4g35052' => 'fve', 'FvH4_5g30862' => 'fve', 'FvH4_6g01541' => 'fve', 'FvH4_6g02021' => 'fve', 'FvH4_6g02041' => 'fve', 'FvH4_6g02071' => 'fve', 'FvH4_6g02171' => 'fve', 'FvH4_6g03181' => 'fve', 'FvH4_6g03182' => 'fve', 'FvH4_6g03221' => 'fve', 'FvH4_6g03380' => 'fve', 'FvH4_6g05201' => 'fve', 'FvH4_6g05203' => 'fve', 'FvH4_6g20231' => 'fve', 'FvH4_6g31981' => 'fve', 'FvH4_6g32061' => 'fve', 'FvH4_6g37041' => 'fve', 'FvH4_6g37932' => 'fve', 'FvH4_6g38731' => 'fve', 'FvH4_6g39370' => 'fve', 'FvH4_6g39371' => 'fve', 'FvH4_6g40891' => 'fve', 'FvH4_6g40892' => 'fve', 'FvH4_6g43143' => 'fve', 'FvH4_6g45251' => 'fve', 'FvH4_6g45260' => 'fve', 'FvH4_6g45291' => 'fve', 'FvH4_6g45890' => 'fve', 'FvH4_6g46240' => 'fve', 'FvH4_6g46241' => 'fve', 'FvH4_6g46242' => 'fve', 'FvH4_6g46260' => 'fve', 'FvH4_6g46280' => 'fve', 'FvH4_6g46380' => 'fve', 'FvH4_7g12841' => 'fve', 'FvH4_7g31431' => 'fve', 'Glyma.09G075900' => 'gma', 'Gohir.A09G096401' => 'ghi', 'Gohir.D09G096101' => 'ghi', 'Gorai.006G112800' => 'gra', 'HanXRQChr04g0121411' => 'han', 'Hund15878' => 'sun', 'Lj2A1107G68' => 'lonja', 'Lj2A630G63' => 'lonja', 'Lj2A946T25' => 'lonja', 'Lj2C714T1' => 'lonja', 'Lj2C966T3' => 'lonja', 'Lj2C966T4' => 'lonja', 'Lj4g0002979' => 'lja', 'Lsat_1_v5_gn_5_30901' => 'lsa', 'Lsat_1_v5_gn_5_31100' => 'lsa', 'Lsat_1_v5_gn_5_38600' => 'lsa', 'Lsat_1_v5_gn_6_92061' => 'lsa', 'Manes.05G071301' => 'mes', 'MD02G1008700' => 'mdo', 'MD02G1008900' => 'mdo', 'MD03G1256400' => 'mdo', 'MD04G1180900' => 'mdo', 'MD04G1181000' => 'mdo', 'MD04G1181200' => 'mdo', 'MD05G1244200' => 'mdo', 'MD05G1324200' => 'mdo', 'MD09G1201600' => 'mdo', 'MD10G1000600' => 'mdo', 'MD14G1026900' => 'mdo', 'MD14G1187900' => 'mdo', 'MD15G1017800' => 'mdo', 'MD15G1018100' => 'mdo', 'Medtr4g124160' => 'mtr', 'Migut.L01260' => 'egut', 'Nitab4.5_0000008g0440' => 'nta', 'Nitab4.5_0000207g0170' => 'nta', 'Nitab4.5_0007671g0030' => 'nta', 'Nitab4.5_0010853g0020' => 'nta', 'Oeu057656.1' => 'oeu', 'PGSC0003DMG400005638' => 'stu', 'PGSC0003DMG400005639' => 'stu', 'Phvul.009G222800' => 'pvu', 'Potri.009G132400' => 'ptr', 'Potri.009G163001' => 'ptr', 'Potri.011G000700' => 'ptr', 'Potri.011G004800' => 'ptr', 'Prupe.1G509300' => 'ppe', 'Prupe.1G509700' => 'ppe', 'Prupe.1G510400' => 'ppe', 'Prupe.1G510700' => 'ppe', 'Prupe.1G512600' => 'ppe', 'Prupe.2G073200' => 'ppe', 'Prupe.3G059500' => 'ppe', 'Prupe.3G059600' => 'ppe', 'Prupe.3G246100' => 'ppe', 'Prupe.3G265100' => 'ppe', 'Prupe.4G034700' => 'ppe', 'Prupe.4G052100' => 'ppe', 'Prupe.4G053600' => 'ppe', 'Prupe.5G068800' => 'ppe', 'Prupe.5G070600' => 'ppe', 'Prupe.6G075400' => 'ppe', 'Prupe.6G075500' => 'ppe', 'Prupe.6G076400' => 'ppe', 'Prupe.8G110700' => 'ppe', 'Psat4g020960' => 'psa', 'PSO135G0788' => 'pso', 'PSO210G6463' => 'pso', 'PSO384G0370' => 'pso', 'PSO386G0056' => 'pso', 'QL01p006048' => 'qlo', 'QL02p054283' => 'qlo', 'QL05p008000' => 'qlo', 'QL05p008212' => 'qlo', 'QL05p008950' => 'qlo', 'QL05p009042' => 'qlo', 'QL05p009518' => 'qlo', 'QL05p012589' => 'qlo', 'QL05p012608' => 'qlo', 'QL05p012650' => 'qlo', 'QL05p012667' => 'qlo', 'QL05p014501' => 'qlo', 'QL05p052800' => 'qlo', 'QL05p065010' => 'qlo', 'QL05p074156' => 'qlo', 'QL05p074160' => 'qlo', 'QL05p074174' => 'qlo', 'QL05p074178' => 'qlo', 'QL05p074214' => 'qlo', 'QL06p001050' => 'qlo', 'QL06p001056' => 'qlo', 'QL06p006093' => 'qlo', 'QL06p006111' => 'qlo', 'QL07p019784' => 'qlo', 'QL07p019801' => 'qlo', 'QL07p036110' => 'qlo', 'QL07p036134' => 'qlo', 'QL07p036147' => 'qlo', 'QL07p036156' => 'qlo', 'QL07p036300' => 'qlo', 'QL07p036320' => 'qlo', 'QL08p014547' => 'qlo', 'QL08p014551' => 'qlo', 'QL08p043319' => 'qlo', 'QL08p043324' => 'qlo', 'QL11p009094' => 'qlo', 'RcHm_v2.0_Chr1g0380481' => 'rch', 'RcHm_v2.0_Chr2g0089331' => 'rch', 'RcHm_v2.0_Chr2g0123691' => 'rch', 'RcHm_v2.0_Chr2g0151111' => 'rch', 'RcHm_v2.0_Chr2g0163011' => 'rch', 'RcHm_v2.0_Chr2g0163051' => 'rch', 'RcHm_v2.0_Chr2g0164671' => 'rch', 'RcHm_v2.0_Chr2g0164681' => 'rch', 'RcHm_v2.0_Chr2g0164721' => 'rch', 'RcHm_v2.0_Chr3g0449911' => 'rch', 'RcHm_v2.0_Chr3g0450211' => 'rch', 'RcHm_v2.0_Chr3g0457271' => 'rch', 'RcHm_v2.0_Chr5g0018111' => 'rch', 'RcHm_v2.0_Chr5g0021011' => 'rch', 'RcHm_v2.0_Chr5g0081171' => 'rch', 'RcHm_v2.0_Chr5g0081211' => 'rch', 'RcHm_v2.0_Chr6g0275871' => 'rch', 'RcHm_v2.0_Chr6g0276071' => 'rch', 'RcHm_v2.0_Chr6g0285591' => 'rch', 'RcHm_v2.0_Chr6g0291931' => 'rch', 'RcHm_v2.0_Chr6g0292091' => 'rch', 'RcHm_v2.0_Chr6g0292271' => 'rch', 'RcHm_v2.0_Chr7g0221261' => 'rch', 'Rhsim08G0219900' => 'rsi', 'Rhsim08G0220200' => 'rsi', 'Rhsim08G0237800' => 'rsi', 'Rhsim08G0238800' => 'rsi', 'Sabra09G0102700' => 'sbr', 'Sabra09G0127200' => 'sbr', 'Sabra11G0003700' => 'sbr', 'Sabra15G0014700' => 'sbr', 'Sc19g0000590' => 'sci', 'Sc19g0001870' => 'sci', 'SGA_v2.0_scaffold1G00346' => 'sas', 'SGA_v2.0_scaffold1G00575' => 'sas', 'SGA_v2.0_scaffold1G00761' => 'sas', 'SGA_v2.0_scaffold232G43501' => 'sas', 'TAR625G1137' => 'tar', 'Thecc.03G222100' => 'tca', 'TPR.G12691' => 'tpr', 'TWI34G0727' => 'twi', 'TWI36G0117' => 'twi', 'VMungo1309G0868' => 'vmu' ), 'gf_id' => 'HOM05D001729', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001729' ), 'data_identifier' => 'HOM05D001729', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001729', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '375', 'num_species' => '42' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'Ah.07g204710' => 'amhyb', 'AUR62006001' => 'cqu', 'AUR62006002' => 'cqu', 'AUR62006003' => 'cqu', 'AUR62015641' => 'cqu', 'AUR62027174' => 'cqu', 'AUR62035623' => 'cqu', 'AUR62035624' => 'cqu', 'AUR62035625' => 'cqu', 'AUR62035626' => 'cqu', 'CAN.G1110.53' => 'can', 'CANSAT80G0415' => 'cansat', 'Ca_21364_v3' => 'car', 'COL.COLO4_30693' => 'col', 'COL.COLO4_30694' => 'col', 'COL.COLO4_30695' => 'col', 'COL.COLO4_30696' => 'col', 'COL.COLO4_34020' => 'col', 'DCAR_004585' => 'dca', 'Dinv04029' => 'din', 'Dinv34857' => 'din', 'Duzib147G0011' => 'dzi', 'Duzib170G0599' => 'dzi', 'Duzib192G1051' => 'dzi', 'FAN01G0708' => 'fan', 'FAN01G0742' => 'fan', 'FAN02G0048' => 'fan', 'FAN02G0583' => 'fan', 'FAN02G0688' => 'fan', 'FAN02G1588' => 'fan', 'FAN02G2194' => 'fan', 'FAN02G2750' => 'fan', 'FAN02G3094' => 'fan', 'FAN02G3887' => 'fan', 'FAN02G3911' => 'fan', 'FAN02G3994' => 'fan', 'FAN02G4432' => 'fan', 'FAN02G4556' => 'fan', 'FAN03G1977' => 'fan', 'FAN03G2781' => 'fan', 'FAN03G2850' => 'fan', 'FAN03G3155' => 'fan', 'FAN04G2487' => 'fan', 'FAN05G0208' => 'fan', 'FAN05G0656' => 'fan', 'FAN05G0696' => 'fan', 'FAN05G0810' => 'fan', 'FAN05G1447' => 'fan', 'FAN05G2640' => 'fan', 'FAN05G2911' => 'fan', 'FAN05G3901' => 'fan', 'FAN05G4859' => 'fan', 'FAN05G4861' => 'fan', 'FAN05G4988' => 'fan', 'FAN05G5187' => 'fan', 'FAN05G5452' => 'fan', 'FAN05G5500' => 'fan', 'FAN05G5688' => 'fan', 'FAN06G0177' => 'fan', 'FAN06G0675' => 'fan', 'FAN06G1290' => 'fan', 'FAN06G2191' => 'fan', 'FAN06G2405' => 'fan', 'FAN06G3231' => 'fan', 'FAN06G3932' => 'fan', 'FAN07G0163' => 'fan', 'FAN07G0471' => 'fan', 'FAN07G1354' => 'fan', 'FAN08G0338' => 'fan', 'FAN08G1373' => 'fan', 'FAN08G2539' => 'fan', 'FAN08G2728' => 'fan', 'FAN09G0608' => 'fan', 'FAN09G1136' => 'fan', 'FAN09G1958' => 'fan', 'FAN09G2508' => 'fan', 'FAN09G2597' => 'fan', 'FAN09G2658' => 'fan', 'FAN09G2757' => 'fan', 'FAN09G2983' => 'fan', 'FAN09G3130' => 'fan', 'FAN09G3565' => 'fan', 'FAN09G3613' => 'fan', 'FAN09G4011' => 'fan', 'FAN09G4239' => 'fan', 'FAN09G4277' => 'fan', 'FAN09G4720' => 'fan', 'FAN11G0139' => 'fan', 'FAN11G1727' => 'fan', 'FAN11G2672' => 'fan', 'FAN11G2795' => 'fan', 'FAN11G3238' => 'fan', 'FAN11G3734' => 'fan', 'FAN12G0631' => 'fan', 'FAN12G2239' => 'fan', 'FAN12G2308' => 'fan', 'FAN12G2569' => 'fan', 'FAN12G2623' => 'fan', 'FAN13G3182' => 'fan', 'FAN14G0053' => 'fan', 'FAN14G0370' => 'fan', 'FAN14G0382' => 'fan', 'FAN14G0421' => 'fan', 'FAN14G0866' => 'fan', 'FAN14G1187' => 'fan', 'FAN14G1727' => 'fan', 'FAN14G1791' => 'fan', 'FAN14G2361' => 'fan', 'FAN14G2668' => 'fan', 'FAN14G2770' => 'fan', 'FAN14G2874' => 'fan', 'FAN14G3193' => 'fan', 'FAN14G3624' => 'fan', 'FAN14G3676' => 'fan', 'FAN14G3807' => 'fan', 'FAN14G4082' => 'fan', 'FAN14G4342' => 'fan', 'FAN14G4985' => 'fan', 'FAN14G5126' => 'fan', 'FAN14G5781' => 'fan', 'FAN14G5808' => 'fan', 'FAN14G5949' => 'fan', 'FAN15G0828' => 'fan', 'FAN15G1054' => 'fan', 'FAN15G2023' => 'fan', 'FAN15G2506' => 'fan', 'FAN16G0128' => 'fan', 'FAN16G0249' => 'fan', 'FAN16G0429' => 'fan', 'FAN16G1493' => 'fan', 'FAN16G2210' => 'fan', 'FAN16G2506' => 'fan', 'FAN18G1542' => 'fan', 'FAN18G4057' => 'fan', 'FAN19G0745' => 'fan', 'FAN19G1216' => 'fan', 'FAN19G1733' => 'fan', 'FAN20G0258' => 'fan', 'FAN20G1095' => 'fan', 'FAN20G1557' => 'fan', 'FAN21G0302' => 'fan', 'FAN21G0519' => 'fan', 'FAN21G0970' => 'fan', 'FAN21G1159' => 'fan', 'FAN21G1312' => 'fan', 'FAN21G1440' => 'fan', 'FAN21G1715' => 'fan', 'FAN23G1584' => 'fan', 'FAN24G0045' => 'fan', 'FAN24G0053' => 'fan', 'FAN24G1500' => 'fan', 'FAN24G1817' => 'fan', 'FAN24G2147' => 'fan', 'FAN24G2236' => 'fan', 'FAN24G2446' => 'fan', 'FAN24G2684' => 'fan', 'FAN25G0187' => 'fan', 'FAN25G0505' => 'fan', 'FAN25G0589' => 'fan', 'FAN25G3663' => 'fan', 'FAN26G1025' => 'fan', 'FAN26G2860' => 'fan', 'FAN27G1329' => 'fan', 'FAN27G3392' => 'fan', 'FvH4_1g02011' => 'fve', 'FvH4_1g06511' => 'fve', 'FvH4_2g19900' => 'fve', 'FvH4_2g19920' => 'fve', 'FvH4_2g24261' => 'fve', 'FvH4_2g24270' => 'fve', 'FvH4_2g24631' => 'fve', 'FvH4_2g30622' => 'fve', 'FvH4_3g12920' => 'fve', 'FvH4_3g30171' => 'fve', 'FvH4_3g35490' => 'fve', 'FvH4_3g43682' => 'fve', 'FvH4_3g43730' => 'fve', 'FvH4_3g43732' => 'fve', 'FvH4_3g43751' => 'fve', 'FvH4_3g43752' => 'fve', 'FvH4_3g43770' => 'fve', 'FvH4_3g44471' => 'fve', 'FvH4_3g44510' => 'fve', 'FvH4_3g44582' => 'fve', 'FvH4_4g16921' => 'fve', 'FvH4_4g17121' => 'fve', 'FvH4_4g17782' => 'fve', 'FvH4_4g17783' => 'fve', 'FvH4_4g18120' => 'fve', 'FvH4_4g31310' => 'fve', 'FvH4_4g35052' => 'fve', 'FvH4_5g30862' => 'fve', 'FvH4_6g01541' => 'fve', 'FvH4_6g02021' => 'fve', 'FvH4_6g02041' => 'fve', 'FvH4_6g02071' => 'fve', 'FvH4_6g02171' => 'fve', 'FvH4_6g03181' => 'fve', 'FvH4_6g03182' => 'fve', 'FvH4_6g03221' => 'fve', 'FvH4_6g03380' => 'fve', 'FvH4_6g05201' => 'fve', 'FvH4_6g05203' => 'fve', 'FvH4_6g20231' => 'fve', 'FvH4_6g31981' => 'fve', 'FvH4_6g32061' => 'fve', 'FvH4_6g37041' => 'fve', 'FvH4_6g37932' => 'fve', 'FvH4_6g38731' => 'fve', 'FvH4_6g39370' => 'fve', 'FvH4_6g39371' => 'fve', 'FvH4_6g40891' => 'fve', 'FvH4_6g40892' => 'fve', 'FvH4_6g43143' => 'fve', 'FvH4_6g45251' => 'fve', 'FvH4_6g45260' => 'fve', 'FvH4_6g45291' => 'fve', 'FvH4_6g45890' => 'fve', 'FvH4_6g46240' => 'fve', 'FvH4_6g46241' => 'fve', 'FvH4_6g46242' => 'fve', 'FvH4_6g46260' => 'fve', 'FvH4_6g46280' => 'fve', 'FvH4_6g46380' => 'fve', 'FvH4_7g12841' => 'fve', 'FvH4_7g31431' => 'fve', 'Glyma.09G075900' => 'gma', 'Gohir.A09G096401' => 'ghi', 'Gohir.D09G096101' => 'ghi', 'Gorai.006G112800' => 'gra', 'HanXRQChr04g0121411' => 'han', 'Hund15878' => 'sun', 'Lj2A1107G68' => 'lonja', 'Lj2A630G63' => 'lonja', 'Lj2A946T25' => 'lonja', 'Lj2C714T1' => 'lonja', 'Lj2C966T3' => 'lonja', 'Lj2C966T4' => 'lonja', 'Lj4g0002979' => 'lja', 'Lsat_1_v5_gn_5_30901' => 'lsa', 'Lsat_1_v5_gn_5_31100' => 'lsa', 'Lsat_1_v5_gn_5_38600' => 'lsa', 'Lsat_1_v5_gn_6_92061' => 'lsa', 'Manes.05G071301' => 'mes', 'MD02G1008700' => 'mdo', 'MD02G1008900' => 'mdo', 'MD03G1256400' => 'mdo', 'MD04G1180900' => 'mdo', 'MD04G1181000' => 'mdo', 'MD04G1181200' => 'mdo', 'MD05G1244200' => 'mdo', 'MD05G1324200' => 'mdo', 'MD09G1201600' => 'mdo', 'MD10G1000600' => 'mdo', 'MD14G1026900' => 'mdo', 'MD14G1187900' => 'mdo', 'MD15G1017800' => 'mdo', 'MD15G1018100' => 'mdo', 'Medtr4g124160' => 'mtr', 'Migut.L01260' => 'egut', 'Nitab4.5_0000008g0440' => 'nta', 'Nitab4.5_0000207g0170' => 'nta', 'Nitab4.5_0007671g0030' => 'nta', 'Nitab4.5_0010853g0020' => 'nta', 'Oeu057656.1' => 'oeu', 'PGSC0003DMG400005638' => 'stu', 'PGSC0003DMG400005639' => 'stu', 'Phvul.009G222800' => 'pvu', 'Potri.009G132400' => 'ptr', 'Potri.009G163001' => 'ptr', 'Potri.011G000700' => 'ptr', 'Potri.011G004800' => 'ptr', 'Prupe.1G509300' => 'ppe', 'Prupe.1G509700' => 'ppe', 'Prupe.1G510400' => 'ppe', 'Prupe.1G510700' => 'ppe', 'Prupe.1G512600' => 'ppe', 'Prupe.2G073200' => 'ppe', 'Prupe.3G059500' => 'ppe', 'Prupe.3G059600' => 'ppe', 'Prupe.3G246100' => 'ppe', 'Prupe.3G265100' => 'ppe', 'Prupe.4G034700' => 'ppe', 'Prupe.4G052100' => 'ppe', 'Prupe.4G053600' => 'ppe', 'Prupe.5G068800' => 'ppe', 'Prupe.5G070600' => 'ppe', 'Prupe.6G075400' => 'ppe', 'Prupe.6G075500' => 'ppe', 'Prupe.6G076400' => 'ppe', 'Prupe.8G110700' => 'ppe', 'Psat4g020960' => 'psa', 'PSO135G0788' => 'pso', 'PSO210G6463' => 'pso', 'PSO384G0370' => 'pso', 'PSO386G0056' => 'pso', 'QL01p006048' => 'qlo', 'QL02p054283' => 'qlo', 'QL05p008000' => 'qlo', 'QL05p008212' => 'qlo', 'QL05p008950' => 'qlo', 'QL05p009042' => 'qlo', 'QL05p009518' => 'qlo', 'QL05p012589' => 'qlo', 'QL05p012608' => 'qlo', 'QL05p012650' => 'qlo', 'QL05p012667' => 'qlo', 'QL05p014501' => 'qlo', 'QL05p052800' => 'qlo', 'QL05p065010' => 'qlo', 'QL05p074156' => 'qlo', 'QL05p074160' => 'qlo', 'QL05p074174' => 'qlo', 'QL05p074178' => 'qlo', 'QL05p074214' => 'qlo', 'QL06p001050' => 'qlo', 'QL06p001056' => 'qlo', 'QL06p006093' => 'qlo', 'QL06p006111' => 'qlo', 'QL07p019784' => 'qlo', 'QL07p019801' => 'qlo', 'QL07p036110' => 'qlo', 'QL07p036134' => 'qlo', 'QL07p036147' => 'qlo', 'QL07p036156' => 'qlo', 'QL07p036300' => 'qlo', 'QL07p036320' => 'qlo', 'QL08p014547' => 'qlo', 'QL08p014551' => 'qlo', 'QL08p043319' => 'qlo', 'QL08p043324' => 'qlo', 'QL11p009094' => 'qlo', 'RcHm_v2.0_Chr1g0380481' => 'rch', 'RcHm_v2.0_Chr2g0089331' => 'rch', 'RcHm_v2.0_Chr2g0123691' => 'rch', 'RcHm_v2.0_Chr2g0151111' => 'rch', 'RcHm_v2.0_Chr2g0163011' => 'rch', 'RcHm_v2.0_Chr2g0163051' => 'rch', 'RcHm_v2.0_Chr2g0164671' => 'rch', 'RcHm_v2.0_Chr2g0164681' => 'rch', 'RcHm_v2.0_Chr2g0164721' => 'rch', 'RcHm_v2.0_Chr3g0449911' => 'rch', 'RcHm_v2.0_Chr3g0450211' => 'rch', 'RcHm_v2.0_Chr3g0457271' => 'rch', 'RcHm_v2.0_Chr5g0018111' => 'rch', 'RcHm_v2.0_Chr5g0021011' => 'rch', 'RcHm_v2.0_Chr5g0081171' => 'rch', 'RcHm_v2.0_Chr5g0081211' => 'rch', 'RcHm_v2.0_Chr6g0275871' => 'rch', 'RcHm_v2.0_Chr6g0276071' => 'rch', 'RcHm_v2.0_Chr6g0285591' => 'rch', 'RcHm_v2.0_Chr6g0291931' => 'rch', 'RcHm_v2.0_Chr6g0292091' => 'rch', 'RcHm_v2.0_Chr6g0292271' => 'rch', 'RcHm_v2.0_Chr7g0221261' => 'rch', 'Rhsim08G0219900' => 'rsi', 'Rhsim08G0220200' => 'rsi', 'Rhsim08G0237800' => 'rsi', 'Rhsim08G0238800' => 'rsi', 'Sabra09G0102700' => 'sbr', 'Sabra09G0127200' => 'sbr', 'Sabra11G0003700' => 'sbr', 'Sabra15G0014700' => 'sbr', 'Sc19g0000590' => 'sci', 'Sc19g0001870' => 'sci', 'SGA_v2.0_scaffold1G00346' => 'sas', 'SGA_v2.0_scaffold1G00575' => 'sas', 'SGA_v2.0_scaffold1G00761' => 'sas', 'SGA_v2.0_scaffold232G43501' => 'sas', 'TAR625G1137' => 'tar', 'Thecc.03G222100' => 'tca', 'TPR.G12691' => 'tpr', 'TWI34G0727' => 'twi', 'TWI36G0117' => 'twi', 'VMungo1309G0868' => 'vmu' ) $gf_id = 'HOM05D001729' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001729' ) $data_identifier = 'HOM05D001729' $data_type = 'gf_id' $species_gene_counts = array( 'amhyb' => (int) 1, 'cqu' => (int) 9, 'can' => (int) 1, 'cansat' => (int) 1, 'car' => (int) 1, 'col' => (int) 5, 'dca' => (int) 1, 'din' => (int) 2, 'dzi' => (int) 3, 'fan' => (int) 140, 'fve' => (int) 62, 'gma' => (int) 1, 'ghi' => (int) 2, 'gra' => (int) 1, 'han' => (int) 1, 'sun' => (int) 1, 'lonja' => (int) 6, 'lja' => (int) 1, 'lsa' => (int) 4, 'mes' => (int) 1, 'mdo' => (int) 14, 'mtr' => (int) 1, 'egut' => (int) 1, 'nta' => (int) 4, 'oeu' => (int) 1, 'stu' => (int) 2, 'pvu' => (int) 1, 'ptr' => (int) 4, 'ppe' => (int) 19, 'psa' => (int) 1, 'pso' => (int) 4, 'qlo' => (int) 36, 'rch' => (int) 23, 'rsi' => (int) 4, 'sbr' => (int) 4, 'sci' => (int) 2, 'sas' => (int) 4, 'tar' => (int) 1, 'tca' => (int) 1, 'tpr' => (int) 1, 'twi' => (int) 2, 'vmu' => (int) 1 ) $gf_gene_species = 'vmu' $gf_gene_id = 'VMungo1309G0868' $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' => 'HOM05D001729', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '375', 'num_species' => '42' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'Ah.07g204710' => 'amhyb', 'AUR62006001' => 'cqu', 'AUR62006002' => 'cqu', 'AUR62006003' => 'cqu', 'AUR62015641' => 'cqu', 'AUR62027174' => 'cqu', 'AUR62035623' => 'cqu', 'AUR62035624' => 'cqu', 'AUR62035625' => 'cqu', 'AUR62035626' => 'cqu', 'CAN.G1110.53' => 'can', 'CANSAT80G0415' => 'cansat', 'Ca_21364_v3' => 'car', 'COL.COLO4_30693' => 'col', 'COL.COLO4_30694' => 'col', 'COL.COLO4_30695' => 'col', 'COL.COLO4_30696' => 'col', 'COL.COLO4_34020' => 'col', 'DCAR_004585' => 'dca', 'Dinv04029' => 'din', 'Dinv34857' => 'din', 'Duzib147G0011' => 'dzi', 'Duzib170G0599' => 'dzi', 'Duzib192G1051' => 'dzi', 'FAN01G0708' => 'fan', 'FAN01G0742' => 'fan', 'FAN02G0048' => 'fan', 'FAN02G0583' => 'fan', 'FAN02G0688' => 'fan', 'FAN02G1588' => 'fan', 'FAN02G2194' => 'fan', 'FAN02G2750' => 'fan', 'FAN02G3094' => 'fan', 'FAN02G3887' => 'fan', 'FAN02G3911' => 'fan', 'FAN02G3994' => 'fan', 'FAN02G4432' => 'fan', 'FAN02G4556' => 'fan', 'FAN03G1977' => 'fan', 'FAN03G2781' => 'fan', 'FAN03G2850' => 'fan', 'FAN03G3155' => 'fan', 'FAN04G2487' => 'fan', 'FAN05G0208' => 'fan', 'FAN05G0656' => 'fan', 'FAN05G0696' => 'fan', 'FAN05G0810' => 'fan', 'FAN05G1447' => 'fan', 'FAN05G2640' => 'fan', 'FAN05G2911' => 'fan', 'FAN05G3901' => 'fan', 'FAN05G4859' => 'fan', 'FAN05G4861' => 'fan', 'FAN05G4988' => 'fan', 'FAN05G5187' => 'fan', 'FAN05G5452' => 'fan', 'FAN05G5500' => 'fan', 'FAN05G5688' => 'fan', 'FAN06G0177' => 'fan', 'FAN06G0675' => 'fan', 'FAN06G1290' => 'fan', 'FAN06G2191' => 'fan', 'FAN06G2405' => 'fan', 'FAN06G3231' => 'fan', 'FAN06G3932' => 'fan', 'FAN07G0163' => 'fan', 'FAN07G0471' => 'fan', 'FAN07G1354' => 'fan', 'FAN08G0338' => 'fan', 'FAN08G1373' => 'fan', 'FAN08G2539' => 'fan', 'FAN08G2728' => 'fan', 'FAN09G0608' => 'fan', 'FAN09G1136' => 'fan', 'FAN09G1958' => 'fan', 'FAN09G2508' => 'fan', 'FAN09G2597' => 'fan', 'FAN09G2658' => 'fan', 'FAN09G2757' => 'fan', 'FAN09G2983' => 'fan', 'FAN09G3130' => 'fan', 'FAN09G3565' => 'fan', 'FAN09G3613' => 'fan', 'FAN09G4011' => 'fan', 'FAN09G4239' => 'fan', 'FAN09G4277' => 'fan', 'FAN09G4720' => 'fan', 'FAN11G0139' => 'fan', 'FAN11G1727' => 'fan', 'FAN11G2672' => 'fan', 'FAN11G2795' => 'fan', 'FAN11G3238' => 'fan', 'FAN11G3734' => 'fan', 'FAN12G0631' => 'fan', 'FAN12G2239' => 'fan', 'FAN12G2308' => 'fan', 'FAN12G2569' => 'fan', 'FAN12G2623' => 'fan', 'FAN13G3182' => 'fan', 'FAN14G0053' => 'fan', 'FAN14G0370' => 'fan', 'FAN14G0382' => 'fan', 'FAN14G0421' => 'fan', 'FAN14G0866' => 'fan', 'FAN14G1187' => 'fan', 'FAN14G1727' => 'fan', 'FAN14G1791' => 'fan', 'FAN14G2361' => 'fan', 'FAN14G2668' => 'fan', 'FAN14G2770' => 'fan', 'FAN14G2874' => 'fan', 'FAN14G3193' => 'fan', 'FAN14G3624' => 'fan', 'FAN14G3676' => 'fan', 'FAN14G3807' => 'fan', 'FAN14G4082' => 'fan', 'FAN14G4342' => 'fan', 'FAN14G4985' => 'fan', 'FAN14G5126' => 'fan', 'FAN14G5781' => 'fan', 'FAN14G5808' => 'fan', 'FAN14G5949' => 'fan', 'FAN15G0828' => 'fan', 'FAN15G1054' => 'fan', 'FAN15G2023' => 'fan', 'FAN15G2506' => 'fan', 'FAN16G0128' => 'fan', 'FAN16G0249' => 'fan', 'FAN16G0429' => 'fan', 'FAN16G1493' => 'fan', 'FAN16G2210' => 'fan', 'FAN16G2506' => 'fan', 'FAN18G1542' => 'fan', 'FAN18G4057' => 'fan', 'FAN19G0745' => 'fan', 'FAN19G1216' => 'fan', 'FAN19G1733' => 'fan', 'FAN20G0258' => 'fan', 'FAN20G1095' => 'fan', 'FAN20G1557' => 'fan', 'FAN21G0302' => 'fan', 'FAN21G0519' => 'fan', 'FAN21G0970' => 'fan', 'FAN21G1159' => 'fan', 'FAN21G1312' => 'fan', 'FAN21G1440' => 'fan', 'FAN21G1715' => 'fan', 'FAN23G1584' => 'fan', 'FAN24G0045' => 'fan', 'FAN24G0053' => 'fan', 'FAN24G1500' => 'fan', 'FAN24G1817' => 'fan', 'FAN24G2147' => 'fan', 'FAN24G2236' => 'fan', 'FAN24G2446' => 'fan', 'FAN24G2684' => 'fan', 'FAN25G0187' => 'fan', 'FAN25G0505' => 'fan', 'FAN25G0589' => 'fan', 'FAN25G3663' => 'fan', 'FAN26G1025' => 'fan', 'FAN26G2860' => 'fan', 'FAN27G1329' => 'fan', 'FAN27G3392' => 'fan', 'FvH4_1g02011' => 'fve', 'FvH4_1g06511' => 'fve', 'FvH4_2g19900' => 'fve', 'FvH4_2g19920' => 'fve', 'FvH4_2g24261' => 'fve', 'FvH4_2g24270' => 'fve', 'FvH4_2g24631' => 'fve', 'FvH4_2g30622' => 'fve', 'FvH4_3g12920' => 'fve', 'FvH4_3g30171' => 'fve', 'FvH4_3g35490' => 'fve', 'FvH4_3g43682' => 'fve', 'FvH4_3g43730' => 'fve', 'FvH4_3g43732' => 'fve', 'FvH4_3g43751' => 'fve', 'FvH4_3g43752' => 'fve', 'FvH4_3g43770' => 'fve', 'FvH4_3g44471' => 'fve', 'FvH4_3g44510' => 'fve', 'FvH4_3g44582' => 'fve', 'FvH4_4g16921' => 'fve', 'FvH4_4g17121' => 'fve', 'FvH4_4g17782' => 'fve', 'FvH4_4g17783' => 'fve', 'FvH4_4g18120' => 'fve', 'FvH4_4g31310' => 'fve', 'FvH4_4g35052' => 'fve', 'FvH4_5g30862' => 'fve', 'FvH4_6g01541' => 'fve', 'FvH4_6g02021' => 'fve', 'FvH4_6g02041' => 'fve', 'FvH4_6g02071' => 'fve', 'FvH4_6g02171' => 'fve', 'FvH4_6g03181' => 'fve', 'FvH4_6g03182' => 'fve', 'FvH4_6g03221' => 'fve', 'FvH4_6g03380' => 'fve', 'FvH4_6g05201' => 'fve', 'FvH4_6g05203' => 'fve', 'FvH4_6g20231' => 'fve', 'FvH4_6g31981' => 'fve', 'FvH4_6g32061' => 'fve', 'FvH4_6g37041' => 'fve', 'FvH4_6g37932' => 'fve', 'FvH4_6g38731' => 'fve', 'FvH4_6g39370' => 'fve', 'FvH4_6g39371' => 'fve', 'FvH4_6g40891' => 'fve', 'FvH4_6g40892' => 'fve', 'FvH4_6g43143' => 'fve', 'FvH4_6g45251' => 'fve', 'FvH4_6g45260' => 'fve', 'FvH4_6g45291' => 'fve', 'FvH4_6g45890' => 'fve', 'FvH4_6g46240' => 'fve', 'FvH4_6g46241' => 'fve', 'FvH4_6g46242' => 'fve', 'FvH4_6g46260' => 'fve', 'FvH4_6g46280' => 'fve', 'FvH4_6g46380' => 'fve', 'FvH4_7g12841' => 'fve', 'FvH4_7g31431' => 'fve', 'Glyma.09G075900' => 'gma', 'Gohir.A09G096401' => 'ghi', 'Gohir.D09G096101' => 'ghi', 'Gorai.006G112800' => 'gra', 'HanXRQChr04g0121411' => 'han', 'Hund15878' => 'sun', 'Lj2A1107G68' => 'lonja', 'Lj2A630G63' => 'lonja', 'Lj2A946T25' => 'lonja', 'Lj2C714T1' => 'lonja', 'Lj2C966T3' => 'lonja', 'Lj2C966T4' => 'lonja', 'Lj4g0002979' => 'lja', 'Lsat_1_v5_gn_5_30901' => 'lsa', 'Lsat_1_v5_gn_5_31100' => 'lsa', 'Lsat_1_v5_gn_5_38600' => 'lsa', 'Lsat_1_v5_gn_6_92061' => 'lsa', 'Manes.05G071301' => 'mes', 'MD02G1008700' => 'mdo', 'MD02G1008900' => 'mdo', 'MD03G1256400' => 'mdo', 'MD04G1180900' => 'mdo', 'MD04G1181000' => 'mdo', 'MD04G1181200' => 'mdo', 'MD05G1244200' => 'mdo', 'MD05G1324200' => 'mdo', 'MD09G1201600' => 'mdo', 'MD10G1000600' => 'mdo', 'MD14G1026900' => 'mdo', 'MD14G1187900' => 'mdo', 'MD15G1017800' => 'mdo', 'MD15G1018100' => 'mdo', 'Medtr4g124160' => 'mtr', 'Migut.L01260' => 'egut', 'Nitab4.5_0000008g0440' => 'nta', 'Nitab4.5_0000207g0170' => 'nta', 'Nitab4.5_0007671g0030' => 'nta', 'Nitab4.5_0010853g0020' => 'nta', 'Oeu057656.1' => 'oeu', 'PGSC0003DMG400005638' => 'stu', 'PGSC0003DMG400005639' => 'stu', 'Phvul.009G222800' => 'pvu', 'Potri.009G132400' => 'ptr', 'Potri.009G163001' => 'ptr', 'Potri.011G000700' => 'ptr', 'Potri.011G004800' => 'ptr', 'Prupe.1G509300' => 'ppe', 'Prupe.1G509700' => 'ppe', 'Prupe.1G510400' => 'ppe', 'Prupe.1G510700' => 'ppe', 'Prupe.1G512600' => 'ppe', 'Prupe.2G073200' => 'ppe', 'Prupe.3G059500' => 'ppe', 'Prupe.3G059600' => 'ppe', 'Prupe.3G246100' => 'ppe', 'Prupe.3G265100' => 'ppe', 'Prupe.4G034700' => 'ppe', 'Prupe.4G052100' => 'ppe', 'Prupe.4G053600' => 'ppe', 'Prupe.5G068800' => 'ppe', 'Prupe.5G070600' => 'ppe', 'Prupe.6G075400' => 'ppe', 'Prupe.6G075500' => 'ppe', 'Prupe.6G076400' => 'ppe', 'Prupe.8G110700' => 'ppe', 'Psat4g020960' => 'psa', 'PSO135G0788' => 'pso', 'PSO210G6463' => 'pso', 'PSO384G0370' => 'pso', 'PSO386G0056' => 'pso', 'QL01p006048' => 'qlo', 'QL02p054283' => 'qlo', 'QL05p008000' => 'qlo', 'QL05p008212' => 'qlo', 'QL05p008950' => 'qlo', 'QL05p009042' => 'qlo', 'QL05p009518' => 'qlo', 'QL05p012589' => 'qlo', 'QL05p012608' => 'qlo', 'QL05p012650' => 'qlo', 'QL05p012667' => 'qlo', 'QL05p014501' => 'qlo', 'QL05p052800' => 'qlo', 'QL05p065010' => 'qlo', 'QL05p074156' => 'qlo', 'QL05p074160' => 'qlo', 'QL05p074174' => 'qlo', 'QL05p074178' => 'qlo', 'QL05p074214' => 'qlo', 'QL06p001050' => 'qlo', 'QL06p001056' => 'qlo', 'QL06p006093' => 'qlo', 'QL06p006111' => 'qlo', 'QL07p019784' => 'qlo', 'QL07p019801' => 'qlo', 'QL07p036110' => 'qlo', 'QL07p036134' => 'qlo', 'QL07p036147' => 'qlo', 'QL07p036156' => 'qlo', 'QL07p036300' => 'qlo', 'QL07p036320' => 'qlo', 'QL08p014547' => 'qlo', 'QL08p014551' => 'qlo', 'QL08p043319' => 'qlo', 'QL08p043324' => 'qlo', 'QL11p009094' => 'qlo', 'RcHm_v2.0_Chr1g0380481' => 'rch', 'RcHm_v2.0_Chr2g0089331' => 'rch', 'RcHm_v2.0_Chr2g0123691' => 'rch', 'RcHm_v2.0_Chr2g0151111' => 'rch', 'RcHm_v2.0_Chr2g0163011' => 'rch', 'RcHm_v2.0_Chr2g0163051' => 'rch', 'RcHm_v2.0_Chr2g0164671' => 'rch', 'RcHm_v2.0_Chr2g0164681' => 'rch', 'RcHm_v2.0_Chr2g0164721' => 'rch', 'RcHm_v2.0_Chr3g0449911' => 'rch', 'RcHm_v2.0_Chr3g0450211' => 'rch', 'RcHm_v2.0_Chr3g0457271' => 'rch', 'RcHm_v2.0_Chr5g0018111' => 'rch', 'RcHm_v2.0_Chr5g0021011' => 'rch', 'RcHm_v2.0_Chr5g0081171' => 'rch', 'RcHm_v2.0_Chr5g0081211' => 'rch', 'RcHm_v2.0_Chr6g0275871' => 'rch', 'RcHm_v2.0_Chr6g0276071' => 'rch', 'RcHm_v2.0_Chr6g0285591' => 'rch', 'RcHm_v2.0_Chr6g0291931' => 'rch', 'RcHm_v2.0_Chr6g0292091' => 'rch', 'RcHm_v2.0_Chr6g0292271' => 'rch', 'RcHm_v2.0_Chr7g0221261' => 'rch', 'Rhsim08G0219900' => 'rsi', 'Rhsim08G0220200' => 'rsi', 'Rhsim08G0237800' => 'rsi', 'Rhsim08G0238800' => 'rsi', 'Sabra09G0102700' => 'sbr', 'Sabra09G0127200' => 'sbr', 'Sabra11G0003700' => 'sbr', 'Sabra15G0014700' => 'sbr', 'Sc19g0000590' => 'sci', 'Sc19g0001870' => 'sci', 'SGA_v2.0_scaffold1G00346' => 'sas', 'SGA_v2.0_scaffold1G00575' => 'sas', 'SGA_v2.0_scaffold1G00761' => 'sas', 'SGA_v2.0_scaffold232G43501' => 'sas', 'TAR625G1137' => 'tar', 'Thecc.03G222100' => 'tca', 'TPR.G12691' => 'tpr', 'TWI34G0727' => 'twi', 'TWI36G0117' => 'twi', 'VMungo1309G0868' => 'vmu' ), 'gf_id' => 'HOM05D001729', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001729' ), 'data_identifier' => 'HOM05D001729', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001729', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '375', 'num_species' => '42' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'Ah.07g204710' => 'amhyb', 'AUR62006001' => 'cqu', 'AUR62006002' => 'cqu', 'AUR62006003' => 'cqu', 'AUR62015641' => 'cqu', 'AUR62027174' => 'cqu', 'AUR62035623' => 'cqu', 'AUR62035624' => 'cqu', 'AUR62035625' => 'cqu', 'AUR62035626' => 'cqu', 'CAN.G1110.53' => 'can', 'CANSAT80G0415' => 'cansat', 'Ca_21364_v3' => 'car', 'COL.COLO4_30693' => 'col', 'COL.COLO4_30694' => 'col', 'COL.COLO4_30695' => 'col', 'COL.COLO4_30696' => 'col', 'COL.COLO4_34020' => 'col', 'DCAR_004585' => 'dca', 'Dinv04029' => 'din', 'Dinv34857' => 'din', 'Duzib147G0011' => 'dzi', 'Duzib170G0599' => 'dzi', 'Duzib192G1051' => 'dzi', 'FAN01G0708' => 'fan', 'FAN01G0742' => 'fan', 'FAN02G0048' => 'fan', 'FAN02G0583' => 'fan', 'FAN02G0688' => 'fan', 'FAN02G1588' => 'fan', 'FAN02G2194' => 'fan', 'FAN02G2750' => 'fan', 'FAN02G3094' => 'fan', 'FAN02G3887' => 'fan', 'FAN02G3911' => 'fan', 'FAN02G3994' => 'fan', 'FAN02G4432' => 'fan', 'FAN02G4556' => 'fan', 'FAN03G1977' => 'fan', 'FAN03G2781' => 'fan', 'FAN03G2850' => 'fan', 'FAN03G3155' => 'fan', 'FAN04G2487' => 'fan', 'FAN05G0208' => 'fan', 'FAN05G0656' => 'fan', 'FAN05G0696' => 'fan', 'FAN05G0810' => 'fan', 'FAN05G1447' => 'fan', 'FAN05G2640' => 'fan', 'FAN05G2911' => 'fan', 'FAN05G3901' => 'fan', 'FAN05G4859' => 'fan', 'FAN05G4861' => 'fan', 'FAN05G4988' => 'fan', 'FAN05G5187' => 'fan', 'FAN05G5452' => 'fan', 'FAN05G5500' => 'fan', 'FAN05G5688' => 'fan', 'FAN06G0177' => 'fan', 'FAN06G0675' => 'fan', 'FAN06G1290' => 'fan', 'FAN06G2191' => 'fan', 'FAN06G2405' => 'fan', 'FAN06G3231' => 'fan', 'FAN06G3932' => 'fan', 'FAN07G0163' => 'fan', 'FAN07G0471' => 'fan', 'FAN07G1354' => 'fan', 'FAN08G0338' => 'fan', 'FAN08G1373' => 'fan', 'FAN08G2539' => 'fan', 'FAN08G2728' => 'fan', 'FAN09G0608' => 'fan', 'FAN09G1136' => 'fan', 'FAN09G1958' => 'fan', 'FAN09G2508' => 'fan', 'FAN09G2597' => 'fan', 'FAN09G2658' => 'fan', 'FAN09G2757' => 'fan', 'FAN09G2983' => 'fan', 'FAN09G3130' => 'fan', 'FAN09G3565' => 'fan', 'FAN09G3613' => 'fan', 'FAN09G4011' => 'fan', 'FAN09G4239' => 'fan', 'FAN09G4277' => 'fan', 'FAN09G4720' => 'fan', 'FAN11G0139' => 'fan', 'FAN11G1727' => 'fan', 'FAN11G2672' => 'fan', 'FAN11G2795' => 'fan', 'FAN11G3238' => 'fan', 'FAN11G3734' => 'fan', 'FAN12G0631' => 'fan', 'FAN12G2239' => 'fan', 'FAN12G2308' => 'fan', 'FAN12G2569' => 'fan', 'FAN12G2623' => 'fan', 'FAN13G3182' => 'fan', 'FAN14G0053' => 'fan', 'FAN14G0370' => 'fan', 'FAN14G0382' => 'fan', 'FAN14G0421' => 'fan', 'FAN14G0866' => 'fan', 'FAN14G1187' => 'fan', 'FAN14G1727' => 'fan', 'FAN14G1791' => 'fan', 'FAN14G2361' => 'fan', 'FAN14G2668' => 'fan', 'FAN14G2770' => 'fan', 'FAN14G2874' => 'fan', 'FAN14G3193' => 'fan', 'FAN14G3624' => 'fan', 'FAN14G3676' => 'fan', 'FAN14G3807' => 'fan', 'FAN14G4082' => 'fan', 'FAN14G4342' => 'fan', 'FAN14G4985' => 'fan', 'FAN14G5126' => 'fan', 'FAN14G5781' => 'fan', 'FAN14G5808' => 'fan', 'FAN14G5949' => 'fan', 'FAN15G0828' => 'fan', 'FAN15G1054' => 'fan', 'FAN15G2023' => 'fan', 'FAN15G2506' => 'fan', 'FAN16G0128' => 'fan', 'FAN16G0249' => 'fan', 'FAN16G0429' => 'fan', 'FAN16G1493' => 'fan', 'FAN16G2210' => 'fan', 'FAN16G2506' => 'fan', 'FAN18G1542' => 'fan', 'FAN18G4057' => 'fan', 'FAN19G0745' => 'fan', 'FAN19G1216' => 'fan', 'FAN19G1733' => 'fan', 'FAN20G0258' => 'fan', 'FAN20G1095' => 'fan', 'FAN20G1557' => 'fan', 'FAN21G0302' => 'fan', 'FAN21G0519' => 'fan', 'FAN21G0970' => 'fan', 'FAN21G1159' => 'fan', 'FAN21G1312' => 'fan', 'FAN21G1440' => 'fan', 'FAN21G1715' => 'fan', 'FAN23G1584' => 'fan', 'FAN24G0045' => 'fan', 'FAN24G0053' => 'fan', 'FAN24G1500' => 'fan', 'FAN24G1817' => 'fan', 'FAN24G2147' => 'fan', 'FAN24G2236' => 'fan', 'FAN24G2446' => 'fan', 'FAN24G2684' => 'fan', 'FAN25G0187' => 'fan', 'FAN25G0505' => 'fan', 'FAN25G0589' => 'fan', 'FAN25G3663' => 'fan', 'FAN26G1025' => 'fan', 'FAN26G2860' => 'fan', 'FAN27G1329' => 'fan', 'FAN27G3392' => 'fan', 'FvH4_1g02011' => 'fve', 'FvH4_1g06511' => 'fve', 'FvH4_2g19900' => 'fve', 'FvH4_2g19920' => 'fve', 'FvH4_2g24261' => 'fve', 'FvH4_2g24270' => 'fve', 'FvH4_2g24631' => 'fve', 'FvH4_2g30622' => 'fve', 'FvH4_3g12920' => 'fve', 'FvH4_3g30171' => 'fve', 'FvH4_3g35490' => 'fve', 'FvH4_3g43682' => 'fve', 'FvH4_3g43730' => 'fve', 'FvH4_3g43732' => 'fve', 'FvH4_3g43751' => 'fve', 'FvH4_3g43752' => 'fve', 'FvH4_3g43770' => 'fve', 'FvH4_3g44471' => 'fve', 'FvH4_3g44510' => 'fve', 'FvH4_3g44582' => 'fve', 'FvH4_4g16921' => 'fve', 'FvH4_4g17121' => 'fve', 'FvH4_4g17782' => 'fve', 'FvH4_4g17783' => 'fve', 'FvH4_4g18120' => 'fve', 'FvH4_4g31310' => 'fve', 'FvH4_4g35052' => 'fve', 'FvH4_5g30862' => 'fve', 'FvH4_6g01541' => 'fve', 'FvH4_6g02021' => 'fve', 'FvH4_6g02041' => 'fve', 'FvH4_6g02071' => 'fve', 'FvH4_6g02171' => 'fve', 'FvH4_6g03181' => 'fve', 'FvH4_6g03182' => 'fve', 'FvH4_6g03221' => 'fve', 'FvH4_6g03380' => 'fve', 'FvH4_6g05201' => 'fve', 'FvH4_6g05203' => 'fve', 'FvH4_6g20231' => 'fve', 'FvH4_6g31981' => 'fve', 'FvH4_6g32061' => 'fve', 'FvH4_6g37041' => 'fve', 'FvH4_6g37932' => 'fve', 'FvH4_6g38731' => 'fve', 'FvH4_6g39370' => 'fve', 'FvH4_6g39371' => 'fve', 'FvH4_6g40891' => 'fve', 'FvH4_6g40892' => 'fve', 'FvH4_6g43143' => 'fve', 'FvH4_6g45251' => 'fve', 'FvH4_6g45260' => 'fve', 'FvH4_6g45291' => 'fve', 'FvH4_6g45890' => 'fve', 'FvH4_6g46240' => 'fve', 'FvH4_6g46241' => 'fve', 'FvH4_6g46242' => 'fve', 'FvH4_6g46260' => 'fve', 'FvH4_6g46280' => 'fve', 'FvH4_6g46380' => 'fve', 'FvH4_7g12841' => 'fve', 'FvH4_7g31431' => 'fve', 'Glyma.09G075900' => 'gma', 'Gohir.A09G096401' => 'ghi', 'Gohir.D09G096101' => 'ghi', 'Gorai.006G112800' => 'gra', 'HanXRQChr04g0121411' => 'han', 'Hund15878' => 'sun', 'Lj2A1107G68' => 'lonja', 'Lj2A630G63' => 'lonja', 'Lj2A946T25' => 'lonja', 'Lj2C714T1' => 'lonja', 'Lj2C966T3' => 'lonja', 'Lj2C966T4' => 'lonja', 'Lj4g0002979' => 'lja', 'Lsat_1_v5_gn_5_30901' => 'lsa', 'Lsat_1_v5_gn_5_31100' => 'lsa', 'Lsat_1_v5_gn_5_38600' => 'lsa', 'Lsat_1_v5_gn_6_92061' => 'lsa', 'Manes.05G071301' => 'mes', 'MD02G1008700' => 'mdo', 'MD02G1008900' => 'mdo', 'MD03G1256400' => 'mdo', 'MD04G1180900' => 'mdo', 'MD04G1181000' => 'mdo', 'MD04G1181200' => 'mdo', 'MD05G1244200' => 'mdo', 'MD05G1324200' => 'mdo', 'MD09G1201600' => 'mdo', 'MD10G1000600' => 'mdo', 'MD14G1026900' => 'mdo', 'MD14G1187900' => 'mdo', 'MD15G1017800' => 'mdo', 'MD15G1018100' => 'mdo', 'Medtr4g124160' => 'mtr', 'Migut.L01260' => 'egut', 'Nitab4.5_0000008g0440' => 'nta', 'Nitab4.5_0000207g0170' => 'nta', 'Nitab4.5_0007671g0030' => 'nta', 'Nitab4.5_0010853g0020' => 'nta', 'Oeu057656.1' => 'oeu', 'PGSC0003DMG400005638' => 'stu', 'PGSC0003DMG400005639' => 'stu', 'Phvul.009G222800' => 'pvu', 'Potri.009G132400' => 'ptr', 'Potri.009G163001' => 'ptr', 'Potri.011G000700' => 'ptr', 'Potri.011G004800' => 'ptr', 'Prupe.1G509300' => 'ppe', 'Prupe.1G509700' => 'ppe', 'Prupe.1G510400' => 'ppe', 'Prupe.1G510700' => 'ppe', 'Prupe.1G512600' => 'ppe', 'Prupe.2G073200' => 'ppe', 'Prupe.3G059500' => 'ppe', 'Prupe.3G059600' => 'ppe', 'Prupe.3G246100' => 'ppe', 'Prupe.3G265100' => 'ppe', 'Prupe.4G034700' => 'ppe', 'Prupe.4G052100' => 'ppe', 'Prupe.4G053600' => 'ppe', 'Prupe.5G068800' => 'ppe', 'Prupe.5G070600' => 'ppe', 'Prupe.6G075400' => 'ppe', 'Prupe.6G075500' => 'ppe', 'Prupe.6G076400' => 'ppe', 'Prupe.8G110700' => 'ppe', 'Psat4g020960' => 'psa', 'PSO135G0788' => 'pso', 'PSO210G6463' => 'pso', 'PSO384G0370' => 'pso', 'PSO386G0056' => 'pso', 'QL01p006048' => 'qlo', 'QL02p054283' => 'qlo', 'QL05p008000' => 'qlo', 'QL05p008212' => 'qlo', 'QL05p008950' => 'qlo', 'QL05p009042' => 'qlo', 'QL05p009518' => 'qlo', 'QL05p012589' => 'qlo', 'QL05p012608' => 'qlo', 'QL05p012650' => 'qlo', 'QL05p012667' => 'qlo', 'QL05p014501' => 'qlo', 'QL05p052800' => 'qlo', 'QL05p065010' => 'qlo', 'QL05p074156' => 'qlo', 'QL05p074160' => 'qlo', 'QL05p074174' => 'qlo', 'QL05p074178' => 'qlo', 'QL05p074214' => 'qlo', 'QL06p001050' => 'qlo', 'QL06p001056' => 'qlo', 'QL06p006093' => 'qlo', 'QL06p006111' => 'qlo', 'QL07p019784' => 'qlo', 'QL07p019801' => 'qlo', 'QL07p036110' => 'qlo', 'QL07p036134' => 'qlo', 'QL07p036147' => 'qlo', 'QL07p036156' => 'qlo', 'QL07p036300' => 'qlo', 'QL07p036320' => 'qlo', 'QL08p014547' => 'qlo', 'QL08p014551' => 'qlo', 'QL08p043319' => 'qlo', 'QL08p043324' => 'qlo', 'QL11p009094' => 'qlo', 'RcHm_v2.0_Chr1g0380481' => 'rch', 'RcHm_v2.0_Chr2g0089331' => 'rch', 'RcHm_v2.0_Chr2g0123691' => 'rch', 'RcHm_v2.0_Chr2g0151111' => 'rch', 'RcHm_v2.0_Chr2g0163011' => 'rch', 'RcHm_v2.0_Chr2g0163051' => 'rch', 'RcHm_v2.0_Chr2g0164671' => 'rch', 'RcHm_v2.0_Chr2g0164681' => 'rch', 'RcHm_v2.0_Chr2g0164721' => 'rch', 'RcHm_v2.0_Chr3g0449911' => 'rch', 'RcHm_v2.0_Chr3g0450211' => 'rch', 'RcHm_v2.0_Chr3g0457271' => 'rch', 'RcHm_v2.0_Chr5g0018111' => 'rch', 'RcHm_v2.0_Chr5g0021011' => 'rch', 'RcHm_v2.0_Chr5g0081171' => 'rch', 'RcHm_v2.0_Chr5g0081211' => 'rch', 'RcHm_v2.0_Chr6g0275871' => 'rch', 'RcHm_v2.0_Chr6g0276071' => 'rch', 'RcHm_v2.0_Chr6g0285591' => 'rch', 'RcHm_v2.0_Chr6g0291931' => 'rch', 'RcHm_v2.0_Chr6g0292091' => 'rch', 'RcHm_v2.0_Chr6g0292271' => 'rch', 'RcHm_v2.0_Chr7g0221261' => 'rch', 'Rhsim08G0219900' => 'rsi', 'Rhsim08G0220200' => 'rsi', 'Rhsim08G0237800' => 'rsi', 'Rhsim08G0238800' => 'rsi', 'Sabra09G0102700' => 'sbr', 'Sabra09G0127200' => 'sbr', 'Sabra11G0003700' => 'sbr', 'Sabra15G0014700' => 'sbr', 'Sc19g0000590' => 'sci', 'Sc19g0001870' => 'sci', 'SGA_v2.0_scaffold1G00346' => 'sas', 'SGA_v2.0_scaffold1G00575' => 'sas', 'SGA_v2.0_scaffold1G00761' => 'sas', 'SGA_v2.0_scaffold232G43501' => 'sas', 'TAR625G1137' => 'tar', 'Thecc.03G222100' => 'tca', 'TPR.G12691' => 'tpr', 'TWI34G0727' => 'twi', 'TWI36G0117' => 'twi', 'VMungo1309G0868' => 'vmu' ) $gf_id = 'HOM05D001729' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001729' ) $data_identifier = 'HOM05D001729' $data_type = 'gf_id' $species_gene_counts = array( 'amhyb' => (int) 1, 'cqu' => (int) 9, 'can' => (int) 1, 'cansat' => (int) 1, 'car' => (int) 1, 'col' => (int) 5, 'dca' => (int) 1, 'din' => (int) 2, 'dzi' => (int) 3, 'fan' => (int) 140, 'fve' => (int) 62, 'gma' => (int) 1, 'ghi' => (int) 2, 'gra' => (int) 1, 'han' => (int) 1, 'sun' => (int) 1, 'lonja' => (int) 6, 'lja' => (int) 1, 'lsa' => (int) 4, 'mes' => (int) 1, 'mdo' => (int) 14, 'mtr' => (int) 1, 'egut' => (int) 1, 'nta' => (int) 4, 'oeu' => (int) 1, 'stu' => (int) 2, 'pvu' => (int) 1, 'ptr' => (int) 4, 'ppe' => (int) 19, 'psa' => (int) 1, 'pso' => (int) 4, 'qlo' => (int) 36, 'rch' => (int) 23, 'rsi' => (int) 4, 'sbr' => (int) 4, 'sci' => (int) 2, 'sas' => (int) 4, 'tar' => (int) 1, 'tca' => (int) 1, 'tpr' => (int) 1, 'twi' => (int) 2, 'vmu' => (int) 1 ) $gf_gene_species = 'vmu' $gf_gene_id = 'VMungo1309G0868' $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' => 'HOM05D001729', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '375', 'num_species' => '42' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'Ah.07g204710' => 'amhyb', 'AUR62006001' => 'cqu', 'AUR62006002' => 'cqu', 'AUR62006003' => 'cqu', 'AUR62015641' => 'cqu', 'AUR62027174' => 'cqu', 'AUR62035623' => 'cqu', 'AUR62035624' => 'cqu', 'AUR62035625' => 'cqu', 'AUR62035626' => 'cqu', 'CAN.G1110.53' => 'can', 'CANSAT80G0415' => 'cansat', 'Ca_21364_v3' => 'car', 'COL.COLO4_30693' => 'col', 'COL.COLO4_30694' => 'col', 'COL.COLO4_30695' => 'col', 'COL.COLO4_30696' => 'col', 'COL.COLO4_34020' => 'col', 'DCAR_004585' => 'dca', 'Dinv04029' => 'din', 'Dinv34857' => 'din', 'Duzib147G0011' => 'dzi', 'Duzib170G0599' => 'dzi', 'Duzib192G1051' => 'dzi', 'FAN01G0708' => 'fan', 'FAN01G0742' => 'fan', 'FAN02G0048' => 'fan', 'FAN02G0583' => 'fan', 'FAN02G0688' => 'fan', 'FAN02G1588' => 'fan', 'FAN02G2194' => 'fan', 'FAN02G2750' => 'fan', 'FAN02G3094' => 'fan', 'FAN02G3887' => 'fan', 'FAN02G3911' => 'fan', 'FAN02G3994' => 'fan', 'FAN02G4432' => 'fan', 'FAN02G4556' => 'fan', 'FAN03G1977' => 'fan', 'FAN03G2781' => 'fan', 'FAN03G2850' => 'fan', 'FAN03G3155' => 'fan', 'FAN04G2487' => 'fan', 'FAN05G0208' => 'fan', 'FAN05G0656' => 'fan', 'FAN05G0696' => 'fan', 'FAN05G0810' => 'fan', 'FAN05G1447' => 'fan', 'FAN05G2640' => 'fan', 'FAN05G2911' => 'fan', 'FAN05G3901' => 'fan', 'FAN05G4859' => 'fan', 'FAN05G4861' => 'fan', 'FAN05G4988' => 'fan', 'FAN05G5187' => 'fan', 'FAN05G5452' => 'fan', 'FAN05G5500' => 'fan', 'FAN05G5688' => 'fan', 'FAN06G0177' => 'fan', 'FAN06G0675' => 'fan', 'FAN06G1290' => 'fan', 'FAN06G2191' => 'fan', 'FAN06G2405' => 'fan', 'FAN06G3231' => 'fan', 'FAN06G3932' => 'fan', 'FAN07G0163' => 'fan', 'FAN07G0471' => 'fan', 'FAN07G1354' => 'fan', 'FAN08G0338' => 'fan', 'FAN08G1373' => 'fan', 'FAN08G2539' => 'fan', 'FAN08G2728' => 'fan', 'FAN09G0608' => 'fan', 'FAN09G1136' => 'fan', 'FAN09G1958' => 'fan', 'FAN09G2508' => 'fan', 'FAN09G2597' => 'fan', 'FAN09G2658' => 'fan', 'FAN09G2757' => 'fan', 'FAN09G2983' => 'fan', 'FAN09G3130' => 'fan', 'FAN09G3565' => 'fan', 'FAN09G3613' => 'fan', 'FAN09G4011' => 'fan', 'FAN09G4239' => 'fan', 'FAN09G4277' => 'fan', 'FAN09G4720' => 'fan', 'FAN11G0139' => 'fan', 'FAN11G1727' => 'fan', 'FAN11G2672' => 'fan', 'FAN11G2795' => 'fan', 'FAN11G3238' => 'fan', 'FAN11G3734' => 'fan', 'FAN12G0631' => 'fan', 'FAN12G2239' => 'fan', 'FAN12G2308' => 'fan', 'FAN12G2569' => 'fan', 'FAN12G2623' => 'fan', 'FAN13G3182' => 'fan', 'FAN14G0053' => 'fan', 'FAN14G0370' => 'fan', 'FAN14G0382' => 'fan', 'FAN14G0421' => 'fan', 'FAN14G0866' => 'fan', 'FAN14G1187' => 'fan', 'FAN14G1727' => 'fan', 'FAN14G1791' => 'fan', 'FAN14G2361' => 'fan', 'FAN14G2668' => 'fan', 'FAN14G2770' => 'fan', 'FAN14G2874' => 'fan', 'FAN14G3193' => 'fan', 'FAN14G3624' => 'fan', 'FAN14G3676' => 'fan', 'FAN14G3807' => 'fan', 'FAN14G4082' => 'fan', 'FAN14G4342' => 'fan', 'FAN14G4985' => 'fan', 'FAN14G5126' => 'fan', 'FAN14G5781' => 'fan', 'FAN14G5808' => 'fan', 'FAN14G5949' => 'fan', 'FAN15G0828' => 'fan', 'FAN15G1054' => 'fan', 'FAN15G2023' => 'fan', 'FAN15G2506' => 'fan', 'FAN16G0128' => 'fan', 'FAN16G0249' => 'fan', 'FAN16G0429' => 'fan', 'FAN16G1493' => 'fan', 'FAN16G2210' => 'fan', 'FAN16G2506' => 'fan', 'FAN18G1542' => 'fan', 'FAN18G4057' => 'fan', 'FAN19G0745' => 'fan', 'FAN19G1216' => 'fan', 'FAN19G1733' => 'fan', 'FAN20G0258' => 'fan', 'FAN20G1095' => 'fan', 'FAN20G1557' => 'fan', 'FAN21G0302' => 'fan', 'FAN21G0519' => 'fan', 'FAN21G0970' => 'fan', 'FAN21G1159' => 'fan', 'FAN21G1312' => 'fan', 'FAN21G1440' => 'fan', 'FAN21G1715' => 'fan', 'FAN23G1584' => 'fan', 'FAN24G0045' => 'fan', 'FAN24G0053' => 'fan', 'FAN24G1500' => 'fan', 'FAN24G1817' => 'fan', 'FAN24G2147' => 'fan', 'FAN24G2236' => 'fan', 'FAN24G2446' => 'fan', 'FAN24G2684' => 'fan', 'FAN25G0187' => 'fan', 'FAN25G0505' => 'fan', 'FAN25G0589' => 'fan', 'FAN25G3663' => 'fan', 'FAN26G1025' => 'fan', 'FAN26G2860' => 'fan', 'FAN27G1329' => 'fan', 'FAN27G3392' => 'fan', 'FvH4_1g02011' => 'fve', 'FvH4_1g06511' => 'fve', 'FvH4_2g19900' => 'fve', 'FvH4_2g19920' => 'fve', 'FvH4_2g24261' => 'fve', 'FvH4_2g24270' => 'fve', 'FvH4_2g24631' => 'fve', 'FvH4_2g30622' => 'fve', 'FvH4_3g12920' => 'fve', 'FvH4_3g30171' => 'fve', 'FvH4_3g35490' => 'fve', 'FvH4_3g43682' => 'fve', 'FvH4_3g43730' => 'fve', 'FvH4_3g43732' => 'fve', 'FvH4_3g43751' => 'fve', 'FvH4_3g43752' => 'fve', 'FvH4_3g43770' => 'fve', 'FvH4_3g44471' => 'fve', 'FvH4_3g44510' => 'fve', 'FvH4_3g44582' => 'fve', 'FvH4_4g16921' => 'fve', 'FvH4_4g17121' => 'fve', 'FvH4_4g17782' => 'fve', 'FvH4_4g17783' => 'fve', 'FvH4_4g18120' => 'fve', 'FvH4_4g31310' => 'fve', 'FvH4_4g35052' => 'fve', 'FvH4_5g30862' => 'fve', 'FvH4_6g01541' => 'fve', 'FvH4_6g02021' => 'fve', 'FvH4_6g02041' => 'fve', 'FvH4_6g02071' => 'fve', 'FvH4_6g02171' => 'fve', 'FvH4_6g03181' => 'fve', 'FvH4_6g03182' => 'fve', 'FvH4_6g03221' => 'fve', 'FvH4_6g03380' => 'fve', 'FvH4_6g05201' => 'fve', 'FvH4_6g05203' => 'fve', 'FvH4_6g20231' => 'fve', 'FvH4_6g31981' => 'fve', 'FvH4_6g32061' => 'fve', 'FvH4_6g37041' => 'fve', 'FvH4_6g37932' => 'fve', 'FvH4_6g38731' => 'fve', 'FvH4_6g39370' => 'fve', 'FvH4_6g39371' => 'fve', 'FvH4_6g40891' => 'fve', 'FvH4_6g40892' => 'fve', 'FvH4_6g43143' => 'fve', 'FvH4_6g45251' => 'fve', 'FvH4_6g45260' => 'fve', 'FvH4_6g45291' => 'fve', 'FvH4_6g45890' => 'fve', 'FvH4_6g46240' => 'fve', 'FvH4_6g46241' => 'fve', 'FvH4_6g46242' => 'fve', 'FvH4_6g46260' => 'fve', 'FvH4_6g46280' => 'fve', 'FvH4_6g46380' => 'fve', 'FvH4_7g12841' => 'fve', 'FvH4_7g31431' => 'fve', 'Glyma.09G075900' => 'gma', 'Gohir.A09G096401' => 'ghi', 'Gohir.D09G096101' => 'ghi', 'Gorai.006G112800' => 'gra', 'HanXRQChr04g0121411' => 'han', 'Hund15878' => 'sun', 'Lj2A1107G68' => 'lonja', 'Lj2A630G63' => 'lonja', 'Lj2A946T25' => 'lonja', 'Lj2C714T1' => 'lonja', 'Lj2C966T3' => 'lonja', 'Lj2C966T4' => 'lonja', 'Lj4g0002979' => 'lja', 'Lsat_1_v5_gn_5_30901' => 'lsa', 'Lsat_1_v5_gn_5_31100' => 'lsa', 'Lsat_1_v5_gn_5_38600' => 'lsa', 'Lsat_1_v5_gn_6_92061' => 'lsa', 'Manes.05G071301' => 'mes', 'MD02G1008700' => 'mdo', 'MD02G1008900' => 'mdo', 'MD03G1256400' => 'mdo', 'MD04G1180900' => 'mdo', 'MD04G1181000' => 'mdo', 'MD04G1181200' => 'mdo', 'MD05G1244200' => 'mdo', 'MD05G1324200' => 'mdo', 'MD09G1201600' => 'mdo', 'MD10G1000600' => 'mdo', 'MD14G1026900' => 'mdo', 'MD14G1187900' => 'mdo', 'MD15G1017800' => 'mdo', 'MD15G1018100' => 'mdo', 'Medtr4g124160' => 'mtr', 'Migut.L01260' => 'egut', 'Nitab4.5_0000008g0440' => 'nta', 'Nitab4.5_0000207g0170' => 'nta', 'Nitab4.5_0007671g0030' => 'nta', 'Nitab4.5_0010853g0020' => 'nta', 'Oeu057656.1' => 'oeu', 'PGSC0003DMG400005638' => 'stu', 'PGSC0003DMG400005639' => 'stu', 'Phvul.009G222800' => 'pvu', 'Potri.009G132400' => 'ptr', 'Potri.009G163001' => 'ptr', 'Potri.011G000700' => 'ptr', 'Potri.011G004800' => 'ptr', 'Prupe.1G509300' => 'ppe', 'Prupe.1G509700' => 'ppe', 'Prupe.1G510400' => 'ppe', 'Prupe.1G510700' => 'ppe', 'Prupe.1G512600' => 'ppe', 'Prupe.2G073200' => 'ppe', 'Prupe.3G059500' => 'ppe', 'Prupe.3G059600' => 'ppe', 'Prupe.3G246100' => 'ppe', 'Prupe.3G265100' => 'ppe', 'Prupe.4G034700' => 'ppe', 'Prupe.4G052100' => 'ppe', 'Prupe.4G053600' => 'ppe', 'Prupe.5G068800' => 'ppe', 'Prupe.5G070600' => 'ppe', 'Prupe.6G075400' => 'ppe', 'Prupe.6G075500' => 'ppe', 'Prupe.6G076400' => 'ppe', 'Prupe.8G110700' => 'ppe', 'Psat4g020960' => 'psa', 'PSO135G0788' => 'pso', 'PSO210G6463' => 'pso', 'PSO384G0370' => 'pso', 'PSO386G0056' => 'pso', 'QL01p006048' => 'qlo', 'QL02p054283' => 'qlo', 'QL05p008000' => 'qlo', 'QL05p008212' => 'qlo', 'QL05p008950' => 'qlo', 'QL05p009042' => 'qlo', 'QL05p009518' => 'qlo', 'QL05p012589' => 'qlo', 'QL05p012608' => 'qlo', 'QL05p012650' => 'qlo', 'QL05p012667' => 'qlo', 'QL05p014501' => 'qlo', 'QL05p052800' => 'qlo', 'QL05p065010' => 'qlo', 'QL05p074156' => 'qlo', 'QL05p074160' => 'qlo', 'QL05p074174' => 'qlo', 'QL05p074178' => 'qlo', 'QL05p074214' => 'qlo', 'QL06p001050' => 'qlo', 'QL06p001056' => 'qlo', 'QL06p006093' => 'qlo', 'QL06p006111' => 'qlo', 'QL07p019784' => 'qlo', 'QL07p019801' => 'qlo', 'QL07p036110' => 'qlo', 'QL07p036134' => 'qlo', 'QL07p036147' => 'qlo', 'QL07p036156' => 'qlo', 'QL07p036300' => 'qlo', 'QL07p036320' => 'qlo', 'QL08p014547' => 'qlo', 'QL08p014551' => 'qlo', 'QL08p043319' => 'qlo', 'QL08p043324' => 'qlo', 'QL11p009094' => 'qlo', 'RcHm_v2.0_Chr1g0380481' => 'rch', 'RcHm_v2.0_Chr2g0089331' => 'rch', 'RcHm_v2.0_Chr2g0123691' => 'rch', 'RcHm_v2.0_Chr2g0151111' => 'rch', 'RcHm_v2.0_Chr2g0163011' => 'rch', 'RcHm_v2.0_Chr2g0163051' => 'rch', 'RcHm_v2.0_Chr2g0164671' => 'rch', 'RcHm_v2.0_Chr2g0164681' => 'rch', 'RcHm_v2.0_Chr2g0164721' => 'rch', 'RcHm_v2.0_Chr3g0449911' => 'rch', 'RcHm_v2.0_Chr3g0450211' => 'rch', 'RcHm_v2.0_Chr3g0457271' => 'rch', 'RcHm_v2.0_Chr5g0018111' => 'rch', 'RcHm_v2.0_Chr5g0021011' => 'rch', 'RcHm_v2.0_Chr5g0081171' => 'rch', 'RcHm_v2.0_Chr5g0081211' => 'rch', 'RcHm_v2.0_Chr6g0275871' => 'rch', 'RcHm_v2.0_Chr6g0276071' => 'rch', 'RcHm_v2.0_Chr6g0285591' => 'rch', 'RcHm_v2.0_Chr6g0291931' => 'rch', 'RcHm_v2.0_Chr6g0292091' => 'rch', 'RcHm_v2.0_Chr6g0292271' => 'rch', 'RcHm_v2.0_Chr7g0221261' => 'rch', 'Rhsim08G0219900' => 'rsi', 'Rhsim08G0220200' => 'rsi', 'Rhsim08G0237800' => 'rsi', 'Rhsim08G0238800' => 'rsi', 'Sabra09G0102700' => 'sbr', 'Sabra09G0127200' => 'sbr', 'Sabra11G0003700' => 'sbr', 'Sabra15G0014700' => 'sbr', 'Sc19g0000590' => 'sci', 'Sc19g0001870' => 'sci', 'SGA_v2.0_scaffold1G00346' => 'sas', 'SGA_v2.0_scaffold1G00575' => 'sas', 'SGA_v2.0_scaffold1G00761' => 'sas', 'SGA_v2.0_scaffold232G43501' => 'sas', 'TAR625G1137' => 'tar', 'Thecc.03G222100' => 'tca', 'TPR.G12691' => 'tpr', 'TWI34G0727' => 'twi', 'TWI36G0117' => 'twi', 'VMungo1309G0868' => 'vmu' ), 'gf_id' => 'HOM05D001729', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001729' ), 'data_identifier' => 'HOM05D001729', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001729', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '375', 'num_species' => '42' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'Ah.07g204710' => 'amhyb', 'AUR62006001' => 'cqu', 'AUR62006002' => 'cqu', 'AUR62006003' => 'cqu', 'AUR62015641' => 'cqu', 'AUR62027174' => 'cqu', 'AUR62035623' => 'cqu', 'AUR62035624' => 'cqu', 'AUR62035625' => 'cqu', 'AUR62035626' => 'cqu', 'CAN.G1110.53' => 'can', 'CANSAT80G0415' => 'cansat', 'Ca_21364_v3' => 'car', 'COL.COLO4_30693' => 'col', 'COL.COLO4_30694' => 'col', 'COL.COLO4_30695' => 'col', 'COL.COLO4_30696' => 'col', 'COL.COLO4_34020' => 'col', 'DCAR_004585' => 'dca', 'Dinv04029' => 'din', 'Dinv34857' => 'din', 'Duzib147G0011' => 'dzi', 'Duzib170G0599' => 'dzi', 'Duzib192G1051' => 'dzi', 'FAN01G0708' => 'fan', 'FAN01G0742' => 'fan', 'FAN02G0048' => 'fan', 'FAN02G0583' => 'fan', 'FAN02G0688' => 'fan', 'FAN02G1588' => 'fan', 'FAN02G2194' => 'fan', 'FAN02G2750' => 'fan', 'FAN02G3094' => 'fan', 'FAN02G3887' => 'fan', 'FAN02G3911' => 'fan', 'FAN02G3994' => 'fan', 'FAN02G4432' => 'fan', 'FAN02G4556' => 'fan', 'FAN03G1977' => 'fan', 'FAN03G2781' => 'fan', 'FAN03G2850' => 'fan', 'FAN03G3155' => 'fan', 'FAN04G2487' => 'fan', 'FAN05G0208' => 'fan', 'FAN05G0656' => 'fan', 'FAN05G0696' => 'fan', 'FAN05G0810' => 'fan', 'FAN05G1447' => 'fan', 'FAN05G2640' => 'fan', 'FAN05G2911' => 'fan', 'FAN05G3901' => 'fan', 'FAN05G4859' => 'fan', 'FAN05G4861' => 'fan', 'FAN05G4988' => 'fan', 'FAN05G5187' => 'fan', 'FAN05G5452' => 'fan', 'FAN05G5500' => 'fan', 'FAN05G5688' => 'fan', 'FAN06G0177' => 'fan', 'FAN06G0675' => 'fan', 'FAN06G1290' => 'fan', 'FAN06G2191' => 'fan', 'FAN06G2405' => 'fan', 'FAN06G3231' => 'fan', 'FAN06G3932' => 'fan', 'FAN07G0163' => 'fan', 'FAN07G0471' => 'fan', 'FAN07G1354' => 'fan', 'FAN08G0338' => 'fan', 'FAN08G1373' => 'fan', 'FAN08G2539' => 'fan', 'FAN08G2728' => 'fan', 'FAN09G0608' => 'fan', 'FAN09G1136' => 'fan', 'FAN09G1958' => 'fan', 'FAN09G2508' => 'fan', 'FAN09G2597' => 'fan', 'FAN09G2658' => 'fan', 'FAN09G2757' => 'fan', 'FAN09G2983' => 'fan', 'FAN09G3130' => 'fan', 'FAN09G3565' => 'fan', 'FAN09G3613' => 'fan', 'FAN09G4011' => 'fan', 'FAN09G4239' => 'fan', 'FAN09G4277' => 'fan', 'FAN09G4720' => 'fan', 'FAN11G0139' => 'fan', 'FAN11G1727' => 'fan', 'FAN11G2672' => 'fan', 'FAN11G2795' => 'fan', 'FAN11G3238' => 'fan', 'FAN11G3734' => 'fan', 'FAN12G0631' => 'fan', 'FAN12G2239' => 'fan', 'FAN12G2308' => 'fan', 'FAN12G2569' => 'fan', 'FAN12G2623' => 'fan', 'FAN13G3182' => 'fan', 'FAN14G0053' => 'fan', 'FAN14G0370' => 'fan', 'FAN14G0382' => 'fan', 'FAN14G0421' => 'fan', 'FAN14G0866' => 'fan', 'FAN14G1187' => 'fan', 'FAN14G1727' => 'fan', 'FAN14G1791' => 'fan', 'FAN14G2361' => 'fan', 'FAN14G2668' => 'fan', 'FAN14G2770' => 'fan', 'FAN14G2874' => 'fan', 'FAN14G3193' => 'fan', 'FAN14G3624' => 'fan', 'FAN14G3676' => 'fan', 'FAN14G3807' => 'fan', 'FAN14G4082' => 'fan', 'FAN14G4342' => 'fan', 'FAN14G4985' => 'fan', 'FAN14G5126' => 'fan', 'FAN14G5781' => 'fan', 'FAN14G5808' => 'fan', 'FAN14G5949' => 'fan', 'FAN15G0828' => 'fan', 'FAN15G1054' => 'fan', 'FAN15G2023' => 'fan', 'FAN15G2506' => 'fan', 'FAN16G0128' => 'fan', 'FAN16G0249' => 'fan', 'FAN16G0429' => 'fan', 'FAN16G1493' => 'fan', 'FAN16G2210' => 'fan', 'FAN16G2506' => 'fan', 'FAN18G1542' => 'fan', 'FAN18G4057' => 'fan', 'FAN19G0745' => 'fan', 'FAN19G1216' => 'fan', 'FAN19G1733' => 'fan', 'FAN20G0258' => 'fan', 'FAN20G1095' => 'fan', 'FAN20G1557' => 'fan', 'FAN21G0302' => 'fan', 'FAN21G0519' => 'fan', 'FAN21G0970' => 'fan', 'FAN21G1159' => 'fan', 'FAN21G1312' => 'fan', 'FAN21G1440' => 'fan', 'FAN21G1715' => 'fan', 'FAN23G1584' => 'fan', 'FAN24G0045' => 'fan', 'FAN24G0053' => 'fan', 'FAN24G1500' => 'fan', 'FAN24G1817' => 'fan', 'FAN24G2147' => 'fan', 'FAN24G2236' => 'fan', 'FAN24G2446' => 'fan', 'FAN24G2684' => 'fan', 'FAN25G0187' => 'fan', 'FAN25G0505' => 'fan', 'FAN25G0589' => 'fan', 'FAN25G3663' => 'fan', 'FAN26G1025' => 'fan', 'FAN26G2860' => 'fan', 'FAN27G1329' => 'fan', 'FAN27G3392' => 'fan', 'FvH4_1g02011' => 'fve', 'FvH4_1g06511' => 'fve', 'FvH4_2g19900' => 'fve', 'FvH4_2g19920' => 'fve', 'FvH4_2g24261' => 'fve', 'FvH4_2g24270' => 'fve', 'FvH4_2g24631' => 'fve', 'FvH4_2g30622' => 'fve', 'FvH4_3g12920' => 'fve', 'FvH4_3g30171' => 'fve', 'FvH4_3g35490' => 'fve', 'FvH4_3g43682' => 'fve', 'FvH4_3g43730' => 'fve', 'FvH4_3g43732' => 'fve', 'FvH4_3g43751' => 'fve', 'FvH4_3g43752' => 'fve', 'FvH4_3g43770' => 'fve', 'FvH4_3g44471' => 'fve', 'FvH4_3g44510' => 'fve', 'FvH4_3g44582' => 'fve', 'FvH4_4g16921' => 'fve', 'FvH4_4g17121' => 'fve', 'FvH4_4g17782' => 'fve', 'FvH4_4g17783' => 'fve', 'FvH4_4g18120' => 'fve', 'FvH4_4g31310' => 'fve', 'FvH4_4g35052' => 'fve', 'FvH4_5g30862' => 'fve', 'FvH4_6g01541' => 'fve', 'FvH4_6g02021' => 'fve', 'FvH4_6g02041' => 'fve', 'FvH4_6g02071' => 'fve', 'FvH4_6g02171' => 'fve', 'FvH4_6g03181' => 'fve', 'FvH4_6g03182' => 'fve', 'FvH4_6g03221' => 'fve', 'FvH4_6g03380' => 'fve', 'FvH4_6g05201' => 'fve', 'FvH4_6g05203' => 'fve', 'FvH4_6g20231' => 'fve', 'FvH4_6g31981' => 'fve', 'FvH4_6g32061' => 'fve', 'FvH4_6g37041' => 'fve', 'FvH4_6g37932' => 'fve', 'FvH4_6g38731' => 'fve', 'FvH4_6g39370' => 'fve', 'FvH4_6g39371' => 'fve', 'FvH4_6g40891' => 'fve', 'FvH4_6g40892' => 'fve', 'FvH4_6g43143' => 'fve', 'FvH4_6g45251' => 'fve', 'FvH4_6g45260' => 'fve', 'FvH4_6g45291' => 'fve', 'FvH4_6g45890' => 'fve', 'FvH4_6g46240' => 'fve', 'FvH4_6g46241' => 'fve', 'FvH4_6g46242' => 'fve', 'FvH4_6g46260' => 'fve', 'FvH4_6g46280' => 'fve', 'FvH4_6g46380' => 'fve', 'FvH4_7g12841' => 'fve', 'FvH4_7g31431' => 'fve', 'Glyma.09G075900' => 'gma', 'Gohir.A09G096401' => 'ghi', 'Gohir.D09G096101' => 'ghi', 'Gorai.006G112800' => 'gra', 'HanXRQChr04g0121411' => 'han', 'Hund15878' => 'sun', 'Lj2A1107G68' => 'lonja', 'Lj2A630G63' => 'lonja', 'Lj2A946T25' => 'lonja', 'Lj2C714T1' => 'lonja', 'Lj2C966T3' => 'lonja', 'Lj2C966T4' => 'lonja', 'Lj4g0002979' => 'lja', 'Lsat_1_v5_gn_5_30901' => 'lsa', 'Lsat_1_v5_gn_5_31100' => 'lsa', 'Lsat_1_v5_gn_5_38600' => 'lsa', 'Lsat_1_v5_gn_6_92061' => 'lsa', 'Manes.05G071301' => 'mes', 'MD02G1008700' => 'mdo', 'MD02G1008900' => 'mdo', 'MD03G1256400' => 'mdo', 'MD04G1180900' => 'mdo', 'MD04G1181000' => 'mdo', 'MD04G1181200' => 'mdo', 'MD05G1244200' => 'mdo', 'MD05G1324200' => 'mdo', 'MD09G1201600' => 'mdo', 'MD10G1000600' => 'mdo', 'MD14G1026900' => 'mdo', 'MD14G1187900' => 'mdo', 'MD15G1017800' => 'mdo', 'MD15G1018100' => 'mdo', 'Medtr4g124160' => 'mtr', 'Migut.L01260' => 'egut', 'Nitab4.5_0000008g0440' => 'nta', 'Nitab4.5_0000207g0170' => 'nta', 'Nitab4.5_0007671g0030' => 'nta', 'Nitab4.5_0010853g0020' => 'nta', 'Oeu057656.1' => 'oeu', 'PGSC0003DMG400005638' => 'stu', 'PGSC0003DMG400005639' => 'stu', 'Phvul.009G222800' => 'pvu', 'Potri.009G132400' => 'ptr', 'Potri.009G163001' => 'ptr', 'Potri.011G000700' => 'ptr', 'Potri.011G004800' => 'ptr', 'Prupe.1G509300' => 'ppe', 'Prupe.1G509700' => 'ppe', 'Prupe.1G510400' => 'ppe', 'Prupe.1G510700' => 'ppe', 'Prupe.1G512600' => 'ppe', 'Prupe.2G073200' => 'ppe', 'Prupe.3G059500' => 'ppe', 'Prupe.3G059600' => 'ppe', 'Prupe.3G246100' => 'ppe', 'Prupe.3G265100' => 'ppe', 'Prupe.4G034700' => 'ppe', 'Prupe.4G052100' => 'ppe', 'Prupe.4G053600' => 'ppe', 'Prupe.5G068800' => 'ppe', 'Prupe.5G070600' => 'ppe', 'Prupe.6G075400' => 'ppe', 'Prupe.6G075500' => 'ppe', 'Prupe.6G076400' => 'ppe', 'Prupe.8G110700' => 'ppe', 'Psat4g020960' => 'psa', 'PSO135G0788' => 'pso', 'PSO210G6463' => 'pso', 'PSO384G0370' => 'pso', 'PSO386G0056' => 'pso', 'QL01p006048' => 'qlo', 'QL02p054283' => 'qlo', 'QL05p008000' => 'qlo', 'QL05p008212' => 'qlo', 'QL05p008950' => 'qlo', 'QL05p009042' => 'qlo', 'QL05p009518' => 'qlo', 'QL05p012589' => 'qlo', 'QL05p012608' => 'qlo', 'QL05p012650' => 'qlo', 'QL05p012667' => 'qlo', 'QL05p014501' => 'qlo', 'QL05p052800' => 'qlo', 'QL05p065010' => 'qlo', 'QL05p074156' => 'qlo', 'QL05p074160' => 'qlo', 'QL05p074174' => 'qlo', 'QL05p074178' => 'qlo', 'QL05p074214' => 'qlo', 'QL06p001050' => 'qlo', 'QL06p001056' => 'qlo', 'QL06p006093' => 'qlo', 'QL06p006111' => 'qlo', 'QL07p019784' => 'qlo', 'QL07p019801' => 'qlo', 'QL07p036110' => 'qlo', 'QL07p036134' => 'qlo', 'QL07p036147' => 'qlo', 'QL07p036156' => 'qlo', 'QL07p036300' => 'qlo', 'QL07p036320' => 'qlo', 'QL08p014547' => 'qlo', 'QL08p014551' => 'qlo', 'QL08p043319' => 'qlo', 'QL08p043324' => 'qlo', 'QL11p009094' => 'qlo', 'RcHm_v2.0_Chr1g0380481' => 'rch', 'RcHm_v2.0_Chr2g0089331' => 'rch', 'RcHm_v2.0_Chr2g0123691' => 'rch', 'RcHm_v2.0_Chr2g0151111' => 'rch', 'RcHm_v2.0_Chr2g0163011' => 'rch', 'RcHm_v2.0_Chr2g0163051' => 'rch', 'RcHm_v2.0_Chr2g0164671' => 'rch', 'RcHm_v2.0_Chr2g0164681' => 'rch', 'RcHm_v2.0_Chr2g0164721' => 'rch', 'RcHm_v2.0_Chr3g0449911' => 'rch', 'RcHm_v2.0_Chr3g0450211' => 'rch', 'RcHm_v2.0_Chr3g0457271' => 'rch', 'RcHm_v2.0_Chr5g0018111' => 'rch', 'RcHm_v2.0_Chr5g0021011' => 'rch', 'RcHm_v2.0_Chr5g0081171' => 'rch', 'RcHm_v2.0_Chr5g0081211' => 'rch', 'RcHm_v2.0_Chr6g0275871' => 'rch', 'RcHm_v2.0_Chr6g0276071' => 'rch', 'RcHm_v2.0_Chr6g0285591' => 'rch', 'RcHm_v2.0_Chr6g0291931' => 'rch', 'RcHm_v2.0_Chr6g0292091' => 'rch', 'RcHm_v2.0_Chr6g0292271' => 'rch', 'RcHm_v2.0_Chr7g0221261' => 'rch', 'Rhsim08G0219900' => 'rsi', 'Rhsim08G0220200' => 'rsi', 'Rhsim08G0237800' => 'rsi', 'Rhsim08G0238800' => 'rsi', 'Sabra09G0102700' => 'sbr', 'Sabra09G0127200' => 'sbr', 'Sabra11G0003700' => 'sbr', 'Sabra15G0014700' => 'sbr', 'Sc19g0000590' => 'sci', 'Sc19g0001870' => 'sci', 'SGA_v2.0_scaffold1G00346' => 'sas', 'SGA_v2.0_scaffold1G00575' => 'sas', 'SGA_v2.0_scaffold1G00761' => 'sas', 'SGA_v2.0_scaffold232G43501' => 'sas', 'TAR625G1137' => 'tar', 'Thecc.03G222100' => 'tca', 'TPR.G12691' => 'tpr', 'TWI34G0727' => 'twi', 'TWI36G0117' => 'twi', 'VMungo1309G0868' => 'vmu' ) $gf_id = 'HOM05D001729' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001729' ) $data_identifier = 'HOM05D001729' $data_type = 'gf_id' $species_gene_counts = array( 'amhyb' => (int) 1, 'cqu' => (int) 9, 'can' => (int) 1, 'cansat' => (int) 1, 'car' => (int) 1, 'col' => (int) 5, 'dca' => (int) 1, 'din' => (int) 2, 'dzi' => (int) 3, 'fan' => (int) 140, 'fve' => (int) 62, 'gma' => (int) 1, 'ghi' => (int) 2, 'gra' => (int) 1, 'han' => (int) 1, 'sun' => (int) 1, 'lonja' => (int) 6, 'lja' => (int) 1, 'lsa' => (int) 4, 'mes' => (int) 1, 'mdo' => (int) 14, 'mtr' => (int) 1, 'egut' => (int) 1, 'nta' => (int) 4, 'oeu' => (int) 1, 'stu' => (int) 2, 'pvu' => (int) 1, 'ptr' => (int) 4, 'ppe' => (int) 19, 'psa' => (int) 1, 'pso' => (int) 4, 'qlo' => (int) 36, 'rch' => (int) 23, 'rsi' => (int) 4, 'sbr' => (int) 4, 'sci' => (int) 2, 'sas' => (int) 4, 'tar' => (int) 1, 'tca' => (int) 1, 'tpr' => (int) 1, 'twi' => (int) 2, 'vmu' => (int) 1 ) $gf_gene_species = 'vmu' $gf_gene_id = 'VMungo1309G0868' $species_info = array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ) $local_species = 'mtr' $disabled = '' $selected = '' $num_hits = (int) 0include - APP/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp, line 33 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933 View::_renderElement() - CORE/Cake/View/View.php, line 1224 View::element() - CORE/Cake/View/View.php, line 418 include - APP/View/Elements/analysis/phylogenetics_module/gf_data_settings.ctp, line 37 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933 View::_renderElement() - CORE/Cake/View/View.php, line 1224 View::element() - CORE/Cake/View/View.php, line 418 include - APP/View/Elements/analysis/phylogenetics_module/parameter_selection.ctp, line 64 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933 View::_renderElement() - CORE/Cake/View/View.php, line 1224 View::element() - CORE/Cake/View/View.php, line 418 include - APP/View/Analysis/custom_tree_creation.ctp, line 27 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933
$viewFile = '/www/bioinformatics01_ro/plaza/_dev_instances/feedback/app/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp' $dataForView = array( 'sidebar_info' => array( 'gf_id' => 'HOM05D001729', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '375', 'num_species' => '42' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'Ah.07g204710' => 'amhyb', 'AUR62006001' => 'cqu', 'AUR62006002' => 'cqu', 'AUR62006003' => 'cqu', 'AUR62015641' => 'cqu', 'AUR62027174' => 'cqu', 'AUR62035623' => 'cqu', 'AUR62035624' => 'cqu', 'AUR62035625' => 'cqu', 'AUR62035626' => 'cqu', 'CAN.G1110.53' => 'can', 'CANSAT80G0415' => 'cansat', 'Ca_21364_v3' => 'car', 'COL.COLO4_30693' => 'col', 'COL.COLO4_30694' => 'col', 'COL.COLO4_30695' => 'col', 'COL.COLO4_30696' => 'col', 'COL.COLO4_34020' => 'col', 'DCAR_004585' => 'dca', 'Dinv04029' => 'din', 'Dinv34857' => 'din', 'Duzib147G0011' => 'dzi', 'Duzib170G0599' => 'dzi', 'Duzib192G1051' => 'dzi', 'FAN01G0708' => 'fan', 'FAN01G0742' => 'fan', 'FAN02G0048' => 'fan', 'FAN02G0583' => 'fan', 'FAN02G0688' => 'fan', 'FAN02G1588' => 'fan', 'FAN02G2194' => 'fan', 'FAN02G2750' => 'fan', 'FAN02G3094' => 'fan', 'FAN02G3887' => 'fan', 'FAN02G3911' => 'fan', 'FAN02G3994' => 'fan', 'FAN02G4432' => 'fan', 'FAN02G4556' => 'fan', 'FAN03G1977' => 'fan', 'FAN03G2781' => 'fan', 'FAN03G2850' => 'fan', 'FAN03G3155' => 'fan', 'FAN04G2487' => 'fan', 'FAN05G0208' => 'fan', 'FAN05G0656' => 'fan', 'FAN05G0696' => 'fan', 'FAN05G0810' => 'fan', 'FAN05G1447' => 'fan', 'FAN05G2640' => 'fan', 'FAN05G2911' => 'fan', 'FAN05G3901' => 'fan', 'FAN05G4859' => 'fan', 'FAN05G4861' => 'fan', 'FAN05G4988' => 'fan', 'FAN05G5187' => 'fan', 'FAN05G5452' => 'fan', 'FAN05G5500' => 'fan', 'FAN05G5688' => 'fan', 'FAN06G0177' => 'fan', 'FAN06G0675' => 'fan', 'FAN06G1290' => 'fan', 'FAN06G2191' => 'fan', 'FAN06G2405' => 'fan', 'FAN06G3231' => 'fan', 'FAN06G3932' => 'fan', 'FAN07G0163' => 'fan', 'FAN07G0471' => 'fan', 'FAN07G1354' => 'fan', 'FAN08G0338' => 'fan', 'FAN08G1373' => 'fan', 'FAN08G2539' => 'fan', 'FAN08G2728' => 'fan', 'FAN09G0608' => 'fan', 'FAN09G1136' => 'fan', 'FAN09G1958' => 'fan', 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'FAN14G5126' => 'fan', 'FAN14G5781' => 'fan', 'FAN14G5808' => 'fan', 'FAN14G5949' => 'fan', 'FAN15G0828' => 'fan', 'FAN15G1054' => 'fan', 'FAN15G2023' => 'fan', 'FAN15G2506' => 'fan', 'FAN16G0128' => 'fan', 'FAN16G0249' => 'fan', 'FAN16G0429' => 'fan', 'FAN16G1493' => 'fan', 'FAN16G2210' => 'fan', 'FAN16G2506' => 'fan', 'FAN18G1542' => 'fan', 'FAN18G4057' => 'fan', 'FAN19G0745' => 'fan', 'FAN19G1216' => 'fan', 'FAN19G1733' => 'fan', 'FAN20G0258' => 'fan', 'FAN20G1095' => 'fan', 'FAN20G1557' => 'fan', 'FAN21G0302' => 'fan', 'FAN21G0519' => 'fan', 'FAN21G0970' => 'fan', 'FAN21G1159' => 'fan', 'FAN21G1312' => 'fan', 'FAN21G1440' => 'fan', 'FAN21G1715' => 'fan', 'FAN23G1584' => 'fan', 'FAN24G0045' => 'fan', 'FAN24G0053' => 'fan', 'FAN24G1500' => 'fan', 'FAN24G1817' => 'fan', 'FAN24G2147' => 'fan', 'FAN24G2236' => 'fan', 'FAN24G2446' => 'fan', 'FAN24G2684' => 'fan', 'FAN25G0187' => 'fan', 'FAN25G0505' => 'fan', 'FAN25G0589' => 'fan', 'FAN25G3663' => 'fan', 'FAN26G1025' => 'fan', 'FAN26G2860' => 'fan', 'FAN27G1329' => 'fan', 'FAN27G3392' => 'fan', 'FvH4_1g02011' => 'fve', 'FvH4_1g06511' => 'fve', 'FvH4_2g19900' => 'fve', 'FvH4_2g19920' => 'fve', 'FvH4_2g24261' => 'fve', 'FvH4_2g24270' => 'fve', 'FvH4_2g24631' => 'fve', 'FvH4_2g30622' => 'fve', 'FvH4_3g12920' => 'fve', 'FvH4_3g30171' => 'fve', 'FvH4_3g35490' => 'fve', 'FvH4_3g43682' => 'fve', 'FvH4_3g43730' => 'fve', 'FvH4_3g43732' => 'fve', 'FvH4_3g43751' => 'fve', 'FvH4_3g43752' => 'fve', 'FvH4_3g43770' => 'fve', 'FvH4_3g44471' => 'fve', 'FvH4_3g44510' => 'fve', 'FvH4_3g44582' => 'fve', 'FvH4_4g16921' => 'fve', 'FvH4_4g17121' => 'fve', 'FvH4_4g17782' => 'fve', 'FvH4_4g17783' => 'fve', 'FvH4_4g18120' => 'fve', 'FvH4_4g31310' => 'fve', 'FvH4_4g35052' => 'fve', 'FvH4_5g30862' => 'fve', 'FvH4_6g01541' => 'fve', 'FvH4_6g02021' => 'fve', 'FvH4_6g02041' => 'fve', 'FvH4_6g02071' => 'fve', 'FvH4_6g02171' => 'fve', 'FvH4_6g03181' => 'fve', 'FvH4_6g03182' => 'fve', 'FvH4_6g03221' => 'fve', 'FvH4_6g03380' => 'fve', 'FvH4_6g05201' => 'fve', 'FvH4_6g05203' => 'fve', 'FvH4_6g20231' => 'fve', 'FvH4_6g31981' => 'fve', 'FvH4_6g32061' => 'fve', 'FvH4_6g37041' => 'fve', 'FvH4_6g37932' => 'fve', 'FvH4_6g38731' => 'fve', 'FvH4_6g39370' => 'fve', 'FvH4_6g39371' => 'fve', 'FvH4_6g40891' => 'fve', 'FvH4_6g40892' => 'fve', 'FvH4_6g43143' => 'fve', 'FvH4_6g45251' => 'fve', 'FvH4_6g45260' => 'fve', 'FvH4_6g45291' => 'fve', 'FvH4_6g45890' => 'fve', 'FvH4_6g46240' => 'fve', 'FvH4_6g46241' => 'fve', 'FvH4_6g46242' => 'fve', 'FvH4_6g46260' => 'fve', 'FvH4_6g46280' => 'fve', 'FvH4_6g46380' => 'fve', 'FvH4_7g12841' => 'fve', 'FvH4_7g31431' => 'fve', 'Glyma.09G075900' => 'gma', 'Gohir.A09G096401' => 'ghi', 'Gohir.D09G096101' => 'ghi', 'Gorai.006G112800' => 'gra', 'HanXRQChr04g0121411' => 'han', 'Hund15878' => 'sun', 'Lj2A1107G68' => 'lonja', 'Lj2A630G63' => 'lonja', 'Lj2A946T25' => 'lonja', 'Lj2C714T1' => 'lonja', 'Lj2C966T3' => 'lonja', 'Lj2C966T4' => 'lonja', 'Lj4g0002979' => 'lja', 'Lsat_1_v5_gn_5_30901' => 'lsa', 'Lsat_1_v5_gn_5_31100' => 'lsa', 'Lsat_1_v5_gn_5_38600' => 'lsa', 'Lsat_1_v5_gn_6_92061' => 'lsa', 'Manes.05G071301' => 'mes', 'MD02G1008700' => 'mdo', 'MD02G1008900' => 'mdo', 'MD03G1256400' => 'mdo', 'MD04G1180900' => 'mdo', 'MD04G1181000' => 'mdo', 'MD04G1181200' => 'mdo', 'MD05G1244200' => 'mdo', 'MD05G1324200' => 'mdo', 'MD09G1201600' => 'mdo', 'MD10G1000600' => 'mdo', 'MD14G1026900' => 'mdo', 'MD14G1187900' => 'mdo', 'MD15G1017800' => 'mdo', 'MD15G1018100' => 'mdo', 'Medtr4g124160' => 'mtr', 'Migut.L01260' => 'egut', 'Nitab4.5_0000008g0440' => 'nta', 'Nitab4.5_0000207g0170' => 'nta', 'Nitab4.5_0007671g0030' => 'nta', 'Nitab4.5_0010853g0020' => 'nta', 'Oeu057656.1' => 'oeu', 'PGSC0003DMG400005638' => 'stu', 'PGSC0003DMG400005639' => 'stu', 'Phvul.009G222800' => 'pvu', 'Potri.009G132400' => 'ptr', 'Potri.009G163001' => 'ptr', 'Potri.011G000700' => 'ptr', 'Potri.011G004800' => 'ptr', 'Prupe.1G509300' => 'ppe', 'Prupe.1G509700' => 'ppe', 'Prupe.1G510400' => 'ppe', 'Prupe.1G510700' => 'ppe', 'Prupe.1G512600' => 'ppe', 'Prupe.2G073200' => 'ppe', 'Prupe.3G059500' => 'ppe', 'Prupe.3G059600' => 'ppe', 'Prupe.3G246100' => 'ppe', 'Prupe.3G265100' => 'ppe', 'Prupe.4G034700' => 'ppe', 'Prupe.4G052100' => 'ppe', 'Prupe.4G053600' => 'ppe', 'Prupe.5G068800' => 'ppe', 'Prupe.5G070600' => 'ppe', 'Prupe.6G075400' => 'ppe', 'Prupe.6G075500' => 'ppe', 'Prupe.6G076400' => 'ppe', 'Prupe.8G110700' => 'ppe', 'Psat4g020960' => 'psa', 'PSO135G0788' => 'pso', 'PSO210G6463' => 'pso', 'PSO384G0370' => 'pso', 'PSO386G0056' => 'pso', 'QL01p006048' => 'qlo', 'QL02p054283' => 'qlo', 'QL05p008000' => 'qlo', 'QL05p008212' => 'qlo', 'QL05p008950' => 'qlo', 'QL05p009042' => 'qlo', 'QL05p009518' => 'qlo', 'QL05p012589' => 'qlo', 'QL05p012608' => 'qlo', 'QL05p012650' => 'qlo', 'QL05p012667' => 'qlo', 'QL05p014501' => 'qlo', 'QL05p052800' => 'qlo', 'QL05p065010' => 'qlo', 'QL05p074156' => 'qlo', 'QL05p074160' => 'qlo', 'QL05p074174' => 'qlo', 'QL05p074178' => 'qlo', 'QL05p074214' => 'qlo', 'QL06p001050' => 'qlo', 'QL06p001056' => 'qlo', 'QL06p006093' => 'qlo', 'QL06p006111' => 'qlo', 'QL07p019784' => 'qlo', 'QL07p019801' => 'qlo', 'QL07p036110' => 'qlo', 'QL07p036134' => 'qlo', 'QL07p036147' => 'qlo', 'QL07p036156' => 'qlo', 'QL07p036300' => 'qlo', 'QL07p036320' => 'qlo', 'QL08p014547' => 'qlo', 'QL08p014551' => 'qlo', 'QL08p043319' => 'qlo', 'QL08p043324' => 'qlo', 'QL11p009094' => 'qlo', 'RcHm_v2.0_Chr1g0380481' => 'rch', 'RcHm_v2.0_Chr2g0089331' => 'rch', 'RcHm_v2.0_Chr2g0123691' => 'rch', 'RcHm_v2.0_Chr2g0151111' => 'rch', 'RcHm_v2.0_Chr2g0163011' => 'rch', 'RcHm_v2.0_Chr2g0163051' => 'rch', 'RcHm_v2.0_Chr2g0164671' => 'rch', 'RcHm_v2.0_Chr2g0164681' => 'rch', 'RcHm_v2.0_Chr2g0164721' => 'rch', 'RcHm_v2.0_Chr3g0449911' => 'rch', 'RcHm_v2.0_Chr3g0450211' => 'rch', 'RcHm_v2.0_Chr3g0457271' => 'rch', 'RcHm_v2.0_Chr5g0018111' => 'rch', 'RcHm_v2.0_Chr5g0021011' => 'rch', 'RcHm_v2.0_Chr5g0081171' => 'rch', 'RcHm_v2.0_Chr5g0081211' => 'rch', 'RcHm_v2.0_Chr6g0275871' => 'rch', 'RcHm_v2.0_Chr6g0276071' => 'rch', 'RcHm_v2.0_Chr6g0285591' => 'rch', 'RcHm_v2.0_Chr6g0291931' => 'rch', 'RcHm_v2.0_Chr6g0292091' => 'rch', 'RcHm_v2.0_Chr6g0292271' => 'rch', 'RcHm_v2.0_Chr7g0221261' => 'rch', 'Rhsim08G0219900' => 'rsi', 'Rhsim08G0220200' => 'rsi', 'Rhsim08G0237800' => 'rsi', 'Rhsim08G0238800' => 'rsi', 'Sabra09G0102700' => 'sbr', 'Sabra09G0127200' => 'sbr', 'Sabra11G0003700' => 'sbr', 'Sabra15G0014700' => 'sbr', 'Sc19g0000590' => 'sci', 'Sc19g0001870' => 'sci', 'SGA_v2.0_scaffold1G00346' => 'sas', 'SGA_v2.0_scaffold1G00575' => 'sas', 'SGA_v2.0_scaffold1G00761' => 'sas', 'SGA_v2.0_scaffold232G43501' => 'sas', 'TAR625G1137' => 'tar', 'Thecc.03G222100' => 'tca', 'TPR.G12691' => 'tpr', 'TWI34G0727' => 'twi', 'TWI36G0117' => 'twi', 'VMungo1309G0868' => 'vmu' ), 'gf_id' => 'HOM05D001729', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001729' ), 'data_identifier' => 'HOM05D001729', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001729', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '375', 'num_species' => '42' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'Ah.07g204710' => 'amhyb', 'AUR62006001' => 'cqu', 'AUR62006002' => 'cqu', 'AUR62006003' => 'cqu', 'AUR62015641' => 'cqu', 'AUR62027174' => 'cqu', 'AUR62035623' => 'cqu', 'AUR62035624' => 'cqu', 'AUR62035625' => 'cqu', 'AUR62035626' => 'cqu', 'CAN.G1110.53' => 'can', 'CANSAT80G0415' => 'cansat', 'Ca_21364_v3' => 'car', 'COL.COLO4_30693' => 'col', 'COL.COLO4_30694' => 'col', 'COL.COLO4_30695' => 'col', 'COL.COLO4_30696' => 'col', 'COL.COLO4_34020' => 'col', 'DCAR_004585' => 'dca', 'Dinv04029' => 'din', 'Dinv34857' => 'din', 'Duzib147G0011' => 'dzi', 'Duzib170G0599' => 'dzi', 'Duzib192G1051' => 'dzi', 'FAN01G0708' => 'fan', 'FAN01G0742' => 'fan', 'FAN02G0048' => 'fan', 'FAN02G0583' => 'fan', 'FAN02G0688' => 'fan', 'FAN02G1588' => 'fan', 'FAN02G2194' => 'fan', 'FAN02G2750' => 'fan', 'FAN02G3094' => 'fan', 'FAN02G3887' => 'fan', 'FAN02G3911' => 'fan', 'FAN02G3994' => 'fan', 'FAN02G4432' => 'fan', 'FAN02G4556' => 'fan', 'FAN03G1977' => 'fan', 'FAN03G2781' => 'fan', 'FAN03G2850' => 'fan', 'FAN03G3155' => 'fan', 'FAN04G2487' => 'fan', 'FAN05G0208' => 'fan', 'FAN05G0656' => 'fan', 'FAN05G0696' => 'fan', 'FAN05G0810' => 'fan', 'FAN05G1447' => 'fan', 'FAN05G2640' => 'fan', 'FAN05G2911' => 'fan', 'FAN05G3901' => 'fan', 'FAN05G4859' => 'fan', 'FAN05G4861' => 'fan', 'FAN05G4988' => 'fan', 'FAN05G5187' => 'fan', 'FAN05G5452' => 'fan', 'FAN05G5500' => 'fan', 'FAN05G5688' => 'fan', 'FAN06G0177' => 'fan', 'FAN06G0675' => 'fan', 'FAN06G1290' => 'fan', 'FAN06G2191' => 'fan', 'FAN06G2405' => 'fan', 'FAN06G3231' => 'fan', 'FAN06G3932' => 'fan', 'FAN07G0163' => 'fan', 'FAN07G0471' => 'fan', 'FAN07G1354' => 'fan', 'FAN08G0338' => 'fan', 'FAN08G1373' => 'fan', 'FAN08G2539' => 'fan', 'FAN08G2728' => 'fan', 'FAN09G0608' => 'fan', 'FAN09G1136' => 'fan', 'FAN09G1958' => 'fan', 'FAN09G2508' => 'fan', 'FAN09G2597' => 'fan', 'FAN09G2658' => 'fan', 'FAN09G2757' => 'fan', 'FAN09G2983' => 'fan', 'FAN09G3130' => 'fan', 'FAN09G3565' => 'fan', 'FAN09G3613' => 'fan', 'FAN09G4011' => 'fan', 'FAN09G4239' => 'fan', 'FAN09G4277' => 'fan', 'FAN09G4720' => 'fan', 'FAN11G0139' => 'fan', 'FAN11G1727' => 'fan', 'FAN11G2672' => 'fan', 'FAN11G2795' => 'fan', 'FAN11G3238' => 'fan', 'FAN11G3734' => 'fan', 'FAN12G0631' => 'fan', 'FAN12G2239' => 'fan', 'FAN12G2308' => 'fan', 'FAN12G2569' => 'fan', 'FAN12G2623' => 'fan', 'FAN13G3182' => 'fan', 'FAN14G0053' => 'fan', 'FAN14G0370' => 'fan', 'FAN14G0382' => 'fan', 'FAN14G0421' => 'fan', 'FAN14G0866' => 'fan', 'FAN14G1187' => 'fan', 'FAN14G1727' => 'fan', 'FAN14G1791' => 'fan', 'FAN14G2361' => 'fan', 'FAN14G2668' => 'fan', 'FAN14G2770' => 'fan', 'FAN14G2874' => 'fan', 'FAN14G3193' => 'fan', 'FAN14G3624' => 'fan', 'FAN14G3676' => 'fan', 'FAN14G3807' => 'fan', 'FAN14G4082' => 'fan', 'FAN14G4342' => 'fan', 'FAN14G4985' => 'fan', 'FAN14G5126' => 'fan', 'FAN14G5781' => 'fan', 'FAN14G5808' => 'fan', 'FAN14G5949' => 'fan', 'FAN15G0828' => 'fan', 'FAN15G1054' => 'fan', 'FAN15G2023' => 'fan', 'FAN15G2506' => 'fan', 'FAN16G0128' => 'fan', 'FAN16G0249' => 'fan', 'FAN16G0429' => 'fan', 'FAN16G1493' => 'fan', 'FAN16G2210' => 'fan', 'FAN16G2506' => 'fan', 'FAN18G1542' => 'fan', 'FAN18G4057' => 'fan', 'FAN19G0745' => 'fan', 'FAN19G1216' => 'fan', 'FAN19G1733' => 'fan', 'FAN20G0258' => 'fan', 'FAN20G1095' => 'fan', 'FAN20G1557' => 'fan', 'FAN21G0302' => 'fan', 'FAN21G0519' => 'fan', 'FAN21G0970' => 'fan', 'FAN21G1159' => 'fan', 'FAN21G1312' => 'fan', 'FAN21G1440' => 'fan', 'FAN21G1715' => 'fan', 'FAN23G1584' => 'fan', 'FAN24G0045' => 'fan', 'FAN24G0053' => 'fan', 'FAN24G1500' => 'fan', 'FAN24G1817' => 'fan', 'FAN24G2147' => 'fan', 'FAN24G2236' => 'fan', 'FAN24G2446' => 'fan', 'FAN24G2684' => 'fan', 'FAN25G0187' => 'fan', 'FAN25G0505' => 'fan', 'FAN25G0589' => 'fan', 'FAN25G3663' => 'fan', 'FAN26G1025' => 'fan', 'FAN26G2860' => 'fan', 'FAN27G1329' => 'fan', 'FAN27G3392' => 'fan', 'FvH4_1g02011' => 'fve', 'FvH4_1g06511' => 'fve', 'FvH4_2g19900' => 'fve', 'FvH4_2g19920' => 'fve', 'FvH4_2g24261' => 'fve', 'FvH4_2g24270' => 'fve', 'FvH4_2g24631' => 'fve', 'FvH4_2g30622' => 'fve', 'FvH4_3g12920' => 'fve', 'FvH4_3g30171' => 'fve', 'FvH4_3g35490' => 'fve', 'FvH4_3g43682' => 'fve', 'FvH4_3g43730' => 'fve', 'FvH4_3g43732' => 'fve', 'FvH4_3g43751' => 'fve', 'FvH4_3g43752' => 'fve', 'FvH4_3g43770' => 'fve', 'FvH4_3g44471' => 'fve', 'FvH4_3g44510' => 'fve', 'FvH4_3g44582' => 'fve', 'FvH4_4g16921' => 'fve', 'FvH4_4g17121' => 'fve', 'FvH4_4g17782' => 'fve', 'FvH4_4g17783' => 'fve', 'FvH4_4g18120' => 'fve', 'FvH4_4g31310' => 'fve', 'FvH4_4g35052' => 'fve', 'FvH4_5g30862' => 'fve', 'FvH4_6g01541' => 'fve', 'FvH4_6g02021' => 'fve', 'FvH4_6g02041' => 'fve', 'FvH4_6g02071' => 'fve', 'FvH4_6g02171' => 'fve', 'FvH4_6g03181' => 'fve', 'FvH4_6g03182' => 'fve', 'FvH4_6g03221' => 'fve', 'FvH4_6g03380' => 'fve', 'FvH4_6g05201' => 'fve', 'FvH4_6g05203' => 'fve', 'FvH4_6g20231' => 'fve', 'FvH4_6g31981' => 'fve', 'FvH4_6g32061' => 'fve', 'FvH4_6g37041' => 'fve', 'FvH4_6g37932' => 'fve', 'FvH4_6g38731' => 'fve', 'FvH4_6g39370' => 'fve', 'FvH4_6g39371' => 'fve', 'FvH4_6g40891' => 'fve', 'FvH4_6g40892' => 'fve', 'FvH4_6g43143' => 'fve', 'FvH4_6g45251' => 'fve', 'FvH4_6g45260' => 'fve', 'FvH4_6g45291' => 'fve', 'FvH4_6g45890' => 'fve', 'FvH4_6g46240' => 'fve', 'FvH4_6g46241' => 'fve', 'FvH4_6g46242' => 'fve', 'FvH4_6g46260' => 'fve', 'FvH4_6g46280' => 'fve', 'FvH4_6g46380' => 'fve', 'FvH4_7g12841' => 'fve', 'FvH4_7g31431' => 'fve', 'Glyma.09G075900' => 'gma', 'Gohir.A09G096401' => 'ghi', 'Gohir.D09G096101' => 'ghi', 'Gorai.006G112800' => 'gra', 'HanXRQChr04g0121411' => 'han', 'Hund15878' => 'sun', 'Lj2A1107G68' => 'lonja', 'Lj2A630G63' => 'lonja', 'Lj2A946T25' => 'lonja', 'Lj2C714T1' => 'lonja', 'Lj2C966T3' => 'lonja', 'Lj2C966T4' => 'lonja', 'Lj4g0002979' => 'lja', 'Lsat_1_v5_gn_5_30901' => 'lsa', 'Lsat_1_v5_gn_5_31100' => 'lsa', 'Lsat_1_v5_gn_5_38600' => 'lsa', 'Lsat_1_v5_gn_6_92061' => 'lsa', 'Manes.05G071301' => 'mes', 'MD02G1008700' => 'mdo', 'MD02G1008900' => 'mdo', 'MD03G1256400' => 'mdo', 'MD04G1180900' => 'mdo', 'MD04G1181000' => 'mdo', 'MD04G1181200' => 'mdo', 'MD05G1244200' => 'mdo', 'MD05G1324200' => 'mdo', 'MD09G1201600' => 'mdo', 'MD10G1000600' => 'mdo', 'MD14G1026900' => 'mdo', 'MD14G1187900' => 'mdo', 'MD15G1017800' => 'mdo', 'MD15G1018100' => 'mdo', 'Medtr4g124160' => 'mtr', 'Migut.L01260' => 'egut', 'Nitab4.5_0000008g0440' => 'nta', 'Nitab4.5_0000207g0170' => 'nta', 'Nitab4.5_0007671g0030' => 'nta', 'Nitab4.5_0010853g0020' => 'nta', 'Oeu057656.1' => 'oeu', 'PGSC0003DMG400005638' => 'stu', 'PGSC0003DMG400005639' => 'stu', 'Phvul.009G222800' => 'pvu', 'Potri.009G132400' => 'ptr', 'Potri.009G163001' => 'ptr', 'Potri.011G000700' => 'ptr', 'Potri.011G004800' => 'ptr', 'Prupe.1G509300' => 'ppe', 'Prupe.1G509700' => 'ppe', 'Prupe.1G510400' => 'ppe', 'Prupe.1G510700' => 'ppe', 'Prupe.1G512600' => 'ppe', 'Prupe.2G073200' => 'ppe', 'Prupe.3G059500' => 'ppe', 'Prupe.3G059600' => 'ppe', 'Prupe.3G246100' => 'ppe', 'Prupe.3G265100' => 'ppe', 'Prupe.4G034700' => 'ppe', 'Prupe.4G052100' => 'ppe', 'Prupe.4G053600' => 'ppe', 'Prupe.5G068800' => 'ppe', 'Prupe.5G070600' => 'ppe', 'Prupe.6G075400' => 'ppe', 'Prupe.6G075500' => 'ppe', 'Prupe.6G076400' => 'ppe', 'Prupe.8G110700' => 'ppe', 'Psat4g020960' => 'psa', 'PSO135G0788' => 'pso', 'PSO210G6463' => 'pso', 'PSO384G0370' => 'pso', 'PSO386G0056' => 'pso', 'QL01p006048' => 'qlo', 'QL02p054283' => 'qlo', 'QL05p008000' => 'qlo', 'QL05p008212' => 'qlo', 'QL05p008950' => 'qlo', 'QL05p009042' => 'qlo', 'QL05p009518' => 'qlo', 'QL05p012589' => 'qlo', 'QL05p012608' => 'qlo', 'QL05p012650' => 'qlo', 'QL05p012667' => 'qlo', 'QL05p014501' => 'qlo', 'QL05p052800' => 'qlo', 'QL05p065010' => 'qlo', 'QL05p074156' => 'qlo', 'QL05p074160' => 'qlo', 'QL05p074174' => 'qlo', 'QL05p074178' => 'qlo', 'QL05p074214' => 'qlo', 'QL06p001050' => 'qlo', 'QL06p001056' => 'qlo', 'QL06p006093' => 'qlo', 'QL06p006111' => 'qlo', 'QL07p019784' => 'qlo', 'QL07p019801' => 'qlo', 'QL07p036110' => 'qlo', 'QL07p036134' => 'qlo', 'QL07p036147' => 'qlo', 'QL07p036156' => 'qlo', 'QL07p036300' => 'qlo', 'QL07p036320' => 'qlo', 'QL08p014547' => 'qlo', 'QL08p014551' => 'qlo', 'QL08p043319' => 'qlo', 'QL08p043324' => 'qlo', 'QL11p009094' => 'qlo', 'RcHm_v2.0_Chr1g0380481' => 'rch', 'RcHm_v2.0_Chr2g0089331' => 'rch', 'RcHm_v2.0_Chr2g0123691' => 'rch', 'RcHm_v2.0_Chr2g0151111' => 'rch', 'RcHm_v2.0_Chr2g0163011' => 'rch', 'RcHm_v2.0_Chr2g0163051' => 'rch', 'RcHm_v2.0_Chr2g0164671' => 'rch', 'RcHm_v2.0_Chr2g0164681' => 'rch', 'RcHm_v2.0_Chr2g0164721' => 'rch', 'RcHm_v2.0_Chr3g0449911' => 'rch', 'RcHm_v2.0_Chr3g0450211' => 'rch', 'RcHm_v2.0_Chr3g0457271' => 'rch', 'RcHm_v2.0_Chr5g0018111' => 'rch', 'RcHm_v2.0_Chr5g0021011' => 'rch', 'RcHm_v2.0_Chr5g0081171' => 'rch', 'RcHm_v2.0_Chr5g0081211' => 'rch', 'RcHm_v2.0_Chr6g0275871' => 'rch', 'RcHm_v2.0_Chr6g0276071' => 'rch', 'RcHm_v2.0_Chr6g0285591' => 'rch', 'RcHm_v2.0_Chr6g0291931' => 'rch', 'RcHm_v2.0_Chr6g0292091' => 'rch', 'RcHm_v2.0_Chr6g0292271' => 'rch', 'RcHm_v2.0_Chr7g0221261' => 'rch', 'Rhsim08G0219900' => 'rsi', 'Rhsim08G0220200' => 'rsi', 'Rhsim08G0237800' => 'rsi', 'Rhsim08G0238800' => 'rsi', 'Sabra09G0102700' => 'sbr', 'Sabra09G0127200' => 'sbr', 'Sabra11G0003700' => 'sbr', 'Sabra15G0014700' => 'sbr', 'Sc19g0000590' => 'sci', 'Sc19g0001870' => 'sci', 'SGA_v2.0_scaffold1G00346' => 'sas', 'SGA_v2.0_scaffold1G00575' => 'sas', 'SGA_v2.0_scaffold1G00761' => 'sas', 'SGA_v2.0_scaffold232G43501' => 'sas', 'TAR625G1137' => 'tar', 'Thecc.03G222100' => 'tca', 'TPR.G12691' => 'tpr', 'TWI34G0727' => 'twi', 'TWI36G0117' => 'twi', 'VMungo1309G0868' => 'vmu' ) $gf_id = 'HOM05D001729' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001729' ) $data_identifier = 'HOM05D001729' $data_type = 'gf_id' $species_gene_counts = array( 'amhyb' => (int) 1, 'cqu' => (int) 9, 'can' => (int) 1, 'cansat' => (int) 1, 'car' => (int) 1, 'col' => (int) 5, 'dca' => (int) 1, 'din' => (int) 2, 'dzi' => (int) 3, 'fan' => (int) 140, 'fve' => (int) 62, 'gma' => (int) 1, 'ghi' => (int) 2, 'gra' => (int) 1, 'han' => (int) 1, 'sun' => (int) 1, 'lonja' => (int) 6, 'lja' => (int) 1, 'lsa' => (int) 4, 'mes' => (int) 1, 'mdo' => (int) 14, 'mtr' => (int) 1, 'egut' => (int) 1, 'nta' => (int) 4, 'oeu' => (int) 1, 'stu' => (int) 2, 'pvu' => (int) 1, 'ptr' => (int) 4, 'ppe' => (int) 19, 'psa' => (int) 1, 'pso' => (int) 4, 'qlo' => (int) 36, 'rch' => (int) 23, 'rsi' => (int) 4, 'sbr' => (int) 4, 'sci' => (int) 2, 'sas' => (int) 4, 'tar' => (int) 1, 'tca' => (int) 1, 'tpr' => (int) 1, 'twi' => (int) 2, 'vmu' => (int) 1 ) $gf_gene_species = 'vmu' $gf_gene_id = 'VMungo1309G0868' $species_info = array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ) $local_species = 'mtr' $disabled = '' $selected = '' $num_hits = (int) 0
Warning (2): count(): Parameter must be an array or an object that implements Countable [APP/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp, line 33]Code Context $disabled = (!array_key_exists($local_species,$species_gene_counts))?"disabled":""; $selected = (isset($selected_species) && array_key_exists($local_species,$selected_species))?"checked='checked'":""; $num_hits = (array_key_exists($local_species,$species_gene_counts))?count($species_gene_counts[$local_species]):0; $viewFile = '/www/bioinformatics01_ro/plaza/_dev_instances/feedback/app/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp' $dataForView = array( 'sidebar_info' => array( 'gf_id' => 'HOM05D001729', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '375', 'num_species' => '42' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'Ah.07g204710' => 'amhyb', 'AUR62006001' => 'cqu', 'AUR62006002' => 'cqu', 'AUR62006003' => 'cqu', 'AUR62015641' => 'cqu', 'AUR62027174' => 'cqu', 'AUR62035623' => 'cqu', 'AUR62035624' => 'cqu', 'AUR62035625' => 'cqu', 'AUR62035626' => 'cqu', 'CAN.G1110.53' => 'can', 'CANSAT80G0415' => 'cansat', 'Ca_21364_v3' => 'car', 'COL.COLO4_30693' => 'col', 'COL.COLO4_30694' => 'col', 'COL.COLO4_30695' => 'col', 'COL.COLO4_30696' => 'col', 'COL.COLO4_34020' => 'col', 'DCAR_004585' => 'dca', 'Dinv04029' => 'din', 'Dinv34857' => 'din', 'Duzib147G0011' => 'dzi', 'Duzib170G0599' => 'dzi', 'Duzib192G1051' => 'dzi', 'FAN01G0708' => 'fan', 'FAN01G0742' => 'fan', 'FAN02G0048' => 'fan', 'FAN02G0583' => 'fan', 'FAN02G0688' => 'fan', 'FAN02G1588' => 'fan', 'FAN02G2194' => 'fan', 'FAN02G2750' => 'fan', 'FAN02G3094' => 'fan', 'FAN02G3887' => 'fan', 'FAN02G3911' => 'fan', 'FAN02G3994' => 'fan', 'FAN02G4432' => 'fan', 'FAN02G4556' => 'fan', 'FAN03G1977' => 'fan', 'FAN03G2781' => 'fan', 'FAN03G2850' => 'fan', 'FAN03G3155' => 'fan', 'FAN04G2487' => 'fan', 'FAN05G0208' => 'fan', 'FAN05G0656' => 'fan', 'FAN05G0696' => 'fan', 'FAN05G0810' => 'fan', 'FAN05G1447' => 'fan', 'FAN05G2640' => 'fan', 'FAN05G2911' => 'fan', 'FAN05G3901' => 'fan', 'FAN05G4859' => 'fan', 'FAN05G4861' => 'fan', 'FAN05G4988' => 'fan', 'FAN05G5187' => 'fan', 'FAN05G5452' => 'fan', 'FAN05G5500' => 'fan', 'FAN05G5688' => 'fan', 'FAN06G0177' => 'fan', 'FAN06G0675' => 'fan', 'FAN06G1290' => 'fan', 'FAN06G2191' => 'fan', 'FAN06G2405' => 'fan', 'FAN06G3231' => 'fan', 'FAN06G3932' => 'fan', 'FAN07G0163' => 'fan', 'FAN07G0471' => 'fan', 'FAN07G1354' => 'fan', 'FAN08G0338' => 'fan', 'FAN08G1373' => 'fan', 'FAN08G2539' => 'fan', 'FAN08G2728' => 'fan', 'FAN09G0608' => 'fan', 'FAN09G1136' => 'fan', 'FAN09G1958' => 'fan', 'FAN09G2508' => 'fan', 'FAN09G2597' => 'fan', 'FAN09G2658' => 'fan', 'FAN09G2757' => 'fan', 'FAN09G2983' => 'fan', 'FAN09G3130' => 'fan', 'FAN09G3565' => 'fan', 'FAN09G3613' => 'fan', 'FAN09G4011' => 'fan', 'FAN09G4239' => 'fan', 'FAN09G4277' => 'fan', 'FAN09G4720' => 'fan', 'FAN11G0139' => 'fan', 'FAN11G1727' => 'fan', 'FAN11G2672' => 'fan', 'FAN11G2795' => 'fan', 'FAN11G3238' => 'fan', 'FAN11G3734' => 'fan', 'FAN12G0631' => 'fan', 'FAN12G2239' => 'fan', 'FAN12G2308' => 'fan', 'FAN12G2569' => 'fan', 'FAN12G2623' => 'fan', 'FAN13G3182' => 'fan', 'FAN14G0053' => 'fan', 'FAN14G0370' => 'fan', 'FAN14G0382' => 'fan', 'FAN14G0421' => 'fan', 'FAN14G0866' => 'fan', 'FAN14G1187' => 'fan', 'FAN14G1727' => 'fan', 'FAN14G1791' => 'fan', 'FAN14G2361' => 'fan', 'FAN14G2668' => 'fan', 'FAN14G2770' => 'fan', 'FAN14G2874' => 'fan', 'FAN14G3193' => 'fan', 'FAN14G3624' => 'fan', 'FAN14G3676' => 'fan', 'FAN14G3807' => 'fan', 'FAN14G4082' => 'fan', 'FAN14G4342' => 'fan', 'FAN14G4985' => 'fan', 'FAN14G5126' => 'fan', 'FAN14G5781' => 'fan', 'FAN14G5808' => 'fan', 'FAN14G5949' => 'fan', 'FAN15G0828' => 'fan', 'FAN15G1054' => 'fan', 'FAN15G2023' => 'fan', 'FAN15G2506' => 'fan', 'FAN16G0128' => 'fan', 'FAN16G0249' => 'fan', 'FAN16G0429' => 'fan', 'FAN16G1493' => 'fan', 'FAN16G2210' => 'fan', 'FAN16G2506' => 'fan', 'FAN18G1542' => 'fan', 'FAN18G4057' => 'fan', 'FAN19G0745' => 'fan', 'FAN19G1216' => 'fan', 'FAN19G1733' => 'fan', 'FAN20G0258' => 'fan', 'FAN20G1095' => 'fan', 'FAN20G1557' => 'fan', 'FAN21G0302' => 'fan', 'FAN21G0519' => 'fan', 'FAN21G0970' => 'fan', 'FAN21G1159' => 'fan', 'FAN21G1312' => 'fan', 'FAN21G1440' => 'fan', 'FAN21G1715' => 'fan', 'FAN23G1584' => 'fan', 'FAN24G0045' => 'fan', 'FAN24G0053' => 'fan', 'FAN24G1500' => 'fan', 'FAN24G1817' => 'fan', 'FAN24G2147' => 'fan', 'FAN24G2236' => 'fan', 'FAN24G2446' => 'fan', 'FAN24G2684' => 'fan', 'FAN25G0187' => 'fan', 'FAN25G0505' => 'fan', 'FAN25G0589' => 'fan', 'FAN25G3663' => 'fan', 'FAN26G1025' => 'fan', 'FAN26G2860' => 'fan', 'FAN27G1329' => 'fan', 'FAN27G3392' => 'fan', 'FvH4_1g02011' => 'fve', 'FvH4_1g06511' => 'fve', 'FvH4_2g19900' => 'fve', 'FvH4_2g19920' => 'fve', 'FvH4_2g24261' => 'fve', 'FvH4_2g24270' => 'fve', 'FvH4_2g24631' => 'fve', 'FvH4_2g30622' => 'fve', 'FvH4_3g12920' => 'fve', 'FvH4_3g30171' => 'fve', 'FvH4_3g35490' => 'fve', 'FvH4_3g43682' => 'fve', 'FvH4_3g43730' => 'fve', 'FvH4_3g43732' => 'fve', 'FvH4_3g43751' => 'fve', 'FvH4_3g43752' => 'fve', 'FvH4_3g43770' => 'fve', 'FvH4_3g44471' => 'fve', 'FvH4_3g44510' => 'fve', 'FvH4_3g44582' => 'fve', 'FvH4_4g16921' => 'fve', 'FvH4_4g17121' => 'fve', 'FvH4_4g17782' => 'fve', 'FvH4_4g17783' => 'fve', 'FvH4_4g18120' => 'fve', 'FvH4_4g31310' => 'fve', 'FvH4_4g35052' => 'fve', 'FvH4_5g30862' => 'fve', 'FvH4_6g01541' => 'fve', 'FvH4_6g02021' => 'fve', 'FvH4_6g02041' => 'fve', 'FvH4_6g02071' => 'fve', 'FvH4_6g02171' => 'fve', 'FvH4_6g03181' => 'fve', 'FvH4_6g03182' => 'fve', 'FvH4_6g03221' => 'fve', 'FvH4_6g03380' => 'fve', 'FvH4_6g05201' => 'fve', 'FvH4_6g05203' => 'fve', 'FvH4_6g20231' => 'fve', 'FvH4_6g31981' => 'fve', 'FvH4_6g32061' => 'fve', 'FvH4_6g37041' => 'fve', 'FvH4_6g37932' => 'fve', 'FvH4_6g38731' => 'fve', 'FvH4_6g39370' => 'fve', 'FvH4_6g39371' => 'fve', 'FvH4_6g40891' => 'fve', 'FvH4_6g40892' => 'fve', 'FvH4_6g43143' => 'fve', 'FvH4_6g45251' => 'fve', 'FvH4_6g45260' => 'fve', 'FvH4_6g45291' => 'fve', 'FvH4_6g45890' => 'fve', 'FvH4_6g46240' => 'fve', 'FvH4_6g46241' => 'fve', 'FvH4_6g46242' => 'fve', 'FvH4_6g46260' => 'fve', 'FvH4_6g46280' => 'fve', 'FvH4_6g46380' => 'fve', 'FvH4_7g12841' => 'fve', 'FvH4_7g31431' => 'fve', 'Glyma.09G075900' => 'gma', 'Gohir.A09G096401' => 'ghi', 'Gohir.D09G096101' => 'ghi', 'Gorai.006G112800' => 'gra', 'HanXRQChr04g0121411' => 'han', 'Hund15878' => 'sun', 'Lj2A1107G68' => 'lonja', 'Lj2A630G63' => 'lonja', 'Lj2A946T25' => 'lonja', 'Lj2C714T1' => 'lonja', 'Lj2C966T3' => 'lonja', 'Lj2C966T4' => 'lonja', 'Lj4g0002979' => 'lja', 'Lsat_1_v5_gn_5_30901' => 'lsa', 'Lsat_1_v5_gn_5_31100' => 'lsa', 'Lsat_1_v5_gn_5_38600' => 'lsa', 'Lsat_1_v5_gn_6_92061' => 'lsa', 'Manes.05G071301' => 'mes', 'MD02G1008700' => 'mdo', 'MD02G1008900' => 'mdo', 'MD03G1256400' => 'mdo', 'MD04G1180900' => 'mdo', 'MD04G1181000' => 'mdo', 'MD04G1181200' => 'mdo', 'MD05G1244200' => 'mdo', 'MD05G1324200' => 'mdo', 'MD09G1201600' => 'mdo', 'MD10G1000600' => 'mdo', 'MD14G1026900' => 'mdo', 'MD14G1187900' => 'mdo', 'MD15G1017800' => 'mdo', 'MD15G1018100' => 'mdo', 'Medtr4g124160' => 'mtr', 'Migut.L01260' => 'egut', 'Nitab4.5_0000008g0440' => 'nta', 'Nitab4.5_0000207g0170' => 'nta', 'Nitab4.5_0007671g0030' => 'nta', 'Nitab4.5_0010853g0020' => 'nta', 'Oeu057656.1' => 'oeu', 'PGSC0003DMG400005638' => 'stu', 'PGSC0003DMG400005639' => 'stu', 'Phvul.009G222800' => 'pvu', 'Potri.009G132400' => 'ptr', 'Potri.009G163001' => 'ptr', 'Potri.011G000700' => 'ptr', 'Potri.011G004800' => 'ptr', 'Prupe.1G509300' => 'ppe', 'Prupe.1G509700' => 'ppe', 'Prupe.1G510400' => 'ppe', 'Prupe.1G510700' => 'ppe', 'Prupe.1G512600' => 'ppe', 'Prupe.2G073200' => 'ppe', 'Prupe.3G059500' => 'ppe', 'Prupe.3G059600' => 'ppe', 'Prupe.3G246100' => 'ppe', 'Prupe.3G265100' => 'ppe', 'Prupe.4G034700' => 'ppe', 'Prupe.4G052100' => 'ppe', 'Prupe.4G053600' => 'ppe', 'Prupe.5G068800' => 'ppe', 'Prupe.5G070600' => 'ppe', 'Prupe.6G075400' => 'ppe', 'Prupe.6G075500' => 'ppe', 'Prupe.6G076400' => 'ppe', 'Prupe.8G110700' => 'ppe', 'Psat4g020960' => 'psa', 'PSO135G0788' => 'pso', 'PSO210G6463' => 'pso', 'PSO384G0370' => 'pso', 'PSO386G0056' => 'pso', 'QL01p006048' => 'qlo', 'QL02p054283' => 'qlo', 'QL05p008000' => 'qlo', 'QL05p008212' => 'qlo', 'QL05p008950' => 'qlo', 'QL05p009042' => 'qlo', 'QL05p009518' => 'qlo', 'QL05p012589' => 'qlo', 'QL05p012608' => 'qlo', 'QL05p012650' => 'qlo', 'QL05p012667' => 'qlo', 'QL05p014501' => 'qlo', 'QL05p052800' => 'qlo', 'QL05p065010' => 'qlo', 'QL05p074156' => 'qlo', 'QL05p074160' => 'qlo', 'QL05p074174' => 'qlo', 'QL05p074178' => 'qlo', 'QL05p074214' => 'qlo', 'QL06p001050' => 'qlo', 'QL06p001056' => 'qlo', 'QL06p006093' => 'qlo', 'QL06p006111' => 'qlo', 'QL07p019784' => 'qlo', 'QL07p019801' => 'qlo', 'QL07p036110' => 'qlo', 'QL07p036134' => 'qlo', 'QL07p036147' => 'qlo', 'QL07p036156' => 'qlo', 'QL07p036300' => 'qlo', 'QL07p036320' => 'qlo', 'QL08p014547' => 'qlo', 'QL08p014551' => 'qlo', 'QL08p043319' => 'qlo', 'QL08p043324' => 'qlo', 'QL11p009094' => 'qlo', 'RcHm_v2.0_Chr1g0380481' => 'rch', 'RcHm_v2.0_Chr2g0089331' => 'rch', 'RcHm_v2.0_Chr2g0123691' => 'rch', 'RcHm_v2.0_Chr2g0151111' => 'rch', 'RcHm_v2.0_Chr2g0163011' => 'rch', 'RcHm_v2.0_Chr2g0163051' => 'rch', 'RcHm_v2.0_Chr2g0164671' => 'rch', 'RcHm_v2.0_Chr2g0164681' => 'rch', 'RcHm_v2.0_Chr2g0164721' => 'rch', 'RcHm_v2.0_Chr3g0449911' => 'rch', 'RcHm_v2.0_Chr3g0450211' => 'rch', 'RcHm_v2.0_Chr3g0457271' => 'rch', 'RcHm_v2.0_Chr5g0018111' => 'rch', 'RcHm_v2.0_Chr5g0021011' => 'rch', 'RcHm_v2.0_Chr5g0081171' => 'rch', 'RcHm_v2.0_Chr5g0081211' => 'rch', 'RcHm_v2.0_Chr6g0275871' => 'rch', 'RcHm_v2.0_Chr6g0276071' => 'rch', 'RcHm_v2.0_Chr6g0285591' => 'rch', 'RcHm_v2.0_Chr6g0291931' => 'rch', 'RcHm_v2.0_Chr6g0292091' => 'rch', 'RcHm_v2.0_Chr6g0292271' => 'rch', 'RcHm_v2.0_Chr7g0221261' => 'rch', 'Rhsim08G0219900' => 'rsi', 'Rhsim08G0220200' => 'rsi', 'Rhsim08G0237800' => 'rsi', 'Rhsim08G0238800' => 'rsi', 'Sabra09G0102700' => 'sbr', 'Sabra09G0127200' => 'sbr', 'Sabra11G0003700' => 'sbr', 'Sabra15G0014700' => 'sbr', 'Sc19g0000590' => 'sci', 'Sc19g0001870' => 'sci', 'SGA_v2.0_scaffold1G00346' => 'sas', 'SGA_v2.0_scaffold1G00575' => 'sas', 'SGA_v2.0_scaffold1G00761' => 'sas', 'SGA_v2.0_scaffold232G43501' => 'sas', 'TAR625G1137' => 'tar', 'Thecc.03G222100' => 'tca', 'TPR.G12691' => 'tpr', 'TWI34G0727' => 'twi', 'TWI36G0117' => 'twi', 'VMungo1309G0868' => 'vmu' ), 'gf_id' => 'HOM05D001729', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001729' ), 'data_identifier' => 'HOM05D001729', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001729', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '375', 'num_species' => '42' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'Ah.07g204710' => 'amhyb', 'AUR62006001' => 'cqu', 'AUR62006002' => 'cqu', 'AUR62006003' => 'cqu', 'AUR62015641' => 'cqu', 'AUR62027174' => 'cqu', 'AUR62035623' => 'cqu', 'AUR62035624' => 'cqu', 'AUR62035625' => 'cqu', 'AUR62035626' => 'cqu', 'CAN.G1110.53' => 'can', 'CANSAT80G0415' => 'cansat', 'Ca_21364_v3' => 'car', 'COL.COLO4_30693' => 'col', 'COL.COLO4_30694' => 'col', 'COL.COLO4_30695' => 'col', 'COL.COLO4_30696' => 'col', 'COL.COLO4_34020' => 'col', 'DCAR_004585' => 'dca', 'Dinv04029' => 'din', 'Dinv34857' => 'din', 'Duzib147G0011' => 'dzi', 'Duzib170G0599' => 'dzi', 'Duzib192G1051' => 'dzi', 'FAN01G0708' => 'fan', 'FAN01G0742' => 'fan', 'FAN02G0048' => 'fan', 'FAN02G0583' => 'fan', 'FAN02G0688' => 'fan', 'FAN02G1588' => 'fan', 'FAN02G2194' => 'fan', 'FAN02G2750' => 'fan', 'FAN02G3094' => 'fan', 'FAN02G3887' => 'fan', 'FAN02G3911' => 'fan', 'FAN02G3994' => 'fan', 'FAN02G4432' => 'fan', 'FAN02G4556' => 'fan', 'FAN03G1977' => 'fan', 'FAN03G2781' => 'fan', 'FAN03G2850' => 'fan', 'FAN03G3155' => 'fan', 'FAN04G2487' => 'fan', 'FAN05G0208' => 'fan', 'FAN05G0656' => 'fan', 'FAN05G0696' => 'fan', 'FAN05G0810' => 'fan', 'FAN05G1447' => 'fan', 'FAN05G2640' => 'fan', 'FAN05G2911' => 'fan', 'FAN05G3901' => 'fan', 'FAN05G4859' => 'fan', 'FAN05G4861' => 'fan', 'FAN05G4988' => 'fan', 'FAN05G5187' => 'fan', 'FAN05G5452' => 'fan', 'FAN05G5500' => 'fan', 'FAN05G5688' => 'fan', 'FAN06G0177' => 'fan', 'FAN06G0675' => 'fan', 'FAN06G1290' => 'fan', 'FAN06G2191' => 'fan', 'FAN06G2405' => 'fan', 'FAN06G3231' => 'fan', 'FAN06G3932' => 'fan', 'FAN07G0163' => 'fan', 'FAN07G0471' => 'fan', 'FAN07G1354' => 'fan', 'FAN08G0338' => 'fan', 'FAN08G1373' => 'fan', 'FAN08G2539' => 'fan', 'FAN08G2728' => 'fan', 'FAN09G0608' => 'fan', 'FAN09G1136' => 'fan', 'FAN09G1958' => 'fan', 'FAN09G2508' => 'fan', 'FAN09G2597' => 'fan', 'FAN09G2658' => 'fan', 'FAN09G2757' => 'fan', 'FAN09G2983' => 'fan', 'FAN09G3130' => 'fan', 'FAN09G3565' => 'fan', 'FAN09G3613' => 'fan', 'FAN09G4011' => 'fan', 'FAN09G4239' => 'fan', 'FAN09G4277' => 'fan', 'FAN09G4720' => 'fan', 'FAN11G0139' => 'fan', 'FAN11G1727' => 'fan', 'FAN11G2672' => 'fan', 'FAN11G2795' => 'fan', 'FAN11G3238' => 'fan', 'FAN11G3734' => 'fan', 'FAN12G0631' => 'fan', 'FAN12G2239' => 'fan', 'FAN12G2308' => 'fan', 'FAN12G2569' => 'fan', 'FAN12G2623' => 'fan', 'FAN13G3182' => 'fan', 'FAN14G0053' => 'fan', 'FAN14G0370' => 'fan', 'FAN14G0382' => 'fan', 'FAN14G0421' => 'fan', 'FAN14G0866' => 'fan', 'FAN14G1187' => 'fan', 'FAN14G1727' => 'fan', 'FAN14G1791' => 'fan', 'FAN14G2361' => 'fan', 'FAN14G2668' => 'fan', 'FAN14G2770' => 'fan', 'FAN14G2874' => 'fan', 'FAN14G3193' => 'fan', 'FAN14G3624' => 'fan', 'FAN14G3676' => 'fan', 'FAN14G3807' => 'fan', 'FAN14G4082' => 'fan', 'FAN14G4342' => 'fan', 'FAN14G4985' => 'fan', 'FAN14G5126' => 'fan', 'FAN14G5781' => 'fan', 'FAN14G5808' => 'fan', 'FAN14G5949' => 'fan', 'FAN15G0828' => 'fan', 'FAN15G1054' => 'fan', 'FAN15G2023' => 'fan', 'FAN15G2506' => 'fan', 'FAN16G0128' => 'fan', 'FAN16G0249' => 'fan', 'FAN16G0429' => 'fan', 'FAN16G1493' => 'fan', 'FAN16G2210' => 'fan', 'FAN16G2506' => 'fan', 'FAN18G1542' => 'fan', 'FAN18G4057' => 'fan', 'FAN19G0745' => 'fan', 'FAN19G1216' => 'fan', 'FAN19G1733' => 'fan', 'FAN20G0258' => 'fan', 'FAN20G1095' => 'fan', 'FAN20G1557' => 'fan', 'FAN21G0302' => 'fan', 'FAN21G0519' => 'fan', 'FAN21G0970' => 'fan', 'FAN21G1159' => 'fan', 'FAN21G1312' => 'fan', 'FAN21G1440' => 'fan', 'FAN21G1715' => 'fan', 'FAN23G1584' => 'fan', 'FAN24G0045' => 'fan', 'FAN24G0053' => 'fan', 'FAN24G1500' => 'fan', 'FAN24G1817' => 'fan', 'FAN24G2147' => 'fan', 'FAN24G2236' => 'fan', 'FAN24G2446' => 'fan', 'FAN24G2684' => 'fan', 'FAN25G0187' => 'fan', 'FAN25G0505' => 'fan', 'FAN25G0589' => 'fan', 'FAN25G3663' => 'fan', 'FAN26G1025' => 'fan', 'FAN26G2860' => 'fan', 'FAN27G1329' => 'fan', 'FAN27G3392' => 'fan', 'FvH4_1g02011' => 'fve', 'FvH4_1g06511' => 'fve', 'FvH4_2g19900' => 'fve', 'FvH4_2g19920' => 'fve', 'FvH4_2g24261' => 'fve', 'FvH4_2g24270' => 'fve', 'FvH4_2g24631' => 'fve', 'FvH4_2g30622' => 'fve', 'FvH4_3g12920' => 'fve', 'FvH4_3g30171' => 'fve', 'FvH4_3g35490' => 'fve', 'FvH4_3g43682' => 'fve', 'FvH4_3g43730' => 'fve', 'FvH4_3g43732' => 'fve', 'FvH4_3g43751' => 'fve', 'FvH4_3g43752' => 'fve', 'FvH4_3g43770' => 'fve', 'FvH4_3g44471' => 'fve', 'FvH4_3g44510' => 'fve', 'FvH4_3g44582' => 'fve', 'FvH4_4g16921' => 'fve', 'FvH4_4g17121' => 'fve', 'FvH4_4g17782' => 'fve', 'FvH4_4g17783' => 'fve', 'FvH4_4g18120' => 'fve', 'FvH4_4g31310' => 'fve', 'FvH4_4g35052' => 'fve', 'FvH4_5g30862' => 'fve', 'FvH4_6g01541' => 'fve', 'FvH4_6g02021' => 'fve', 'FvH4_6g02041' => 'fve', 'FvH4_6g02071' => 'fve', 'FvH4_6g02171' => 'fve', 'FvH4_6g03181' => 'fve', 'FvH4_6g03182' => 'fve', 'FvH4_6g03221' => 'fve', 'FvH4_6g03380' => 'fve', 'FvH4_6g05201' => 'fve', 'FvH4_6g05203' => 'fve', 'FvH4_6g20231' => 'fve', 'FvH4_6g31981' => 'fve', 'FvH4_6g32061' => 'fve', 'FvH4_6g37041' => 'fve', 'FvH4_6g37932' => 'fve', 'FvH4_6g38731' => 'fve', 'FvH4_6g39370' => 'fve', 'FvH4_6g39371' => 'fve', 'FvH4_6g40891' => 'fve', 'FvH4_6g40892' => 'fve', 'FvH4_6g43143' => 'fve', 'FvH4_6g45251' => 'fve', 'FvH4_6g45260' => 'fve', 'FvH4_6g45291' => 'fve', 'FvH4_6g45890' => 'fve', 'FvH4_6g46240' => 'fve', 'FvH4_6g46241' => 'fve', 'FvH4_6g46242' => 'fve', 'FvH4_6g46260' => 'fve', 'FvH4_6g46280' => 'fve', 'FvH4_6g46380' => 'fve', 'FvH4_7g12841' => 'fve', 'FvH4_7g31431' => 'fve', 'Glyma.09G075900' => 'gma', 'Gohir.A09G096401' => 'ghi', 'Gohir.D09G096101' => 'ghi', 'Gorai.006G112800' => 'gra', 'HanXRQChr04g0121411' => 'han', 'Hund15878' => 'sun', 'Lj2A1107G68' => 'lonja', 'Lj2A630G63' => 'lonja', 'Lj2A946T25' => 'lonja', 'Lj2C714T1' => 'lonja', 'Lj2C966T3' => 'lonja', 'Lj2C966T4' => 'lonja', 'Lj4g0002979' => 'lja', 'Lsat_1_v5_gn_5_30901' => 'lsa', 'Lsat_1_v5_gn_5_31100' => 'lsa', 'Lsat_1_v5_gn_5_38600' => 'lsa', 'Lsat_1_v5_gn_6_92061' => 'lsa', 'Manes.05G071301' => 'mes', 'MD02G1008700' => 'mdo', 'MD02G1008900' => 'mdo', 'MD03G1256400' => 'mdo', 'MD04G1180900' => 'mdo', 'MD04G1181000' => 'mdo', 'MD04G1181200' => 'mdo', 'MD05G1244200' => 'mdo', 'MD05G1324200' => 'mdo', 'MD09G1201600' => 'mdo', 'MD10G1000600' => 'mdo', 'MD14G1026900' => 'mdo', 'MD14G1187900' => 'mdo', 'MD15G1017800' => 'mdo', 'MD15G1018100' => 'mdo', 'Medtr4g124160' => 'mtr', 'Migut.L01260' => 'egut', 'Nitab4.5_0000008g0440' => 'nta', 'Nitab4.5_0000207g0170' => 'nta', 'Nitab4.5_0007671g0030' => 'nta', 'Nitab4.5_0010853g0020' => 'nta', 'Oeu057656.1' => 'oeu', 'PGSC0003DMG400005638' => 'stu', 'PGSC0003DMG400005639' => 'stu', 'Phvul.009G222800' => 'pvu', 'Potri.009G132400' => 'ptr', 'Potri.009G163001' => 'ptr', 'Potri.011G000700' => 'ptr', 'Potri.011G004800' => 'ptr', 'Prupe.1G509300' => 'ppe', 'Prupe.1G509700' => 'ppe', 'Prupe.1G510400' => 'ppe', 'Prupe.1G510700' => 'ppe', 'Prupe.1G512600' => 'ppe', 'Prupe.2G073200' => 'ppe', 'Prupe.3G059500' => 'ppe', 'Prupe.3G059600' => 'ppe', 'Prupe.3G246100' => 'ppe', 'Prupe.3G265100' => 'ppe', 'Prupe.4G034700' => 'ppe', 'Prupe.4G052100' => 'ppe', 'Prupe.4G053600' => 'ppe', 'Prupe.5G068800' => 'ppe', 'Prupe.5G070600' => 'ppe', 'Prupe.6G075400' => 'ppe', 'Prupe.6G075500' => 'ppe', 'Prupe.6G076400' => 'ppe', 'Prupe.8G110700' => 'ppe', 'Psat4g020960' => 'psa', 'PSO135G0788' => 'pso', 'PSO210G6463' => 'pso', 'PSO384G0370' => 'pso', 'PSO386G0056' => 'pso', 'QL01p006048' => 'qlo', 'QL02p054283' => 'qlo', 'QL05p008000' => 'qlo', 'QL05p008212' => 'qlo', 'QL05p008950' => 'qlo', 'QL05p009042' => 'qlo', 'QL05p009518' => 'qlo', 'QL05p012589' => 'qlo', 'QL05p012608' => 'qlo', 'QL05p012650' => 'qlo', 'QL05p012667' => 'qlo', 'QL05p014501' => 'qlo', 'QL05p052800' => 'qlo', 'QL05p065010' => 'qlo', 'QL05p074156' => 'qlo', 'QL05p074160' => 'qlo', 'QL05p074174' => 'qlo', 'QL05p074178' => 'qlo', 'QL05p074214' => 'qlo', 'QL06p001050' => 'qlo', 'QL06p001056' => 'qlo', 'QL06p006093' => 'qlo', 'QL06p006111' => 'qlo', 'QL07p019784' => 'qlo', 'QL07p019801' => 'qlo', 'QL07p036110' => 'qlo', 'QL07p036134' => 'qlo', 'QL07p036147' => 'qlo', 'QL07p036156' => 'qlo', 'QL07p036300' => 'qlo', 'QL07p036320' => 'qlo', 'QL08p014547' => 'qlo', 'QL08p014551' => 'qlo', 'QL08p043319' => 'qlo', 'QL08p043324' => 'qlo', 'QL11p009094' => 'qlo', 'RcHm_v2.0_Chr1g0380481' => 'rch', 'RcHm_v2.0_Chr2g0089331' => 'rch', 'RcHm_v2.0_Chr2g0123691' => 'rch', 'RcHm_v2.0_Chr2g0151111' => 'rch', 'RcHm_v2.0_Chr2g0163011' => 'rch', 'RcHm_v2.0_Chr2g0163051' => 'rch', 'RcHm_v2.0_Chr2g0164671' => 'rch', 'RcHm_v2.0_Chr2g0164681' => 'rch', 'RcHm_v2.0_Chr2g0164721' => 'rch', 'RcHm_v2.0_Chr3g0449911' => 'rch', 'RcHm_v2.0_Chr3g0450211' => 'rch', 'RcHm_v2.0_Chr3g0457271' => 'rch', 'RcHm_v2.0_Chr5g0018111' => 'rch', 'RcHm_v2.0_Chr5g0021011' => 'rch', 'RcHm_v2.0_Chr5g0081171' => 'rch', 'RcHm_v2.0_Chr5g0081211' => 'rch', 'RcHm_v2.0_Chr6g0275871' => 'rch', 'RcHm_v2.0_Chr6g0276071' => 'rch', 'RcHm_v2.0_Chr6g0285591' => 'rch', 'RcHm_v2.0_Chr6g0291931' => 'rch', 'RcHm_v2.0_Chr6g0292091' => 'rch', 'RcHm_v2.0_Chr6g0292271' => 'rch', 'RcHm_v2.0_Chr7g0221261' => 'rch', 'Rhsim08G0219900' => 'rsi', 'Rhsim08G0220200' => 'rsi', 'Rhsim08G0237800' => 'rsi', 'Rhsim08G0238800' => 'rsi', 'Sabra09G0102700' => 'sbr', 'Sabra09G0127200' => 'sbr', 'Sabra11G0003700' => 'sbr', 'Sabra15G0014700' => 'sbr', 'Sc19g0000590' => 'sci', 'Sc19g0001870' => 'sci', 'SGA_v2.0_scaffold1G00346' => 'sas', 'SGA_v2.0_scaffold1G00575' => 'sas', 'SGA_v2.0_scaffold1G00761' => 'sas', 'SGA_v2.0_scaffold232G43501' => 'sas', 'TAR625G1137' => 'tar', 'Thecc.03G222100' => 'tca', 'TPR.G12691' => 'tpr', 'TWI34G0727' => 'twi', 'TWI36G0117' => 'twi', 'VMungo1309G0868' => 'vmu' ) $gf_id = 'HOM05D001729' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001729' ) $data_identifier = 'HOM05D001729' $data_type = 'gf_id' $species_gene_counts = array( 'amhyb' => (int) 1, 'cqu' => (int) 9, 'can' => (int) 1, 'cansat' => (int) 1, 'car' => (int) 1, 'col' => (int) 5, 'dca' => (int) 1, 'din' => (int) 2, 'dzi' => (int) 3, 'fan' => (int) 140, 'fve' => (int) 62, 'gma' => (int) 1, 'ghi' => (int) 2, 'gra' => (int) 1, 'han' => (int) 1, 'sun' => (int) 1, 'lonja' => (int) 6, 'lja' => (int) 1, 'lsa' => (int) 4, 'mes' => (int) 1, 'mdo' => (int) 14, 'mtr' => (int) 1, 'egut' => (int) 1, 'nta' => (int) 4, 'oeu' => (int) 1, 'stu' => (int) 2, 'pvu' => (int) 1, 'ptr' => (int) 4, 'ppe' => (int) 19, 'psa' => (int) 1, 'pso' => (int) 4, 'qlo' => (int) 36, 'rch' => (int) 23, 'rsi' => (int) 4, 'sbr' => (int) 4, 'sci' => (int) 2, 'sas' => (int) 4, 'tar' => (int) 1, 'tca' => (int) 1, 'tpr' => (int) 1, 'twi' => (int) 2, 'vmu' => (int) 1 ) $gf_gene_species = 'vmu' $gf_gene_id = 'VMungo1309G0868' $species_info = array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ) $local_species = 'nta' $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' => 'HOM05D001729', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '375', 'num_species' => '42' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'Ah.07g204710' => 'amhyb', 'AUR62006001' => 'cqu', 'AUR62006002' => 'cqu', 'AUR62006003' => 'cqu', 'AUR62015641' => 'cqu', 'AUR62027174' => 'cqu', 'AUR62035623' => 'cqu', 'AUR62035624' => 'cqu', 'AUR62035625' => 'cqu', 'AUR62035626' => 'cqu', 'CAN.G1110.53' => 'can', 'CANSAT80G0415' => 'cansat', 'Ca_21364_v3' => 'car', 'COL.COLO4_30693' => 'col', 'COL.COLO4_30694' => 'col', 'COL.COLO4_30695' => 'col', 'COL.COLO4_30696' => 'col', 'COL.COLO4_34020' => 'col', 'DCAR_004585' => 'dca', 'Dinv04029' => 'din', 'Dinv34857' => 'din', 'Duzib147G0011' => 'dzi', 'Duzib170G0599' => 'dzi', 'Duzib192G1051' => 'dzi', 'FAN01G0708' => 'fan', 'FAN01G0742' => 'fan', 'FAN02G0048' => 'fan', 'FAN02G0583' => 'fan', 'FAN02G0688' => 'fan', 'FAN02G1588' => 'fan', 'FAN02G2194' => 'fan', 'FAN02G2750' => 'fan', 'FAN02G3094' => 'fan', 'FAN02G3887' => 'fan', 'FAN02G3911' => 'fan', 'FAN02G3994' => 'fan', 'FAN02G4432' => 'fan', 'FAN02G4556' => 'fan', 'FAN03G1977' => 'fan', 'FAN03G2781' => 'fan', 'FAN03G2850' => 'fan', 'FAN03G3155' => 'fan', 'FAN04G2487' => 'fan', 'FAN05G0208' => 'fan', 'FAN05G0656' => 'fan', 'FAN05G0696' => 'fan', 'FAN05G0810' => 'fan', 'FAN05G1447' => 'fan', 'FAN05G2640' => 'fan', 'FAN05G2911' => 'fan', 'FAN05G3901' => 'fan', 'FAN05G4859' => 'fan', 'FAN05G4861' => 'fan', 'FAN05G4988' => 'fan', 'FAN05G5187' => 'fan', 'FAN05G5452' => 'fan', 'FAN05G5500' => 'fan', 'FAN05G5688' => 'fan', 'FAN06G0177' => 'fan', 'FAN06G0675' => 'fan', 'FAN06G1290' => 'fan', 'FAN06G2191' => 'fan', 'FAN06G2405' => 'fan', 'FAN06G3231' => 'fan', 'FAN06G3932' => 'fan', 'FAN07G0163' => 'fan', 'FAN07G0471' => 'fan', 'FAN07G1354' => 'fan', 'FAN08G0338' => 'fan', 'FAN08G1373' => 'fan', 'FAN08G2539' => 'fan', 'FAN08G2728' => 'fan', 'FAN09G0608' => 'fan', 'FAN09G1136' => 'fan', 'FAN09G1958' => 'fan', 'FAN09G2508' => 'fan', 'FAN09G2597' => 'fan', 'FAN09G2658' => 'fan', 'FAN09G2757' => 'fan', 'FAN09G2983' => 'fan', 'FAN09G3130' => 'fan', 'FAN09G3565' => 'fan', 'FAN09G3613' => 'fan', 'FAN09G4011' => 'fan', 'FAN09G4239' => 'fan', 'FAN09G4277' => 'fan', 'FAN09G4720' => 'fan', 'FAN11G0139' => 'fan', 'FAN11G1727' => 'fan', 'FAN11G2672' => 'fan', 'FAN11G2795' => 'fan', 'FAN11G3238' => 'fan', 'FAN11G3734' => 'fan', 'FAN12G0631' => 'fan', 'FAN12G2239' => 'fan', 'FAN12G2308' => 'fan', 'FAN12G2569' => 'fan', 'FAN12G2623' => 'fan', 'FAN13G3182' => 'fan', 'FAN14G0053' => 'fan', 'FAN14G0370' => 'fan', 'FAN14G0382' => 'fan', 'FAN14G0421' => 'fan', 'FAN14G0866' => 'fan', 'FAN14G1187' => 'fan', 'FAN14G1727' => 'fan', 'FAN14G1791' => 'fan', 'FAN14G2361' => 'fan', 'FAN14G2668' => 'fan', 'FAN14G2770' => 'fan', 'FAN14G2874' => 'fan', 'FAN14G3193' => 'fan', 'FAN14G3624' => 'fan', 'FAN14G3676' => 'fan', 'FAN14G3807' => 'fan', 'FAN14G4082' => 'fan', 'FAN14G4342' => 'fan', 'FAN14G4985' => 'fan', 'FAN14G5126' => 'fan', 'FAN14G5781' => 'fan', 'FAN14G5808' => 'fan', 'FAN14G5949' => 'fan', 'FAN15G0828' => 'fan', 'FAN15G1054' => 'fan', 'FAN15G2023' => 'fan', 'FAN15G2506' => 'fan', 'FAN16G0128' => 'fan', 'FAN16G0249' => 'fan', 'FAN16G0429' => 'fan', 'FAN16G1493' => 'fan', 'FAN16G2210' => 'fan', 'FAN16G2506' => 'fan', 'FAN18G1542' => 'fan', 'FAN18G4057' => 'fan', 'FAN19G0745' => 'fan', 'FAN19G1216' => 'fan', 'FAN19G1733' => 'fan', 'FAN20G0258' => 'fan', 'FAN20G1095' => 'fan', 'FAN20G1557' => 'fan', 'FAN21G0302' => 'fan', 'FAN21G0519' => 'fan', 'FAN21G0970' => 'fan', 'FAN21G1159' => 'fan', 'FAN21G1312' => 'fan', 'FAN21G1440' => 'fan', 'FAN21G1715' => 'fan', 'FAN23G1584' => 'fan', 'FAN24G0045' => 'fan', 'FAN24G0053' => 'fan', 'FAN24G1500' => 'fan', 'FAN24G1817' => 'fan', 'FAN24G2147' => 'fan', 'FAN24G2236' => 'fan', 'FAN24G2446' => 'fan', 'FAN24G2684' => 'fan', 'FAN25G0187' => 'fan', 'FAN25G0505' => 'fan', 'FAN25G0589' => 'fan', 'FAN25G3663' => 'fan', 'FAN26G1025' => 'fan', 'FAN26G2860' => 'fan', 'FAN27G1329' => 'fan', 'FAN27G3392' => 'fan', 'FvH4_1g02011' => 'fve', 'FvH4_1g06511' => 'fve', 'FvH4_2g19900' => 'fve', 'FvH4_2g19920' => 'fve', 'FvH4_2g24261' => 'fve', 'FvH4_2g24270' => 'fve', 'FvH4_2g24631' => 'fve', 'FvH4_2g30622' => 'fve', 'FvH4_3g12920' => 'fve', 'FvH4_3g30171' => 'fve', 'FvH4_3g35490' => 'fve', 'FvH4_3g43682' => 'fve', 'FvH4_3g43730' => 'fve', 'FvH4_3g43732' => 'fve', 'FvH4_3g43751' => 'fve', 'FvH4_3g43752' => 'fve', 'FvH4_3g43770' => 'fve', 'FvH4_3g44471' => 'fve', 'FvH4_3g44510' => 'fve', 'FvH4_3g44582' => 'fve', 'FvH4_4g16921' => 'fve', 'FvH4_4g17121' => 'fve', 'FvH4_4g17782' => 'fve', 'FvH4_4g17783' => 'fve', 'FvH4_4g18120' => 'fve', 'FvH4_4g31310' => 'fve', 'FvH4_4g35052' => 'fve', 'FvH4_5g30862' => 'fve', 'FvH4_6g01541' => 'fve', 'FvH4_6g02021' => 'fve', 'FvH4_6g02041' => 'fve', 'FvH4_6g02071' => 'fve', 'FvH4_6g02171' => 'fve', 'FvH4_6g03181' => 'fve', 'FvH4_6g03182' => 'fve', 'FvH4_6g03221' => 'fve', 'FvH4_6g03380' => 'fve', 'FvH4_6g05201' => 'fve', 'FvH4_6g05203' => 'fve', 'FvH4_6g20231' => 'fve', 'FvH4_6g31981' => 'fve', 'FvH4_6g32061' => 'fve', 'FvH4_6g37041' => 'fve', 'FvH4_6g37932' => 'fve', 'FvH4_6g38731' => 'fve', 'FvH4_6g39370' => 'fve', 'FvH4_6g39371' => 'fve', 'FvH4_6g40891' => 'fve', 'FvH4_6g40892' => 'fve', 'FvH4_6g43143' => 'fve', 'FvH4_6g45251' => 'fve', 'FvH4_6g45260' => 'fve', 'FvH4_6g45291' => 'fve', 'FvH4_6g45890' => 'fve', 'FvH4_6g46240' => 'fve', 'FvH4_6g46241' => 'fve', 'FvH4_6g46242' => 'fve', 'FvH4_6g46260' => 'fve', 'FvH4_6g46280' => 'fve', 'FvH4_6g46380' => 'fve', 'FvH4_7g12841' => 'fve', 'FvH4_7g31431' => 'fve', 'Glyma.09G075900' => 'gma', 'Gohir.A09G096401' => 'ghi', 'Gohir.D09G096101' => 'ghi', 'Gorai.006G112800' => 'gra', 'HanXRQChr04g0121411' => 'han', 'Hund15878' => 'sun', 'Lj2A1107G68' => 'lonja', 'Lj2A630G63' => 'lonja', 'Lj2A946T25' => 'lonja', 'Lj2C714T1' => 'lonja', 'Lj2C966T3' => 'lonja', 'Lj2C966T4' => 'lonja', 'Lj4g0002979' => 'lja', 'Lsat_1_v5_gn_5_30901' => 'lsa', 'Lsat_1_v5_gn_5_31100' => 'lsa', 'Lsat_1_v5_gn_5_38600' => 'lsa', 'Lsat_1_v5_gn_6_92061' => 'lsa', 'Manes.05G071301' => 'mes', 'MD02G1008700' => 'mdo', 'MD02G1008900' => 'mdo', 'MD03G1256400' => 'mdo', 'MD04G1180900' => 'mdo', 'MD04G1181000' => 'mdo', 'MD04G1181200' => 'mdo', 'MD05G1244200' => 'mdo', 'MD05G1324200' => 'mdo', 'MD09G1201600' => 'mdo', 'MD10G1000600' => 'mdo', 'MD14G1026900' => 'mdo', 'MD14G1187900' => 'mdo', 'MD15G1017800' => 'mdo', 'MD15G1018100' => 'mdo', 'Medtr4g124160' => 'mtr', 'Migut.L01260' => 'egut', 'Nitab4.5_0000008g0440' => 'nta', 'Nitab4.5_0000207g0170' => 'nta', 'Nitab4.5_0007671g0030' => 'nta', 'Nitab4.5_0010853g0020' => 'nta', 'Oeu057656.1' => 'oeu', 'PGSC0003DMG400005638' => 'stu', 'PGSC0003DMG400005639' => 'stu', 'Phvul.009G222800' => 'pvu', 'Potri.009G132400' => 'ptr', 'Potri.009G163001' => 'ptr', 'Potri.011G000700' => 'ptr', 'Potri.011G004800' => 'ptr', 'Prupe.1G509300' => 'ppe', 'Prupe.1G509700' => 'ppe', 'Prupe.1G510400' => 'ppe', 'Prupe.1G510700' => 'ppe', 'Prupe.1G512600' => 'ppe', 'Prupe.2G073200' => 'ppe', 'Prupe.3G059500' => 'ppe', 'Prupe.3G059600' => 'ppe', 'Prupe.3G246100' => 'ppe', 'Prupe.3G265100' => 'ppe', 'Prupe.4G034700' => 'ppe', 'Prupe.4G052100' => 'ppe', 'Prupe.4G053600' => 'ppe', 'Prupe.5G068800' => 'ppe', 'Prupe.5G070600' => 'ppe', 'Prupe.6G075400' => 'ppe', 'Prupe.6G075500' => 'ppe', 'Prupe.6G076400' => 'ppe', 'Prupe.8G110700' => 'ppe', 'Psat4g020960' => 'psa', 'PSO135G0788' => 'pso', 'PSO210G6463' => 'pso', 'PSO384G0370' => 'pso', 'PSO386G0056' => 'pso', 'QL01p006048' => 'qlo', 'QL02p054283' => 'qlo', 'QL05p008000' => 'qlo', 'QL05p008212' => 'qlo', 'QL05p008950' => 'qlo', 'QL05p009042' => 'qlo', 'QL05p009518' => 'qlo', 'QL05p012589' => 'qlo', 'QL05p012608' => 'qlo', 'QL05p012650' => 'qlo', 'QL05p012667' => 'qlo', 'QL05p014501' => 'qlo', 'QL05p052800' => 'qlo', 'QL05p065010' => 'qlo', 'QL05p074156' => 'qlo', 'QL05p074160' => 'qlo', 'QL05p074174' => 'qlo', 'QL05p074178' => 'qlo', 'QL05p074214' => 'qlo', 'QL06p001050' => 'qlo', 'QL06p001056' => 'qlo', 'QL06p006093' => 'qlo', 'QL06p006111' => 'qlo', 'QL07p019784' => 'qlo', 'QL07p019801' => 'qlo', 'QL07p036110' => 'qlo', 'QL07p036134' => 'qlo', 'QL07p036147' => 'qlo', 'QL07p036156' => 'qlo', 'QL07p036300' => 'qlo', 'QL07p036320' => 'qlo', 'QL08p014547' => 'qlo', 'QL08p014551' => 'qlo', 'QL08p043319' => 'qlo', 'QL08p043324' => 'qlo', 'QL11p009094' => 'qlo', 'RcHm_v2.0_Chr1g0380481' => 'rch', 'RcHm_v2.0_Chr2g0089331' => 'rch', 'RcHm_v2.0_Chr2g0123691' => 'rch', 'RcHm_v2.0_Chr2g0151111' => 'rch', 'RcHm_v2.0_Chr2g0163011' => 'rch', 'RcHm_v2.0_Chr2g0163051' => 'rch', 'RcHm_v2.0_Chr2g0164671' => 'rch', 'RcHm_v2.0_Chr2g0164681' => 'rch', 'RcHm_v2.0_Chr2g0164721' => 'rch', 'RcHm_v2.0_Chr3g0449911' => 'rch', 'RcHm_v2.0_Chr3g0450211' => 'rch', 'RcHm_v2.0_Chr3g0457271' => 'rch', 'RcHm_v2.0_Chr5g0018111' => 'rch', 'RcHm_v2.0_Chr5g0021011' => 'rch', 'RcHm_v2.0_Chr5g0081171' => 'rch', 'RcHm_v2.0_Chr5g0081211' => 'rch', 'RcHm_v2.0_Chr6g0275871' => 'rch', 'RcHm_v2.0_Chr6g0276071' => 'rch', 'RcHm_v2.0_Chr6g0285591' => 'rch', 'RcHm_v2.0_Chr6g0291931' => 'rch', 'RcHm_v2.0_Chr6g0292091' => 'rch', 'RcHm_v2.0_Chr6g0292271' => 'rch', 'RcHm_v2.0_Chr7g0221261' => 'rch', 'Rhsim08G0219900' => 'rsi', 'Rhsim08G0220200' => 'rsi', 'Rhsim08G0237800' => 'rsi', 'Rhsim08G0238800' => 'rsi', 'Sabra09G0102700' => 'sbr', 'Sabra09G0127200' => 'sbr', 'Sabra11G0003700' => 'sbr', 'Sabra15G0014700' => 'sbr', 'Sc19g0000590' => 'sci', 'Sc19g0001870' => 'sci', 'SGA_v2.0_scaffold1G00346' => 'sas', 'SGA_v2.0_scaffold1G00575' => 'sas', 'SGA_v2.0_scaffold1G00761' => 'sas', 'SGA_v2.0_scaffold232G43501' => 'sas', 'TAR625G1137' => 'tar', 'Thecc.03G222100' => 'tca', 'TPR.G12691' => 'tpr', 'TWI34G0727' => 'twi', 'TWI36G0117' => 'twi', 'VMungo1309G0868' => 'vmu' ), 'gf_id' => 'HOM05D001729', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001729' ), 'data_identifier' => 'HOM05D001729', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001729', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '375', 'num_species' => '42' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'Ah.07g204710' => 'amhyb', 'AUR62006001' => 'cqu', 'AUR62006002' => 'cqu', 'AUR62006003' => 'cqu', 'AUR62015641' => 'cqu', 'AUR62027174' => 'cqu', 'AUR62035623' => 'cqu', 'AUR62035624' => 'cqu', 'AUR62035625' => 'cqu', 'AUR62035626' => 'cqu', 'CAN.G1110.53' => 'can', 'CANSAT80G0415' => 'cansat', 'Ca_21364_v3' => 'car', 'COL.COLO4_30693' => 'col', 'COL.COLO4_30694' => 'col', 'COL.COLO4_30695' => 'col', 'COL.COLO4_30696' => 'col', 'COL.COLO4_34020' => 'col', 'DCAR_004585' => 'dca', 'Dinv04029' => 'din', 'Dinv34857' => 'din', 'Duzib147G0011' => 'dzi', 'Duzib170G0599' => 'dzi', 'Duzib192G1051' => 'dzi', 'FAN01G0708' => 'fan', 'FAN01G0742' => 'fan', 'FAN02G0048' => 'fan', 'FAN02G0583' => 'fan', 'FAN02G0688' => 'fan', 'FAN02G1588' => 'fan', 'FAN02G2194' => 'fan', 'FAN02G2750' => 'fan', 'FAN02G3094' => 'fan', 'FAN02G3887' => 'fan', 'FAN02G3911' => 'fan', 'FAN02G3994' => 'fan', 'FAN02G4432' => 'fan', 'FAN02G4556' => 'fan', 'FAN03G1977' => 'fan', 'FAN03G2781' => 'fan', 'FAN03G2850' => 'fan', 'FAN03G3155' => 'fan', 'FAN04G2487' => 'fan', 'FAN05G0208' => 'fan', 'FAN05G0656' => 'fan', 'FAN05G0696' => 'fan', 'FAN05G0810' => 'fan', 'FAN05G1447' => 'fan', 'FAN05G2640' => 'fan', 'FAN05G2911' => 'fan', 'FAN05G3901' => 'fan', 'FAN05G4859' => 'fan', 'FAN05G4861' => 'fan', 'FAN05G4988' => 'fan', 'FAN05G5187' => 'fan', 'FAN05G5452' => 'fan', 'FAN05G5500' => 'fan', 'FAN05G5688' => 'fan', 'FAN06G0177' => 'fan', 'FAN06G0675' => 'fan', 'FAN06G1290' => 'fan', 'FAN06G2191' => 'fan', 'FAN06G2405' => 'fan', 'FAN06G3231' => 'fan', 'FAN06G3932' => 'fan', 'FAN07G0163' => 'fan', 'FAN07G0471' => 'fan', 'FAN07G1354' => 'fan', 'FAN08G0338' => 'fan', 'FAN08G1373' => 'fan', 'FAN08G2539' => 'fan', 'FAN08G2728' => 'fan', 'FAN09G0608' => 'fan', 'FAN09G1136' => 'fan', 'FAN09G1958' => 'fan', 'FAN09G2508' => 'fan', 'FAN09G2597' => 'fan', 'FAN09G2658' => 'fan', 'FAN09G2757' => 'fan', 'FAN09G2983' => 'fan', 'FAN09G3130' => 'fan', 'FAN09G3565' => 'fan', 'FAN09G3613' => 'fan', 'FAN09G4011' => 'fan', 'FAN09G4239' => 'fan', 'FAN09G4277' => 'fan', 'FAN09G4720' => 'fan', 'FAN11G0139' => 'fan', 'FAN11G1727' => 'fan', 'FAN11G2672' => 'fan', 'FAN11G2795' => 'fan', 'FAN11G3238' => 'fan', 'FAN11G3734' => 'fan', 'FAN12G0631' => 'fan', 'FAN12G2239' => 'fan', 'FAN12G2308' => 'fan', 'FAN12G2569' => 'fan', 'FAN12G2623' => 'fan', 'FAN13G3182' => 'fan', 'FAN14G0053' => 'fan', 'FAN14G0370' => 'fan', 'FAN14G0382' => 'fan', 'FAN14G0421' => 'fan', 'FAN14G0866' => 'fan', 'FAN14G1187' => 'fan', 'FAN14G1727' => 'fan', 'FAN14G1791' => 'fan', 'FAN14G2361' => 'fan', 'FAN14G2668' => 'fan', 'FAN14G2770' => 'fan', 'FAN14G2874' => 'fan', 'FAN14G3193' => 'fan', 'FAN14G3624' => 'fan', 'FAN14G3676' => 'fan', 'FAN14G3807' => 'fan', 'FAN14G4082' => 'fan', 'FAN14G4342' => 'fan', 'FAN14G4985' => 'fan', 'FAN14G5126' => 'fan', 'FAN14G5781' => 'fan', 'FAN14G5808' => 'fan', 'FAN14G5949' => 'fan', 'FAN15G0828' => 'fan', 'FAN15G1054' => 'fan', 'FAN15G2023' => 'fan', 'FAN15G2506' => 'fan', 'FAN16G0128' => 'fan', 'FAN16G0249' => 'fan', 'FAN16G0429' => 'fan', 'FAN16G1493' => 'fan', 'FAN16G2210' => 'fan', 'FAN16G2506' => 'fan', 'FAN18G1542' => 'fan', 'FAN18G4057' => 'fan', 'FAN19G0745' => 'fan', 'FAN19G1216' => 'fan', 'FAN19G1733' => 'fan', 'FAN20G0258' => 'fan', 'FAN20G1095' => 'fan', 'FAN20G1557' => 'fan', 'FAN21G0302' => 'fan', 'FAN21G0519' => 'fan', 'FAN21G0970' => 'fan', 'FAN21G1159' => 'fan', 'FAN21G1312' => 'fan', 'FAN21G1440' => 'fan', 'FAN21G1715' => 'fan', 'FAN23G1584' => 'fan', 'FAN24G0045' => 'fan', 'FAN24G0053' => 'fan', 'FAN24G1500' => 'fan', 'FAN24G1817' => 'fan', 'FAN24G2147' => 'fan', 'FAN24G2236' => 'fan', 'FAN24G2446' => 'fan', 'FAN24G2684' => 'fan', 'FAN25G0187' => 'fan', 'FAN25G0505' => 'fan', 'FAN25G0589' => 'fan', 'FAN25G3663' => 'fan', 'FAN26G1025' => 'fan', 'FAN26G2860' => 'fan', 'FAN27G1329' => 'fan', 'FAN27G3392' => 'fan', 'FvH4_1g02011' => 'fve', 'FvH4_1g06511' => 'fve', 'FvH4_2g19900' => 'fve', 'FvH4_2g19920' => 'fve', 'FvH4_2g24261' => 'fve', 'FvH4_2g24270' => 'fve', 'FvH4_2g24631' => 'fve', 'FvH4_2g30622' => 'fve', 'FvH4_3g12920' => 'fve', 'FvH4_3g30171' => 'fve', 'FvH4_3g35490' => 'fve', 'FvH4_3g43682' => 'fve', 'FvH4_3g43730' => 'fve', 'FvH4_3g43732' => 'fve', 'FvH4_3g43751' => 'fve', 'FvH4_3g43752' => 'fve', 'FvH4_3g43770' => 'fve', 'FvH4_3g44471' => 'fve', 'FvH4_3g44510' => 'fve', 'FvH4_3g44582' => 'fve', 'FvH4_4g16921' => 'fve', 'FvH4_4g17121' => 'fve', 'FvH4_4g17782' => 'fve', 'FvH4_4g17783' => 'fve', 'FvH4_4g18120' => 'fve', 'FvH4_4g31310' => 'fve', 'FvH4_4g35052' => 'fve', 'FvH4_5g30862' => 'fve', 'FvH4_6g01541' => 'fve', 'FvH4_6g02021' => 'fve', 'FvH4_6g02041' => 'fve', 'FvH4_6g02071' => 'fve', 'FvH4_6g02171' => 'fve', 'FvH4_6g03181' => 'fve', 'FvH4_6g03182' => 'fve', 'FvH4_6g03221' => 'fve', 'FvH4_6g03380' => 'fve', 'FvH4_6g05201' => 'fve', 'FvH4_6g05203' => 'fve', 'FvH4_6g20231' => 'fve', 'FvH4_6g31981' => 'fve', 'FvH4_6g32061' => 'fve', 'FvH4_6g37041' => 'fve', 'FvH4_6g37932' => 'fve', 'FvH4_6g38731' => 'fve', 'FvH4_6g39370' => 'fve', 'FvH4_6g39371' => 'fve', 'FvH4_6g40891' => 'fve', 'FvH4_6g40892' => 'fve', 'FvH4_6g43143' => 'fve', 'FvH4_6g45251' => 'fve', 'FvH4_6g45260' => 'fve', 'FvH4_6g45291' => 'fve', 'FvH4_6g45890' => 'fve', 'FvH4_6g46240' => 'fve', 'FvH4_6g46241' => 'fve', 'FvH4_6g46242' => 'fve', 'FvH4_6g46260' => 'fve', 'FvH4_6g46280' => 'fve', 'FvH4_6g46380' => 'fve', 'FvH4_7g12841' => 'fve', 'FvH4_7g31431' => 'fve', 'Glyma.09G075900' => 'gma', 'Gohir.A09G096401' => 'ghi', 'Gohir.D09G096101' => 'ghi', 'Gorai.006G112800' => 'gra', 'HanXRQChr04g0121411' => 'han', 'Hund15878' => 'sun', 'Lj2A1107G68' => 'lonja', 'Lj2A630G63' => 'lonja', 'Lj2A946T25' => 'lonja', 'Lj2C714T1' => 'lonja', 'Lj2C966T3' => 'lonja', 'Lj2C966T4' => 'lonja', 'Lj4g0002979' => 'lja', 'Lsat_1_v5_gn_5_30901' => 'lsa', 'Lsat_1_v5_gn_5_31100' => 'lsa', 'Lsat_1_v5_gn_5_38600' => 'lsa', 'Lsat_1_v5_gn_6_92061' => 'lsa', 'Manes.05G071301' => 'mes', 'MD02G1008700' => 'mdo', 'MD02G1008900' => 'mdo', 'MD03G1256400' => 'mdo', 'MD04G1180900' => 'mdo', 'MD04G1181000' => 'mdo', 'MD04G1181200' => 'mdo', 'MD05G1244200' => 'mdo', 'MD05G1324200' => 'mdo', 'MD09G1201600' => 'mdo', 'MD10G1000600' => 'mdo', 'MD14G1026900' => 'mdo', 'MD14G1187900' => 'mdo', 'MD15G1017800' => 'mdo', 'MD15G1018100' => 'mdo', 'Medtr4g124160' => 'mtr', 'Migut.L01260' => 'egut', 'Nitab4.5_0000008g0440' => 'nta', 'Nitab4.5_0000207g0170' => 'nta', 'Nitab4.5_0007671g0030' => 'nta', 'Nitab4.5_0010853g0020' => 'nta', 'Oeu057656.1' => 'oeu', 'PGSC0003DMG400005638' => 'stu', 'PGSC0003DMG400005639' => 'stu', 'Phvul.009G222800' => 'pvu', 'Potri.009G132400' => 'ptr', 'Potri.009G163001' => 'ptr', 'Potri.011G000700' => 'ptr', 'Potri.011G004800' => 'ptr', 'Prupe.1G509300' => 'ppe', 'Prupe.1G509700' => 'ppe', 'Prupe.1G510400' => 'ppe', 'Prupe.1G510700' => 'ppe', 'Prupe.1G512600' => 'ppe', 'Prupe.2G073200' => 'ppe', 'Prupe.3G059500' => 'ppe', 'Prupe.3G059600' => 'ppe', 'Prupe.3G246100' => 'ppe', 'Prupe.3G265100' => 'ppe', 'Prupe.4G034700' => 'ppe', 'Prupe.4G052100' => 'ppe', 'Prupe.4G053600' => 'ppe', 'Prupe.5G068800' => 'ppe', 'Prupe.5G070600' => 'ppe', 'Prupe.6G075400' => 'ppe', 'Prupe.6G075500' => 'ppe', 'Prupe.6G076400' => 'ppe', 'Prupe.8G110700' => 'ppe', 'Psat4g020960' => 'psa', 'PSO135G0788' => 'pso', 'PSO210G6463' => 'pso', 'PSO384G0370' => 'pso', 'PSO386G0056' => 'pso', 'QL01p006048' => 'qlo', 'QL02p054283' => 'qlo', 'QL05p008000' => 'qlo', 'QL05p008212' => 'qlo', 'QL05p008950' => 'qlo', 'QL05p009042' => 'qlo', 'QL05p009518' => 'qlo', 'QL05p012589' => 'qlo', 'QL05p012608' => 'qlo', 'QL05p012650' => 'qlo', 'QL05p012667' => 'qlo', 'QL05p014501' => 'qlo', 'QL05p052800' => 'qlo', 'QL05p065010' => 'qlo', 'QL05p074156' => 'qlo', 'QL05p074160' => 'qlo', 'QL05p074174' => 'qlo', 'QL05p074178' => 'qlo', 'QL05p074214' => 'qlo', 'QL06p001050' => 'qlo', 'QL06p001056' => 'qlo', 'QL06p006093' => 'qlo', 'QL06p006111' => 'qlo', 'QL07p019784' => 'qlo', 'QL07p019801' => 'qlo', 'QL07p036110' => 'qlo', 'QL07p036134' => 'qlo', 'QL07p036147' => 'qlo', 'QL07p036156' => 'qlo', 'QL07p036300' => 'qlo', 'QL07p036320' => 'qlo', 'QL08p014547' => 'qlo', 'QL08p014551' => 'qlo', 'QL08p043319' => 'qlo', 'QL08p043324' => 'qlo', 'QL11p009094' => 'qlo', 'RcHm_v2.0_Chr1g0380481' => 'rch', 'RcHm_v2.0_Chr2g0089331' => 'rch', 'RcHm_v2.0_Chr2g0123691' => 'rch', 'RcHm_v2.0_Chr2g0151111' => 'rch', 'RcHm_v2.0_Chr2g0163011' => 'rch', 'RcHm_v2.0_Chr2g0163051' => 'rch', 'RcHm_v2.0_Chr2g0164671' => 'rch', 'RcHm_v2.0_Chr2g0164681' => 'rch', 'RcHm_v2.0_Chr2g0164721' => 'rch', 'RcHm_v2.0_Chr3g0449911' => 'rch', 'RcHm_v2.0_Chr3g0450211' => 'rch', 'RcHm_v2.0_Chr3g0457271' => 'rch', 'RcHm_v2.0_Chr5g0018111' => 'rch', 'RcHm_v2.0_Chr5g0021011' => 'rch', 'RcHm_v2.0_Chr5g0081171' => 'rch', 'RcHm_v2.0_Chr5g0081211' => 'rch', 'RcHm_v2.0_Chr6g0275871' => 'rch', 'RcHm_v2.0_Chr6g0276071' => 'rch', 'RcHm_v2.0_Chr6g0285591' => 'rch', 'RcHm_v2.0_Chr6g0291931' => 'rch', 'RcHm_v2.0_Chr6g0292091' => 'rch', 'RcHm_v2.0_Chr6g0292271' => 'rch', 'RcHm_v2.0_Chr7g0221261' => 'rch', 'Rhsim08G0219900' => 'rsi', 'Rhsim08G0220200' => 'rsi', 'Rhsim08G0237800' => 'rsi', 'Rhsim08G0238800' => 'rsi', 'Sabra09G0102700' => 'sbr', 'Sabra09G0127200' => 'sbr', 'Sabra11G0003700' => 'sbr', 'Sabra15G0014700' => 'sbr', 'Sc19g0000590' => 'sci', 'Sc19g0001870' => 'sci', 'SGA_v2.0_scaffold1G00346' => 'sas', 'SGA_v2.0_scaffold1G00575' => 'sas', 'SGA_v2.0_scaffold1G00761' => 'sas', 'SGA_v2.0_scaffold232G43501' => 'sas', 'TAR625G1137' => 'tar', 'Thecc.03G222100' => 'tca', 'TPR.G12691' => 'tpr', 'TWI34G0727' => 'twi', 'TWI36G0117' => 'twi', 'VMungo1309G0868' => 'vmu' ) $gf_id = 'HOM05D001729' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001729' ) $data_identifier = 'HOM05D001729' $data_type = 'gf_id' $species_gene_counts = array( 'amhyb' => (int) 1, 'cqu' => (int) 9, 'can' => (int) 1, 'cansat' => (int) 1, 'car' => (int) 1, 'col' => (int) 5, 'dca' => (int) 1, 'din' => (int) 2, 'dzi' => (int) 3, 'fan' => (int) 140, 'fve' => (int) 62, 'gma' => (int) 1, 'ghi' => (int) 2, 'gra' => (int) 1, 'han' => (int) 1, 'sun' => (int) 1, 'lonja' => (int) 6, 'lja' => (int) 1, 'lsa' => (int) 4, 'mes' => (int) 1, 'mdo' => (int) 14, 'mtr' => (int) 1, 'egut' => (int) 1, 'nta' => (int) 4, 'oeu' => (int) 1, 'stu' => (int) 2, 'pvu' => (int) 1, 'ptr' => (int) 4, 'ppe' => (int) 19, 'psa' => (int) 1, 'pso' => (int) 4, 'qlo' => (int) 36, 'rch' => (int) 23, 'rsi' => (int) 4, 'sbr' => (int) 4, 'sci' => (int) 2, 'sas' => (int) 4, 'tar' => (int) 1, 'tca' => (int) 1, 'tpr' => (int) 1, 'twi' => (int) 2, 'vmu' => (int) 1 ) $gf_gene_species = 'vmu' $gf_gene_id = 'VMungo1309G0868' $species_info = array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ) $local_species = 'nta' $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' => 'HOM05D001729', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '375', 'num_species' => '42' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'Ah.07g204710' => 'amhyb', 'AUR62006001' => 'cqu', 'AUR62006002' => 'cqu', 'AUR62006003' => 'cqu', 'AUR62015641' => 'cqu', 'AUR62027174' => 'cqu', 'AUR62035623' => 'cqu', 'AUR62035624' => 'cqu', 'AUR62035625' => 'cqu', 'AUR62035626' => 'cqu', 'CAN.G1110.53' => 'can', 'CANSAT80G0415' => 'cansat', 'Ca_21364_v3' => 'car', 'COL.COLO4_30693' => 'col', 'COL.COLO4_30694' => 'col', 'COL.COLO4_30695' => 'col', 'COL.COLO4_30696' => 'col', 'COL.COLO4_34020' => 'col', 'DCAR_004585' => 'dca', 'Dinv04029' => 'din', 'Dinv34857' => 'din', 'Duzib147G0011' => 'dzi', 'Duzib170G0599' => 'dzi', 'Duzib192G1051' => 'dzi', 'FAN01G0708' => 'fan', 'FAN01G0742' => 'fan', 'FAN02G0048' => 'fan', 'FAN02G0583' => 'fan', 'FAN02G0688' => 'fan', 'FAN02G1588' => 'fan', 'FAN02G2194' => 'fan', 'FAN02G2750' => 'fan', 'FAN02G3094' => 'fan', 'FAN02G3887' => 'fan', 'FAN02G3911' => 'fan', 'FAN02G3994' => 'fan', 'FAN02G4432' => 'fan', 'FAN02G4556' => 'fan', 'FAN03G1977' => 'fan', 'FAN03G2781' => 'fan', 'FAN03G2850' => 'fan', 'FAN03G3155' => 'fan', 'FAN04G2487' => 'fan', 'FAN05G0208' => 'fan', 'FAN05G0656' => 'fan', 'FAN05G0696' => 'fan', 'FAN05G0810' => 'fan', 'FAN05G1447' => 'fan', 'FAN05G2640' => 'fan', 'FAN05G2911' => 'fan', 'FAN05G3901' => 'fan', 'FAN05G4859' => 'fan', 'FAN05G4861' => 'fan', 'FAN05G4988' => 'fan', 'FAN05G5187' => 'fan', 'FAN05G5452' => 'fan', 'FAN05G5500' => 'fan', 'FAN05G5688' => 'fan', 'FAN06G0177' => 'fan', 'FAN06G0675' => 'fan', 'FAN06G1290' => 'fan', 'FAN06G2191' => 'fan', 'FAN06G2405' => 'fan', 'FAN06G3231' => 'fan', 'FAN06G3932' => 'fan', 'FAN07G0163' => 'fan', 'FAN07G0471' => 'fan', 'FAN07G1354' => 'fan', 'FAN08G0338' => 'fan', 'FAN08G1373' => 'fan', 'FAN08G2539' => 'fan', 'FAN08G2728' => 'fan', 'FAN09G0608' => 'fan', 'FAN09G1136' => 'fan', 'FAN09G1958' => 'fan', 'FAN09G2508' => 'fan', 'FAN09G2597' => 'fan', 'FAN09G2658' => 'fan', 'FAN09G2757' => 'fan', 'FAN09G2983' => 'fan', 'FAN09G3130' => 'fan', 'FAN09G3565' => 'fan', 'FAN09G3613' => 'fan', 'FAN09G4011' => 'fan', 'FAN09G4239' => 'fan', 'FAN09G4277' => 'fan', 'FAN09G4720' => 'fan', 'FAN11G0139' => 'fan', 'FAN11G1727' => 'fan', 'FAN11G2672' => 'fan', 'FAN11G2795' => 'fan', 'FAN11G3238' => 'fan', 'FAN11G3734' => 'fan', 'FAN12G0631' => 'fan', 'FAN12G2239' => 'fan', 'FAN12G2308' => 'fan', 'FAN12G2569' => 'fan', 'FAN12G2623' => 'fan', 'FAN13G3182' => 'fan', 'FAN14G0053' => 'fan', 'FAN14G0370' => 'fan', 'FAN14G0382' => 'fan', 'FAN14G0421' => 'fan', 'FAN14G0866' => 'fan', 'FAN14G1187' => 'fan', 'FAN14G1727' => 'fan', 'FAN14G1791' => 'fan', 'FAN14G2361' => 'fan', 'FAN14G2668' => 'fan', 'FAN14G2770' => 'fan', 'FAN14G2874' => 'fan', 'FAN14G3193' => 'fan', 'FAN14G3624' => 'fan', 'FAN14G3676' => 'fan', 'FAN14G3807' => 'fan', 'FAN14G4082' => 'fan', 'FAN14G4342' => 'fan', 'FAN14G4985' => 'fan', 'FAN14G5126' => 'fan', 'FAN14G5781' => 'fan', 'FAN14G5808' => 'fan', 'FAN14G5949' => 'fan', 'FAN15G0828' => 'fan', 'FAN15G1054' => 'fan', 'FAN15G2023' => 'fan', 'FAN15G2506' => 'fan', 'FAN16G0128' => 'fan', 'FAN16G0249' => 'fan', 'FAN16G0429' => 'fan', 'FAN16G1493' => 'fan', 'FAN16G2210' => 'fan', 'FAN16G2506' => 'fan', 'FAN18G1542' => 'fan', 'FAN18G4057' => 'fan', 'FAN19G0745' => 'fan', 'FAN19G1216' => 'fan', 'FAN19G1733' => 'fan', 'FAN20G0258' => 'fan', 'FAN20G1095' => 'fan', 'FAN20G1557' => 'fan', 'FAN21G0302' => 'fan', 'FAN21G0519' => 'fan', 'FAN21G0970' => 'fan', 'FAN21G1159' => 'fan', 'FAN21G1312' => 'fan', 'FAN21G1440' => 'fan', 'FAN21G1715' => 'fan', 'FAN23G1584' => 'fan', 'FAN24G0045' => 'fan', 'FAN24G0053' => 'fan', 'FAN24G1500' => 'fan', 'FAN24G1817' => 'fan', 'FAN24G2147' => 'fan', 'FAN24G2236' => 'fan', 'FAN24G2446' => 'fan', 'FAN24G2684' => 'fan', 'FAN25G0187' => 'fan', 'FAN25G0505' => 'fan', 'FAN25G0589' => 'fan', 'FAN25G3663' => 'fan', 'FAN26G1025' => 'fan', 'FAN26G2860' => 'fan', 'FAN27G1329' => 'fan', 'FAN27G3392' => 'fan', 'FvH4_1g02011' => 'fve', 'FvH4_1g06511' => 'fve', 'FvH4_2g19900' => 'fve', 'FvH4_2g19920' => 'fve', 'FvH4_2g24261' => 'fve', 'FvH4_2g24270' => 'fve', 'FvH4_2g24631' => 'fve', 'FvH4_2g30622' => 'fve', 'FvH4_3g12920' => 'fve', 'FvH4_3g30171' => 'fve', 'FvH4_3g35490' => 'fve', 'FvH4_3g43682' => 'fve', 'FvH4_3g43730' => 'fve', 'FvH4_3g43732' => 'fve', 'FvH4_3g43751' => 'fve', 'FvH4_3g43752' => 'fve', 'FvH4_3g43770' => 'fve', 'FvH4_3g44471' => 'fve', 'FvH4_3g44510' => 'fve', 'FvH4_3g44582' => 'fve', 'FvH4_4g16921' => 'fve', 'FvH4_4g17121' => 'fve', 'FvH4_4g17782' => 'fve', 'FvH4_4g17783' => 'fve', 'FvH4_4g18120' => 'fve', 'FvH4_4g31310' => 'fve', 'FvH4_4g35052' => 'fve', 'FvH4_5g30862' => 'fve', 'FvH4_6g01541' => 'fve', 'FvH4_6g02021' => 'fve', 'FvH4_6g02041' => 'fve', 'FvH4_6g02071' => 'fve', 'FvH4_6g02171' => 'fve', 'FvH4_6g03181' => 'fve', 'FvH4_6g03182' => 'fve', 'FvH4_6g03221' => 'fve', 'FvH4_6g03380' => 'fve', 'FvH4_6g05201' => 'fve', 'FvH4_6g05203' => 'fve', 'FvH4_6g20231' => 'fve', 'FvH4_6g31981' => 'fve', 'FvH4_6g32061' => 'fve', 'FvH4_6g37041' => 'fve', 'FvH4_6g37932' => 'fve', 'FvH4_6g38731' => 'fve', 'FvH4_6g39370' => 'fve', 'FvH4_6g39371' => 'fve', 'FvH4_6g40891' => 'fve', 'FvH4_6g40892' => 'fve', 'FvH4_6g43143' => 'fve', 'FvH4_6g45251' => 'fve', 'FvH4_6g45260' => 'fve', 'FvH4_6g45291' => 'fve', 'FvH4_6g45890' => 'fve', 'FvH4_6g46240' => 'fve', 'FvH4_6g46241' => 'fve', 'FvH4_6g46242' => 'fve', 'FvH4_6g46260' => 'fve', 'FvH4_6g46280' => 'fve', 'FvH4_6g46380' => 'fve', 'FvH4_7g12841' => 'fve', 'FvH4_7g31431' => 'fve', 'Glyma.09G075900' => 'gma', 'Gohir.A09G096401' => 'ghi', 'Gohir.D09G096101' => 'ghi', 'Gorai.006G112800' => 'gra', 'HanXRQChr04g0121411' => 'han', 'Hund15878' => 'sun', 'Lj2A1107G68' => 'lonja', 'Lj2A630G63' => 'lonja', 'Lj2A946T25' => 'lonja', 'Lj2C714T1' => 'lonja', 'Lj2C966T3' => 'lonja', 'Lj2C966T4' => 'lonja', 'Lj4g0002979' => 'lja', 'Lsat_1_v5_gn_5_30901' => 'lsa', 'Lsat_1_v5_gn_5_31100' => 'lsa', 'Lsat_1_v5_gn_5_38600' => 'lsa', 'Lsat_1_v5_gn_6_92061' => 'lsa', 'Manes.05G071301' => 'mes', 'MD02G1008700' => 'mdo', 'MD02G1008900' => 'mdo', 'MD03G1256400' => 'mdo', 'MD04G1180900' => 'mdo', 'MD04G1181000' => 'mdo', 'MD04G1181200' => 'mdo', 'MD05G1244200' => 'mdo', 'MD05G1324200' => 'mdo', 'MD09G1201600' => 'mdo', 'MD10G1000600' => 'mdo', 'MD14G1026900' => 'mdo', 'MD14G1187900' => 'mdo', 'MD15G1017800' => 'mdo', 'MD15G1018100' => 'mdo', 'Medtr4g124160' => 'mtr', 'Migut.L01260' => 'egut', 'Nitab4.5_0000008g0440' => 'nta', 'Nitab4.5_0000207g0170' => 'nta', 'Nitab4.5_0007671g0030' => 'nta', 'Nitab4.5_0010853g0020' => 'nta', 'Oeu057656.1' => 'oeu', 'PGSC0003DMG400005638' => 'stu', 'PGSC0003DMG400005639' => 'stu', 'Phvul.009G222800' => 'pvu', 'Potri.009G132400' => 'ptr', 'Potri.009G163001' => 'ptr', 'Potri.011G000700' => 'ptr', 'Potri.011G004800' => 'ptr', 'Prupe.1G509300' => 'ppe', 'Prupe.1G509700' => 'ppe', 'Prupe.1G510400' => 'ppe', 'Prupe.1G510700' => 'ppe', 'Prupe.1G512600' => 'ppe', 'Prupe.2G073200' => 'ppe', 'Prupe.3G059500' => 'ppe', 'Prupe.3G059600' => 'ppe', 'Prupe.3G246100' => 'ppe', 'Prupe.3G265100' => 'ppe', 'Prupe.4G034700' => 'ppe', 'Prupe.4G052100' => 'ppe', 'Prupe.4G053600' => 'ppe', 'Prupe.5G068800' => 'ppe', 'Prupe.5G070600' => 'ppe', 'Prupe.6G075400' => 'ppe', 'Prupe.6G075500' => 'ppe', 'Prupe.6G076400' => 'ppe', 'Prupe.8G110700' => 'ppe', 'Psat4g020960' => 'psa', 'PSO135G0788' => 'pso', 'PSO210G6463' => 'pso', 'PSO384G0370' => 'pso', 'PSO386G0056' => 'pso', 'QL01p006048' => 'qlo', 'QL02p054283' => 'qlo', 'QL05p008000' => 'qlo', 'QL05p008212' => 'qlo', 'QL05p008950' => 'qlo', 'QL05p009042' => 'qlo', 'QL05p009518' => 'qlo', 'QL05p012589' => 'qlo', 'QL05p012608' => 'qlo', 'QL05p012650' => 'qlo', 'QL05p012667' => 'qlo', 'QL05p014501' => 'qlo', 'QL05p052800' => 'qlo', 'QL05p065010' => 'qlo', 'QL05p074156' => 'qlo', 'QL05p074160' => 'qlo', 'QL05p074174' => 'qlo', 'QL05p074178' => 'qlo', 'QL05p074214' => 'qlo', 'QL06p001050' => 'qlo', 'QL06p001056' => 'qlo', 'QL06p006093' => 'qlo', 'QL06p006111' => 'qlo', 'QL07p019784' => 'qlo', 'QL07p019801' => 'qlo', 'QL07p036110' => 'qlo', 'QL07p036134' => 'qlo', 'QL07p036147' => 'qlo', 'QL07p036156' => 'qlo', 'QL07p036300' => 'qlo', 'QL07p036320' => 'qlo', 'QL08p014547' => 'qlo', 'QL08p014551' => 'qlo', 'QL08p043319' => 'qlo', 'QL08p043324' => 'qlo', 'QL11p009094' => 'qlo', 'RcHm_v2.0_Chr1g0380481' => 'rch', 'RcHm_v2.0_Chr2g0089331' => 'rch', 'RcHm_v2.0_Chr2g0123691' => 'rch', 'RcHm_v2.0_Chr2g0151111' => 'rch', 'RcHm_v2.0_Chr2g0163011' => 'rch', 'RcHm_v2.0_Chr2g0163051' => 'rch', 'RcHm_v2.0_Chr2g0164671' => 'rch', 'RcHm_v2.0_Chr2g0164681' => 'rch', 'RcHm_v2.0_Chr2g0164721' => 'rch', 'RcHm_v2.0_Chr3g0449911' => 'rch', 'RcHm_v2.0_Chr3g0450211' => 'rch', 'RcHm_v2.0_Chr3g0457271' => 'rch', 'RcHm_v2.0_Chr5g0018111' => 'rch', 'RcHm_v2.0_Chr5g0021011' => 'rch', 'RcHm_v2.0_Chr5g0081171' => 'rch', 'RcHm_v2.0_Chr5g0081211' => 'rch', 'RcHm_v2.0_Chr6g0275871' => 'rch', 'RcHm_v2.0_Chr6g0276071' => 'rch', 'RcHm_v2.0_Chr6g0285591' => 'rch', 'RcHm_v2.0_Chr6g0291931' => 'rch', 'RcHm_v2.0_Chr6g0292091' => 'rch', 'RcHm_v2.0_Chr6g0292271' => 'rch', 'RcHm_v2.0_Chr7g0221261' => 'rch', 'Rhsim08G0219900' => 'rsi', 'Rhsim08G0220200' => 'rsi', 'Rhsim08G0237800' => 'rsi', 'Rhsim08G0238800' => 'rsi', 'Sabra09G0102700' => 'sbr', 'Sabra09G0127200' => 'sbr', 'Sabra11G0003700' => 'sbr', 'Sabra15G0014700' => 'sbr', 'Sc19g0000590' => 'sci', 'Sc19g0001870' => 'sci', 'SGA_v2.0_scaffold1G00346' => 'sas', 'SGA_v2.0_scaffold1G00575' => 'sas', 'SGA_v2.0_scaffold1G00761' => 'sas', 'SGA_v2.0_scaffold232G43501' => 'sas', 'TAR625G1137' => 'tar', 'Thecc.03G222100' => 'tca', 'TPR.G12691' => 'tpr', 'TWI34G0727' => 'twi', 'TWI36G0117' => 'twi', 'VMungo1309G0868' => 'vmu' ), 'gf_id' => 'HOM05D001729', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001729' ), 'data_identifier' => 'HOM05D001729', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001729', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '375', 'num_species' => '42' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'Ah.07g204710' => 'amhyb', 'AUR62006001' => 'cqu', 'AUR62006002' => 'cqu', 'AUR62006003' => 'cqu', 'AUR62015641' => 'cqu', 'AUR62027174' => 'cqu', 'AUR62035623' => 'cqu', 'AUR62035624' => 'cqu', 'AUR62035625' => 'cqu', 'AUR62035626' => 'cqu', 'CAN.G1110.53' => 'can', 'CANSAT80G0415' => 'cansat', 'Ca_21364_v3' => 'car', 'COL.COLO4_30693' => 'col', 'COL.COLO4_30694' => 'col', 'COL.COLO4_30695' => 'col', 'COL.COLO4_30696' => 'col', 'COL.COLO4_34020' => 'col', 'DCAR_004585' => 'dca', 'Dinv04029' => 'din', 'Dinv34857' => 'din', 'Duzib147G0011' => 'dzi', 'Duzib170G0599' => 'dzi', 'Duzib192G1051' => 'dzi', 'FAN01G0708' => 'fan', 'FAN01G0742' => 'fan', 'FAN02G0048' => 'fan', 'FAN02G0583' => 'fan', 'FAN02G0688' => 'fan', 'FAN02G1588' => 'fan', 'FAN02G2194' => 'fan', 'FAN02G2750' => 'fan', 'FAN02G3094' => 'fan', 'FAN02G3887' => 'fan', 'FAN02G3911' => 'fan', 'FAN02G3994' => 'fan', 'FAN02G4432' => 'fan', 'FAN02G4556' => 'fan', 'FAN03G1977' => 'fan', 'FAN03G2781' => 'fan', 'FAN03G2850' => 'fan', 'FAN03G3155' => 'fan', 'FAN04G2487' => 'fan', 'FAN05G0208' => 'fan', 'FAN05G0656' => 'fan', 'FAN05G0696' => 'fan', 'FAN05G0810' => 'fan', 'FAN05G1447' => 'fan', 'FAN05G2640' => 'fan', 'FAN05G2911' => 'fan', 'FAN05G3901' => 'fan', 'FAN05G4859' => 'fan', 'FAN05G4861' => 'fan', 'FAN05G4988' => 'fan', 'FAN05G5187' => 'fan', 'FAN05G5452' => 'fan', 'FAN05G5500' => 'fan', 'FAN05G5688' => 'fan', 'FAN06G0177' => 'fan', 'FAN06G0675' => 'fan', 'FAN06G1290' => 'fan', 'FAN06G2191' => 'fan', 'FAN06G2405' => 'fan', 'FAN06G3231' => 'fan', 'FAN06G3932' => 'fan', 'FAN07G0163' => 'fan', 'FAN07G0471' => 'fan', 'FAN07G1354' => 'fan', 'FAN08G0338' => 'fan', 'FAN08G1373' => 'fan', 'FAN08G2539' => 'fan', 'FAN08G2728' => 'fan', 'FAN09G0608' => 'fan', 'FAN09G1136' => 'fan', 'FAN09G1958' => 'fan', 'FAN09G2508' => 'fan', 'FAN09G2597' => 'fan', 'FAN09G2658' => 'fan', 'FAN09G2757' => 'fan', 'FAN09G2983' => 'fan', 'FAN09G3130' => 'fan', 'FAN09G3565' => 'fan', 'FAN09G3613' => 'fan', 'FAN09G4011' => 'fan', 'FAN09G4239' => 'fan', 'FAN09G4277' => 'fan', 'FAN09G4720' => 'fan', 'FAN11G0139' => 'fan', 'FAN11G1727' => 'fan', 'FAN11G2672' => 'fan', 'FAN11G2795' => 'fan', 'FAN11G3238' => 'fan', 'FAN11G3734' => 'fan', 'FAN12G0631' => 'fan', 'FAN12G2239' => 'fan', 'FAN12G2308' => 'fan', 'FAN12G2569' => 'fan', 'FAN12G2623' => 'fan', 'FAN13G3182' => 'fan', 'FAN14G0053' => 'fan', 'FAN14G0370' => 'fan', 'FAN14G0382' => 'fan', 'FAN14G0421' => 'fan', 'FAN14G0866' => 'fan', 'FAN14G1187' => 'fan', 'FAN14G1727' => 'fan', 'FAN14G1791' => 'fan', 'FAN14G2361' => 'fan', 'FAN14G2668' => 'fan', 'FAN14G2770' => 'fan', 'FAN14G2874' => 'fan', 'FAN14G3193' => 'fan', 'FAN14G3624' => 'fan', 'FAN14G3676' => 'fan', 'FAN14G3807' => 'fan', 'FAN14G4082' => 'fan', 'FAN14G4342' => 'fan', 'FAN14G4985' => 'fan', 'FAN14G5126' => 'fan', 'FAN14G5781' => 'fan', 'FAN14G5808' => 'fan', 'FAN14G5949' => 'fan', 'FAN15G0828' => 'fan', 'FAN15G1054' => 'fan', 'FAN15G2023' => 'fan', 'FAN15G2506' => 'fan', 'FAN16G0128' => 'fan', 'FAN16G0249' => 'fan', 'FAN16G0429' => 'fan', 'FAN16G1493' => 'fan', 'FAN16G2210' => 'fan', 'FAN16G2506' => 'fan', 'FAN18G1542' => 'fan', 'FAN18G4057' => 'fan', 'FAN19G0745' => 'fan', 'FAN19G1216' => 'fan', 'FAN19G1733' => 'fan', 'FAN20G0258' => 'fan', 'FAN20G1095' => 'fan', 'FAN20G1557' => 'fan', 'FAN21G0302' => 'fan', 'FAN21G0519' => 'fan', 'FAN21G0970' => 'fan', 'FAN21G1159' => 'fan', 'FAN21G1312' => 'fan', 'FAN21G1440' => 'fan', 'FAN21G1715' => 'fan', 'FAN23G1584' => 'fan', 'FAN24G0045' => 'fan', 'FAN24G0053' => 'fan', 'FAN24G1500' => 'fan', 'FAN24G1817' => 'fan', 'FAN24G2147' => 'fan', 'FAN24G2236' => 'fan', 'FAN24G2446' => 'fan', 'FAN24G2684' => 'fan', 'FAN25G0187' => 'fan', 'FAN25G0505' => 'fan', 'FAN25G0589' => 'fan', 'FAN25G3663' => 'fan', 'FAN26G1025' => 'fan', 'FAN26G2860' => 'fan', 'FAN27G1329' => 'fan', 'FAN27G3392' => 'fan', 'FvH4_1g02011' => 'fve', 'FvH4_1g06511' => 'fve', 'FvH4_2g19900' => 'fve', 'FvH4_2g19920' => 'fve', 'FvH4_2g24261' => 'fve', 'FvH4_2g24270' => 'fve', 'FvH4_2g24631' => 'fve', 'FvH4_2g30622' => 'fve', 'FvH4_3g12920' => 'fve', 'FvH4_3g30171' => 'fve', 'FvH4_3g35490' => 'fve', 'FvH4_3g43682' => 'fve', 'FvH4_3g43730' => 'fve', 'FvH4_3g43732' => 'fve', 'FvH4_3g43751' => 'fve', 'FvH4_3g43752' => 'fve', 'FvH4_3g43770' => 'fve', 'FvH4_3g44471' => 'fve', 'FvH4_3g44510' => 'fve', 'FvH4_3g44582' => 'fve', 'FvH4_4g16921' => 'fve', 'FvH4_4g17121' => 'fve', 'FvH4_4g17782' => 'fve', 'FvH4_4g17783' => 'fve', 'FvH4_4g18120' => 'fve', 'FvH4_4g31310' => 'fve', 'FvH4_4g35052' => 'fve', 'FvH4_5g30862' => 'fve', 'FvH4_6g01541' => 'fve', 'FvH4_6g02021' => 'fve', 'FvH4_6g02041' => 'fve', 'FvH4_6g02071' => 'fve', 'FvH4_6g02171' => 'fve', 'FvH4_6g03181' => 'fve', 'FvH4_6g03182' => 'fve', 'FvH4_6g03221' => 'fve', 'FvH4_6g03380' => 'fve', 'FvH4_6g05201' => 'fve', 'FvH4_6g05203' => 'fve', 'FvH4_6g20231' => 'fve', 'FvH4_6g31981' => 'fve', 'FvH4_6g32061' => 'fve', 'FvH4_6g37041' => 'fve', 'FvH4_6g37932' => 'fve', 'FvH4_6g38731' => 'fve', 'FvH4_6g39370' => 'fve', 'FvH4_6g39371' => 'fve', 'FvH4_6g40891' => 'fve', 'FvH4_6g40892' => 'fve', 'FvH4_6g43143' => 'fve', 'FvH4_6g45251' => 'fve', 'FvH4_6g45260' => 'fve', 'FvH4_6g45291' => 'fve', 'FvH4_6g45890' => 'fve', 'FvH4_6g46240' => 'fve', 'FvH4_6g46241' => 'fve', 'FvH4_6g46242' => 'fve', 'FvH4_6g46260' => 'fve', 'FvH4_6g46280' => 'fve', 'FvH4_6g46380' => 'fve', 'FvH4_7g12841' => 'fve', 'FvH4_7g31431' => 'fve', 'Glyma.09G075900' => 'gma', 'Gohir.A09G096401' => 'ghi', 'Gohir.D09G096101' => 'ghi', 'Gorai.006G112800' => 'gra', 'HanXRQChr04g0121411' => 'han', 'Hund15878' => 'sun', 'Lj2A1107G68' => 'lonja', 'Lj2A630G63' => 'lonja', 'Lj2A946T25' => 'lonja', 'Lj2C714T1' => 'lonja', 'Lj2C966T3' => 'lonja', 'Lj2C966T4' => 'lonja', 'Lj4g0002979' => 'lja', 'Lsat_1_v5_gn_5_30901' => 'lsa', 'Lsat_1_v5_gn_5_31100' => 'lsa', 'Lsat_1_v5_gn_5_38600' => 'lsa', 'Lsat_1_v5_gn_6_92061' => 'lsa', 'Manes.05G071301' => 'mes', 'MD02G1008700' => 'mdo', 'MD02G1008900' => 'mdo', 'MD03G1256400' => 'mdo', 'MD04G1180900' => 'mdo', 'MD04G1181000' => 'mdo', 'MD04G1181200' => 'mdo', 'MD05G1244200' => 'mdo', 'MD05G1324200' => 'mdo', 'MD09G1201600' => 'mdo', 'MD10G1000600' => 'mdo', 'MD14G1026900' => 'mdo', 'MD14G1187900' => 'mdo', 'MD15G1017800' => 'mdo', 'MD15G1018100' => 'mdo', 'Medtr4g124160' => 'mtr', 'Migut.L01260' => 'egut', 'Nitab4.5_0000008g0440' => 'nta', 'Nitab4.5_0000207g0170' => 'nta', 'Nitab4.5_0007671g0030' => 'nta', 'Nitab4.5_0010853g0020' => 'nta', 'Oeu057656.1' => 'oeu', 'PGSC0003DMG400005638' => 'stu', 'PGSC0003DMG400005639' => 'stu', 'Phvul.009G222800' => 'pvu', 'Potri.009G132400' => 'ptr', 'Potri.009G163001' => 'ptr', 'Potri.011G000700' => 'ptr', 'Potri.011G004800' => 'ptr', 'Prupe.1G509300' => 'ppe', 'Prupe.1G509700' => 'ppe', 'Prupe.1G510400' => 'ppe', 'Prupe.1G510700' => 'ppe', 'Prupe.1G512600' => 'ppe', 'Prupe.2G073200' => 'ppe', 'Prupe.3G059500' => 'ppe', 'Prupe.3G059600' => 'ppe', 'Prupe.3G246100' => 'ppe', 'Prupe.3G265100' => 'ppe', 'Prupe.4G034700' => 'ppe', 'Prupe.4G052100' => 'ppe', 'Prupe.4G053600' => 'ppe', 'Prupe.5G068800' => 'ppe', 'Prupe.5G070600' => 'ppe', 'Prupe.6G075400' => 'ppe', 'Prupe.6G075500' => 'ppe', 'Prupe.6G076400' => 'ppe', 'Prupe.8G110700' => 'ppe', 'Psat4g020960' => 'psa', 'PSO135G0788' => 'pso', 'PSO210G6463' => 'pso', 'PSO384G0370' => 'pso', 'PSO386G0056' => 'pso', 'QL01p006048' => 'qlo', 'QL02p054283' => 'qlo', 'QL05p008000' => 'qlo', 'QL05p008212' => 'qlo', 'QL05p008950' => 'qlo', 'QL05p009042' => 'qlo', 'QL05p009518' => 'qlo', 'QL05p012589' => 'qlo', 'QL05p012608' => 'qlo', 'QL05p012650' => 'qlo', 'QL05p012667' => 'qlo', 'QL05p014501' => 'qlo', 'QL05p052800' => 'qlo', 'QL05p065010' => 'qlo', 'QL05p074156' => 'qlo', 'QL05p074160' => 'qlo', 'QL05p074174' => 'qlo', 'QL05p074178' => 'qlo', 'QL05p074214' => 'qlo', 'QL06p001050' => 'qlo', 'QL06p001056' => 'qlo', 'QL06p006093' => 'qlo', 'QL06p006111' => 'qlo', 'QL07p019784' => 'qlo', 'QL07p019801' => 'qlo', 'QL07p036110' => 'qlo', 'QL07p036134' => 'qlo', 'QL07p036147' => 'qlo', 'QL07p036156' => 'qlo', 'QL07p036300' => 'qlo', 'QL07p036320' => 'qlo', 'QL08p014547' => 'qlo', 'QL08p014551' => 'qlo', 'QL08p043319' => 'qlo', 'QL08p043324' => 'qlo', 'QL11p009094' => 'qlo', 'RcHm_v2.0_Chr1g0380481' => 'rch', 'RcHm_v2.0_Chr2g0089331' => 'rch', 'RcHm_v2.0_Chr2g0123691' => 'rch', 'RcHm_v2.0_Chr2g0151111' => 'rch', 'RcHm_v2.0_Chr2g0163011' => 'rch', 'RcHm_v2.0_Chr2g0163051' => 'rch', 'RcHm_v2.0_Chr2g0164671' => 'rch', 'RcHm_v2.0_Chr2g0164681' => 'rch', 'RcHm_v2.0_Chr2g0164721' => 'rch', 'RcHm_v2.0_Chr3g0449911' => 'rch', 'RcHm_v2.0_Chr3g0450211' => 'rch', 'RcHm_v2.0_Chr3g0457271' => 'rch', 'RcHm_v2.0_Chr5g0018111' => 'rch', 'RcHm_v2.0_Chr5g0021011' => 'rch', 'RcHm_v2.0_Chr5g0081171' => 'rch', 'RcHm_v2.0_Chr5g0081211' => 'rch', 'RcHm_v2.0_Chr6g0275871' => 'rch', 'RcHm_v2.0_Chr6g0276071' => 'rch', 'RcHm_v2.0_Chr6g0285591' => 'rch', 'RcHm_v2.0_Chr6g0291931' => 'rch', 'RcHm_v2.0_Chr6g0292091' => 'rch', 'RcHm_v2.0_Chr6g0292271' => 'rch', 'RcHm_v2.0_Chr7g0221261' => 'rch', 'Rhsim08G0219900' => 'rsi', 'Rhsim08G0220200' => 'rsi', 'Rhsim08G0237800' => 'rsi', 'Rhsim08G0238800' => 'rsi', 'Sabra09G0102700' => 'sbr', 'Sabra09G0127200' => 'sbr', 'Sabra11G0003700' => 'sbr', 'Sabra15G0014700' => 'sbr', 'Sc19g0000590' => 'sci', 'Sc19g0001870' => 'sci', 'SGA_v2.0_scaffold1G00346' => 'sas', 'SGA_v2.0_scaffold1G00575' => 'sas', 'SGA_v2.0_scaffold1G00761' => 'sas', 'SGA_v2.0_scaffold232G43501' => 'sas', 'TAR625G1137' => 'tar', 'Thecc.03G222100' => 'tca', 'TPR.G12691' => 'tpr', 'TWI34G0727' => 'twi', 'TWI36G0117' => 'twi', 'VMungo1309G0868' => 'vmu' ) $gf_id = 'HOM05D001729' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001729' ) $data_identifier = 'HOM05D001729' $data_type = 'gf_id' $species_gene_counts = array( 'amhyb' => (int) 1, 'cqu' => (int) 9, 'can' => (int) 1, 'cansat' => (int) 1, 'car' => (int) 1, 'col' => (int) 5, 'dca' => (int) 1, 'din' => (int) 2, 'dzi' => (int) 3, 'fan' => (int) 140, 'fve' => (int) 62, 'gma' => (int) 1, 'ghi' => (int) 2, 'gra' => (int) 1, 'han' => (int) 1, 'sun' => (int) 1, 'lonja' => (int) 6, 'lja' => (int) 1, 'lsa' => (int) 4, 'mes' => (int) 1, 'mdo' => (int) 14, 'mtr' => (int) 1, 'egut' => (int) 1, 'nta' => (int) 4, 'oeu' => (int) 1, 'stu' => (int) 2, 'pvu' => (int) 1, 'ptr' => (int) 4, 'ppe' => (int) 19, 'psa' => (int) 1, 'pso' => (int) 4, 'qlo' => (int) 36, 'rch' => (int) 23, 'rsi' => (int) 4, 'sbr' => (int) 4, 'sci' => (int) 2, 'sas' => (int) 4, 'tar' => (int) 1, 'tca' => (int) 1, 'tpr' => (int) 1, 'twi' => (int) 2, 'vmu' => (int) 1 ) $gf_gene_species = 'vmu' $gf_gene_id = 'VMungo1309G0868' $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' => 'HOM05D001729', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '375', 'num_species' => '42' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'Ah.07g204710' => 'amhyb', 'AUR62006001' => 'cqu', 'AUR62006002' => 'cqu', 'AUR62006003' => 'cqu', 'AUR62015641' => 'cqu', 'AUR62027174' => 'cqu', 'AUR62035623' => 'cqu', 'AUR62035624' => 'cqu', 'AUR62035625' => 'cqu', 'AUR62035626' => 'cqu', 'CAN.G1110.53' => 'can', 'CANSAT80G0415' => 'cansat', 'Ca_21364_v3' => 'car', 'COL.COLO4_30693' => 'col', 'COL.COLO4_30694' => 'col', 'COL.COLO4_30695' => 'col', 'COL.COLO4_30696' => 'col', 'COL.COLO4_34020' => 'col', 'DCAR_004585' => 'dca', 'Dinv04029' => 'din', 'Dinv34857' => 'din', 'Duzib147G0011' => 'dzi', 'Duzib170G0599' => 'dzi', 'Duzib192G1051' => 'dzi', 'FAN01G0708' => 'fan', 'FAN01G0742' => 'fan', 'FAN02G0048' => 'fan', 'FAN02G0583' => 'fan', 'FAN02G0688' => 'fan', 'FAN02G1588' => 'fan', 'FAN02G2194' => 'fan', 'FAN02G2750' => 'fan', 'FAN02G3094' => 'fan', 'FAN02G3887' => 'fan', 'FAN02G3911' => 'fan', 'FAN02G3994' => 'fan', 'FAN02G4432' => 'fan', 'FAN02G4556' => 'fan', 'FAN03G1977' => 'fan', 'FAN03G2781' => 'fan', 'FAN03G2850' => 'fan', 'FAN03G3155' => 'fan', 'FAN04G2487' => 'fan', 'FAN05G0208' => 'fan', 'FAN05G0656' => 'fan', 'FAN05G0696' => 'fan', 'FAN05G0810' => 'fan', 'FAN05G1447' => 'fan', 'FAN05G2640' => 'fan', 'FAN05G2911' => 'fan', 'FAN05G3901' => 'fan', 'FAN05G4859' => 'fan', 'FAN05G4861' => 'fan', 'FAN05G4988' => 'fan', 'FAN05G5187' => 'fan', 'FAN05G5452' => 'fan', 'FAN05G5500' => 'fan', 'FAN05G5688' => 'fan', 'FAN06G0177' => 'fan', 'FAN06G0675' => 'fan', 'FAN06G1290' => 'fan', 'FAN06G2191' => 'fan', 'FAN06G2405' => 'fan', 'FAN06G3231' => 'fan', 'FAN06G3932' => 'fan', 'FAN07G0163' => 'fan', 'FAN07G0471' => 'fan', 'FAN07G1354' => 'fan', 'FAN08G0338' => 'fan', 'FAN08G1373' => 'fan', 'FAN08G2539' => 'fan', 'FAN08G2728' => 'fan', 'FAN09G0608' => 'fan', 'FAN09G1136' => 'fan', 'FAN09G1958' => 'fan', 'FAN09G2508' => 'fan', 'FAN09G2597' => 'fan', 'FAN09G2658' => 'fan', 'FAN09G2757' => 'fan', 'FAN09G2983' => 'fan', 'FAN09G3130' => 'fan', 'FAN09G3565' => 'fan', 'FAN09G3613' => 'fan', 'FAN09G4011' => 'fan', 'FAN09G4239' => 'fan', 'FAN09G4277' => 'fan', 'FAN09G4720' => 'fan', 'FAN11G0139' => 'fan', 'FAN11G1727' => 'fan', 'FAN11G2672' => 'fan', 'FAN11G2795' => 'fan', 'FAN11G3238' => 'fan', 'FAN11G3734' => 'fan', 'FAN12G0631' => 'fan', 'FAN12G2239' => 'fan', 'FAN12G2308' => 'fan', 'FAN12G2569' => 'fan', 'FAN12G2623' => 'fan', 'FAN13G3182' => 'fan', 'FAN14G0053' => 'fan', 'FAN14G0370' => 'fan', 'FAN14G0382' => 'fan', 'FAN14G0421' => 'fan', 'FAN14G0866' => 'fan', 'FAN14G1187' => 'fan', 'FAN14G1727' => 'fan', 'FAN14G1791' => 'fan', 'FAN14G2361' => 'fan', 'FAN14G2668' => 'fan', 'FAN14G2770' => 'fan', 'FAN14G2874' => 'fan', 'FAN14G3193' => 'fan', 'FAN14G3624' => 'fan', 'FAN14G3676' => 'fan', 'FAN14G3807' => 'fan', 'FAN14G4082' => 'fan', 'FAN14G4342' => 'fan', 'FAN14G4985' => 'fan', 'FAN14G5126' => 'fan', 'FAN14G5781' => 'fan', 'FAN14G5808' => 'fan', 'FAN14G5949' => 'fan', 'FAN15G0828' => 'fan', 'FAN15G1054' => 'fan', 'FAN15G2023' => 'fan', 'FAN15G2506' => 'fan', 'FAN16G0128' => 'fan', 'FAN16G0249' => 'fan', 'FAN16G0429' => 'fan', 'FAN16G1493' => 'fan', 'FAN16G2210' => 'fan', 'FAN16G2506' => 'fan', 'FAN18G1542' => 'fan', 'FAN18G4057' => 'fan', 'FAN19G0745' => 'fan', 'FAN19G1216' => 'fan', 'FAN19G1733' => 'fan', 'FAN20G0258' => 'fan', 'FAN20G1095' => 'fan', 'FAN20G1557' => 'fan', 'FAN21G0302' => 'fan', 'FAN21G0519' => 'fan', 'FAN21G0970' => 'fan', 'FAN21G1159' => 'fan', 'FAN21G1312' => 'fan', 'FAN21G1440' => 'fan', 'FAN21G1715' => 'fan', 'FAN23G1584' => 'fan', 'FAN24G0045' => 'fan', 'FAN24G0053' => 'fan', 'FAN24G1500' => 'fan', 'FAN24G1817' => 'fan', 'FAN24G2147' => 'fan', 'FAN24G2236' => 'fan', 'FAN24G2446' => 'fan', 'FAN24G2684' => 'fan', 'FAN25G0187' => 'fan', 'FAN25G0505' => 'fan', 'FAN25G0589' => 'fan', 'FAN25G3663' => 'fan', 'FAN26G1025' => 'fan', 'FAN26G2860' => 'fan', 'FAN27G1329' => 'fan', 'FAN27G3392' => 'fan', 'FvH4_1g02011' => 'fve', 'FvH4_1g06511' => 'fve', 'FvH4_2g19900' => 'fve', 'FvH4_2g19920' => 'fve', 'FvH4_2g24261' => 'fve', 'FvH4_2g24270' => 'fve', 'FvH4_2g24631' => 'fve', 'FvH4_2g30622' => 'fve', 'FvH4_3g12920' => 'fve', 'FvH4_3g30171' => 'fve', 'FvH4_3g35490' => 'fve', 'FvH4_3g43682' => 'fve', 'FvH4_3g43730' => 'fve', 'FvH4_3g43732' => 'fve', 'FvH4_3g43751' => 'fve', 'FvH4_3g43752' => 'fve', 'FvH4_3g43770' => 'fve', 'FvH4_3g44471' => 'fve', 'FvH4_3g44510' => 'fve', 'FvH4_3g44582' => 'fve', 'FvH4_4g16921' => 'fve', 'FvH4_4g17121' => 'fve', 'FvH4_4g17782' => 'fve', 'FvH4_4g17783' => 'fve', 'FvH4_4g18120' => 'fve', 'FvH4_4g31310' => 'fve', 'FvH4_4g35052' => 'fve', 'FvH4_5g30862' => 'fve', 'FvH4_6g01541' => 'fve', 'FvH4_6g02021' => 'fve', 'FvH4_6g02041' => 'fve', 'FvH4_6g02071' => 'fve', 'FvH4_6g02171' => 'fve', 'FvH4_6g03181' => 'fve', 'FvH4_6g03182' => 'fve', 'FvH4_6g03221' => 'fve', 'FvH4_6g03380' => 'fve', 'FvH4_6g05201' => 'fve', 'FvH4_6g05203' => 'fve', 'FvH4_6g20231' => 'fve', 'FvH4_6g31981' => 'fve', 'FvH4_6g32061' => 'fve', 'FvH4_6g37041' => 'fve', 'FvH4_6g37932' => 'fve', 'FvH4_6g38731' => 'fve', 'FvH4_6g39370' => 'fve', 'FvH4_6g39371' => 'fve', 'FvH4_6g40891' => 'fve', 'FvH4_6g40892' => 'fve', 'FvH4_6g43143' => 'fve', 'FvH4_6g45251' => 'fve', 'FvH4_6g45260' => 'fve', 'FvH4_6g45291' => 'fve', 'FvH4_6g45890' => 'fve', 'FvH4_6g46240' => 'fve', 'FvH4_6g46241' => 'fve', 'FvH4_6g46242' => 'fve', 'FvH4_6g46260' => 'fve', 'FvH4_6g46280' => 'fve', 'FvH4_6g46380' => 'fve', 'FvH4_7g12841' => 'fve', 'FvH4_7g31431' => 'fve', 'Glyma.09G075900' => 'gma', 'Gohir.A09G096401' => 'ghi', 'Gohir.D09G096101' => 'ghi', 'Gorai.006G112800' => 'gra', 'HanXRQChr04g0121411' => 'han', 'Hund15878' => 'sun', 'Lj2A1107G68' => 'lonja', 'Lj2A630G63' => 'lonja', 'Lj2A946T25' => 'lonja', 'Lj2C714T1' => 'lonja', 'Lj2C966T3' => 'lonja', 'Lj2C966T4' => 'lonja', 'Lj4g0002979' => 'lja', 'Lsat_1_v5_gn_5_30901' => 'lsa', 'Lsat_1_v5_gn_5_31100' => 'lsa', 'Lsat_1_v5_gn_5_38600' => 'lsa', 'Lsat_1_v5_gn_6_92061' => 'lsa', 'Manes.05G071301' => 'mes', 'MD02G1008700' => 'mdo', 'MD02G1008900' => 'mdo', 'MD03G1256400' => 'mdo', 'MD04G1180900' => 'mdo', 'MD04G1181000' => 'mdo', 'MD04G1181200' => 'mdo', 'MD05G1244200' => 'mdo', 'MD05G1324200' => 'mdo', 'MD09G1201600' => 'mdo', 'MD10G1000600' => 'mdo', 'MD14G1026900' => 'mdo', 'MD14G1187900' => 'mdo', 'MD15G1017800' => 'mdo', 'MD15G1018100' => 'mdo', 'Medtr4g124160' => 'mtr', 'Migut.L01260' => 'egut', 'Nitab4.5_0000008g0440' => 'nta', 'Nitab4.5_0000207g0170' => 'nta', 'Nitab4.5_0007671g0030' => 'nta', 'Nitab4.5_0010853g0020' => 'nta', 'Oeu057656.1' => 'oeu', 'PGSC0003DMG400005638' => 'stu', 'PGSC0003DMG400005639' => 'stu', 'Phvul.009G222800' => 'pvu', 'Potri.009G132400' => 'ptr', 'Potri.009G163001' => 'ptr', 'Potri.011G000700' => 'ptr', 'Potri.011G004800' => 'ptr', 'Prupe.1G509300' => 'ppe', 'Prupe.1G509700' => 'ppe', 'Prupe.1G510400' => 'ppe', 'Prupe.1G510700' => 'ppe', 'Prupe.1G512600' => 'ppe', 'Prupe.2G073200' => 'ppe', 'Prupe.3G059500' => 'ppe', 'Prupe.3G059600' => 'ppe', 'Prupe.3G246100' => 'ppe', 'Prupe.3G265100' => 'ppe', 'Prupe.4G034700' => 'ppe', 'Prupe.4G052100' => 'ppe', 'Prupe.4G053600' => 'ppe', 'Prupe.5G068800' => 'ppe', 'Prupe.5G070600' => 'ppe', 'Prupe.6G075400' => 'ppe', 'Prupe.6G075500' => 'ppe', 'Prupe.6G076400' => 'ppe', 'Prupe.8G110700' => 'ppe', 'Psat4g020960' => 'psa', 'PSO135G0788' => 'pso', 'PSO210G6463' => 'pso', 'PSO384G0370' => 'pso', 'PSO386G0056' => 'pso', 'QL01p006048' => 'qlo', 'QL02p054283' => 'qlo', 'QL05p008000' => 'qlo', 'QL05p008212' => 'qlo', 'QL05p008950' => 'qlo', 'QL05p009042' => 'qlo', 'QL05p009518' => 'qlo', 'QL05p012589' => 'qlo', 'QL05p012608' => 'qlo', 'QL05p012650' => 'qlo', 'QL05p012667' => 'qlo', 'QL05p014501' => 'qlo', 'QL05p052800' => 'qlo', 'QL05p065010' => 'qlo', 'QL05p074156' => 'qlo', 'QL05p074160' => 'qlo', 'QL05p074174' => 'qlo', 'QL05p074178' => 'qlo', 'QL05p074214' => 'qlo', 'QL06p001050' => 'qlo', 'QL06p001056' => 'qlo', 'QL06p006093' => 'qlo', 'QL06p006111' => 'qlo', 'QL07p019784' => 'qlo', 'QL07p019801' => 'qlo', 'QL07p036110' => 'qlo', 'QL07p036134' => 'qlo', 'QL07p036147' => 'qlo', 'QL07p036156' => 'qlo', 'QL07p036300' => 'qlo', 'QL07p036320' => 'qlo', 'QL08p014547' => 'qlo', 'QL08p014551' => 'qlo', 'QL08p043319' => 'qlo', 'QL08p043324' => 'qlo', 'QL11p009094' => 'qlo', 'RcHm_v2.0_Chr1g0380481' => 'rch', 'RcHm_v2.0_Chr2g0089331' => 'rch', 'RcHm_v2.0_Chr2g0123691' => 'rch', 'RcHm_v2.0_Chr2g0151111' => 'rch', 'RcHm_v2.0_Chr2g0163011' => 'rch', 'RcHm_v2.0_Chr2g0163051' => 'rch', 'RcHm_v2.0_Chr2g0164671' => 'rch', 'RcHm_v2.0_Chr2g0164681' => 'rch', 'RcHm_v2.0_Chr2g0164721' => 'rch', 'RcHm_v2.0_Chr3g0449911' => 'rch', 'RcHm_v2.0_Chr3g0450211' => 'rch', 'RcHm_v2.0_Chr3g0457271' => 'rch', 'RcHm_v2.0_Chr5g0018111' => 'rch', 'RcHm_v2.0_Chr5g0021011' => 'rch', 'RcHm_v2.0_Chr5g0081171' => 'rch', 'RcHm_v2.0_Chr5g0081211' => 'rch', 'RcHm_v2.0_Chr6g0275871' => 'rch', 'RcHm_v2.0_Chr6g0276071' => 'rch', 'RcHm_v2.0_Chr6g0285591' => 'rch', 'RcHm_v2.0_Chr6g0291931' => 'rch', 'RcHm_v2.0_Chr6g0292091' => 'rch', 'RcHm_v2.0_Chr6g0292271' => 'rch', 'RcHm_v2.0_Chr7g0221261' => 'rch', 'Rhsim08G0219900' => 'rsi', 'Rhsim08G0220200' => 'rsi', 'Rhsim08G0237800' => 'rsi', 'Rhsim08G0238800' => 'rsi', 'Sabra09G0102700' => 'sbr', 'Sabra09G0127200' => 'sbr', 'Sabra11G0003700' => 'sbr', 'Sabra15G0014700' => 'sbr', 'Sc19g0000590' => 'sci', 'Sc19g0001870' => 'sci', 'SGA_v2.0_scaffold1G00346' => 'sas', 'SGA_v2.0_scaffold1G00575' => 'sas', 'SGA_v2.0_scaffold1G00761' => 'sas', 'SGA_v2.0_scaffold232G43501' => 'sas', 'TAR625G1137' => 'tar', 'Thecc.03G222100' => 'tca', 'TPR.G12691' => 'tpr', 'TWI34G0727' => 'twi', 'TWI36G0117' => 'twi', 'VMungo1309G0868' => 'vmu' ), 'gf_id' => 'HOM05D001729', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001729' ), 'data_identifier' => 'HOM05D001729', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001729', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '375', 'num_species' => '42' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'Ah.07g204710' => 'amhyb', 'AUR62006001' => 'cqu', 'AUR62006002' => 'cqu', 'AUR62006003' => 'cqu', 'AUR62015641' => 'cqu', 'AUR62027174' => 'cqu', 'AUR62035623' => 'cqu', 'AUR62035624' => 'cqu', 'AUR62035625' => 'cqu', 'AUR62035626' => 'cqu', 'CAN.G1110.53' => 'can', 'CANSAT80G0415' => 'cansat', 'Ca_21364_v3' => 'car', 'COL.COLO4_30693' => 'col', 'COL.COLO4_30694' => 'col', 'COL.COLO4_30695' => 'col', 'COL.COLO4_30696' => 'col', 'COL.COLO4_34020' => 'col', 'DCAR_004585' => 'dca', 'Dinv04029' => 'din', 'Dinv34857' => 'din', 'Duzib147G0011' => 'dzi', 'Duzib170G0599' => 'dzi', 'Duzib192G1051' => 'dzi', 'FAN01G0708' => 'fan', 'FAN01G0742' => 'fan', 'FAN02G0048' => 'fan', 'FAN02G0583' => 'fan', 'FAN02G0688' => 'fan', 'FAN02G1588' => 'fan', 'FAN02G2194' => 'fan', 'FAN02G2750' => 'fan', 'FAN02G3094' => 'fan', 'FAN02G3887' => 'fan', 'FAN02G3911' => 'fan', 'FAN02G3994' => 'fan', 'FAN02G4432' => 'fan', 'FAN02G4556' => 'fan', 'FAN03G1977' => 'fan', 'FAN03G2781' => 'fan', 'FAN03G2850' => 'fan', 'FAN03G3155' => 'fan', 'FAN04G2487' => 'fan', 'FAN05G0208' => 'fan', 'FAN05G0656' => 'fan', 'FAN05G0696' => 'fan', 'FAN05G0810' => 'fan', 'FAN05G1447' => 'fan', 'FAN05G2640' => 'fan', 'FAN05G2911' => 'fan', 'FAN05G3901' => 'fan', 'FAN05G4859' => 'fan', 'FAN05G4861' => 'fan', 'FAN05G4988' => 'fan', 'FAN05G5187' => 'fan', 'FAN05G5452' => 'fan', 'FAN05G5500' => 'fan', 'FAN05G5688' => 'fan', 'FAN06G0177' => 'fan', 'FAN06G0675' => 'fan', 'FAN06G1290' => 'fan', 'FAN06G2191' => 'fan', 'FAN06G2405' => 'fan', 'FAN06G3231' => 'fan', 'FAN06G3932' => 'fan', 'FAN07G0163' => 'fan', 'FAN07G0471' => 'fan', 'FAN07G1354' => 'fan', 'FAN08G0338' => 'fan', 'FAN08G1373' => 'fan', 'FAN08G2539' => 'fan', 'FAN08G2728' => 'fan', 'FAN09G0608' => 'fan', 'FAN09G1136' => 'fan', 'FAN09G1958' => 'fan', 'FAN09G2508' => 'fan', 'FAN09G2597' => 'fan', 'FAN09G2658' => 'fan', 'FAN09G2757' => 'fan', 'FAN09G2983' => 'fan', 'FAN09G3130' => 'fan', 'FAN09G3565' => 'fan', 'FAN09G3613' => 'fan', 'FAN09G4011' => 'fan', 'FAN09G4239' => 'fan', 'FAN09G4277' => 'fan', 'FAN09G4720' => 'fan', 'FAN11G0139' => 'fan', 'FAN11G1727' => 'fan', 'FAN11G2672' => 'fan', 'FAN11G2795' => 'fan', 'FAN11G3238' => 'fan', 'FAN11G3734' => 'fan', 'FAN12G0631' => 'fan', 'FAN12G2239' => 'fan', 'FAN12G2308' => 'fan', 'FAN12G2569' => 'fan', 'FAN12G2623' => 'fan', 'FAN13G3182' => 'fan', 'FAN14G0053' => 'fan', 'FAN14G0370' => 'fan', 'FAN14G0382' => 'fan', 'FAN14G0421' => 'fan', 'FAN14G0866' => 'fan', 'FAN14G1187' => 'fan', 'FAN14G1727' => 'fan', 'FAN14G1791' => 'fan', 'FAN14G2361' => 'fan', 'FAN14G2668' => 'fan', 'FAN14G2770' => 'fan', 'FAN14G2874' => 'fan', 'FAN14G3193' => 'fan', 'FAN14G3624' => 'fan', 'FAN14G3676' => 'fan', 'FAN14G3807' => 'fan', 'FAN14G4082' => 'fan', 'FAN14G4342' => 'fan', 'FAN14G4985' => 'fan', 'FAN14G5126' => 'fan', 'FAN14G5781' => 'fan', 'FAN14G5808' => 'fan', 'FAN14G5949' => 'fan', 'FAN15G0828' => 'fan', 'FAN15G1054' => 'fan', 'FAN15G2023' => 'fan', 'FAN15G2506' => 'fan', 'FAN16G0128' => 'fan', 'FAN16G0249' => 'fan', 'FAN16G0429' => 'fan', 'FAN16G1493' => 'fan', 'FAN16G2210' => 'fan', 'FAN16G2506' => 'fan', 'FAN18G1542' => 'fan', 'FAN18G4057' => 'fan', 'FAN19G0745' => 'fan', 'FAN19G1216' => 'fan', 'FAN19G1733' => 'fan', 'FAN20G0258' => 'fan', 'FAN20G1095' => 'fan', 'FAN20G1557' => 'fan', 'FAN21G0302' => 'fan', 'FAN21G0519' => 'fan', 'FAN21G0970' => 'fan', 'FAN21G1159' => 'fan', 'FAN21G1312' => 'fan', 'FAN21G1440' => 'fan', 'FAN21G1715' => 'fan', 'FAN23G1584' => 'fan', 'FAN24G0045' => 'fan', 'FAN24G0053' => 'fan', 'FAN24G1500' => 'fan', 'FAN24G1817' => 'fan', 'FAN24G2147' => 'fan', 'FAN24G2236' => 'fan', 'FAN24G2446' => 'fan', 'FAN24G2684' => 'fan', 'FAN25G0187' => 'fan', 'FAN25G0505' => 'fan', 'FAN25G0589' => 'fan', 'FAN25G3663' => 'fan', 'FAN26G1025' => 'fan', 'FAN26G2860' => 'fan', 'FAN27G1329' => 'fan', 'FAN27G3392' => 'fan', 'FvH4_1g02011' => 'fve', 'FvH4_1g06511' => 'fve', 'FvH4_2g19900' => 'fve', 'FvH4_2g19920' => 'fve', 'FvH4_2g24261' => 'fve', 'FvH4_2g24270' => 'fve', 'FvH4_2g24631' => 'fve', 'FvH4_2g30622' => 'fve', 'FvH4_3g12920' => 'fve', 'FvH4_3g30171' => 'fve', 'FvH4_3g35490' => 'fve', 'FvH4_3g43682' => 'fve', 'FvH4_3g43730' => 'fve', 'FvH4_3g43732' => 'fve', 'FvH4_3g43751' => 'fve', 'FvH4_3g43752' => 'fve', 'FvH4_3g43770' => 'fve', 'FvH4_3g44471' => 'fve', 'FvH4_3g44510' => 'fve', 'FvH4_3g44582' => 'fve', 'FvH4_4g16921' => 'fve', 'FvH4_4g17121' => 'fve', 'FvH4_4g17782' => 'fve', 'FvH4_4g17783' => 'fve', 'FvH4_4g18120' => 'fve', 'FvH4_4g31310' => 'fve', 'FvH4_4g35052' => 'fve', 'FvH4_5g30862' => 'fve', 'FvH4_6g01541' => 'fve', 'FvH4_6g02021' => 'fve', 'FvH4_6g02041' => 'fve', 'FvH4_6g02071' => 'fve', 'FvH4_6g02171' => 'fve', 'FvH4_6g03181' => 'fve', 'FvH4_6g03182' => 'fve', 'FvH4_6g03221' => 'fve', 'FvH4_6g03380' => 'fve', 'FvH4_6g05201' => 'fve', 'FvH4_6g05203' => 'fve', 'FvH4_6g20231' => 'fve', 'FvH4_6g31981' => 'fve', 'FvH4_6g32061' => 'fve', 'FvH4_6g37041' => 'fve', 'FvH4_6g37932' => 'fve', 'FvH4_6g38731' => 'fve', 'FvH4_6g39370' => 'fve', 'FvH4_6g39371' => 'fve', 'FvH4_6g40891' => 'fve', 'FvH4_6g40892' => 'fve', 'FvH4_6g43143' => 'fve', 'FvH4_6g45251' => 'fve', 'FvH4_6g45260' => 'fve', 'FvH4_6g45291' => 'fve', 'FvH4_6g45890' => 'fve', 'FvH4_6g46240' => 'fve', 'FvH4_6g46241' => 'fve', 'FvH4_6g46242' => 'fve', 'FvH4_6g46260' => 'fve', 'FvH4_6g46280' => 'fve', 'FvH4_6g46380' => 'fve', 'FvH4_7g12841' => 'fve', 'FvH4_7g31431' => 'fve', 'Glyma.09G075900' => 'gma', 'Gohir.A09G096401' => 'ghi', 'Gohir.D09G096101' => 'ghi', 'Gorai.006G112800' => 'gra', 'HanXRQChr04g0121411' => 'han', 'Hund15878' => 'sun', 'Lj2A1107G68' => 'lonja', 'Lj2A630G63' => 'lonja', 'Lj2A946T25' => 'lonja', 'Lj2C714T1' => 'lonja', 'Lj2C966T3' => 'lonja', 'Lj2C966T4' => 'lonja', 'Lj4g0002979' => 'lja', 'Lsat_1_v5_gn_5_30901' => 'lsa', 'Lsat_1_v5_gn_5_31100' => 'lsa', 'Lsat_1_v5_gn_5_38600' => 'lsa', 'Lsat_1_v5_gn_6_92061' => 'lsa', 'Manes.05G071301' => 'mes', 'MD02G1008700' => 'mdo', 'MD02G1008900' => 'mdo', 'MD03G1256400' => 'mdo', 'MD04G1180900' => 'mdo', 'MD04G1181000' => 'mdo', 'MD04G1181200' => 'mdo', 'MD05G1244200' => 'mdo', 'MD05G1324200' => 'mdo', 'MD09G1201600' => 'mdo', 'MD10G1000600' => 'mdo', 'MD14G1026900' => 'mdo', 'MD14G1187900' => 'mdo', 'MD15G1017800' => 'mdo', 'MD15G1018100' => 'mdo', 'Medtr4g124160' => 'mtr', 'Migut.L01260' => 'egut', 'Nitab4.5_0000008g0440' => 'nta', 'Nitab4.5_0000207g0170' => 'nta', 'Nitab4.5_0007671g0030' => 'nta', 'Nitab4.5_0010853g0020' => 'nta', 'Oeu057656.1' => 'oeu', 'PGSC0003DMG400005638' => 'stu', 'PGSC0003DMG400005639' => 'stu', 'Phvul.009G222800' => 'pvu', 'Potri.009G132400' => 'ptr', 'Potri.009G163001' => 'ptr', 'Potri.011G000700' => 'ptr', 'Potri.011G004800' => 'ptr', 'Prupe.1G509300' => 'ppe', 'Prupe.1G509700' => 'ppe', 'Prupe.1G510400' => 'ppe', 'Prupe.1G510700' => 'ppe', 'Prupe.1G512600' => 'ppe', 'Prupe.2G073200' => 'ppe', 'Prupe.3G059500' => 'ppe', 'Prupe.3G059600' => 'ppe', 'Prupe.3G246100' => 'ppe', 'Prupe.3G265100' => 'ppe', 'Prupe.4G034700' => 'ppe', 'Prupe.4G052100' => 'ppe', 'Prupe.4G053600' => 'ppe', 'Prupe.5G068800' => 'ppe', 'Prupe.5G070600' => 'ppe', 'Prupe.6G075400' => 'ppe', 'Prupe.6G075500' => 'ppe', 'Prupe.6G076400' => 'ppe', 'Prupe.8G110700' => 'ppe', 'Psat4g020960' => 'psa', 'PSO135G0788' => 'pso', 'PSO210G6463' => 'pso', 'PSO384G0370' => 'pso', 'PSO386G0056' => 'pso', 'QL01p006048' => 'qlo', 'QL02p054283' => 'qlo', 'QL05p008000' => 'qlo', 'QL05p008212' => 'qlo', 'QL05p008950' => 'qlo', 'QL05p009042' => 'qlo', 'QL05p009518' => 'qlo', 'QL05p012589' => 'qlo', 'QL05p012608' => 'qlo', 'QL05p012650' => 'qlo', 'QL05p012667' => 'qlo', 'QL05p014501' => 'qlo', 'QL05p052800' => 'qlo', 'QL05p065010' => 'qlo', 'QL05p074156' => 'qlo', 'QL05p074160' => 'qlo', 'QL05p074174' => 'qlo', 'QL05p074178' => 'qlo', 'QL05p074214' => 'qlo', 'QL06p001050' => 'qlo', 'QL06p001056' => 'qlo', 'QL06p006093' => 'qlo', 'QL06p006111' => 'qlo', 'QL07p019784' => 'qlo', 'QL07p019801' => 'qlo', 'QL07p036110' => 'qlo', 'QL07p036134' => 'qlo', 'QL07p036147' => 'qlo', 'QL07p036156' => 'qlo', 'QL07p036300' => 'qlo', 'QL07p036320' => 'qlo', 'QL08p014547' => 'qlo', 'QL08p014551' => 'qlo', 'QL08p043319' => 'qlo', 'QL08p043324' => 'qlo', 'QL11p009094' => 'qlo', 'RcHm_v2.0_Chr1g0380481' => 'rch', 'RcHm_v2.0_Chr2g0089331' => 'rch', 'RcHm_v2.0_Chr2g0123691' => 'rch', 'RcHm_v2.0_Chr2g0151111' => 'rch', 'RcHm_v2.0_Chr2g0163011' => 'rch', 'RcHm_v2.0_Chr2g0163051' => 'rch', 'RcHm_v2.0_Chr2g0164671' => 'rch', 'RcHm_v2.0_Chr2g0164681' => 'rch', 'RcHm_v2.0_Chr2g0164721' => 'rch', 'RcHm_v2.0_Chr3g0449911' => 'rch', 'RcHm_v2.0_Chr3g0450211' => 'rch', 'RcHm_v2.0_Chr3g0457271' => 'rch', 'RcHm_v2.0_Chr5g0018111' => 'rch', 'RcHm_v2.0_Chr5g0021011' => 'rch', 'RcHm_v2.0_Chr5g0081171' => 'rch', 'RcHm_v2.0_Chr5g0081211' => 'rch', 'RcHm_v2.0_Chr6g0275871' => 'rch', 'RcHm_v2.0_Chr6g0276071' => 'rch', 'RcHm_v2.0_Chr6g0285591' => 'rch', 'RcHm_v2.0_Chr6g0291931' => 'rch', 'RcHm_v2.0_Chr6g0292091' => 'rch', 'RcHm_v2.0_Chr6g0292271' => 'rch', 'RcHm_v2.0_Chr7g0221261' => 'rch', 'Rhsim08G0219900' => 'rsi', 'Rhsim08G0220200' => 'rsi', 'Rhsim08G0237800' => 'rsi', 'Rhsim08G0238800' => 'rsi', 'Sabra09G0102700' => 'sbr', 'Sabra09G0127200' => 'sbr', 'Sabra11G0003700' => 'sbr', 'Sabra15G0014700' => 'sbr', 'Sc19g0000590' => 'sci', 'Sc19g0001870' => 'sci', 'SGA_v2.0_scaffold1G00346' => 'sas', 'SGA_v2.0_scaffold1G00575' => 'sas', 'SGA_v2.0_scaffold1G00761' => 'sas', 'SGA_v2.0_scaffold232G43501' => 'sas', 'TAR625G1137' => 'tar', 'Thecc.03G222100' => 'tca', 'TPR.G12691' => 'tpr', 'TWI34G0727' => 'twi', 'TWI36G0117' => 'twi', 'VMungo1309G0868' => 'vmu' ) $gf_id = 'HOM05D001729' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001729' ) $data_identifier = 'HOM05D001729' $data_type = 'gf_id' $species_gene_counts = array( 'amhyb' => (int) 1, 'cqu' => (int) 9, 'can' => (int) 1, 'cansat' => (int) 1, 'car' => (int) 1, 'col' => (int) 5, 'dca' => (int) 1, 'din' => (int) 2, 'dzi' => (int) 3, 'fan' => (int) 140, 'fve' => (int) 62, 'gma' => (int) 1, 'ghi' => (int) 2, 'gra' => (int) 1, 'han' => (int) 1, 'sun' => (int) 1, 'lonja' => (int) 6, 'lja' => (int) 1, 'lsa' => (int) 4, 'mes' => (int) 1, 'mdo' => (int) 14, 'mtr' => (int) 1, 'egut' => (int) 1, 'nta' => (int) 4, 'oeu' => (int) 1, 'stu' => (int) 2, 'pvu' => (int) 1, 'ptr' => (int) 4, 'ppe' => (int) 19, 'psa' => (int) 1, 'pso' => (int) 4, 'qlo' => (int) 36, 'rch' => (int) 23, 'rsi' => (int) 4, 'sbr' => (int) 4, 'sci' => (int) 2, 'sas' => (int) 4, 'tar' => (int) 1, 'tca' => (int) 1, 'tpr' => (int) 1, 'twi' => (int) 2, 'vmu' => (int) 1 ) $gf_gene_species = 'vmu' $gf_gene_id = 'VMungo1309G0868' $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' => 'HOM05D001729', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '375', 'num_species' => '42' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'Ah.07g204710' => 'amhyb', 'AUR62006001' => 'cqu', 'AUR62006002' => 'cqu', 'AUR62006003' => 'cqu', 'AUR62015641' => 'cqu', 'AUR62027174' => 'cqu', 'AUR62035623' => 'cqu', 'AUR62035624' => 'cqu', 'AUR62035625' => 'cqu', 'AUR62035626' => 'cqu', 'CAN.G1110.53' => 'can', 'CANSAT80G0415' => 'cansat', 'Ca_21364_v3' => 'car', 'COL.COLO4_30693' => 'col', 'COL.COLO4_30694' => 'col', 'COL.COLO4_30695' => 'col', 'COL.COLO4_30696' => 'col', 'COL.COLO4_34020' => 'col', 'DCAR_004585' => 'dca', 'Dinv04029' => 'din', 'Dinv34857' => 'din', 'Duzib147G0011' => 'dzi', 'Duzib170G0599' => 'dzi', 'Duzib192G1051' => 'dzi', 'FAN01G0708' => 'fan', 'FAN01G0742' => 'fan', 'FAN02G0048' => 'fan', 'FAN02G0583' => 'fan', 'FAN02G0688' => 'fan', 'FAN02G1588' => 'fan', 'FAN02G2194' => 'fan', 'FAN02G2750' => 'fan', 'FAN02G3094' => 'fan', 'FAN02G3887' => 'fan', 'FAN02G3911' => 'fan', 'FAN02G3994' => 'fan', 'FAN02G4432' => 'fan', 'FAN02G4556' => 'fan', 'FAN03G1977' => 'fan', 'FAN03G2781' => 'fan', 'FAN03G2850' => 'fan', 'FAN03G3155' => 'fan', 'FAN04G2487' => 'fan', 'FAN05G0208' => 'fan', 'FAN05G0656' => 'fan', 'FAN05G0696' => 'fan', 'FAN05G0810' => 'fan', 'FAN05G1447' => 'fan', 'FAN05G2640' => 'fan', 'FAN05G2911' => 'fan', 'FAN05G3901' => 'fan', 'FAN05G4859' => 'fan', 'FAN05G4861' => 'fan', 'FAN05G4988' => 'fan', 'FAN05G5187' => 'fan', 'FAN05G5452' => 'fan', 'FAN05G5500' => 'fan', 'FAN05G5688' => 'fan', 'FAN06G0177' => 'fan', 'FAN06G0675' => 'fan', 'FAN06G1290' => 'fan', 'FAN06G2191' => 'fan', 'FAN06G2405' => 'fan', 'FAN06G3231' => 'fan', 'FAN06G3932' => 'fan', 'FAN07G0163' => 'fan', 'FAN07G0471' => 'fan', 'FAN07G1354' => 'fan', 'FAN08G0338' => 'fan', 'FAN08G1373' => 'fan', 'FAN08G2539' => 'fan', 'FAN08G2728' => 'fan', 'FAN09G0608' => 'fan', 'FAN09G1136' => 'fan', 'FAN09G1958' => 'fan', 'FAN09G2508' => 'fan', 'FAN09G2597' => 'fan', 'FAN09G2658' => 'fan', 'FAN09G2757' => 'fan', 'FAN09G2983' => 'fan', 'FAN09G3130' => 'fan', 'FAN09G3565' => 'fan', 'FAN09G3613' => 'fan', 'FAN09G4011' => 'fan', 'FAN09G4239' => 'fan', 'FAN09G4277' => 'fan', 'FAN09G4720' => 'fan', 'FAN11G0139' => 'fan', 'FAN11G1727' => 'fan', 'FAN11G2672' => 'fan', 'FAN11G2795' => 'fan', 'FAN11G3238' => 'fan', 'FAN11G3734' => 'fan', 'FAN12G0631' => 'fan', 'FAN12G2239' => 'fan', 'FAN12G2308' => 'fan', 'FAN12G2569' => 'fan', 'FAN12G2623' => 'fan', 'FAN13G3182' => 'fan', 'FAN14G0053' => 'fan', 'FAN14G0370' => 'fan', 'FAN14G0382' => 'fan', 'FAN14G0421' => 'fan', 'FAN14G0866' => 'fan', 'FAN14G1187' => 'fan', 'FAN14G1727' => 'fan', 'FAN14G1791' => 'fan', 'FAN14G2361' => 'fan', 'FAN14G2668' => 'fan', 'FAN14G2770' => 'fan', 'FAN14G2874' => 'fan', 'FAN14G3193' => 'fan', 'FAN14G3624' => 'fan', 'FAN14G3676' => 'fan', 'FAN14G3807' => 'fan', 'FAN14G4082' => 'fan', 'FAN14G4342' => 'fan', 'FAN14G4985' => 'fan', 'FAN14G5126' => 'fan', 'FAN14G5781' => 'fan', 'FAN14G5808' => 'fan', 'FAN14G5949' => 'fan', 'FAN15G0828' => 'fan', 'FAN15G1054' => 'fan', 'FAN15G2023' => 'fan', 'FAN15G2506' => 'fan', 'FAN16G0128' => 'fan', 'FAN16G0249' => 'fan', 'FAN16G0429' => 'fan', 'FAN16G1493' => 'fan', 'FAN16G2210' => 'fan', 'FAN16G2506' => 'fan', 'FAN18G1542' => 'fan', 'FAN18G4057' => 'fan', 'FAN19G0745' => 'fan', 'FAN19G1216' => 'fan', 'FAN19G1733' => 'fan', 'FAN20G0258' => 'fan', 'FAN20G1095' => 'fan', 'FAN20G1557' => 'fan', 'FAN21G0302' => 'fan', 'FAN21G0519' => 'fan', 'FAN21G0970' => 'fan', 'FAN21G1159' => 'fan', 'FAN21G1312' => 'fan', 'FAN21G1440' => 'fan', 'FAN21G1715' => 'fan', 'FAN23G1584' => 'fan', 'FAN24G0045' => 'fan', 'FAN24G0053' => 'fan', 'FAN24G1500' => 'fan', 'FAN24G1817' => 'fan', 'FAN24G2147' => 'fan', 'FAN24G2236' => 'fan', 'FAN24G2446' => 'fan', 'FAN24G2684' => 'fan', 'FAN25G0187' => 'fan', 'FAN25G0505' => 'fan', 'FAN25G0589' => 'fan', 'FAN25G3663' => 'fan', 'FAN26G1025' => 'fan', 'FAN26G2860' => 'fan', 'FAN27G1329' => 'fan', 'FAN27G3392' => 'fan', 'FvH4_1g02011' => 'fve', 'FvH4_1g06511' => 'fve', 'FvH4_2g19900' => 'fve', 'FvH4_2g19920' => 'fve', 'FvH4_2g24261' => 'fve', 'FvH4_2g24270' => 'fve', 'FvH4_2g24631' => 'fve', 'FvH4_2g30622' => 'fve', 'FvH4_3g12920' => 'fve', 'FvH4_3g30171' => 'fve', 'FvH4_3g35490' => 'fve', 'FvH4_3g43682' => 'fve', 'FvH4_3g43730' => 'fve', 'FvH4_3g43732' => 'fve', 'FvH4_3g43751' => 'fve', 'FvH4_3g43752' => 'fve', 'FvH4_3g43770' => 'fve', 'FvH4_3g44471' => 'fve', 'FvH4_3g44510' => 'fve', 'FvH4_3g44582' => 'fve', 'FvH4_4g16921' => 'fve', 'FvH4_4g17121' => 'fve', 'FvH4_4g17782' => 'fve', 'FvH4_4g17783' => 'fve', 'FvH4_4g18120' => 'fve', 'FvH4_4g31310' => 'fve', 'FvH4_4g35052' => 'fve', 'FvH4_5g30862' => 'fve', 'FvH4_6g01541' => 'fve', 'FvH4_6g02021' => 'fve', 'FvH4_6g02041' => 'fve', 'FvH4_6g02071' => 'fve', 'FvH4_6g02171' => 'fve', 'FvH4_6g03181' => 'fve', 'FvH4_6g03182' => 'fve', 'FvH4_6g03221' => 'fve', 'FvH4_6g03380' => 'fve', 'FvH4_6g05201' => 'fve', 'FvH4_6g05203' => 'fve', 'FvH4_6g20231' => 'fve', 'FvH4_6g31981' => 'fve', 'FvH4_6g32061' => 'fve', 'FvH4_6g37041' => 'fve', 'FvH4_6g37932' => 'fve', 'FvH4_6g38731' => 'fve', 'FvH4_6g39370' => 'fve', 'FvH4_6g39371' => 'fve', 'FvH4_6g40891' => 'fve', 'FvH4_6g40892' => 'fve', 'FvH4_6g43143' => 'fve', 'FvH4_6g45251' => 'fve', 'FvH4_6g45260' => 'fve', 'FvH4_6g45291' => 'fve', 'FvH4_6g45890' => 'fve', 'FvH4_6g46240' => 'fve', 'FvH4_6g46241' => 'fve', 'FvH4_6g46242' => 'fve', 'FvH4_6g46260' => 'fve', 'FvH4_6g46280' => 'fve', 'FvH4_6g46380' => 'fve', 'FvH4_7g12841' => 'fve', 'FvH4_7g31431' => 'fve', 'Glyma.09G075900' => 'gma', 'Gohir.A09G096401' => 'ghi', 'Gohir.D09G096101' => 'ghi', 'Gorai.006G112800' => 'gra', 'HanXRQChr04g0121411' => 'han', 'Hund15878' => 'sun', 'Lj2A1107G68' => 'lonja', 'Lj2A630G63' => 'lonja', 'Lj2A946T25' => 'lonja', 'Lj2C714T1' => 'lonja', 'Lj2C966T3' => 'lonja', 'Lj2C966T4' => 'lonja', 'Lj4g0002979' => 'lja', 'Lsat_1_v5_gn_5_30901' => 'lsa', 'Lsat_1_v5_gn_5_31100' => 'lsa', 'Lsat_1_v5_gn_5_38600' => 'lsa', 'Lsat_1_v5_gn_6_92061' => 'lsa', 'Manes.05G071301' => 'mes', 'MD02G1008700' => 'mdo', 'MD02G1008900' => 'mdo', 'MD03G1256400' => 'mdo', 'MD04G1180900' => 'mdo', 'MD04G1181000' => 'mdo', 'MD04G1181200' => 'mdo', 'MD05G1244200' => 'mdo', 'MD05G1324200' => 'mdo', 'MD09G1201600' => 'mdo', 'MD10G1000600' => 'mdo', 'MD14G1026900' => 'mdo', 'MD14G1187900' => 'mdo', 'MD15G1017800' => 'mdo', 'MD15G1018100' => 'mdo', 'Medtr4g124160' => 'mtr', 'Migut.L01260' => 'egut', 'Nitab4.5_0000008g0440' => 'nta', 'Nitab4.5_0000207g0170' => 'nta', 'Nitab4.5_0007671g0030' => 'nta', 'Nitab4.5_0010853g0020' => 'nta', 'Oeu057656.1' => 'oeu', 'PGSC0003DMG400005638' => 'stu', 'PGSC0003DMG400005639' => 'stu', 'Phvul.009G222800' => 'pvu', 'Potri.009G132400' => 'ptr', 'Potri.009G163001' => 'ptr', 'Potri.011G000700' => 'ptr', 'Potri.011G004800' => 'ptr', 'Prupe.1G509300' => 'ppe', 'Prupe.1G509700' => 'ppe', 'Prupe.1G510400' => 'ppe', 'Prupe.1G510700' => 'ppe', 'Prupe.1G512600' => 'ppe', 'Prupe.2G073200' => 'ppe', 'Prupe.3G059500' => 'ppe', 'Prupe.3G059600' => 'ppe', 'Prupe.3G246100' => 'ppe', 'Prupe.3G265100' => 'ppe', 'Prupe.4G034700' => 'ppe', 'Prupe.4G052100' => 'ppe', 'Prupe.4G053600' => 'ppe', 'Prupe.5G068800' => 'ppe', 'Prupe.5G070600' => 'ppe', 'Prupe.6G075400' => 'ppe', 'Prupe.6G075500' => 'ppe', 'Prupe.6G076400' => 'ppe', 'Prupe.8G110700' => 'ppe', 'Psat4g020960' => 'psa', 'PSO135G0788' => 'pso', 'PSO210G6463' => 'pso', 'PSO384G0370' => 'pso', 'PSO386G0056' => 'pso', 'QL01p006048' => 'qlo', 'QL02p054283' => 'qlo', 'QL05p008000' => 'qlo', 'QL05p008212' => 'qlo', 'QL05p008950' => 'qlo', 'QL05p009042' => 'qlo', 'QL05p009518' => 'qlo', 'QL05p012589' => 'qlo', 'QL05p012608' => 'qlo', 'QL05p012650' => 'qlo', 'QL05p012667' => 'qlo', 'QL05p014501' => 'qlo', 'QL05p052800' => 'qlo', 'QL05p065010' => 'qlo', 'QL05p074156' => 'qlo', 'QL05p074160' => 'qlo', 'QL05p074174' => 'qlo', 'QL05p074178' => 'qlo', 'QL05p074214' => 'qlo', 'QL06p001050' => 'qlo', 'QL06p001056' => 'qlo', 'QL06p006093' => 'qlo', 'QL06p006111' => 'qlo', 'QL07p019784' => 'qlo', 'QL07p019801' => 'qlo', 'QL07p036110' => 'qlo', 'QL07p036134' => 'qlo', 'QL07p036147' => 'qlo', 'QL07p036156' => 'qlo', 'QL07p036300' => 'qlo', 'QL07p036320' => 'qlo', 'QL08p014547' => 'qlo', 'QL08p014551' => 'qlo', 'QL08p043319' => 'qlo', 'QL08p043324' => 'qlo', 'QL11p009094' => 'qlo', 'RcHm_v2.0_Chr1g0380481' => 'rch', 'RcHm_v2.0_Chr2g0089331' => 'rch', 'RcHm_v2.0_Chr2g0123691' => 'rch', 'RcHm_v2.0_Chr2g0151111' => 'rch', 'RcHm_v2.0_Chr2g0163011' => 'rch', 'RcHm_v2.0_Chr2g0163051' => 'rch', 'RcHm_v2.0_Chr2g0164671' => 'rch', 'RcHm_v2.0_Chr2g0164681' => 'rch', 'RcHm_v2.0_Chr2g0164721' => 'rch', 'RcHm_v2.0_Chr3g0449911' => 'rch', 'RcHm_v2.0_Chr3g0450211' => 'rch', 'RcHm_v2.0_Chr3g0457271' => 'rch', 'RcHm_v2.0_Chr5g0018111' => 'rch', 'RcHm_v2.0_Chr5g0021011' => 'rch', 'RcHm_v2.0_Chr5g0081171' => 'rch', 'RcHm_v2.0_Chr5g0081211' => 'rch', 'RcHm_v2.0_Chr6g0275871' => 'rch', 'RcHm_v2.0_Chr6g0276071' => 'rch', 'RcHm_v2.0_Chr6g0285591' => 'rch', 'RcHm_v2.0_Chr6g0291931' => 'rch', 'RcHm_v2.0_Chr6g0292091' => 'rch', 'RcHm_v2.0_Chr6g0292271' => 'rch', 'RcHm_v2.0_Chr7g0221261' => 'rch', 'Rhsim08G0219900' => 'rsi', 'Rhsim08G0220200' => 'rsi', 'Rhsim08G0237800' => 'rsi', 'Rhsim08G0238800' => 'rsi', 'Sabra09G0102700' => 'sbr', 'Sabra09G0127200' => 'sbr', 'Sabra11G0003700' => 'sbr', 'Sabra15G0014700' => 'sbr', 'Sc19g0000590' => 'sci', 'Sc19g0001870' => 'sci', 'SGA_v2.0_scaffold1G00346' => 'sas', 'SGA_v2.0_scaffold1G00575' => 'sas', 'SGA_v2.0_scaffold1G00761' => 'sas', 'SGA_v2.0_scaffold232G43501' => 'sas', 'TAR625G1137' => 'tar', 'Thecc.03G222100' => 'tca', 'TPR.G12691' => 'tpr', 'TWI34G0727' => 'twi', 'TWI36G0117' => 'twi', 'VMungo1309G0868' => 'vmu' ), 'gf_id' => 'HOM05D001729', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001729' ), 'data_identifier' => 'HOM05D001729', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001729', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '375', 'num_species' => '42' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'Ah.07g204710' => 'amhyb', 'AUR62006001' => 'cqu', 'AUR62006002' => 'cqu', 'AUR62006003' => 'cqu', 'AUR62015641' => 'cqu', 'AUR62027174' => 'cqu', 'AUR62035623' => 'cqu', 'AUR62035624' => 'cqu', 'AUR62035625' => 'cqu', 'AUR62035626' => 'cqu', 'CAN.G1110.53' => 'can', 'CANSAT80G0415' => 'cansat', 'Ca_21364_v3' => 'car', 'COL.COLO4_30693' => 'col', 'COL.COLO4_30694' => 'col', 'COL.COLO4_30695' => 'col', 'COL.COLO4_30696' => 'col', 'COL.COLO4_34020' => 'col', 'DCAR_004585' => 'dca', 'Dinv04029' => 'din', 'Dinv34857' => 'din', 'Duzib147G0011' => 'dzi', 'Duzib170G0599' => 'dzi', 'Duzib192G1051' => 'dzi', 'FAN01G0708' => 'fan', 'FAN01G0742' => 'fan', 'FAN02G0048' => 'fan', 'FAN02G0583' => 'fan', 'FAN02G0688' => 'fan', 'FAN02G1588' => 'fan', 'FAN02G2194' => 'fan', 'FAN02G2750' => 'fan', 'FAN02G3094' => 'fan', 'FAN02G3887' => 'fan', 'FAN02G3911' => 'fan', 'FAN02G3994' => 'fan', 'FAN02G4432' => 'fan', 'FAN02G4556' => 'fan', 'FAN03G1977' => 'fan', 'FAN03G2781' => 'fan', 'FAN03G2850' => 'fan', 'FAN03G3155' => 'fan', 'FAN04G2487' => 'fan', 'FAN05G0208' => 'fan', 'FAN05G0656' => 'fan', 'FAN05G0696' => 'fan', 'FAN05G0810' => 'fan', 'FAN05G1447' => 'fan', 'FAN05G2640' => 'fan', 'FAN05G2911' => 'fan', 'FAN05G3901' => 'fan', 'FAN05G4859' => 'fan', 'FAN05G4861' => 'fan', 'FAN05G4988' => 'fan', 'FAN05G5187' => 'fan', 'FAN05G5452' => 'fan', 'FAN05G5500' => 'fan', 'FAN05G5688' => 'fan', 'FAN06G0177' => 'fan', 'FAN06G0675' => 'fan', 'FAN06G1290' => 'fan', 'FAN06G2191' => 'fan', 'FAN06G2405' => 'fan', 'FAN06G3231' => 'fan', 'FAN06G3932' => 'fan', 'FAN07G0163' => 'fan', 'FAN07G0471' => 'fan', 'FAN07G1354' => 'fan', 'FAN08G0338' => 'fan', 'FAN08G1373' => 'fan', 'FAN08G2539' => 'fan', 'FAN08G2728' => 'fan', 'FAN09G0608' => 'fan', 'FAN09G1136' => 'fan', 'FAN09G1958' => 'fan', 'FAN09G2508' => 'fan', 'FAN09G2597' => 'fan', 'FAN09G2658' => 'fan', 'FAN09G2757' => 'fan', 'FAN09G2983' => 'fan', 'FAN09G3130' => 'fan', 'FAN09G3565' => 'fan', 'FAN09G3613' => 'fan', 'FAN09G4011' => 'fan', 'FAN09G4239' => 'fan', 'FAN09G4277' => 'fan', 'FAN09G4720' => 'fan', 'FAN11G0139' => 'fan', 'FAN11G1727' => 'fan', 'FAN11G2672' => 'fan', 'FAN11G2795' => 'fan', 'FAN11G3238' => 'fan', 'FAN11G3734' => 'fan', 'FAN12G0631' => 'fan', 'FAN12G2239' => 'fan', 'FAN12G2308' => 'fan', 'FAN12G2569' => 'fan', 'FAN12G2623' => 'fan', 'FAN13G3182' => 'fan', 'FAN14G0053' => 'fan', 'FAN14G0370' => 'fan', 'FAN14G0382' => 'fan', 'FAN14G0421' => 'fan', 'FAN14G0866' => 'fan', 'FAN14G1187' => 'fan', 'FAN14G1727' => 'fan', 'FAN14G1791' => 'fan', 'FAN14G2361' => 'fan', 'FAN14G2668' => 'fan', 'FAN14G2770' => 'fan', 'FAN14G2874' => 'fan', 'FAN14G3193' => 'fan', 'FAN14G3624' => 'fan', 'FAN14G3676' => 'fan', 'FAN14G3807' => 'fan', 'FAN14G4082' => 'fan', 'FAN14G4342' => 'fan', 'FAN14G4985' => 'fan', 'FAN14G5126' => 'fan', 'FAN14G5781' => 'fan', 'FAN14G5808' => 'fan', 'FAN14G5949' => 'fan', 'FAN15G0828' => 'fan', 'FAN15G1054' => 'fan', 'FAN15G2023' => 'fan', 'FAN15G2506' => 'fan', 'FAN16G0128' => 'fan', 'FAN16G0249' => 'fan', 'FAN16G0429' => 'fan', 'FAN16G1493' => 'fan', 'FAN16G2210' => 'fan', 'FAN16G2506' => 'fan', 'FAN18G1542' => 'fan', 'FAN18G4057' => 'fan', 'FAN19G0745' => 'fan', 'FAN19G1216' => 'fan', 'FAN19G1733' => 'fan', 'FAN20G0258' => 'fan', 'FAN20G1095' => 'fan', 'FAN20G1557' => 'fan', 'FAN21G0302' => 'fan', 'FAN21G0519' => 'fan', 'FAN21G0970' => 'fan', 'FAN21G1159' => 'fan', 'FAN21G1312' => 'fan', 'FAN21G1440' => 'fan', 'FAN21G1715' => 'fan', 'FAN23G1584' => 'fan', 'FAN24G0045' => 'fan', 'FAN24G0053' => 'fan', 'FAN24G1500' => 'fan', 'FAN24G1817' => 'fan', 'FAN24G2147' => 'fan', 'FAN24G2236' => 'fan', 'FAN24G2446' => 'fan', 'FAN24G2684' => 'fan', 'FAN25G0187' => 'fan', 'FAN25G0505' => 'fan', 'FAN25G0589' => 'fan', 'FAN25G3663' => 'fan', 'FAN26G1025' => 'fan', 'FAN26G2860' => 'fan', 'FAN27G1329' => 'fan', 'FAN27G3392' => 'fan', 'FvH4_1g02011' => 'fve', 'FvH4_1g06511' => 'fve', 'FvH4_2g19900' => 'fve', 'FvH4_2g19920' => 'fve', 'FvH4_2g24261' => 'fve', 'FvH4_2g24270' => 'fve', 'FvH4_2g24631' => 'fve', 'FvH4_2g30622' => 'fve', 'FvH4_3g12920' => 'fve', 'FvH4_3g30171' => 'fve', 'FvH4_3g35490' => 'fve', 'FvH4_3g43682' => 'fve', 'FvH4_3g43730' => 'fve', 'FvH4_3g43732' => 'fve', 'FvH4_3g43751' => 'fve', 'FvH4_3g43752' => 'fve', 'FvH4_3g43770' => 'fve', 'FvH4_3g44471' => 'fve', 'FvH4_3g44510' => 'fve', 'FvH4_3g44582' => 'fve', 'FvH4_4g16921' => 'fve', 'FvH4_4g17121' => 'fve', 'FvH4_4g17782' => 'fve', 'FvH4_4g17783' => 'fve', 'FvH4_4g18120' => 'fve', 'FvH4_4g31310' => 'fve', 'FvH4_4g35052' => 'fve', 'FvH4_5g30862' => 'fve', 'FvH4_6g01541' => 'fve', 'FvH4_6g02021' => 'fve', 'FvH4_6g02041' => 'fve', 'FvH4_6g02071' => 'fve', 'FvH4_6g02171' => 'fve', 'FvH4_6g03181' => 'fve', 'FvH4_6g03182' => 'fve', 'FvH4_6g03221' => 'fve', 'FvH4_6g03380' => 'fve', 'FvH4_6g05201' => 'fve', 'FvH4_6g05203' => 'fve', 'FvH4_6g20231' => 'fve', 'FvH4_6g31981' => 'fve', 'FvH4_6g32061' => 'fve', 'FvH4_6g37041' => 'fve', 'FvH4_6g37932' => 'fve', 'FvH4_6g38731' => 'fve', 'FvH4_6g39370' => 'fve', 'FvH4_6g39371' => 'fve', 'FvH4_6g40891' => 'fve', 'FvH4_6g40892' => 'fve', 'FvH4_6g43143' => 'fve', 'FvH4_6g45251' => 'fve', 'FvH4_6g45260' => 'fve', 'FvH4_6g45291' => 'fve', 'FvH4_6g45890' => 'fve', 'FvH4_6g46240' => 'fve', 'FvH4_6g46241' => 'fve', 'FvH4_6g46242' => 'fve', 'FvH4_6g46260' => 'fve', 'FvH4_6g46280' => 'fve', 'FvH4_6g46380' => 'fve', 'FvH4_7g12841' => 'fve', 'FvH4_7g31431' => 'fve', 'Glyma.09G075900' => 'gma', 'Gohir.A09G096401' => 'ghi', 'Gohir.D09G096101' => 'ghi', 'Gorai.006G112800' => 'gra', 'HanXRQChr04g0121411' => 'han', 'Hund15878' => 'sun', 'Lj2A1107G68' => 'lonja', 'Lj2A630G63' => 'lonja', 'Lj2A946T25' => 'lonja', 'Lj2C714T1' => 'lonja', 'Lj2C966T3' => 'lonja', 'Lj2C966T4' => 'lonja', 'Lj4g0002979' => 'lja', 'Lsat_1_v5_gn_5_30901' => 'lsa', 'Lsat_1_v5_gn_5_31100' => 'lsa', 'Lsat_1_v5_gn_5_38600' => 'lsa', 'Lsat_1_v5_gn_6_92061' => 'lsa', 'Manes.05G071301' => 'mes', 'MD02G1008700' => 'mdo', 'MD02G1008900' => 'mdo', 'MD03G1256400' => 'mdo', 'MD04G1180900' => 'mdo', 'MD04G1181000' => 'mdo', 'MD04G1181200' => 'mdo', 'MD05G1244200' => 'mdo', 'MD05G1324200' => 'mdo', 'MD09G1201600' => 'mdo', 'MD10G1000600' => 'mdo', 'MD14G1026900' => 'mdo', 'MD14G1187900' => 'mdo', 'MD15G1017800' => 'mdo', 'MD15G1018100' => 'mdo', 'Medtr4g124160' => 'mtr', 'Migut.L01260' => 'egut', 'Nitab4.5_0000008g0440' => 'nta', 'Nitab4.5_0000207g0170' => 'nta', 'Nitab4.5_0007671g0030' => 'nta', 'Nitab4.5_0010853g0020' => 'nta', 'Oeu057656.1' => 'oeu', 'PGSC0003DMG400005638' => 'stu', 'PGSC0003DMG400005639' => 'stu', 'Phvul.009G222800' => 'pvu', 'Potri.009G132400' => 'ptr', 'Potri.009G163001' => 'ptr', 'Potri.011G000700' => 'ptr', 'Potri.011G004800' => 'ptr', 'Prupe.1G509300' => 'ppe', 'Prupe.1G509700' => 'ppe', 'Prupe.1G510400' => 'ppe', 'Prupe.1G510700' => 'ppe', 'Prupe.1G512600' => 'ppe', 'Prupe.2G073200' => 'ppe', 'Prupe.3G059500' => 'ppe', 'Prupe.3G059600' => 'ppe', 'Prupe.3G246100' => 'ppe', 'Prupe.3G265100' => 'ppe', 'Prupe.4G034700' => 'ppe', 'Prupe.4G052100' => 'ppe', 'Prupe.4G053600' => 'ppe', 'Prupe.5G068800' => 'ppe', 'Prupe.5G070600' => 'ppe', 'Prupe.6G075400' => 'ppe', 'Prupe.6G075500' => 'ppe', 'Prupe.6G076400' => 'ppe', 'Prupe.8G110700' => 'ppe', 'Psat4g020960' => 'psa', 'PSO135G0788' => 'pso', 'PSO210G6463' => 'pso', 'PSO384G0370' => 'pso', 'PSO386G0056' => 'pso', 'QL01p006048' => 'qlo', 'QL02p054283' => 'qlo', 'QL05p008000' => 'qlo', 'QL05p008212' => 'qlo', 'QL05p008950' => 'qlo', 'QL05p009042' => 'qlo', 'QL05p009518' => 'qlo', 'QL05p012589' => 'qlo', 'QL05p012608' => 'qlo', 'QL05p012650' => 'qlo', 'QL05p012667' => 'qlo', 'QL05p014501' => 'qlo', 'QL05p052800' => 'qlo', 'QL05p065010' => 'qlo', 'QL05p074156' => 'qlo', 'QL05p074160' => 'qlo', 'QL05p074174' => 'qlo', 'QL05p074178' => 'qlo', 'QL05p074214' => 'qlo', 'QL06p001050' => 'qlo', 'QL06p001056' => 'qlo', 'QL06p006093' => 'qlo', 'QL06p006111' => 'qlo', 'QL07p019784' => 'qlo', 'QL07p019801' => 'qlo', 'QL07p036110' => 'qlo', 'QL07p036134' => 'qlo', 'QL07p036147' => 'qlo', 'QL07p036156' => 'qlo', 'QL07p036300' => 'qlo', 'QL07p036320' => 'qlo', 'QL08p014547' => 'qlo', 'QL08p014551' => 'qlo', 'QL08p043319' => 'qlo', 'QL08p043324' => 'qlo', 'QL11p009094' => 'qlo', 'RcHm_v2.0_Chr1g0380481' => 'rch', 'RcHm_v2.0_Chr2g0089331' => 'rch', 'RcHm_v2.0_Chr2g0123691' => 'rch', 'RcHm_v2.0_Chr2g0151111' => 'rch', 'RcHm_v2.0_Chr2g0163011' => 'rch', 'RcHm_v2.0_Chr2g0163051' => 'rch', 'RcHm_v2.0_Chr2g0164671' => 'rch', 'RcHm_v2.0_Chr2g0164681' => 'rch', 'RcHm_v2.0_Chr2g0164721' => 'rch', 'RcHm_v2.0_Chr3g0449911' => 'rch', 'RcHm_v2.0_Chr3g0450211' => 'rch', 'RcHm_v2.0_Chr3g0457271' => 'rch', 'RcHm_v2.0_Chr5g0018111' => 'rch', 'RcHm_v2.0_Chr5g0021011' => 'rch', 'RcHm_v2.0_Chr5g0081171' => 'rch', 'RcHm_v2.0_Chr5g0081211' => 'rch', 'RcHm_v2.0_Chr6g0275871' => 'rch', 'RcHm_v2.0_Chr6g0276071' => 'rch', 'RcHm_v2.0_Chr6g0285591' => 'rch', 'RcHm_v2.0_Chr6g0291931' => 'rch', 'RcHm_v2.0_Chr6g0292091' => 'rch', 'RcHm_v2.0_Chr6g0292271' => 'rch', 'RcHm_v2.0_Chr7g0221261' => 'rch', 'Rhsim08G0219900' => 'rsi', 'Rhsim08G0220200' => 'rsi', 'Rhsim08G0237800' => 'rsi', 'Rhsim08G0238800' => 'rsi', 'Sabra09G0102700' => 'sbr', 'Sabra09G0127200' => 'sbr', 'Sabra11G0003700' => 'sbr', 'Sabra15G0014700' => 'sbr', 'Sc19g0000590' => 'sci', 'Sc19g0001870' => 'sci', 'SGA_v2.0_scaffold1G00346' => 'sas', 'SGA_v2.0_scaffold1G00575' => 'sas', 'SGA_v2.0_scaffold1G00761' => 'sas', 'SGA_v2.0_scaffold232G43501' => 'sas', 'TAR625G1137' => 'tar', 'Thecc.03G222100' => 'tca', 'TPR.G12691' => 'tpr', 'TWI34G0727' => 'twi', 'TWI36G0117' => 'twi', 'VMungo1309G0868' => 'vmu' ) $gf_id = 'HOM05D001729' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001729' ) $data_identifier = 'HOM05D001729' $data_type = 'gf_id' $species_gene_counts = array( 'amhyb' => (int) 1, 'cqu' => (int) 9, 'can' => (int) 1, 'cansat' => (int) 1, 'car' => (int) 1, 'col' => (int) 5, 'dca' => (int) 1, 'din' => (int) 2, 'dzi' => (int) 3, 'fan' => (int) 140, 'fve' => (int) 62, 'gma' => (int) 1, 'ghi' => (int) 2, 'gra' => (int) 1, 'han' => (int) 1, 'sun' => (int) 1, 'lonja' => (int) 6, 'lja' => (int) 1, 'lsa' => (int) 4, 'mes' => (int) 1, 'mdo' => (int) 14, 'mtr' => (int) 1, 'egut' => (int) 1, 'nta' => (int) 4, 'oeu' => (int) 1, 'stu' => (int) 2, 'pvu' => (int) 1, 'ptr' => (int) 4, 'ppe' => (int) 19, 'psa' => (int) 1, 'pso' => (int) 4, 'qlo' => (int) 36, 'rch' => (int) 23, 'rsi' => (int) 4, 'sbr' => (int) 4, 'sci' => (int) 2, 'sas' => (int) 4, 'tar' => (int) 1, 'tca' => (int) 1, 'tpr' => (int) 1, 'twi' => (int) 2, 'vmu' => (int) 1 ) $gf_gene_species = 'vmu' $gf_gene_id = 'VMungo1309G0868' $species_info = array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ) $local_species = 'pso' $disabled = '' $selected = '' $num_hits = (int) 0include - APP/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp, line 33 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933 View::_renderElement() - CORE/Cake/View/View.php, line 1224 View::element() - CORE/Cake/View/View.php, line 418 include - APP/View/Elements/analysis/phylogenetics_module/gf_data_settings.ctp, line 37 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933 View::_renderElement() - CORE/Cake/View/View.php, line 1224 View::element() - CORE/Cake/View/View.php, line 418 include - APP/View/Elements/analysis/phylogenetics_module/parameter_selection.ctp, line 64 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933 View::_renderElement() - CORE/Cake/View/View.php, line 1224 View::element() - CORE/Cake/View/View.php, line 418 include - APP/View/Analysis/custom_tree_creation.ctp, line 27 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933
$viewFile = '/www/bioinformatics01_ro/plaza/_dev_instances/feedback/app/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp' $dataForView = array( 'sidebar_info' => array( 'gf_id' => 'HOM05D001729', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '375', 'num_species' => '42' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'Ah.07g204710' => 'amhyb', 'AUR62006001' => 'cqu', 'AUR62006002' => 'cqu', 'AUR62006003' => 'cqu', 'AUR62015641' => 'cqu', 'AUR62027174' => 'cqu', 'AUR62035623' => 'cqu', 'AUR62035624' => 'cqu', 'AUR62035625' => 'cqu', 'AUR62035626' => 'cqu', 'CAN.G1110.53' => 'can', 'CANSAT80G0415' => 'cansat', 'Ca_21364_v3' => 'car', 'COL.COLO4_30693' => 'col', 'COL.COLO4_30694' => 'col', 'COL.COLO4_30695' => 'col', 'COL.COLO4_30696' => 'col', 'COL.COLO4_34020' => 'col', 'DCAR_004585' => 'dca', 'Dinv04029' => 'din', 'Dinv34857' => 'din', 'Duzib147G0011' => 'dzi', 'Duzib170G0599' => 'dzi', 'Duzib192G1051' => 'dzi', 'FAN01G0708' => 'fan', 'FAN01G0742' => 'fan', 'FAN02G0048' => 'fan', 'FAN02G0583' => 'fan', 'FAN02G0688' => 'fan', 'FAN02G1588' => 'fan', 'FAN02G2194' => 'fan', 'FAN02G2750' => 'fan', 'FAN02G3094' => 'fan', 'FAN02G3887' => 'fan', 'FAN02G3911' => 'fan', 'FAN02G3994' => 'fan', 'FAN02G4432' => 'fan', 'FAN02G4556' => 'fan', 'FAN03G1977' => 'fan', 'FAN03G2781' => 'fan', 'FAN03G2850' => 'fan', 'FAN03G3155' => 'fan', 'FAN04G2487' => 'fan', 'FAN05G0208' => 'fan', 'FAN05G0656' => 'fan', 'FAN05G0696' => 'fan', 'FAN05G0810' => 'fan', 'FAN05G1447' => 'fan', 'FAN05G2640' => 'fan', 'FAN05G2911' => 'fan', 'FAN05G3901' => 'fan', 'FAN05G4859' => 'fan', 'FAN05G4861' => 'fan', 'FAN05G4988' => 'fan', 'FAN05G5187' => 'fan', 'FAN05G5452' => 'fan', 'FAN05G5500' => 'fan', 'FAN05G5688' => 'fan', 'FAN06G0177' => 'fan', 'FAN06G0675' => 'fan', 'FAN06G1290' => 'fan', 'FAN06G2191' => 'fan', 'FAN06G2405' => 'fan', 'FAN06G3231' => 'fan', 'FAN06G3932' => 'fan', 'FAN07G0163' => 'fan', 'FAN07G0471' => 'fan', 'FAN07G1354' => 'fan', 'FAN08G0338' => 'fan', 'FAN08G1373' => 'fan', 'FAN08G2539' => 'fan', 'FAN08G2728' => 'fan', 'FAN09G0608' => 'fan', 'FAN09G1136' => 'fan', 'FAN09G1958' => 'fan', 'FAN09G2508' => 'fan', 'FAN09G2597' => 'fan', 'FAN09G2658' => 'fan', 'FAN09G2757' => 'fan', 'FAN09G2983' => 'fan', 'FAN09G3130' => 'fan', 'FAN09G3565' => 'fan', 'FAN09G3613' => 'fan', 'FAN09G4011' => 'fan', 'FAN09G4239' => 'fan', 'FAN09G4277' => 'fan', 'FAN09G4720' => 'fan', 'FAN11G0139' => 'fan', 'FAN11G1727' => 'fan', 'FAN11G2672' => 'fan', 'FAN11G2795' => 'fan', 'FAN11G3238' => 'fan', 'FAN11G3734' => 'fan', 'FAN12G0631' => 'fan', 'FAN12G2239' => 'fan', 'FAN12G2308' => 'fan', 'FAN12G2569' => 'fan', 'FAN12G2623' => 'fan', 'FAN13G3182' => 'fan', 'FAN14G0053' => 'fan', 'FAN14G0370' => 'fan', 'FAN14G0382' => 'fan', 'FAN14G0421' => 'fan', 'FAN14G0866' => 'fan', 'FAN14G1187' => 'fan', 'FAN14G1727' => 'fan', 'FAN14G1791' => 'fan', 'FAN14G2361' => 'fan', 'FAN14G2668' => 'fan', 'FAN14G2770' => 'fan', 'FAN14G2874' => 'fan', 'FAN14G3193' => 'fan', 'FAN14G3624' => 'fan', 'FAN14G3676' => 'fan', 'FAN14G3807' => 'fan', 'FAN14G4082' => 'fan', 'FAN14G4342' => 'fan', 'FAN14G4985' => 'fan', 'FAN14G5126' => 'fan', 'FAN14G5781' => 'fan', 'FAN14G5808' => 'fan', 'FAN14G5949' => 'fan', 'FAN15G0828' => 'fan', 'FAN15G1054' => 'fan', 'FAN15G2023' => 'fan', 'FAN15G2506' => 'fan', 'FAN16G0128' => 'fan', 'FAN16G0249' => 'fan', 'FAN16G0429' => 'fan', 'FAN16G1493' => 'fan', 'FAN16G2210' => 'fan', 'FAN16G2506' => 'fan', 'FAN18G1542' => 'fan', 'FAN18G4057' => 'fan', 'FAN19G0745' => 'fan', 'FAN19G1216' => 'fan', 'FAN19G1733' => 'fan', 'FAN20G0258' => 'fan', 'FAN20G1095' => 'fan', 'FAN20G1557' => 'fan', 'FAN21G0302' => 'fan', 'FAN21G0519' => 'fan', 'FAN21G0970' => 'fan', 'FAN21G1159' => 'fan', 'FAN21G1312' => 'fan', 'FAN21G1440' => 'fan', 'FAN21G1715' => 'fan', 'FAN23G1584' => 'fan', 'FAN24G0045' => 'fan', 'FAN24G0053' => 'fan', 'FAN24G1500' => 'fan', 'FAN24G1817' => 'fan', 'FAN24G2147' => 'fan', 'FAN24G2236' => 'fan', 'FAN24G2446' => 'fan', 'FAN24G2684' => 'fan', 'FAN25G0187' => 'fan', 'FAN25G0505' => 'fan', 'FAN25G0589' => 'fan', 'FAN25G3663' => 'fan', 'FAN26G1025' => 'fan', 'FAN26G2860' => 'fan', 'FAN27G1329' => 'fan', 'FAN27G3392' => 'fan', 'FvH4_1g02011' => 'fve', 'FvH4_1g06511' => 'fve', 'FvH4_2g19900' => 'fve', 'FvH4_2g19920' => 'fve', 'FvH4_2g24261' => 'fve', 'FvH4_2g24270' => 'fve', 'FvH4_2g24631' => 'fve', 'FvH4_2g30622' => 'fve', 'FvH4_3g12920' => 'fve', 'FvH4_3g30171' => 'fve', 'FvH4_3g35490' => 'fve', 'FvH4_3g43682' => 'fve', 'FvH4_3g43730' => 'fve', 'FvH4_3g43732' => 'fve', 'FvH4_3g43751' => 'fve', 'FvH4_3g43752' => 'fve', 'FvH4_3g43770' => 'fve', 'FvH4_3g44471' => 'fve', 'FvH4_3g44510' => 'fve', 'FvH4_3g44582' => 'fve', 'FvH4_4g16921' => 'fve', 'FvH4_4g17121' => 'fve', 'FvH4_4g17782' => 'fve', 'FvH4_4g17783' => 'fve', 'FvH4_4g18120' => 'fve', 'FvH4_4g31310' => 'fve', 'FvH4_4g35052' => 'fve', 'FvH4_5g30862' => 'fve', 'FvH4_6g01541' => 'fve', 'FvH4_6g02021' => 'fve', 'FvH4_6g02041' => 'fve', 'FvH4_6g02071' => 'fve', 'FvH4_6g02171' => 'fve', 'FvH4_6g03181' => 'fve', 'FvH4_6g03182' => 'fve', 'FvH4_6g03221' => 'fve', 'FvH4_6g03380' => 'fve', 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'ppe', 'Prupe.1G512600' => 'ppe', 'Prupe.2G073200' => 'ppe', 'Prupe.3G059500' => 'ppe', 'Prupe.3G059600' => 'ppe', 'Prupe.3G246100' => 'ppe', 'Prupe.3G265100' => 'ppe', 'Prupe.4G034700' => 'ppe', 'Prupe.4G052100' => 'ppe', 'Prupe.4G053600' => 'ppe', 'Prupe.5G068800' => 'ppe', 'Prupe.5G070600' => 'ppe', 'Prupe.6G075400' => 'ppe', 'Prupe.6G075500' => 'ppe', 'Prupe.6G076400' => 'ppe', 'Prupe.8G110700' => 'ppe', 'Psat4g020960' => 'psa', 'PSO135G0788' => 'pso', 'PSO210G6463' => 'pso', 'PSO384G0370' => 'pso', 'PSO386G0056' => 'pso', 'QL01p006048' => 'qlo', 'QL02p054283' => 'qlo', 'QL05p008000' => 'qlo', 'QL05p008212' => 'qlo', 'QL05p008950' => 'qlo', 'QL05p009042' => 'qlo', 'QL05p009518' => 'qlo', 'QL05p012589' => 'qlo', 'QL05p012608' => 'qlo', 'QL05p012650' => 'qlo', 'QL05p012667' => 'qlo', 'QL05p014501' => 'qlo', 'QL05p052800' => 'qlo', 'QL05p065010' => 'qlo', 'QL05p074156' => 'qlo', 'QL05p074160' => 'qlo', 'QL05p074174' => 'qlo', 'QL05p074178' => 'qlo', 'QL05p074214' => 'qlo', 'QL06p001050' => 'qlo', 'QL06p001056' => 'qlo', 'QL06p006093' => 'qlo', 'QL06p006111' => 'qlo', 'QL07p019784' => 'qlo', 'QL07p019801' => 'qlo', 'QL07p036110' => 'qlo', 'QL07p036134' => 'qlo', 'QL07p036147' => 'qlo', 'QL07p036156' => 'qlo', 'QL07p036300' => 'qlo', 'QL07p036320' => 'qlo', 'QL08p014547' => 'qlo', 'QL08p014551' => 'qlo', 'QL08p043319' => 'qlo', 'QL08p043324' => 'qlo', 'QL11p009094' => 'qlo', 'RcHm_v2.0_Chr1g0380481' => 'rch', 'RcHm_v2.0_Chr2g0089331' => 'rch', 'RcHm_v2.0_Chr2g0123691' => 'rch', 'RcHm_v2.0_Chr2g0151111' => 'rch', 'RcHm_v2.0_Chr2g0163011' => 'rch', 'RcHm_v2.0_Chr2g0163051' => 'rch', 'RcHm_v2.0_Chr2g0164671' => 'rch', 'RcHm_v2.0_Chr2g0164681' => 'rch', 'RcHm_v2.0_Chr2g0164721' => 'rch', 'RcHm_v2.0_Chr3g0449911' => 'rch', 'RcHm_v2.0_Chr3g0450211' => 'rch', 'RcHm_v2.0_Chr3g0457271' => 'rch', 'RcHm_v2.0_Chr5g0018111' => 'rch', 'RcHm_v2.0_Chr5g0021011' => 'rch', 'RcHm_v2.0_Chr5g0081171' => 'rch', 'RcHm_v2.0_Chr5g0081211' => 'rch', 'RcHm_v2.0_Chr6g0275871' => 'rch', 'RcHm_v2.0_Chr6g0276071' => 'rch', 'RcHm_v2.0_Chr6g0285591' => 'rch', 'RcHm_v2.0_Chr6g0291931' => 'rch', 'RcHm_v2.0_Chr6g0292091' => 'rch', 'RcHm_v2.0_Chr6g0292271' => 'rch', 'RcHm_v2.0_Chr7g0221261' => 'rch', 'Rhsim08G0219900' => 'rsi', 'Rhsim08G0220200' => 'rsi', 'Rhsim08G0237800' => 'rsi', 'Rhsim08G0238800' => 'rsi', 'Sabra09G0102700' => 'sbr', 'Sabra09G0127200' => 'sbr', 'Sabra11G0003700' => 'sbr', 'Sabra15G0014700' => 'sbr', 'Sc19g0000590' => 'sci', 'Sc19g0001870' => 'sci', 'SGA_v2.0_scaffold1G00346' => 'sas', 'SGA_v2.0_scaffold1G00575' => 'sas', 'SGA_v2.0_scaffold1G00761' => 'sas', 'SGA_v2.0_scaffold232G43501' => 'sas', 'TAR625G1137' => 'tar', 'Thecc.03G222100' => 'tca', 'TPR.G12691' => 'tpr', 'TWI34G0727' => 'twi', 'TWI36G0117' => 'twi', 'VMungo1309G0868' => 'vmu' ), 'gf_id' => 'HOM05D001729', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001729' ), 'data_identifier' => 'HOM05D001729', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001729', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '375', 'num_species' => '42' ) 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'AUR62035624' => 'cqu', 'AUR62035625' => 'cqu', 'AUR62035626' => 'cqu', 'CAN.G1110.53' => 'can', 'CANSAT80G0415' => 'cansat', 'Ca_21364_v3' => 'car', 'COL.COLO4_30693' => 'col', 'COL.COLO4_30694' => 'col', 'COL.COLO4_30695' => 'col', 'COL.COLO4_30696' => 'col', 'COL.COLO4_34020' => 'col', 'DCAR_004585' => 'dca', 'Dinv04029' => 'din', 'Dinv34857' => 'din', 'Duzib147G0011' => 'dzi', 'Duzib170G0599' => 'dzi', 'Duzib192G1051' => 'dzi', 'FAN01G0708' => 'fan', 'FAN01G0742' => 'fan', 'FAN02G0048' => 'fan', 'FAN02G0583' => 'fan', 'FAN02G0688' => 'fan', 'FAN02G1588' => 'fan', 'FAN02G2194' => 'fan', 'FAN02G2750' => 'fan', 'FAN02G3094' => 'fan', 'FAN02G3887' => 'fan', 'FAN02G3911' => 'fan', 'FAN02G3994' => 'fan', 'FAN02G4432' => 'fan', 'FAN02G4556' => 'fan', 'FAN03G1977' => 'fan', 'FAN03G2781' => 'fan', 'FAN03G2850' => 'fan', 'FAN03G3155' => 'fan', 'FAN04G2487' => 'fan', 'FAN05G0208' => 'fan', 'FAN05G0656' => 'fan', 'FAN05G0696' => 'fan', 'FAN05G0810' => 'fan', 'FAN05G1447' => 'fan', 'FAN05G2640' => 'fan', 'FAN05G2911' => 'fan', 'FAN05G3901' => 'fan', 'FAN05G4859' => 'fan', 'FAN05G4861' => 'fan', 'FAN05G4988' => 'fan', 'FAN05G5187' => 'fan', 'FAN05G5452' => 'fan', 'FAN05G5500' => 'fan', 'FAN05G5688' => 'fan', 'FAN06G0177' => 'fan', 'FAN06G0675' => 'fan', 'FAN06G1290' => 'fan', 'FAN06G2191' => 'fan', 'FAN06G2405' => 'fan', 'FAN06G3231' => 'fan', 'FAN06G3932' => 'fan', 'FAN07G0163' => 'fan', 'FAN07G0471' => 'fan', 'FAN07G1354' => 'fan', 'FAN08G0338' => 'fan', 'FAN08G1373' => 'fan', 'FAN08G2539' => 'fan', 'FAN08G2728' => 'fan', 'FAN09G0608' => 'fan', 'FAN09G1136' => 'fan', 'FAN09G1958' => 'fan', 'FAN09G2508' => 'fan', 'FAN09G2597' => 'fan', 'FAN09G2658' => 'fan', 'FAN09G2757' => 'fan', 'FAN09G2983' => 'fan', 'FAN09G3130' => 'fan', 'FAN09G3565' => 'fan', 'FAN09G3613' => 'fan', 'FAN09G4011' => 'fan', 'FAN09G4239' => 'fan', 'FAN09G4277' => 'fan', 'FAN09G4720' => 'fan', 'FAN11G0139' => 'fan', 'FAN11G1727' => 'fan', 'FAN11G2672' => 'fan', 'FAN11G2795' => 'fan', 'FAN11G3238' => 'fan', 'FAN11G3734' => 'fan', 'FAN12G0631' => 'fan', 'FAN12G2239' => 'fan', 'FAN12G2308' => 'fan', 'FAN12G2569' => 'fan', 'FAN12G2623' => 'fan', 'FAN13G3182' => 'fan', 'FAN14G0053' => 'fan', 'FAN14G0370' => 'fan', 'FAN14G0382' => 'fan', 'FAN14G0421' => 'fan', 'FAN14G0866' => 'fan', 'FAN14G1187' => 'fan', 'FAN14G1727' => 'fan', 'FAN14G1791' => 'fan', 'FAN14G2361' => 'fan', 'FAN14G2668' => 'fan', 'FAN14G2770' => 'fan', 'FAN14G2874' => 'fan', 'FAN14G3193' => 'fan', 'FAN14G3624' => 'fan', 'FAN14G3676' => 'fan', 'FAN14G3807' => 'fan', 'FAN14G4082' => 'fan', 'FAN14G4342' => 'fan', 'FAN14G4985' => 'fan', 'FAN14G5126' => 'fan', 'FAN14G5781' => 'fan', 'FAN14G5808' => 'fan', 'FAN14G5949' => 'fan', 'FAN15G0828' => 'fan', 'FAN15G1054' => 'fan', 'FAN15G2023' => 'fan', 'FAN15G2506' => 'fan', 'FAN16G0128' => 'fan', 'FAN16G0249' => 'fan', 'FAN16G0429' => 'fan', 'FAN16G1493' => 'fan', 'FAN16G2210' => 'fan', 'FAN16G2506' => 'fan', 'FAN18G1542' => 'fan', 'FAN18G4057' => 'fan', 'FAN19G0745' => 'fan', 'FAN19G1216' => 'fan', 'FAN19G1733' => 'fan', 'FAN20G0258' => 'fan', 'FAN20G1095' => 'fan', 'FAN20G1557' => 'fan', 'FAN21G0302' => 'fan', 'FAN21G0519' => 'fan', 'FAN21G0970' => 'fan', 'FAN21G1159' => 'fan', 'FAN21G1312' => 'fan', 'FAN21G1440' => 'fan', 'FAN21G1715' => 'fan', 'FAN23G1584' => 'fan', 'FAN24G0045' => 'fan', 'FAN24G0053' => 'fan', 'FAN24G1500' => 'fan', 'FAN24G1817' => 'fan', 'FAN24G2147' => 'fan', 'FAN24G2236' => 'fan', 'FAN24G2446' => 'fan', 'FAN24G2684' => 'fan', 'FAN25G0187' => 'fan', 'FAN25G0505' => 'fan', 'FAN25G0589' => 'fan', 'FAN25G3663' => 'fan', 'FAN26G1025' => 'fan', 'FAN26G2860' => 'fan', 'FAN27G1329' => 'fan', 'FAN27G3392' => 'fan', 'FvH4_1g02011' => 'fve', 'FvH4_1g06511' => 'fve', 'FvH4_2g19900' => 'fve', 'FvH4_2g19920' => 'fve', 'FvH4_2g24261' => 'fve', 'FvH4_2g24270' => 'fve', 'FvH4_2g24631' => 'fve', 'FvH4_2g30622' => 'fve', 'FvH4_3g12920' => 'fve', 'FvH4_3g30171' => 'fve', 'FvH4_3g35490' => 'fve', 'FvH4_3g43682' => 'fve', 'FvH4_3g43730' => 'fve', 'FvH4_3g43732' => 'fve', 'FvH4_3g43751' => 'fve', 'FvH4_3g43752' => 'fve', 'FvH4_3g43770' => 'fve', 'FvH4_3g44471' => 'fve', 'FvH4_3g44510' => 'fve', 'FvH4_3g44582' => 'fve', 'FvH4_4g16921' => 'fve', 'FvH4_4g17121' => 'fve', 'FvH4_4g17782' => 'fve', 'FvH4_4g17783' => 'fve', 'FvH4_4g18120' => 'fve', 'FvH4_4g31310' => 'fve', 'FvH4_4g35052' => 'fve', 'FvH4_5g30862' => 'fve', 'FvH4_6g01541' => 'fve', 'FvH4_6g02021' => 'fve', 'FvH4_6g02041' => 'fve', 'FvH4_6g02071' => 'fve', 'FvH4_6g02171' => 'fve', 'FvH4_6g03181' => 'fve', 'FvH4_6g03182' => 'fve', 'FvH4_6g03221' => 'fve', 'FvH4_6g03380' => 'fve', 'FvH4_6g05201' => 'fve', 'FvH4_6g05203' => 'fve', 'FvH4_6g20231' => 'fve', 'FvH4_6g31981' => 'fve', 'FvH4_6g32061' => 'fve', 'FvH4_6g37041' => 'fve', 'FvH4_6g37932' => 'fve', 'FvH4_6g38731' => 'fve', 'FvH4_6g39370' => 'fve', 'FvH4_6g39371' => 'fve', 'FvH4_6g40891' => 'fve', 'FvH4_6g40892' => 'fve', 'FvH4_6g43143' => 'fve', 'FvH4_6g45251' => 'fve', 'FvH4_6g45260' => 'fve', 'FvH4_6g45291' => 'fve', 'FvH4_6g45890' => 'fve', 'FvH4_6g46240' => 'fve', 'FvH4_6g46241' => 'fve', 'FvH4_6g46242' => 'fve', 'FvH4_6g46260' => 'fve', 'FvH4_6g46280' => 'fve', 'FvH4_6g46380' => 'fve', 'FvH4_7g12841' => 'fve', 'FvH4_7g31431' => 'fve', 'Glyma.09G075900' => 'gma', 'Gohir.A09G096401' => 'ghi', 'Gohir.D09G096101' => 'ghi', 'Gorai.006G112800' => 'gra', 'HanXRQChr04g0121411' => 'han', 'Hund15878' => 'sun', 'Lj2A1107G68' => 'lonja', 'Lj2A630G63' => 'lonja', 'Lj2A946T25' => 'lonja', 'Lj2C714T1' => 'lonja', 'Lj2C966T3' => 'lonja', 'Lj2C966T4' => 'lonja', 'Lj4g0002979' => 'lja', 'Lsat_1_v5_gn_5_30901' => 'lsa', 'Lsat_1_v5_gn_5_31100' => 'lsa', 'Lsat_1_v5_gn_5_38600' => 'lsa', 'Lsat_1_v5_gn_6_92061' => 'lsa', 'Manes.05G071301' => 'mes', 'MD02G1008700' => 'mdo', 'MD02G1008900' => 'mdo', 'MD03G1256400' => 'mdo', 'MD04G1180900' => 'mdo', 'MD04G1181000' => 'mdo', 'MD04G1181200' => 'mdo', 'MD05G1244200' => 'mdo', 'MD05G1324200' => 'mdo', 'MD09G1201600' => 'mdo', 'MD10G1000600' => 'mdo', 'MD14G1026900' => 'mdo', 'MD14G1187900' => 'mdo', 'MD15G1017800' => 'mdo', 'MD15G1018100' => 'mdo', 'Medtr4g124160' => 'mtr', 'Migut.L01260' => 'egut', 'Nitab4.5_0000008g0440' => 'nta', 'Nitab4.5_0000207g0170' => 'nta', 'Nitab4.5_0007671g0030' => 'nta', 'Nitab4.5_0010853g0020' => 'nta', 'Oeu057656.1' => 'oeu', 'PGSC0003DMG400005638' => 'stu', 'PGSC0003DMG400005639' => 'stu', 'Phvul.009G222800' => 'pvu', 'Potri.009G132400' => 'ptr', 'Potri.009G163001' => 'ptr', 'Potri.011G000700' => 'ptr', 'Potri.011G004800' => 'ptr', 'Prupe.1G509300' => 'ppe', 'Prupe.1G509700' => 'ppe', 'Prupe.1G510400' => 'ppe', 'Prupe.1G510700' => 'ppe', 'Prupe.1G512600' => 'ppe', 'Prupe.2G073200' => 'ppe', 'Prupe.3G059500' => 'ppe', 'Prupe.3G059600' => 'ppe', 'Prupe.3G246100' => 'ppe', 'Prupe.3G265100' => 'ppe', 'Prupe.4G034700' => 'ppe', 'Prupe.4G052100' => 'ppe', 'Prupe.4G053600' => 'ppe', 'Prupe.5G068800' => 'ppe', 'Prupe.5G070600' => 'ppe', 'Prupe.6G075400' => 'ppe', 'Prupe.6G075500' => 'ppe', 'Prupe.6G076400' => 'ppe', 'Prupe.8G110700' => 'ppe', 'Psat4g020960' => 'psa', 'PSO135G0788' => 'pso', 'PSO210G6463' => 'pso', 'PSO384G0370' => 'pso', 'PSO386G0056' => 'pso', 'QL01p006048' => 'qlo', 'QL02p054283' => 'qlo', 'QL05p008000' => 'qlo', 'QL05p008212' => 'qlo', 'QL05p008950' => 'qlo', 'QL05p009042' => 'qlo', 'QL05p009518' => 'qlo', 'QL05p012589' => 'qlo', 'QL05p012608' => 'qlo', 'QL05p012650' => 'qlo', 'QL05p012667' => 'qlo', 'QL05p014501' => 'qlo', 'QL05p052800' => 'qlo', 'QL05p065010' => 'qlo', 'QL05p074156' => 'qlo', 'QL05p074160' => 'qlo', 'QL05p074174' => 'qlo', 'QL05p074178' => 'qlo', 'QL05p074214' => 'qlo', 'QL06p001050' => 'qlo', 'QL06p001056' => 'qlo', 'QL06p006093' => 'qlo', 'QL06p006111' => 'qlo', 'QL07p019784' => 'qlo', 'QL07p019801' => 'qlo', 'QL07p036110' => 'qlo', 'QL07p036134' => 'qlo', 'QL07p036147' => 'qlo', 'QL07p036156' => 'qlo', 'QL07p036300' => 'qlo', 'QL07p036320' => 'qlo', 'QL08p014547' => 'qlo', 'QL08p014551' => 'qlo', 'QL08p043319' => 'qlo', 'QL08p043324' => 'qlo', 'QL11p009094' => 'qlo', 'RcHm_v2.0_Chr1g0380481' => 'rch', 'RcHm_v2.0_Chr2g0089331' => 'rch', 'RcHm_v2.0_Chr2g0123691' => 'rch', 'RcHm_v2.0_Chr2g0151111' => 'rch', 'RcHm_v2.0_Chr2g0163011' => 'rch', 'RcHm_v2.0_Chr2g0163051' => 'rch', 'RcHm_v2.0_Chr2g0164671' => 'rch', 'RcHm_v2.0_Chr2g0164681' => 'rch', 'RcHm_v2.0_Chr2g0164721' => 'rch', 'RcHm_v2.0_Chr3g0449911' => 'rch', 'RcHm_v2.0_Chr3g0450211' => 'rch', 'RcHm_v2.0_Chr3g0457271' => 'rch', 'RcHm_v2.0_Chr5g0018111' => 'rch', 'RcHm_v2.0_Chr5g0021011' => 'rch', 'RcHm_v2.0_Chr5g0081171' => 'rch', 'RcHm_v2.0_Chr5g0081211' => 'rch', 'RcHm_v2.0_Chr6g0275871' => 'rch', 'RcHm_v2.0_Chr6g0276071' => 'rch', 'RcHm_v2.0_Chr6g0285591' => 'rch', 'RcHm_v2.0_Chr6g0291931' => 'rch', 'RcHm_v2.0_Chr6g0292091' => 'rch', 'RcHm_v2.0_Chr6g0292271' => 'rch', 'RcHm_v2.0_Chr7g0221261' => 'rch', 'Rhsim08G0219900' => 'rsi', 'Rhsim08G0220200' => 'rsi', 'Rhsim08G0237800' => 'rsi', 'Rhsim08G0238800' => 'rsi', 'Sabra09G0102700' => 'sbr', 'Sabra09G0127200' => 'sbr', 'Sabra11G0003700' => 'sbr', 'Sabra15G0014700' => 'sbr', 'Sc19g0000590' => 'sci', 'Sc19g0001870' => 'sci', 'SGA_v2.0_scaffold1G00346' => 'sas', 'SGA_v2.0_scaffold1G00575' => 'sas', 'SGA_v2.0_scaffold1G00761' => 'sas', 'SGA_v2.0_scaffold232G43501' => 'sas', 'TAR625G1137' => 'tar', 'Thecc.03G222100' => 'tca', 'TPR.G12691' => 'tpr', 'TWI34G0727' => 'twi', 'TWI36G0117' => 'twi', 'VMungo1309G0868' => 'vmu' ) $gf_id = 'HOM05D001729' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001729' ) $data_identifier = 'HOM05D001729' $data_type = 'gf_id' $species_gene_counts = array( 'amhyb' => (int) 1, 'cqu' => (int) 9, 'can' => (int) 1, 'cansat' => (int) 1, 'car' => (int) 1, 'col' => (int) 5, 'dca' => (int) 1, 'din' => (int) 2, 'dzi' => (int) 3, 'fan' => (int) 140, 'fve' => (int) 62, 'gma' => (int) 1, 'ghi' => (int) 2, 'gra' => (int) 1, 'han' => (int) 1, 'sun' => (int) 1, 'lonja' => (int) 6, 'lja' => (int) 1, 'lsa' => (int) 4, 'mes' => (int) 1, 'mdo' => (int) 14, 'mtr' => (int) 1, 'egut' => (int) 1, 'nta' => (int) 4, 'oeu' => (int) 1, 'stu' => (int) 2, 'pvu' => (int) 1, 'ptr' => (int) 4, 'ppe' => (int) 19, 'psa' => (int) 1, 'pso' => (int) 4, 'qlo' => (int) 36, 'rch' => (int) 23, 'rsi' => (int) 4, 'sbr' => (int) 4, 'sci' => (int) 2, 'sas' => (int) 4, 'tar' => (int) 1, 'tca' => (int) 1, 'tpr' => (int) 1, 'twi' => (int) 2, 'vmu' => (int) 1 ) $gf_gene_species = 'vmu' $gf_gene_id = 'VMungo1309G0868' $species_info = array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ) $local_species = 'pso' $disabled = '' $selected = '' $num_hits = (int) 0
Warning (2): count(): Parameter must be an array or an object that implements Countable [APP/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp, line 33]Code Context $disabled = (!array_key_exists($local_species,$species_gene_counts))?"disabled":""; $selected = (isset($selected_species) && array_key_exists($local_species,$selected_species))?"checked='checked'":""; $num_hits = (array_key_exists($local_species,$species_gene_counts))?count($species_gene_counts[$local_species]):0; $viewFile = '/www/bioinformatics01_ro/plaza/_dev_instances/feedback/app/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp' $dataForView = array( 'sidebar_info' => array( 'gf_id' => 'HOM05D001729', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '375', 'num_species' => '42' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'Ah.07g204710' => 'amhyb', 'AUR62006001' => 'cqu', 'AUR62006002' => 'cqu', 'AUR62006003' => 'cqu', 'AUR62015641' => 'cqu', 'AUR62027174' => 'cqu', 'AUR62035623' => 'cqu', 'AUR62035624' => 'cqu', 'AUR62035625' => 'cqu', 'AUR62035626' => 'cqu', 'CAN.G1110.53' => 'can', 'CANSAT80G0415' => 'cansat', 'Ca_21364_v3' => 'car', 'COL.COLO4_30693' => 'col', 'COL.COLO4_30694' => 'col', 'COL.COLO4_30695' => 'col', 'COL.COLO4_30696' => 'col', 'COL.COLO4_34020' => 'col', 'DCAR_004585' => 'dca', 'Dinv04029' => 'din', 'Dinv34857' => 'din', 'Duzib147G0011' => 'dzi', 'Duzib170G0599' => 'dzi', 'Duzib192G1051' => 'dzi', 'FAN01G0708' => 'fan', 'FAN01G0742' => 'fan', 'FAN02G0048' => 'fan', 'FAN02G0583' => 'fan', 'FAN02G0688' => 'fan', 'FAN02G1588' => 'fan', 'FAN02G2194' => 'fan', 'FAN02G2750' => 'fan', 'FAN02G3094' => 'fan', 'FAN02G3887' => 'fan', 'FAN02G3911' => 'fan', 'FAN02G3994' => 'fan', 'FAN02G4432' => 'fan', 'FAN02G4556' => 'fan', 'FAN03G1977' => 'fan', 'FAN03G2781' => 'fan', 'FAN03G2850' => 'fan', 'FAN03G3155' => 'fan', 'FAN04G2487' => 'fan', 'FAN05G0208' => 'fan', 'FAN05G0656' => 'fan', 'FAN05G0696' => 'fan', 'FAN05G0810' => 'fan', 'FAN05G1447' => 'fan', 'FAN05G2640' => 'fan', 'FAN05G2911' => 'fan', 'FAN05G3901' => 'fan', 'FAN05G4859' => 'fan', 'FAN05G4861' => 'fan', 'FAN05G4988' => 'fan', 'FAN05G5187' => 'fan', 'FAN05G5452' => 'fan', 'FAN05G5500' => 'fan', 'FAN05G5688' => 'fan', 'FAN06G0177' => 'fan', 'FAN06G0675' => 'fan', 'FAN06G1290' => 'fan', 'FAN06G2191' => 'fan', 'FAN06G2405' => 'fan', 'FAN06G3231' => 'fan', 'FAN06G3932' => 'fan', 'FAN07G0163' => 'fan', 'FAN07G0471' => 'fan', 'FAN07G1354' => 'fan', 'FAN08G0338' => 'fan', 'FAN08G1373' => 'fan', 'FAN08G2539' => 'fan', 'FAN08G2728' => 'fan', 'FAN09G0608' => 'fan', 'FAN09G1136' => 'fan', 'FAN09G1958' => 'fan', 'FAN09G2508' => 'fan', 'FAN09G2597' => 'fan', 'FAN09G2658' => 'fan', 'FAN09G2757' => 'fan', 'FAN09G2983' => 'fan', 'FAN09G3130' => 'fan', 'FAN09G3565' => 'fan', 'FAN09G3613' => 'fan', 'FAN09G4011' => 'fan', 'FAN09G4239' => 'fan', 'FAN09G4277' => 'fan', 'FAN09G4720' => 'fan', 'FAN11G0139' => 'fan', 'FAN11G1727' => 'fan', 'FAN11G2672' => 'fan', 'FAN11G2795' => 'fan', 'FAN11G3238' => 'fan', 'FAN11G3734' => 'fan', 'FAN12G0631' => 'fan', 'FAN12G2239' => 'fan', 'FAN12G2308' => 'fan', 'FAN12G2569' => 'fan', 'FAN12G2623' => 'fan', 'FAN13G3182' => 'fan', 'FAN14G0053' => 'fan', 'FAN14G0370' => 'fan', 'FAN14G0382' => 'fan', 'FAN14G0421' => 'fan', 'FAN14G0866' => 'fan', 'FAN14G1187' => 'fan', 'FAN14G1727' => 'fan', 'FAN14G1791' => 'fan', 'FAN14G2361' => 'fan', 'FAN14G2668' => 'fan', 'FAN14G2770' => 'fan', 'FAN14G2874' => 'fan', 'FAN14G3193' => 'fan', 'FAN14G3624' => 'fan', 'FAN14G3676' => 'fan', 'FAN14G3807' => 'fan', 'FAN14G4082' => 'fan', 'FAN14G4342' => 'fan', 'FAN14G4985' => 'fan', 'FAN14G5126' => 'fan', 'FAN14G5781' => 'fan', 'FAN14G5808' => 'fan', 'FAN14G5949' => 'fan', 'FAN15G0828' => 'fan', 'FAN15G1054' => 'fan', 'FAN15G2023' => 'fan', 'FAN15G2506' => 'fan', 'FAN16G0128' => 'fan', 'FAN16G0249' => 'fan', 'FAN16G0429' => 'fan', 'FAN16G1493' => 'fan', 'FAN16G2210' => 'fan', 'FAN16G2506' => 'fan', 'FAN18G1542' => 'fan', 'FAN18G4057' => 'fan', 'FAN19G0745' => 'fan', 'FAN19G1216' => 'fan', 'FAN19G1733' => 'fan', 'FAN20G0258' => 'fan', 'FAN20G1095' => 'fan', 'FAN20G1557' => 'fan', 'FAN21G0302' => 'fan', 'FAN21G0519' => 'fan', 'FAN21G0970' => 'fan', 'FAN21G1159' => 'fan', 'FAN21G1312' => 'fan', 'FAN21G1440' => 'fan', 'FAN21G1715' => 'fan', 'FAN23G1584' => 'fan', 'FAN24G0045' => 'fan', 'FAN24G0053' => 'fan', 'FAN24G1500' => 'fan', 'FAN24G1817' => 'fan', 'FAN24G2147' => 'fan', 'FAN24G2236' => 'fan', 'FAN24G2446' => 'fan', 'FAN24G2684' => 'fan', 'FAN25G0187' => 'fan', 'FAN25G0505' => 'fan', 'FAN25G0589' => 'fan', 'FAN25G3663' => 'fan', 'FAN26G1025' => 'fan', 'FAN26G2860' => 'fan', 'FAN27G1329' => 'fan', 'FAN27G3392' => 'fan', 'FvH4_1g02011' => 'fve', 'FvH4_1g06511' => 'fve', 'FvH4_2g19900' => 'fve', 'FvH4_2g19920' => 'fve', 'FvH4_2g24261' => 'fve', 'FvH4_2g24270' => 'fve', 'FvH4_2g24631' => 'fve', 'FvH4_2g30622' => 'fve', 'FvH4_3g12920' => 'fve', 'FvH4_3g30171' => 'fve', 'FvH4_3g35490' => 'fve', 'FvH4_3g43682' => 'fve', 'FvH4_3g43730' => 'fve', 'FvH4_3g43732' => 'fve', 'FvH4_3g43751' => 'fve', 'FvH4_3g43752' => 'fve', 'FvH4_3g43770' => 'fve', 'FvH4_3g44471' => 'fve', 'FvH4_3g44510' => 'fve', 'FvH4_3g44582' => 'fve', 'FvH4_4g16921' => 'fve', 'FvH4_4g17121' => 'fve', 'FvH4_4g17782' => 'fve', 'FvH4_4g17783' => 'fve', 'FvH4_4g18120' => 'fve', 'FvH4_4g31310' => 'fve', 'FvH4_4g35052' => 'fve', 'FvH4_5g30862' => 'fve', 'FvH4_6g01541' => 'fve', 'FvH4_6g02021' => 'fve', 'FvH4_6g02041' => 'fve', 'FvH4_6g02071' => 'fve', 'FvH4_6g02171' => 'fve', 'FvH4_6g03181' => 'fve', 'FvH4_6g03182' => 'fve', 'FvH4_6g03221' => 'fve', 'FvH4_6g03380' => 'fve', 'FvH4_6g05201' => 'fve', 'FvH4_6g05203' => 'fve', 'FvH4_6g20231' => 'fve', 'FvH4_6g31981' => 'fve', 'FvH4_6g32061' => 'fve', 'FvH4_6g37041' => 'fve', 'FvH4_6g37932' => 'fve', 'FvH4_6g38731' => 'fve', 'FvH4_6g39370' => 'fve', 'FvH4_6g39371' => 'fve', 'FvH4_6g40891' => 'fve', 'FvH4_6g40892' => 'fve', 'FvH4_6g43143' => 'fve', 'FvH4_6g45251' => 'fve', 'FvH4_6g45260' => 'fve', 'FvH4_6g45291' => 'fve', 'FvH4_6g45890' => 'fve', 'FvH4_6g46240' => 'fve', 'FvH4_6g46241' => 'fve', 'FvH4_6g46242' => 'fve', 'FvH4_6g46260' => 'fve', 'FvH4_6g46280' => 'fve', 'FvH4_6g46380' => 'fve', 'FvH4_7g12841' => 'fve', 'FvH4_7g31431' => 'fve', 'Glyma.09G075900' => 'gma', 'Gohir.A09G096401' => 'ghi', 'Gohir.D09G096101' => 'ghi', 'Gorai.006G112800' => 'gra', 'HanXRQChr04g0121411' => 'han', 'Hund15878' => 'sun', 'Lj2A1107G68' => 'lonja', 'Lj2A630G63' => 'lonja', 'Lj2A946T25' => 'lonja', 'Lj2C714T1' => 'lonja', 'Lj2C966T3' => 'lonja', 'Lj2C966T4' => 'lonja', 'Lj4g0002979' => 'lja', 'Lsat_1_v5_gn_5_30901' => 'lsa', 'Lsat_1_v5_gn_5_31100' => 'lsa', 'Lsat_1_v5_gn_5_38600' => 'lsa', 'Lsat_1_v5_gn_6_92061' => 'lsa', 'Manes.05G071301' => 'mes', 'MD02G1008700' => 'mdo', 'MD02G1008900' => 'mdo', 'MD03G1256400' => 'mdo', 'MD04G1180900' => 'mdo', 'MD04G1181000' => 'mdo', 'MD04G1181200' => 'mdo', 'MD05G1244200' => 'mdo', 'MD05G1324200' => 'mdo', 'MD09G1201600' => 'mdo', 'MD10G1000600' => 'mdo', 'MD14G1026900' => 'mdo', 'MD14G1187900' => 'mdo', 'MD15G1017800' => 'mdo', 'MD15G1018100' => 'mdo', 'Medtr4g124160' => 'mtr', 'Migut.L01260' => 'egut', 'Nitab4.5_0000008g0440' => 'nta', 'Nitab4.5_0000207g0170' => 'nta', 'Nitab4.5_0007671g0030' => 'nta', 'Nitab4.5_0010853g0020' => 'nta', 'Oeu057656.1' => 'oeu', 'PGSC0003DMG400005638' => 'stu', 'PGSC0003DMG400005639' => 'stu', 'Phvul.009G222800' => 'pvu', 'Potri.009G132400' => 'ptr', 'Potri.009G163001' => 'ptr', 'Potri.011G000700' => 'ptr', 'Potri.011G004800' => 'ptr', 'Prupe.1G509300' => 'ppe', 'Prupe.1G509700' => 'ppe', 'Prupe.1G510400' => 'ppe', 'Prupe.1G510700' => 'ppe', 'Prupe.1G512600' => 'ppe', 'Prupe.2G073200' => 'ppe', 'Prupe.3G059500' => 'ppe', 'Prupe.3G059600' => 'ppe', 'Prupe.3G246100' => 'ppe', 'Prupe.3G265100' => 'ppe', 'Prupe.4G034700' => 'ppe', 'Prupe.4G052100' => 'ppe', 'Prupe.4G053600' => 'ppe', 'Prupe.5G068800' => 'ppe', 'Prupe.5G070600' => 'ppe', 'Prupe.6G075400' => 'ppe', 'Prupe.6G075500' => 'ppe', 'Prupe.6G076400' => 'ppe', 'Prupe.8G110700' => 'ppe', 'Psat4g020960' => 'psa', 'PSO135G0788' => 'pso', 'PSO210G6463' => 'pso', 'PSO384G0370' => 'pso', 'PSO386G0056' => 'pso', 'QL01p006048' => 'qlo', 'QL02p054283' => 'qlo', 'QL05p008000' => 'qlo', 'QL05p008212' => 'qlo', 'QL05p008950' => 'qlo', 'QL05p009042' => 'qlo', 'QL05p009518' => 'qlo', 'QL05p012589' => 'qlo', 'QL05p012608' => 'qlo', 'QL05p012650' => 'qlo', 'QL05p012667' => 'qlo', 'QL05p014501' => 'qlo', 'QL05p052800' => 'qlo', 'QL05p065010' => 'qlo', 'QL05p074156' => 'qlo', 'QL05p074160' => 'qlo', 'QL05p074174' => 'qlo', 'QL05p074178' => 'qlo', 'QL05p074214' => 'qlo', 'QL06p001050' => 'qlo', 'QL06p001056' => 'qlo', 'QL06p006093' => 'qlo', 'QL06p006111' => 'qlo', 'QL07p019784' => 'qlo', 'QL07p019801' => 'qlo', 'QL07p036110' => 'qlo', 'QL07p036134' => 'qlo', 'QL07p036147' => 'qlo', 'QL07p036156' => 'qlo', 'QL07p036300' => 'qlo', 'QL07p036320' => 'qlo', 'QL08p014547' => 'qlo', 'QL08p014551' => 'qlo', 'QL08p043319' => 'qlo', 'QL08p043324' => 'qlo', 'QL11p009094' => 'qlo', 'RcHm_v2.0_Chr1g0380481' => 'rch', 'RcHm_v2.0_Chr2g0089331' => 'rch', 'RcHm_v2.0_Chr2g0123691' => 'rch', 'RcHm_v2.0_Chr2g0151111' => 'rch', 'RcHm_v2.0_Chr2g0163011' => 'rch', 'RcHm_v2.0_Chr2g0163051' => 'rch', 'RcHm_v2.0_Chr2g0164671' => 'rch', 'RcHm_v2.0_Chr2g0164681' => 'rch', 'RcHm_v2.0_Chr2g0164721' => 'rch', 'RcHm_v2.0_Chr3g0449911' => 'rch', 'RcHm_v2.0_Chr3g0450211' => 'rch', 'RcHm_v2.0_Chr3g0457271' => 'rch', 'RcHm_v2.0_Chr5g0018111' => 'rch', 'RcHm_v2.0_Chr5g0021011' => 'rch', 'RcHm_v2.0_Chr5g0081171' => 'rch', 'RcHm_v2.0_Chr5g0081211' => 'rch', 'RcHm_v2.0_Chr6g0275871' => 'rch', 'RcHm_v2.0_Chr6g0276071' => 'rch', 'RcHm_v2.0_Chr6g0285591' => 'rch', 'RcHm_v2.0_Chr6g0291931' => 'rch', 'RcHm_v2.0_Chr6g0292091' => 'rch', 'RcHm_v2.0_Chr6g0292271' => 'rch', 'RcHm_v2.0_Chr7g0221261' => 'rch', 'Rhsim08G0219900' => 'rsi', 'Rhsim08G0220200' => 'rsi', 'Rhsim08G0237800' => 'rsi', 'Rhsim08G0238800' => 'rsi', 'Sabra09G0102700' => 'sbr', 'Sabra09G0127200' => 'sbr', 'Sabra11G0003700' => 'sbr', 'Sabra15G0014700' => 'sbr', 'Sc19g0000590' => 'sci', 'Sc19g0001870' => 'sci', 'SGA_v2.0_scaffold1G00346' => 'sas', 'SGA_v2.0_scaffold1G00575' => 'sas', 'SGA_v2.0_scaffold1G00761' => 'sas', 'SGA_v2.0_scaffold232G43501' => 'sas', 'TAR625G1137' => 'tar', 'Thecc.03G222100' => 'tca', 'TPR.G12691' => 'tpr', 'TWI34G0727' => 'twi', 'TWI36G0117' => 'twi', 'VMungo1309G0868' => 'vmu' ), 'gf_id' => 'HOM05D001729', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001729' ), 'data_identifier' => 'HOM05D001729', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001729', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '375', 'num_species' => '42' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'Ah.07g204710' => 'amhyb', 'AUR62006001' => 'cqu', 'AUR62006002' => 'cqu', 'AUR62006003' => 'cqu', 'AUR62015641' => 'cqu', 'AUR62027174' => 'cqu', 'AUR62035623' => 'cqu', 'AUR62035624' => 'cqu', 'AUR62035625' => 'cqu', 'AUR62035626' => 'cqu', 'CAN.G1110.53' => 'can', 'CANSAT80G0415' => 'cansat', 'Ca_21364_v3' => 'car', 'COL.COLO4_30693' => 'col', 'COL.COLO4_30694' => 'col', 'COL.COLO4_30695' => 'col', 'COL.COLO4_30696' => 'col', 'COL.COLO4_34020' => 'col', 'DCAR_004585' => 'dca', 'Dinv04029' => 'din', 'Dinv34857' => 'din', 'Duzib147G0011' => 'dzi', 'Duzib170G0599' => 'dzi', 'Duzib192G1051' => 'dzi', 'FAN01G0708' => 'fan', 'FAN01G0742' => 'fan', 'FAN02G0048' => 'fan', 'FAN02G0583' => 'fan', 'FAN02G0688' => 'fan', 'FAN02G1588' => 'fan', 'FAN02G2194' => 'fan', 'FAN02G2750' => 'fan', 'FAN02G3094' => 'fan', 'FAN02G3887' => 'fan', 'FAN02G3911' => 'fan', 'FAN02G3994' => 'fan', 'FAN02G4432' => 'fan', 'FAN02G4556' => 'fan', 'FAN03G1977' => 'fan', 'FAN03G2781' => 'fan', 'FAN03G2850' => 'fan', 'FAN03G3155' => 'fan', 'FAN04G2487' => 'fan', 'FAN05G0208' => 'fan', 'FAN05G0656' => 'fan', 'FAN05G0696' => 'fan', 'FAN05G0810' => 'fan', 'FAN05G1447' => 'fan', 'FAN05G2640' => 'fan', 'FAN05G2911' => 'fan', 'FAN05G3901' => 'fan', 'FAN05G4859' => 'fan', 'FAN05G4861' => 'fan', 'FAN05G4988' => 'fan', 'FAN05G5187' => 'fan', 'FAN05G5452' => 'fan', 'FAN05G5500' => 'fan', 'FAN05G5688' => 'fan', 'FAN06G0177' => 'fan', 'FAN06G0675' => 'fan', 'FAN06G1290' => 'fan', 'FAN06G2191' => 'fan', 'FAN06G2405' => 'fan', 'FAN06G3231' => 'fan', 'FAN06G3932' => 'fan', 'FAN07G0163' => 'fan', 'FAN07G0471' => 'fan', 'FAN07G1354' => 'fan', 'FAN08G0338' => 'fan', 'FAN08G1373' => 'fan', 'FAN08G2539' => 'fan', 'FAN08G2728' => 'fan', 'FAN09G0608' => 'fan', 'FAN09G1136' => 'fan', 'FAN09G1958' => 'fan', 'FAN09G2508' => 'fan', 'FAN09G2597' => 'fan', 'FAN09G2658' => 'fan', 'FAN09G2757' => 'fan', 'FAN09G2983' => 'fan', 'FAN09G3130' => 'fan', 'FAN09G3565' => 'fan', 'FAN09G3613' => 'fan', 'FAN09G4011' => 'fan', 'FAN09G4239' => 'fan', 'FAN09G4277' => 'fan', 'FAN09G4720' => 'fan', 'FAN11G0139' => 'fan', 'FAN11G1727' => 'fan', 'FAN11G2672' => 'fan', 'FAN11G2795' => 'fan', 'FAN11G3238' => 'fan', 'FAN11G3734' => 'fan', 'FAN12G0631' => 'fan', 'FAN12G2239' => 'fan', 'FAN12G2308' => 'fan', 'FAN12G2569' => 'fan', 'FAN12G2623' => 'fan', 'FAN13G3182' => 'fan', 'FAN14G0053' => 'fan', 'FAN14G0370' => 'fan', 'FAN14G0382' => 'fan', 'FAN14G0421' => 'fan', 'FAN14G0866' => 'fan', 'FAN14G1187' => 'fan', 'FAN14G1727' => 'fan', 'FAN14G1791' => 'fan', 'FAN14G2361' => 'fan', 'FAN14G2668' => 'fan', 'FAN14G2770' => 'fan', 'FAN14G2874' => 'fan', 'FAN14G3193' => 'fan', 'FAN14G3624' => 'fan', 'FAN14G3676' => 'fan', 'FAN14G3807' => 'fan', 'FAN14G4082' => 'fan', 'FAN14G4342' => 'fan', 'FAN14G4985' => 'fan', 'FAN14G5126' => 'fan', 'FAN14G5781' => 'fan', 'FAN14G5808' => 'fan', 'FAN14G5949' => 'fan', 'FAN15G0828' => 'fan', 'FAN15G1054' => 'fan', 'FAN15G2023' => 'fan', 'FAN15G2506' => 'fan', 'FAN16G0128' => 'fan', 'FAN16G0249' => 'fan', 'FAN16G0429' => 'fan', 'FAN16G1493' => 'fan', 'FAN16G2210' => 'fan', 'FAN16G2506' => 'fan', 'FAN18G1542' => 'fan', 'FAN18G4057' => 'fan', 'FAN19G0745' => 'fan', 'FAN19G1216' => 'fan', 'FAN19G1733' => 'fan', 'FAN20G0258' => 'fan', 'FAN20G1095' => 'fan', 'FAN20G1557' => 'fan', 'FAN21G0302' => 'fan', 'FAN21G0519' => 'fan', 'FAN21G0970' => 'fan', 'FAN21G1159' => 'fan', 'FAN21G1312' => 'fan', 'FAN21G1440' => 'fan', 'FAN21G1715' => 'fan', 'FAN23G1584' => 'fan', 'FAN24G0045' => 'fan', 'FAN24G0053' => 'fan', 'FAN24G1500' => 'fan', 'FAN24G1817' => 'fan', 'FAN24G2147' => 'fan', 'FAN24G2236' => 'fan', 'FAN24G2446' => 'fan', 'FAN24G2684' => 'fan', 'FAN25G0187' => 'fan', 'FAN25G0505' => 'fan', 'FAN25G0589' => 'fan', 'FAN25G3663' => 'fan', 'FAN26G1025' => 'fan', 'FAN26G2860' => 'fan', 'FAN27G1329' => 'fan', 'FAN27G3392' => 'fan', 'FvH4_1g02011' => 'fve', 'FvH4_1g06511' => 'fve', 'FvH4_2g19900' => 'fve', 'FvH4_2g19920' => 'fve', 'FvH4_2g24261' => 'fve', 'FvH4_2g24270' => 'fve', 'FvH4_2g24631' => 'fve', 'FvH4_2g30622' => 'fve', 'FvH4_3g12920' => 'fve', 'FvH4_3g30171' => 'fve', 'FvH4_3g35490' => 'fve', 'FvH4_3g43682' => 'fve', 'FvH4_3g43730' => 'fve', 'FvH4_3g43732' => 'fve', 'FvH4_3g43751' => 'fve', 'FvH4_3g43752' => 'fve', 'FvH4_3g43770' => 'fve', 'FvH4_3g44471' => 'fve', 'FvH4_3g44510' => 'fve', 'FvH4_3g44582' => 'fve', 'FvH4_4g16921' => 'fve', 'FvH4_4g17121' => 'fve', 'FvH4_4g17782' => 'fve', 'FvH4_4g17783' => 'fve', 'FvH4_4g18120' => 'fve', 'FvH4_4g31310' => 'fve', 'FvH4_4g35052' => 'fve', 'FvH4_5g30862' => 'fve', 'FvH4_6g01541' => 'fve', 'FvH4_6g02021' => 'fve', 'FvH4_6g02041' => 'fve', 'FvH4_6g02071' => 'fve', 'FvH4_6g02171' => 'fve', 'FvH4_6g03181' => 'fve', 'FvH4_6g03182' => 'fve', 'FvH4_6g03221' => 'fve', 'FvH4_6g03380' => 'fve', 'FvH4_6g05201' => 'fve', 'FvH4_6g05203' => 'fve', 'FvH4_6g20231' => 'fve', 'FvH4_6g31981' => 'fve', 'FvH4_6g32061' => 'fve', 'FvH4_6g37041' => 'fve', 'FvH4_6g37932' => 'fve', 'FvH4_6g38731' => 'fve', 'FvH4_6g39370' => 'fve', 'FvH4_6g39371' => 'fve', 'FvH4_6g40891' => 'fve', 'FvH4_6g40892' => 'fve', 'FvH4_6g43143' => 'fve', 'FvH4_6g45251' => 'fve', 'FvH4_6g45260' => 'fve', 'FvH4_6g45291' => 'fve', 'FvH4_6g45890' => 'fve', 'FvH4_6g46240' => 'fve', 'FvH4_6g46241' => 'fve', 'FvH4_6g46242' => 'fve', 'FvH4_6g46260' => 'fve', 'FvH4_6g46280' => 'fve', 'FvH4_6g46380' => 'fve', 'FvH4_7g12841' => 'fve', 'FvH4_7g31431' => 'fve', 'Glyma.09G075900' => 'gma', 'Gohir.A09G096401' => 'ghi', 'Gohir.D09G096101' => 'ghi', 'Gorai.006G112800' => 'gra', 'HanXRQChr04g0121411' => 'han', 'Hund15878' => 'sun', 'Lj2A1107G68' => 'lonja', 'Lj2A630G63' => 'lonja', 'Lj2A946T25' => 'lonja', 'Lj2C714T1' => 'lonja', 'Lj2C966T3' => 'lonja', 'Lj2C966T4' => 'lonja', 'Lj4g0002979' => 'lja', 'Lsat_1_v5_gn_5_30901' => 'lsa', 'Lsat_1_v5_gn_5_31100' => 'lsa', 'Lsat_1_v5_gn_5_38600' => 'lsa', 'Lsat_1_v5_gn_6_92061' => 'lsa', 'Manes.05G071301' => 'mes', 'MD02G1008700' => 'mdo', 'MD02G1008900' => 'mdo', 'MD03G1256400' => 'mdo', 'MD04G1180900' => 'mdo', 'MD04G1181000' => 'mdo', 'MD04G1181200' => 'mdo', 'MD05G1244200' => 'mdo', 'MD05G1324200' => 'mdo', 'MD09G1201600' => 'mdo', 'MD10G1000600' => 'mdo', 'MD14G1026900' => 'mdo', 'MD14G1187900' => 'mdo', 'MD15G1017800' => 'mdo', 'MD15G1018100' => 'mdo', 'Medtr4g124160' => 'mtr', 'Migut.L01260' => 'egut', 'Nitab4.5_0000008g0440' => 'nta', 'Nitab4.5_0000207g0170' => 'nta', 'Nitab4.5_0007671g0030' => 'nta', 'Nitab4.5_0010853g0020' => 'nta', 'Oeu057656.1' => 'oeu', 'PGSC0003DMG400005638' => 'stu', 'PGSC0003DMG400005639' => 'stu', 'Phvul.009G222800' => 'pvu', 'Potri.009G132400' => 'ptr', 'Potri.009G163001' => 'ptr', 'Potri.011G000700' => 'ptr', 'Potri.011G004800' => 'ptr', 'Prupe.1G509300' => 'ppe', 'Prupe.1G509700' => 'ppe', 'Prupe.1G510400' => 'ppe', 'Prupe.1G510700' => 'ppe', 'Prupe.1G512600' => 'ppe', 'Prupe.2G073200' => 'ppe', 'Prupe.3G059500' => 'ppe', 'Prupe.3G059600' => 'ppe', 'Prupe.3G246100' => 'ppe', 'Prupe.3G265100' => 'ppe', 'Prupe.4G034700' => 'ppe', 'Prupe.4G052100' => 'ppe', 'Prupe.4G053600' => 'ppe', 'Prupe.5G068800' => 'ppe', 'Prupe.5G070600' => 'ppe', 'Prupe.6G075400' => 'ppe', 'Prupe.6G075500' => 'ppe', 'Prupe.6G076400' => 'ppe', 'Prupe.8G110700' => 'ppe', 'Psat4g020960' => 'psa', 'PSO135G0788' => 'pso', 'PSO210G6463' => 'pso', 'PSO384G0370' => 'pso', 'PSO386G0056' => 'pso', 'QL01p006048' => 'qlo', 'QL02p054283' => 'qlo', 'QL05p008000' => 'qlo', 'QL05p008212' => 'qlo', 'QL05p008950' => 'qlo', 'QL05p009042' => 'qlo', 'QL05p009518' => 'qlo', 'QL05p012589' => 'qlo', 'QL05p012608' => 'qlo', 'QL05p012650' => 'qlo', 'QL05p012667' => 'qlo', 'QL05p014501' => 'qlo', 'QL05p052800' => 'qlo', 'QL05p065010' => 'qlo', 'QL05p074156' => 'qlo', 'QL05p074160' => 'qlo', 'QL05p074174' => 'qlo', 'QL05p074178' => 'qlo', 'QL05p074214' => 'qlo', 'QL06p001050' => 'qlo', 'QL06p001056' => 'qlo', 'QL06p006093' => 'qlo', 'QL06p006111' => 'qlo', 'QL07p019784' => 'qlo', 'QL07p019801' => 'qlo', 'QL07p036110' => 'qlo', 'QL07p036134' => 'qlo', 'QL07p036147' => 'qlo', 'QL07p036156' => 'qlo', 'QL07p036300' => 'qlo', 'QL07p036320' => 'qlo', 'QL08p014547' => 'qlo', 'QL08p014551' => 'qlo', 'QL08p043319' => 'qlo', 'QL08p043324' => 'qlo', 'QL11p009094' => 'qlo', 'RcHm_v2.0_Chr1g0380481' => 'rch', 'RcHm_v2.0_Chr2g0089331' => 'rch', 'RcHm_v2.0_Chr2g0123691' => 'rch', 'RcHm_v2.0_Chr2g0151111' => 'rch', 'RcHm_v2.0_Chr2g0163011' => 'rch', 'RcHm_v2.0_Chr2g0163051' => 'rch', 'RcHm_v2.0_Chr2g0164671' => 'rch', 'RcHm_v2.0_Chr2g0164681' => 'rch', 'RcHm_v2.0_Chr2g0164721' => 'rch', 'RcHm_v2.0_Chr3g0449911' => 'rch', 'RcHm_v2.0_Chr3g0450211' => 'rch', 'RcHm_v2.0_Chr3g0457271' => 'rch', 'RcHm_v2.0_Chr5g0018111' => 'rch', 'RcHm_v2.0_Chr5g0021011' => 'rch', 'RcHm_v2.0_Chr5g0081171' => 'rch', 'RcHm_v2.0_Chr5g0081211' => 'rch', 'RcHm_v2.0_Chr6g0275871' => 'rch', 'RcHm_v2.0_Chr6g0276071' => 'rch', 'RcHm_v2.0_Chr6g0285591' => 'rch', 'RcHm_v2.0_Chr6g0291931' => 'rch', 'RcHm_v2.0_Chr6g0292091' => 'rch', 'RcHm_v2.0_Chr6g0292271' => 'rch', 'RcHm_v2.0_Chr7g0221261' => 'rch', 'Rhsim08G0219900' => 'rsi', 'Rhsim08G0220200' => 'rsi', 'Rhsim08G0237800' => 'rsi', 'Rhsim08G0238800' => 'rsi', 'Sabra09G0102700' => 'sbr', 'Sabra09G0127200' => 'sbr', 'Sabra11G0003700' => 'sbr', 'Sabra15G0014700' => 'sbr', 'Sc19g0000590' => 'sci', 'Sc19g0001870' => 'sci', 'SGA_v2.0_scaffold1G00346' => 'sas', 'SGA_v2.0_scaffold1G00575' => 'sas', 'SGA_v2.0_scaffold1G00761' => 'sas', 'SGA_v2.0_scaffold232G43501' => 'sas', 'TAR625G1137' => 'tar', 'Thecc.03G222100' => 'tca', 'TPR.G12691' => 'tpr', 'TWI34G0727' => 'twi', 'TWI36G0117' => 'twi', 'VMungo1309G0868' => 'vmu' ) $gf_id = 'HOM05D001729' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001729' ) $data_identifier = 'HOM05D001729' $data_type = 'gf_id' $species_gene_counts = array( 'amhyb' => (int) 1, 'cqu' => (int) 9, 'can' => (int) 1, 'cansat' => (int) 1, 'car' => (int) 1, 'col' => (int) 5, 'dca' => (int) 1, 'din' => (int) 2, 'dzi' => (int) 3, 'fan' => (int) 140, 'fve' => (int) 62, 'gma' => (int) 1, 'ghi' => (int) 2, 'gra' => (int) 1, 'han' => (int) 1, 'sun' => (int) 1, 'lonja' => (int) 6, 'lja' => (int) 1, 'lsa' => (int) 4, 'mes' => (int) 1, 'mdo' => (int) 14, 'mtr' => (int) 1, 'egut' => (int) 1, 'nta' => (int) 4, 'oeu' => (int) 1, 'stu' => (int) 2, 'pvu' => (int) 1, 'ptr' => (int) 4, 'ppe' => (int) 19, 'psa' => (int) 1, 'pso' => (int) 4, 'qlo' => (int) 36, 'rch' => (int) 23, 'rsi' => (int) 4, 'sbr' => (int) 4, 'sci' => (int) 2, 'sas' => (int) 4, 'tar' => (int) 1, 'tca' => (int) 1, 'tpr' => (int) 1, 'twi' => (int) 2, 'vmu' => (int) 1 ) $gf_gene_species = 'vmu' $gf_gene_id = 'VMungo1309G0868' $species_info = array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ) $local_species = 'pvu' $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' => 'HOM05D001729', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '375', 'num_species' => '42' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'Ah.07g204710' => 'amhyb', 'AUR62006001' => 'cqu', 'AUR62006002' => 'cqu', 'AUR62006003' => 'cqu', 'AUR62015641' => 'cqu', 'AUR62027174' => 'cqu', 'AUR62035623' => 'cqu', 'AUR62035624' => 'cqu', 'AUR62035625' => 'cqu', 'AUR62035626' => 'cqu', 'CAN.G1110.53' => 'can', 'CANSAT80G0415' => 'cansat', 'Ca_21364_v3' => 'car', 'COL.COLO4_30693' => 'col', 'COL.COLO4_30694' => 'col', 'COL.COLO4_30695' => 'col', 'COL.COLO4_30696' => 'col', 'COL.COLO4_34020' => 'col', 'DCAR_004585' => 'dca', 'Dinv04029' => 'din', 'Dinv34857' => 'din', 'Duzib147G0011' => 'dzi', 'Duzib170G0599' => 'dzi', 'Duzib192G1051' => 'dzi', 'FAN01G0708' => 'fan', 'FAN01G0742' => 'fan', 'FAN02G0048' => 'fan', 'FAN02G0583' => 'fan', 'FAN02G0688' => 'fan', 'FAN02G1588' => 'fan', 'FAN02G2194' => 'fan', 'FAN02G2750' => 'fan', 'FAN02G3094' => 'fan', 'FAN02G3887' => 'fan', 'FAN02G3911' => 'fan', 'FAN02G3994' => 'fan', 'FAN02G4432' => 'fan', 'FAN02G4556' => 'fan', 'FAN03G1977' => 'fan', 'FAN03G2781' => 'fan', 'FAN03G2850' => 'fan', 'FAN03G3155' => 'fan', 'FAN04G2487' => 'fan', 'FAN05G0208' => 'fan', 'FAN05G0656' => 'fan', 'FAN05G0696' => 'fan', 'FAN05G0810' => 'fan', 'FAN05G1447' => 'fan', 'FAN05G2640' => 'fan', 'FAN05G2911' => 'fan', 'FAN05G3901' => 'fan', 'FAN05G4859' => 'fan', 'FAN05G4861' => 'fan', 'FAN05G4988' => 'fan', 'FAN05G5187' => 'fan', 'FAN05G5452' => 'fan', 'FAN05G5500' => 'fan', 'FAN05G5688' => 'fan', 'FAN06G0177' => 'fan', 'FAN06G0675' => 'fan', 'FAN06G1290' => 'fan', 'FAN06G2191' => 'fan', 'FAN06G2405' => 'fan', 'FAN06G3231' => 'fan', 'FAN06G3932' => 'fan', 'FAN07G0163' => 'fan', 'FAN07G0471' => 'fan', 'FAN07G1354' => 'fan', 'FAN08G0338' => 'fan', 'FAN08G1373' => 'fan', 'FAN08G2539' => 'fan', 'FAN08G2728' => 'fan', 'FAN09G0608' => 'fan', 'FAN09G1136' => 'fan', 'FAN09G1958' => 'fan', 'FAN09G2508' => 'fan', 'FAN09G2597' => 'fan', 'FAN09G2658' => 'fan', 'FAN09G2757' => 'fan', 'FAN09G2983' => 'fan', 'FAN09G3130' => 'fan', 'FAN09G3565' => 'fan', 'FAN09G3613' => 'fan', 'FAN09G4011' => 'fan', 'FAN09G4239' => 'fan', 'FAN09G4277' => 'fan', 'FAN09G4720' => 'fan', 'FAN11G0139' => 'fan', 'FAN11G1727' => 'fan', 'FAN11G2672' => 'fan', 'FAN11G2795' => 'fan', 'FAN11G3238' => 'fan', 'FAN11G3734' => 'fan', 'FAN12G0631' => 'fan', 'FAN12G2239' => 'fan', 'FAN12G2308' => 'fan', 'FAN12G2569' => 'fan', 'FAN12G2623' => 'fan', 'FAN13G3182' => 'fan', 'FAN14G0053' => 'fan', 'FAN14G0370' => 'fan', 'FAN14G0382' => 'fan', 'FAN14G0421' => 'fan', 'FAN14G0866' => 'fan', 'FAN14G1187' => 'fan', 'FAN14G1727' => 'fan', 'FAN14G1791' => 'fan', 'FAN14G2361' => 'fan', 'FAN14G2668' => 'fan', 'FAN14G2770' => 'fan', 'FAN14G2874' => 'fan', 'FAN14G3193' => 'fan', 'FAN14G3624' => 'fan', 'FAN14G3676' => 'fan', 'FAN14G3807' => 'fan', 'FAN14G4082' => 'fan', 'FAN14G4342' => 'fan', 'FAN14G4985' => 'fan', 'FAN14G5126' => 'fan', 'FAN14G5781' => 'fan', 'FAN14G5808' => 'fan', 'FAN14G5949' => 'fan', 'FAN15G0828' => 'fan', 'FAN15G1054' => 'fan', 'FAN15G2023' => 'fan', 'FAN15G2506' => 'fan', 'FAN16G0128' => 'fan', 'FAN16G0249' => 'fan', 'FAN16G0429' => 'fan', 'FAN16G1493' => 'fan', 'FAN16G2210' => 'fan', 'FAN16G2506' => 'fan', 'FAN18G1542' => 'fan', 'FAN18G4057' => 'fan', 'FAN19G0745' => 'fan', 'FAN19G1216' => 'fan', 'FAN19G1733' => 'fan', 'FAN20G0258' => 'fan', 'FAN20G1095' => 'fan', 'FAN20G1557' => 'fan', 'FAN21G0302' => 'fan', 'FAN21G0519' => 'fan', 'FAN21G0970' => 'fan', 'FAN21G1159' => 'fan', 'FAN21G1312' => 'fan', 'FAN21G1440' => 'fan', 'FAN21G1715' => 'fan', 'FAN23G1584' => 'fan', 'FAN24G0045' => 'fan', 'FAN24G0053' => 'fan', 'FAN24G1500' => 'fan', 'FAN24G1817' => 'fan', 'FAN24G2147' => 'fan', 'FAN24G2236' => 'fan', 'FAN24G2446' => 'fan', 'FAN24G2684' => 'fan', 'FAN25G0187' => 'fan', 'FAN25G0505' => 'fan', 'FAN25G0589' => 'fan', 'FAN25G3663' => 'fan', 'FAN26G1025' => 'fan', 'FAN26G2860' => 'fan', 'FAN27G1329' => 'fan', 'FAN27G3392' => 'fan', 'FvH4_1g02011' => 'fve', 'FvH4_1g06511' => 'fve', 'FvH4_2g19900' => 'fve', 'FvH4_2g19920' => 'fve', 'FvH4_2g24261' => 'fve', 'FvH4_2g24270' => 'fve', 'FvH4_2g24631' => 'fve', 'FvH4_2g30622' => 'fve', 'FvH4_3g12920' => 'fve', 'FvH4_3g30171' => 'fve', 'FvH4_3g35490' => 'fve', 'FvH4_3g43682' => 'fve', 'FvH4_3g43730' => 'fve', 'FvH4_3g43732' => 'fve', 'FvH4_3g43751' => 'fve', 'FvH4_3g43752' => 'fve', 'FvH4_3g43770' => 'fve', 'FvH4_3g44471' => 'fve', 'FvH4_3g44510' => 'fve', 'FvH4_3g44582' => 'fve', 'FvH4_4g16921' => 'fve', 'FvH4_4g17121' => 'fve', 'FvH4_4g17782' => 'fve', 'FvH4_4g17783' => 'fve', 'FvH4_4g18120' => 'fve', 'FvH4_4g31310' => 'fve', 'FvH4_4g35052' => 'fve', 'FvH4_5g30862' => 'fve', 'FvH4_6g01541' => 'fve', 'FvH4_6g02021' => 'fve', 'FvH4_6g02041' => 'fve', 'FvH4_6g02071' => 'fve', 'FvH4_6g02171' => 'fve', 'FvH4_6g03181' => 'fve', 'FvH4_6g03182' => 'fve', 'FvH4_6g03221' => 'fve', 'FvH4_6g03380' => 'fve', 'FvH4_6g05201' => 'fve', 'FvH4_6g05203' => 'fve', 'FvH4_6g20231' => 'fve', 'FvH4_6g31981' => 'fve', 'FvH4_6g32061' => 'fve', 'FvH4_6g37041' => 'fve', 'FvH4_6g37932' => 'fve', 'FvH4_6g38731' => 'fve', 'FvH4_6g39370' => 'fve', 'FvH4_6g39371' => 'fve', 'FvH4_6g40891' => 'fve', 'FvH4_6g40892' => 'fve', 'FvH4_6g43143' => 'fve', 'FvH4_6g45251' => 'fve', 'FvH4_6g45260' => 'fve', 'FvH4_6g45291' => 'fve', 'FvH4_6g45890' => 'fve', 'FvH4_6g46240' => 'fve', 'FvH4_6g46241' => 'fve', 'FvH4_6g46242' => 'fve', 'FvH4_6g46260' => 'fve', 'FvH4_6g46280' => 'fve', 'FvH4_6g46380' => 'fve', 'FvH4_7g12841' => 'fve', 'FvH4_7g31431' => 'fve', 'Glyma.09G075900' => 'gma', 'Gohir.A09G096401' => 'ghi', 'Gohir.D09G096101' => 'ghi', 'Gorai.006G112800' => 'gra', 'HanXRQChr04g0121411' => 'han', 'Hund15878' => 'sun', 'Lj2A1107G68' => 'lonja', 'Lj2A630G63' => 'lonja', 'Lj2A946T25' => 'lonja', 'Lj2C714T1' => 'lonja', 'Lj2C966T3' => 'lonja', 'Lj2C966T4' => 'lonja', 'Lj4g0002979' => 'lja', 'Lsat_1_v5_gn_5_30901' => 'lsa', 'Lsat_1_v5_gn_5_31100' => 'lsa', 'Lsat_1_v5_gn_5_38600' => 'lsa', 'Lsat_1_v5_gn_6_92061' => 'lsa', 'Manes.05G071301' => 'mes', 'MD02G1008700' => 'mdo', 'MD02G1008900' => 'mdo', 'MD03G1256400' => 'mdo', 'MD04G1180900' => 'mdo', 'MD04G1181000' => 'mdo', 'MD04G1181200' => 'mdo', 'MD05G1244200' => 'mdo', 'MD05G1324200' => 'mdo', 'MD09G1201600' => 'mdo', 'MD10G1000600' => 'mdo', 'MD14G1026900' => 'mdo', 'MD14G1187900' => 'mdo', 'MD15G1017800' => 'mdo', 'MD15G1018100' => 'mdo', 'Medtr4g124160' => 'mtr', 'Migut.L01260' => 'egut', 'Nitab4.5_0000008g0440' => 'nta', 'Nitab4.5_0000207g0170' => 'nta', 'Nitab4.5_0007671g0030' => 'nta', 'Nitab4.5_0010853g0020' => 'nta', 'Oeu057656.1' => 'oeu', 'PGSC0003DMG400005638' => 'stu', 'PGSC0003DMG400005639' => 'stu', 'Phvul.009G222800' => 'pvu', 'Potri.009G132400' => 'ptr', 'Potri.009G163001' => 'ptr', 'Potri.011G000700' => 'ptr', 'Potri.011G004800' => 'ptr', 'Prupe.1G509300' => 'ppe', 'Prupe.1G509700' => 'ppe', 'Prupe.1G510400' => 'ppe', 'Prupe.1G510700' => 'ppe', 'Prupe.1G512600' => 'ppe', 'Prupe.2G073200' => 'ppe', 'Prupe.3G059500' => 'ppe', 'Prupe.3G059600' => 'ppe', 'Prupe.3G246100' => 'ppe', 'Prupe.3G265100' => 'ppe', 'Prupe.4G034700' => 'ppe', 'Prupe.4G052100' => 'ppe', 'Prupe.4G053600' => 'ppe', 'Prupe.5G068800' => 'ppe', 'Prupe.5G070600' => 'ppe', 'Prupe.6G075400' => 'ppe', 'Prupe.6G075500' => 'ppe', 'Prupe.6G076400' => 'ppe', 'Prupe.8G110700' => 'ppe', 'Psat4g020960' => 'psa', 'PSO135G0788' => 'pso', 'PSO210G6463' => 'pso', 'PSO384G0370' => 'pso', 'PSO386G0056' => 'pso', 'QL01p006048' => 'qlo', 'QL02p054283' => 'qlo', 'QL05p008000' => 'qlo', 'QL05p008212' => 'qlo', 'QL05p008950' => 'qlo', 'QL05p009042' => 'qlo', 'QL05p009518' => 'qlo', 'QL05p012589' => 'qlo', 'QL05p012608' => 'qlo', 'QL05p012650' => 'qlo', 'QL05p012667' => 'qlo', 'QL05p014501' => 'qlo', 'QL05p052800' => 'qlo', 'QL05p065010' => 'qlo', 'QL05p074156' => 'qlo', 'QL05p074160' => 'qlo', 'QL05p074174' => 'qlo', 'QL05p074178' => 'qlo', 'QL05p074214' => 'qlo', 'QL06p001050' => 'qlo', 'QL06p001056' => 'qlo', 'QL06p006093' => 'qlo', 'QL06p006111' => 'qlo', 'QL07p019784' => 'qlo', 'QL07p019801' => 'qlo', 'QL07p036110' => 'qlo', 'QL07p036134' => 'qlo', 'QL07p036147' => 'qlo', 'QL07p036156' => 'qlo', 'QL07p036300' => 'qlo', 'QL07p036320' => 'qlo', 'QL08p014547' => 'qlo', 'QL08p014551' => 'qlo', 'QL08p043319' => 'qlo', 'QL08p043324' => 'qlo', 'QL11p009094' => 'qlo', 'RcHm_v2.0_Chr1g0380481' => 'rch', 'RcHm_v2.0_Chr2g0089331' => 'rch', 'RcHm_v2.0_Chr2g0123691' => 'rch', 'RcHm_v2.0_Chr2g0151111' => 'rch', 'RcHm_v2.0_Chr2g0163011' => 'rch', 'RcHm_v2.0_Chr2g0163051' => 'rch', 'RcHm_v2.0_Chr2g0164671' => 'rch', 'RcHm_v2.0_Chr2g0164681' => 'rch', 'RcHm_v2.0_Chr2g0164721' => 'rch', 'RcHm_v2.0_Chr3g0449911' => 'rch', 'RcHm_v2.0_Chr3g0450211' => 'rch', 'RcHm_v2.0_Chr3g0457271' => 'rch', 'RcHm_v2.0_Chr5g0018111' => 'rch', 'RcHm_v2.0_Chr5g0021011' => 'rch', 'RcHm_v2.0_Chr5g0081171' => 'rch', 'RcHm_v2.0_Chr5g0081211' => 'rch', 'RcHm_v2.0_Chr6g0275871' => 'rch', 'RcHm_v2.0_Chr6g0276071' => 'rch', 'RcHm_v2.0_Chr6g0285591' => 'rch', 'RcHm_v2.0_Chr6g0291931' => 'rch', 'RcHm_v2.0_Chr6g0292091' => 'rch', 'RcHm_v2.0_Chr6g0292271' => 'rch', 'RcHm_v2.0_Chr7g0221261' => 'rch', 'Rhsim08G0219900' => 'rsi', 'Rhsim08G0220200' => 'rsi', 'Rhsim08G0237800' => 'rsi', 'Rhsim08G0238800' => 'rsi', 'Sabra09G0102700' => 'sbr', 'Sabra09G0127200' => 'sbr', 'Sabra11G0003700' => 'sbr', 'Sabra15G0014700' => 'sbr', 'Sc19g0000590' => 'sci', 'Sc19g0001870' => 'sci', 'SGA_v2.0_scaffold1G00346' => 'sas', 'SGA_v2.0_scaffold1G00575' => 'sas', 'SGA_v2.0_scaffold1G00761' => 'sas', 'SGA_v2.0_scaffold232G43501' => 'sas', 'TAR625G1137' => 'tar', 'Thecc.03G222100' => 'tca', 'TPR.G12691' => 'tpr', 'TWI34G0727' => 'twi', 'TWI36G0117' => 'twi', 'VMungo1309G0868' => 'vmu' ), 'gf_id' => 'HOM05D001729', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001729' ), 'data_identifier' => 'HOM05D001729', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001729', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '375', 'num_species' => '42' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'Ah.07g204710' => 'amhyb', 'AUR62006001' => 'cqu', 'AUR62006002' => 'cqu', 'AUR62006003' => 'cqu', 'AUR62015641' => 'cqu', 'AUR62027174' => 'cqu', 'AUR62035623' => 'cqu', 'AUR62035624' => 'cqu', 'AUR62035625' => 'cqu', 'AUR62035626' => 'cqu', 'CAN.G1110.53' => 'can', 'CANSAT80G0415' => 'cansat', 'Ca_21364_v3' => 'car', 'COL.COLO4_30693' => 'col', 'COL.COLO4_30694' => 'col', 'COL.COLO4_30695' => 'col', 'COL.COLO4_30696' => 'col', 'COL.COLO4_34020' => 'col', 'DCAR_004585' => 'dca', 'Dinv04029' => 'din', 'Dinv34857' => 'din', 'Duzib147G0011' => 'dzi', 'Duzib170G0599' => 'dzi', 'Duzib192G1051' => 'dzi', 'FAN01G0708' => 'fan', 'FAN01G0742' => 'fan', 'FAN02G0048' => 'fan', 'FAN02G0583' => 'fan', 'FAN02G0688' => 'fan', 'FAN02G1588' => 'fan', 'FAN02G2194' => 'fan', 'FAN02G2750' => 'fan', 'FAN02G3094' => 'fan', 'FAN02G3887' => 'fan', 'FAN02G3911' => 'fan', 'FAN02G3994' => 'fan', 'FAN02G4432' => 'fan', 'FAN02G4556' => 'fan', 'FAN03G1977' => 'fan', 'FAN03G2781' => 'fan', 'FAN03G2850' => 'fan', 'FAN03G3155' => 'fan', 'FAN04G2487' => 'fan', 'FAN05G0208' => 'fan', 'FAN05G0656' => 'fan', 'FAN05G0696' => 'fan', 'FAN05G0810' => 'fan', 'FAN05G1447' => 'fan', 'FAN05G2640' => 'fan', 'FAN05G2911' => 'fan', 'FAN05G3901' => 'fan', 'FAN05G4859' => 'fan', 'FAN05G4861' => 'fan', 'FAN05G4988' => 'fan', 'FAN05G5187' => 'fan', 'FAN05G5452' => 'fan', 'FAN05G5500' => 'fan', 'FAN05G5688' => 'fan', 'FAN06G0177' => 'fan', 'FAN06G0675' => 'fan', 'FAN06G1290' => 'fan', 'FAN06G2191' => 'fan', 'FAN06G2405' => 'fan', 'FAN06G3231' => 'fan', 'FAN06G3932' => 'fan', 'FAN07G0163' => 'fan', 'FAN07G0471' => 'fan', 'FAN07G1354' => 'fan', 'FAN08G0338' => 'fan', 'FAN08G1373' => 'fan', 'FAN08G2539' => 'fan', 'FAN08G2728' => 'fan', 'FAN09G0608' => 'fan', 'FAN09G1136' => 'fan', 'FAN09G1958' => 'fan', 'FAN09G2508' => 'fan', 'FAN09G2597' => 'fan', 'FAN09G2658' => 'fan', 'FAN09G2757' => 'fan', 'FAN09G2983' => 'fan', 'FAN09G3130' => 'fan', 'FAN09G3565' => 'fan', 'FAN09G3613' => 'fan', 'FAN09G4011' => 'fan', 'FAN09G4239' => 'fan', 'FAN09G4277' => 'fan', 'FAN09G4720' => 'fan', 'FAN11G0139' => 'fan', 'FAN11G1727' => 'fan', 'FAN11G2672' => 'fan', 'FAN11G2795' => 'fan', 'FAN11G3238' => 'fan', 'FAN11G3734' => 'fan', 'FAN12G0631' => 'fan', 'FAN12G2239' => 'fan', 'FAN12G2308' => 'fan', 'FAN12G2569' => 'fan', 'FAN12G2623' => 'fan', 'FAN13G3182' => 'fan', 'FAN14G0053' => 'fan', 'FAN14G0370' => 'fan', 'FAN14G0382' => 'fan', 'FAN14G0421' => 'fan', 'FAN14G0866' => 'fan', 'FAN14G1187' => 'fan', 'FAN14G1727' => 'fan', 'FAN14G1791' => 'fan', 'FAN14G2361' => 'fan', 'FAN14G2668' => 'fan', 'FAN14G2770' => 'fan', 'FAN14G2874' => 'fan', 'FAN14G3193' => 'fan', 'FAN14G3624' => 'fan', 'FAN14G3676' => 'fan', 'FAN14G3807' => 'fan', 'FAN14G4082' => 'fan', 'FAN14G4342' => 'fan', 'FAN14G4985' => 'fan', 'FAN14G5126' => 'fan', 'FAN14G5781' => 'fan', 'FAN14G5808' => 'fan', 'FAN14G5949' => 'fan', 'FAN15G0828' => 'fan', 'FAN15G1054' => 'fan', 'FAN15G2023' => 'fan', 'FAN15G2506' => 'fan', 'FAN16G0128' => 'fan', 'FAN16G0249' => 'fan', 'FAN16G0429' => 'fan', 'FAN16G1493' => 'fan', 'FAN16G2210' => 'fan', 'FAN16G2506' => 'fan', 'FAN18G1542' => 'fan', 'FAN18G4057' => 'fan', 'FAN19G0745' => 'fan', 'FAN19G1216' => 'fan', 'FAN19G1733' => 'fan', 'FAN20G0258' => 'fan', 'FAN20G1095' => 'fan', 'FAN20G1557' => 'fan', 'FAN21G0302' => 'fan', 'FAN21G0519' => 'fan', 'FAN21G0970' => 'fan', 'FAN21G1159' => 'fan', 'FAN21G1312' => 'fan', 'FAN21G1440' => 'fan', 'FAN21G1715' => 'fan', 'FAN23G1584' => 'fan', 'FAN24G0045' => 'fan', 'FAN24G0053' => 'fan', 'FAN24G1500' => 'fan', 'FAN24G1817' => 'fan', 'FAN24G2147' => 'fan', 'FAN24G2236' => 'fan', 'FAN24G2446' => 'fan', 'FAN24G2684' => 'fan', 'FAN25G0187' => 'fan', 'FAN25G0505' => 'fan', 'FAN25G0589' => 'fan', 'FAN25G3663' => 'fan', 'FAN26G1025' => 'fan', 'FAN26G2860' => 'fan', 'FAN27G1329' => 'fan', 'FAN27G3392' => 'fan', 'FvH4_1g02011' => 'fve', 'FvH4_1g06511' => 'fve', 'FvH4_2g19900' => 'fve', 'FvH4_2g19920' => 'fve', 'FvH4_2g24261' => 'fve', 'FvH4_2g24270' => 'fve', 'FvH4_2g24631' => 'fve', 'FvH4_2g30622' => 'fve', 'FvH4_3g12920' => 'fve', 'FvH4_3g30171' => 'fve', 'FvH4_3g35490' => 'fve', 'FvH4_3g43682' => 'fve', 'FvH4_3g43730' => 'fve', 'FvH4_3g43732' => 'fve', 'FvH4_3g43751' => 'fve', 'FvH4_3g43752' => 'fve', 'FvH4_3g43770' => 'fve', 'FvH4_3g44471' => 'fve', 'FvH4_3g44510' => 'fve', 'FvH4_3g44582' => 'fve', 'FvH4_4g16921' => 'fve', 'FvH4_4g17121' => 'fve', 'FvH4_4g17782' => 'fve', 'FvH4_4g17783' => 'fve', 'FvH4_4g18120' => 'fve', 'FvH4_4g31310' => 'fve', 'FvH4_4g35052' => 'fve', 'FvH4_5g30862' => 'fve', 'FvH4_6g01541' => 'fve', 'FvH4_6g02021' => 'fve', 'FvH4_6g02041' => 'fve', 'FvH4_6g02071' => 'fve', 'FvH4_6g02171' => 'fve', 'FvH4_6g03181' => 'fve', 'FvH4_6g03182' => 'fve', 'FvH4_6g03221' => 'fve', 'FvH4_6g03380' => 'fve', 'FvH4_6g05201' => 'fve', 'FvH4_6g05203' => 'fve', 'FvH4_6g20231' => 'fve', 'FvH4_6g31981' => 'fve', 'FvH4_6g32061' => 'fve', 'FvH4_6g37041' => 'fve', 'FvH4_6g37932' => 'fve', 'FvH4_6g38731' => 'fve', 'FvH4_6g39370' => 'fve', 'FvH4_6g39371' => 'fve', 'FvH4_6g40891' => 'fve', 'FvH4_6g40892' => 'fve', 'FvH4_6g43143' => 'fve', 'FvH4_6g45251' => 'fve', 'FvH4_6g45260' => 'fve', 'FvH4_6g45291' => 'fve', 'FvH4_6g45890' => 'fve', 'FvH4_6g46240' => 'fve', 'FvH4_6g46241' => 'fve', 'FvH4_6g46242' => 'fve', 'FvH4_6g46260' => 'fve', 'FvH4_6g46280' => 'fve', 'FvH4_6g46380' => 'fve', 'FvH4_7g12841' => 'fve', 'FvH4_7g31431' => 'fve', 'Glyma.09G075900' => 'gma', 'Gohir.A09G096401' => 'ghi', 'Gohir.D09G096101' => 'ghi', 'Gorai.006G112800' => 'gra', 'HanXRQChr04g0121411' => 'han', 'Hund15878' => 'sun', 'Lj2A1107G68' => 'lonja', 'Lj2A630G63' => 'lonja', 'Lj2A946T25' => 'lonja', 'Lj2C714T1' => 'lonja', 'Lj2C966T3' => 'lonja', 'Lj2C966T4' => 'lonja', 'Lj4g0002979' => 'lja', 'Lsat_1_v5_gn_5_30901' => 'lsa', 'Lsat_1_v5_gn_5_31100' => 'lsa', 'Lsat_1_v5_gn_5_38600' => 'lsa', 'Lsat_1_v5_gn_6_92061' => 'lsa', 'Manes.05G071301' => 'mes', 'MD02G1008700' => 'mdo', 'MD02G1008900' => 'mdo', 'MD03G1256400' => 'mdo', 'MD04G1180900' => 'mdo', 'MD04G1181000' => 'mdo', 'MD04G1181200' => 'mdo', 'MD05G1244200' => 'mdo', 'MD05G1324200' => 'mdo', 'MD09G1201600' => 'mdo', 'MD10G1000600' => 'mdo', 'MD14G1026900' => 'mdo', 'MD14G1187900' => 'mdo', 'MD15G1017800' => 'mdo', 'MD15G1018100' => 'mdo', 'Medtr4g124160' => 'mtr', 'Migut.L01260' => 'egut', 'Nitab4.5_0000008g0440' => 'nta', 'Nitab4.5_0000207g0170' => 'nta', 'Nitab4.5_0007671g0030' => 'nta', 'Nitab4.5_0010853g0020' => 'nta', 'Oeu057656.1' => 'oeu', 'PGSC0003DMG400005638' => 'stu', 'PGSC0003DMG400005639' => 'stu', 'Phvul.009G222800' => 'pvu', 'Potri.009G132400' => 'ptr', 'Potri.009G163001' => 'ptr', 'Potri.011G000700' => 'ptr', 'Potri.011G004800' => 'ptr', 'Prupe.1G509300' => 'ppe', 'Prupe.1G509700' => 'ppe', 'Prupe.1G510400' => 'ppe', 'Prupe.1G510700' => 'ppe', 'Prupe.1G512600' => 'ppe', 'Prupe.2G073200' => 'ppe', 'Prupe.3G059500' => 'ppe', 'Prupe.3G059600' => 'ppe', 'Prupe.3G246100' => 'ppe', 'Prupe.3G265100' => 'ppe', 'Prupe.4G034700' => 'ppe', 'Prupe.4G052100' => 'ppe', 'Prupe.4G053600' => 'ppe', 'Prupe.5G068800' => 'ppe', 'Prupe.5G070600' => 'ppe', 'Prupe.6G075400' => 'ppe', 'Prupe.6G075500' => 'ppe', 'Prupe.6G076400' => 'ppe', 'Prupe.8G110700' => 'ppe', 'Psat4g020960' => 'psa', 'PSO135G0788' => 'pso', 'PSO210G6463' => 'pso', 'PSO384G0370' => 'pso', 'PSO386G0056' => 'pso', 'QL01p006048' => 'qlo', 'QL02p054283' => 'qlo', 'QL05p008000' => 'qlo', 'QL05p008212' => 'qlo', 'QL05p008950' => 'qlo', 'QL05p009042' => 'qlo', 'QL05p009518' => 'qlo', 'QL05p012589' => 'qlo', 'QL05p012608' => 'qlo', 'QL05p012650' => 'qlo', 'QL05p012667' => 'qlo', 'QL05p014501' => 'qlo', 'QL05p052800' => 'qlo', 'QL05p065010' => 'qlo', 'QL05p074156' => 'qlo', 'QL05p074160' => 'qlo', 'QL05p074174' => 'qlo', 'QL05p074178' => 'qlo', 'QL05p074214' => 'qlo', 'QL06p001050' => 'qlo', 'QL06p001056' => 'qlo', 'QL06p006093' => 'qlo', 'QL06p006111' => 'qlo', 'QL07p019784' => 'qlo', 'QL07p019801' => 'qlo', 'QL07p036110' => 'qlo', 'QL07p036134' => 'qlo', 'QL07p036147' => 'qlo', 'QL07p036156' => 'qlo', 'QL07p036300' => 'qlo', 'QL07p036320' => 'qlo', 'QL08p014547' => 'qlo', 'QL08p014551' => 'qlo', 'QL08p043319' => 'qlo', 'QL08p043324' => 'qlo', 'QL11p009094' => 'qlo', 'RcHm_v2.0_Chr1g0380481' => 'rch', 'RcHm_v2.0_Chr2g0089331' => 'rch', 'RcHm_v2.0_Chr2g0123691' => 'rch', 'RcHm_v2.0_Chr2g0151111' => 'rch', 'RcHm_v2.0_Chr2g0163011' => 'rch', 'RcHm_v2.0_Chr2g0163051' => 'rch', 'RcHm_v2.0_Chr2g0164671' => 'rch', 'RcHm_v2.0_Chr2g0164681' => 'rch', 'RcHm_v2.0_Chr2g0164721' => 'rch', 'RcHm_v2.0_Chr3g0449911' => 'rch', 'RcHm_v2.0_Chr3g0450211' => 'rch', 'RcHm_v2.0_Chr3g0457271' => 'rch', 'RcHm_v2.0_Chr5g0018111' => 'rch', 'RcHm_v2.0_Chr5g0021011' => 'rch', 'RcHm_v2.0_Chr5g0081171' => 'rch', 'RcHm_v2.0_Chr5g0081211' => 'rch', 'RcHm_v2.0_Chr6g0275871' => 'rch', 'RcHm_v2.0_Chr6g0276071' => 'rch', 'RcHm_v2.0_Chr6g0285591' => 'rch', 'RcHm_v2.0_Chr6g0291931' => 'rch', 'RcHm_v2.0_Chr6g0292091' => 'rch', 'RcHm_v2.0_Chr6g0292271' => 'rch', 'RcHm_v2.0_Chr7g0221261' => 'rch', 'Rhsim08G0219900' => 'rsi', 'Rhsim08G0220200' => 'rsi', 'Rhsim08G0237800' => 'rsi', 'Rhsim08G0238800' => 'rsi', 'Sabra09G0102700' => 'sbr', 'Sabra09G0127200' => 'sbr', 'Sabra11G0003700' => 'sbr', 'Sabra15G0014700' => 'sbr', 'Sc19g0000590' => 'sci', 'Sc19g0001870' => 'sci', 'SGA_v2.0_scaffold1G00346' => 'sas', 'SGA_v2.0_scaffold1G00575' => 'sas', 'SGA_v2.0_scaffold1G00761' => 'sas', 'SGA_v2.0_scaffold232G43501' => 'sas', 'TAR625G1137' => 'tar', 'Thecc.03G222100' => 'tca', 'TPR.G12691' => 'tpr', 'TWI34G0727' => 'twi', 'TWI36G0117' => 'twi', 'VMungo1309G0868' => 'vmu' ) $gf_id = 'HOM05D001729' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001729' ) $data_identifier = 'HOM05D001729' $data_type = 'gf_id' $species_gene_counts = array( 'amhyb' => (int) 1, 'cqu' => (int) 9, 'can' => (int) 1, 'cansat' => (int) 1, 'car' => (int) 1, 'col' => (int) 5, 'dca' => (int) 1, 'din' => (int) 2, 'dzi' => (int) 3, 'fan' => (int) 140, 'fve' => (int) 62, 'gma' => (int) 1, 'ghi' => (int) 2, 'gra' => (int) 1, 'han' => (int) 1, 'sun' => (int) 1, 'lonja' => (int) 6, 'lja' => (int) 1, 'lsa' => (int) 4, 'mes' => (int) 1, 'mdo' => (int) 14, 'mtr' => (int) 1, 'egut' => (int) 1, 'nta' => (int) 4, 'oeu' => (int) 1, 'stu' => (int) 2, 'pvu' => (int) 1, 'ptr' => (int) 4, 'ppe' => (int) 19, 'psa' => (int) 1, 'pso' => (int) 4, 'qlo' => (int) 36, 'rch' => (int) 23, 'rsi' => (int) 4, 'sbr' => (int) 4, 'sci' => (int) 2, 'sas' => (int) 4, 'tar' => (int) 1, 'tca' => (int) 1, 'tpr' => (int) 1, 'twi' => (int) 2, 'vmu' => (int) 1 ) $gf_gene_species = 'vmu' $gf_gene_id = 'VMungo1309G0868' $species_info = array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ) $local_species = 'pvu' $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' => 'HOM05D001729', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '375', 'num_species' => '42' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'Ah.07g204710' => 'amhyb', 'AUR62006001' => 'cqu', 'AUR62006002' => 'cqu', 'AUR62006003' => 'cqu', 'AUR62015641' => 'cqu', 'AUR62027174' => 'cqu', 'AUR62035623' => 'cqu', 'AUR62035624' => 'cqu', 'AUR62035625' => 'cqu', 'AUR62035626' => 'cqu', 'CAN.G1110.53' => 'can', 'CANSAT80G0415' => 'cansat', 'Ca_21364_v3' => 'car', 'COL.COLO4_30693' => 'col', 'COL.COLO4_30694' => 'col', 'COL.COLO4_30695' => 'col', 'COL.COLO4_30696' => 'col', 'COL.COLO4_34020' => 'col', 'DCAR_004585' => 'dca', 'Dinv04029' => 'din', 'Dinv34857' => 'din', 'Duzib147G0011' => 'dzi', 'Duzib170G0599' => 'dzi', 'Duzib192G1051' => 'dzi', 'FAN01G0708' => 'fan', 'FAN01G0742' => 'fan', 'FAN02G0048' => 'fan', 'FAN02G0583' => 'fan', 'FAN02G0688' => 'fan', 'FAN02G1588' => 'fan', 'FAN02G2194' => 'fan', 'FAN02G2750' => 'fan', 'FAN02G3094' => 'fan', 'FAN02G3887' => 'fan', 'FAN02G3911' => 'fan', 'FAN02G3994' => 'fan', 'FAN02G4432' => 'fan', 'FAN02G4556' => 'fan', 'FAN03G1977' => 'fan', 'FAN03G2781' => 'fan', 'FAN03G2850' => 'fan', 'FAN03G3155' => 'fan', 'FAN04G2487' => 'fan', 'FAN05G0208' => 'fan', 'FAN05G0656' => 'fan', 'FAN05G0696' => 'fan', 'FAN05G0810' => 'fan', 'FAN05G1447' => 'fan', 'FAN05G2640' => 'fan', 'FAN05G2911' => 'fan', 'FAN05G3901' => 'fan', 'FAN05G4859' => 'fan', 'FAN05G4861' => 'fan', 'FAN05G4988' => 'fan', 'FAN05G5187' => 'fan', 'FAN05G5452' => 'fan', 'FAN05G5500' => 'fan', 'FAN05G5688' => 'fan', 'FAN06G0177' => 'fan', 'FAN06G0675' => 'fan', 'FAN06G1290' => 'fan', 'FAN06G2191' => 'fan', 'FAN06G2405' => 'fan', 'FAN06G3231' => 'fan', 'FAN06G3932' => 'fan', 'FAN07G0163' => 'fan', 'FAN07G0471' => 'fan', 'FAN07G1354' => 'fan', 'FAN08G0338' => 'fan', 'FAN08G1373' => 'fan', 'FAN08G2539' => 'fan', 'FAN08G2728' => 'fan', 'FAN09G0608' => 'fan', 'FAN09G1136' => 'fan', 'FAN09G1958' => 'fan', 'FAN09G2508' => 'fan', 'FAN09G2597' => 'fan', 'FAN09G2658' => 'fan', 'FAN09G2757' => 'fan', 'FAN09G2983' => 'fan', 'FAN09G3130' => 'fan', 'FAN09G3565' => 'fan', 'FAN09G3613' => 'fan', 'FAN09G4011' => 'fan', 'FAN09G4239' => 'fan', 'FAN09G4277' => 'fan', 'FAN09G4720' => 'fan', 'FAN11G0139' => 'fan', 'FAN11G1727' => 'fan', 'FAN11G2672' => 'fan', 'FAN11G2795' => 'fan', 'FAN11G3238' => 'fan', 'FAN11G3734' => 'fan', 'FAN12G0631' => 'fan', 'FAN12G2239' => 'fan', 'FAN12G2308' => 'fan', 'FAN12G2569' => 'fan', 'FAN12G2623' => 'fan', 'FAN13G3182' => 'fan', 'FAN14G0053' => 'fan', 'FAN14G0370' => 'fan', 'FAN14G0382' => 'fan', 'FAN14G0421' => 'fan', 'FAN14G0866' => 'fan', 'FAN14G1187' => 'fan', 'FAN14G1727' => 'fan', 'FAN14G1791' => 'fan', 'FAN14G2361' => 'fan', 'FAN14G2668' => 'fan', 'FAN14G2770' => 'fan', 'FAN14G2874' => 'fan', 'FAN14G3193' => 'fan', 'FAN14G3624' => 'fan', 'FAN14G3676' => 'fan', 'FAN14G3807' => 'fan', 'FAN14G4082' => 'fan', 'FAN14G4342' => 'fan', 'FAN14G4985' => 'fan', 'FAN14G5126' => 'fan', 'FAN14G5781' => 'fan', 'FAN14G5808' => 'fan', 'FAN14G5949' => 'fan', 'FAN15G0828' => 'fan', 'FAN15G1054' => 'fan', 'FAN15G2023' => 'fan', 'FAN15G2506' => 'fan', 'FAN16G0128' => 'fan', 'FAN16G0249' => 'fan', 'FAN16G0429' => 'fan', 'FAN16G1493' => 'fan', 'FAN16G2210' => 'fan', 'FAN16G2506' => 'fan', 'FAN18G1542' => 'fan', 'FAN18G4057' => 'fan', 'FAN19G0745' => 'fan', 'FAN19G1216' => 'fan', 'FAN19G1733' => 'fan', 'FAN20G0258' => 'fan', 'FAN20G1095' => 'fan', 'FAN20G1557' => 'fan', 'FAN21G0302' => 'fan', 'FAN21G0519' => 'fan', 'FAN21G0970' => 'fan', 'FAN21G1159' => 'fan', 'FAN21G1312' => 'fan', 'FAN21G1440' => 'fan', 'FAN21G1715' => 'fan', 'FAN23G1584' => 'fan', 'FAN24G0045' => 'fan', 'FAN24G0053' => 'fan', 'FAN24G1500' => 'fan', 'FAN24G1817' => 'fan', 'FAN24G2147' => 'fan', 'FAN24G2236' => 'fan', 'FAN24G2446' => 'fan', 'FAN24G2684' => 'fan', 'FAN25G0187' => 'fan', 'FAN25G0505' => 'fan', 'FAN25G0589' => 'fan', 'FAN25G3663' => 'fan', 'FAN26G1025' => 'fan', 'FAN26G2860' => 'fan', 'FAN27G1329' => 'fan', 'FAN27G3392' => 'fan', 'FvH4_1g02011' => 'fve', 'FvH4_1g06511' => 'fve', 'FvH4_2g19900' => 'fve', 'FvH4_2g19920' => 'fve', 'FvH4_2g24261' => 'fve', 'FvH4_2g24270' => 'fve', 'FvH4_2g24631' => 'fve', 'FvH4_2g30622' => 'fve', 'FvH4_3g12920' => 'fve', 'FvH4_3g30171' => 'fve', 'FvH4_3g35490' => 'fve', 'FvH4_3g43682' => 'fve', 'FvH4_3g43730' => 'fve', 'FvH4_3g43732' => 'fve', 'FvH4_3g43751' => 'fve', 'FvH4_3g43752' => 'fve', 'FvH4_3g43770' => 'fve', 'FvH4_3g44471' => 'fve', 'FvH4_3g44510' => 'fve', 'FvH4_3g44582' => 'fve', 'FvH4_4g16921' => 'fve', 'FvH4_4g17121' => 'fve', 'FvH4_4g17782' => 'fve', 'FvH4_4g17783' => 'fve', 'FvH4_4g18120' => 'fve', 'FvH4_4g31310' => 'fve', 'FvH4_4g35052' => 'fve', 'FvH4_5g30862' => 'fve', 'FvH4_6g01541' => 'fve', 'FvH4_6g02021' => 'fve', 'FvH4_6g02041' => 'fve', 'FvH4_6g02071' => 'fve', 'FvH4_6g02171' => 'fve', 'FvH4_6g03181' => 'fve', 'FvH4_6g03182' => 'fve', 'FvH4_6g03221' => 'fve', 'FvH4_6g03380' => 'fve', 'FvH4_6g05201' => 'fve', 'FvH4_6g05203' => 'fve', 'FvH4_6g20231' => 'fve', 'FvH4_6g31981' => 'fve', 'FvH4_6g32061' => 'fve', 'FvH4_6g37041' => 'fve', 'FvH4_6g37932' => 'fve', 'FvH4_6g38731' => 'fve', 'FvH4_6g39370' => 'fve', 'FvH4_6g39371' => 'fve', 'FvH4_6g40891' => 'fve', 'FvH4_6g40892' => 'fve', 'FvH4_6g43143' => 'fve', 'FvH4_6g45251' => 'fve', 'FvH4_6g45260' => 'fve', 'FvH4_6g45291' => 'fve', 'FvH4_6g45890' => 'fve', 'FvH4_6g46240' => 'fve', 'FvH4_6g46241' => 'fve', 'FvH4_6g46242' => 'fve', 'FvH4_6g46260' => 'fve', 'FvH4_6g46280' => 'fve', 'FvH4_6g46380' => 'fve', 'FvH4_7g12841' => 'fve', 'FvH4_7g31431' => 'fve', 'Glyma.09G075900' => 'gma', 'Gohir.A09G096401' => 'ghi', 'Gohir.D09G096101' => 'ghi', 'Gorai.006G112800' => 'gra', 'HanXRQChr04g0121411' => 'han', 'Hund15878' => 'sun', 'Lj2A1107G68' => 'lonja', 'Lj2A630G63' => 'lonja', 'Lj2A946T25' => 'lonja', 'Lj2C714T1' => 'lonja', 'Lj2C966T3' => 'lonja', 'Lj2C966T4' => 'lonja', 'Lj4g0002979' => 'lja', 'Lsat_1_v5_gn_5_30901' => 'lsa', 'Lsat_1_v5_gn_5_31100' => 'lsa', 'Lsat_1_v5_gn_5_38600' => 'lsa', 'Lsat_1_v5_gn_6_92061' => 'lsa', 'Manes.05G071301' => 'mes', 'MD02G1008700' => 'mdo', 'MD02G1008900' => 'mdo', 'MD03G1256400' => 'mdo', 'MD04G1180900' => 'mdo', 'MD04G1181000' => 'mdo', 'MD04G1181200' => 'mdo', 'MD05G1244200' => 'mdo', 'MD05G1324200' => 'mdo', 'MD09G1201600' => 'mdo', 'MD10G1000600' => 'mdo', 'MD14G1026900' => 'mdo', 'MD14G1187900' => 'mdo', 'MD15G1017800' => 'mdo', 'MD15G1018100' => 'mdo', 'Medtr4g124160' => 'mtr', 'Migut.L01260' => 'egut', 'Nitab4.5_0000008g0440' => 'nta', 'Nitab4.5_0000207g0170' => 'nta', 'Nitab4.5_0007671g0030' => 'nta', 'Nitab4.5_0010853g0020' => 'nta', 'Oeu057656.1' => 'oeu', 'PGSC0003DMG400005638' => 'stu', 'PGSC0003DMG400005639' => 'stu', 'Phvul.009G222800' => 'pvu', 'Potri.009G132400' => 'ptr', 'Potri.009G163001' => 'ptr', 'Potri.011G000700' => 'ptr', 'Potri.011G004800' => 'ptr', 'Prupe.1G509300' => 'ppe', 'Prupe.1G509700' => 'ppe', 'Prupe.1G510400' => 'ppe', 'Prupe.1G510700' => 'ppe', 'Prupe.1G512600' => 'ppe', 'Prupe.2G073200' => 'ppe', 'Prupe.3G059500' => 'ppe', 'Prupe.3G059600' => 'ppe', 'Prupe.3G246100' => 'ppe', 'Prupe.3G265100' => 'ppe', 'Prupe.4G034700' => 'ppe', 'Prupe.4G052100' => 'ppe', 'Prupe.4G053600' => 'ppe', 'Prupe.5G068800' => 'ppe', 'Prupe.5G070600' => 'ppe', 'Prupe.6G075400' => 'ppe', 'Prupe.6G075500' => 'ppe', 'Prupe.6G076400' => 'ppe', 'Prupe.8G110700' => 'ppe', 'Psat4g020960' => 'psa', 'PSO135G0788' => 'pso', 'PSO210G6463' => 'pso', 'PSO384G0370' => 'pso', 'PSO386G0056' => 'pso', 'QL01p006048' => 'qlo', 'QL02p054283' => 'qlo', 'QL05p008000' => 'qlo', 'QL05p008212' => 'qlo', 'QL05p008950' => 'qlo', 'QL05p009042' => 'qlo', 'QL05p009518' => 'qlo', 'QL05p012589' => 'qlo', 'QL05p012608' => 'qlo', 'QL05p012650' => 'qlo', 'QL05p012667' => 'qlo', 'QL05p014501' => 'qlo', 'QL05p052800' => 'qlo', 'QL05p065010' => 'qlo', 'QL05p074156' => 'qlo', 'QL05p074160' => 'qlo', 'QL05p074174' => 'qlo', 'QL05p074178' => 'qlo', 'QL05p074214' => 'qlo', 'QL06p001050' => 'qlo', 'QL06p001056' => 'qlo', 'QL06p006093' => 'qlo', 'QL06p006111' => 'qlo', 'QL07p019784' => 'qlo', 'QL07p019801' => 'qlo', 'QL07p036110' => 'qlo', 'QL07p036134' => 'qlo', 'QL07p036147' => 'qlo', 'QL07p036156' => 'qlo', 'QL07p036300' => 'qlo', 'QL07p036320' => 'qlo', 'QL08p014547' => 'qlo', 'QL08p014551' => 'qlo', 'QL08p043319' => 'qlo', 'QL08p043324' => 'qlo', 'QL11p009094' => 'qlo', 'RcHm_v2.0_Chr1g0380481' => 'rch', 'RcHm_v2.0_Chr2g0089331' => 'rch', 'RcHm_v2.0_Chr2g0123691' => 'rch', 'RcHm_v2.0_Chr2g0151111' => 'rch', 'RcHm_v2.0_Chr2g0163011' => 'rch', 'RcHm_v2.0_Chr2g0163051' => 'rch', 'RcHm_v2.0_Chr2g0164671' => 'rch', 'RcHm_v2.0_Chr2g0164681' => 'rch', 'RcHm_v2.0_Chr2g0164721' => 'rch', 'RcHm_v2.0_Chr3g0449911' => 'rch', 'RcHm_v2.0_Chr3g0450211' => 'rch', 'RcHm_v2.0_Chr3g0457271' => 'rch', 'RcHm_v2.0_Chr5g0018111' => 'rch', 'RcHm_v2.0_Chr5g0021011' => 'rch', 'RcHm_v2.0_Chr5g0081171' => 'rch', 'RcHm_v2.0_Chr5g0081211' => 'rch', 'RcHm_v2.0_Chr6g0275871' => 'rch', 'RcHm_v2.0_Chr6g0276071' => 'rch', 'RcHm_v2.0_Chr6g0285591' => 'rch', 'RcHm_v2.0_Chr6g0291931' => 'rch', 'RcHm_v2.0_Chr6g0292091' => 'rch', 'RcHm_v2.0_Chr6g0292271' => 'rch', 'RcHm_v2.0_Chr7g0221261' => 'rch', 'Rhsim08G0219900' => 'rsi', 'Rhsim08G0220200' => 'rsi', 'Rhsim08G0237800' => 'rsi', 'Rhsim08G0238800' => 'rsi', 'Sabra09G0102700' => 'sbr', 'Sabra09G0127200' => 'sbr', 'Sabra11G0003700' => 'sbr', 'Sabra15G0014700' => 'sbr', 'Sc19g0000590' => 'sci', 'Sc19g0001870' => 'sci', 'SGA_v2.0_scaffold1G00346' => 'sas', 'SGA_v2.0_scaffold1G00575' => 'sas', 'SGA_v2.0_scaffold1G00761' => 'sas', 'SGA_v2.0_scaffold232G43501' => 'sas', 'TAR625G1137' => 'tar', 'Thecc.03G222100' => 'tca', 'TPR.G12691' => 'tpr', 'TWI34G0727' => 'twi', 'TWI36G0117' => 'twi', 'VMungo1309G0868' => 'vmu' ), 'gf_id' => 'HOM05D001729', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001729' ), 'data_identifier' => 'HOM05D001729', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001729', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '375', 'num_species' => '42' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'Ah.07g204710' => 'amhyb', 'AUR62006001' => 'cqu', 'AUR62006002' => 'cqu', 'AUR62006003' => 'cqu', 'AUR62015641' => 'cqu', 'AUR62027174' => 'cqu', 'AUR62035623' => 'cqu', 'AUR62035624' => 'cqu', 'AUR62035625' => 'cqu', 'AUR62035626' => 'cqu', 'CAN.G1110.53' => 'can', 'CANSAT80G0415' => 'cansat', 'Ca_21364_v3' => 'car', 'COL.COLO4_30693' => 'col', 'COL.COLO4_30694' => 'col', 'COL.COLO4_30695' => 'col', 'COL.COLO4_30696' => 'col', 'COL.COLO4_34020' => 'col', 'DCAR_004585' => 'dca', 'Dinv04029' => 'din', 'Dinv34857' => 'din', 'Duzib147G0011' => 'dzi', 'Duzib170G0599' => 'dzi', 'Duzib192G1051' => 'dzi', 'FAN01G0708' => 'fan', 'FAN01G0742' => 'fan', 'FAN02G0048' => 'fan', 'FAN02G0583' => 'fan', 'FAN02G0688' => 'fan', 'FAN02G1588' => 'fan', 'FAN02G2194' => 'fan', 'FAN02G2750' => 'fan', 'FAN02G3094' => 'fan', 'FAN02G3887' => 'fan', 'FAN02G3911' => 'fan', 'FAN02G3994' => 'fan', 'FAN02G4432' => 'fan', 'FAN02G4556' => 'fan', 'FAN03G1977' => 'fan', 'FAN03G2781' => 'fan', 'FAN03G2850' => 'fan', 'FAN03G3155' => 'fan', 'FAN04G2487' => 'fan', 'FAN05G0208' => 'fan', 'FAN05G0656' => 'fan', 'FAN05G0696' => 'fan', 'FAN05G0810' => 'fan', 'FAN05G1447' => 'fan', 'FAN05G2640' => 'fan', 'FAN05G2911' => 'fan', 'FAN05G3901' => 'fan', 'FAN05G4859' => 'fan', 'FAN05G4861' => 'fan', 'FAN05G4988' => 'fan', 'FAN05G5187' => 'fan', 'FAN05G5452' => 'fan', 'FAN05G5500' => 'fan', 'FAN05G5688' => 'fan', 'FAN06G0177' => 'fan', 'FAN06G0675' => 'fan', 'FAN06G1290' => 'fan', 'FAN06G2191' => 'fan', 'FAN06G2405' => 'fan', 'FAN06G3231' => 'fan', 'FAN06G3932' => 'fan', 'FAN07G0163' => 'fan', 'FAN07G0471' => 'fan', 'FAN07G1354' => 'fan', 'FAN08G0338' => 'fan', 'FAN08G1373' => 'fan', 'FAN08G2539' => 'fan', 'FAN08G2728' => 'fan', 'FAN09G0608' => 'fan', 'FAN09G1136' => 'fan', 'FAN09G1958' => 'fan', 'FAN09G2508' => 'fan', 'FAN09G2597' => 'fan', 'FAN09G2658' => 'fan', 'FAN09G2757' => 'fan', 'FAN09G2983' => 'fan', 'FAN09G3130' => 'fan', 'FAN09G3565' => 'fan', 'FAN09G3613' => 'fan', 'FAN09G4011' => 'fan', 'FAN09G4239' => 'fan', 'FAN09G4277' => 'fan', 'FAN09G4720' => 'fan', 'FAN11G0139' => 'fan', 'FAN11G1727' => 'fan', 'FAN11G2672' => 'fan', 'FAN11G2795' => 'fan', 'FAN11G3238' => 'fan', 'FAN11G3734' => 'fan', 'FAN12G0631' => 'fan', 'FAN12G2239' => 'fan', 'FAN12G2308' => 'fan', 'FAN12G2569' => 'fan', 'FAN12G2623' => 'fan', 'FAN13G3182' => 'fan', 'FAN14G0053' => 'fan', 'FAN14G0370' => 'fan', 'FAN14G0382' => 'fan', 'FAN14G0421' => 'fan', 'FAN14G0866' => 'fan', 'FAN14G1187' => 'fan', 'FAN14G1727' => 'fan', 'FAN14G1791' => 'fan', 'FAN14G2361' => 'fan', 'FAN14G2668' => 'fan', 'FAN14G2770' => 'fan', 'FAN14G2874' => 'fan', 'FAN14G3193' => 'fan', 'FAN14G3624' => 'fan', 'FAN14G3676' => 'fan', 'FAN14G3807' => 'fan', 'FAN14G4082' => 'fan', 'FAN14G4342' => 'fan', 'FAN14G4985' => 'fan', 'FAN14G5126' => 'fan', 'FAN14G5781' => 'fan', 'FAN14G5808' => 'fan', 'FAN14G5949' => 'fan', 'FAN15G0828' => 'fan', 'FAN15G1054' => 'fan', 'FAN15G2023' => 'fan', 'FAN15G2506' => 'fan', 'FAN16G0128' => 'fan', 'FAN16G0249' => 'fan', 'FAN16G0429' => 'fan', 'FAN16G1493' => 'fan', 'FAN16G2210' => 'fan', 'FAN16G2506' => 'fan', 'FAN18G1542' => 'fan', 'FAN18G4057' => 'fan', 'FAN19G0745' => 'fan', 'FAN19G1216' => 'fan', 'FAN19G1733' => 'fan', 'FAN20G0258' => 'fan', 'FAN20G1095' => 'fan', 'FAN20G1557' => 'fan', 'FAN21G0302' => 'fan', 'FAN21G0519' => 'fan', 'FAN21G0970' => 'fan', 'FAN21G1159' => 'fan', 'FAN21G1312' => 'fan', 'FAN21G1440' => 'fan', 'FAN21G1715' => 'fan', 'FAN23G1584' => 'fan', 'FAN24G0045' => 'fan', 'FAN24G0053' => 'fan', 'FAN24G1500' => 'fan', 'FAN24G1817' => 'fan', 'FAN24G2147' => 'fan', 'FAN24G2236' => 'fan', 'FAN24G2446' => 'fan', 'FAN24G2684' => 'fan', 'FAN25G0187' => 'fan', 'FAN25G0505' => 'fan', 'FAN25G0589' => 'fan', 'FAN25G3663' => 'fan', 'FAN26G1025' => 'fan', 'FAN26G2860' => 'fan', 'FAN27G1329' => 'fan', 'FAN27G3392' => 'fan', 'FvH4_1g02011' => 'fve', 'FvH4_1g06511' => 'fve', 'FvH4_2g19900' => 'fve', 'FvH4_2g19920' => 'fve', 'FvH4_2g24261' => 'fve', 'FvH4_2g24270' => 'fve', 'FvH4_2g24631' => 'fve', 'FvH4_2g30622' => 'fve', 'FvH4_3g12920' => 'fve', 'FvH4_3g30171' => 'fve', 'FvH4_3g35490' => 'fve', 'FvH4_3g43682' => 'fve', 'FvH4_3g43730' => 'fve', 'FvH4_3g43732' => 'fve', 'FvH4_3g43751' => 'fve', 'FvH4_3g43752' => 'fve', 'FvH4_3g43770' => 'fve', 'FvH4_3g44471' => 'fve', 'FvH4_3g44510' => 'fve', 'FvH4_3g44582' => 'fve', 'FvH4_4g16921' => 'fve', 'FvH4_4g17121' => 'fve', 'FvH4_4g17782' => 'fve', 'FvH4_4g17783' => 'fve', 'FvH4_4g18120' => 'fve', 'FvH4_4g31310' => 'fve', 'FvH4_4g35052' => 'fve', 'FvH4_5g30862' => 'fve', 'FvH4_6g01541' => 'fve', 'FvH4_6g02021' => 'fve', 'FvH4_6g02041' => 'fve', 'FvH4_6g02071' => 'fve', 'FvH4_6g02171' => 'fve', 'FvH4_6g03181' => 'fve', 'FvH4_6g03182' => 'fve', 'FvH4_6g03221' => 'fve', 'FvH4_6g03380' => 'fve', 'FvH4_6g05201' => 'fve', 'FvH4_6g05203' => 'fve', 'FvH4_6g20231' => 'fve', 'FvH4_6g31981' => 'fve', 'FvH4_6g32061' => 'fve', 'FvH4_6g37041' => 'fve', 'FvH4_6g37932' => 'fve', 'FvH4_6g38731' => 'fve', 'FvH4_6g39370' => 'fve', 'FvH4_6g39371' => 'fve', 'FvH4_6g40891' => 'fve', 'FvH4_6g40892' => 'fve', 'FvH4_6g43143' => 'fve', 'FvH4_6g45251' => 'fve', 'FvH4_6g45260' => 'fve', 'FvH4_6g45291' => 'fve', 'FvH4_6g45890' => 'fve', 'FvH4_6g46240' => 'fve', 'FvH4_6g46241' => 'fve', 'FvH4_6g46242' => 'fve', 'FvH4_6g46260' => 'fve', 'FvH4_6g46280' => 'fve', 'FvH4_6g46380' => 'fve', 'FvH4_7g12841' => 'fve', 'FvH4_7g31431' => 'fve', 'Glyma.09G075900' => 'gma', 'Gohir.A09G096401' => 'ghi', 'Gohir.D09G096101' => 'ghi', 'Gorai.006G112800' => 'gra', 'HanXRQChr04g0121411' => 'han', 'Hund15878' => 'sun', 'Lj2A1107G68' => 'lonja', 'Lj2A630G63' => 'lonja', 'Lj2A946T25' => 'lonja', 'Lj2C714T1' => 'lonja', 'Lj2C966T3' => 'lonja', 'Lj2C966T4' => 'lonja', 'Lj4g0002979' => 'lja', 'Lsat_1_v5_gn_5_30901' => 'lsa', 'Lsat_1_v5_gn_5_31100' => 'lsa', 'Lsat_1_v5_gn_5_38600' => 'lsa', 'Lsat_1_v5_gn_6_92061' => 'lsa', 'Manes.05G071301' => 'mes', 'MD02G1008700' => 'mdo', 'MD02G1008900' => 'mdo', 'MD03G1256400' => 'mdo', 'MD04G1180900' => 'mdo', 'MD04G1181000' => 'mdo', 'MD04G1181200' => 'mdo', 'MD05G1244200' => 'mdo', 'MD05G1324200' => 'mdo', 'MD09G1201600' => 'mdo', 'MD10G1000600' => 'mdo', 'MD14G1026900' => 'mdo', 'MD14G1187900' => 'mdo', 'MD15G1017800' => 'mdo', 'MD15G1018100' => 'mdo', 'Medtr4g124160' => 'mtr', 'Migut.L01260' => 'egut', 'Nitab4.5_0000008g0440' => 'nta', 'Nitab4.5_0000207g0170' => 'nta', 'Nitab4.5_0007671g0030' => 'nta', 'Nitab4.5_0010853g0020' => 'nta', 'Oeu057656.1' => 'oeu', 'PGSC0003DMG400005638' => 'stu', 'PGSC0003DMG400005639' => 'stu', 'Phvul.009G222800' => 'pvu', 'Potri.009G132400' => 'ptr', 'Potri.009G163001' => 'ptr', 'Potri.011G000700' => 'ptr', 'Potri.011G004800' => 'ptr', 'Prupe.1G509300' => 'ppe', 'Prupe.1G509700' => 'ppe', 'Prupe.1G510400' => 'ppe', 'Prupe.1G510700' => 'ppe', 'Prupe.1G512600' => 'ppe', 'Prupe.2G073200' => 'ppe', 'Prupe.3G059500' => 'ppe', 'Prupe.3G059600' => 'ppe', 'Prupe.3G246100' => 'ppe', 'Prupe.3G265100' => 'ppe', 'Prupe.4G034700' => 'ppe', 'Prupe.4G052100' => 'ppe', 'Prupe.4G053600' => 'ppe', 'Prupe.5G068800' => 'ppe', 'Prupe.5G070600' => 'ppe', 'Prupe.6G075400' => 'ppe', 'Prupe.6G075500' => 'ppe', 'Prupe.6G076400' => 'ppe', 'Prupe.8G110700' => 'ppe', 'Psat4g020960' => 'psa', 'PSO135G0788' => 'pso', 'PSO210G6463' => 'pso', 'PSO384G0370' => 'pso', 'PSO386G0056' => 'pso', 'QL01p006048' => 'qlo', 'QL02p054283' => 'qlo', 'QL05p008000' => 'qlo', 'QL05p008212' => 'qlo', 'QL05p008950' => 'qlo', 'QL05p009042' => 'qlo', 'QL05p009518' => 'qlo', 'QL05p012589' => 'qlo', 'QL05p012608' => 'qlo', 'QL05p012650' => 'qlo', 'QL05p012667' => 'qlo', 'QL05p014501' => 'qlo', 'QL05p052800' => 'qlo', 'QL05p065010' => 'qlo', 'QL05p074156' => 'qlo', 'QL05p074160' => 'qlo', 'QL05p074174' => 'qlo', 'QL05p074178' => 'qlo', 'QL05p074214' => 'qlo', 'QL06p001050' => 'qlo', 'QL06p001056' => 'qlo', 'QL06p006093' => 'qlo', 'QL06p006111' => 'qlo', 'QL07p019784' => 'qlo', 'QL07p019801' => 'qlo', 'QL07p036110' => 'qlo', 'QL07p036134' => 'qlo', 'QL07p036147' => 'qlo', 'QL07p036156' => 'qlo', 'QL07p036300' => 'qlo', 'QL07p036320' => 'qlo', 'QL08p014547' => 'qlo', 'QL08p014551' => 'qlo', 'QL08p043319' => 'qlo', 'QL08p043324' => 'qlo', 'QL11p009094' => 'qlo', 'RcHm_v2.0_Chr1g0380481' => 'rch', 'RcHm_v2.0_Chr2g0089331' => 'rch', 'RcHm_v2.0_Chr2g0123691' => 'rch', 'RcHm_v2.0_Chr2g0151111' => 'rch', 'RcHm_v2.0_Chr2g0163011' => 'rch', 'RcHm_v2.0_Chr2g0163051' => 'rch', 'RcHm_v2.0_Chr2g0164671' => 'rch', 'RcHm_v2.0_Chr2g0164681' => 'rch', 'RcHm_v2.0_Chr2g0164721' => 'rch', 'RcHm_v2.0_Chr3g0449911' => 'rch', 'RcHm_v2.0_Chr3g0450211' => 'rch', 'RcHm_v2.0_Chr3g0457271' => 'rch', 'RcHm_v2.0_Chr5g0018111' => 'rch', 'RcHm_v2.0_Chr5g0021011' => 'rch', 'RcHm_v2.0_Chr5g0081171' => 'rch', 'RcHm_v2.0_Chr5g0081211' => 'rch', 'RcHm_v2.0_Chr6g0275871' => 'rch', 'RcHm_v2.0_Chr6g0276071' => 'rch', 'RcHm_v2.0_Chr6g0285591' => 'rch', 'RcHm_v2.0_Chr6g0291931' => 'rch', 'RcHm_v2.0_Chr6g0292091' => 'rch', 'RcHm_v2.0_Chr6g0292271' => 'rch', 'RcHm_v2.0_Chr7g0221261' => 'rch', 'Rhsim08G0219900' => 'rsi', 'Rhsim08G0220200' => 'rsi', 'Rhsim08G0237800' => 'rsi', 'Rhsim08G0238800' => 'rsi', 'Sabra09G0102700' => 'sbr', 'Sabra09G0127200' => 'sbr', 'Sabra11G0003700' => 'sbr', 'Sabra15G0014700' => 'sbr', 'Sc19g0000590' => 'sci', 'Sc19g0001870' => 'sci', 'SGA_v2.0_scaffold1G00346' => 'sas', 'SGA_v2.0_scaffold1G00575' => 'sas', 'SGA_v2.0_scaffold1G00761' => 'sas', 'SGA_v2.0_scaffold232G43501' => 'sas', 'TAR625G1137' => 'tar', 'Thecc.03G222100' => 'tca', 'TPR.G12691' => 'tpr', 'TWI34G0727' => 'twi', 'TWI36G0117' => 'twi', 'VMungo1309G0868' => 'vmu' ) $gf_id = 'HOM05D001729' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001729' ) $data_identifier = 'HOM05D001729' $data_type = 'gf_id' $species_gene_counts = array( 'amhyb' => (int) 1, 'cqu' => (int) 9, 'can' => (int) 1, 'cansat' => (int) 1, 'car' => (int) 1, 'col' => (int) 5, 'dca' => (int) 1, 'din' => (int) 2, 'dzi' => (int) 3, 'fan' => (int) 140, 'fve' => (int) 62, 'gma' => (int) 1, 'ghi' => (int) 2, 'gra' => (int) 1, 'han' => (int) 1, 'sun' => (int) 1, 'lonja' => (int) 6, 'lja' => (int) 1, 'lsa' => (int) 4, 'mes' => (int) 1, 'mdo' => (int) 14, 'mtr' => (int) 1, 'egut' => (int) 1, 'nta' => (int) 4, 'oeu' => (int) 1, 'stu' => (int) 2, 'pvu' => (int) 1, 'ptr' => (int) 4, 'ppe' => (int) 19, 'psa' => (int) 1, 'pso' => (int) 4, 'qlo' => (int) 36, 'rch' => (int) 23, 'rsi' => (int) 4, 'sbr' => (int) 4, 'sci' => (int) 2, 'sas' => (int) 4, 'tar' => (int) 1, 'tca' => (int) 1, 'tpr' => (int) 1, 'twi' => (int) 2, 'vmu' => (int) 1 ) $gf_gene_species = 'vmu' $gf_gene_id = 'VMungo1309G0868' $species_info = array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ) $local_species = 'psa' $disabled = '' $selected = '' $num_hits = (int) 0include - APP/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp, line 33 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933 View::_renderElement() - CORE/Cake/View/View.php, line 1224 View::element() - CORE/Cake/View/View.php, line 418 include - APP/View/Elements/analysis/phylogenetics_module/gf_data_settings.ctp, line 37 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933 View::_renderElement() - CORE/Cake/View/View.php, line 1224 View::element() - CORE/Cake/View/View.php, line 418 include - APP/View/Elements/analysis/phylogenetics_module/parameter_selection.ctp, line 64 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933 View::_renderElement() - CORE/Cake/View/View.php, line 1224 View::element() - CORE/Cake/View/View.php, line 418 include - APP/View/Analysis/custom_tree_creation.ctp, line 27 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933
$viewFile = '/www/bioinformatics01_ro/plaza/_dev_instances/feedback/app/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp' $dataForView = array( 'sidebar_info' => array( 'gf_id' => 'HOM05D001729', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '375', 'num_species' => '42' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'Ah.07g204710' => 'amhyb', 'AUR62006001' => 'cqu', 'AUR62006002' => 'cqu', 'AUR62006003' => 'cqu', 'AUR62015641' => 'cqu', 'AUR62027174' => 'cqu', 'AUR62035623' => 'cqu', 'AUR62035624' => 'cqu', 'AUR62035625' => 'cqu', 'AUR62035626' => 'cqu', 'CAN.G1110.53' => 'can', 'CANSAT80G0415' => 'cansat', 'Ca_21364_v3' => 'car', 'COL.COLO4_30693' => 'col', 'COL.COLO4_30694' => 'col', 'COL.COLO4_30695' => 'col', 'COL.COLO4_30696' => 'col', 'COL.COLO4_34020' => 'col', 'DCAR_004585' => 'dca', 'Dinv04029' => 'din', 'Dinv34857' => 'din', 'Duzib147G0011' => 'dzi', 'Duzib170G0599' => 'dzi', 'Duzib192G1051' => 'dzi', 'FAN01G0708' => 'fan', 'FAN01G0742' => 'fan', 'FAN02G0048' => 'fan', 'FAN02G0583' => 'fan', 'FAN02G0688' => 'fan', 'FAN02G1588' => 'fan', 'FAN02G2194' => 'fan', 'FAN02G2750' => 'fan', 'FAN02G3094' => 'fan', 'FAN02G3887' => 'fan', 'FAN02G3911' => 'fan', 'FAN02G3994' => 'fan', 'FAN02G4432' => 'fan', 'FAN02G4556' => 'fan', 'FAN03G1977' => 'fan', 'FAN03G2781' => 'fan', 'FAN03G2850' => 'fan', 'FAN03G3155' => 'fan', 'FAN04G2487' => 'fan', 'FAN05G0208' => 'fan', 'FAN05G0656' => 'fan', 'FAN05G0696' => 'fan', 'FAN05G0810' => 'fan', 'FAN05G1447' => 'fan', 'FAN05G2640' => 'fan', 'FAN05G2911' => 'fan', 'FAN05G3901' => 'fan', 'FAN05G4859' => 'fan', 'FAN05G4861' => 'fan', 'FAN05G4988' => 'fan', 'FAN05G5187' => 'fan', 'FAN05G5452' => 'fan', 'FAN05G5500' => 'fan', 'FAN05G5688' => 'fan', 'FAN06G0177' => 'fan', 'FAN06G0675' => 'fan', 'FAN06G1290' => 'fan', 'FAN06G2191' => 'fan', 'FAN06G2405' => 'fan', 'FAN06G3231' => 'fan', 'FAN06G3932' => 'fan', 'FAN07G0163' => 'fan', 'FAN07G0471' => 'fan', 'FAN07G1354' => 'fan', 'FAN08G0338' => 'fan', 'FAN08G1373' => 'fan', 'FAN08G2539' => 'fan', 'FAN08G2728' => 'fan', 'FAN09G0608' => 'fan', 'FAN09G1136' => 'fan', 'FAN09G1958' => 'fan', 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'FAN14G5126' => 'fan', 'FAN14G5781' => 'fan', 'FAN14G5808' => 'fan', 'FAN14G5949' => 'fan', 'FAN15G0828' => 'fan', 'FAN15G1054' => 'fan', 'FAN15G2023' => 'fan', 'FAN15G2506' => 'fan', 'FAN16G0128' => 'fan', 'FAN16G0249' => 'fan', 'FAN16G0429' => 'fan', 'FAN16G1493' => 'fan', 'FAN16G2210' => 'fan', 'FAN16G2506' => 'fan', 'FAN18G1542' => 'fan', 'FAN18G4057' => 'fan', 'FAN19G0745' => 'fan', 'FAN19G1216' => 'fan', 'FAN19G1733' => 'fan', 'FAN20G0258' => 'fan', 'FAN20G1095' => 'fan', 'FAN20G1557' => 'fan', 'FAN21G0302' => 'fan', 'FAN21G0519' => 'fan', 'FAN21G0970' => 'fan', 'FAN21G1159' => 'fan', 'FAN21G1312' => 'fan', 'FAN21G1440' => 'fan', 'FAN21G1715' => 'fan', 'FAN23G1584' => 'fan', 'FAN24G0045' => 'fan', 'FAN24G0053' => 'fan', 'FAN24G1500' => 'fan', 'FAN24G1817' => 'fan', 'FAN24G2147' => 'fan', 'FAN24G2236' => 'fan', 'FAN24G2446' => 'fan', 'FAN24G2684' => 'fan', 'FAN25G0187' => 'fan', 'FAN25G0505' => 'fan', 'FAN25G0589' => 'fan', 'FAN25G3663' => 'fan', 'FAN26G1025' => 'fan', 'FAN26G2860' => 'fan', 'FAN27G1329' => 'fan', 'FAN27G3392' => 'fan', 'FvH4_1g02011' => 'fve', 'FvH4_1g06511' => 'fve', 'FvH4_2g19900' => 'fve', 'FvH4_2g19920' => 'fve', 'FvH4_2g24261' => 'fve', 'FvH4_2g24270' => 'fve', 'FvH4_2g24631' => 'fve', 'FvH4_2g30622' => 'fve', 'FvH4_3g12920' => 'fve', 'FvH4_3g30171' => 'fve', 'FvH4_3g35490' => 'fve', 'FvH4_3g43682' => 'fve', 'FvH4_3g43730' => 'fve', 'FvH4_3g43732' => 'fve', 'FvH4_3g43751' => 'fve', 'FvH4_3g43752' => 'fve', 'FvH4_3g43770' => 'fve', 'FvH4_3g44471' => 'fve', 'FvH4_3g44510' => 'fve', 'FvH4_3g44582' => 'fve', 'FvH4_4g16921' => 'fve', 'FvH4_4g17121' => 'fve', 'FvH4_4g17782' => 'fve', 'FvH4_4g17783' => 'fve', 'FvH4_4g18120' => 'fve', 'FvH4_4g31310' => 'fve', 'FvH4_4g35052' => 'fve', 'FvH4_5g30862' => 'fve', 'FvH4_6g01541' => 'fve', 'FvH4_6g02021' => 'fve', 'FvH4_6g02041' => 'fve', 'FvH4_6g02071' => 'fve', 'FvH4_6g02171' => 'fve', 'FvH4_6g03181' => 'fve', 'FvH4_6g03182' => 'fve', 'FvH4_6g03221' => 'fve', 'FvH4_6g03380' => 'fve', 'FvH4_6g05201' => 'fve', 'FvH4_6g05203' => 'fve', 'FvH4_6g20231' => 'fve', 'FvH4_6g31981' => 'fve', 'FvH4_6g32061' => 'fve', 'FvH4_6g37041' => 'fve', 'FvH4_6g37932' => 'fve', 'FvH4_6g38731' => 'fve', 'FvH4_6g39370' => 'fve', 'FvH4_6g39371' => 'fve', 'FvH4_6g40891' => 'fve', 'FvH4_6g40892' => 'fve', 'FvH4_6g43143' => 'fve', 'FvH4_6g45251' => 'fve', 'FvH4_6g45260' => 'fve', 'FvH4_6g45291' => 'fve', 'FvH4_6g45890' => 'fve', 'FvH4_6g46240' => 'fve', 'FvH4_6g46241' => 'fve', 'FvH4_6g46242' => 'fve', 'FvH4_6g46260' => 'fve', 'FvH4_6g46280' => 'fve', 'FvH4_6g46380' => 'fve', 'FvH4_7g12841' => 'fve', 'FvH4_7g31431' => 'fve', 'Glyma.09G075900' => 'gma', 'Gohir.A09G096401' => 'ghi', 'Gohir.D09G096101' => 'ghi', 'Gorai.006G112800' => 'gra', 'HanXRQChr04g0121411' => 'han', 'Hund15878' => 'sun', 'Lj2A1107G68' => 'lonja', 'Lj2A630G63' => 'lonja', 'Lj2A946T25' => 'lonja', 'Lj2C714T1' => 'lonja', 'Lj2C966T3' => 'lonja', 'Lj2C966T4' => 'lonja', 'Lj4g0002979' => 'lja', 'Lsat_1_v5_gn_5_30901' => 'lsa', 'Lsat_1_v5_gn_5_31100' => 'lsa', 'Lsat_1_v5_gn_5_38600' => 'lsa', 'Lsat_1_v5_gn_6_92061' => 'lsa', 'Manes.05G071301' => 'mes', 'MD02G1008700' => 'mdo', 'MD02G1008900' => 'mdo', 'MD03G1256400' => 'mdo', 'MD04G1180900' => 'mdo', 'MD04G1181000' => 'mdo', 'MD04G1181200' => 'mdo', 'MD05G1244200' => 'mdo', 'MD05G1324200' => 'mdo', 'MD09G1201600' => 'mdo', 'MD10G1000600' => 'mdo', 'MD14G1026900' => 'mdo', 'MD14G1187900' => 'mdo', 'MD15G1017800' => 'mdo', 'MD15G1018100' => 'mdo', 'Medtr4g124160' => 'mtr', 'Migut.L01260' => 'egut', 'Nitab4.5_0000008g0440' => 'nta', 'Nitab4.5_0000207g0170' => 'nta', 'Nitab4.5_0007671g0030' => 'nta', 'Nitab4.5_0010853g0020' => 'nta', 'Oeu057656.1' => 'oeu', 'PGSC0003DMG400005638' => 'stu', 'PGSC0003DMG400005639' => 'stu', 'Phvul.009G222800' => 'pvu', 'Potri.009G132400' => 'ptr', 'Potri.009G163001' => 'ptr', 'Potri.011G000700' => 'ptr', 'Potri.011G004800' => 'ptr', 'Prupe.1G509300' => 'ppe', 'Prupe.1G509700' => 'ppe', 'Prupe.1G510400' => 'ppe', 'Prupe.1G510700' => 'ppe', 'Prupe.1G512600' => 'ppe', 'Prupe.2G073200' => 'ppe', 'Prupe.3G059500' => 'ppe', 'Prupe.3G059600' => 'ppe', 'Prupe.3G246100' => 'ppe', 'Prupe.3G265100' => 'ppe', 'Prupe.4G034700' => 'ppe', 'Prupe.4G052100' => 'ppe', 'Prupe.4G053600' => 'ppe', 'Prupe.5G068800' => 'ppe', 'Prupe.5G070600' => 'ppe', 'Prupe.6G075400' => 'ppe', 'Prupe.6G075500' => 'ppe', 'Prupe.6G076400' => 'ppe', 'Prupe.8G110700' => 'ppe', 'Psat4g020960' => 'psa', 'PSO135G0788' => 'pso', 'PSO210G6463' => 'pso', 'PSO384G0370' => 'pso', 'PSO386G0056' => 'pso', 'QL01p006048' => 'qlo', 'QL02p054283' => 'qlo', 'QL05p008000' => 'qlo', 'QL05p008212' => 'qlo', 'QL05p008950' => 'qlo', 'QL05p009042' => 'qlo', 'QL05p009518' => 'qlo', 'QL05p012589' => 'qlo', 'QL05p012608' => 'qlo', 'QL05p012650' => 'qlo', 'QL05p012667' => 'qlo', 'QL05p014501' => 'qlo', 'QL05p052800' => 'qlo', 'QL05p065010' => 'qlo', 'QL05p074156' => 'qlo', 'QL05p074160' => 'qlo', 'QL05p074174' => 'qlo', 'QL05p074178' => 'qlo', 'QL05p074214' => 'qlo', 'QL06p001050' => 'qlo', 'QL06p001056' => 'qlo', 'QL06p006093' => 'qlo', 'QL06p006111' => 'qlo', 'QL07p019784' => 'qlo', 'QL07p019801' => 'qlo', 'QL07p036110' => 'qlo', 'QL07p036134' => 'qlo', 'QL07p036147' => 'qlo', 'QL07p036156' => 'qlo', 'QL07p036300' => 'qlo', 'QL07p036320' => 'qlo', 'QL08p014547' => 'qlo', 'QL08p014551' => 'qlo', 'QL08p043319' => 'qlo', 'QL08p043324' => 'qlo', 'QL11p009094' => 'qlo', 'RcHm_v2.0_Chr1g0380481' => 'rch', 'RcHm_v2.0_Chr2g0089331' => 'rch', 'RcHm_v2.0_Chr2g0123691' => 'rch', 'RcHm_v2.0_Chr2g0151111' => 'rch', 'RcHm_v2.0_Chr2g0163011' => 'rch', 'RcHm_v2.0_Chr2g0163051' => 'rch', 'RcHm_v2.0_Chr2g0164671' => 'rch', 'RcHm_v2.0_Chr2g0164681' => 'rch', 'RcHm_v2.0_Chr2g0164721' => 'rch', 'RcHm_v2.0_Chr3g0449911' => 'rch', 'RcHm_v2.0_Chr3g0450211' => 'rch', 'RcHm_v2.0_Chr3g0457271' => 'rch', 'RcHm_v2.0_Chr5g0018111' => 'rch', 'RcHm_v2.0_Chr5g0021011' => 'rch', 'RcHm_v2.0_Chr5g0081171' => 'rch', 'RcHm_v2.0_Chr5g0081211' => 'rch', 'RcHm_v2.0_Chr6g0275871' => 'rch', 'RcHm_v2.0_Chr6g0276071' => 'rch', 'RcHm_v2.0_Chr6g0285591' => 'rch', 'RcHm_v2.0_Chr6g0291931' => 'rch', 'RcHm_v2.0_Chr6g0292091' => 'rch', 'RcHm_v2.0_Chr6g0292271' => 'rch', 'RcHm_v2.0_Chr7g0221261' => 'rch', 'Rhsim08G0219900' => 'rsi', 'Rhsim08G0220200' => 'rsi', 'Rhsim08G0237800' => 'rsi', 'Rhsim08G0238800' => 'rsi', 'Sabra09G0102700' => 'sbr', 'Sabra09G0127200' => 'sbr', 'Sabra11G0003700' => 'sbr', 'Sabra15G0014700' => 'sbr', 'Sc19g0000590' => 'sci', 'Sc19g0001870' => 'sci', 'SGA_v2.0_scaffold1G00346' => 'sas', 'SGA_v2.0_scaffold1G00575' => 'sas', 'SGA_v2.0_scaffold1G00761' => 'sas', 'SGA_v2.0_scaffold232G43501' => 'sas', 'TAR625G1137' => 'tar', 'Thecc.03G222100' => 'tca', 'TPR.G12691' => 'tpr', 'TWI34G0727' => 'twi', 'TWI36G0117' => 'twi', 'VMungo1309G0868' => 'vmu' ), 'gf_id' => 'HOM05D001729', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001729' ), 'data_identifier' => 'HOM05D001729', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001729', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '375', 'num_species' => '42' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'Ah.07g204710' => 'amhyb', 'AUR62006001' => 'cqu', 'AUR62006002' => 'cqu', 'AUR62006003' => 'cqu', 'AUR62015641' => 'cqu', 'AUR62027174' => 'cqu', 'AUR62035623' => 'cqu', 'AUR62035624' => 'cqu', 'AUR62035625' => 'cqu', 'AUR62035626' => 'cqu', 'CAN.G1110.53' => 'can', 'CANSAT80G0415' => 'cansat', 'Ca_21364_v3' => 'car', 'COL.COLO4_30693' => 'col', 'COL.COLO4_30694' => 'col', 'COL.COLO4_30695' => 'col', 'COL.COLO4_30696' => 'col', 'COL.COLO4_34020' => 'col', 'DCAR_004585' => 'dca', 'Dinv04029' => 'din', 'Dinv34857' => 'din', 'Duzib147G0011' => 'dzi', 'Duzib170G0599' => 'dzi', 'Duzib192G1051' => 'dzi', 'FAN01G0708' => 'fan', 'FAN01G0742' => 'fan', 'FAN02G0048' => 'fan', 'FAN02G0583' => 'fan', 'FAN02G0688' => 'fan', 'FAN02G1588' => 'fan', 'FAN02G2194' => 'fan', 'FAN02G2750' => 'fan', 'FAN02G3094' => 'fan', 'FAN02G3887' => 'fan', 'FAN02G3911' => 'fan', 'FAN02G3994' => 'fan', 'FAN02G4432' => 'fan', 'FAN02G4556' => 'fan', 'FAN03G1977' => 'fan', 'FAN03G2781' => 'fan', 'FAN03G2850' => 'fan', 'FAN03G3155' => 'fan', 'FAN04G2487' => 'fan', 'FAN05G0208' => 'fan', 'FAN05G0656' => 'fan', 'FAN05G0696' => 'fan', 'FAN05G0810' => 'fan', 'FAN05G1447' => 'fan', 'FAN05G2640' => 'fan', 'FAN05G2911' => 'fan', 'FAN05G3901' => 'fan', 'FAN05G4859' => 'fan', 'FAN05G4861' => 'fan', 'FAN05G4988' => 'fan', 'FAN05G5187' => 'fan', 'FAN05G5452' => 'fan', 'FAN05G5500' => 'fan', 'FAN05G5688' => 'fan', 'FAN06G0177' => 'fan', 'FAN06G0675' => 'fan', 'FAN06G1290' => 'fan', 'FAN06G2191' => 'fan', 'FAN06G2405' => 'fan', 'FAN06G3231' => 'fan', 'FAN06G3932' => 'fan', 'FAN07G0163' => 'fan', 'FAN07G0471' => 'fan', 'FAN07G1354' => 'fan', 'FAN08G0338' => 'fan', 'FAN08G1373' => 'fan', 'FAN08G2539' => 'fan', 'FAN08G2728' => 'fan', 'FAN09G0608' => 'fan', 'FAN09G1136' => 'fan', 'FAN09G1958' => 'fan', 'FAN09G2508' => 'fan', 'FAN09G2597' => 'fan', 'FAN09G2658' => 'fan', 'FAN09G2757' => 'fan', 'FAN09G2983' => 'fan', 'FAN09G3130' => 'fan', 'FAN09G3565' => 'fan', 'FAN09G3613' => 'fan', 'FAN09G4011' => 'fan', 'FAN09G4239' => 'fan', 'FAN09G4277' => 'fan', 'FAN09G4720' => 'fan', 'FAN11G0139' => 'fan', 'FAN11G1727' => 'fan', 'FAN11G2672' => 'fan', 'FAN11G2795' => 'fan', 'FAN11G3238' => 'fan', 'FAN11G3734' => 'fan', 'FAN12G0631' => 'fan', 'FAN12G2239' => 'fan', 'FAN12G2308' => 'fan', 'FAN12G2569' => 'fan', 'FAN12G2623' => 'fan', 'FAN13G3182' => 'fan', 'FAN14G0053' => 'fan', 'FAN14G0370' => 'fan', 'FAN14G0382' => 'fan', 'FAN14G0421' => 'fan', 'FAN14G0866' => 'fan', 'FAN14G1187' => 'fan', 'FAN14G1727' => 'fan', 'FAN14G1791' => 'fan', 'FAN14G2361' => 'fan', 'FAN14G2668' => 'fan', 'FAN14G2770' => 'fan', 'FAN14G2874' => 'fan', 'FAN14G3193' => 'fan', 'FAN14G3624' => 'fan', 'FAN14G3676' => 'fan', 'FAN14G3807' => 'fan', 'FAN14G4082' => 'fan', 'FAN14G4342' => 'fan', 'FAN14G4985' => 'fan', 'FAN14G5126' => 'fan', 'FAN14G5781' => 'fan', 'FAN14G5808' => 'fan', 'FAN14G5949' => 'fan', 'FAN15G0828' => 'fan', 'FAN15G1054' => 'fan', 'FAN15G2023' => 'fan', 'FAN15G2506' => 'fan', 'FAN16G0128' => 'fan', 'FAN16G0249' => 'fan', 'FAN16G0429' => 'fan', 'FAN16G1493' => 'fan', 'FAN16G2210' => 'fan', 'FAN16G2506' => 'fan', 'FAN18G1542' => 'fan', 'FAN18G4057' => 'fan', 'FAN19G0745' => 'fan', 'FAN19G1216' => 'fan', 'FAN19G1733' => 'fan', 'FAN20G0258' => 'fan', 'FAN20G1095' => 'fan', 'FAN20G1557' => 'fan', 'FAN21G0302' => 'fan', 'FAN21G0519' => 'fan', 'FAN21G0970' => 'fan', 'FAN21G1159' => 'fan', 'FAN21G1312' => 'fan', 'FAN21G1440' => 'fan', 'FAN21G1715' => 'fan', 'FAN23G1584' => 'fan', 'FAN24G0045' => 'fan', 'FAN24G0053' => 'fan', 'FAN24G1500' => 'fan', 'FAN24G1817' => 'fan', 'FAN24G2147' => 'fan', 'FAN24G2236' => 'fan', 'FAN24G2446' => 'fan', 'FAN24G2684' => 'fan', 'FAN25G0187' => 'fan', 'FAN25G0505' => 'fan', 'FAN25G0589' => 'fan', 'FAN25G3663' => 'fan', 'FAN26G1025' => 'fan', 'FAN26G2860' => 'fan', 'FAN27G1329' => 'fan', 'FAN27G3392' => 'fan', 'FvH4_1g02011' => 'fve', 'FvH4_1g06511' => 'fve', 'FvH4_2g19900' => 'fve', 'FvH4_2g19920' => 'fve', 'FvH4_2g24261' => 'fve', 'FvH4_2g24270' => 'fve', 'FvH4_2g24631' => 'fve', 'FvH4_2g30622' => 'fve', 'FvH4_3g12920' => 'fve', 'FvH4_3g30171' => 'fve', 'FvH4_3g35490' => 'fve', 'FvH4_3g43682' => 'fve', 'FvH4_3g43730' => 'fve', 'FvH4_3g43732' => 'fve', 'FvH4_3g43751' => 'fve', 'FvH4_3g43752' => 'fve', 'FvH4_3g43770' => 'fve', 'FvH4_3g44471' => 'fve', 'FvH4_3g44510' => 'fve', 'FvH4_3g44582' => 'fve', 'FvH4_4g16921' => 'fve', 'FvH4_4g17121' => 'fve', 'FvH4_4g17782' => 'fve', 'FvH4_4g17783' => 'fve', 'FvH4_4g18120' => 'fve', 'FvH4_4g31310' => 'fve', 'FvH4_4g35052' => 'fve', 'FvH4_5g30862' => 'fve', 'FvH4_6g01541' => 'fve', 'FvH4_6g02021' => 'fve', 'FvH4_6g02041' => 'fve', 'FvH4_6g02071' => 'fve', 'FvH4_6g02171' => 'fve', 'FvH4_6g03181' => 'fve', 'FvH4_6g03182' => 'fve', 'FvH4_6g03221' => 'fve', 'FvH4_6g03380' => 'fve', 'FvH4_6g05201' => 'fve', 'FvH4_6g05203' => 'fve', 'FvH4_6g20231' => 'fve', 'FvH4_6g31981' => 'fve', 'FvH4_6g32061' => 'fve', 'FvH4_6g37041' => 'fve', 'FvH4_6g37932' => 'fve', 'FvH4_6g38731' => 'fve', 'FvH4_6g39370' => 'fve', 'FvH4_6g39371' => 'fve', 'FvH4_6g40891' => 'fve', 'FvH4_6g40892' => 'fve', 'FvH4_6g43143' => 'fve', 'FvH4_6g45251' => 'fve', 'FvH4_6g45260' => 'fve', 'FvH4_6g45291' => 'fve', 'FvH4_6g45890' => 'fve', 'FvH4_6g46240' => 'fve', 'FvH4_6g46241' => 'fve', 'FvH4_6g46242' => 'fve', 'FvH4_6g46260' => 'fve', 'FvH4_6g46280' => 'fve', 'FvH4_6g46380' => 'fve', 'FvH4_7g12841' => 'fve', 'FvH4_7g31431' => 'fve', 'Glyma.09G075900' => 'gma', 'Gohir.A09G096401' => 'ghi', 'Gohir.D09G096101' => 'ghi', 'Gorai.006G112800' => 'gra', 'HanXRQChr04g0121411' => 'han', 'Hund15878' => 'sun', 'Lj2A1107G68' => 'lonja', 'Lj2A630G63' => 'lonja', 'Lj2A946T25' => 'lonja', 'Lj2C714T1' => 'lonja', 'Lj2C966T3' => 'lonja', 'Lj2C966T4' => 'lonja', 'Lj4g0002979' => 'lja', 'Lsat_1_v5_gn_5_30901' => 'lsa', 'Lsat_1_v5_gn_5_31100' => 'lsa', 'Lsat_1_v5_gn_5_38600' => 'lsa', 'Lsat_1_v5_gn_6_92061' => 'lsa', 'Manes.05G071301' => 'mes', 'MD02G1008700' => 'mdo', 'MD02G1008900' => 'mdo', 'MD03G1256400' => 'mdo', 'MD04G1180900' => 'mdo', 'MD04G1181000' => 'mdo', 'MD04G1181200' => 'mdo', 'MD05G1244200' => 'mdo', 'MD05G1324200' => 'mdo', 'MD09G1201600' => 'mdo', 'MD10G1000600' => 'mdo', 'MD14G1026900' => 'mdo', 'MD14G1187900' => 'mdo', 'MD15G1017800' => 'mdo', 'MD15G1018100' => 'mdo', 'Medtr4g124160' => 'mtr', 'Migut.L01260' => 'egut', 'Nitab4.5_0000008g0440' => 'nta', 'Nitab4.5_0000207g0170' => 'nta', 'Nitab4.5_0007671g0030' => 'nta', 'Nitab4.5_0010853g0020' => 'nta', 'Oeu057656.1' => 'oeu', 'PGSC0003DMG400005638' => 'stu', 'PGSC0003DMG400005639' => 'stu', 'Phvul.009G222800' => 'pvu', 'Potri.009G132400' => 'ptr', 'Potri.009G163001' => 'ptr', 'Potri.011G000700' => 'ptr', 'Potri.011G004800' => 'ptr', 'Prupe.1G509300' => 'ppe', 'Prupe.1G509700' => 'ppe', 'Prupe.1G510400' => 'ppe', 'Prupe.1G510700' => 'ppe', 'Prupe.1G512600' => 'ppe', 'Prupe.2G073200' => 'ppe', 'Prupe.3G059500' => 'ppe', 'Prupe.3G059600' => 'ppe', 'Prupe.3G246100' => 'ppe', 'Prupe.3G265100' => 'ppe', 'Prupe.4G034700' => 'ppe', 'Prupe.4G052100' => 'ppe', 'Prupe.4G053600' => 'ppe', 'Prupe.5G068800' => 'ppe', 'Prupe.5G070600' => 'ppe', 'Prupe.6G075400' => 'ppe', 'Prupe.6G075500' => 'ppe', 'Prupe.6G076400' => 'ppe', 'Prupe.8G110700' => 'ppe', 'Psat4g020960' => 'psa', 'PSO135G0788' => 'pso', 'PSO210G6463' => 'pso', 'PSO384G0370' => 'pso', 'PSO386G0056' => 'pso', 'QL01p006048' => 'qlo', 'QL02p054283' => 'qlo', 'QL05p008000' => 'qlo', 'QL05p008212' => 'qlo', 'QL05p008950' => 'qlo', 'QL05p009042' => 'qlo', 'QL05p009518' => 'qlo', 'QL05p012589' => 'qlo', 'QL05p012608' => 'qlo', 'QL05p012650' => 'qlo', 'QL05p012667' => 'qlo', 'QL05p014501' => 'qlo', 'QL05p052800' => 'qlo', 'QL05p065010' => 'qlo', 'QL05p074156' => 'qlo', 'QL05p074160' => 'qlo', 'QL05p074174' => 'qlo', 'QL05p074178' => 'qlo', 'QL05p074214' => 'qlo', 'QL06p001050' => 'qlo', 'QL06p001056' => 'qlo', 'QL06p006093' => 'qlo', 'QL06p006111' => 'qlo', 'QL07p019784' => 'qlo', 'QL07p019801' => 'qlo', 'QL07p036110' => 'qlo', 'QL07p036134' => 'qlo', 'QL07p036147' => 'qlo', 'QL07p036156' => 'qlo', 'QL07p036300' => 'qlo', 'QL07p036320' => 'qlo', 'QL08p014547' => 'qlo', 'QL08p014551' => 'qlo', 'QL08p043319' => 'qlo', 'QL08p043324' => 'qlo', 'QL11p009094' => 'qlo', 'RcHm_v2.0_Chr1g0380481' => 'rch', 'RcHm_v2.0_Chr2g0089331' => 'rch', 'RcHm_v2.0_Chr2g0123691' => 'rch', 'RcHm_v2.0_Chr2g0151111' => 'rch', 'RcHm_v2.0_Chr2g0163011' => 'rch', 'RcHm_v2.0_Chr2g0163051' => 'rch', 'RcHm_v2.0_Chr2g0164671' => 'rch', 'RcHm_v2.0_Chr2g0164681' => 'rch', 'RcHm_v2.0_Chr2g0164721' => 'rch', 'RcHm_v2.0_Chr3g0449911' => 'rch', 'RcHm_v2.0_Chr3g0450211' => 'rch', 'RcHm_v2.0_Chr3g0457271' => 'rch', 'RcHm_v2.0_Chr5g0018111' => 'rch', 'RcHm_v2.0_Chr5g0021011' => 'rch', 'RcHm_v2.0_Chr5g0081171' => 'rch', 'RcHm_v2.0_Chr5g0081211' => 'rch', 'RcHm_v2.0_Chr6g0275871' => 'rch', 'RcHm_v2.0_Chr6g0276071' => 'rch', 'RcHm_v2.0_Chr6g0285591' => 'rch', 'RcHm_v2.0_Chr6g0291931' => 'rch', 'RcHm_v2.0_Chr6g0292091' => 'rch', 'RcHm_v2.0_Chr6g0292271' => 'rch', 'RcHm_v2.0_Chr7g0221261' => 'rch', 'Rhsim08G0219900' => 'rsi', 'Rhsim08G0220200' => 'rsi', 'Rhsim08G0237800' => 'rsi', 'Rhsim08G0238800' => 'rsi', 'Sabra09G0102700' => 'sbr', 'Sabra09G0127200' => 'sbr', 'Sabra11G0003700' => 'sbr', 'Sabra15G0014700' => 'sbr', 'Sc19g0000590' => 'sci', 'Sc19g0001870' => 'sci', 'SGA_v2.0_scaffold1G00346' => 'sas', 'SGA_v2.0_scaffold1G00575' => 'sas', 'SGA_v2.0_scaffold1G00761' => 'sas', 'SGA_v2.0_scaffold232G43501' => 'sas', 'TAR625G1137' => 'tar', 'Thecc.03G222100' => 'tca', 'TPR.G12691' => 'tpr', 'TWI34G0727' => 'twi', 'TWI36G0117' => 'twi', 'VMungo1309G0868' => 'vmu' ) $gf_id = 'HOM05D001729' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001729' ) $data_identifier = 'HOM05D001729' $data_type = 'gf_id' $species_gene_counts = array( 'amhyb' => (int) 1, 'cqu' => (int) 9, 'can' => (int) 1, 'cansat' => (int) 1, 'car' => (int) 1, 'col' => (int) 5, 'dca' => (int) 1, 'din' => (int) 2, 'dzi' => (int) 3, 'fan' => (int) 140, 'fve' => (int) 62, 'gma' => (int) 1, 'ghi' => (int) 2, 'gra' => (int) 1, 'han' => (int) 1, 'sun' => (int) 1, 'lonja' => (int) 6, 'lja' => (int) 1, 'lsa' => (int) 4, 'mes' => (int) 1, 'mdo' => (int) 14, 'mtr' => (int) 1, 'egut' => (int) 1, 'nta' => (int) 4, 'oeu' => (int) 1, 'stu' => (int) 2, 'pvu' => (int) 1, 'ptr' => (int) 4, 'ppe' => (int) 19, 'psa' => (int) 1, 'pso' => (int) 4, 'qlo' => (int) 36, 'rch' => (int) 23, 'rsi' => (int) 4, 'sbr' => (int) 4, 'sci' => (int) 2, 'sas' => (int) 4, 'tar' => (int) 1, 'tca' => (int) 1, 'tpr' => (int) 1, 'twi' => (int) 2, 'vmu' => (int) 1 ) $gf_gene_species = 'vmu' $gf_gene_id = 'VMungo1309G0868' $species_info = array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ) $local_species = 'psa' $disabled = '' $selected = '' $num_hits = (int) 0
Warning (2): count(): Parameter must be an array or an object that implements Countable [APP/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp, line 33]Code Context $disabled = (!array_key_exists($local_species,$species_gene_counts))?"disabled":""; $selected = (isset($selected_species) && array_key_exists($local_species,$selected_species))?"checked='checked'":""; $num_hits = (array_key_exists($local_species,$species_gene_counts))?count($species_gene_counts[$local_species]):0; $viewFile = '/www/bioinformatics01_ro/plaza/_dev_instances/feedback/app/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp' $dataForView = array( 'sidebar_info' => array( 'gf_id' => 'HOM05D001729', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '375', 'num_species' => '42' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'Ah.07g204710' => 'amhyb', 'AUR62006001' => 'cqu', 'AUR62006002' => 'cqu', 'AUR62006003' => 'cqu', 'AUR62015641' => 'cqu', 'AUR62027174' => 'cqu', 'AUR62035623' => 'cqu', 'AUR62035624' => 'cqu', 'AUR62035625' => 'cqu', 'AUR62035626' => 'cqu', 'CAN.G1110.53' => 'can', 'CANSAT80G0415' => 'cansat', 'Ca_21364_v3' => 'car', 'COL.COLO4_30693' => 'col', 'COL.COLO4_30694' => 'col', 'COL.COLO4_30695' => 'col', 'COL.COLO4_30696' => 'col', 'COL.COLO4_34020' => 'col', 'DCAR_004585' => 'dca', 'Dinv04029' => 'din', 'Dinv34857' => 'din', 'Duzib147G0011' => 'dzi', 'Duzib170G0599' => 'dzi', 'Duzib192G1051' => 'dzi', 'FAN01G0708' => 'fan', 'FAN01G0742' => 'fan', 'FAN02G0048' => 'fan', 'FAN02G0583' => 'fan', 'FAN02G0688' => 'fan', 'FAN02G1588' => 'fan', 'FAN02G2194' => 'fan', 'FAN02G2750' => 'fan', 'FAN02G3094' => 'fan', 'FAN02G3887' => 'fan', 'FAN02G3911' => 'fan', 'FAN02G3994' => 'fan', 'FAN02G4432' => 'fan', 'FAN02G4556' => 'fan', 'FAN03G1977' => 'fan', 'FAN03G2781' => 'fan', 'FAN03G2850' => 'fan', 'FAN03G3155' => 'fan', 'FAN04G2487' => 'fan', 'FAN05G0208' => 'fan', 'FAN05G0656' => 'fan', 'FAN05G0696' => 'fan', 'FAN05G0810' => 'fan', 'FAN05G1447' => 'fan', 'FAN05G2640' => 'fan', 'FAN05G2911' => 'fan', 'FAN05G3901' => 'fan', 'FAN05G4859' => 'fan', 'FAN05G4861' => 'fan', 'FAN05G4988' => 'fan', 'FAN05G5187' => 'fan', 'FAN05G5452' => 'fan', 'FAN05G5500' => 'fan', 'FAN05G5688' => 'fan', 'FAN06G0177' => 'fan', 'FAN06G0675' => 'fan', 'FAN06G1290' => 'fan', 'FAN06G2191' => 'fan', 'FAN06G2405' => 'fan', 'FAN06G3231' => 'fan', 'FAN06G3932' => 'fan', 'FAN07G0163' => 'fan', 'FAN07G0471' => 'fan', 'FAN07G1354' => 'fan', 'FAN08G0338' => 'fan', 'FAN08G1373' => 'fan', 'FAN08G2539' => 'fan', 'FAN08G2728' => 'fan', 'FAN09G0608' => 'fan', 'FAN09G1136' => 'fan', 'FAN09G1958' => 'fan', 'FAN09G2508' => 'fan', 'FAN09G2597' => 'fan', 'FAN09G2658' => 'fan', 'FAN09G2757' => 'fan', 'FAN09G2983' => 'fan', 'FAN09G3130' => 'fan', 'FAN09G3565' => 'fan', 'FAN09G3613' => 'fan', 'FAN09G4011' => 'fan', 'FAN09G4239' => 'fan', 'FAN09G4277' => 'fan', 'FAN09G4720' => 'fan', 'FAN11G0139' => 'fan', 'FAN11G1727' => 'fan', 'FAN11G2672' => 'fan', 'FAN11G2795' => 'fan', 'FAN11G3238' => 'fan', 'FAN11G3734' => 'fan', 'FAN12G0631' => 'fan', 'FAN12G2239' => 'fan', 'FAN12G2308' => 'fan', 'FAN12G2569' => 'fan', 'FAN12G2623' => 'fan', 'FAN13G3182' => 'fan', 'FAN14G0053' => 'fan', 'FAN14G0370' => 'fan', 'FAN14G0382' => 'fan', 'FAN14G0421' => 'fan', 'FAN14G0866' => 'fan', 'FAN14G1187' => 'fan', 'FAN14G1727' => 'fan', 'FAN14G1791' => 'fan', 'FAN14G2361' => 'fan', 'FAN14G2668' => 'fan', 'FAN14G2770' => 'fan', 'FAN14G2874' => 'fan', 'FAN14G3193' => 'fan', 'FAN14G3624' => 'fan', 'FAN14G3676' => 'fan', 'FAN14G3807' => 'fan', 'FAN14G4082' => 'fan', 'FAN14G4342' => 'fan', 'FAN14G4985' => 'fan', 'FAN14G5126' => 'fan', 'FAN14G5781' => 'fan', 'FAN14G5808' => 'fan', 'FAN14G5949' => 'fan', 'FAN15G0828' => 'fan', 'FAN15G1054' => 'fan', 'FAN15G2023' => 'fan', 'FAN15G2506' => 'fan', 'FAN16G0128' => 'fan', 'FAN16G0249' => 'fan', 'FAN16G0429' => 'fan', 'FAN16G1493' => 'fan', 'FAN16G2210' => 'fan', 'FAN16G2506' => 'fan', 'FAN18G1542' => 'fan', 'FAN18G4057' => 'fan', 'FAN19G0745' => 'fan', 'FAN19G1216' => 'fan', 'FAN19G1733' => 'fan', 'FAN20G0258' => 'fan', 'FAN20G1095' => 'fan', 'FAN20G1557' => 'fan', 'FAN21G0302' => 'fan', 'FAN21G0519' => 'fan', 'FAN21G0970' => 'fan', 'FAN21G1159' => 'fan', 'FAN21G1312' => 'fan', 'FAN21G1440' => 'fan', 'FAN21G1715' => 'fan', 'FAN23G1584' => 'fan', 'FAN24G0045' => 'fan', 'FAN24G0053' => 'fan', 'FAN24G1500' => 'fan', 'FAN24G1817' => 'fan', 'FAN24G2147' => 'fan', 'FAN24G2236' => 'fan', 'FAN24G2446' => 'fan', 'FAN24G2684' => 'fan', 'FAN25G0187' => 'fan', 'FAN25G0505' => 'fan', 'FAN25G0589' => 'fan', 'FAN25G3663' => 'fan', 'FAN26G1025' => 'fan', 'FAN26G2860' => 'fan', 'FAN27G1329' => 'fan', 'FAN27G3392' => 'fan', 'FvH4_1g02011' => 'fve', 'FvH4_1g06511' => 'fve', 'FvH4_2g19900' => 'fve', 'FvH4_2g19920' => 'fve', 'FvH4_2g24261' => 'fve', 'FvH4_2g24270' => 'fve', 'FvH4_2g24631' => 'fve', 'FvH4_2g30622' => 'fve', 'FvH4_3g12920' => 'fve', 'FvH4_3g30171' => 'fve', 'FvH4_3g35490' => 'fve', 'FvH4_3g43682' => 'fve', 'FvH4_3g43730' => 'fve', 'FvH4_3g43732' => 'fve', 'FvH4_3g43751' => 'fve', 'FvH4_3g43752' => 'fve', 'FvH4_3g43770' => 'fve', 'FvH4_3g44471' => 'fve', 'FvH4_3g44510' => 'fve', 'FvH4_3g44582' => 'fve', 'FvH4_4g16921' => 'fve', 'FvH4_4g17121' => 'fve', 'FvH4_4g17782' => 'fve', 'FvH4_4g17783' => 'fve', 'FvH4_4g18120' => 'fve', 'FvH4_4g31310' => 'fve', 'FvH4_4g35052' => 'fve', 'FvH4_5g30862' => 'fve', 'FvH4_6g01541' => 'fve', 'FvH4_6g02021' => 'fve', 'FvH4_6g02041' => 'fve', 'FvH4_6g02071' => 'fve', 'FvH4_6g02171' => 'fve', 'FvH4_6g03181' => 'fve', 'FvH4_6g03182' => 'fve', 'FvH4_6g03221' => 'fve', 'FvH4_6g03380' => 'fve', 'FvH4_6g05201' => 'fve', 'FvH4_6g05203' => 'fve', 'FvH4_6g20231' => 'fve', 'FvH4_6g31981' => 'fve', 'FvH4_6g32061' => 'fve', 'FvH4_6g37041' => 'fve', 'FvH4_6g37932' => 'fve', 'FvH4_6g38731' => 'fve', 'FvH4_6g39370' => 'fve', 'FvH4_6g39371' => 'fve', 'FvH4_6g40891' => 'fve', 'FvH4_6g40892' => 'fve', 'FvH4_6g43143' => 'fve', 'FvH4_6g45251' => 'fve', 'FvH4_6g45260' => 'fve', 'FvH4_6g45291' => 'fve', 'FvH4_6g45890' => 'fve', 'FvH4_6g46240' => 'fve', 'FvH4_6g46241' => 'fve', 'FvH4_6g46242' => 'fve', 'FvH4_6g46260' => 'fve', 'FvH4_6g46280' => 'fve', 'FvH4_6g46380' => 'fve', 'FvH4_7g12841' => 'fve', 'FvH4_7g31431' => 'fve', 'Glyma.09G075900' => 'gma', 'Gohir.A09G096401' => 'ghi', 'Gohir.D09G096101' => 'ghi', 'Gorai.006G112800' => 'gra', 'HanXRQChr04g0121411' => 'han', 'Hund15878' => 'sun', 'Lj2A1107G68' => 'lonja', 'Lj2A630G63' => 'lonja', 'Lj2A946T25' => 'lonja', 'Lj2C714T1' => 'lonja', 'Lj2C966T3' => 'lonja', 'Lj2C966T4' => 'lonja', 'Lj4g0002979' => 'lja', 'Lsat_1_v5_gn_5_30901' => 'lsa', 'Lsat_1_v5_gn_5_31100' => 'lsa', 'Lsat_1_v5_gn_5_38600' => 'lsa', 'Lsat_1_v5_gn_6_92061' => 'lsa', 'Manes.05G071301' => 'mes', 'MD02G1008700' => 'mdo', 'MD02G1008900' => 'mdo', 'MD03G1256400' => 'mdo', 'MD04G1180900' => 'mdo', 'MD04G1181000' => 'mdo', 'MD04G1181200' => 'mdo', 'MD05G1244200' => 'mdo', 'MD05G1324200' => 'mdo', 'MD09G1201600' => 'mdo', 'MD10G1000600' => 'mdo', 'MD14G1026900' => 'mdo', 'MD14G1187900' => 'mdo', 'MD15G1017800' => 'mdo', 'MD15G1018100' => 'mdo', 'Medtr4g124160' => 'mtr', 'Migut.L01260' => 'egut', 'Nitab4.5_0000008g0440' => 'nta', 'Nitab4.5_0000207g0170' => 'nta', 'Nitab4.5_0007671g0030' => 'nta', 'Nitab4.5_0010853g0020' => 'nta', 'Oeu057656.1' => 'oeu', 'PGSC0003DMG400005638' => 'stu', 'PGSC0003DMG400005639' => 'stu', 'Phvul.009G222800' => 'pvu', 'Potri.009G132400' => 'ptr', 'Potri.009G163001' => 'ptr', 'Potri.011G000700' => 'ptr', 'Potri.011G004800' => 'ptr', 'Prupe.1G509300' => 'ppe', 'Prupe.1G509700' => 'ppe', 'Prupe.1G510400' => 'ppe', 'Prupe.1G510700' => 'ppe', 'Prupe.1G512600' => 'ppe', 'Prupe.2G073200' => 'ppe', 'Prupe.3G059500' => 'ppe', 'Prupe.3G059600' => 'ppe', 'Prupe.3G246100' => 'ppe', 'Prupe.3G265100' => 'ppe', 'Prupe.4G034700' => 'ppe', 'Prupe.4G052100' => 'ppe', 'Prupe.4G053600' => 'ppe', 'Prupe.5G068800' => 'ppe', 'Prupe.5G070600' => 'ppe', 'Prupe.6G075400' => 'ppe', 'Prupe.6G075500' => 'ppe', 'Prupe.6G076400' => 'ppe', 'Prupe.8G110700' => 'ppe', 'Psat4g020960' => 'psa', 'PSO135G0788' => 'pso', 'PSO210G6463' => 'pso', 'PSO384G0370' => 'pso', 'PSO386G0056' => 'pso', 'QL01p006048' => 'qlo', 'QL02p054283' => 'qlo', 'QL05p008000' => 'qlo', 'QL05p008212' => 'qlo', 'QL05p008950' => 'qlo', 'QL05p009042' => 'qlo', 'QL05p009518' => 'qlo', 'QL05p012589' => 'qlo', 'QL05p012608' => 'qlo', 'QL05p012650' => 'qlo', 'QL05p012667' => 'qlo', 'QL05p014501' => 'qlo', 'QL05p052800' => 'qlo', 'QL05p065010' => 'qlo', 'QL05p074156' => 'qlo', 'QL05p074160' => 'qlo', 'QL05p074174' => 'qlo', 'QL05p074178' => 'qlo', 'QL05p074214' => 'qlo', 'QL06p001050' => 'qlo', 'QL06p001056' => 'qlo', 'QL06p006093' => 'qlo', 'QL06p006111' => 'qlo', 'QL07p019784' => 'qlo', 'QL07p019801' => 'qlo', 'QL07p036110' => 'qlo', 'QL07p036134' => 'qlo', 'QL07p036147' => 'qlo', 'QL07p036156' => 'qlo', 'QL07p036300' => 'qlo', 'QL07p036320' => 'qlo', 'QL08p014547' => 'qlo', 'QL08p014551' => 'qlo', 'QL08p043319' => 'qlo', 'QL08p043324' => 'qlo', 'QL11p009094' => 'qlo', 'RcHm_v2.0_Chr1g0380481' => 'rch', 'RcHm_v2.0_Chr2g0089331' => 'rch', 'RcHm_v2.0_Chr2g0123691' => 'rch', 'RcHm_v2.0_Chr2g0151111' => 'rch', 'RcHm_v2.0_Chr2g0163011' => 'rch', 'RcHm_v2.0_Chr2g0163051' => 'rch', 'RcHm_v2.0_Chr2g0164671' => 'rch', 'RcHm_v2.0_Chr2g0164681' => 'rch', 'RcHm_v2.0_Chr2g0164721' => 'rch', 'RcHm_v2.0_Chr3g0449911' => 'rch', 'RcHm_v2.0_Chr3g0450211' => 'rch', 'RcHm_v2.0_Chr3g0457271' => 'rch', 'RcHm_v2.0_Chr5g0018111' => 'rch', 'RcHm_v2.0_Chr5g0021011' => 'rch', 'RcHm_v2.0_Chr5g0081171' => 'rch', 'RcHm_v2.0_Chr5g0081211' => 'rch', 'RcHm_v2.0_Chr6g0275871' => 'rch', 'RcHm_v2.0_Chr6g0276071' => 'rch', 'RcHm_v2.0_Chr6g0285591' => 'rch', 'RcHm_v2.0_Chr6g0291931' => 'rch', 'RcHm_v2.0_Chr6g0292091' => 'rch', 'RcHm_v2.0_Chr6g0292271' => 'rch', 'RcHm_v2.0_Chr7g0221261' => 'rch', 'Rhsim08G0219900' => 'rsi', 'Rhsim08G0220200' => 'rsi', 'Rhsim08G0237800' => 'rsi', 'Rhsim08G0238800' => 'rsi', 'Sabra09G0102700' => 'sbr', 'Sabra09G0127200' => 'sbr', 'Sabra11G0003700' => 'sbr', 'Sabra15G0014700' => 'sbr', 'Sc19g0000590' => 'sci', 'Sc19g0001870' => 'sci', 'SGA_v2.0_scaffold1G00346' => 'sas', 'SGA_v2.0_scaffold1G00575' => 'sas', 'SGA_v2.0_scaffold1G00761' => 'sas', 'SGA_v2.0_scaffold232G43501' => 'sas', 'TAR625G1137' => 'tar', 'Thecc.03G222100' => 'tca', 'TPR.G12691' => 'tpr', 'TWI34G0727' => 'twi', 'TWI36G0117' => 'twi', 'VMungo1309G0868' => 'vmu' ), 'gf_id' => 'HOM05D001729', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001729' ), 'data_identifier' => 'HOM05D001729', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001729', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '375', 'num_species' => '42' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'Ah.07g204710' => 'amhyb', 'AUR62006001' => 'cqu', 'AUR62006002' => 'cqu', 'AUR62006003' => 'cqu', 'AUR62015641' => 'cqu', 'AUR62027174' => 'cqu', 'AUR62035623' => 'cqu', 'AUR62035624' => 'cqu', 'AUR62035625' => 'cqu', 'AUR62035626' => 'cqu', 'CAN.G1110.53' => 'can', 'CANSAT80G0415' => 'cansat', 'Ca_21364_v3' => 'car', 'COL.COLO4_30693' => 'col', 'COL.COLO4_30694' => 'col', 'COL.COLO4_30695' => 'col', 'COL.COLO4_30696' => 'col', 'COL.COLO4_34020' => 'col', 'DCAR_004585' => 'dca', 'Dinv04029' => 'din', 'Dinv34857' => 'din', 'Duzib147G0011' => 'dzi', 'Duzib170G0599' => 'dzi', 'Duzib192G1051' => 'dzi', 'FAN01G0708' => 'fan', 'FAN01G0742' => 'fan', 'FAN02G0048' => 'fan', 'FAN02G0583' => 'fan', 'FAN02G0688' => 'fan', 'FAN02G1588' => 'fan', 'FAN02G2194' => 'fan', 'FAN02G2750' => 'fan', 'FAN02G3094' => 'fan', 'FAN02G3887' => 'fan', 'FAN02G3911' => 'fan', 'FAN02G3994' => 'fan', 'FAN02G4432' => 'fan', 'FAN02G4556' => 'fan', 'FAN03G1977' => 'fan', 'FAN03G2781' => 'fan', 'FAN03G2850' => 'fan', 'FAN03G3155' => 'fan', 'FAN04G2487' => 'fan', 'FAN05G0208' => 'fan', 'FAN05G0656' => 'fan', 'FAN05G0696' => 'fan', 'FAN05G0810' => 'fan', 'FAN05G1447' => 'fan', 'FAN05G2640' => 'fan', 'FAN05G2911' => 'fan', 'FAN05G3901' => 'fan', 'FAN05G4859' => 'fan', 'FAN05G4861' => 'fan', 'FAN05G4988' => 'fan', 'FAN05G5187' => 'fan', 'FAN05G5452' => 'fan', 'FAN05G5500' => 'fan', 'FAN05G5688' => 'fan', 'FAN06G0177' => 'fan', 'FAN06G0675' => 'fan', 'FAN06G1290' => 'fan', 'FAN06G2191' => 'fan', 'FAN06G2405' => 'fan', 'FAN06G3231' => 'fan', 'FAN06G3932' => 'fan', 'FAN07G0163' => 'fan', 'FAN07G0471' => 'fan', 'FAN07G1354' => 'fan', 'FAN08G0338' => 'fan', 'FAN08G1373' => 'fan', 'FAN08G2539' => 'fan', 'FAN08G2728' => 'fan', 'FAN09G0608' => 'fan', 'FAN09G1136' => 'fan', 'FAN09G1958' => 'fan', 'FAN09G2508' => 'fan', 'FAN09G2597' => 'fan', 'FAN09G2658' => 'fan', 'FAN09G2757' => 'fan', 'FAN09G2983' => 'fan', 'FAN09G3130' => 'fan', 'FAN09G3565' => 'fan', 'FAN09G3613' => 'fan', 'FAN09G4011' => 'fan', 'FAN09G4239' => 'fan', 'FAN09G4277' => 'fan', 'FAN09G4720' => 'fan', 'FAN11G0139' => 'fan', 'FAN11G1727' => 'fan', 'FAN11G2672' => 'fan', 'FAN11G2795' => 'fan', 'FAN11G3238' => 'fan', 'FAN11G3734' => 'fan', 'FAN12G0631' => 'fan', 'FAN12G2239' => 'fan', 'FAN12G2308' => 'fan', 'FAN12G2569' => 'fan', 'FAN12G2623' => 'fan', 'FAN13G3182' => 'fan', 'FAN14G0053' => 'fan', 'FAN14G0370' => 'fan', 'FAN14G0382' => 'fan', 'FAN14G0421' => 'fan', 'FAN14G0866' => 'fan', 'FAN14G1187' => 'fan', 'FAN14G1727' => 'fan', 'FAN14G1791' => 'fan', 'FAN14G2361' => 'fan', 'FAN14G2668' => 'fan', 'FAN14G2770' => 'fan', 'FAN14G2874' => 'fan', 'FAN14G3193' => 'fan', 'FAN14G3624' => 'fan', 'FAN14G3676' => 'fan', 'FAN14G3807' => 'fan', 'FAN14G4082' => 'fan', 'FAN14G4342' => 'fan', 'FAN14G4985' => 'fan', 'FAN14G5126' => 'fan', 'FAN14G5781' => 'fan', 'FAN14G5808' => 'fan', 'FAN14G5949' => 'fan', 'FAN15G0828' => 'fan', 'FAN15G1054' => 'fan', 'FAN15G2023' => 'fan', 'FAN15G2506' => 'fan', 'FAN16G0128' => 'fan', 'FAN16G0249' => 'fan', 'FAN16G0429' => 'fan', 'FAN16G1493' => 'fan', 'FAN16G2210' => 'fan', 'FAN16G2506' => 'fan', 'FAN18G1542' => 'fan', 'FAN18G4057' => 'fan', 'FAN19G0745' => 'fan', 'FAN19G1216' => 'fan', 'FAN19G1733' => 'fan', 'FAN20G0258' => 'fan', 'FAN20G1095' => 'fan', 'FAN20G1557' => 'fan', 'FAN21G0302' => 'fan', 'FAN21G0519' => 'fan', 'FAN21G0970' => 'fan', 'FAN21G1159' => 'fan', 'FAN21G1312' => 'fan', 'FAN21G1440' => 'fan', 'FAN21G1715' => 'fan', 'FAN23G1584' => 'fan', 'FAN24G0045' => 'fan', 'FAN24G0053' => 'fan', 'FAN24G1500' => 'fan', 'FAN24G1817' => 'fan', 'FAN24G2147' => 'fan', 'FAN24G2236' => 'fan', 'FAN24G2446' => 'fan', 'FAN24G2684' => 'fan', 'FAN25G0187' => 'fan', 'FAN25G0505' => 'fan', 'FAN25G0589' => 'fan', 'FAN25G3663' => 'fan', 'FAN26G1025' => 'fan', 'FAN26G2860' => 'fan', 'FAN27G1329' => 'fan', 'FAN27G3392' => 'fan', 'FvH4_1g02011' => 'fve', 'FvH4_1g06511' => 'fve', 'FvH4_2g19900' => 'fve', 'FvH4_2g19920' => 'fve', 'FvH4_2g24261' => 'fve', 'FvH4_2g24270' => 'fve', 'FvH4_2g24631' => 'fve', 'FvH4_2g30622' => 'fve', 'FvH4_3g12920' => 'fve', 'FvH4_3g30171' => 'fve', 'FvH4_3g35490' => 'fve', 'FvH4_3g43682' => 'fve', 'FvH4_3g43730' => 'fve', 'FvH4_3g43732' => 'fve', 'FvH4_3g43751' => 'fve', 'FvH4_3g43752' => 'fve', 'FvH4_3g43770' => 'fve', 'FvH4_3g44471' => 'fve', 'FvH4_3g44510' => 'fve', 'FvH4_3g44582' => 'fve', 'FvH4_4g16921' => 'fve', 'FvH4_4g17121' => 'fve', 'FvH4_4g17782' => 'fve', 'FvH4_4g17783' => 'fve', 'FvH4_4g18120' => 'fve', 'FvH4_4g31310' => 'fve', 'FvH4_4g35052' => 'fve', 'FvH4_5g30862' => 'fve', 'FvH4_6g01541' => 'fve', 'FvH4_6g02021' => 'fve', 'FvH4_6g02041' => 'fve', 'FvH4_6g02071' => 'fve', 'FvH4_6g02171' => 'fve', 'FvH4_6g03181' => 'fve', 'FvH4_6g03182' => 'fve', 'FvH4_6g03221' => 'fve', 'FvH4_6g03380' => 'fve', 'FvH4_6g05201' => 'fve', 'FvH4_6g05203' => 'fve', 'FvH4_6g20231' => 'fve', 'FvH4_6g31981' => 'fve', 'FvH4_6g32061' => 'fve', 'FvH4_6g37041' => 'fve', 'FvH4_6g37932' => 'fve', 'FvH4_6g38731' => 'fve', 'FvH4_6g39370' => 'fve', 'FvH4_6g39371' => 'fve', 'FvH4_6g40891' => 'fve', 'FvH4_6g40892' => 'fve', 'FvH4_6g43143' => 'fve', 'FvH4_6g45251' => 'fve', 'FvH4_6g45260' => 'fve', 'FvH4_6g45291' => 'fve', 'FvH4_6g45890' => 'fve', 'FvH4_6g46240' => 'fve', 'FvH4_6g46241' => 'fve', 'FvH4_6g46242' => 'fve', 'FvH4_6g46260' => 'fve', 'FvH4_6g46280' => 'fve', 'FvH4_6g46380' => 'fve', 'FvH4_7g12841' => 'fve', 'FvH4_7g31431' => 'fve', 'Glyma.09G075900' => 'gma', 'Gohir.A09G096401' => 'ghi', 'Gohir.D09G096101' => 'ghi', 'Gorai.006G112800' => 'gra', 'HanXRQChr04g0121411' => 'han', 'Hund15878' => 'sun', 'Lj2A1107G68' => 'lonja', 'Lj2A630G63' => 'lonja', 'Lj2A946T25' => 'lonja', 'Lj2C714T1' => 'lonja', 'Lj2C966T3' => 'lonja', 'Lj2C966T4' => 'lonja', 'Lj4g0002979' => 'lja', 'Lsat_1_v5_gn_5_30901' => 'lsa', 'Lsat_1_v5_gn_5_31100' => 'lsa', 'Lsat_1_v5_gn_5_38600' => 'lsa', 'Lsat_1_v5_gn_6_92061' => 'lsa', 'Manes.05G071301' => 'mes', 'MD02G1008700' => 'mdo', 'MD02G1008900' => 'mdo', 'MD03G1256400' => 'mdo', 'MD04G1180900' => 'mdo', 'MD04G1181000' => 'mdo', 'MD04G1181200' => 'mdo', 'MD05G1244200' => 'mdo', 'MD05G1324200' => 'mdo', 'MD09G1201600' => 'mdo', 'MD10G1000600' => 'mdo', 'MD14G1026900' => 'mdo', 'MD14G1187900' => 'mdo', 'MD15G1017800' => 'mdo', 'MD15G1018100' => 'mdo', 'Medtr4g124160' => 'mtr', 'Migut.L01260' => 'egut', 'Nitab4.5_0000008g0440' => 'nta', 'Nitab4.5_0000207g0170' => 'nta', 'Nitab4.5_0007671g0030' => 'nta', 'Nitab4.5_0010853g0020' => 'nta', 'Oeu057656.1' => 'oeu', 'PGSC0003DMG400005638' => 'stu', 'PGSC0003DMG400005639' => 'stu', 'Phvul.009G222800' => 'pvu', 'Potri.009G132400' => 'ptr', 'Potri.009G163001' => 'ptr', 'Potri.011G000700' => 'ptr', 'Potri.011G004800' => 'ptr', 'Prupe.1G509300' => 'ppe', 'Prupe.1G509700' => 'ppe', 'Prupe.1G510400' => 'ppe', 'Prupe.1G510700' => 'ppe', 'Prupe.1G512600' => 'ppe', 'Prupe.2G073200' => 'ppe', 'Prupe.3G059500' => 'ppe', 'Prupe.3G059600' => 'ppe', 'Prupe.3G246100' => 'ppe', 'Prupe.3G265100' => 'ppe', 'Prupe.4G034700' => 'ppe', 'Prupe.4G052100' => 'ppe', 'Prupe.4G053600' => 'ppe', 'Prupe.5G068800' => 'ppe', 'Prupe.5G070600' => 'ppe', 'Prupe.6G075400' => 'ppe', 'Prupe.6G075500' => 'ppe', 'Prupe.6G076400' => 'ppe', 'Prupe.8G110700' => 'ppe', 'Psat4g020960' => 'psa', 'PSO135G0788' => 'pso', 'PSO210G6463' => 'pso', 'PSO384G0370' => 'pso', 'PSO386G0056' => 'pso', 'QL01p006048' => 'qlo', 'QL02p054283' => 'qlo', 'QL05p008000' => 'qlo', 'QL05p008212' => 'qlo', 'QL05p008950' => 'qlo', 'QL05p009042' => 'qlo', 'QL05p009518' => 'qlo', 'QL05p012589' => 'qlo', 'QL05p012608' => 'qlo', 'QL05p012650' => 'qlo', 'QL05p012667' => 'qlo', 'QL05p014501' => 'qlo', 'QL05p052800' => 'qlo', 'QL05p065010' => 'qlo', 'QL05p074156' => 'qlo', 'QL05p074160' => 'qlo', 'QL05p074174' => 'qlo', 'QL05p074178' => 'qlo', 'QL05p074214' => 'qlo', 'QL06p001050' => 'qlo', 'QL06p001056' => 'qlo', 'QL06p006093' => 'qlo', 'QL06p006111' => 'qlo', 'QL07p019784' => 'qlo', 'QL07p019801' => 'qlo', 'QL07p036110' => 'qlo', 'QL07p036134' => 'qlo', 'QL07p036147' => 'qlo', 'QL07p036156' => 'qlo', 'QL07p036300' => 'qlo', 'QL07p036320' => 'qlo', 'QL08p014547' => 'qlo', 'QL08p014551' => 'qlo', 'QL08p043319' => 'qlo', 'QL08p043324' => 'qlo', 'QL11p009094' => 'qlo', 'RcHm_v2.0_Chr1g0380481' => 'rch', 'RcHm_v2.0_Chr2g0089331' => 'rch', 'RcHm_v2.0_Chr2g0123691' => 'rch', 'RcHm_v2.0_Chr2g0151111' => 'rch', 'RcHm_v2.0_Chr2g0163011' => 'rch', 'RcHm_v2.0_Chr2g0163051' => 'rch', 'RcHm_v2.0_Chr2g0164671' => 'rch', 'RcHm_v2.0_Chr2g0164681' => 'rch', 'RcHm_v2.0_Chr2g0164721' => 'rch', 'RcHm_v2.0_Chr3g0449911' => 'rch', 'RcHm_v2.0_Chr3g0450211' => 'rch', 'RcHm_v2.0_Chr3g0457271' => 'rch', 'RcHm_v2.0_Chr5g0018111' => 'rch', 'RcHm_v2.0_Chr5g0021011' => 'rch', 'RcHm_v2.0_Chr5g0081171' => 'rch', 'RcHm_v2.0_Chr5g0081211' => 'rch', 'RcHm_v2.0_Chr6g0275871' => 'rch', 'RcHm_v2.0_Chr6g0276071' => 'rch', 'RcHm_v2.0_Chr6g0285591' => 'rch', 'RcHm_v2.0_Chr6g0291931' => 'rch', 'RcHm_v2.0_Chr6g0292091' => 'rch', 'RcHm_v2.0_Chr6g0292271' => 'rch', 'RcHm_v2.0_Chr7g0221261' => 'rch', 'Rhsim08G0219900' => 'rsi', 'Rhsim08G0220200' => 'rsi', 'Rhsim08G0237800' => 'rsi', 'Rhsim08G0238800' => 'rsi', 'Sabra09G0102700' => 'sbr', 'Sabra09G0127200' => 'sbr', 'Sabra11G0003700' => 'sbr', 'Sabra15G0014700' => 'sbr', 'Sc19g0000590' => 'sci', 'Sc19g0001870' => 'sci', 'SGA_v2.0_scaffold1G00346' => 'sas', 'SGA_v2.0_scaffold1G00575' => 'sas', 'SGA_v2.0_scaffold1G00761' => 'sas', 'SGA_v2.0_scaffold232G43501' => 'sas', 'TAR625G1137' => 'tar', 'Thecc.03G222100' => 'tca', 'TPR.G12691' => 'tpr', 'TWI34G0727' => 'twi', 'TWI36G0117' => 'twi', 'VMungo1309G0868' => 'vmu' ) $gf_id = 'HOM05D001729' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001729' ) $data_identifier = 'HOM05D001729' $data_type = 'gf_id' $species_gene_counts = array( 'amhyb' => (int) 1, 'cqu' => (int) 9, 'can' => (int) 1, 'cansat' => (int) 1, 'car' => (int) 1, 'col' => (int) 5, 'dca' => (int) 1, 'din' => (int) 2, 'dzi' => (int) 3, 'fan' => (int) 140, 'fve' => (int) 62, 'gma' => (int) 1, 'ghi' => (int) 2, 'gra' => (int) 1, 'han' => (int) 1, 'sun' => (int) 1, 'lonja' => (int) 6, 'lja' => (int) 1, 'lsa' => (int) 4, 'mes' => (int) 1, 'mdo' => (int) 14, 'mtr' => (int) 1, 'egut' => (int) 1, 'nta' => (int) 4, 'oeu' => (int) 1, 'stu' => (int) 2, 'pvu' => (int) 1, 'ptr' => (int) 4, 'ppe' => (int) 19, 'psa' => (int) 1, 'pso' => (int) 4, 'qlo' => (int) 36, 'rch' => (int) 23, 'rsi' => (int) 4, 'sbr' => (int) 4, 'sci' => (int) 2, 'sas' => (int) 4, 'tar' => (int) 1, 'tca' => (int) 1, 'tpr' => (int) 1, 'twi' => (int) 2, 'vmu' => (int) 1 ) $gf_gene_species = 'vmu' $gf_gene_id = 'VMungo1309G0868' $species_info = array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ) $local_species = 'ptr' $disabled = '' $selected = '' $num_hits = (int) 1include - APP/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp, line 33 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933 View::_renderElement() - CORE/Cake/View/View.php, line 1224 View::element() - CORE/Cake/View/View.php, line 418 include - APP/View/Elements/analysis/phylogenetics_module/gf_data_settings.ctp, line 37 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933 View::_renderElement() - CORE/Cake/View/View.php, line 1224 View::element() - CORE/Cake/View/View.php, line 418 include - APP/View/Elements/analysis/phylogenetics_module/parameter_selection.ctp, line 64 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933 View::_renderElement() - CORE/Cake/View/View.php, line 1224 View::element() - CORE/Cake/View/View.php, line 418 include - APP/View/Analysis/custom_tree_creation.ctp, line 27 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933
$viewFile = '/www/bioinformatics01_ro/plaza/_dev_instances/feedback/app/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp' $dataForView = array( 'sidebar_info' => array( 'gf_id' => 'HOM05D001729', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '375', 'num_species' => '42' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'Ah.07g204710' => 'amhyb', 'AUR62006001' => 'cqu', 'AUR62006002' => 'cqu', 'AUR62006003' => 'cqu', 'AUR62015641' => 'cqu', 'AUR62027174' => 'cqu', 'AUR62035623' => 'cqu', 'AUR62035624' => 'cqu', 'AUR62035625' => 'cqu', 'AUR62035626' => 'cqu', 'CAN.G1110.53' => 'can', 'CANSAT80G0415' => 'cansat', 'Ca_21364_v3' => 'car', 'COL.COLO4_30693' => 'col', 'COL.COLO4_30694' => 'col', 'COL.COLO4_30695' => 'col', 'COL.COLO4_30696' => 'col', 'COL.COLO4_34020' => 'col', 'DCAR_004585' => 'dca', 'Dinv04029' => 'din', 'Dinv34857' => 'din', 'Duzib147G0011' => 'dzi', 'Duzib170G0599' => 'dzi', 'Duzib192G1051' => 'dzi', 'FAN01G0708' => 'fan', 'FAN01G0742' => 'fan', 'FAN02G0048' => 'fan', 'FAN02G0583' => 'fan', 'FAN02G0688' => 'fan', 'FAN02G1588' => 'fan', 'FAN02G2194' => 'fan', 'FAN02G2750' => 'fan', 'FAN02G3094' => 'fan', 'FAN02G3887' => 'fan', 'FAN02G3911' => 'fan', 'FAN02G3994' => 'fan', 'FAN02G4432' => 'fan', 'FAN02G4556' => 'fan', 'FAN03G1977' => 'fan', 'FAN03G2781' => 'fan', 'FAN03G2850' => 'fan', 'FAN03G3155' => 'fan', 'FAN04G2487' => 'fan', 'FAN05G0208' => 'fan', 'FAN05G0656' => 'fan', 'FAN05G0696' => 'fan', 'FAN05G0810' => 'fan', 'FAN05G1447' => 'fan', 'FAN05G2640' => 'fan', 'FAN05G2911' => 'fan', 'FAN05G3901' => 'fan', 'FAN05G4859' => 'fan', 'FAN05G4861' => 'fan', 'FAN05G4988' => 'fan', 'FAN05G5187' => 'fan', 'FAN05G5452' => 'fan', 'FAN05G5500' => 'fan', 'FAN05G5688' => 'fan', 'FAN06G0177' => 'fan', 'FAN06G0675' => 'fan', 'FAN06G1290' => 'fan', 'FAN06G2191' => 'fan', 'FAN06G2405' => 'fan', 'FAN06G3231' => 'fan', 'FAN06G3932' => 'fan', 'FAN07G0163' => 'fan', 'FAN07G0471' => 'fan', 'FAN07G1354' => 'fan', 'FAN08G0338' => 'fan', 'FAN08G1373' => 'fan', 'FAN08G2539' => 'fan', 'FAN08G2728' => 'fan', 'FAN09G0608' => 'fan', 'FAN09G1136' => 'fan', 'FAN09G1958' => 'fan', 'FAN09G2508' => 'fan', 'FAN09G2597' => 'fan', 'FAN09G2658' => 'fan', 'FAN09G2757' => 'fan', 'FAN09G2983' => 'fan', 'FAN09G3130' => 'fan', 'FAN09G3565' => 'fan', 'FAN09G3613' => 'fan', 'FAN09G4011' => 'fan', 'FAN09G4239' => 'fan', 'FAN09G4277' => 'fan', 'FAN09G4720' => 'fan', 'FAN11G0139' => 'fan', 'FAN11G1727' => 'fan', 'FAN11G2672' => 'fan', 'FAN11G2795' => 'fan', 'FAN11G3238' => 'fan', 'FAN11G3734' => 'fan', 'FAN12G0631' => 'fan', 'FAN12G2239' => 'fan', 'FAN12G2308' => 'fan', 'FAN12G2569' => 'fan', 'FAN12G2623' => 'fan', 'FAN13G3182' => 'fan', 'FAN14G0053' => 'fan', 'FAN14G0370' => 'fan', 'FAN14G0382' => 'fan', 'FAN14G0421' => 'fan', 'FAN14G0866' => 'fan', 'FAN14G1187' => 'fan', 'FAN14G1727' => 'fan', 'FAN14G1791' => 'fan', 'FAN14G2361' => 'fan', 'FAN14G2668' => 'fan', 'FAN14G2770' => 'fan', 'FAN14G2874' => 'fan', 'FAN14G3193' => 'fan', 'FAN14G3624' => 'fan', 'FAN14G3676' => 'fan', 'FAN14G3807' => 'fan', 'FAN14G4082' => 'fan', 'FAN14G4342' => 'fan', 'FAN14G4985' => 'fan', 'FAN14G5126' => 'fan', 'FAN14G5781' => 'fan', 'FAN14G5808' => 'fan', 'FAN14G5949' => 'fan', 'FAN15G0828' => 'fan', 'FAN15G1054' => 'fan', 'FAN15G2023' => 'fan', 'FAN15G2506' => 'fan', 'FAN16G0128' => 'fan', 'FAN16G0249' => 'fan', 'FAN16G0429' => 'fan', 'FAN16G1493' => 'fan', 'FAN16G2210' => 'fan', 'FAN16G2506' => 'fan', 'FAN18G1542' => 'fan', 'FAN18G4057' => 'fan', 'FAN19G0745' => 'fan', 'FAN19G1216' => 'fan', 'FAN19G1733' => 'fan', 'FAN20G0258' => 'fan', 'FAN20G1095' => 'fan', 'FAN20G1557' => 'fan', 'FAN21G0302' => 'fan', 'FAN21G0519' => 'fan', 'FAN21G0970' => 'fan', 'FAN21G1159' => 'fan', 'FAN21G1312' => 'fan', 'FAN21G1440' => 'fan', 'FAN21G1715' => 'fan', 'FAN23G1584' => 'fan', 'FAN24G0045' => 'fan', 'FAN24G0053' => 'fan', 'FAN24G1500' => 'fan', 'FAN24G1817' => 'fan', 'FAN24G2147' => 'fan', 'FAN24G2236' => 'fan', 'FAN24G2446' => 'fan', 'FAN24G2684' => 'fan', 'FAN25G0187' => 'fan', 'FAN25G0505' => 'fan', 'FAN25G0589' => 'fan', 'FAN25G3663' => 'fan', 'FAN26G1025' => 'fan', 'FAN26G2860' => 'fan', 'FAN27G1329' => 'fan', 'FAN27G3392' => 'fan', 'FvH4_1g02011' => 'fve', 'FvH4_1g06511' => 'fve', 'FvH4_2g19900' => 'fve', 'FvH4_2g19920' => 'fve', 'FvH4_2g24261' => 'fve', 'FvH4_2g24270' => 'fve', 'FvH4_2g24631' => 'fve', 'FvH4_2g30622' => 'fve', 'FvH4_3g12920' => 'fve', 'FvH4_3g30171' => 'fve', 'FvH4_3g35490' => 'fve', 'FvH4_3g43682' => 'fve', 'FvH4_3g43730' => 'fve', 'FvH4_3g43732' => 'fve', 'FvH4_3g43751' => 'fve', 'FvH4_3g43752' => 'fve', 'FvH4_3g43770' => 'fve', 'FvH4_3g44471' => 'fve', 'FvH4_3g44510' => 'fve', 'FvH4_3g44582' => 'fve', 'FvH4_4g16921' => 'fve', 'FvH4_4g17121' => 'fve', 'FvH4_4g17782' => 'fve', 'FvH4_4g17783' => 'fve', 'FvH4_4g18120' => 'fve', 'FvH4_4g31310' => 'fve', 'FvH4_4g35052' => 'fve', 'FvH4_5g30862' => 'fve', 'FvH4_6g01541' => 'fve', 'FvH4_6g02021' => 'fve', 'FvH4_6g02041' => 'fve', 'FvH4_6g02071' => 'fve', 'FvH4_6g02171' => 'fve', 'FvH4_6g03181' => 'fve', 'FvH4_6g03182' => 'fve', 'FvH4_6g03221' => 'fve', 'FvH4_6g03380' => 'fve', 'FvH4_6g05201' => 'fve', 'FvH4_6g05203' => 'fve', 'FvH4_6g20231' => 'fve', 'FvH4_6g31981' => 'fve', 'FvH4_6g32061' => 'fve', 'FvH4_6g37041' => 'fve', 'FvH4_6g37932' => 'fve', 'FvH4_6g38731' => 'fve', 'FvH4_6g39370' => 'fve', 'FvH4_6g39371' => 'fve', 'FvH4_6g40891' => 'fve', 'FvH4_6g40892' => 'fve', 'FvH4_6g43143' => 'fve', 'FvH4_6g45251' => 'fve', 'FvH4_6g45260' => 'fve', 'FvH4_6g45291' => 'fve', 'FvH4_6g45890' => 'fve', 'FvH4_6g46240' => 'fve', 'FvH4_6g46241' => 'fve', 'FvH4_6g46242' => 'fve', 'FvH4_6g46260' => 'fve', 'FvH4_6g46280' => 'fve', 'FvH4_6g46380' => 'fve', 'FvH4_7g12841' => 'fve', 'FvH4_7g31431' => 'fve', 'Glyma.09G075900' => 'gma', 'Gohir.A09G096401' => 'ghi', 'Gohir.D09G096101' => 'ghi', 'Gorai.006G112800' => 'gra', 'HanXRQChr04g0121411' => 'han', 'Hund15878' => 'sun', 'Lj2A1107G68' => 'lonja', 'Lj2A630G63' => 'lonja', 'Lj2A946T25' => 'lonja', 'Lj2C714T1' => 'lonja', 'Lj2C966T3' => 'lonja', 'Lj2C966T4' => 'lonja', 'Lj4g0002979' => 'lja', 'Lsat_1_v5_gn_5_30901' => 'lsa', 'Lsat_1_v5_gn_5_31100' => 'lsa', 'Lsat_1_v5_gn_5_38600' => 'lsa', 'Lsat_1_v5_gn_6_92061' => 'lsa', 'Manes.05G071301' => 'mes', 'MD02G1008700' => 'mdo', 'MD02G1008900' => 'mdo', 'MD03G1256400' => 'mdo', 'MD04G1180900' => 'mdo', 'MD04G1181000' => 'mdo', 'MD04G1181200' => 'mdo', 'MD05G1244200' => 'mdo', 'MD05G1324200' => 'mdo', 'MD09G1201600' => 'mdo', 'MD10G1000600' => 'mdo', 'MD14G1026900' => 'mdo', 'MD14G1187900' => 'mdo', 'MD15G1017800' => 'mdo', 'MD15G1018100' => 'mdo', 'Medtr4g124160' => 'mtr', 'Migut.L01260' => 'egut', 'Nitab4.5_0000008g0440' => 'nta', 'Nitab4.5_0000207g0170' => 'nta', 'Nitab4.5_0007671g0030' => 'nta', 'Nitab4.5_0010853g0020' => 'nta', 'Oeu057656.1' => 'oeu', 'PGSC0003DMG400005638' => 'stu', 'PGSC0003DMG400005639' => 'stu', 'Phvul.009G222800' => 'pvu', 'Potri.009G132400' => 'ptr', 'Potri.009G163001' => 'ptr', 'Potri.011G000700' => 'ptr', 'Potri.011G004800' => 'ptr', 'Prupe.1G509300' => 'ppe', 'Prupe.1G509700' => 'ppe', 'Prupe.1G510400' => 'ppe', 'Prupe.1G510700' => 'ppe', 'Prupe.1G512600' => 'ppe', 'Prupe.2G073200' => 'ppe', 'Prupe.3G059500' => 'ppe', 'Prupe.3G059600' => 'ppe', 'Prupe.3G246100' => 'ppe', 'Prupe.3G265100' => 'ppe', 'Prupe.4G034700' => 'ppe', 'Prupe.4G052100' => 'ppe', 'Prupe.4G053600' => 'ppe', 'Prupe.5G068800' => 'ppe', 'Prupe.5G070600' => 'ppe', 'Prupe.6G075400' => 'ppe', 'Prupe.6G075500' => 'ppe', 'Prupe.6G076400' => 'ppe', 'Prupe.8G110700' => 'ppe', 'Psat4g020960' => 'psa', 'PSO135G0788' => 'pso', 'PSO210G6463' => 'pso', 'PSO384G0370' => 'pso', 'PSO386G0056' => 'pso', 'QL01p006048' => 'qlo', 'QL02p054283' => 'qlo', 'QL05p008000' => 'qlo', 'QL05p008212' => 'qlo', 'QL05p008950' => 'qlo', 'QL05p009042' => 'qlo', 'QL05p009518' => 'qlo', 'QL05p012589' => 'qlo', 'QL05p012608' => 'qlo', 'QL05p012650' => 'qlo', 'QL05p012667' => 'qlo', 'QL05p014501' => 'qlo', 'QL05p052800' => 'qlo', 'QL05p065010' => 'qlo', 'QL05p074156' => 'qlo', 'QL05p074160' => 'qlo', 'QL05p074174' => 'qlo', 'QL05p074178' => 'qlo', 'QL05p074214' => 'qlo', 'QL06p001050' => 'qlo', 'QL06p001056' => 'qlo', 'QL06p006093' => 'qlo', 'QL06p006111' => 'qlo', 'QL07p019784' => 'qlo', 'QL07p019801' => 'qlo', 'QL07p036110' => 'qlo', 'QL07p036134' => 'qlo', 'QL07p036147' => 'qlo', 'QL07p036156' => 'qlo', 'QL07p036300' => 'qlo', 'QL07p036320' => 'qlo', 'QL08p014547' => 'qlo', 'QL08p014551' => 'qlo', 'QL08p043319' => 'qlo', 'QL08p043324' => 'qlo', 'QL11p009094' => 'qlo', 'RcHm_v2.0_Chr1g0380481' => 'rch', 'RcHm_v2.0_Chr2g0089331' => 'rch', 'RcHm_v2.0_Chr2g0123691' => 'rch', 'RcHm_v2.0_Chr2g0151111' => 'rch', 'RcHm_v2.0_Chr2g0163011' => 'rch', 'RcHm_v2.0_Chr2g0163051' => 'rch', 'RcHm_v2.0_Chr2g0164671' => 'rch', 'RcHm_v2.0_Chr2g0164681' => 'rch', 'RcHm_v2.0_Chr2g0164721' => 'rch', 'RcHm_v2.0_Chr3g0449911' => 'rch', 'RcHm_v2.0_Chr3g0450211' => 'rch', 'RcHm_v2.0_Chr3g0457271' => 'rch', 'RcHm_v2.0_Chr5g0018111' => 'rch', 'RcHm_v2.0_Chr5g0021011' => 'rch', 'RcHm_v2.0_Chr5g0081171' => 'rch', 'RcHm_v2.0_Chr5g0081211' => 'rch', 'RcHm_v2.0_Chr6g0275871' => 'rch', 'RcHm_v2.0_Chr6g0276071' => 'rch', 'RcHm_v2.0_Chr6g0285591' => 'rch', 'RcHm_v2.0_Chr6g0291931' => 'rch', 'RcHm_v2.0_Chr6g0292091' => 'rch', 'RcHm_v2.0_Chr6g0292271' => 'rch', 'RcHm_v2.0_Chr7g0221261' => 'rch', 'Rhsim08G0219900' => 'rsi', 'Rhsim08G0220200' => 'rsi', 'Rhsim08G0237800' => 'rsi', 'Rhsim08G0238800' => 'rsi', 'Sabra09G0102700' => 'sbr', 'Sabra09G0127200' => 'sbr', 'Sabra11G0003700' => 'sbr', 'Sabra15G0014700' => 'sbr', 'Sc19g0000590' => 'sci', 'Sc19g0001870' => 'sci', 'SGA_v2.0_scaffold1G00346' => 'sas', 'SGA_v2.0_scaffold1G00575' => 'sas', 'SGA_v2.0_scaffold1G00761' => 'sas', 'SGA_v2.0_scaffold232G43501' => 'sas', 'TAR625G1137' => 'tar', 'Thecc.03G222100' => 'tca', 'TPR.G12691' => 'tpr', 'TWI34G0727' => 'twi', 'TWI36G0117' => 'twi', 'VMungo1309G0868' => 'vmu' ), 'gf_id' => 'HOM05D001729', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001729' ), 'data_identifier' => 'HOM05D001729', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001729', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '375', 'num_species' => '42' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'Ah.07g204710' => 'amhyb', 'AUR62006001' => 'cqu', 'AUR62006002' => 'cqu', 'AUR62006003' => 'cqu', 'AUR62015641' => 'cqu', 'AUR62027174' => 'cqu', 'AUR62035623' => 'cqu', 'AUR62035624' => 'cqu', 'AUR62035625' => 'cqu', 'AUR62035626' => 'cqu', 'CAN.G1110.53' => 'can', 'CANSAT80G0415' => 'cansat', 'Ca_21364_v3' => 'car', 'COL.COLO4_30693' => 'col', 'COL.COLO4_30694' => 'col', 'COL.COLO4_30695' => 'col', 'COL.COLO4_30696' => 'col', 'COL.COLO4_34020' => 'col', 'DCAR_004585' => 'dca', 'Dinv04029' => 'din', 'Dinv34857' => 'din', 'Duzib147G0011' => 'dzi', 'Duzib170G0599' => 'dzi', 'Duzib192G1051' => 'dzi', 'FAN01G0708' => 'fan', 'FAN01G0742' => 'fan', 'FAN02G0048' => 'fan', 'FAN02G0583' => 'fan', 'FAN02G0688' => 'fan', 'FAN02G1588' => 'fan', 'FAN02G2194' => 'fan', 'FAN02G2750' => 'fan', 'FAN02G3094' => 'fan', 'FAN02G3887' => 'fan', 'FAN02G3911' => 'fan', 'FAN02G3994' => 'fan', 'FAN02G4432' => 'fan', 'FAN02G4556' => 'fan', 'FAN03G1977' => 'fan', 'FAN03G2781' => 'fan', 'FAN03G2850' => 'fan', 'FAN03G3155' => 'fan', 'FAN04G2487' => 'fan', 'FAN05G0208' => 'fan', 'FAN05G0656' => 'fan', 'FAN05G0696' => 'fan', 'FAN05G0810' => 'fan', 'FAN05G1447' => 'fan', 'FAN05G2640' => 'fan', 'FAN05G2911' => 'fan', 'FAN05G3901' => 'fan', 'FAN05G4859' => 'fan', 'FAN05G4861' => 'fan', 'FAN05G4988' => 'fan', 'FAN05G5187' => 'fan', 'FAN05G5452' => 'fan', 'FAN05G5500' => 'fan', 'FAN05G5688' => 'fan', 'FAN06G0177' => 'fan', 'FAN06G0675' => 'fan', 'FAN06G1290' => 'fan', 'FAN06G2191' => 'fan', 'FAN06G2405' => 'fan', 'FAN06G3231' => 'fan', 'FAN06G3932' => 'fan', 'FAN07G0163' => 'fan', 'FAN07G0471' => 'fan', 'FAN07G1354' => 'fan', 'FAN08G0338' => 'fan', 'FAN08G1373' => 'fan', 'FAN08G2539' => 'fan', 'FAN08G2728' => 'fan', 'FAN09G0608' => 'fan', 'FAN09G1136' => 'fan', 'FAN09G1958' => 'fan', 'FAN09G2508' => 'fan', 'FAN09G2597' => 'fan', 'FAN09G2658' => 'fan', 'FAN09G2757' => 'fan', 'FAN09G2983' => 'fan', 'FAN09G3130' => 'fan', 'FAN09G3565' => 'fan', 'FAN09G3613' => 'fan', 'FAN09G4011' => 'fan', 'FAN09G4239' => 'fan', 'FAN09G4277' => 'fan', 'FAN09G4720' => 'fan', 'FAN11G0139' => 'fan', 'FAN11G1727' => 'fan', 'FAN11G2672' => 'fan', 'FAN11G2795' => 'fan', 'FAN11G3238' => 'fan', 'FAN11G3734' => 'fan', 'FAN12G0631' => 'fan', 'FAN12G2239' => 'fan', 'FAN12G2308' => 'fan', 'FAN12G2569' => 'fan', 'FAN12G2623' => 'fan', 'FAN13G3182' => 'fan', 'FAN14G0053' => 'fan', 'FAN14G0370' => 'fan', 'FAN14G0382' => 'fan', 'FAN14G0421' => 'fan', 'FAN14G0866' => 'fan', 'FAN14G1187' => 'fan', 'FAN14G1727' => 'fan', 'FAN14G1791' => 'fan', 'FAN14G2361' => 'fan', 'FAN14G2668' => 'fan', 'FAN14G2770' => 'fan', 'FAN14G2874' => 'fan', 'FAN14G3193' => 'fan', 'FAN14G3624' => 'fan', 'FAN14G3676' => 'fan', 'FAN14G3807' => 'fan', 'FAN14G4082' => 'fan', 'FAN14G4342' => 'fan', 'FAN14G4985' => 'fan', 'FAN14G5126' => 'fan', 'FAN14G5781' => 'fan', 'FAN14G5808' => 'fan', 'FAN14G5949' => 'fan', 'FAN15G0828' => 'fan', 'FAN15G1054' => 'fan', 'FAN15G2023' => 'fan', 'FAN15G2506' => 'fan', 'FAN16G0128' => 'fan', 'FAN16G0249' => 'fan', 'FAN16G0429' => 'fan', 'FAN16G1493' => 'fan', 'FAN16G2210' => 'fan', 'FAN16G2506' => 'fan', 'FAN18G1542' => 'fan', 'FAN18G4057' => 'fan', 'FAN19G0745' => 'fan', 'FAN19G1216' => 'fan', 'FAN19G1733' => 'fan', 'FAN20G0258' => 'fan', 'FAN20G1095' => 'fan', 'FAN20G1557' => 'fan', 'FAN21G0302' => 'fan', 'FAN21G0519' => 'fan', 'FAN21G0970' => 'fan', 'FAN21G1159' => 'fan', 'FAN21G1312' => 'fan', 'FAN21G1440' => 'fan', 'FAN21G1715' => 'fan', 'FAN23G1584' => 'fan', 'FAN24G0045' => 'fan', 'FAN24G0053' => 'fan', 'FAN24G1500' => 'fan', 'FAN24G1817' => 'fan', 'FAN24G2147' => 'fan', 'FAN24G2236' => 'fan', 'FAN24G2446' => 'fan', 'FAN24G2684' => 'fan', 'FAN25G0187' => 'fan', 'FAN25G0505' => 'fan', 'FAN25G0589' => 'fan', 'FAN25G3663' => 'fan', 'FAN26G1025' => 'fan', 'FAN26G2860' => 'fan', 'FAN27G1329' => 'fan', 'FAN27G3392' => 'fan', 'FvH4_1g02011' => 'fve', 'FvH4_1g06511' => 'fve', 'FvH4_2g19900' => 'fve', 'FvH4_2g19920' => 'fve', 'FvH4_2g24261' => 'fve', 'FvH4_2g24270' => 'fve', 'FvH4_2g24631' => 'fve', 'FvH4_2g30622' => 'fve', 'FvH4_3g12920' => 'fve', 'FvH4_3g30171' => 'fve', 'FvH4_3g35490' => 'fve', 'FvH4_3g43682' => 'fve', 'FvH4_3g43730' => 'fve', 'FvH4_3g43732' => 'fve', 'FvH4_3g43751' => 'fve', 'FvH4_3g43752' => 'fve', 'FvH4_3g43770' => 'fve', 'FvH4_3g44471' => 'fve', 'FvH4_3g44510' => 'fve', 'FvH4_3g44582' => 'fve', 'FvH4_4g16921' => 'fve', 'FvH4_4g17121' => 'fve', 'FvH4_4g17782' => 'fve', 'FvH4_4g17783' => 'fve', 'FvH4_4g18120' => 'fve', 'FvH4_4g31310' => 'fve', 'FvH4_4g35052' => 'fve', 'FvH4_5g30862' => 'fve', 'FvH4_6g01541' => 'fve', 'FvH4_6g02021' => 'fve', 'FvH4_6g02041' => 'fve', 'FvH4_6g02071' => 'fve', 'FvH4_6g02171' => 'fve', 'FvH4_6g03181' => 'fve', 'FvH4_6g03182' => 'fve', 'FvH4_6g03221' => 'fve', 'FvH4_6g03380' => 'fve', 'FvH4_6g05201' => 'fve', 'FvH4_6g05203' => 'fve', 'FvH4_6g20231' => 'fve', 'FvH4_6g31981' => 'fve', 'FvH4_6g32061' => 'fve', 'FvH4_6g37041' => 'fve', 'FvH4_6g37932' => 'fve', 'FvH4_6g38731' => 'fve', 'FvH4_6g39370' => 'fve', 'FvH4_6g39371' => 'fve', 'FvH4_6g40891' => 'fve', 'FvH4_6g40892' => 'fve', 'FvH4_6g43143' => 'fve', 'FvH4_6g45251' => 'fve', 'FvH4_6g45260' => 'fve', 'FvH4_6g45291' => 'fve', 'FvH4_6g45890' => 'fve', 'FvH4_6g46240' => 'fve', 'FvH4_6g46241' => 'fve', 'FvH4_6g46242' => 'fve', 'FvH4_6g46260' => 'fve', 'FvH4_6g46280' => 'fve', 'FvH4_6g46380' => 'fve', 'FvH4_7g12841' => 'fve', 'FvH4_7g31431' => 'fve', 'Glyma.09G075900' => 'gma', 'Gohir.A09G096401' => 'ghi', 'Gohir.D09G096101' => 'ghi', 'Gorai.006G112800' => 'gra', 'HanXRQChr04g0121411' => 'han', 'Hund15878' => 'sun', 'Lj2A1107G68' => 'lonja', 'Lj2A630G63' => 'lonja', 'Lj2A946T25' => 'lonja', 'Lj2C714T1' => 'lonja', 'Lj2C966T3' => 'lonja', 'Lj2C966T4' => 'lonja', 'Lj4g0002979' => 'lja', 'Lsat_1_v5_gn_5_30901' => 'lsa', 'Lsat_1_v5_gn_5_31100' => 'lsa', 'Lsat_1_v5_gn_5_38600' => 'lsa', 'Lsat_1_v5_gn_6_92061' => 'lsa', 'Manes.05G071301' => 'mes', 'MD02G1008700' => 'mdo', 'MD02G1008900' => 'mdo', 'MD03G1256400' => 'mdo', 'MD04G1180900' => 'mdo', 'MD04G1181000' => 'mdo', 'MD04G1181200' => 'mdo', 'MD05G1244200' => 'mdo', 'MD05G1324200' => 'mdo', 'MD09G1201600' => 'mdo', 'MD10G1000600' => 'mdo', 'MD14G1026900' => 'mdo', 'MD14G1187900' => 'mdo', 'MD15G1017800' => 'mdo', 'MD15G1018100' => 'mdo', 'Medtr4g124160' => 'mtr', 'Migut.L01260' => 'egut', 'Nitab4.5_0000008g0440' => 'nta', 'Nitab4.5_0000207g0170' => 'nta', 'Nitab4.5_0007671g0030' => 'nta', 'Nitab4.5_0010853g0020' => 'nta', 'Oeu057656.1' => 'oeu', 'PGSC0003DMG400005638' => 'stu', 'PGSC0003DMG400005639' => 'stu', 'Phvul.009G222800' => 'pvu', 'Potri.009G132400' => 'ptr', 'Potri.009G163001' => 'ptr', 'Potri.011G000700' => 'ptr', 'Potri.011G004800' => 'ptr', 'Prupe.1G509300' => 'ppe', 'Prupe.1G509700' => 'ppe', 'Prupe.1G510400' => 'ppe', 'Prupe.1G510700' => 'ppe', 'Prupe.1G512600' => 'ppe', 'Prupe.2G073200' => 'ppe', 'Prupe.3G059500' => 'ppe', 'Prupe.3G059600' => 'ppe', 'Prupe.3G246100' => 'ppe', 'Prupe.3G265100' => 'ppe', 'Prupe.4G034700' => 'ppe', 'Prupe.4G052100' => 'ppe', 'Prupe.4G053600' => 'ppe', 'Prupe.5G068800' => 'ppe', 'Prupe.5G070600' => 'ppe', 'Prupe.6G075400' => 'ppe', 'Prupe.6G075500' => 'ppe', 'Prupe.6G076400' => 'ppe', 'Prupe.8G110700' => 'ppe', 'Psat4g020960' => 'psa', 'PSO135G0788' => 'pso', 'PSO210G6463' => 'pso', 'PSO384G0370' => 'pso', 'PSO386G0056' => 'pso', 'QL01p006048' => 'qlo', 'QL02p054283' => 'qlo', 'QL05p008000' => 'qlo', 'QL05p008212' => 'qlo', 'QL05p008950' => 'qlo', 'QL05p009042' => 'qlo', 'QL05p009518' => 'qlo', 'QL05p012589' => 'qlo', 'QL05p012608' => 'qlo', 'QL05p012650' => 'qlo', 'QL05p012667' => 'qlo', 'QL05p014501' => 'qlo', 'QL05p052800' => 'qlo', 'QL05p065010' => 'qlo', 'QL05p074156' => 'qlo', 'QL05p074160' => 'qlo', 'QL05p074174' => 'qlo', 'QL05p074178' => 'qlo', 'QL05p074214' => 'qlo', 'QL06p001050' => 'qlo', 'QL06p001056' => 'qlo', 'QL06p006093' => 'qlo', 'QL06p006111' => 'qlo', 'QL07p019784' => 'qlo', 'QL07p019801' => 'qlo', 'QL07p036110' => 'qlo', 'QL07p036134' => 'qlo', 'QL07p036147' => 'qlo', 'QL07p036156' => 'qlo', 'QL07p036300' => 'qlo', 'QL07p036320' => 'qlo', 'QL08p014547' => 'qlo', 'QL08p014551' => 'qlo', 'QL08p043319' => 'qlo', 'QL08p043324' => 'qlo', 'QL11p009094' => 'qlo', 'RcHm_v2.0_Chr1g0380481' => 'rch', 'RcHm_v2.0_Chr2g0089331' => 'rch', 'RcHm_v2.0_Chr2g0123691' => 'rch', 'RcHm_v2.0_Chr2g0151111' => 'rch', 'RcHm_v2.0_Chr2g0163011' => 'rch', 'RcHm_v2.0_Chr2g0163051' => 'rch', 'RcHm_v2.0_Chr2g0164671' => 'rch', 'RcHm_v2.0_Chr2g0164681' => 'rch', 'RcHm_v2.0_Chr2g0164721' => 'rch', 'RcHm_v2.0_Chr3g0449911' => 'rch', 'RcHm_v2.0_Chr3g0450211' => 'rch', 'RcHm_v2.0_Chr3g0457271' => 'rch', 'RcHm_v2.0_Chr5g0018111' => 'rch', 'RcHm_v2.0_Chr5g0021011' => 'rch', 'RcHm_v2.0_Chr5g0081171' => 'rch', 'RcHm_v2.0_Chr5g0081211' => 'rch', 'RcHm_v2.0_Chr6g0275871' => 'rch', 'RcHm_v2.0_Chr6g0276071' => 'rch', 'RcHm_v2.0_Chr6g0285591' => 'rch', 'RcHm_v2.0_Chr6g0291931' => 'rch', 'RcHm_v2.0_Chr6g0292091' => 'rch', 'RcHm_v2.0_Chr6g0292271' => 'rch', 'RcHm_v2.0_Chr7g0221261' => 'rch', 'Rhsim08G0219900' => 'rsi', 'Rhsim08G0220200' => 'rsi', 'Rhsim08G0237800' => 'rsi', 'Rhsim08G0238800' => 'rsi', 'Sabra09G0102700' => 'sbr', 'Sabra09G0127200' => 'sbr', 'Sabra11G0003700' => 'sbr', 'Sabra15G0014700' => 'sbr', 'Sc19g0000590' => 'sci', 'Sc19g0001870' => 'sci', 'SGA_v2.0_scaffold1G00346' => 'sas', 'SGA_v2.0_scaffold1G00575' => 'sas', 'SGA_v2.0_scaffold1G00761' => 'sas', 'SGA_v2.0_scaffold232G43501' => 'sas', 'TAR625G1137' => 'tar', 'Thecc.03G222100' => 'tca', 'TPR.G12691' => 'tpr', 'TWI34G0727' => 'twi', 'TWI36G0117' => 'twi', 'VMungo1309G0868' => 'vmu' ) $gf_id = 'HOM05D001729' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001729' ) $data_identifier = 'HOM05D001729' $data_type = 'gf_id' $species_gene_counts = array( 'amhyb' => (int) 1, 'cqu' => (int) 9, 'can' => (int) 1, 'cansat' => (int) 1, 'car' => (int) 1, 'col' => (int) 5, 'dca' => (int) 1, 'din' => (int) 2, 'dzi' => (int) 3, 'fan' => (int) 140, 'fve' => (int) 62, 'gma' => (int) 1, 'ghi' => (int) 2, 'gra' => (int) 1, 'han' => (int) 1, 'sun' => (int) 1, 'lonja' => (int) 6, 'lja' => (int) 1, 'lsa' => (int) 4, 'mes' => (int) 1, 'mdo' => (int) 14, 'mtr' => (int) 1, 'egut' => (int) 1, 'nta' => (int) 4, 'oeu' => (int) 1, 'stu' => (int) 2, 'pvu' => (int) 1, 'ptr' => (int) 4, 'ppe' => (int) 19, 'psa' => (int) 1, 'pso' => (int) 4, 'qlo' => (int) 36, 'rch' => (int) 23, 'rsi' => (int) 4, 'sbr' => (int) 4, 'sci' => (int) 2, 'sas' => (int) 4, 'tar' => (int) 1, 'tca' => (int) 1, 'tpr' => (int) 1, 'twi' => (int) 2, 'vmu' => (int) 1 ) $gf_gene_species = 'vmu' $gf_gene_id = 'VMungo1309G0868' $species_info = array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ) $local_species = 'ptr' $disabled = '' $selected = '' $num_hits = (int) 1
Warning (2): count(): Parameter must be an array or an object that implements Countable [APP/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp, line 33]Code Context $disabled = (!array_key_exists($local_species,$species_gene_counts))?"disabled":""; $selected = (isset($selected_species) && array_key_exists($local_species,$selected_species))?"checked='checked'":""; $num_hits = (array_key_exists($local_species,$species_gene_counts))?count($species_gene_counts[$local_species]):0; $viewFile = '/www/bioinformatics01_ro/plaza/_dev_instances/feedback/app/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp' $dataForView = array( 'sidebar_info' => array( 'gf_id' => 'HOM05D001729', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '375', 'num_species' => '42' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'Ah.07g204710' => 'amhyb', 'AUR62006001' => 'cqu', 'AUR62006002' => 'cqu', 'AUR62006003' => 'cqu', 'AUR62015641' => 'cqu', 'AUR62027174' => 'cqu', 'AUR62035623' => 'cqu', 'AUR62035624' => 'cqu', 'AUR62035625' => 'cqu', 'AUR62035626' => 'cqu', 'CAN.G1110.53' => 'can', 'CANSAT80G0415' => 'cansat', 'Ca_21364_v3' => 'car', 'COL.COLO4_30693' => 'col', 'COL.COLO4_30694' => 'col', 'COL.COLO4_30695' => 'col', 'COL.COLO4_30696' => 'col', 'COL.COLO4_34020' => 'col', 'DCAR_004585' => 'dca', 'Dinv04029' => 'din', 'Dinv34857' => 'din', 'Duzib147G0011' => 'dzi', 'Duzib170G0599' => 'dzi', 'Duzib192G1051' => 'dzi', 'FAN01G0708' => 'fan', 'FAN01G0742' => 'fan', 'FAN02G0048' => 'fan', 'FAN02G0583' => 'fan', 'FAN02G0688' => 'fan', 'FAN02G1588' => 'fan', 'FAN02G2194' => 'fan', 'FAN02G2750' => 'fan', 'FAN02G3094' => 'fan', 'FAN02G3887' => 'fan', 'FAN02G3911' => 'fan', 'FAN02G3994' => 'fan', 'FAN02G4432' => 'fan', 'FAN02G4556' => 'fan', 'FAN03G1977' => 'fan', 'FAN03G2781' => 'fan', 'FAN03G2850' => 'fan', 'FAN03G3155' => 'fan', 'FAN04G2487' => 'fan', 'FAN05G0208' => 'fan', 'FAN05G0656' => 'fan', 'FAN05G0696' => 'fan', 'FAN05G0810' => 'fan', 'FAN05G1447' => 'fan', 'FAN05G2640' => 'fan', 'FAN05G2911' => 'fan', 'FAN05G3901' => 'fan', 'FAN05G4859' => 'fan', 'FAN05G4861' => 'fan', 'FAN05G4988' => 'fan', 'FAN05G5187' => 'fan', 'FAN05G5452' => 'fan', 'FAN05G5500' => 'fan', 'FAN05G5688' => 'fan', 'FAN06G0177' => 'fan', 'FAN06G0675' => 'fan', 'FAN06G1290' => 'fan', 'FAN06G2191' => 'fan', 'FAN06G2405' => 'fan', 'FAN06G3231' => 'fan', 'FAN06G3932' => 'fan', 'FAN07G0163' => 'fan', 'FAN07G0471' => 'fan', 'FAN07G1354' => 'fan', 'FAN08G0338' => 'fan', 'FAN08G1373' => 'fan', 'FAN08G2539' => 'fan', 'FAN08G2728' => 'fan', 'FAN09G0608' => 'fan', 'FAN09G1136' => 'fan', 'FAN09G1958' => 'fan', 'FAN09G2508' => 'fan', 'FAN09G2597' => 'fan', 'FAN09G2658' => 'fan', 'FAN09G2757' => 'fan', 'FAN09G2983' => 'fan', 'FAN09G3130' => 'fan', 'FAN09G3565' => 'fan', 'FAN09G3613' => 'fan', 'FAN09G4011' => 'fan', 'FAN09G4239' => 'fan', 'FAN09G4277' => 'fan', 'FAN09G4720' => 'fan', 'FAN11G0139' => 'fan', 'FAN11G1727' => 'fan', 'FAN11G2672' => 'fan', 'FAN11G2795' => 'fan', 'FAN11G3238' => 'fan', 'FAN11G3734' => 'fan', 'FAN12G0631' => 'fan', 'FAN12G2239' => 'fan', 'FAN12G2308' => 'fan', 'FAN12G2569' => 'fan', 'FAN12G2623' => 'fan', 'FAN13G3182' => 'fan', 'FAN14G0053' => 'fan', 'FAN14G0370' => 'fan', 'FAN14G0382' => 'fan', 'FAN14G0421' => 'fan', 'FAN14G0866' => 'fan', 'FAN14G1187' => 'fan', 'FAN14G1727' => 'fan', 'FAN14G1791' => 'fan', 'FAN14G2361' => 'fan', 'FAN14G2668' => 'fan', 'FAN14G2770' => 'fan', 'FAN14G2874' => 'fan', 'FAN14G3193' => 'fan', 'FAN14G3624' => 'fan', 'FAN14G3676' => 'fan', 'FAN14G3807' => 'fan', 'FAN14G4082' => 'fan', 'FAN14G4342' => 'fan', 'FAN14G4985' => 'fan', 'FAN14G5126' => 'fan', 'FAN14G5781' => 'fan', 'FAN14G5808' => 'fan', 'FAN14G5949' => 'fan', 'FAN15G0828' => 'fan', 'FAN15G1054' => 'fan', 'FAN15G2023' => 'fan', 'FAN15G2506' => 'fan', 'FAN16G0128' => 'fan', 'FAN16G0249' => 'fan', 'FAN16G0429' => 'fan', 'FAN16G1493' => 'fan', 'FAN16G2210' => 'fan', 'FAN16G2506' => 'fan', 'FAN18G1542' => 'fan', 'FAN18G4057' => 'fan', 'FAN19G0745' => 'fan', 'FAN19G1216' => 'fan', 'FAN19G1733' => 'fan', 'FAN20G0258' => 'fan', 'FAN20G1095' => 'fan', 'FAN20G1557' => 'fan', 'FAN21G0302' => 'fan', 'FAN21G0519' => 'fan', 'FAN21G0970' => 'fan', 'FAN21G1159' => 'fan', 'FAN21G1312' => 'fan', 'FAN21G1440' => 'fan', 'FAN21G1715' => 'fan', 'FAN23G1584' => 'fan', 'FAN24G0045' => 'fan', 'FAN24G0053' => 'fan', 'FAN24G1500' => 'fan', 'FAN24G1817' => 'fan', 'FAN24G2147' => 'fan', 'FAN24G2236' => 'fan', 'FAN24G2446' => 'fan', 'FAN24G2684' => 'fan', 'FAN25G0187' => 'fan', 'FAN25G0505' => 'fan', 'FAN25G0589' => 'fan', 'FAN25G3663' => 'fan', 'FAN26G1025' => 'fan', 'FAN26G2860' => 'fan', 'FAN27G1329' => 'fan', 'FAN27G3392' => 'fan', 'FvH4_1g02011' => 'fve', 'FvH4_1g06511' => 'fve', 'FvH4_2g19900' => 'fve', 'FvH4_2g19920' => 'fve', 'FvH4_2g24261' => 'fve', 'FvH4_2g24270' => 'fve', 'FvH4_2g24631' => 'fve', 'FvH4_2g30622' => 'fve', 'FvH4_3g12920' => 'fve', 'FvH4_3g30171' => 'fve', 'FvH4_3g35490' => 'fve', 'FvH4_3g43682' => 'fve', 'FvH4_3g43730' => 'fve', 'FvH4_3g43732' => 'fve', 'FvH4_3g43751' => 'fve', 'FvH4_3g43752' => 'fve', 'FvH4_3g43770' => 'fve', 'FvH4_3g44471' => 'fve', 'FvH4_3g44510' => 'fve', 'FvH4_3g44582' => 'fve', 'FvH4_4g16921' => 'fve', 'FvH4_4g17121' => 'fve', 'FvH4_4g17782' => 'fve', 'FvH4_4g17783' => 'fve', 'FvH4_4g18120' => 'fve', 'FvH4_4g31310' => 'fve', 'FvH4_4g35052' => 'fve', 'FvH4_5g30862' => 'fve', 'FvH4_6g01541' => 'fve', 'FvH4_6g02021' => 'fve', 'FvH4_6g02041' => 'fve', 'FvH4_6g02071' => 'fve', 'FvH4_6g02171' => 'fve', 'FvH4_6g03181' => 'fve', 'FvH4_6g03182' => 'fve', 'FvH4_6g03221' => 'fve', 'FvH4_6g03380' => 'fve', 'FvH4_6g05201' => 'fve', 'FvH4_6g05203' => 'fve', 'FvH4_6g20231' => 'fve', 'FvH4_6g31981' => 'fve', 'FvH4_6g32061' => 'fve', 'FvH4_6g37041' => 'fve', 'FvH4_6g37932' => 'fve', 'FvH4_6g38731' => 'fve', 'FvH4_6g39370' => 'fve', 'FvH4_6g39371' => 'fve', 'FvH4_6g40891' => 'fve', 'FvH4_6g40892' => 'fve', 'FvH4_6g43143' => 'fve', 'FvH4_6g45251' => 'fve', 'FvH4_6g45260' => 'fve', 'FvH4_6g45291' => 'fve', 'FvH4_6g45890' => 'fve', 'FvH4_6g46240' => 'fve', 'FvH4_6g46241' => 'fve', 'FvH4_6g46242' => 'fve', 'FvH4_6g46260' => 'fve', 'FvH4_6g46280' => 'fve', 'FvH4_6g46380' => 'fve', 'FvH4_7g12841' => 'fve', 'FvH4_7g31431' => 'fve', 'Glyma.09G075900' => 'gma', 'Gohir.A09G096401' => 'ghi', 'Gohir.D09G096101' => 'ghi', 'Gorai.006G112800' => 'gra', 'HanXRQChr04g0121411' => 'han', 'Hund15878' => 'sun', 'Lj2A1107G68' => 'lonja', 'Lj2A630G63' => 'lonja', 'Lj2A946T25' => 'lonja', 'Lj2C714T1' => 'lonja', 'Lj2C966T3' => 'lonja', 'Lj2C966T4' => 'lonja', 'Lj4g0002979' => 'lja', 'Lsat_1_v5_gn_5_30901' => 'lsa', 'Lsat_1_v5_gn_5_31100' => 'lsa', 'Lsat_1_v5_gn_5_38600' => 'lsa', 'Lsat_1_v5_gn_6_92061' => 'lsa', 'Manes.05G071301' => 'mes', 'MD02G1008700' => 'mdo', 'MD02G1008900' => 'mdo', 'MD03G1256400' => 'mdo', 'MD04G1180900' => 'mdo', 'MD04G1181000' => 'mdo', 'MD04G1181200' => 'mdo', 'MD05G1244200' => 'mdo', 'MD05G1324200' => 'mdo', 'MD09G1201600' => 'mdo', 'MD10G1000600' => 'mdo', 'MD14G1026900' => 'mdo', 'MD14G1187900' => 'mdo', 'MD15G1017800' => 'mdo', 'MD15G1018100' => 'mdo', 'Medtr4g124160' => 'mtr', 'Migut.L01260' => 'egut', 'Nitab4.5_0000008g0440' => 'nta', 'Nitab4.5_0000207g0170' => 'nta', 'Nitab4.5_0007671g0030' => 'nta', 'Nitab4.5_0010853g0020' => 'nta', 'Oeu057656.1' => 'oeu', 'PGSC0003DMG400005638' => 'stu', 'PGSC0003DMG400005639' => 'stu', 'Phvul.009G222800' => 'pvu', 'Potri.009G132400' => 'ptr', 'Potri.009G163001' => 'ptr', 'Potri.011G000700' => 'ptr', 'Potri.011G004800' => 'ptr', 'Prupe.1G509300' => 'ppe', 'Prupe.1G509700' => 'ppe', 'Prupe.1G510400' => 'ppe', 'Prupe.1G510700' => 'ppe', 'Prupe.1G512600' => 'ppe', 'Prupe.2G073200' => 'ppe', 'Prupe.3G059500' => 'ppe', 'Prupe.3G059600' => 'ppe', 'Prupe.3G246100' => 'ppe', 'Prupe.3G265100' => 'ppe', 'Prupe.4G034700' => 'ppe', 'Prupe.4G052100' => 'ppe', 'Prupe.4G053600' => 'ppe', 'Prupe.5G068800' => 'ppe', 'Prupe.5G070600' => 'ppe', 'Prupe.6G075400' => 'ppe', 'Prupe.6G075500' => 'ppe', 'Prupe.6G076400' => 'ppe', 'Prupe.8G110700' => 'ppe', 'Psat4g020960' => 'psa', 'PSO135G0788' => 'pso', 'PSO210G6463' => 'pso', 'PSO384G0370' => 'pso', 'PSO386G0056' => 'pso', 'QL01p006048' => 'qlo', 'QL02p054283' => 'qlo', 'QL05p008000' => 'qlo', 'QL05p008212' => 'qlo', 'QL05p008950' => 'qlo', 'QL05p009042' => 'qlo', 'QL05p009518' => 'qlo', 'QL05p012589' => 'qlo', 'QL05p012608' => 'qlo', 'QL05p012650' => 'qlo', 'QL05p012667' => 'qlo', 'QL05p014501' => 'qlo', 'QL05p052800' => 'qlo', 'QL05p065010' => 'qlo', 'QL05p074156' => 'qlo', 'QL05p074160' => 'qlo', 'QL05p074174' => 'qlo', 'QL05p074178' => 'qlo', 'QL05p074214' => 'qlo', 'QL06p001050' => 'qlo', 'QL06p001056' => 'qlo', 'QL06p006093' => 'qlo', 'QL06p006111' => 'qlo', 'QL07p019784' => 'qlo', 'QL07p019801' => 'qlo', 'QL07p036110' => 'qlo', 'QL07p036134' => 'qlo', 'QL07p036147' => 'qlo', 'QL07p036156' => 'qlo', 'QL07p036300' => 'qlo', 'QL07p036320' => 'qlo', 'QL08p014547' => 'qlo', 'QL08p014551' => 'qlo', 'QL08p043319' => 'qlo', 'QL08p043324' => 'qlo', 'QL11p009094' => 'qlo', 'RcHm_v2.0_Chr1g0380481' => 'rch', 'RcHm_v2.0_Chr2g0089331' => 'rch', 'RcHm_v2.0_Chr2g0123691' => 'rch', 'RcHm_v2.0_Chr2g0151111' => 'rch', 'RcHm_v2.0_Chr2g0163011' => 'rch', 'RcHm_v2.0_Chr2g0163051' => 'rch', 'RcHm_v2.0_Chr2g0164671' => 'rch', 'RcHm_v2.0_Chr2g0164681' => 'rch', 'RcHm_v2.0_Chr2g0164721' => 'rch', 'RcHm_v2.0_Chr3g0449911' => 'rch', 'RcHm_v2.0_Chr3g0450211' => 'rch', 'RcHm_v2.0_Chr3g0457271' => 'rch', 'RcHm_v2.0_Chr5g0018111' => 'rch', 'RcHm_v2.0_Chr5g0021011' => 'rch', 'RcHm_v2.0_Chr5g0081171' => 'rch', 'RcHm_v2.0_Chr5g0081211' => 'rch', 'RcHm_v2.0_Chr6g0275871' => 'rch', 'RcHm_v2.0_Chr6g0276071' => 'rch', 'RcHm_v2.0_Chr6g0285591' => 'rch', 'RcHm_v2.0_Chr6g0291931' => 'rch', 'RcHm_v2.0_Chr6g0292091' => 'rch', 'RcHm_v2.0_Chr6g0292271' => 'rch', 'RcHm_v2.0_Chr7g0221261' => 'rch', 'Rhsim08G0219900' => 'rsi', 'Rhsim08G0220200' => 'rsi', 'Rhsim08G0237800' => 'rsi', 'Rhsim08G0238800' => 'rsi', 'Sabra09G0102700' => 'sbr', 'Sabra09G0127200' => 'sbr', 'Sabra11G0003700' => 'sbr', 'Sabra15G0014700' => 'sbr', 'Sc19g0000590' => 'sci', 'Sc19g0001870' => 'sci', 'SGA_v2.0_scaffold1G00346' => 'sas', 'SGA_v2.0_scaffold1G00575' => 'sas', 'SGA_v2.0_scaffold1G00761' => 'sas', 'SGA_v2.0_scaffold232G43501' => 'sas', 'TAR625G1137' => 'tar', 'Thecc.03G222100' => 'tca', 'TPR.G12691' => 'tpr', 'TWI34G0727' => 'twi', 'TWI36G0117' => 'twi', 'VMungo1309G0868' => 'vmu' ), 'gf_id' => 'HOM05D001729', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001729' ), 'data_identifier' => 'HOM05D001729', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001729', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '375', 'num_species' => '42' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'Ah.07g204710' => 'amhyb', 'AUR62006001' => 'cqu', 'AUR62006002' => 'cqu', 'AUR62006003' => 'cqu', 'AUR62015641' => 'cqu', 'AUR62027174' => 'cqu', 'AUR62035623' => 'cqu', 'AUR62035624' => 'cqu', 'AUR62035625' => 'cqu', 'AUR62035626' => 'cqu', 'CAN.G1110.53' => 'can', 'CANSAT80G0415' => 'cansat', 'Ca_21364_v3' => 'car', 'COL.COLO4_30693' => 'col', 'COL.COLO4_30694' => 'col', 'COL.COLO4_30695' => 'col', 'COL.COLO4_30696' => 'col', 'COL.COLO4_34020' => 'col', 'DCAR_004585' => 'dca', 'Dinv04029' => 'din', 'Dinv34857' => 'din', 'Duzib147G0011' => 'dzi', 'Duzib170G0599' => 'dzi', 'Duzib192G1051' => 'dzi', 'FAN01G0708' => 'fan', 'FAN01G0742' => 'fan', 'FAN02G0048' => 'fan', 'FAN02G0583' => 'fan', 'FAN02G0688' => 'fan', 'FAN02G1588' => 'fan', 'FAN02G2194' => 'fan', 'FAN02G2750' => 'fan', 'FAN02G3094' => 'fan', 'FAN02G3887' => 'fan', 'FAN02G3911' => 'fan', 'FAN02G3994' => 'fan', 'FAN02G4432' => 'fan', 'FAN02G4556' => 'fan', 'FAN03G1977' => 'fan', 'FAN03G2781' => 'fan', 'FAN03G2850' => 'fan', 'FAN03G3155' => 'fan', 'FAN04G2487' => 'fan', 'FAN05G0208' => 'fan', 'FAN05G0656' => 'fan', 'FAN05G0696' => 'fan', 'FAN05G0810' => 'fan', 'FAN05G1447' => 'fan', 'FAN05G2640' => 'fan', 'FAN05G2911' => 'fan', 'FAN05G3901' => 'fan', 'FAN05G4859' => 'fan', 'FAN05G4861' => 'fan', 'FAN05G4988' => 'fan', 'FAN05G5187' => 'fan', 'FAN05G5452' => 'fan', 'FAN05G5500' => 'fan', 'FAN05G5688' => 'fan', 'FAN06G0177' => 'fan', 'FAN06G0675' => 'fan', 'FAN06G1290' => 'fan', 'FAN06G2191' => 'fan', 'FAN06G2405' => 'fan', 'FAN06G3231' => 'fan', 'FAN06G3932' => 'fan', 'FAN07G0163' => 'fan', 'FAN07G0471' => 'fan', 'FAN07G1354' => 'fan', 'FAN08G0338' => 'fan', 'FAN08G1373' => 'fan', 'FAN08G2539' => 'fan', 'FAN08G2728' => 'fan', 'FAN09G0608' => 'fan', 'FAN09G1136' => 'fan', 'FAN09G1958' => 'fan', 'FAN09G2508' => 'fan', 'FAN09G2597' => 'fan', 'FAN09G2658' => 'fan', 'FAN09G2757' => 'fan', 'FAN09G2983' => 'fan', 'FAN09G3130' => 'fan', 'FAN09G3565' => 'fan', 'FAN09G3613' => 'fan', 'FAN09G4011' => 'fan', 'FAN09G4239' => 'fan', 'FAN09G4277' => 'fan', 'FAN09G4720' => 'fan', 'FAN11G0139' => 'fan', 'FAN11G1727' => 'fan', 'FAN11G2672' => 'fan', 'FAN11G2795' => 'fan', 'FAN11G3238' => 'fan', 'FAN11G3734' => 'fan', 'FAN12G0631' => 'fan', 'FAN12G2239' => 'fan', 'FAN12G2308' => 'fan', 'FAN12G2569' => 'fan', 'FAN12G2623' => 'fan', 'FAN13G3182' => 'fan', 'FAN14G0053' => 'fan', 'FAN14G0370' => 'fan', 'FAN14G0382' => 'fan', 'FAN14G0421' => 'fan', 'FAN14G0866' => 'fan', 'FAN14G1187' => 'fan', 'FAN14G1727' => 'fan', 'FAN14G1791' => 'fan', 'FAN14G2361' => 'fan', 'FAN14G2668' => 'fan', 'FAN14G2770' => 'fan', 'FAN14G2874' => 'fan', 'FAN14G3193' => 'fan', 'FAN14G3624' => 'fan', 'FAN14G3676' => 'fan', 'FAN14G3807' => 'fan', 'FAN14G4082' => 'fan', 'FAN14G4342' => 'fan', 'FAN14G4985' => 'fan', 'FAN14G5126' => 'fan', 'FAN14G5781' => 'fan', 'FAN14G5808' => 'fan', 'FAN14G5949' => 'fan', 'FAN15G0828' => 'fan', 'FAN15G1054' => 'fan', 'FAN15G2023' => 'fan', 'FAN15G2506' => 'fan', 'FAN16G0128' => 'fan', 'FAN16G0249' => 'fan', 'FAN16G0429' => 'fan', 'FAN16G1493' => 'fan', 'FAN16G2210' => 'fan', 'FAN16G2506' => 'fan', 'FAN18G1542' => 'fan', 'FAN18G4057' => 'fan', 'FAN19G0745' => 'fan', 'FAN19G1216' => 'fan', 'FAN19G1733' => 'fan', 'FAN20G0258' => 'fan', 'FAN20G1095' => 'fan', 'FAN20G1557' => 'fan', 'FAN21G0302' => 'fan', 'FAN21G0519' => 'fan', 'FAN21G0970' => 'fan', 'FAN21G1159' => 'fan', 'FAN21G1312' => 'fan', 'FAN21G1440' => 'fan', 'FAN21G1715' => 'fan', 'FAN23G1584' => 'fan', 'FAN24G0045' => 'fan', 'FAN24G0053' => 'fan', 'FAN24G1500' => 'fan', 'FAN24G1817' => 'fan', 'FAN24G2147' => 'fan', 'FAN24G2236' => 'fan', 'FAN24G2446' => 'fan', 'FAN24G2684' => 'fan', 'FAN25G0187' => 'fan', 'FAN25G0505' => 'fan', 'FAN25G0589' => 'fan', 'FAN25G3663' => 'fan', 'FAN26G1025' => 'fan', 'FAN26G2860' => 'fan', 'FAN27G1329' => 'fan', 'FAN27G3392' => 'fan', 'FvH4_1g02011' => 'fve', 'FvH4_1g06511' => 'fve', 'FvH4_2g19900' => 'fve', 'FvH4_2g19920' => 'fve', 'FvH4_2g24261' => 'fve', 'FvH4_2g24270' => 'fve', 'FvH4_2g24631' => 'fve', 'FvH4_2g30622' => 'fve', 'FvH4_3g12920' => 'fve', 'FvH4_3g30171' => 'fve', 'FvH4_3g35490' => 'fve', 'FvH4_3g43682' => 'fve', 'FvH4_3g43730' => 'fve', 'FvH4_3g43732' => 'fve', 'FvH4_3g43751' => 'fve', 'FvH4_3g43752' => 'fve', 'FvH4_3g43770' => 'fve', 'FvH4_3g44471' => 'fve', 'FvH4_3g44510' => 'fve', 'FvH4_3g44582' => 'fve', 'FvH4_4g16921' => 'fve', 'FvH4_4g17121' => 'fve', 'FvH4_4g17782' => 'fve', 'FvH4_4g17783' => 'fve', 'FvH4_4g18120' => 'fve', 'FvH4_4g31310' => 'fve', 'FvH4_4g35052' => 'fve', 'FvH4_5g30862' => 'fve', 'FvH4_6g01541' => 'fve', 'FvH4_6g02021' => 'fve', 'FvH4_6g02041' => 'fve', 'FvH4_6g02071' => 'fve', 'FvH4_6g02171' => 'fve', 'FvH4_6g03181' => 'fve', 'FvH4_6g03182' => 'fve', 'FvH4_6g03221' => 'fve', 'FvH4_6g03380' => 'fve', 'FvH4_6g05201' => 'fve', 'FvH4_6g05203' => 'fve', 'FvH4_6g20231' => 'fve', 'FvH4_6g31981' => 'fve', 'FvH4_6g32061' => 'fve', 'FvH4_6g37041' => 'fve', 'FvH4_6g37932' => 'fve', 'FvH4_6g38731' => 'fve', 'FvH4_6g39370' => 'fve', 'FvH4_6g39371' => 'fve', 'FvH4_6g40891' => 'fve', 'FvH4_6g40892' => 'fve', 'FvH4_6g43143' => 'fve', 'FvH4_6g45251' => 'fve', 'FvH4_6g45260' => 'fve', 'FvH4_6g45291' => 'fve', 'FvH4_6g45890' => 'fve', 'FvH4_6g46240' => 'fve', 'FvH4_6g46241' => 'fve', 'FvH4_6g46242' => 'fve', 'FvH4_6g46260' => 'fve', 'FvH4_6g46280' => 'fve', 'FvH4_6g46380' => 'fve', 'FvH4_7g12841' => 'fve', 'FvH4_7g31431' => 'fve', 'Glyma.09G075900' => 'gma', 'Gohir.A09G096401' => 'ghi', 'Gohir.D09G096101' => 'ghi', 'Gorai.006G112800' => 'gra', 'HanXRQChr04g0121411' => 'han', 'Hund15878' => 'sun', 'Lj2A1107G68' => 'lonja', 'Lj2A630G63' => 'lonja', 'Lj2A946T25' => 'lonja', 'Lj2C714T1' => 'lonja', 'Lj2C966T3' => 'lonja', 'Lj2C966T4' => 'lonja', 'Lj4g0002979' => 'lja', 'Lsat_1_v5_gn_5_30901' => 'lsa', 'Lsat_1_v5_gn_5_31100' => 'lsa', 'Lsat_1_v5_gn_5_38600' => 'lsa', 'Lsat_1_v5_gn_6_92061' => 'lsa', 'Manes.05G071301' => 'mes', 'MD02G1008700' => 'mdo', 'MD02G1008900' => 'mdo', 'MD03G1256400' => 'mdo', 'MD04G1180900' => 'mdo', 'MD04G1181000' => 'mdo', 'MD04G1181200' => 'mdo', 'MD05G1244200' => 'mdo', 'MD05G1324200' => 'mdo', 'MD09G1201600' => 'mdo', 'MD10G1000600' => 'mdo', 'MD14G1026900' => 'mdo', 'MD14G1187900' => 'mdo', 'MD15G1017800' => 'mdo', 'MD15G1018100' => 'mdo', 'Medtr4g124160' => 'mtr', 'Migut.L01260' => 'egut', 'Nitab4.5_0000008g0440' => 'nta', 'Nitab4.5_0000207g0170' => 'nta', 'Nitab4.5_0007671g0030' => 'nta', 'Nitab4.5_0010853g0020' => 'nta', 'Oeu057656.1' => 'oeu', 'PGSC0003DMG400005638' => 'stu', 'PGSC0003DMG400005639' => 'stu', 'Phvul.009G222800' => 'pvu', 'Potri.009G132400' => 'ptr', 'Potri.009G163001' => 'ptr', 'Potri.011G000700' => 'ptr', 'Potri.011G004800' => 'ptr', 'Prupe.1G509300' => 'ppe', 'Prupe.1G509700' => 'ppe', 'Prupe.1G510400' => 'ppe', 'Prupe.1G510700' => 'ppe', 'Prupe.1G512600' => 'ppe', 'Prupe.2G073200' => 'ppe', 'Prupe.3G059500' => 'ppe', 'Prupe.3G059600' => 'ppe', 'Prupe.3G246100' => 'ppe', 'Prupe.3G265100' => 'ppe', 'Prupe.4G034700' => 'ppe', 'Prupe.4G052100' => 'ppe', 'Prupe.4G053600' => 'ppe', 'Prupe.5G068800' => 'ppe', 'Prupe.5G070600' => 'ppe', 'Prupe.6G075400' => 'ppe', 'Prupe.6G075500' => 'ppe', 'Prupe.6G076400' => 'ppe', 'Prupe.8G110700' => 'ppe', 'Psat4g020960' => 'psa', 'PSO135G0788' => 'pso', 'PSO210G6463' => 'pso', 'PSO384G0370' => 'pso', 'PSO386G0056' => 'pso', 'QL01p006048' => 'qlo', 'QL02p054283' => 'qlo', 'QL05p008000' => 'qlo', 'QL05p008212' => 'qlo', 'QL05p008950' => 'qlo', 'QL05p009042' => 'qlo', 'QL05p009518' => 'qlo', 'QL05p012589' => 'qlo', 'QL05p012608' => 'qlo', 'QL05p012650' => 'qlo', 'QL05p012667' => 'qlo', 'QL05p014501' => 'qlo', 'QL05p052800' => 'qlo', 'QL05p065010' => 'qlo', 'QL05p074156' => 'qlo', 'QL05p074160' => 'qlo', 'QL05p074174' => 'qlo', 'QL05p074178' => 'qlo', 'QL05p074214' => 'qlo', 'QL06p001050' => 'qlo', 'QL06p001056' => 'qlo', 'QL06p006093' => 'qlo', 'QL06p006111' => 'qlo', 'QL07p019784' => 'qlo', 'QL07p019801' => 'qlo', 'QL07p036110' => 'qlo', 'QL07p036134' => 'qlo', 'QL07p036147' => 'qlo', 'QL07p036156' => 'qlo', 'QL07p036300' => 'qlo', 'QL07p036320' => 'qlo', 'QL08p014547' => 'qlo', 'QL08p014551' => 'qlo', 'QL08p043319' => 'qlo', 'QL08p043324' => 'qlo', 'QL11p009094' => 'qlo', 'RcHm_v2.0_Chr1g0380481' => 'rch', 'RcHm_v2.0_Chr2g0089331' => 'rch', 'RcHm_v2.0_Chr2g0123691' => 'rch', 'RcHm_v2.0_Chr2g0151111' => 'rch', 'RcHm_v2.0_Chr2g0163011' => 'rch', 'RcHm_v2.0_Chr2g0163051' => 'rch', 'RcHm_v2.0_Chr2g0164671' => 'rch', 'RcHm_v2.0_Chr2g0164681' => 'rch', 'RcHm_v2.0_Chr2g0164721' => 'rch', 'RcHm_v2.0_Chr3g0449911' => 'rch', 'RcHm_v2.0_Chr3g0450211' => 'rch', 'RcHm_v2.0_Chr3g0457271' => 'rch', 'RcHm_v2.0_Chr5g0018111' => 'rch', 'RcHm_v2.0_Chr5g0021011' => 'rch', 'RcHm_v2.0_Chr5g0081171' => 'rch', 'RcHm_v2.0_Chr5g0081211' => 'rch', 'RcHm_v2.0_Chr6g0275871' => 'rch', 'RcHm_v2.0_Chr6g0276071' => 'rch', 'RcHm_v2.0_Chr6g0285591' => 'rch', 'RcHm_v2.0_Chr6g0291931' => 'rch', 'RcHm_v2.0_Chr6g0292091' => 'rch', 'RcHm_v2.0_Chr6g0292271' => 'rch', 'RcHm_v2.0_Chr7g0221261' => 'rch', 'Rhsim08G0219900' => 'rsi', 'Rhsim08G0220200' => 'rsi', 'Rhsim08G0237800' => 'rsi', 'Rhsim08G0238800' => 'rsi', 'Sabra09G0102700' => 'sbr', 'Sabra09G0127200' => 'sbr', 'Sabra11G0003700' => 'sbr', 'Sabra15G0014700' => 'sbr', 'Sc19g0000590' => 'sci', 'Sc19g0001870' => 'sci', 'SGA_v2.0_scaffold1G00346' => 'sas', 'SGA_v2.0_scaffold1G00575' => 'sas', 'SGA_v2.0_scaffold1G00761' => 'sas', 'SGA_v2.0_scaffold232G43501' => 'sas', 'TAR625G1137' => 'tar', 'Thecc.03G222100' => 'tca', 'TPR.G12691' => 'tpr', 'TWI34G0727' => 'twi', 'TWI36G0117' => 'twi', 'VMungo1309G0868' => 'vmu' ) $gf_id = 'HOM05D001729' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001729' ) $data_identifier = 'HOM05D001729' $data_type = 'gf_id' $species_gene_counts = array( 'amhyb' => (int) 1, 'cqu' => (int) 9, 'can' => (int) 1, 'cansat' => (int) 1, 'car' => (int) 1, 'col' => (int) 5, 'dca' => (int) 1, 'din' => (int) 2, 'dzi' => (int) 3, 'fan' => (int) 140, 'fve' => (int) 62, 'gma' => (int) 1, 'ghi' => (int) 2, 'gra' => (int) 1, 'han' => (int) 1, 'sun' => (int) 1, 'lonja' => (int) 6, 'lja' => (int) 1, 'lsa' => (int) 4, 'mes' => (int) 1, 'mdo' => (int) 14, 'mtr' => (int) 1, 'egut' => (int) 1, 'nta' => (int) 4, 'oeu' => (int) 1, 'stu' => (int) 2, 'pvu' => (int) 1, 'ptr' => (int) 4, 'ppe' => (int) 19, 'psa' => (int) 1, 'pso' => (int) 4, 'qlo' => (int) 36, 'rch' => (int) 23, 'rsi' => (int) 4, 'sbr' => (int) 4, 'sci' => (int) 2, 'sas' => (int) 4, 'tar' => (int) 1, 'tca' => (int) 1, 'tpr' => (int) 1, 'twi' => (int) 2, 'vmu' => (int) 1 ) $gf_gene_species = 'vmu' $gf_gene_id = 'VMungo1309G0868' $species_info = array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ) $local_species = 'ppe' $disabled = '' $selected = '' $num_hits = (int) 0include - APP/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp, line 33 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933 View::_renderElement() - CORE/Cake/View/View.php, line 1224 View::element() - CORE/Cake/View/View.php, line 418 include - APP/View/Elements/analysis/phylogenetics_module/gf_data_settings.ctp, line 37 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933 View::_renderElement() - CORE/Cake/View/View.php, line 1224 View::element() - CORE/Cake/View/View.php, line 418 include - APP/View/Elements/analysis/phylogenetics_module/parameter_selection.ctp, line 64 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933 View::_renderElement() - CORE/Cake/View/View.php, line 1224 View::element() - CORE/Cake/View/View.php, line 418 include - APP/View/Analysis/custom_tree_creation.ctp, line 27 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933
$viewFile = '/www/bioinformatics01_ro/plaza/_dev_instances/feedback/app/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp' $dataForView = array( 'sidebar_info' => array( 'gf_id' => 'HOM05D001729', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '375', 'num_species' => '42' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'Ah.07g204710' => 'amhyb', 'AUR62006001' => 'cqu', 'AUR62006002' => 'cqu', 'AUR62006003' => 'cqu', 'AUR62015641' => 'cqu', 'AUR62027174' => 'cqu', 'AUR62035623' => 'cqu', 'AUR62035624' => 'cqu', 'AUR62035625' => 'cqu', 'AUR62035626' => 'cqu', 'CAN.G1110.53' => 'can', 'CANSAT80G0415' => 'cansat', 'Ca_21364_v3' => 'car', 'COL.COLO4_30693' => 'col', 'COL.COLO4_30694' => 'col', 'COL.COLO4_30695' => 'col', 'COL.COLO4_30696' => 'col', 'COL.COLO4_34020' => 'col', 'DCAR_004585' => 'dca', 'Dinv04029' => 'din', 'Dinv34857' => 'din', 'Duzib147G0011' => 'dzi', 'Duzib170G0599' => 'dzi', 'Duzib192G1051' => 'dzi', 'FAN01G0708' => 'fan', 'FAN01G0742' => 'fan', 'FAN02G0048' => 'fan', 'FAN02G0583' => 'fan', 'FAN02G0688' => 'fan', 'FAN02G1588' => 'fan', 'FAN02G2194' => 'fan', 'FAN02G2750' => 'fan', 'FAN02G3094' => 'fan', 'FAN02G3887' => 'fan', 'FAN02G3911' => 'fan', 'FAN02G3994' => 'fan', 'FAN02G4432' => 'fan', 'FAN02G4556' => 'fan', 'FAN03G1977' => 'fan', 'FAN03G2781' => 'fan', 'FAN03G2850' => 'fan', 'FAN03G3155' => 'fan', 'FAN04G2487' => 'fan', 'FAN05G0208' => 'fan', 'FAN05G0656' => 'fan', 'FAN05G0696' => 'fan', 'FAN05G0810' => 'fan', 'FAN05G1447' => 'fan', 'FAN05G2640' => 'fan', 'FAN05G2911' => 'fan', 'FAN05G3901' => 'fan', 'FAN05G4859' => 'fan', 'FAN05G4861' => 'fan', 'FAN05G4988' => 'fan', 'FAN05G5187' => 'fan', 'FAN05G5452' => 'fan', 'FAN05G5500' => 'fan', 'FAN05G5688' => 'fan', 'FAN06G0177' => 'fan', 'FAN06G0675' => 'fan', 'FAN06G1290' => 'fan', 'FAN06G2191' => 'fan', 'FAN06G2405' => 'fan', 'FAN06G3231' => 'fan', 'FAN06G3932' => 'fan', 'FAN07G0163' => 'fan', 'FAN07G0471' => 'fan', 'FAN07G1354' => 'fan', 'FAN08G0338' => 'fan', 'FAN08G1373' => 'fan', 'FAN08G2539' => 'fan', 'FAN08G2728' => 'fan', 'FAN09G0608' => 'fan', 'FAN09G1136' => 'fan', 'FAN09G1958' => 'fan', 'FAN09G2508' => 'fan', 'FAN09G2597' => 'fan', 'FAN09G2658' => 'fan', 'FAN09G2757' => 'fan', 'FAN09G2983' => 'fan', 'FAN09G3130' => 'fan', 'FAN09G3565' => 'fan', 'FAN09G3613' => 'fan', 'FAN09G4011' => 'fan', 'FAN09G4239' => 'fan', 'FAN09G4277' => 'fan', 'FAN09G4720' => 'fan', 'FAN11G0139' => 'fan', 'FAN11G1727' => 'fan', 'FAN11G2672' => 'fan', 'FAN11G2795' => 'fan', 'FAN11G3238' => 'fan', 'FAN11G3734' => 'fan', 'FAN12G0631' => 'fan', 'FAN12G2239' => 'fan', 'FAN12G2308' => 'fan', 'FAN12G2569' => 'fan', 'FAN12G2623' => 'fan', 'FAN13G3182' => 'fan', 'FAN14G0053' => 'fan', 'FAN14G0370' => 'fan', 'FAN14G0382' => 'fan', 'FAN14G0421' => 'fan', 'FAN14G0866' => 'fan', 'FAN14G1187' => 'fan', 'FAN14G1727' => 'fan', 'FAN14G1791' => 'fan', 'FAN14G2361' => 'fan', 'FAN14G2668' => 'fan', 'FAN14G2770' => 'fan', 'FAN14G2874' => 'fan', 'FAN14G3193' => 'fan', 'FAN14G3624' => 'fan', 'FAN14G3676' => 'fan', 'FAN14G3807' => 'fan', 'FAN14G4082' => 'fan', 'FAN14G4342' => 'fan', 'FAN14G4985' => 'fan', 'FAN14G5126' => 'fan', 'FAN14G5781' => 'fan', 'FAN14G5808' => 'fan', 'FAN14G5949' => 'fan', 'FAN15G0828' => 'fan', 'FAN15G1054' => 'fan', 'FAN15G2023' => 'fan', 'FAN15G2506' => 'fan', 'FAN16G0128' => 'fan', 'FAN16G0249' => 'fan', 'FAN16G0429' => 'fan', 'FAN16G1493' => 'fan', 'FAN16G2210' => 'fan', 'FAN16G2506' => 'fan', 'FAN18G1542' => 'fan', 'FAN18G4057' => 'fan', 'FAN19G0745' => 'fan', 'FAN19G1216' => 'fan', 'FAN19G1733' => 'fan', 'FAN20G0258' => 'fan', 'FAN20G1095' => 'fan', 'FAN20G1557' => 'fan', 'FAN21G0302' => 'fan', 'FAN21G0519' => 'fan', 'FAN21G0970' => 'fan', 'FAN21G1159' => 'fan', 'FAN21G1312' => 'fan', 'FAN21G1440' => 'fan', 'FAN21G1715' => 'fan', 'FAN23G1584' => 'fan', 'FAN24G0045' => 'fan', 'FAN24G0053' => 'fan', 'FAN24G1500' => 'fan', 'FAN24G1817' => 'fan', 'FAN24G2147' => 'fan', 'FAN24G2236' => 'fan', 'FAN24G2446' => 'fan', 'FAN24G2684' => 'fan', 'FAN25G0187' => 'fan', 'FAN25G0505' => 'fan', 'FAN25G0589' => 'fan', 'FAN25G3663' => 'fan', 'FAN26G1025' => 'fan', 'FAN26G2860' => 'fan', 'FAN27G1329' => 'fan', 'FAN27G3392' => 'fan', 'FvH4_1g02011' => 'fve', 'FvH4_1g06511' => 'fve', 'FvH4_2g19900' => 'fve', 'FvH4_2g19920' => 'fve', 'FvH4_2g24261' => 'fve', 'FvH4_2g24270' => 'fve', 'FvH4_2g24631' => 'fve', 'FvH4_2g30622' => 'fve', 'FvH4_3g12920' => 'fve', 'FvH4_3g30171' => 'fve', 'FvH4_3g35490' => 'fve', 'FvH4_3g43682' => 'fve', 'FvH4_3g43730' => 'fve', 'FvH4_3g43732' => 'fve', 'FvH4_3g43751' => 'fve', 'FvH4_3g43752' => 'fve', 'FvH4_3g43770' => 'fve', 'FvH4_3g44471' => 'fve', 'FvH4_3g44510' => 'fve', 'FvH4_3g44582' => 'fve', 'FvH4_4g16921' => 'fve', 'FvH4_4g17121' => 'fve', 'FvH4_4g17782' => 'fve', 'FvH4_4g17783' => 'fve', 'FvH4_4g18120' => 'fve', 'FvH4_4g31310' => 'fve', 'FvH4_4g35052' => 'fve', 'FvH4_5g30862' => 'fve', 'FvH4_6g01541' => 'fve', 'FvH4_6g02021' => 'fve', 'FvH4_6g02041' => 'fve', 'FvH4_6g02071' => 'fve', 'FvH4_6g02171' => 'fve', 'FvH4_6g03181' => 'fve', 'FvH4_6g03182' => 'fve', 'FvH4_6g03221' => 'fve', 'FvH4_6g03380' => 'fve', 'FvH4_6g05201' => 'fve', 'FvH4_6g05203' => 'fve', 'FvH4_6g20231' => 'fve', 'FvH4_6g31981' => 'fve', 'FvH4_6g32061' => 'fve', 'FvH4_6g37041' => 'fve', 'FvH4_6g37932' => 'fve', 'FvH4_6g38731' => 'fve', 'FvH4_6g39370' => 'fve', 'FvH4_6g39371' => 'fve', 'FvH4_6g40891' => 'fve', 'FvH4_6g40892' => 'fve', 'FvH4_6g43143' => 'fve', 'FvH4_6g45251' => 'fve', 'FvH4_6g45260' => 'fve', 'FvH4_6g45291' => 'fve', 'FvH4_6g45890' => 'fve', 'FvH4_6g46240' => 'fve', 'FvH4_6g46241' => 'fve', 'FvH4_6g46242' => 'fve', 'FvH4_6g46260' => 'fve', 'FvH4_6g46280' => 'fve', 'FvH4_6g46380' => 'fve', 'FvH4_7g12841' => 'fve', 'FvH4_7g31431' => 'fve', 'Glyma.09G075900' => 'gma', 'Gohir.A09G096401' => 'ghi', 'Gohir.D09G096101' => 'ghi', 'Gorai.006G112800' => 'gra', 'HanXRQChr04g0121411' => 'han', 'Hund15878' => 'sun', 'Lj2A1107G68' => 'lonja', 'Lj2A630G63' => 'lonja', 'Lj2A946T25' => 'lonja', 'Lj2C714T1' => 'lonja', 'Lj2C966T3' => 'lonja', 'Lj2C966T4' => 'lonja', 'Lj4g0002979' => 'lja', 'Lsat_1_v5_gn_5_30901' => 'lsa', 'Lsat_1_v5_gn_5_31100' => 'lsa', 'Lsat_1_v5_gn_5_38600' => 'lsa', 'Lsat_1_v5_gn_6_92061' => 'lsa', 'Manes.05G071301' => 'mes', 'MD02G1008700' => 'mdo', 'MD02G1008900' => 'mdo', 'MD03G1256400' => 'mdo', 'MD04G1180900' => 'mdo', 'MD04G1181000' => 'mdo', 'MD04G1181200' => 'mdo', 'MD05G1244200' => 'mdo', 'MD05G1324200' => 'mdo', 'MD09G1201600' => 'mdo', 'MD10G1000600' => 'mdo', 'MD14G1026900' => 'mdo', 'MD14G1187900' => 'mdo', 'MD15G1017800' => 'mdo', 'MD15G1018100' => 'mdo', 'Medtr4g124160' => 'mtr', 'Migut.L01260' => 'egut', 'Nitab4.5_0000008g0440' => 'nta', 'Nitab4.5_0000207g0170' => 'nta', 'Nitab4.5_0007671g0030' => 'nta', 'Nitab4.5_0010853g0020' => 'nta', 'Oeu057656.1' => 'oeu', 'PGSC0003DMG400005638' => 'stu', 'PGSC0003DMG400005639' => 'stu', 'Phvul.009G222800' => 'pvu', 'Potri.009G132400' => 'ptr', 'Potri.009G163001' => 'ptr', 'Potri.011G000700' => 'ptr', 'Potri.011G004800' => 'ptr', 'Prupe.1G509300' => 'ppe', 'Prupe.1G509700' => 'ppe', 'Prupe.1G510400' => 'ppe', 'Prupe.1G510700' => 'ppe', 'Prupe.1G512600' => 'ppe', 'Prupe.2G073200' => 'ppe', 'Prupe.3G059500' => 'ppe', 'Prupe.3G059600' => 'ppe', 'Prupe.3G246100' => 'ppe', 'Prupe.3G265100' => 'ppe', 'Prupe.4G034700' => 'ppe', 'Prupe.4G052100' => 'ppe', 'Prupe.4G053600' => 'ppe', 'Prupe.5G068800' => 'ppe', 'Prupe.5G070600' => 'ppe', 'Prupe.6G075400' => 'ppe', 'Prupe.6G075500' => 'ppe', 'Prupe.6G076400' => 'ppe', 'Prupe.8G110700' => 'ppe', 'Psat4g020960' => 'psa', 'PSO135G0788' => 'pso', 'PSO210G6463' => 'pso', 'PSO384G0370' => 'pso', 'PSO386G0056' => 'pso', 'QL01p006048' => 'qlo', 'QL02p054283' => 'qlo', 'QL05p008000' => 'qlo', 'QL05p008212' => 'qlo', 'QL05p008950' => 'qlo', 'QL05p009042' => 'qlo', 'QL05p009518' => 'qlo', 'QL05p012589' => 'qlo', 'QL05p012608' => 'qlo', 'QL05p012650' => 'qlo', 'QL05p012667' => 'qlo', 'QL05p014501' => 'qlo', 'QL05p052800' => 'qlo', 'QL05p065010' => 'qlo', 'QL05p074156' => 'qlo', 'QL05p074160' => 'qlo', 'QL05p074174' => 'qlo', 'QL05p074178' => 'qlo', 'QL05p074214' => 'qlo', 'QL06p001050' => 'qlo', 'QL06p001056' => 'qlo', 'QL06p006093' => 'qlo', 'QL06p006111' => 'qlo', 'QL07p019784' => 'qlo', 'QL07p019801' => 'qlo', 'QL07p036110' => 'qlo', 'QL07p036134' => 'qlo', 'QL07p036147' => 'qlo', 'QL07p036156' => 'qlo', 'QL07p036300' => 'qlo', 'QL07p036320' => 'qlo', 'QL08p014547' => 'qlo', 'QL08p014551' => 'qlo', 'QL08p043319' => 'qlo', 'QL08p043324' => 'qlo', 'QL11p009094' => 'qlo', 'RcHm_v2.0_Chr1g0380481' => 'rch', 'RcHm_v2.0_Chr2g0089331' => 'rch', 'RcHm_v2.0_Chr2g0123691' => 'rch', 'RcHm_v2.0_Chr2g0151111' => 'rch', 'RcHm_v2.0_Chr2g0163011' => 'rch', 'RcHm_v2.0_Chr2g0163051' => 'rch', 'RcHm_v2.0_Chr2g0164671' => 'rch', 'RcHm_v2.0_Chr2g0164681' => 'rch', 'RcHm_v2.0_Chr2g0164721' => 'rch', 'RcHm_v2.0_Chr3g0449911' => 'rch', 'RcHm_v2.0_Chr3g0450211' => 'rch', 'RcHm_v2.0_Chr3g0457271' => 'rch', 'RcHm_v2.0_Chr5g0018111' => 'rch', 'RcHm_v2.0_Chr5g0021011' => 'rch', 'RcHm_v2.0_Chr5g0081171' => 'rch', 'RcHm_v2.0_Chr5g0081211' => 'rch', 'RcHm_v2.0_Chr6g0275871' => 'rch', 'RcHm_v2.0_Chr6g0276071' => 'rch', 'RcHm_v2.0_Chr6g0285591' => 'rch', 'RcHm_v2.0_Chr6g0291931' => 'rch', 'RcHm_v2.0_Chr6g0292091' => 'rch', 'RcHm_v2.0_Chr6g0292271' => 'rch', 'RcHm_v2.0_Chr7g0221261' => 'rch', 'Rhsim08G0219900' => 'rsi', 'Rhsim08G0220200' => 'rsi', 'Rhsim08G0237800' => 'rsi', 'Rhsim08G0238800' => 'rsi', 'Sabra09G0102700' => 'sbr', 'Sabra09G0127200' => 'sbr', 'Sabra11G0003700' => 'sbr', 'Sabra15G0014700' => 'sbr', 'Sc19g0000590' => 'sci', 'Sc19g0001870' => 'sci', 'SGA_v2.0_scaffold1G00346' => 'sas', 'SGA_v2.0_scaffold1G00575' => 'sas', 'SGA_v2.0_scaffold1G00761' => 'sas', 'SGA_v2.0_scaffold232G43501' => 'sas', 'TAR625G1137' => 'tar', 'Thecc.03G222100' => 'tca', 'TPR.G12691' => 'tpr', 'TWI34G0727' => 'twi', 'TWI36G0117' => 'twi', 'VMungo1309G0868' => 'vmu' ), 'gf_id' => 'HOM05D001729', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001729' ), 'data_identifier' => 'HOM05D001729', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001729', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '375', 'num_species' => '42' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'Ah.07g204710' => 'amhyb', 'AUR62006001' => 'cqu', 'AUR62006002' => 'cqu', 'AUR62006003' => 'cqu', 'AUR62015641' => 'cqu', 'AUR62027174' => 'cqu', 'AUR62035623' => 'cqu', 'AUR62035624' => 'cqu', 'AUR62035625' => 'cqu', 'AUR62035626' => 'cqu', 'CAN.G1110.53' => 'can', 'CANSAT80G0415' => 'cansat', 'Ca_21364_v3' => 'car', 'COL.COLO4_30693' => 'col', 'COL.COLO4_30694' => 'col', 'COL.COLO4_30695' => 'col', 'COL.COLO4_30696' => 'col', 'COL.COLO4_34020' => 'col', 'DCAR_004585' => 'dca', 'Dinv04029' => 'din', 'Dinv34857' => 'din', 'Duzib147G0011' => 'dzi', 'Duzib170G0599' => 'dzi', 'Duzib192G1051' => 'dzi', 'FAN01G0708' => 'fan', 'FAN01G0742' => 'fan', 'FAN02G0048' => 'fan', 'FAN02G0583' => 'fan', 'FAN02G0688' => 'fan', 'FAN02G1588' => 'fan', 'FAN02G2194' => 'fan', 'FAN02G2750' => 'fan', 'FAN02G3094' => 'fan', 'FAN02G3887' => 'fan', 'FAN02G3911' => 'fan', 'FAN02G3994' => 'fan', 'FAN02G4432' => 'fan', 'FAN02G4556' => 'fan', 'FAN03G1977' => 'fan', 'FAN03G2781' => 'fan', 'FAN03G2850' => 'fan', 'FAN03G3155' => 'fan', 'FAN04G2487' => 'fan', 'FAN05G0208' => 'fan', 'FAN05G0656' => 'fan', 'FAN05G0696' => 'fan', 'FAN05G0810' => 'fan', 'FAN05G1447' => 'fan', 'FAN05G2640' => 'fan', 'FAN05G2911' => 'fan', 'FAN05G3901' => 'fan', 'FAN05G4859' => 'fan', 'FAN05G4861' => 'fan', 'FAN05G4988' => 'fan', 'FAN05G5187' => 'fan', 'FAN05G5452' => 'fan', 'FAN05G5500' => 'fan', 'FAN05G5688' => 'fan', 'FAN06G0177' => 'fan', 'FAN06G0675' => 'fan', 'FAN06G1290' => 'fan', 'FAN06G2191' => 'fan', 'FAN06G2405' => 'fan', 'FAN06G3231' => 'fan', 'FAN06G3932' => 'fan', 'FAN07G0163' => 'fan', 'FAN07G0471' => 'fan', 'FAN07G1354' => 'fan', 'FAN08G0338' => 'fan', 'FAN08G1373' => 'fan', 'FAN08G2539' => 'fan', 'FAN08G2728' => 'fan', 'FAN09G0608' => 'fan', 'FAN09G1136' => 'fan', 'FAN09G1958' => 'fan', 'FAN09G2508' => 'fan', 'FAN09G2597' => 'fan', 'FAN09G2658' => 'fan', 'FAN09G2757' => 'fan', 'FAN09G2983' => 'fan', 'FAN09G3130' => 'fan', 'FAN09G3565' => 'fan', 'FAN09G3613' => 'fan', 'FAN09G4011' => 'fan', 'FAN09G4239' => 'fan', 'FAN09G4277' => 'fan', 'FAN09G4720' => 'fan', 'FAN11G0139' => 'fan', 'FAN11G1727' => 'fan', 'FAN11G2672' => 'fan', 'FAN11G2795' => 'fan', 'FAN11G3238' => 'fan', 'FAN11G3734' => 'fan', 'FAN12G0631' => 'fan', 'FAN12G2239' => 'fan', 'FAN12G2308' => 'fan', 'FAN12G2569' => 'fan', 'FAN12G2623' => 'fan', 'FAN13G3182' => 'fan', 'FAN14G0053' => 'fan', 'FAN14G0370' => 'fan', 'FAN14G0382' => 'fan', 'FAN14G0421' => 'fan', 'FAN14G0866' => 'fan', 'FAN14G1187' => 'fan', 'FAN14G1727' => 'fan', 'FAN14G1791' => 'fan', 'FAN14G2361' => 'fan', 'FAN14G2668' => 'fan', 'FAN14G2770' => 'fan', 'FAN14G2874' => 'fan', 'FAN14G3193' => 'fan', 'FAN14G3624' => 'fan', 'FAN14G3676' => 'fan', 'FAN14G3807' => 'fan', 'FAN14G4082' => 'fan', 'FAN14G4342' => 'fan', 'FAN14G4985' => 'fan', 'FAN14G5126' => 'fan', 'FAN14G5781' => 'fan', 'FAN14G5808' => 'fan', 'FAN14G5949' => 'fan', 'FAN15G0828' => 'fan', 'FAN15G1054' => 'fan', 'FAN15G2023' => 'fan', 'FAN15G2506' => 'fan', 'FAN16G0128' => 'fan', 'FAN16G0249' => 'fan', 'FAN16G0429' => 'fan', 'FAN16G1493' => 'fan', 'FAN16G2210' => 'fan', 'FAN16G2506' => 'fan', 'FAN18G1542' => 'fan', 'FAN18G4057' => 'fan', 'FAN19G0745' => 'fan', 'FAN19G1216' => 'fan', 'FAN19G1733' => 'fan', 'FAN20G0258' => 'fan', 'FAN20G1095' => 'fan', 'FAN20G1557' => 'fan', 'FAN21G0302' => 'fan', 'FAN21G0519' => 'fan', 'FAN21G0970' => 'fan', 'FAN21G1159' => 'fan', 'FAN21G1312' => 'fan', 'FAN21G1440' => 'fan', 'FAN21G1715' => 'fan', 'FAN23G1584' => 'fan', 'FAN24G0045' => 'fan', 'FAN24G0053' => 'fan', 'FAN24G1500' => 'fan', 'FAN24G1817' => 'fan', 'FAN24G2147' => 'fan', 'FAN24G2236' => 'fan', 'FAN24G2446' => 'fan', 'FAN24G2684' => 'fan', 'FAN25G0187' => 'fan', 'FAN25G0505' => 'fan', 'FAN25G0589' => 'fan', 'FAN25G3663' => 'fan', 'FAN26G1025' => 'fan', 'FAN26G2860' => 'fan', 'FAN27G1329' => 'fan', 'FAN27G3392' => 'fan', 'FvH4_1g02011' => 'fve', 'FvH4_1g06511' => 'fve', 'FvH4_2g19900' => 'fve', 'FvH4_2g19920' => 'fve', 'FvH4_2g24261' => 'fve', 'FvH4_2g24270' => 'fve', 'FvH4_2g24631' => 'fve', 'FvH4_2g30622' => 'fve', 'FvH4_3g12920' => 'fve', 'FvH4_3g30171' => 'fve', 'FvH4_3g35490' => 'fve', 'FvH4_3g43682' => 'fve', 'FvH4_3g43730' => 'fve', 'FvH4_3g43732' => 'fve', 'FvH4_3g43751' => 'fve', 'FvH4_3g43752' => 'fve', 'FvH4_3g43770' => 'fve', 'FvH4_3g44471' => 'fve', 'FvH4_3g44510' => 'fve', 'FvH4_3g44582' => 'fve', 'FvH4_4g16921' => 'fve', 'FvH4_4g17121' => 'fve', 'FvH4_4g17782' => 'fve', 'FvH4_4g17783' => 'fve', 'FvH4_4g18120' => 'fve', 'FvH4_4g31310' => 'fve', 'FvH4_4g35052' => 'fve', 'FvH4_5g30862' => 'fve', 'FvH4_6g01541' => 'fve', 'FvH4_6g02021' => 'fve', 'FvH4_6g02041' => 'fve', 'FvH4_6g02071' => 'fve', 'FvH4_6g02171' => 'fve', 'FvH4_6g03181' => 'fve', 'FvH4_6g03182' => 'fve', 'FvH4_6g03221' => 'fve', 'FvH4_6g03380' => 'fve', 'FvH4_6g05201' => 'fve', 'FvH4_6g05203' => 'fve', 'FvH4_6g20231' => 'fve', 'FvH4_6g31981' => 'fve', 'FvH4_6g32061' => 'fve', 'FvH4_6g37041' => 'fve', 'FvH4_6g37932' => 'fve', 'FvH4_6g38731' => 'fve', 'FvH4_6g39370' => 'fve', 'FvH4_6g39371' => 'fve', 'FvH4_6g40891' => 'fve', 'FvH4_6g40892' => 'fve', 'FvH4_6g43143' => 'fve', 'FvH4_6g45251' => 'fve', 'FvH4_6g45260' => 'fve', 'FvH4_6g45291' => 'fve', 'FvH4_6g45890' => 'fve', 'FvH4_6g46240' => 'fve', 'FvH4_6g46241' => 'fve', 'FvH4_6g46242' => 'fve', 'FvH4_6g46260' => 'fve', 'FvH4_6g46280' => 'fve', 'FvH4_6g46380' => 'fve', 'FvH4_7g12841' => 'fve', 'FvH4_7g31431' => 'fve', 'Glyma.09G075900' => 'gma', 'Gohir.A09G096401' => 'ghi', 'Gohir.D09G096101' => 'ghi', 'Gorai.006G112800' => 'gra', 'HanXRQChr04g0121411' => 'han', 'Hund15878' => 'sun', 'Lj2A1107G68' => 'lonja', 'Lj2A630G63' => 'lonja', 'Lj2A946T25' => 'lonja', 'Lj2C714T1' => 'lonja', 'Lj2C966T3' => 'lonja', 'Lj2C966T4' => 'lonja', 'Lj4g0002979' => 'lja', 'Lsat_1_v5_gn_5_30901' => 'lsa', 'Lsat_1_v5_gn_5_31100' => 'lsa', 'Lsat_1_v5_gn_5_38600' => 'lsa', 'Lsat_1_v5_gn_6_92061' => 'lsa', 'Manes.05G071301' => 'mes', 'MD02G1008700' => 'mdo', 'MD02G1008900' => 'mdo', 'MD03G1256400' => 'mdo', 'MD04G1180900' => 'mdo', 'MD04G1181000' => 'mdo', 'MD04G1181200' => 'mdo', 'MD05G1244200' => 'mdo', 'MD05G1324200' => 'mdo', 'MD09G1201600' => 'mdo', 'MD10G1000600' => 'mdo', 'MD14G1026900' => 'mdo', 'MD14G1187900' => 'mdo', 'MD15G1017800' => 'mdo', 'MD15G1018100' => 'mdo', 'Medtr4g124160' => 'mtr', 'Migut.L01260' => 'egut', 'Nitab4.5_0000008g0440' => 'nta', 'Nitab4.5_0000207g0170' => 'nta', 'Nitab4.5_0007671g0030' => 'nta', 'Nitab4.5_0010853g0020' => 'nta', 'Oeu057656.1' => 'oeu', 'PGSC0003DMG400005638' => 'stu', 'PGSC0003DMG400005639' => 'stu', 'Phvul.009G222800' => 'pvu', 'Potri.009G132400' => 'ptr', 'Potri.009G163001' => 'ptr', 'Potri.011G000700' => 'ptr', 'Potri.011G004800' => 'ptr', 'Prupe.1G509300' => 'ppe', 'Prupe.1G509700' => 'ppe', 'Prupe.1G510400' => 'ppe', 'Prupe.1G510700' => 'ppe', 'Prupe.1G512600' => 'ppe', 'Prupe.2G073200' => 'ppe', 'Prupe.3G059500' => 'ppe', 'Prupe.3G059600' => 'ppe', 'Prupe.3G246100' => 'ppe', 'Prupe.3G265100' => 'ppe', 'Prupe.4G034700' => 'ppe', 'Prupe.4G052100' => 'ppe', 'Prupe.4G053600' => 'ppe', 'Prupe.5G068800' => 'ppe', 'Prupe.5G070600' => 'ppe', 'Prupe.6G075400' => 'ppe', 'Prupe.6G075500' => 'ppe', 'Prupe.6G076400' => 'ppe', 'Prupe.8G110700' => 'ppe', 'Psat4g020960' => 'psa', 'PSO135G0788' => 'pso', 'PSO210G6463' => 'pso', 'PSO384G0370' => 'pso', 'PSO386G0056' => 'pso', 'QL01p006048' => 'qlo', 'QL02p054283' => 'qlo', 'QL05p008000' => 'qlo', 'QL05p008212' => 'qlo', 'QL05p008950' => 'qlo', 'QL05p009042' => 'qlo', 'QL05p009518' => 'qlo', 'QL05p012589' => 'qlo', 'QL05p012608' => 'qlo', 'QL05p012650' => 'qlo', 'QL05p012667' => 'qlo', 'QL05p014501' => 'qlo', 'QL05p052800' => 'qlo', 'QL05p065010' => 'qlo', 'QL05p074156' => 'qlo', 'QL05p074160' => 'qlo', 'QL05p074174' => 'qlo', 'QL05p074178' => 'qlo', 'QL05p074214' => 'qlo', 'QL06p001050' => 'qlo', 'QL06p001056' => 'qlo', 'QL06p006093' => 'qlo', 'QL06p006111' => 'qlo', 'QL07p019784' => 'qlo', 'QL07p019801' => 'qlo', 'QL07p036110' => 'qlo', 'QL07p036134' => 'qlo', 'QL07p036147' => 'qlo', 'QL07p036156' => 'qlo', 'QL07p036300' => 'qlo', 'QL07p036320' => 'qlo', 'QL08p014547' => 'qlo', 'QL08p014551' => 'qlo', 'QL08p043319' => 'qlo', 'QL08p043324' => 'qlo', 'QL11p009094' => 'qlo', 'RcHm_v2.0_Chr1g0380481' => 'rch', 'RcHm_v2.0_Chr2g0089331' => 'rch', 'RcHm_v2.0_Chr2g0123691' => 'rch', 'RcHm_v2.0_Chr2g0151111' => 'rch', 'RcHm_v2.0_Chr2g0163011' => 'rch', 'RcHm_v2.0_Chr2g0163051' => 'rch', 'RcHm_v2.0_Chr2g0164671' => 'rch', 'RcHm_v2.0_Chr2g0164681' => 'rch', 'RcHm_v2.0_Chr2g0164721' => 'rch', 'RcHm_v2.0_Chr3g0449911' => 'rch', 'RcHm_v2.0_Chr3g0450211' => 'rch', 'RcHm_v2.0_Chr3g0457271' => 'rch', 'RcHm_v2.0_Chr5g0018111' => 'rch', 'RcHm_v2.0_Chr5g0021011' => 'rch', 'RcHm_v2.0_Chr5g0081171' => 'rch', 'RcHm_v2.0_Chr5g0081211' => 'rch', 'RcHm_v2.0_Chr6g0275871' => 'rch', 'RcHm_v2.0_Chr6g0276071' => 'rch', 'RcHm_v2.0_Chr6g0285591' => 'rch', 'RcHm_v2.0_Chr6g0291931' => 'rch', 'RcHm_v2.0_Chr6g0292091' => 'rch', 'RcHm_v2.0_Chr6g0292271' => 'rch', 'RcHm_v2.0_Chr7g0221261' => 'rch', 'Rhsim08G0219900' => 'rsi', 'Rhsim08G0220200' => 'rsi', 'Rhsim08G0237800' => 'rsi', 'Rhsim08G0238800' => 'rsi', 'Sabra09G0102700' => 'sbr', 'Sabra09G0127200' => 'sbr', 'Sabra11G0003700' => 'sbr', 'Sabra15G0014700' => 'sbr', 'Sc19g0000590' => 'sci', 'Sc19g0001870' => 'sci', 'SGA_v2.0_scaffold1G00346' => 'sas', 'SGA_v2.0_scaffold1G00575' => 'sas', 'SGA_v2.0_scaffold1G00761' => 'sas', 'SGA_v2.0_scaffold232G43501' => 'sas', 'TAR625G1137' => 'tar', 'Thecc.03G222100' => 'tca', 'TPR.G12691' => 'tpr', 'TWI34G0727' => 'twi', 'TWI36G0117' => 'twi', 'VMungo1309G0868' => 'vmu' ) $gf_id = 'HOM05D001729' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001729' ) $data_identifier = 'HOM05D001729' $data_type = 'gf_id' $species_gene_counts = array( 'amhyb' => (int) 1, 'cqu' => (int) 9, 'can' => (int) 1, 'cansat' => (int) 1, 'car' => (int) 1, 'col' => (int) 5, 'dca' => (int) 1, 'din' => (int) 2, 'dzi' => (int) 3, 'fan' => (int) 140, 'fve' => (int) 62, 'gma' => (int) 1, 'ghi' => (int) 2, 'gra' => (int) 1, 'han' => (int) 1, 'sun' => (int) 1, 'lonja' => (int) 6, 'lja' => (int) 1, 'lsa' => (int) 4, 'mes' => (int) 1, 'mdo' => (int) 14, 'mtr' => (int) 1, 'egut' => (int) 1, 'nta' => (int) 4, 'oeu' => (int) 1, 'stu' => (int) 2, 'pvu' => (int) 1, 'ptr' => (int) 4, 'ppe' => (int) 19, 'psa' => (int) 1, 'pso' => (int) 4, 'qlo' => (int) 36, 'rch' => (int) 23, 'rsi' => (int) 4, 'sbr' => (int) 4, 'sci' => (int) 2, 'sas' => (int) 4, 'tar' => (int) 1, 'tca' => (int) 1, 'tpr' => (int) 1, 'twi' => (int) 2, 'vmu' => (int) 1 ) $gf_gene_species = 'vmu' $gf_gene_id = 'VMungo1309G0868' $species_info = array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ) $local_species = 'ppe' $disabled = '' $selected = '' $num_hits = (int) 0
Warning (2): count(): Parameter must be an array or an object that implements Countable [APP/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp, line 33]Code Context $disabled = (!array_key_exists($local_species,$species_gene_counts))?"disabled":""; $selected = (isset($selected_species) && array_key_exists($local_species,$selected_species))?"checked='checked'":""; $num_hits = (array_key_exists($local_species,$species_gene_counts))?count($species_gene_counts[$local_species]):0; $viewFile = '/www/bioinformatics01_ro/plaza/_dev_instances/feedback/app/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp' $dataForView = array( 'sidebar_info' => array( 'gf_id' => 'HOM05D001729', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '375', 'num_species' => '42' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'Ah.07g204710' => 'amhyb', 'AUR62006001' => 'cqu', 'AUR62006002' => 'cqu', 'AUR62006003' => 'cqu', 'AUR62015641' => 'cqu', 'AUR62027174' => 'cqu', 'AUR62035623' => 'cqu', 'AUR62035624' => 'cqu', 'AUR62035625' => 'cqu', 'AUR62035626' => 'cqu', 'CAN.G1110.53' => 'can', 'CANSAT80G0415' => 'cansat', 'Ca_21364_v3' => 'car', 'COL.COLO4_30693' => 'col', 'COL.COLO4_30694' => 'col', 'COL.COLO4_30695' => 'col', 'COL.COLO4_30696' => 'col', 'COL.COLO4_34020' => 'col', 'DCAR_004585' => 'dca', 'Dinv04029' => 'din', 'Dinv34857' => 'din', 'Duzib147G0011' => 'dzi', 'Duzib170G0599' => 'dzi', 'Duzib192G1051' => 'dzi', 'FAN01G0708' => 'fan', 'FAN01G0742' => 'fan', 'FAN02G0048' => 'fan', 'FAN02G0583' => 'fan', 'FAN02G0688' => 'fan', 'FAN02G1588' => 'fan', 'FAN02G2194' => 'fan', 'FAN02G2750' => 'fan', 'FAN02G3094' => 'fan', 'FAN02G3887' => 'fan', 'FAN02G3911' => 'fan', 'FAN02G3994' => 'fan', 'FAN02G4432' => 'fan', 'FAN02G4556' => 'fan', 'FAN03G1977' => 'fan', 'FAN03G2781' => 'fan', 'FAN03G2850' => 'fan', 'FAN03G3155' => 'fan', 'FAN04G2487' => 'fan', 'FAN05G0208' => 'fan', 'FAN05G0656' => 'fan', 'FAN05G0696' => 'fan', 'FAN05G0810' => 'fan', 'FAN05G1447' => 'fan', 'FAN05G2640' => 'fan', 'FAN05G2911' => 'fan', 'FAN05G3901' => 'fan', 'FAN05G4859' => 'fan', 'FAN05G4861' => 'fan', 'FAN05G4988' => 'fan', 'FAN05G5187' => 'fan', 'FAN05G5452' => 'fan', 'FAN05G5500' => 'fan', 'FAN05G5688' => 'fan', 'FAN06G0177' => 'fan', 'FAN06G0675' => 'fan', 'FAN06G1290' => 'fan', 'FAN06G2191' => 'fan', 'FAN06G2405' => 'fan', 'FAN06G3231' => 'fan', 'FAN06G3932' => 'fan', 'FAN07G0163' => 'fan', 'FAN07G0471' => 'fan', 'FAN07G1354' => 'fan', 'FAN08G0338' => 'fan', 'FAN08G1373' => 'fan', 'FAN08G2539' => 'fan', 'FAN08G2728' => 'fan', 'FAN09G0608' => 'fan', 'FAN09G1136' => 'fan', 'FAN09G1958' => 'fan', 'FAN09G2508' => 'fan', 'FAN09G2597' => 'fan', 'FAN09G2658' => 'fan', 'FAN09G2757' => 'fan', 'FAN09G2983' => 'fan', 'FAN09G3130' => 'fan', 'FAN09G3565' => 'fan', 'FAN09G3613' => 'fan', 'FAN09G4011' => 'fan', 'FAN09G4239' => 'fan', 'FAN09G4277' => 'fan', 'FAN09G4720' => 'fan', 'FAN11G0139' => 'fan', 'FAN11G1727' => 'fan', 'FAN11G2672' => 'fan', 'FAN11G2795' => 'fan', 'FAN11G3238' => 'fan', 'FAN11G3734' => 'fan', 'FAN12G0631' => 'fan', 'FAN12G2239' => 'fan', 'FAN12G2308' => 'fan', 'FAN12G2569' => 'fan', 'FAN12G2623' => 'fan', 'FAN13G3182' => 'fan', 'FAN14G0053' => 'fan', 'FAN14G0370' => 'fan', 'FAN14G0382' => 'fan', 'FAN14G0421' => 'fan', 'FAN14G0866' => 'fan', 'FAN14G1187' => 'fan', 'FAN14G1727' => 'fan', 'FAN14G1791' => 'fan', 'FAN14G2361' => 'fan', 'FAN14G2668' => 'fan', 'FAN14G2770' => 'fan', 'FAN14G2874' => 'fan', 'FAN14G3193' => 'fan', 'FAN14G3624' => 'fan', 'FAN14G3676' => 'fan', 'FAN14G3807' => 'fan', 'FAN14G4082' => 'fan', 'FAN14G4342' => 'fan', 'FAN14G4985' => 'fan', 'FAN14G5126' => 'fan', 'FAN14G5781' => 'fan', 'FAN14G5808' => 'fan', 'FAN14G5949' => 'fan', 'FAN15G0828' => 'fan', 'FAN15G1054' => 'fan', 'FAN15G2023' => 'fan', 'FAN15G2506' => 'fan', 'FAN16G0128' => 'fan', 'FAN16G0249' => 'fan', 'FAN16G0429' => 'fan', 'FAN16G1493' => 'fan', 'FAN16G2210' => 'fan', 'FAN16G2506' => 'fan', 'FAN18G1542' => 'fan', 'FAN18G4057' => 'fan', 'FAN19G0745' => 'fan', 'FAN19G1216' => 'fan', 'FAN19G1733' => 'fan', 'FAN20G0258' => 'fan', 'FAN20G1095' => 'fan', 'FAN20G1557' => 'fan', 'FAN21G0302' => 'fan', 'FAN21G0519' => 'fan', 'FAN21G0970' => 'fan', 'FAN21G1159' => 'fan', 'FAN21G1312' => 'fan', 'FAN21G1440' => 'fan', 'FAN21G1715' => 'fan', 'FAN23G1584' => 'fan', 'FAN24G0045' => 'fan', 'FAN24G0053' => 'fan', 'FAN24G1500' => 'fan', 'FAN24G1817' => 'fan', 'FAN24G2147' => 'fan', 'FAN24G2236' => 'fan', 'FAN24G2446' => 'fan', 'FAN24G2684' => 'fan', 'FAN25G0187' => 'fan', 'FAN25G0505' => 'fan', 'FAN25G0589' => 'fan', 'FAN25G3663' => 'fan', 'FAN26G1025' => 'fan', 'FAN26G2860' => 'fan', 'FAN27G1329' => 'fan', 'FAN27G3392' => 'fan', 'FvH4_1g02011' => 'fve', 'FvH4_1g06511' => 'fve', 'FvH4_2g19900' => 'fve', 'FvH4_2g19920' => 'fve', 'FvH4_2g24261' => 'fve', 'FvH4_2g24270' => 'fve', 'FvH4_2g24631' => 'fve', 'FvH4_2g30622' => 'fve', 'FvH4_3g12920' => 'fve', 'FvH4_3g30171' => 'fve', 'FvH4_3g35490' => 'fve', 'FvH4_3g43682' => 'fve', 'FvH4_3g43730' => 'fve', 'FvH4_3g43732' => 'fve', 'FvH4_3g43751' => 'fve', 'FvH4_3g43752' => 'fve', 'FvH4_3g43770' => 'fve', 'FvH4_3g44471' => 'fve', 'FvH4_3g44510' => 'fve', 'FvH4_3g44582' => 'fve', 'FvH4_4g16921' => 'fve', 'FvH4_4g17121' => 'fve', 'FvH4_4g17782' => 'fve', 'FvH4_4g17783' => 'fve', 'FvH4_4g18120' => 'fve', 'FvH4_4g31310' => 'fve', 'FvH4_4g35052' => 'fve', 'FvH4_5g30862' => 'fve', 'FvH4_6g01541' => 'fve', 'FvH4_6g02021' => 'fve', 'FvH4_6g02041' => 'fve', 'FvH4_6g02071' => 'fve', 'FvH4_6g02171' => 'fve', 'FvH4_6g03181' => 'fve', 'FvH4_6g03182' => 'fve', 'FvH4_6g03221' => 'fve', 'FvH4_6g03380' => 'fve', 'FvH4_6g05201' => 'fve', 'FvH4_6g05203' => 'fve', 'FvH4_6g20231' => 'fve', 'FvH4_6g31981' => 'fve', 'FvH4_6g32061' => 'fve', 'FvH4_6g37041' => 'fve', 'FvH4_6g37932' => 'fve', 'FvH4_6g38731' => 'fve', 'FvH4_6g39370' => 'fve', 'FvH4_6g39371' => 'fve', 'FvH4_6g40891' => 'fve', 'FvH4_6g40892' => 'fve', 'FvH4_6g43143' => 'fve', 'FvH4_6g45251' => 'fve', 'FvH4_6g45260' => 'fve', 'FvH4_6g45291' => 'fve', 'FvH4_6g45890' => 'fve', 'FvH4_6g46240' => 'fve', 'FvH4_6g46241' => 'fve', 'FvH4_6g46242' => 'fve', 'FvH4_6g46260' => 'fve', 'FvH4_6g46280' => 'fve', 'FvH4_6g46380' => 'fve', 'FvH4_7g12841' => 'fve', 'FvH4_7g31431' => 'fve', 'Glyma.09G075900' => 'gma', 'Gohir.A09G096401' => 'ghi', 'Gohir.D09G096101' => 'ghi', 'Gorai.006G112800' => 'gra', 'HanXRQChr04g0121411' => 'han', 'Hund15878' => 'sun', 'Lj2A1107G68' => 'lonja', 'Lj2A630G63' => 'lonja', 'Lj2A946T25' => 'lonja', 'Lj2C714T1' => 'lonja', 'Lj2C966T3' => 'lonja', 'Lj2C966T4' => 'lonja', 'Lj4g0002979' => 'lja', 'Lsat_1_v5_gn_5_30901' => 'lsa', 'Lsat_1_v5_gn_5_31100' => 'lsa', 'Lsat_1_v5_gn_5_38600' => 'lsa', 'Lsat_1_v5_gn_6_92061' => 'lsa', 'Manes.05G071301' => 'mes', 'MD02G1008700' => 'mdo', 'MD02G1008900' => 'mdo', 'MD03G1256400' => 'mdo', 'MD04G1180900' => 'mdo', 'MD04G1181000' => 'mdo', 'MD04G1181200' => 'mdo', 'MD05G1244200' => 'mdo', 'MD05G1324200' => 'mdo', 'MD09G1201600' => 'mdo', 'MD10G1000600' => 'mdo', 'MD14G1026900' => 'mdo', 'MD14G1187900' => 'mdo', 'MD15G1017800' => 'mdo', 'MD15G1018100' => 'mdo', 'Medtr4g124160' => 'mtr', 'Migut.L01260' => 'egut', 'Nitab4.5_0000008g0440' => 'nta', 'Nitab4.5_0000207g0170' => 'nta', 'Nitab4.5_0007671g0030' => 'nta', 'Nitab4.5_0010853g0020' => 'nta', 'Oeu057656.1' => 'oeu', 'PGSC0003DMG400005638' => 'stu', 'PGSC0003DMG400005639' => 'stu', 'Phvul.009G222800' => 'pvu', 'Potri.009G132400' => 'ptr', 'Potri.009G163001' => 'ptr', 'Potri.011G000700' => 'ptr', 'Potri.011G004800' => 'ptr', 'Prupe.1G509300' => 'ppe', 'Prupe.1G509700' => 'ppe', 'Prupe.1G510400' => 'ppe', 'Prupe.1G510700' => 'ppe', 'Prupe.1G512600' => 'ppe', 'Prupe.2G073200' => 'ppe', 'Prupe.3G059500' => 'ppe', 'Prupe.3G059600' => 'ppe', 'Prupe.3G246100' => 'ppe', 'Prupe.3G265100' => 'ppe', 'Prupe.4G034700' => 'ppe', 'Prupe.4G052100' => 'ppe', 'Prupe.4G053600' => 'ppe', 'Prupe.5G068800' => 'ppe', 'Prupe.5G070600' => 'ppe', 'Prupe.6G075400' => 'ppe', 'Prupe.6G075500' => 'ppe', 'Prupe.6G076400' => 'ppe', 'Prupe.8G110700' => 'ppe', 'Psat4g020960' => 'psa', 'PSO135G0788' => 'pso', 'PSO210G6463' => 'pso', 'PSO384G0370' => 'pso', 'PSO386G0056' => 'pso', 'QL01p006048' => 'qlo', 'QL02p054283' => 'qlo', 'QL05p008000' => 'qlo', 'QL05p008212' => 'qlo', 'QL05p008950' => 'qlo', 'QL05p009042' => 'qlo', 'QL05p009518' => 'qlo', 'QL05p012589' => 'qlo', 'QL05p012608' => 'qlo', 'QL05p012650' => 'qlo', 'QL05p012667' => 'qlo', 'QL05p014501' => 'qlo', 'QL05p052800' => 'qlo', 'QL05p065010' => 'qlo', 'QL05p074156' => 'qlo', 'QL05p074160' => 'qlo', 'QL05p074174' => 'qlo', 'QL05p074178' => 'qlo', 'QL05p074214' => 'qlo', 'QL06p001050' => 'qlo', 'QL06p001056' => 'qlo', 'QL06p006093' => 'qlo', 'QL06p006111' => 'qlo', 'QL07p019784' => 'qlo', 'QL07p019801' => 'qlo', 'QL07p036110' => 'qlo', 'QL07p036134' => 'qlo', 'QL07p036147' => 'qlo', 'QL07p036156' => 'qlo', 'QL07p036300' => 'qlo', 'QL07p036320' => 'qlo', 'QL08p014547' => 'qlo', 'QL08p014551' => 'qlo', 'QL08p043319' => 'qlo', 'QL08p043324' => 'qlo', 'QL11p009094' => 'qlo', 'RcHm_v2.0_Chr1g0380481' => 'rch', 'RcHm_v2.0_Chr2g0089331' => 'rch', 'RcHm_v2.0_Chr2g0123691' => 'rch', 'RcHm_v2.0_Chr2g0151111' => 'rch', 'RcHm_v2.0_Chr2g0163011' => 'rch', 'RcHm_v2.0_Chr2g0163051' => 'rch', 'RcHm_v2.0_Chr2g0164671' => 'rch', 'RcHm_v2.0_Chr2g0164681' => 'rch', 'RcHm_v2.0_Chr2g0164721' => 'rch', 'RcHm_v2.0_Chr3g0449911' => 'rch', 'RcHm_v2.0_Chr3g0450211' => 'rch', 'RcHm_v2.0_Chr3g0457271' => 'rch', 'RcHm_v2.0_Chr5g0018111' => 'rch', 'RcHm_v2.0_Chr5g0021011' => 'rch', 'RcHm_v2.0_Chr5g0081171' => 'rch', 'RcHm_v2.0_Chr5g0081211' => 'rch', 'RcHm_v2.0_Chr6g0275871' => 'rch', 'RcHm_v2.0_Chr6g0276071' => 'rch', 'RcHm_v2.0_Chr6g0285591' => 'rch', 'RcHm_v2.0_Chr6g0291931' => 'rch', 'RcHm_v2.0_Chr6g0292091' => 'rch', 'RcHm_v2.0_Chr6g0292271' => 'rch', 'RcHm_v2.0_Chr7g0221261' => 'rch', 'Rhsim08G0219900' => 'rsi', 'Rhsim08G0220200' => 'rsi', 'Rhsim08G0237800' => 'rsi', 'Rhsim08G0238800' => 'rsi', 'Sabra09G0102700' => 'sbr', 'Sabra09G0127200' => 'sbr', 'Sabra11G0003700' => 'sbr', 'Sabra15G0014700' => 'sbr', 'Sc19g0000590' => 'sci', 'Sc19g0001870' => 'sci', 'SGA_v2.0_scaffold1G00346' => 'sas', 'SGA_v2.0_scaffold1G00575' => 'sas', 'SGA_v2.0_scaffold1G00761' => 'sas', 'SGA_v2.0_scaffold232G43501' => 'sas', 'TAR625G1137' => 'tar', 'Thecc.03G222100' => 'tca', 'TPR.G12691' => 'tpr', 'TWI34G0727' => 'twi', 'TWI36G0117' => 'twi', 'VMungo1309G0868' => 'vmu' ), 'gf_id' => 'HOM05D001729', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001729' ), 'data_identifier' => 'HOM05D001729', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001729', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '375', 'num_species' => '42' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'Ah.07g204710' => 'amhyb', 'AUR62006001' => 'cqu', 'AUR62006002' => 'cqu', 'AUR62006003' => 'cqu', 'AUR62015641' => 'cqu', 'AUR62027174' => 'cqu', 'AUR62035623' => 'cqu', 'AUR62035624' => 'cqu', 'AUR62035625' => 'cqu', 'AUR62035626' => 'cqu', 'CAN.G1110.53' => 'can', 'CANSAT80G0415' => 'cansat', 'Ca_21364_v3' => 'car', 'COL.COLO4_30693' => 'col', 'COL.COLO4_30694' => 'col', 'COL.COLO4_30695' => 'col', 'COL.COLO4_30696' => 'col', 'COL.COLO4_34020' => 'col', 'DCAR_004585' => 'dca', 'Dinv04029' => 'din', 'Dinv34857' => 'din', 'Duzib147G0011' => 'dzi', 'Duzib170G0599' => 'dzi', 'Duzib192G1051' => 'dzi', 'FAN01G0708' => 'fan', 'FAN01G0742' => 'fan', 'FAN02G0048' => 'fan', 'FAN02G0583' => 'fan', 'FAN02G0688' => 'fan', 'FAN02G1588' => 'fan', 'FAN02G2194' => 'fan', 'FAN02G2750' => 'fan', 'FAN02G3094' => 'fan', 'FAN02G3887' => 'fan', 'FAN02G3911' => 'fan', 'FAN02G3994' => 'fan', 'FAN02G4432' => 'fan', 'FAN02G4556' => 'fan', 'FAN03G1977' => 'fan', 'FAN03G2781' => 'fan', 'FAN03G2850' => 'fan', 'FAN03G3155' => 'fan', 'FAN04G2487' => 'fan', 'FAN05G0208' => 'fan', 'FAN05G0656' => 'fan', 'FAN05G0696' => 'fan', 'FAN05G0810' => 'fan', 'FAN05G1447' => 'fan', 'FAN05G2640' => 'fan', 'FAN05G2911' => 'fan', 'FAN05G3901' => 'fan', 'FAN05G4859' => 'fan', 'FAN05G4861' => 'fan', 'FAN05G4988' => 'fan', 'FAN05G5187' => 'fan', 'FAN05G5452' => 'fan', 'FAN05G5500' => 'fan', 'FAN05G5688' => 'fan', 'FAN06G0177' => 'fan', 'FAN06G0675' => 'fan', 'FAN06G1290' => 'fan', 'FAN06G2191' => 'fan', 'FAN06G2405' => 'fan', 'FAN06G3231' => 'fan', 'FAN06G3932' => 'fan', 'FAN07G0163' => 'fan', 'FAN07G0471' => 'fan', 'FAN07G1354' => 'fan', 'FAN08G0338' => 'fan', 'FAN08G1373' => 'fan', 'FAN08G2539' => 'fan', 'FAN08G2728' => 'fan', 'FAN09G0608' => 'fan', 'FAN09G1136' => 'fan', 'FAN09G1958' => 'fan', 'FAN09G2508' => 'fan', 'FAN09G2597' => 'fan', 'FAN09G2658' => 'fan', 'FAN09G2757' => 'fan', 'FAN09G2983' => 'fan', 'FAN09G3130' => 'fan', 'FAN09G3565' => 'fan', 'FAN09G3613' => 'fan', 'FAN09G4011' => 'fan', 'FAN09G4239' => 'fan', 'FAN09G4277' => 'fan', 'FAN09G4720' => 'fan', 'FAN11G0139' => 'fan', 'FAN11G1727' => 'fan', 'FAN11G2672' => 'fan', 'FAN11G2795' => 'fan', 'FAN11G3238' => 'fan', 'FAN11G3734' => 'fan', 'FAN12G0631' => 'fan', 'FAN12G2239' => 'fan', 'FAN12G2308' => 'fan', 'FAN12G2569' => 'fan', 'FAN12G2623' => 'fan', 'FAN13G3182' => 'fan', 'FAN14G0053' => 'fan', 'FAN14G0370' => 'fan', 'FAN14G0382' => 'fan', 'FAN14G0421' => 'fan', 'FAN14G0866' => 'fan', 'FAN14G1187' => 'fan', 'FAN14G1727' => 'fan', 'FAN14G1791' => 'fan', 'FAN14G2361' => 'fan', 'FAN14G2668' => 'fan', 'FAN14G2770' => 'fan', 'FAN14G2874' => 'fan', 'FAN14G3193' => 'fan', 'FAN14G3624' => 'fan', 'FAN14G3676' => 'fan', 'FAN14G3807' => 'fan', 'FAN14G4082' => 'fan', 'FAN14G4342' => 'fan', 'FAN14G4985' => 'fan', 'FAN14G5126' => 'fan', 'FAN14G5781' => 'fan', 'FAN14G5808' => 'fan', 'FAN14G5949' => 'fan', 'FAN15G0828' => 'fan', 'FAN15G1054' => 'fan', 'FAN15G2023' => 'fan', 'FAN15G2506' => 'fan', 'FAN16G0128' => 'fan', 'FAN16G0249' => 'fan', 'FAN16G0429' => 'fan', 'FAN16G1493' => 'fan', 'FAN16G2210' => 'fan', 'FAN16G2506' => 'fan', 'FAN18G1542' => 'fan', 'FAN18G4057' => 'fan', 'FAN19G0745' => 'fan', 'FAN19G1216' => 'fan', 'FAN19G1733' => 'fan', 'FAN20G0258' => 'fan', 'FAN20G1095' => 'fan', 'FAN20G1557' => 'fan', 'FAN21G0302' => 'fan', 'FAN21G0519' => 'fan', 'FAN21G0970' => 'fan', 'FAN21G1159' => 'fan', 'FAN21G1312' => 'fan', 'FAN21G1440' => 'fan', 'FAN21G1715' => 'fan', 'FAN23G1584' => 'fan', 'FAN24G0045' => 'fan', 'FAN24G0053' => 'fan', 'FAN24G1500' => 'fan', 'FAN24G1817' => 'fan', 'FAN24G2147' => 'fan', 'FAN24G2236' => 'fan', 'FAN24G2446' => 'fan', 'FAN24G2684' => 'fan', 'FAN25G0187' => 'fan', 'FAN25G0505' => 'fan', 'FAN25G0589' => 'fan', 'FAN25G3663' => 'fan', 'FAN26G1025' => 'fan', 'FAN26G2860' => 'fan', 'FAN27G1329' => 'fan', 'FAN27G3392' => 'fan', 'FvH4_1g02011' => 'fve', 'FvH4_1g06511' => 'fve', 'FvH4_2g19900' => 'fve', 'FvH4_2g19920' => 'fve', 'FvH4_2g24261' => 'fve', 'FvH4_2g24270' => 'fve', 'FvH4_2g24631' => 'fve', 'FvH4_2g30622' => 'fve', 'FvH4_3g12920' => 'fve', 'FvH4_3g30171' => 'fve', 'FvH4_3g35490' => 'fve', 'FvH4_3g43682' => 'fve', 'FvH4_3g43730' => 'fve', 'FvH4_3g43732' => 'fve', 'FvH4_3g43751' => 'fve', 'FvH4_3g43752' => 'fve', 'FvH4_3g43770' => 'fve', 'FvH4_3g44471' => 'fve', 'FvH4_3g44510' => 'fve', 'FvH4_3g44582' => 'fve', 'FvH4_4g16921' => 'fve', 'FvH4_4g17121' => 'fve', 'FvH4_4g17782' => 'fve', 'FvH4_4g17783' => 'fve', 'FvH4_4g18120' => 'fve', 'FvH4_4g31310' => 'fve', 'FvH4_4g35052' => 'fve', 'FvH4_5g30862' => 'fve', 'FvH4_6g01541' => 'fve', 'FvH4_6g02021' => 'fve', 'FvH4_6g02041' => 'fve', 'FvH4_6g02071' => 'fve', 'FvH4_6g02171' => 'fve', 'FvH4_6g03181' => 'fve', 'FvH4_6g03182' => 'fve', 'FvH4_6g03221' => 'fve', 'FvH4_6g03380' => 'fve', 'FvH4_6g05201' => 'fve', 'FvH4_6g05203' => 'fve', 'FvH4_6g20231' => 'fve', 'FvH4_6g31981' => 'fve', 'FvH4_6g32061' => 'fve', 'FvH4_6g37041' => 'fve', 'FvH4_6g37932' => 'fve', 'FvH4_6g38731' => 'fve', 'FvH4_6g39370' => 'fve', 'FvH4_6g39371' => 'fve', 'FvH4_6g40891' => 'fve', 'FvH4_6g40892' => 'fve', 'FvH4_6g43143' => 'fve', 'FvH4_6g45251' => 'fve', 'FvH4_6g45260' => 'fve', 'FvH4_6g45291' => 'fve', 'FvH4_6g45890' => 'fve', 'FvH4_6g46240' => 'fve', 'FvH4_6g46241' => 'fve', 'FvH4_6g46242' => 'fve', 'FvH4_6g46260' => 'fve', 'FvH4_6g46280' => 'fve', 'FvH4_6g46380' => 'fve', 'FvH4_7g12841' => 'fve', 'FvH4_7g31431' => 'fve', 'Glyma.09G075900' => 'gma', 'Gohir.A09G096401' => 'ghi', 'Gohir.D09G096101' => 'ghi', 'Gorai.006G112800' => 'gra', 'HanXRQChr04g0121411' => 'han', 'Hund15878' => 'sun', 'Lj2A1107G68' => 'lonja', 'Lj2A630G63' => 'lonja', 'Lj2A946T25' => 'lonja', 'Lj2C714T1' => 'lonja', 'Lj2C966T3' => 'lonja', 'Lj2C966T4' => 'lonja', 'Lj4g0002979' => 'lja', 'Lsat_1_v5_gn_5_30901' => 'lsa', 'Lsat_1_v5_gn_5_31100' => 'lsa', 'Lsat_1_v5_gn_5_38600' => 'lsa', 'Lsat_1_v5_gn_6_92061' => 'lsa', 'Manes.05G071301' => 'mes', 'MD02G1008700' => 'mdo', 'MD02G1008900' => 'mdo', 'MD03G1256400' => 'mdo', 'MD04G1180900' => 'mdo', 'MD04G1181000' => 'mdo', 'MD04G1181200' => 'mdo', 'MD05G1244200' => 'mdo', 'MD05G1324200' => 'mdo', 'MD09G1201600' => 'mdo', 'MD10G1000600' => 'mdo', 'MD14G1026900' => 'mdo', 'MD14G1187900' => 'mdo', 'MD15G1017800' => 'mdo', 'MD15G1018100' => 'mdo', 'Medtr4g124160' => 'mtr', 'Migut.L01260' => 'egut', 'Nitab4.5_0000008g0440' => 'nta', 'Nitab4.5_0000207g0170' => 'nta', 'Nitab4.5_0007671g0030' => 'nta', 'Nitab4.5_0010853g0020' => 'nta', 'Oeu057656.1' => 'oeu', 'PGSC0003DMG400005638' => 'stu', 'PGSC0003DMG400005639' => 'stu', 'Phvul.009G222800' => 'pvu', 'Potri.009G132400' => 'ptr', 'Potri.009G163001' => 'ptr', 'Potri.011G000700' => 'ptr', 'Potri.011G004800' => 'ptr', 'Prupe.1G509300' => 'ppe', 'Prupe.1G509700' => 'ppe', 'Prupe.1G510400' => 'ppe', 'Prupe.1G510700' => 'ppe', 'Prupe.1G512600' => 'ppe', 'Prupe.2G073200' => 'ppe', 'Prupe.3G059500' => 'ppe', 'Prupe.3G059600' => 'ppe', 'Prupe.3G246100' => 'ppe', 'Prupe.3G265100' => 'ppe', 'Prupe.4G034700' => 'ppe', 'Prupe.4G052100' => 'ppe', 'Prupe.4G053600' => 'ppe', 'Prupe.5G068800' => 'ppe', 'Prupe.5G070600' => 'ppe', 'Prupe.6G075400' => 'ppe', 'Prupe.6G075500' => 'ppe', 'Prupe.6G076400' => 'ppe', 'Prupe.8G110700' => 'ppe', 'Psat4g020960' => 'psa', 'PSO135G0788' => 'pso', 'PSO210G6463' => 'pso', 'PSO384G0370' => 'pso', 'PSO386G0056' => 'pso', 'QL01p006048' => 'qlo', 'QL02p054283' => 'qlo', 'QL05p008000' => 'qlo', 'QL05p008212' => 'qlo', 'QL05p008950' => 'qlo', 'QL05p009042' => 'qlo', 'QL05p009518' => 'qlo', 'QL05p012589' => 'qlo', 'QL05p012608' => 'qlo', 'QL05p012650' => 'qlo', 'QL05p012667' => 'qlo', 'QL05p014501' => 'qlo', 'QL05p052800' => 'qlo', 'QL05p065010' => 'qlo', 'QL05p074156' => 'qlo', 'QL05p074160' => 'qlo', 'QL05p074174' => 'qlo', 'QL05p074178' => 'qlo', 'QL05p074214' => 'qlo', 'QL06p001050' => 'qlo', 'QL06p001056' => 'qlo', 'QL06p006093' => 'qlo', 'QL06p006111' => 'qlo', 'QL07p019784' => 'qlo', 'QL07p019801' => 'qlo', 'QL07p036110' => 'qlo', 'QL07p036134' => 'qlo', 'QL07p036147' => 'qlo', 'QL07p036156' => 'qlo', 'QL07p036300' => 'qlo', 'QL07p036320' => 'qlo', 'QL08p014547' => 'qlo', 'QL08p014551' => 'qlo', 'QL08p043319' => 'qlo', 'QL08p043324' => 'qlo', 'QL11p009094' => 'qlo', 'RcHm_v2.0_Chr1g0380481' => 'rch', 'RcHm_v2.0_Chr2g0089331' => 'rch', 'RcHm_v2.0_Chr2g0123691' => 'rch', 'RcHm_v2.0_Chr2g0151111' => 'rch', 'RcHm_v2.0_Chr2g0163011' => 'rch', 'RcHm_v2.0_Chr2g0163051' => 'rch', 'RcHm_v2.0_Chr2g0164671' => 'rch', 'RcHm_v2.0_Chr2g0164681' => 'rch', 'RcHm_v2.0_Chr2g0164721' => 'rch', 'RcHm_v2.0_Chr3g0449911' => 'rch', 'RcHm_v2.0_Chr3g0450211' => 'rch', 'RcHm_v2.0_Chr3g0457271' => 'rch', 'RcHm_v2.0_Chr5g0018111' => 'rch', 'RcHm_v2.0_Chr5g0021011' => 'rch', 'RcHm_v2.0_Chr5g0081171' => 'rch', 'RcHm_v2.0_Chr5g0081211' => 'rch', 'RcHm_v2.0_Chr6g0275871' => 'rch', 'RcHm_v2.0_Chr6g0276071' => 'rch', 'RcHm_v2.0_Chr6g0285591' => 'rch', 'RcHm_v2.0_Chr6g0291931' => 'rch', 'RcHm_v2.0_Chr6g0292091' => 'rch', 'RcHm_v2.0_Chr6g0292271' => 'rch', 'RcHm_v2.0_Chr7g0221261' => 'rch', 'Rhsim08G0219900' => 'rsi', 'Rhsim08G0220200' => 'rsi', 'Rhsim08G0237800' => 'rsi', 'Rhsim08G0238800' => 'rsi', 'Sabra09G0102700' => 'sbr', 'Sabra09G0127200' => 'sbr', 'Sabra11G0003700' => 'sbr', 'Sabra15G0014700' => 'sbr', 'Sc19g0000590' => 'sci', 'Sc19g0001870' => 'sci', 'SGA_v2.0_scaffold1G00346' => 'sas', 'SGA_v2.0_scaffold1G00575' => 'sas', 'SGA_v2.0_scaffold1G00761' => 'sas', 'SGA_v2.0_scaffold232G43501' => 'sas', 'TAR625G1137' => 'tar', 'Thecc.03G222100' => 'tca', 'TPR.G12691' => 'tpr', 'TWI34G0727' => 'twi', 'TWI36G0117' => 'twi', 'VMungo1309G0868' => 'vmu' ) $gf_id = 'HOM05D001729' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001729' ) $data_identifier = 'HOM05D001729' $data_type = 'gf_id' $species_gene_counts = array( 'amhyb' => (int) 1, 'cqu' => (int) 9, 'can' => (int) 1, 'cansat' => (int) 1, 'car' => (int) 1, 'col' => (int) 5, 'dca' => (int) 1, 'din' => (int) 2, 'dzi' => (int) 3, 'fan' => (int) 140, 'fve' => (int) 62, 'gma' => (int) 1, 'ghi' => (int) 2, 'gra' => (int) 1, 'han' => (int) 1, 'sun' => (int) 1, 'lonja' => (int) 6, 'lja' => (int) 1, 'lsa' => (int) 4, 'mes' => (int) 1, 'mdo' => (int) 14, 'mtr' => (int) 1, 'egut' => (int) 1, 'nta' => (int) 4, 'oeu' => (int) 1, 'stu' => (int) 2, 'pvu' => (int) 1, 'ptr' => (int) 4, 'ppe' => (int) 19, 'psa' => (int) 1, 'pso' => (int) 4, 'qlo' => (int) 36, 'rch' => (int) 23, 'rsi' => (int) 4, 'sbr' => (int) 4, 'sci' => (int) 2, 'sas' => (int) 4, 'tar' => (int) 1, 'tca' => (int) 1, 'tpr' => (int) 1, 'twi' => (int) 2, 'vmu' => (int) 1 ) $gf_gene_species = 'vmu' $gf_gene_id = 'VMungo1309G0868' $species_info = array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ) $local_species = 'qlo' $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' => 'HOM05D001729', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '375', 'num_species' => '42' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'Ah.07g204710' => 'amhyb', 'AUR62006001' => 'cqu', 'AUR62006002' => 'cqu', 'AUR62006003' => 'cqu', 'AUR62015641' => 'cqu', 'AUR62027174' => 'cqu', 'AUR62035623' => 'cqu', 'AUR62035624' => 'cqu', 'AUR62035625' => 'cqu', 'AUR62035626' => 'cqu', 'CAN.G1110.53' => 'can', 'CANSAT80G0415' => 'cansat', 'Ca_21364_v3' => 'car', 'COL.COLO4_30693' => 'col', 'COL.COLO4_30694' => 'col', 'COL.COLO4_30695' => 'col', 'COL.COLO4_30696' => 'col', 'COL.COLO4_34020' => 'col', 'DCAR_004585' => 'dca', 'Dinv04029' => 'din', 'Dinv34857' => 'din', 'Duzib147G0011' => 'dzi', 'Duzib170G0599' => 'dzi', 'Duzib192G1051' => 'dzi', 'FAN01G0708' => 'fan', 'FAN01G0742' => 'fan', 'FAN02G0048' => 'fan', 'FAN02G0583' => 'fan', 'FAN02G0688' => 'fan', 'FAN02G1588' => 'fan', 'FAN02G2194' => 'fan', 'FAN02G2750' => 'fan', 'FAN02G3094' => 'fan', 'FAN02G3887' => 'fan', 'FAN02G3911' => 'fan', 'FAN02G3994' => 'fan', 'FAN02G4432' => 'fan', 'FAN02G4556' => 'fan', 'FAN03G1977' => 'fan', 'FAN03G2781' => 'fan', 'FAN03G2850' => 'fan', 'FAN03G3155' => 'fan', 'FAN04G2487' => 'fan', 'FAN05G0208' => 'fan', 'FAN05G0656' => 'fan', 'FAN05G0696' => 'fan', 'FAN05G0810' => 'fan', 'FAN05G1447' => 'fan', 'FAN05G2640' => 'fan', 'FAN05G2911' => 'fan', 'FAN05G3901' => 'fan', 'FAN05G4859' => 'fan', 'FAN05G4861' => 'fan', 'FAN05G4988' => 'fan', 'FAN05G5187' => 'fan', 'FAN05G5452' => 'fan', 'FAN05G5500' => 'fan', 'FAN05G5688' => 'fan', 'FAN06G0177' => 'fan', 'FAN06G0675' => 'fan', 'FAN06G1290' => 'fan', 'FAN06G2191' => 'fan', 'FAN06G2405' => 'fan', 'FAN06G3231' => 'fan', 'FAN06G3932' => 'fan', 'FAN07G0163' => 'fan', 'FAN07G0471' => 'fan', 'FAN07G1354' => 'fan', 'FAN08G0338' => 'fan', 'FAN08G1373' => 'fan', 'FAN08G2539' => 'fan', 'FAN08G2728' => 'fan', 'FAN09G0608' => 'fan', 'FAN09G1136' => 'fan', 'FAN09G1958' => 'fan', 'FAN09G2508' => 'fan', 'FAN09G2597' => 'fan', 'FAN09G2658' => 'fan', 'FAN09G2757' => 'fan', 'FAN09G2983' => 'fan', 'FAN09G3130' => 'fan', 'FAN09G3565' => 'fan', 'FAN09G3613' => 'fan', 'FAN09G4011' => 'fan', 'FAN09G4239' => 'fan', 'FAN09G4277' => 'fan', 'FAN09G4720' => 'fan', 'FAN11G0139' => 'fan', 'FAN11G1727' => 'fan', 'FAN11G2672' => 'fan', 'FAN11G2795' => 'fan', 'FAN11G3238' => 'fan', 'FAN11G3734' => 'fan', 'FAN12G0631' => 'fan', 'FAN12G2239' => 'fan', 'FAN12G2308' => 'fan', 'FAN12G2569' => 'fan', 'FAN12G2623' => 'fan', 'FAN13G3182' => 'fan', 'FAN14G0053' => 'fan', 'FAN14G0370' => 'fan', 'FAN14G0382' => 'fan', 'FAN14G0421' => 'fan', 'FAN14G0866' => 'fan', 'FAN14G1187' => 'fan', 'FAN14G1727' => 'fan', 'FAN14G1791' => 'fan', 'FAN14G2361' => 'fan', 'FAN14G2668' => 'fan', 'FAN14G2770' => 'fan', 'FAN14G2874' => 'fan', 'FAN14G3193' => 'fan', 'FAN14G3624' => 'fan', 'FAN14G3676' => 'fan', 'FAN14G3807' => 'fan', 'FAN14G4082' => 'fan', 'FAN14G4342' => 'fan', 'FAN14G4985' => 'fan', 'FAN14G5126' => 'fan', 'FAN14G5781' => 'fan', 'FAN14G5808' => 'fan', 'FAN14G5949' => 'fan', 'FAN15G0828' => 'fan', 'FAN15G1054' => 'fan', 'FAN15G2023' => 'fan', 'FAN15G2506' => 'fan', 'FAN16G0128' => 'fan', 'FAN16G0249' => 'fan', 'FAN16G0429' => 'fan', 'FAN16G1493' => 'fan', 'FAN16G2210' => 'fan', 'FAN16G2506' => 'fan', 'FAN18G1542' => 'fan', 'FAN18G4057' => 'fan', 'FAN19G0745' => 'fan', 'FAN19G1216' => 'fan', 'FAN19G1733' => 'fan', 'FAN20G0258' => 'fan', 'FAN20G1095' => 'fan', 'FAN20G1557' => 'fan', 'FAN21G0302' => 'fan', 'FAN21G0519' => 'fan', 'FAN21G0970' => 'fan', 'FAN21G1159' => 'fan', 'FAN21G1312' => 'fan', 'FAN21G1440' => 'fan', 'FAN21G1715' => 'fan', 'FAN23G1584' => 'fan', 'FAN24G0045' => 'fan', 'FAN24G0053' => 'fan', 'FAN24G1500' => 'fan', 'FAN24G1817' => 'fan', 'FAN24G2147' => 'fan', 'FAN24G2236' => 'fan', 'FAN24G2446' => 'fan', 'FAN24G2684' => 'fan', 'FAN25G0187' => 'fan', 'FAN25G0505' => 'fan', 'FAN25G0589' => 'fan', 'FAN25G3663' => 'fan', 'FAN26G1025' => 'fan', 'FAN26G2860' => 'fan', 'FAN27G1329' => 'fan', 'FAN27G3392' => 'fan', 'FvH4_1g02011' => 'fve', 'FvH4_1g06511' => 'fve', 'FvH4_2g19900' => 'fve', 'FvH4_2g19920' => 'fve', 'FvH4_2g24261' => 'fve', 'FvH4_2g24270' => 'fve', 'FvH4_2g24631' => 'fve', 'FvH4_2g30622' => 'fve', 'FvH4_3g12920' => 'fve', 'FvH4_3g30171' => 'fve', 'FvH4_3g35490' => 'fve', 'FvH4_3g43682' => 'fve', 'FvH4_3g43730' => 'fve', 'FvH4_3g43732' => 'fve', 'FvH4_3g43751' => 'fve', 'FvH4_3g43752' => 'fve', 'FvH4_3g43770' => 'fve', 'FvH4_3g44471' => 'fve', 'FvH4_3g44510' => 'fve', 'FvH4_3g44582' => 'fve', 'FvH4_4g16921' => 'fve', 'FvH4_4g17121' => 'fve', 'FvH4_4g17782' => 'fve', 'FvH4_4g17783' => 'fve', 'FvH4_4g18120' => 'fve', 'FvH4_4g31310' => 'fve', 'FvH4_4g35052' => 'fve', 'FvH4_5g30862' => 'fve', 'FvH4_6g01541' => 'fve', 'FvH4_6g02021' => 'fve', 'FvH4_6g02041' => 'fve', 'FvH4_6g02071' => 'fve', 'FvH4_6g02171' => 'fve', 'FvH4_6g03181' => 'fve', 'FvH4_6g03182' => 'fve', 'FvH4_6g03221' => 'fve', 'FvH4_6g03380' => 'fve', 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'ppe', 'Prupe.1G512600' => 'ppe', 'Prupe.2G073200' => 'ppe', 'Prupe.3G059500' => 'ppe', 'Prupe.3G059600' => 'ppe', 'Prupe.3G246100' => 'ppe', 'Prupe.3G265100' => 'ppe', 'Prupe.4G034700' => 'ppe', 'Prupe.4G052100' => 'ppe', 'Prupe.4G053600' => 'ppe', 'Prupe.5G068800' => 'ppe', 'Prupe.5G070600' => 'ppe', 'Prupe.6G075400' => 'ppe', 'Prupe.6G075500' => 'ppe', 'Prupe.6G076400' => 'ppe', 'Prupe.8G110700' => 'ppe', 'Psat4g020960' => 'psa', 'PSO135G0788' => 'pso', 'PSO210G6463' => 'pso', 'PSO384G0370' => 'pso', 'PSO386G0056' => 'pso', 'QL01p006048' => 'qlo', 'QL02p054283' => 'qlo', 'QL05p008000' => 'qlo', 'QL05p008212' => 'qlo', 'QL05p008950' => 'qlo', 'QL05p009042' => 'qlo', 'QL05p009518' => 'qlo', 'QL05p012589' => 'qlo', 'QL05p012608' => 'qlo', 'QL05p012650' => 'qlo', 'QL05p012667' => 'qlo', 'QL05p014501' => 'qlo', 'QL05p052800' => 'qlo', 'QL05p065010' => 'qlo', 'QL05p074156' => 'qlo', 'QL05p074160' => 'qlo', 'QL05p074174' => 'qlo', 'QL05p074178' => 'qlo', 'QL05p074214' => 'qlo', 'QL06p001050' => 'qlo', 'QL06p001056' => 'qlo', 'QL06p006093' => 'qlo', 'QL06p006111' => 'qlo', 'QL07p019784' => 'qlo', 'QL07p019801' => 'qlo', 'QL07p036110' => 'qlo', 'QL07p036134' => 'qlo', 'QL07p036147' => 'qlo', 'QL07p036156' => 'qlo', 'QL07p036300' => 'qlo', 'QL07p036320' => 'qlo', 'QL08p014547' => 'qlo', 'QL08p014551' => 'qlo', 'QL08p043319' => 'qlo', 'QL08p043324' => 'qlo', 'QL11p009094' => 'qlo', 'RcHm_v2.0_Chr1g0380481' => 'rch', 'RcHm_v2.0_Chr2g0089331' => 'rch', 'RcHm_v2.0_Chr2g0123691' => 'rch', 'RcHm_v2.0_Chr2g0151111' => 'rch', 'RcHm_v2.0_Chr2g0163011' => 'rch', 'RcHm_v2.0_Chr2g0163051' => 'rch', 'RcHm_v2.0_Chr2g0164671' => 'rch', 'RcHm_v2.0_Chr2g0164681' => 'rch', 'RcHm_v2.0_Chr2g0164721' => 'rch', 'RcHm_v2.0_Chr3g0449911' => 'rch', 'RcHm_v2.0_Chr3g0450211' => 'rch', 'RcHm_v2.0_Chr3g0457271' => 'rch', 'RcHm_v2.0_Chr5g0018111' => 'rch', 'RcHm_v2.0_Chr5g0021011' => 'rch', 'RcHm_v2.0_Chr5g0081171' => 'rch', 'RcHm_v2.0_Chr5g0081211' => 'rch', 'RcHm_v2.0_Chr6g0275871' => 'rch', 'RcHm_v2.0_Chr6g0276071' => 'rch', 'RcHm_v2.0_Chr6g0285591' => 'rch', 'RcHm_v2.0_Chr6g0291931' => 'rch', 'RcHm_v2.0_Chr6g0292091' => 'rch', 'RcHm_v2.0_Chr6g0292271' => 'rch', 'RcHm_v2.0_Chr7g0221261' => 'rch', 'Rhsim08G0219900' => 'rsi', 'Rhsim08G0220200' => 'rsi', 'Rhsim08G0237800' => 'rsi', 'Rhsim08G0238800' => 'rsi', 'Sabra09G0102700' => 'sbr', 'Sabra09G0127200' => 'sbr', 'Sabra11G0003700' => 'sbr', 'Sabra15G0014700' => 'sbr', 'Sc19g0000590' => 'sci', 'Sc19g0001870' => 'sci', 'SGA_v2.0_scaffold1G00346' => 'sas', 'SGA_v2.0_scaffold1G00575' => 'sas', 'SGA_v2.0_scaffold1G00761' => 'sas', 'SGA_v2.0_scaffold232G43501' => 'sas', 'TAR625G1137' => 'tar', 'Thecc.03G222100' => 'tca', 'TPR.G12691' => 'tpr', 'TWI34G0727' => 'twi', 'TWI36G0117' => 'twi', 'VMungo1309G0868' => 'vmu' ), 'gf_id' => 'HOM05D001729', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001729' ), 'data_identifier' => 'HOM05D001729', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001729', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '375', 'num_species' => '42' ) 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'AUR62035624' => 'cqu', 'AUR62035625' => 'cqu', 'AUR62035626' => 'cqu', 'CAN.G1110.53' => 'can', 'CANSAT80G0415' => 'cansat', 'Ca_21364_v3' => 'car', 'COL.COLO4_30693' => 'col', 'COL.COLO4_30694' => 'col', 'COL.COLO4_30695' => 'col', 'COL.COLO4_30696' => 'col', 'COL.COLO4_34020' => 'col', 'DCAR_004585' => 'dca', 'Dinv04029' => 'din', 'Dinv34857' => 'din', 'Duzib147G0011' => 'dzi', 'Duzib170G0599' => 'dzi', 'Duzib192G1051' => 'dzi', 'FAN01G0708' => 'fan', 'FAN01G0742' => 'fan', 'FAN02G0048' => 'fan', 'FAN02G0583' => 'fan', 'FAN02G0688' => 'fan', 'FAN02G1588' => 'fan', 'FAN02G2194' => 'fan', 'FAN02G2750' => 'fan', 'FAN02G3094' => 'fan', 'FAN02G3887' => 'fan', 'FAN02G3911' => 'fan', 'FAN02G3994' => 'fan', 'FAN02G4432' => 'fan', 'FAN02G4556' => 'fan', 'FAN03G1977' => 'fan', 'FAN03G2781' => 'fan', 'FAN03G2850' => 'fan', 'FAN03G3155' => 'fan', 'FAN04G2487' => 'fan', 'FAN05G0208' => 'fan', 'FAN05G0656' => 'fan', 'FAN05G0696' => 'fan', 'FAN05G0810' => 'fan', 'FAN05G1447' => 'fan', 'FAN05G2640' => 'fan', 'FAN05G2911' => 'fan', 'FAN05G3901' => 'fan', 'FAN05G4859' => 'fan', 'FAN05G4861' => 'fan', 'FAN05G4988' => 'fan', 'FAN05G5187' => 'fan', 'FAN05G5452' => 'fan', 'FAN05G5500' => 'fan', 'FAN05G5688' => 'fan', 'FAN06G0177' => 'fan', 'FAN06G0675' => 'fan', 'FAN06G1290' => 'fan', 'FAN06G2191' => 'fan', 'FAN06G2405' => 'fan', 'FAN06G3231' => 'fan', 'FAN06G3932' => 'fan', 'FAN07G0163' => 'fan', 'FAN07G0471' => 'fan', 'FAN07G1354' => 'fan', 'FAN08G0338' => 'fan', 'FAN08G1373' => 'fan', 'FAN08G2539' => 'fan', 'FAN08G2728' => 'fan', 'FAN09G0608' => 'fan', 'FAN09G1136' => 'fan', 'FAN09G1958' => 'fan', 'FAN09G2508' => 'fan', 'FAN09G2597' => 'fan', 'FAN09G2658' => 'fan', 'FAN09G2757' => 'fan', 'FAN09G2983' => 'fan', 'FAN09G3130' => 'fan', 'FAN09G3565' => 'fan', 'FAN09G3613' => 'fan', 'FAN09G4011' => 'fan', 'FAN09G4239' => 'fan', 'FAN09G4277' => 'fan', 'FAN09G4720' => 'fan', 'FAN11G0139' => 'fan', 'FAN11G1727' => 'fan', 'FAN11G2672' => 'fan', 'FAN11G2795' => 'fan', 'FAN11G3238' => 'fan', 'FAN11G3734' => 'fan', 'FAN12G0631' => 'fan', 'FAN12G2239' => 'fan', 'FAN12G2308' => 'fan', 'FAN12G2569' => 'fan', 'FAN12G2623' => 'fan', 'FAN13G3182' => 'fan', 'FAN14G0053' => 'fan', 'FAN14G0370' => 'fan', 'FAN14G0382' => 'fan', 'FAN14G0421' => 'fan', 'FAN14G0866' => 'fan', 'FAN14G1187' => 'fan', 'FAN14G1727' => 'fan', 'FAN14G1791' => 'fan', 'FAN14G2361' => 'fan', 'FAN14G2668' => 'fan', 'FAN14G2770' => 'fan', 'FAN14G2874' => 'fan', 'FAN14G3193' => 'fan', 'FAN14G3624' => 'fan', 'FAN14G3676' => 'fan', 'FAN14G3807' => 'fan', 'FAN14G4082' => 'fan', 'FAN14G4342' => 'fan', 'FAN14G4985' => 'fan', 'FAN14G5126' => 'fan', 'FAN14G5781' => 'fan', 'FAN14G5808' => 'fan', 'FAN14G5949' => 'fan', 'FAN15G0828' => 'fan', 'FAN15G1054' => 'fan', 'FAN15G2023' => 'fan', 'FAN15G2506' => 'fan', 'FAN16G0128' => 'fan', 'FAN16G0249' => 'fan', 'FAN16G0429' => 'fan', 'FAN16G1493' => 'fan', 'FAN16G2210' => 'fan', 'FAN16G2506' => 'fan', 'FAN18G1542' => 'fan', 'FAN18G4057' => 'fan', 'FAN19G0745' => 'fan', 'FAN19G1216' => 'fan', 'FAN19G1733' => 'fan', 'FAN20G0258' => 'fan', 'FAN20G1095' => 'fan', 'FAN20G1557' => 'fan', 'FAN21G0302' => 'fan', 'FAN21G0519' => 'fan', 'FAN21G0970' => 'fan', 'FAN21G1159' => 'fan', 'FAN21G1312' => 'fan', 'FAN21G1440' => 'fan', 'FAN21G1715' => 'fan', 'FAN23G1584' => 'fan', 'FAN24G0045' => 'fan', 'FAN24G0053' => 'fan', 'FAN24G1500' => 'fan', 'FAN24G1817' => 'fan', 'FAN24G2147' => 'fan', 'FAN24G2236' => 'fan', 'FAN24G2446' => 'fan', 'FAN24G2684' => 'fan', 'FAN25G0187' => 'fan', 'FAN25G0505' => 'fan', 'FAN25G0589' => 'fan', 'FAN25G3663' => 'fan', 'FAN26G1025' => 'fan', 'FAN26G2860' => 'fan', 'FAN27G1329' => 'fan', 'FAN27G3392' => 'fan', 'FvH4_1g02011' => 'fve', 'FvH4_1g06511' => 'fve', 'FvH4_2g19900' => 'fve', 'FvH4_2g19920' => 'fve', 'FvH4_2g24261' => 'fve', 'FvH4_2g24270' => 'fve', 'FvH4_2g24631' => 'fve', 'FvH4_2g30622' => 'fve', 'FvH4_3g12920' => 'fve', 'FvH4_3g30171' => 'fve', 'FvH4_3g35490' => 'fve', 'FvH4_3g43682' => 'fve', 'FvH4_3g43730' => 'fve', 'FvH4_3g43732' => 'fve', 'FvH4_3g43751' => 'fve', 'FvH4_3g43752' => 'fve', 'FvH4_3g43770' => 'fve', 'FvH4_3g44471' => 'fve', 'FvH4_3g44510' => 'fve', 'FvH4_3g44582' => 'fve', 'FvH4_4g16921' => 'fve', 'FvH4_4g17121' => 'fve', 'FvH4_4g17782' => 'fve', 'FvH4_4g17783' => 'fve', 'FvH4_4g18120' => 'fve', 'FvH4_4g31310' => 'fve', 'FvH4_4g35052' => 'fve', 'FvH4_5g30862' => 'fve', 'FvH4_6g01541' => 'fve', 'FvH4_6g02021' => 'fve', 'FvH4_6g02041' => 'fve', 'FvH4_6g02071' => 'fve', 'FvH4_6g02171' => 'fve', 'FvH4_6g03181' => 'fve', 'FvH4_6g03182' => 'fve', 'FvH4_6g03221' => 'fve', 'FvH4_6g03380' => 'fve', 'FvH4_6g05201' => 'fve', 'FvH4_6g05203' => 'fve', 'FvH4_6g20231' => 'fve', 'FvH4_6g31981' => 'fve', 'FvH4_6g32061' => 'fve', 'FvH4_6g37041' => 'fve', 'FvH4_6g37932' => 'fve', 'FvH4_6g38731' => 'fve', 'FvH4_6g39370' => 'fve', 'FvH4_6g39371' => 'fve', 'FvH4_6g40891' => 'fve', 'FvH4_6g40892' => 'fve', 'FvH4_6g43143' => 'fve', 'FvH4_6g45251' => 'fve', 'FvH4_6g45260' => 'fve', 'FvH4_6g45291' => 'fve', 'FvH4_6g45890' => 'fve', 'FvH4_6g46240' => 'fve', 'FvH4_6g46241' => 'fve', 'FvH4_6g46242' => 'fve', 'FvH4_6g46260' => 'fve', 'FvH4_6g46280' => 'fve', 'FvH4_6g46380' => 'fve', 'FvH4_7g12841' => 'fve', 'FvH4_7g31431' => 'fve', 'Glyma.09G075900' => 'gma', 'Gohir.A09G096401' => 'ghi', 'Gohir.D09G096101' => 'ghi', 'Gorai.006G112800' => 'gra', 'HanXRQChr04g0121411' => 'han', 'Hund15878' => 'sun', 'Lj2A1107G68' => 'lonja', 'Lj2A630G63' => 'lonja', 'Lj2A946T25' => 'lonja', 'Lj2C714T1' => 'lonja', 'Lj2C966T3' => 'lonja', 'Lj2C966T4' => 'lonja', 'Lj4g0002979' => 'lja', 'Lsat_1_v5_gn_5_30901' => 'lsa', 'Lsat_1_v5_gn_5_31100' => 'lsa', 'Lsat_1_v5_gn_5_38600' => 'lsa', 'Lsat_1_v5_gn_6_92061' => 'lsa', 'Manes.05G071301' => 'mes', 'MD02G1008700' => 'mdo', 'MD02G1008900' => 'mdo', 'MD03G1256400' => 'mdo', 'MD04G1180900' => 'mdo', 'MD04G1181000' => 'mdo', 'MD04G1181200' => 'mdo', 'MD05G1244200' => 'mdo', 'MD05G1324200' => 'mdo', 'MD09G1201600' => 'mdo', 'MD10G1000600' => 'mdo', 'MD14G1026900' => 'mdo', 'MD14G1187900' => 'mdo', 'MD15G1017800' => 'mdo', 'MD15G1018100' => 'mdo', 'Medtr4g124160' => 'mtr', 'Migut.L01260' => 'egut', 'Nitab4.5_0000008g0440' => 'nta', 'Nitab4.5_0000207g0170' => 'nta', 'Nitab4.5_0007671g0030' => 'nta', 'Nitab4.5_0010853g0020' => 'nta', 'Oeu057656.1' => 'oeu', 'PGSC0003DMG400005638' => 'stu', 'PGSC0003DMG400005639' => 'stu', 'Phvul.009G222800' => 'pvu', 'Potri.009G132400' => 'ptr', 'Potri.009G163001' => 'ptr', 'Potri.011G000700' => 'ptr', 'Potri.011G004800' => 'ptr', 'Prupe.1G509300' => 'ppe', 'Prupe.1G509700' => 'ppe', 'Prupe.1G510400' => 'ppe', 'Prupe.1G510700' => 'ppe', 'Prupe.1G512600' => 'ppe', 'Prupe.2G073200' => 'ppe', 'Prupe.3G059500' => 'ppe', 'Prupe.3G059600' => 'ppe', 'Prupe.3G246100' => 'ppe', 'Prupe.3G265100' => 'ppe', 'Prupe.4G034700' => 'ppe', 'Prupe.4G052100' => 'ppe', 'Prupe.4G053600' => 'ppe', 'Prupe.5G068800' => 'ppe', 'Prupe.5G070600' => 'ppe', 'Prupe.6G075400' => 'ppe', 'Prupe.6G075500' => 'ppe', 'Prupe.6G076400' => 'ppe', 'Prupe.8G110700' => 'ppe', 'Psat4g020960' => 'psa', 'PSO135G0788' => 'pso', 'PSO210G6463' => 'pso', 'PSO384G0370' => 'pso', 'PSO386G0056' => 'pso', 'QL01p006048' => 'qlo', 'QL02p054283' => 'qlo', 'QL05p008000' => 'qlo', 'QL05p008212' => 'qlo', 'QL05p008950' => 'qlo', 'QL05p009042' => 'qlo', 'QL05p009518' => 'qlo', 'QL05p012589' => 'qlo', 'QL05p012608' => 'qlo', 'QL05p012650' => 'qlo', 'QL05p012667' => 'qlo', 'QL05p014501' => 'qlo', 'QL05p052800' => 'qlo', 'QL05p065010' => 'qlo', 'QL05p074156' => 'qlo', 'QL05p074160' => 'qlo', 'QL05p074174' => 'qlo', 'QL05p074178' => 'qlo', 'QL05p074214' => 'qlo', 'QL06p001050' => 'qlo', 'QL06p001056' => 'qlo', 'QL06p006093' => 'qlo', 'QL06p006111' => 'qlo', 'QL07p019784' => 'qlo', 'QL07p019801' => 'qlo', 'QL07p036110' => 'qlo', 'QL07p036134' => 'qlo', 'QL07p036147' => 'qlo', 'QL07p036156' => 'qlo', 'QL07p036300' => 'qlo', 'QL07p036320' => 'qlo', 'QL08p014547' => 'qlo', 'QL08p014551' => 'qlo', 'QL08p043319' => 'qlo', 'QL08p043324' => 'qlo', 'QL11p009094' => 'qlo', 'RcHm_v2.0_Chr1g0380481' => 'rch', 'RcHm_v2.0_Chr2g0089331' => 'rch', 'RcHm_v2.0_Chr2g0123691' => 'rch', 'RcHm_v2.0_Chr2g0151111' => 'rch', 'RcHm_v2.0_Chr2g0163011' => 'rch', 'RcHm_v2.0_Chr2g0163051' => 'rch', 'RcHm_v2.0_Chr2g0164671' => 'rch', 'RcHm_v2.0_Chr2g0164681' => 'rch', 'RcHm_v2.0_Chr2g0164721' => 'rch', 'RcHm_v2.0_Chr3g0449911' => 'rch', 'RcHm_v2.0_Chr3g0450211' => 'rch', 'RcHm_v2.0_Chr3g0457271' => 'rch', 'RcHm_v2.0_Chr5g0018111' => 'rch', 'RcHm_v2.0_Chr5g0021011' => 'rch', 'RcHm_v2.0_Chr5g0081171' => 'rch', 'RcHm_v2.0_Chr5g0081211' => 'rch', 'RcHm_v2.0_Chr6g0275871' => 'rch', 'RcHm_v2.0_Chr6g0276071' => 'rch', 'RcHm_v2.0_Chr6g0285591' => 'rch', 'RcHm_v2.0_Chr6g0291931' => 'rch', 'RcHm_v2.0_Chr6g0292091' => 'rch', 'RcHm_v2.0_Chr6g0292271' => 'rch', 'RcHm_v2.0_Chr7g0221261' => 'rch', 'Rhsim08G0219900' => 'rsi', 'Rhsim08G0220200' => 'rsi', 'Rhsim08G0237800' => 'rsi', 'Rhsim08G0238800' => 'rsi', 'Sabra09G0102700' => 'sbr', 'Sabra09G0127200' => 'sbr', 'Sabra11G0003700' => 'sbr', 'Sabra15G0014700' => 'sbr', 'Sc19g0000590' => 'sci', 'Sc19g0001870' => 'sci', 'SGA_v2.0_scaffold1G00346' => 'sas', 'SGA_v2.0_scaffold1G00575' => 'sas', 'SGA_v2.0_scaffold1G00761' => 'sas', 'SGA_v2.0_scaffold232G43501' => 'sas', 'TAR625G1137' => 'tar', 'Thecc.03G222100' => 'tca', 'TPR.G12691' => 'tpr', 'TWI34G0727' => 'twi', 'TWI36G0117' => 'twi', 'VMungo1309G0868' => 'vmu' ) $gf_id = 'HOM05D001729' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001729' ) $data_identifier = 'HOM05D001729' $data_type = 'gf_id' $species_gene_counts = array( 'amhyb' => (int) 1, 'cqu' => (int) 9, 'can' => (int) 1, 'cansat' => (int) 1, 'car' => (int) 1, 'col' => (int) 5, 'dca' => (int) 1, 'din' => (int) 2, 'dzi' => (int) 3, 'fan' => (int) 140, 'fve' => (int) 62, 'gma' => (int) 1, 'ghi' => (int) 2, 'gra' => (int) 1, 'han' => (int) 1, 'sun' => (int) 1, 'lonja' => (int) 6, 'lja' => (int) 1, 'lsa' => (int) 4, 'mes' => (int) 1, 'mdo' => (int) 14, 'mtr' => (int) 1, 'egut' => (int) 1, 'nta' => (int) 4, 'oeu' => (int) 1, 'stu' => (int) 2, 'pvu' => (int) 1, 'ptr' => (int) 4, 'ppe' => (int) 19, 'psa' => (int) 1, 'pso' => (int) 4, 'qlo' => (int) 36, 'rch' => (int) 23, 'rsi' => (int) 4, 'sbr' => (int) 4, 'sci' => (int) 2, 'sas' => (int) 4, 'tar' => (int) 1, 'tca' => (int) 1, 'tpr' => (int) 1, 'twi' => (int) 2, 'vmu' => (int) 1 ) $gf_gene_species = 'vmu' $gf_gene_id = 'VMungo1309G0868' $species_info = array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ) $local_species = 'qlo' $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' => 'HOM05D001729', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '375', 'num_species' => '42' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'Ah.07g204710' => 'amhyb', 'AUR62006001' => 'cqu', 'AUR62006002' => 'cqu', 'AUR62006003' => 'cqu', 'AUR62015641' => 'cqu', 'AUR62027174' => 'cqu', 'AUR62035623' => 'cqu', 'AUR62035624' => 'cqu', 'AUR62035625' => 'cqu', 'AUR62035626' => 'cqu', 'CAN.G1110.53' => 'can', 'CANSAT80G0415' => 'cansat', 'Ca_21364_v3' => 'car', 'COL.COLO4_30693' => 'col', 'COL.COLO4_30694' => 'col', 'COL.COLO4_30695' => 'col', 'COL.COLO4_30696' => 'col', 'COL.COLO4_34020' => 'col', 'DCAR_004585' => 'dca', 'Dinv04029' => 'din', 'Dinv34857' => 'din', 'Duzib147G0011' => 'dzi', 'Duzib170G0599' => 'dzi', 'Duzib192G1051' => 'dzi', 'FAN01G0708' => 'fan', 'FAN01G0742' => 'fan', 'FAN02G0048' => 'fan', 'FAN02G0583' => 'fan', 'FAN02G0688' => 'fan', 'FAN02G1588' => 'fan', 'FAN02G2194' => 'fan', 'FAN02G2750' => 'fan', 'FAN02G3094' => 'fan', 'FAN02G3887' => 'fan', 'FAN02G3911' => 'fan', 'FAN02G3994' => 'fan', 'FAN02G4432' => 'fan', 'FAN02G4556' => 'fan', 'FAN03G1977' => 'fan', 'FAN03G2781' => 'fan', 'FAN03G2850' => 'fan', 'FAN03G3155' => 'fan', 'FAN04G2487' => 'fan', 'FAN05G0208' => 'fan', 'FAN05G0656' => 'fan', 'FAN05G0696' => 'fan', 'FAN05G0810' => 'fan', 'FAN05G1447' => 'fan', 'FAN05G2640' => 'fan', 'FAN05G2911' => 'fan', 'FAN05G3901' => 'fan', 'FAN05G4859' => 'fan', 'FAN05G4861' => 'fan', 'FAN05G4988' => 'fan', 'FAN05G5187' => 'fan', 'FAN05G5452' => 'fan', 'FAN05G5500' => 'fan', 'FAN05G5688' => 'fan', 'FAN06G0177' => 'fan', 'FAN06G0675' => 'fan', 'FAN06G1290' => 'fan', 'FAN06G2191' => 'fan', 'FAN06G2405' => 'fan', 'FAN06G3231' => 'fan', 'FAN06G3932' => 'fan', 'FAN07G0163' => 'fan', 'FAN07G0471' => 'fan', 'FAN07G1354' => 'fan', 'FAN08G0338' => 'fan', 'FAN08G1373' => 'fan', 'FAN08G2539' => 'fan', 'FAN08G2728' => 'fan', 'FAN09G0608' => 'fan', 'FAN09G1136' => 'fan', 'FAN09G1958' => 'fan', 'FAN09G2508' => 'fan', 'FAN09G2597' => 'fan', 'FAN09G2658' => 'fan', 'FAN09G2757' => 'fan', 'FAN09G2983' => 'fan', 'FAN09G3130' => 'fan', 'FAN09G3565' => 'fan', 'FAN09G3613' => 'fan', 'FAN09G4011' => 'fan', 'FAN09G4239' => 'fan', 'FAN09G4277' => 'fan', 'FAN09G4720' => 'fan', 'FAN11G0139' => 'fan', 'FAN11G1727' => 'fan', 'FAN11G2672' => 'fan', 'FAN11G2795' => 'fan', 'FAN11G3238' => 'fan', 'FAN11G3734' => 'fan', 'FAN12G0631' => 'fan', 'FAN12G2239' => 'fan', 'FAN12G2308' => 'fan', 'FAN12G2569' => 'fan', 'FAN12G2623' => 'fan', 'FAN13G3182' => 'fan', 'FAN14G0053' => 'fan', 'FAN14G0370' => 'fan', 'FAN14G0382' => 'fan', 'FAN14G0421' => 'fan', 'FAN14G0866' => 'fan', 'FAN14G1187' => 'fan', 'FAN14G1727' => 'fan', 'FAN14G1791' => 'fan', 'FAN14G2361' => 'fan', 'FAN14G2668' => 'fan', 'FAN14G2770' => 'fan', 'FAN14G2874' => 'fan', 'FAN14G3193' => 'fan', 'FAN14G3624' => 'fan', 'FAN14G3676' => 'fan', 'FAN14G3807' => 'fan', 'FAN14G4082' => 'fan', 'FAN14G4342' => 'fan', 'FAN14G4985' => 'fan', 'FAN14G5126' => 'fan', 'FAN14G5781' => 'fan', 'FAN14G5808' => 'fan', 'FAN14G5949' => 'fan', 'FAN15G0828' => 'fan', 'FAN15G1054' => 'fan', 'FAN15G2023' => 'fan', 'FAN15G2506' => 'fan', 'FAN16G0128' => 'fan', 'FAN16G0249' => 'fan', 'FAN16G0429' => 'fan', 'FAN16G1493' => 'fan', 'FAN16G2210' => 'fan', 'FAN16G2506' => 'fan', 'FAN18G1542' => 'fan', 'FAN18G4057' => 'fan', 'FAN19G0745' => 'fan', 'FAN19G1216' => 'fan', 'FAN19G1733' => 'fan', 'FAN20G0258' => 'fan', 'FAN20G1095' => 'fan', 'FAN20G1557' => 'fan', 'FAN21G0302' => 'fan', 'FAN21G0519' => 'fan', 'FAN21G0970' => 'fan', 'FAN21G1159' => 'fan', 'FAN21G1312' => 'fan', 'FAN21G1440' => 'fan', 'FAN21G1715' => 'fan', 'FAN23G1584' => 'fan', 'FAN24G0045' => 'fan', 'FAN24G0053' => 'fan', 'FAN24G1500' => 'fan', 'FAN24G1817' => 'fan', 'FAN24G2147' => 'fan', 'FAN24G2236' => 'fan', 'FAN24G2446' => 'fan', 'FAN24G2684' => 'fan', 'FAN25G0187' => 'fan', 'FAN25G0505' => 'fan', 'FAN25G0589' => 'fan', 'FAN25G3663' => 'fan', 'FAN26G1025' => 'fan', 'FAN26G2860' => 'fan', 'FAN27G1329' => 'fan', 'FAN27G3392' => 'fan', 'FvH4_1g02011' => 'fve', 'FvH4_1g06511' => 'fve', 'FvH4_2g19900' => 'fve', 'FvH4_2g19920' => 'fve', 'FvH4_2g24261' => 'fve', 'FvH4_2g24270' => 'fve', 'FvH4_2g24631' => 'fve', 'FvH4_2g30622' => 'fve', 'FvH4_3g12920' => 'fve', 'FvH4_3g30171' => 'fve', 'FvH4_3g35490' => 'fve', 'FvH4_3g43682' => 'fve', 'FvH4_3g43730' => 'fve', 'FvH4_3g43732' => 'fve', 'FvH4_3g43751' => 'fve', 'FvH4_3g43752' => 'fve', 'FvH4_3g43770' => 'fve', 'FvH4_3g44471' => 'fve', 'FvH4_3g44510' => 'fve', 'FvH4_3g44582' => 'fve', 'FvH4_4g16921' => 'fve', 'FvH4_4g17121' => 'fve', 'FvH4_4g17782' => 'fve', 'FvH4_4g17783' => 'fve', 'FvH4_4g18120' => 'fve', 'FvH4_4g31310' => 'fve', 'FvH4_4g35052' => 'fve', 'FvH4_5g30862' => 'fve', 'FvH4_6g01541' => 'fve', 'FvH4_6g02021' => 'fve', 'FvH4_6g02041' => 'fve', 'FvH4_6g02071' => 'fve', 'FvH4_6g02171' => 'fve', 'FvH4_6g03181' => 'fve', 'FvH4_6g03182' => 'fve', 'FvH4_6g03221' => 'fve', 'FvH4_6g03380' => 'fve', 'FvH4_6g05201' => 'fve', 'FvH4_6g05203' => 'fve', 'FvH4_6g20231' => 'fve', 'FvH4_6g31981' => 'fve', 'FvH4_6g32061' => 'fve', 'FvH4_6g37041' => 'fve', 'FvH4_6g37932' => 'fve', 'FvH4_6g38731' => 'fve', 'FvH4_6g39370' => 'fve', 'FvH4_6g39371' => 'fve', 'FvH4_6g40891' => 'fve', 'FvH4_6g40892' => 'fve', 'FvH4_6g43143' => 'fve', 'FvH4_6g45251' => 'fve', 'FvH4_6g45260' => 'fve', 'FvH4_6g45291' => 'fve', 'FvH4_6g45890' => 'fve', 'FvH4_6g46240' => 'fve', 'FvH4_6g46241' => 'fve', 'FvH4_6g46242' => 'fve', 'FvH4_6g46260' => 'fve', 'FvH4_6g46280' => 'fve', 'FvH4_6g46380' => 'fve', 'FvH4_7g12841' => 'fve', 'FvH4_7g31431' => 'fve', 'Glyma.09G075900' => 'gma', 'Gohir.A09G096401' => 'ghi', 'Gohir.D09G096101' => 'ghi', 'Gorai.006G112800' => 'gra', 'HanXRQChr04g0121411' => 'han', 'Hund15878' => 'sun', 'Lj2A1107G68' => 'lonja', 'Lj2A630G63' => 'lonja', 'Lj2A946T25' => 'lonja', 'Lj2C714T1' => 'lonja', 'Lj2C966T3' => 'lonja', 'Lj2C966T4' => 'lonja', 'Lj4g0002979' => 'lja', 'Lsat_1_v5_gn_5_30901' => 'lsa', 'Lsat_1_v5_gn_5_31100' => 'lsa', 'Lsat_1_v5_gn_5_38600' => 'lsa', 'Lsat_1_v5_gn_6_92061' => 'lsa', 'Manes.05G071301' => 'mes', 'MD02G1008700' => 'mdo', 'MD02G1008900' => 'mdo', 'MD03G1256400' => 'mdo', 'MD04G1180900' => 'mdo', 'MD04G1181000' => 'mdo', 'MD04G1181200' => 'mdo', 'MD05G1244200' => 'mdo', 'MD05G1324200' => 'mdo', 'MD09G1201600' => 'mdo', 'MD10G1000600' => 'mdo', 'MD14G1026900' => 'mdo', 'MD14G1187900' => 'mdo', 'MD15G1017800' => 'mdo', 'MD15G1018100' => 'mdo', 'Medtr4g124160' => 'mtr', 'Migut.L01260' => 'egut', 'Nitab4.5_0000008g0440' => 'nta', 'Nitab4.5_0000207g0170' => 'nta', 'Nitab4.5_0007671g0030' => 'nta', 'Nitab4.5_0010853g0020' => 'nta', 'Oeu057656.1' => 'oeu', 'PGSC0003DMG400005638' => 'stu', 'PGSC0003DMG400005639' => 'stu', 'Phvul.009G222800' => 'pvu', 'Potri.009G132400' => 'ptr', 'Potri.009G163001' => 'ptr', 'Potri.011G000700' => 'ptr', 'Potri.011G004800' => 'ptr', 'Prupe.1G509300' => 'ppe', 'Prupe.1G509700' => 'ppe', 'Prupe.1G510400' => 'ppe', 'Prupe.1G510700' => 'ppe', 'Prupe.1G512600' => 'ppe', 'Prupe.2G073200' => 'ppe', 'Prupe.3G059500' => 'ppe', 'Prupe.3G059600' => 'ppe', 'Prupe.3G246100' => 'ppe', 'Prupe.3G265100' => 'ppe', 'Prupe.4G034700' => 'ppe', 'Prupe.4G052100' => 'ppe', 'Prupe.4G053600' => 'ppe', 'Prupe.5G068800' => 'ppe', 'Prupe.5G070600' => 'ppe', 'Prupe.6G075400' => 'ppe', 'Prupe.6G075500' => 'ppe', 'Prupe.6G076400' => 'ppe', 'Prupe.8G110700' => 'ppe', 'Psat4g020960' => 'psa', 'PSO135G0788' => 'pso', 'PSO210G6463' => 'pso', 'PSO384G0370' => 'pso', 'PSO386G0056' => 'pso', 'QL01p006048' => 'qlo', 'QL02p054283' => 'qlo', 'QL05p008000' => 'qlo', 'QL05p008212' => 'qlo', 'QL05p008950' => 'qlo', 'QL05p009042' => 'qlo', 'QL05p009518' => 'qlo', 'QL05p012589' => 'qlo', 'QL05p012608' => 'qlo', 'QL05p012650' => 'qlo', 'QL05p012667' => 'qlo', 'QL05p014501' => 'qlo', 'QL05p052800' => 'qlo', 'QL05p065010' => 'qlo', 'QL05p074156' => 'qlo', 'QL05p074160' => 'qlo', 'QL05p074174' => 'qlo', 'QL05p074178' => 'qlo', 'QL05p074214' => 'qlo', 'QL06p001050' => 'qlo', 'QL06p001056' => 'qlo', 'QL06p006093' => 'qlo', 'QL06p006111' => 'qlo', 'QL07p019784' => 'qlo', 'QL07p019801' => 'qlo', 'QL07p036110' => 'qlo', 'QL07p036134' => 'qlo', 'QL07p036147' => 'qlo', 'QL07p036156' => 'qlo', 'QL07p036300' => 'qlo', 'QL07p036320' => 'qlo', 'QL08p014547' => 'qlo', 'QL08p014551' => 'qlo', 'QL08p043319' => 'qlo', 'QL08p043324' => 'qlo', 'QL11p009094' => 'qlo', 'RcHm_v2.0_Chr1g0380481' => 'rch', 'RcHm_v2.0_Chr2g0089331' => 'rch', 'RcHm_v2.0_Chr2g0123691' => 'rch', 'RcHm_v2.0_Chr2g0151111' => 'rch', 'RcHm_v2.0_Chr2g0163011' => 'rch', 'RcHm_v2.0_Chr2g0163051' => 'rch', 'RcHm_v2.0_Chr2g0164671' => 'rch', 'RcHm_v2.0_Chr2g0164681' => 'rch', 'RcHm_v2.0_Chr2g0164721' => 'rch', 'RcHm_v2.0_Chr3g0449911' => 'rch', 'RcHm_v2.0_Chr3g0450211' => 'rch', 'RcHm_v2.0_Chr3g0457271' => 'rch', 'RcHm_v2.0_Chr5g0018111' => 'rch', 'RcHm_v2.0_Chr5g0021011' => 'rch', 'RcHm_v2.0_Chr5g0081171' => 'rch', 'RcHm_v2.0_Chr5g0081211' => 'rch', 'RcHm_v2.0_Chr6g0275871' => 'rch', 'RcHm_v2.0_Chr6g0276071' => 'rch', 'RcHm_v2.0_Chr6g0285591' => 'rch', 'RcHm_v2.0_Chr6g0291931' => 'rch', 'RcHm_v2.0_Chr6g0292091' => 'rch', 'RcHm_v2.0_Chr6g0292271' => 'rch', 'RcHm_v2.0_Chr7g0221261' => 'rch', 'Rhsim08G0219900' => 'rsi', 'Rhsim08G0220200' => 'rsi', 'Rhsim08G0237800' => 'rsi', 'Rhsim08G0238800' => 'rsi', 'Sabra09G0102700' => 'sbr', 'Sabra09G0127200' => 'sbr', 'Sabra11G0003700' => 'sbr', 'Sabra15G0014700' => 'sbr', 'Sc19g0000590' => 'sci', 'Sc19g0001870' => 'sci', 'SGA_v2.0_scaffold1G00346' => 'sas', 'SGA_v2.0_scaffold1G00575' => 'sas', 'SGA_v2.0_scaffold1G00761' => 'sas', 'SGA_v2.0_scaffold232G43501' => 'sas', 'TAR625G1137' => 'tar', 'Thecc.03G222100' => 'tca', 'TPR.G12691' => 'tpr', 'TWI34G0727' => 'twi', 'TWI36G0117' => 'twi', 'VMungo1309G0868' => 'vmu' ), 'gf_id' => 'HOM05D001729', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001729' ), 'data_identifier' => 'HOM05D001729', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001729', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '375', 'num_species' => '42' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'Ah.07g204710' => 'amhyb', 'AUR62006001' => 'cqu', 'AUR62006002' => 'cqu', 'AUR62006003' => 'cqu', 'AUR62015641' => 'cqu', 'AUR62027174' => 'cqu', 'AUR62035623' => 'cqu', 'AUR62035624' => 'cqu', 'AUR62035625' => 'cqu', 'AUR62035626' => 'cqu', 'CAN.G1110.53' => 'can', 'CANSAT80G0415' => 'cansat', 'Ca_21364_v3' => 'car', 'COL.COLO4_30693' => 'col', 'COL.COLO4_30694' => 'col', 'COL.COLO4_30695' => 'col', 'COL.COLO4_30696' => 'col', 'COL.COLO4_34020' => 'col', 'DCAR_004585' => 'dca', 'Dinv04029' => 'din', 'Dinv34857' => 'din', 'Duzib147G0011' => 'dzi', 'Duzib170G0599' => 'dzi', 'Duzib192G1051' => 'dzi', 'FAN01G0708' => 'fan', 'FAN01G0742' => 'fan', 'FAN02G0048' => 'fan', 'FAN02G0583' => 'fan', 'FAN02G0688' => 'fan', 'FAN02G1588' => 'fan', 'FAN02G2194' => 'fan', 'FAN02G2750' => 'fan', 'FAN02G3094' => 'fan', 'FAN02G3887' => 'fan', 'FAN02G3911' => 'fan', 'FAN02G3994' => 'fan', 'FAN02G4432' => 'fan', 'FAN02G4556' => 'fan', 'FAN03G1977' => 'fan', 'FAN03G2781' => 'fan', 'FAN03G2850' => 'fan', 'FAN03G3155' => 'fan', 'FAN04G2487' => 'fan', 'FAN05G0208' => 'fan', 'FAN05G0656' => 'fan', 'FAN05G0696' => 'fan', 'FAN05G0810' => 'fan', 'FAN05G1447' => 'fan', 'FAN05G2640' => 'fan', 'FAN05G2911' => 'fan', 'FAN05G3901' => 'fan', 'FAN05G4859' => 'fan', 'FAN05G4861' => 'fan', 'FAN05G4988' => 'fan', 'FAN05G5187' => 'fan', 'FAN05G5452' => 'fan', 'FAN05G5500' => 'fan', 'FAN05G5688' => 'fan', 'FAN06G0177' => 'fan', 'FAN06G0675' => 'fan', 'FAN06G1290' => 'fan', 'FAN06G2191' => 'fan', 'FAN06G2405' => 'fan', 'FAN06G3231' => 'fan', 'FAN06G3932' => 'fan', 'FAN07G0163' => 'fan', 'FAN07G0471' => 'fan', 'FAN07G1354' => 'fan', 'FAN08G0338' => 'fan', 'FAN08G1373' => 'fan', 'FAN08G2539' => 'fan', 'FAN08G2728' => 'fan', 'FAN09G0608' => 'fan', 'FAN09G1136' => 'fan', 'FAN09G1958' => 'fan', 'FAN09G2508' => 'fan', 'FAN09G2597' => 'fan', 'FAN09G2658' => 'fan', 'FAN09G2757' => 'fan', 'FAN09G2983' => 'fan', 'FAN09G3130' => 'fan', 'FAN09G3565' => 'fan', 'FAN09G3613' => 'fan', 'FAN09G4011' => 'fan', 'FAN09G4239' => 'fan', 'FAN09G4277' => 'fan', 'FAN09G4720' => 'fan', 'FAN11G0139' => 'fan', 'FAN11G1727' => 'fan', 'FAN11G2672' => 'fan', 'FAN11G2795' => 'fan', 'FAN11G3238' => 'fan', 'FAN11G3734' => 'fan', 'FAN12G0631' => 'fan', 'FAN12G2239' => 'fan', 'FAN12G2308' => 'fan', 'FAN12G2569' => 'fan', 'FAN12G2623' => 'fan', 'FAN13G3182' => 'fan', 'FAN14G0053' => 'fan', 'FAN14G0370' => 'fan', 'FAN14G0382' => 'fan', 'FAN14G0421' => 'fan', 'FAN14G0866' => 'fan', 'FAN14G1187' => 'fan', 'FAN14G1727' => 'fan', 'FAN14G1791' => 'fan', 'FAN14G2361' => 'fan', 'FAN14G2668' => 'fan', 'FAN14G2770' => 'fan', 'FAN14G2874' => 'fan', 'FAN14G3193' => 'fan', 'FAN14G3624' => 'fan', 'FAN14G3676' => 'fan', 'FAN14G3807' => 'fan', 'FAN14G4082' => 'fan', 'FAN14G4342' => 'fan', 'FAN14G4985' => 'fan', 'FAN14G5126' => 'fan', 'FAN14G5781' => 'fan', 'FAN14G5808' => 'fan', 'FAN14G5949' => 'fan', 'FAN15G0828' => 'fan', 'FAN15G1054' => 'fan', 'FAN15G2023' => 'fan', 'FAN15G2506' => 'fan', 'FAN16G0128' => 'fan', 'FAN16G0249' => 'fan', 'FAN16G0429' => 'fan', 'FAN16G1493' => 'fan', 'FAN16G2210' => 'fan', 'FAN16G2506' => 'fan', 'FAN18G1542' => 'fan', 'FAN18G4057' => 'fan', 'FAN19G0745' => 'fan', 'FAN19G1216' => 'fan', 'FAN19G1733' => 'fan', 'FAN20G0258' => 'fan', 'FAN20G1095' => 'fan', 'FAN20G1557' => 'fan', 'FAN21G0302' => 'fan', 'FAN21G0519' => 'fan', 'FAN21G0970' => 'fan', 'FAN21G1159' => 'fan', 'FAN21G1312' => 'fan', 'FAN21G1440' => 'fan', 'FAN21G1715' => 'fan', 'FAN23G1584' => 'fan', 'FAN24G0045' => 'fan', 'FAN24G0053' => 'fan', 'FAN24G1500' => 'fan', 'FAN24G1817' => 'fan', 'FAN24G2147' => 'fan', 'FAN24G2236' => 'fan', 'FAN24G2446' => 'fan', 'FAN24G2684' => 'fan', 'FAN25G0187' => 'fan', 'FAN25G0505' => 'fan', 'FAN25G0589' => 'fan', 'FAN25G3663' => 'fan', 'FAN26G1025' => 'fan', 'FAN26G2860' => 'fan', 'FAN27G1329' => 'fan', 'FAN27G3392' => 'fan', 'FvH4_1g02011' => 'fve', 'FvH4_1g06511' => 'fve', 'FvH4_2g19900' => 'fve', 'FvH4_2g19920' => 'fve', 'FvH4_2g24261' => 'fve', 'FvH4_2g24270' => 'fve', 'FvH4_2g24631' => 'fve', 'FvH4_2g30622' => 'fve', 'FvH4_3g12920' => 'fve', 'FvH4_3g30171' => 'fve', 'FvH4_3g35490' => 'fve', 'FvH4_3g43682' => 'fve', 'FvH4_3g43730' => 'fve', 'FvH4_3g43732' => 'fve', 'FvH4_3g43751' => 'fve', 'FvH4_3g43752' => 'fve', 'FvH4_3g43770' => 'fve', 'FvH4_3g44471' => 'fve', 'FvH4_3g44510' => 'fve', 'FvH4_3g44582' => 'fve', 'FvH4_4g16921' => 'fve', 'FvH4_4g17121' => 'fve', 'FvH4_4g17782' => 'fve', 'FvH4_4g17783' => 'fve', 'FvH4_4g18120' => 'fve', 'FvH4_4g31310' => 'fve', 'FvH4_4g35052' => 'fve', 'FvH4_5g30862' => 'fve', 'FvH4_6g01541' => 'fve', 'FvH4_6g02021' => 'fve', 'FvH4_6g02041' => 'fve', 'FvH4_6g02071' => 'fve', 'FvH4_6g02171' => 'fve', 'FvH4_6g03181' => 'fve', 'FvH4_6g03182' => 'fve', 'FvH4_6g03221' => 'fve', 'FvH4_6g03380' => 'fve', 'FvH4_6g05201' => 'fve', 'FvH4_6g05203' => 'fve', 'FvH4_6g20231' => 'fve', 'FvH4_6g31981' => 'fve', 'FvH4_6g32061' => 'fve', 'FvH4_6g37041' => 'fve', 'FvH4_6g37932' => 'fve', 'FvH4_6g38731' => 'fve', 'FvH4_6g39370' => 'fve', 'FvH4_6g39371' => 'fve', 'FvH4_6g40891' => 'fve', 'FvH4_6g40892' => 'fve', 'FvH4_6g43143' => 'fve', 'FvH4_6g45251' => 'fve', 'FvH4_6g45260' => 'fve', 'FvH4_6g45291' => 'fve', 'FvH4_6g45890' => 'fve', 'FvH4_6g46240' => 'fve', 'FvH4_6g46241' => 'fve', 'FvH4_6g46242' => 'fve', 'FvH4_6g46260' => 'fve', 'FvH4_6g46280' => 'fve', 'FvH4_6g46380' => 'fve', 'FvH4_7g12841' => 'fve', 'FvH4_7g31431' => 'fve', 'Glyma.09G075900' => 'gma', 'Gohir.A09G096401' => 'ghi', 'Gohir.D09G096101' => 'ghi', 'Gorai.006G112800' => 'gra', 'HanXRQChr04g0121411' => 'han', 'Hund15878' => 'sun', 'Lj2A1107G68' => 'lonja', 'Lj2A630G63' => 'lonja', 'Lj2A946T25' => 'lonja', 'Lj2C714T1' => 'lonja', 'Lj2C966T3' => 'lonja', 'Lj2C966T4' => 'lonja', 'Lj4g0002979' => 'lja', 'Lsat_1_v5_gn_5_30901' => 'lsa', 'Lsat_1_v5_gn_5_31100' => 'lsa', 'Lsat_1_v5_gn_5_38600' => 'lsa', 'Lsat_1_v5_gn_6_92061' => 'lsa', 'Manes.05G071301' => 'mes', 'MD02G1008700' => 'mdo', 'MD02G1008900' => 'mdo', 'MD03G1256400' => 'mdo', 'MD04G1180900' => 'mdo', 'MD04G1181000' => 'mdo', 'MD04G1181200' => 'mdo', 'MD05G1244200' => 'mdo', 'MD05G1324200' => 'mdo', 'MD09G1201600' => 'mdo', 'MD10G1000600' => 'mdo', 'MD14G1026900' => 'mdo', 'MD14G1187900' => 'mdo', 'MD15G1017800' => 'mdo', 'MD15G1018100' => 'mdo', 'Medtr4g124160' => 'mtr', 'Migut.L01260' => 'egut', 'Nitab4.5_0000008g0440' => 'nta', 'Nitab4.5_0000207g0170' => 'nta', 'Nitab4.5_0007671g0030' => 'nta', 'Nitab4.5_0010853g0020' => 'nta', 'Oeu057656.1' => 'oeu', 'PGSC0003DMG400005638' => 'stu', 'PGSC0003DMG400005639' => 'stu', 'Phvul.009G222800' => 'pvu', 'Potri.009G132400' => 'ptr', 'Potri.009G163001' => 'ptr', 'Potri.011G000700' => 'ptr', 'Potri.011G004800' => 'ptr', 'Prupe.1G509300' => 'ppe', 'Prupe.1G509700' => 'ppe', 'Prupe.1G510400' => 'ppe', 'Prupe.1G510700' => 'ppe', 'Prupe.1G512600' => 'ppe', 'Prupe.2G073200' => 'ppe', 'Prupe.3G059500' => 'ppe', 'Prupe.3G059600' => 'ppe', 'Prupe.3G246100' => 'ppe', 'Prupe.3G265100' => 'ppe', 'Prupe.4G034700' => 'ppe', 'Prupe.4G052100' => 'ppe', 'Prupe.4G053600' => 'ppe', 'Prupe.5G068800' => 'ppe', 'Prupe.5G070600' => 'ppe', 'Prupe.6G075400' => 'ppe', 'Prupe.6G075500' => 'ppe', 'Prupe.6G076400' => 'ppe', 'Prupe.8G110700' => 'ppe', 'Psat4g020960' => 'psa', 'PSO135G0788' => 'pso', 'PSO210G6463' => 'pso', 'PSO384G0370' => 'pso', 'PSO386G0056' => 'pso', 'QL01p006048' => 'qlo', 'QL02p054283' => 'qlo', 'QL05p008000' => 'qlo', 'QL05p008212' => 'qlo', 'QL05p008950' => 'qlo', 'QL05p009042' => 'qlo', 'QL05p009518' => 'qlo', 'QL05p012589' => 'qlo', 'QL05p012608' => 'qlo', 'QL05p012650' => 'qlo', 'QL05p012667' => 'qlo', 'QL05p014501' => 'qlo', 'QL05p052800' => 'qlo', 'QL05p065010' => 'qlo', 'QL05p074156' => 'qlo', 'QL05p074160' => 'qlo', 'QL05p074174' => 'qlo', 'QL05p074178' => 'qlo', 'QL05p074214' => 'qlo', 'QL06p001050' => 'qlo', 'QL06p001056' => 'qlo', 'QL06p006093' => 'qlo', 'QL06p006111' => 'qlo', 'QL07p019784' => 'qlo', 'QL07p019801' => 'qlo', 'QL07p036110' => 'qlo', 'QL07p036134' => 'qlo', 'QL07p036147' => 'qlo', 'QL07p036156' => 'qlo', 'QL07p036300' => 'qlo', 'QL07p036320' => 'qlo', 'QL08p014547' => 'qlo', 'QL08p014551' => 'qlo', 'QL08p043319' => 'qlo', 'QL08p043324' => 'qlo', 'QL11p009094' => 'qlo', 'RcHm_v2.0_Chr1g0380481' => 'rch', 'RcHm_v2.0_Chr2g0089331' => 'rch', 'RcHm_v2.0_Chr2g0123691' => 'rch', 'RcHm_v2.0_Chr2g0151111' => 'rch', 'RcHm_v2.0_Chr2g0163011' => 'rch', 'RcHm_v2.0_Chr2g0163051' => 'rch', 'RcHm_v2.0_Chr2g0164671' => 'rch', 'RcHm_v2.0_Chr2g0164681' => 'rch', 'RcHm_v2.0_Chr2g0164721' => 'rch', 'RcHm_v2.0_Chr3g0449911' => 'rch', 'RcHm_v2.0_Chr3g0450211' => 'rch', 'RcHm_v2.0_Chr3g0457271' => 'rch', 'RcHm_v2.0_Chr5g0018111' => 'rch', 'RcHm_v2.0_Chr5g0021011' => 'rch', 'RcHm_v2.0_Chr5g0081171' => 'rch', 'RcHm_v2.0_Chr5g0081211' => 'rch', 'RcHm_v2.0_Chr6g0275871' => 'rch', 'RcHm_v2.0_Chr6g0276071' => 'rch', 'RcHm_v2.0_Chr6g0285591' => 'rch', 'RcHm_v2.0_Chr6g0291931' => 'rch', 'RcHm_v2.0_Chr6g0292091' => 'rch', 'RcHm_v2.0_Chr6g0292271' => 'rch', 'RcHm_v2.0_Chr7g0221261' => 'rch', 'Rhsim08G0219900' => 'rsi', 'Rhsim08G0220200' => 'rsi', 'Rhsim08G0237800' => 'rsi', 'Rhsim08G0238800' => 'rsi', 'Sabra09G0102700' => 'sbr', 'Sabra09G0127200' => 'sbr', 'Sabra11G0003700' => 'sbr', 'Sabra15G0014700' => 'sbr', 'Sc19g0000590' => 'sci', 'Sc19g0001870' => 'sci', 'SGA_v2.0_scaffold1G00346' => 'sas', 'SGA_v2.0_scaffold1G00575' => 'sas', 'SGA_v2.0_scaffold1G00761' => 'sas', 'SGA_v2.0_scaffold232G43501' => 'sas', 'TAR625G1137' => 'tar', 'Thecc.03G222100' => 'tca', 'TPR.G12691' => 'tpr', 'TWI34G0727' => 'twi', 'TWI36G0117' => 'twi', 'VMungo1309G0868' => 'vmu' ) $gf_id = 'HOM05D001729' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001729' ) $data_identifier = 'HOM05D001729' $data_type = 'gf_id' $species_gene_counts = array( 'amhyb' => (int) 1, 'cqu' => (int) 9, 'can' => (int) 1, 'cansat' => (int) 1, 'car' => (int) 1, 'col' => (int) 5, 'dca' => (int) 1, 'din' => (int) 2, 'dzi' => (int) 3, 'fan' => (int) 140, 'fve' => (int) 62, 'gma' => (int) 1, 'ghi' => (int) 2, 'gra' => (int) 1, 'han' => (int) 1, 'sun' => (int) 1, 'lonja' => (int) 6, 'lja' => (int) 1, 'lsa' => (int) 4, 'mes' => (int) 1, 'mdo' => (int) 14, 'mtr' => (int) 1, 'egut' => (int) 1, 'nta' => (int) 4, 'oeu' => (int) 1, 'stu' => (int) 2, 'pvu' => (int) 1, 'ptr' => (int) 4, 'ppe' => (int) 19, 'psa' => (int) 1, 'pso' => (int) 4, 'qlo' => (int) 36, 'rch' => (int) 23, 'rsi' => (int) 4, 'sbr' => (int) 4, 'sci' => (int) 2, 'sas' => (int) 4, 'tar' => (int) 1, 'tca' => (int) 1, 'tpr' => (int) 1, 'twi' => (int) 2, 'vmu' => (int) 1 ) $gf_gene_species = 'vmu' $gf_gene_id = 'VMungo1309G0868' $species_info = array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ) $local_species = 'rsi' $disabled = '' $selected = '' $num_hits = (int) 1include - APP/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp, line 33 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933 View::_renderElement() - CORE/Cake/View/View.php, line 1224 View::element() - CORE/Cake/View/View.php, line 418 include - APP/View/Elements/analysis/phylogenetics_module/gf_data_settings.ctp, line 37 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933 View::_renderElement() - CORE/Cake/View/View.php, line 1224 View::element() - CORE/Cake/View/View.php, line 418 include - APP/View/Elements/analysis/phylogenetics_module/parameter_selection.ctp, line 64 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933 View::_renderElement() - CORE/Cake/View/View.php, line 1224 View::element() - CORE/Cake/View/View.php, line 418 include - APP/View/Analysis/custom_tree_creation.ctp, line 27 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933
$viewFile = '/www/bioinformatics01_ro/plaza/_dev_instances/feedback/app/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp' $dataForView = array( 'sidebar_info' => array( 'gf_id' => 'HOM05D001729', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '375', 'num_species' => '42' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'Ah.07g204710' => 'amhyb', 'AUR62006001' => 'cqu', 'AUR62006002' => 'cqu', 'AUR62006003' => 'cqu', 'AUR62015641' => 'cqu', 'AUR62027174' => 'cqu', 'AUR62035623' => 'cqu', 'AUR62035624' => 'cqu', 'AUR62035625' => 'cqu', 'AUR62035626' => 'cqu', 'CAN.G1110.53' => 'can', 'CANSAT80G0415' => 'cansat', 'Ca_21364_v3' => 'car', 'COL.COLO4_30693' => 'col', 'COL.COLO4_30694' => 'col', 'COL.COLO4_30695' => 'col', 'COL.COLO4_30696' => 'col', 'COL.COLO4_34020' => 'col', 'DCAR_004585' => 'dca', 'Dinv04029' => 'din', 'Dinv34857' => 'din', 'Duzib147G0011' => 'dzi', 'Duzib170G0599' => 'dzi', 'Duzib192G1051' => 'dzi', 'FAN01G0708' => 'fan', 'FAN01G0742' => 'fan', 'FAN02G0048' => 'fan', 'FAN02G0583' => 'fan', 'FAN02G0688' => 'fan', 'FAN02G1588' => 'fan', 'FAN02G2194' => 'fan', 'FAN02G2750' => 'fan', 'FAN02G3094' => 'fan', 'FAN02G3887' => 'fan', 'FAN02G3911' => 'fan', 'FAN02G3994' => 'fan', 'FAN02G4432' => 'fan', 'FAN02G4556' => 'fan', 'FAN03G1977' => 'fan', 'FAN03G2781' => 'fan', 'FAN03G2850' => 'fan', 'FAN03G3155' => 'fan', 'FAN04G2487' => 'fan', 'FAN05G0208' => 'fan', 'FAN05G0656' => 'fan', 'FAN05G0696' => 'fan', 'FAN05G0810' => 'fan', 'FAN05G1447' => 'fan', 'FAN05G2640' => 'fan', 'FAN05G2911' => 'fan', 'FAN05G3901' => 'fan', 'FAN05G4859' => 'fan', 'FAN05G4861' => 'fan', 'FAN05G4988' => 'fan', 'FAN05G5187' => 'fan', 'FAN05G5452' => 'fan', 'FAN05G5500' => 'fan', 'FAN05G5688' => 'fan', 'FAN06G0177' => 'fan', 'FAN06G0675' => 'fan', 'FAN06G1290' => 'fan', 'FAN06G2191' => 'fan', 'FAN06G2405' => 'fan', 'FAN06G3231' => 'fan', 'FAN06G3932' => 'fan', 'FAN07G0163' => 'fan', 'FAN07G0471' => 'fan', 'FAN07G1354' => 'fan', 'FAN08G0338' => 'fan', 'FAN08G1373' => 'fan', 'FAN08G2539' => 'fan', 'FAN08G2728' => 'fan', 'FAN09G0608' => 'fan', 'FAN09G1136' => 'fan', 'FAN09G1958' => 'fan', 'FAN09G2508' => 'fan', 'FAN09G2597' => 'fan', 'FAN09G2658' => 'fan', 'FAN09G2757' => 'fan', 'FAN09G2983' => 'fan', 'FAN09G3130' => 'fan', 'FAN09G3565' => 'fan', 'FAN09G3613' => 'fan', 'FAN09G4011' => 'fan', 'FAN09G4239' => 'fan', 'FAN09G4277' => 'fan', 'FAN09G4720' => 'fan', 'FAN11G0139' => 'fan', 'FAN11G1727' => 'fan', 'FAN11G2672' => 'fan', 'FAN11G2795' => 'fan', 'FAN11G3238' => 'fan', 'FAN11G3734' => 'fan', 'FAN12G0631' => 'fan', 'FAN12G2239' => 'fan', 'FAN12G2308' => 'fan', 'FAN12G2569' => 'fan', 'FAN12G2623' => 'fan', 'FAN13G3182' => 'fan', 'FAN14G0053' => 'fan', 'FAN14G0370' => 'fan', 'FAN14G0382' => 'fan', 'FAN14G0421' => 'fan', 'FAN14G0866' => 'fan', 'FAN14G1187' => 'fan', 'FAN14G1727' => 'fan', 'FAN14G1791' => 'fan', 'FAN14G2361' => 'fan', 'FAN14G2668' => 'fan', 'FAN14G2770' => 'fan', 'FAN14G2874' => 'fan', 'FAN14G3193' => 'fan', 'FAN14G3624' => 'fan', 'FAN14G3676' => 'fan', 'FAN14G3807' => 'fan', 'FAN14G4082' => 'fan', 'FAN14G4342' => 'fan', 'FAN14G4985' => 'fan', 'FAN14G5126' => 'fan', 'FAN14G5781' => 'fan', 'FAN14G5808' => 'fan', 'FAN14G5949' => 'fan', 'FAN15G0828' => 'fan', 'FAN15G1054' => 'fan', 'FAN15G2023' => 'fan', 'FAN15G2506' => 'fan', 'FAN16G0128' => 'fan', 'FAN16G0249' => 'fan', 'FAN16G0429' => 'fan', 'FAN16G1493' => 'fan', 'FAN16G2210' => 'fan', 'FAN16G2506' => 'fan', 'FAN18G1542' => 'fan', 'FAN18G4057' => 'fan', 'FAN19G0745' => 'fan', 'FAN19G1216' => 'fan', 'FAN19G1733' => 'fan', 'FAN20G0258' => 'fan', 'FAN20G1095' => 'fan', 'FAN20G1557' => 'fan', 'FAN21G0302' => 'fan', 'FAN21G0519' => 'fan', 'FAN21G0970' => 'fan', 'FAN21G1159' => 'fan', 'FAN21G1312' => 'fan', 'FAN21G1440' => 'fan', 'FAN21G1715' => 'fan', 'FAN23G1584' => 'fan', 'FAN24G0045' => 'fan', 'FAN24G0053' => 'fan', 'FAN24G1500' => 'fan', 'FAN24G1817' => 'fan', 'FAN24G2147' => 'fan', 'FAN24G2236' => 'fan', 'FAN24G2446' => 'fan', 'FAN24G2684' => 'fan', 'FAN25G0187' => 'fan', 'FAN25G0505' => 'fan', 'FAN25G0589' => 'fan', 'FAN25G3663' => 'fan', 'FAN26G1025' => 'fan', 'FAN26G2860' => 'fan', 'FAN27G1329' => 'fan', 'FAN27G3392' => 'fan', 'FvH4_1g02011' => 'fve', 'FvH4_1g06511' => 'fve', 'FvH4_2g19900' => 'fve', 'FvH4_2g19920' => 'fve', 'FvH4_2g24261' => 'fve', 'FvH4_2g24270' => 'fve', 'FvH4_2g24631' => 'fve', 'FvH4_2g30622' => 'fve', 'FvH4_3g12920' => 'fve', 'FvH4_3g30171' => 'fve', 'FvH4_3g35490' => 'fve', 'FvH4_3g43682' => 'fve', 'FvH4_3g43730' => 'fve', 'FvH4_3g43732' => 'fve', 'FvH4_3g43751' => 'fve', 'FvH4_3g43752' => 'fve', 'FvH4_3g43770' => 'fve', 'FvH4_3g44471' => 'fve', 'FvH4_3g44510' => 'fve', 'FvH4_3g44582' => 'fve', 'FvH4_4g16921' => 'fve', 'FvH4_4g17121' => 'fve', 'FvH4_4g17782' => 'fve', 'FvH4_4g17783' => 'fve', 'FvH4_4g18120' => 'fve', 'FvH4_4g31310' => 'fve', 'FvH4_4g35052' => 'fve', 'FvH4_5g30862' => 'fve', 'FvH4_6g01541' => 'fve', 'FvH4_6g02021' => 'fve', 'FvH4_6g02041' => 'fve', 'FvH4_6g02071' => 'fve', 'FvH4_6g02171' => 'fve', 'FvH4_6g03181' => 'fve', 'FvH4_6g03182' => 'fve', 'FvH4_6g03221' => 'fve', 'FvH4_6g03380' => 'fve', 'FvH4_6g05201' => 'fve', 'FvH4_6g05203' => 'fve', 'FvH4_6g20231' => 'fve', 'FvH4_6g31981' => 'fve', 'FvH4_6g32061' => 'fve', 'FvH4_6g37041' => 'fve', 'FvH4_6g37932' => 'fve', 'FvH4_6g38731' => 'fve', 'FvH4_6g39370' => 'fve', 'FvH4_6g39371' => 'fve', 'FvH4_6g40891' => 'fve', 'FvH4_6g40892' => 'fve', 'FvH4_6g43143' => 'fve', 'FvH4_6g45251' => 'fve', 'FvH4_6g45260' => 'fve', 'FvH4_6g45291' => 'fve', 'FvH4_6g45890' => 'fve', 'FvH4_6g46240' => 'fve', 'FvH4_6g46241' => 'fve', 'FvH4_6g46242' => 'fve', 'FvH4_6g46260' => 'fve', 'FvH4_6g46280' => 'fve', 'FvH4_6g46380' => 'fve', 'FvH4_7g12841' => 'fve', 'FvH4_7g31431' => 'fve', 'Glyma.09G075900' => 'gma', 'Gohir.A09G096401' => 'ghi', 'Gohir.D09G096101' => 'ghi', 'Gorai.006G112800' => 'gra', 'HanXRQChr04g0121411' => 'han', 'Hund15878' => 'sun', 'Lj2A1107G68' => 'lonja', 'Lj2A630G63' => 'lonja', 'Lj2A946T25' => 'lonja', 'Lj2C714T1' => 'lonja', 'Lj2C966T3' => 'lonja', 'Lj2C966T4' => 'lonja', 'Lj4g0002979' => 'lja', 'Lsat_1_v5_gn_5_30901' => 'lsa', 'Lsat_1_v5_gn_5_31100' => 'lsa', 'Lsat_1_v5_gn_5_38600' => 'lsa', 'Lsat_1_v5_gn_6_92061' => 'lsa', 'Manes.05G071301' => 'mes', 'MD02G1008700' => 'mdo', 'MD02G1008900' => 'mdo', 'MD03G1256400' => 'mdo', 'MD04G1180900' => 'mdo', 'MD04G1181000' => 'mdo', 'MD04G1181200' => 'mdo', 'MD05G1244200' => 'mdo', 'MD05G1324200' => 'mdo', 'MD09G1201600' => 'mdo', 'MD10G1000600' => 'mdo', 'MD14G1026900' => 'mdo', 'MD14G1187900' => 'mdo', 'MD15G1017800' => 'mdo', 'MD15G1018100' => 'mdo', 'Medtr4g124160' => 'mtr', 'Migut.L01260' => 'egut', 'Nitab4.5_0000008g0440' => 'nta', 'Nitab4.5_0000207g0170' => 'nta', 'Nitab4.5_0007671g0030' => 'nta', 'Nitab4.5_0010853g0020' => 'nta', 'Oeu057656.1' => 'oeu', 'PGSC0003DMG400005638' => 'stu', 'PGSC0003DMG400005639' => 'stu', 'Phvul.009G222800' => 'pvu', 'Potri.009G132400' => 'ptr', 'Potri.009G163001' => 'ptr', 'Potri.011G000700' => 'ptr', 'Potri.011G004800' => 'ptr', 'Prupe.1G509300' => 'ppe', 'Prupe.1G509700' => 'ppe', 'Prupe.1G510400' => 'ppe', 'Prupe.1G510700' => 'ppe', 'Prupe.1G512600' => 'ppe', 'Prupe.2G073200' => 'ppe', 'Prupe.3G059500' => 'ppe', 'Prupe.3G059600' => 'ppe', 'Prupe.3G246100' => 'ppe', 'Prupe.3G265100' => 'ppe', 'Prupe.4G034700' => 'ppe', 'Prupe.4G052100' => 'ppe', 'Prupe.4G053600' => 'ppe', 'Prupe.5G068800' => 'ppe', 'Prupe.5G070600' => 'ppe', 'Prupe.6G075400' => 'ppe', 'Prupe.6G075500' => 'ppe', 'Prupe.6G076400' => 'ppe', 'Prupe.8G110700' => 'ppe', 'Psat4g020960' => 'psa', 'PSO135G0788' => 'pso', 'PSO210G6463' => 'pso', 'PSO384G0370' => 'pso', 'PSO386G0056' => 'pso', 'QL01p006048' => 'qlo', 'QL02p054283' => 'qlo', 'QL05p008000' => 'qlo', 'QL05p008212' => 'qlo', 'QL05p008950' => 'qlo', 'QL05p009042' => 'qlo', 'QL05p009518' => 'qlo', 'QL05p012589' => 'qlo', 'QL05p012608' => 'qlo', 'QL05p012650' => 'qlo', 'QL05p012667' => 'qlo', 'QL05p014501' => 'qlo', 'QL05p052800' => 'qlo', 'QL05p065010' => 'qlo', 'QL05p074156' => 'qlo', 'QL05p074160' => 'qlo', 'QL05p074174' => 'qlo', 'QL05p074178' => 'qlo', 'QL05p074214' => 'qlo', 'QL06p001050' => 'qlo', 'QL06p001056' => 'qlo', 'QL06p006093' => 'qlo', 'QL06p006111' => 'qlo', 'QL07p019784' => 'qlo', 'QL07p019801' => 'qlo', 'QL07p036110' => 'qlo', 'QL07p036134' => 'qlo', 'QL07p036147' => 'qlo', 'QL07p036156' => 'qlo', 'QL07p036300' => 'qlo', 'QL07p036320' => 'qlo', 'QL08p014547' => 'qlo', 'QL08p014551' => 'qlo', 'QL08p043319' => 'qlo', 'QL08p043324' => 'qlo', 'QL11p009094' => 'qlo', 'RcHm_v2.0_Chr1g0380481' => 'rch', 'RcHm_v2.0_Chr2g0089331' => 'rch', 'RcHm_v2.0_Chr2g0123691' => 'rch', 'RcHm_v2.0_Chr2g0151111' => 'rch', 'RcHm_v2.0_Chr2g0163011' => 'rch', 'RcHm_v2.0_Chr2g0163051' => 'rch', 'RcHm_v2.0_Chr2g0164671' => 'rch', 'RcHm_v2.0_Chr2g0164681' => 'rch', 'RcHm_v2.0_Chr2g0164721' => 'rch', 'RcHm_v2.0_Chr3g0449911' => 'rch', 'RcHm_v2.0_Chr3g0450211' => 'rch', 'RcHm_v2.0_Chr3g0457271' => 'rch', 'RcHm_v2.0_Chr5g0018111' => 'rch', 'RcHm_v2.0_Chr5g0021011' => 'rch', 'RcHm_v2.0_Chr5g0081171' => 'rch', 'RcHm_v2.0_Chr5g0081211' => 'rch', 'RcHm_v2.0_Chr6g0275871' => 'rch', 'RcHm_v2.0_Chr6g0276071' => 'rch', 'RcHm_v2.0_Chr6g0285591' => 'rch', 'RcHm_v2.0_Chr6g0291931' => 'rch', 'RcHm_v2.0_Chr6g0292091' => 'rch', 'RcHm_v2.0_Chr6g0292271' => 'rch', 'RcHm_v2.0_Chr7g0221261' => 'rch', 'Rhsim08G0219900' => 'rsi', 'Rhsim08G0220200' => 'rsi', 'Rhsim08G0237800' => 'rsi', 'Rhsim08G0238800' => 'rsi', 'Sabra09G0102700' => 'sbr', 'Sabra09G0127200' => 'sbr', 'Sabra11G0003700' => 'sbr', 'Sabra15G0014700' => 'sbr', 'Sc19g0000590' => 'sci', 'Sc19g0001870' => 'sci', 'SGA_v2.0_scaffold1G00346' => 'sas', 'SGA_v2.0_scaffold1G00575' => 'sas', 'SGA_v2.0_scaffold1G00761' => 'sas', 'SGA_v2.0_scaffold232G43501' => 'sas', 'TAR625G1137' => 'tar', 'Thecc.03G222100' => 'tca', 'TPR.G12691' => 'tpr', 'TWI34G0727' => 'twi', 'TWI36G0117' => 'twi', 'VMungo1309G0868' => 'vmu' ), 'gf_id' => 'HOM05D001729', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001729' ), 'data_identifier' => 'HOM05D001729', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001729', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '375', 'num_species' => '42' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'Ah.07g204710' => 'amhyb', 'AUR62006001' => 'cqu', 'AUR62006002' => 'cqu', 'AUR62006003' => 'cqu', 'AUR62015641' => 'cqu', 'AUR62027174' => 'cqu', 'AUR62035623' => 'cqu', 'AUR62035624' => 'cqu', 'AUR62035625' => 'cqu', 'AUR62035626' => 'cqu', 'CAN.G1110.53' => 'can', 'CANSAT80G0415' => 'cansat', 'Ca_21364_v3' => 'car', 'COL.COLO4_30693' => 'col', 'COL.COLO4_30694' => 'col', 'COL.COLO4_30695' => 'col', 'COL.COLO4_30696' => 'col', 'COL.COLO4_34020' => 'col', 'DCAR_004585' => 'dca', 'Dinv04029' => 'din', 'Dinv34857' => 'din', 'Duzib147G0011' => 'dzi', 'Duzib170G0599' => 'dzi', 'Duzib192G1051' => 'dzi', 'FAN01G0708' => 'fan', 'FAN01G0742' => 'fan', 'FAN02G0048' => 'fan', 'FAN02G0583' => 'fan', 'FAN02G0688' => 'fan', 'FAN02G1588' => 'fan', 'FAN02G2194' => 'fan', 'FAN02G2750' => 'fan', 'FAN02G3094' => 'fan', 'FAN02G3887' => 'fan', 'FAN02G3911' => 'fan', 'FAN02G3994' => 'fan', 'FAN02G4432' => 'fan', 'FAN02G4556' => 'fan', 'FAN03G1977' => 'fan', 'FAN03G2781' => 'fan', 'FAN03G2850' => 'fan', 'FAN03G3155' => 'fan', 'FAN04G2487' => 'fan', 'FAN05G0208' => 'fan', 'FAN05G0656' => 'fan', 'FAN05G0696' => 'fan', 'FAN05G0810' => 'fan', 'FAN05G1447' => 'fan', 'FAN05G2640' => 'fan', 'FAN05G2911' => 'fan', 'FAN05G3901' => 'fan', 'FAN05G4859' => 'fan', 'FAN05G4861' => 'fan', 'FAN05G4988' => 'fan', 'FAN05G5187' => 'fan', 'FAN05G5452' => 'fan', 'FAN05G5500' => 'fan', 'FAN05G5688' => 'fan', 'FAN06G0177' => 'fan', 'FAN06G0675' => 'fan', 'FAN06G1290' => 'fan', 'FAN06G2191' => 'fan', 'FAN06G2405' => 'fan', 'FAN06G3231' => 'fan', 'FAN06G3932' => 'fan', 'FAN07G0163' => 'fan', 'FAN07G0471' => 'fan', 'FAN07G1354' => 'fan', 'FAN08G0338' => 'fan', 'FAN08G1373' => 'fan', 'FAN08G2539' => 'fan', 'FAN08G2728' => 'fan', 'FAN09G0608' => 'fan', 'FAN09G1136' => 'fan', 'FAN09G1958' => 'fan', 'FAN09G2508' => 'fan', 'FAN09G2597' => 'fan', 'FAN09G2658' => 'fan', 'FAN09G2757' => 'fan', 'FAN09G2983' => 'fan', 'FAN09G3130' => 'fan', 'FAN09G3565' => 'fan', 'FAN09G3613' => 'fan', 'FAN09G4011' => 'fan', 'FAN09G4239' => 'fan', 'FAN09G4277' => 'fan', 'FAN09G4720' => 'fan', 'FAN11G0139' => 'fan', 'FAN11G1727' => 'fan', 'FAN11G2672' => 'fan', 'FAN11G2795' => 'fan', 'FAN11G3238' => 'fan', 'FAN11G3734' => 'fan', 'FAN12G0631' => 'fan', 'FAN12G2239' => 'fan', 'FAN12G2308' => 'fan', 'FAN12G2569' => 'fan', 'FAN12G2623' => 'fan', 'FAN13G3182' => 'fan', 'FAN14G0053' => 'fan', 'FAN14G0370' => 'fan', 'FAN14G0382' => 'fan', 'FAN14G0421' => 'fan', 'FAN14G0866' => 'fan', 'FAN14G1187' => 'fan', 'FAN14G1727' => 'fan', 'FAN14G1791' => 'fan', 'FAN14G2361' => 'fan', 'FAN14G2668' => 'fan', 'FAN14G2770' => 'fan', 'FAN14G2874' => 'fan', 'FAN14G3193' => 'fan', 'FAN14G3624' => 'fan', 'FAN14G3676' => 'fan', 'FAN14G3807' => 'fan', 'FAN14G4082' => 'fan', 'FAN14G4342' => 'fan', 'FAN14G4985' => 'fan', 'FAN14G5126' => 'fan', 'FAN14G5781' => 'fan', 'FAN14G5808' => 'fan', 'FAN14G5949' => 'fan', 'FAN15G0828' => 'fan', 'FAN15G1054' => 'fan', 'FAN15G2023' => 'fan', 'FAN15G2506' => 'fan', 'FAN16G0128' => 'fan', 'FAN16G0249' => 'fan', 'FAN16G0429' => 'fan', 'FAN16G1493' => 'fan', 'FAN16G2210' => 'fan', 'FAN16G2506' => 'fan', 'FAN18G1542' => 'fan', 'FAN18G4057' => 'fan', 'FAN19G0745' => 'fan', 'FAN19G1216' => 'fan', 'FAN19G1733' => 'fan', 'FAN20G0258' => 'fan', 'FAN20G1095' => 'fan', 'FAN20G1557' => 'fan', 'FAN21G0302' => 'fan', 'FAN21G0519' => 'fan', 'FAN21G0970' => 'fan', 'FAN21G1159' => 'fan', 'FAN21G1312' => 'fan', 'FAN21G1440' => 'fan', 'FAN21G1715' => 'fan', 'FAN23G1584' => 'fan', 'FAN24G0045' => 'fan', 'FAN24G0053' => 'fan', 'FAN24G1500' => 'fan', 'FAN24G1817' => 'fan', 'FAN24G2147' => 'fan', 'FAN24G2236' => 'fan', 'FAN24G2446' => 'fan', 'FAN24G2684' => 'fan', 'FAN25G0187' => 'fan', 'FAN25G0505' => 'fan', 'FAN25G0589' => 'fan', 'FAN25G3663' => 'fan', 'FAN26G1025' => 'fan', 'FAN26G2860' => 'fan', 'FAN27G1329' => 'fan', 'FAN27G3392' => 'fan', 'FvH4_1g02011' => 'fve', 'FvH4_1g06511' => 'fve', 'FvH4_2g19900' => 'fve', 'FvH4_2g19920' => 'fve', 'FvH4_2g24261' => 'fve', 'FvH4_2g24270' => 'fve', 'FvH4_2g24631' => 'fve', 'FvH4_2g30622' => 'fve', 'FvH4_3g12920' => 'fve', 'FvH4_3g30171' => 'fve', 'FvH4_3g35490' => 'fve', 'FvH4_3g43682' => 'fve', 'FvH4_3g43730' => 'fve', 'FvH4_3g43732' => 'fve', 'FvH4_3g43751' => 'fve', 'FvH4_3g43752' => 'fve', 'FvH4_3g43770' => 'fve', 'FvH4_3g44471' => 'fve', 'FvH4_3g44510' => 'fve', 'FvH4_3g44582' => 'fve', 'FvH4_4g16921' => 'fve', 'FvH4_4g17121' => 'fve', 'FvH4_4g17782' => 'fve', 'FvH4_4g17783' => 'fve', 'FvH4_4g18120' => 'fve', 'FvH4_4g31310' => 'fve', 'FvH4_4g35052' => 'fve', 'FvH4_5g30862' => 'fve', 'FvH4_6g01541' => 'fve', 'FvH4_6g02021' => 'fve', 'FvH4_6g02041' => 'fve', 'FvH4_6g02071' => 'fve', 'FvH4_6g02171' => 'fve', 'FvH4_6g03181' => 'fve', 'FvH4_6g03182' => 'fve', 'FvH4_6g03221' => 'fve', 'FvH4_6g03380' => 'fve', 'FvH4_6g05201' => 'fve', 'FvH4_6g05203' => 'fve', 'FvH4_6g20231' => 'fve', 'FvH4_6g31981' => 'fve', 'FvH4_6g32061' => 'fve', 'FvH4_6g37041' => 'fve', 'FvH4_6g37932' => 'fve', 'FvH4_6g38731' => 'fve', 'FvH4_6g39370' => 'fve', 'FvH4_6g39371' => 'fve', 'FvH4_6g40891' => 'fve', 'FvH4_6g40892' => 'fve', 'FvH4_6g43143' => 'fve', 'FvH4_6g45251' => 'fve', 'FvH4_6g45260' => 'fve', 'FvH4_6g45291' => 'fve', 'FvH4_6g45890' => 'fve', 'FvH4_6g46240' => 'fve', 'FvH4_6g46241' => 'fve', 'FvH4_6g46242' => 'fve', 'FvH4_6g46260' => 'fve', 'FvH4_6g46280' => 'fve', 'FvH4_6g46380' => 'fve', 'FvH4_7g12841' => 'fve', 'FvH4_7g31431' => 'fve', 'Glyma.09G075900' => 'gma', 'Gohir.A09G096401' => 'ghi', 'Gohir.D09G096101' => 'ghi', 'Gorai.006G112800' => 'gra', 'HanXRQChr04g0121411' => 'han', 'Hund15878' => 'sun', 'Lj2A1107G68' => 'lonja', 'Lj2A630G63' => 'lonja', 'Lj2A946T25' => 'lonja', 'Lj2C714T1' => 'lonja', 'Lj2C966T3' => 'lonja', 'Lj2C966T4' => 'lonja', 'Lj4g0002979' => 'lja', 'Lsat_1_v5_gn_5_30901' => 'lsa', 'Lsat_1_v5_gn_5_31100' => 'lsa', 'Lsat_1_v5_gn_5_38600' => 'lsa', 'Lsat_1_v5_gn_6_92061' => 'lsa', 'Manes.05G071301' => 'mes', 'MD02G1008700' => 'mdo', 'MD02G1008900' => 'mdo', 'MD03G1256400' => 'mdo', 'MD04G1180900' => 'mdo', 'MD04G1181000' => 'mdo', 'MD04G1181200' => 'mdo', 'MD05G1244200' => 'mdo', 'MD05G1324200' => 'mdo', 'MD09G1201600' => 'mdo', 'MD10G1000600' => 'mdo', 'MD14G1026900' => 'mdo', 'MD14G1187900' => 'mdo', 'MD15G1017800' => 'mdo', 'MD15G1018100' => 'mdo', 'Medtr4g124160' => 'mtr', 'Migut.L01260' => 'egut', 'Nitab4.5_0000008g0440' => 'nta', 'Nitab4.5_0000207g0170' => 'nta', 'Nitab4.5_0007671g0030' => 'nta', 'Nitab4.5_0010853g0020' => 'nta', 'Oeu057656.1' => 'oeu', 'PGSC0003DMG400005638' => 'stu', 'PGSC0003DMG400005639' => 'stu', 'Phvul.009G222800' => 'pvu', 'Potri.009G132400' => 'ptr', 'Potri.009G163001' => 'ptr', 'Potri.011G000700' => 'ptr', 'Potri.011G004800' => 'ptr', 'Prupe.1G509300' => 'ppe', 'Prupe.1G509700' => 'ppe', 'Prupe.1G510400' => 'ppe', 'Prupe.1G510700' => 'ppe', 'Prupe.1G512600' => 'ppe', 'Prupe.2G073200' => 'ppe', 'Prupe.3G059500' => 'ppe', 'Prupe.3G059600' => 'ppe', 'Prupe.3G246100' => 'ppe', 'Prupe.3G265100' => 'ppe', 'Prupe.4G034700' => 'ppe', 'Prupe.4G052100' => 'ppe', 'Prupe.4G053600' => 'ppe', 'Prupe.5G068800' => 'ppe', 'Prupe.5G070600' => 'ppe', 'Prupe.6G075400' => 'ppe', 'Prupe.6G075500' => 'ppe', 'Prupe.6G076400' => 'ppe', 'Prupe.8G110700' => 'ppe', 'Psat4g020960' => 'psa', 'PSO135G0788' => 'pso', 'PSO210G6463' => 'pso', 'PSO384G0370' => 'pso', 'PSO386G0056' => 'pso', 'QL01p006048' => 'qlo', 'QL02p054283' => 'qlo', 'QL05p008000' => 'qlo', 'QL05p008212' => 'qlo', 'QL05p008950' => 'qlo', 'QL05p009042' => 'qlo', 'QL05p009518' => 'qlo', 'QL05p012589' => 'qlo', 'QL05p012608' => 'qlo', 'QL05p012650' => 'qlo', 'QL05p012667' => 'qlo', 'QL05p014501' => 'qlo', 'QL05p052800' => 'qlo', 'QL05p065010' => 'qlo', 'QL05p074156' => 'qlo', 'QL05p074160' => 'qlo', 'QL05p074174' => 'qlo', 'QL05p074178' => 'qlo', 'QL05p074214' => 'qlo', 'QL06p001050' => 'qlo', 'QL06p001056' => 'qlo', 'QL06p006093' => 'qlo', 'QL06p006111' => 'qlo', 'QL07p019784' => 'qlo', 'QL07p019801' => 'qlo', 'QL07p036110' => 'qlo', 'QL07p036134' => 'qlo', 'QL07p036147' => 'qlo', 'QL07p036156' => 'qlo', 'QL07p036300' => 'qlo', 'QL07p036320' => 'qlo', 'QL08p014547' => 'qlo', 'QL08p014551' => 'qlo', 'QL08p043319' => 'qlo', 'QL08p043324' => 'qlo', 'QL11p009094' => 'qlo', 'RcHm_v2.0_Chr1g0380481' => 'rch', 'RcHm_v2.0_Chr2g0089331' => 'rch', 'RcHm_v2.0_Chr2g0123691' => 'rch', 'RcHm_v2.0_Chr2g0151111' => 'rch', 'RcHm_v2.0_Chr2g0163011' => 'rch', 'RcHm_v2.0_Chr2g0163051' => 'rch', 'RcHm_v2.0_Chr2g0164671' => 'rch', 'RcHm_v2.0_Chr2g0164681' => 'rch', 'RcHm_v2.0_Chr2g0164721' => 'rch', 'RcHm_v2.0_Chr3g0449911' => 'rch', 'RcHm_v2.0_Chr3g0450211' => 'rch', 'RcHm_v2.0_Chr3g0457271' => 'rch', 'RcHm_v2.0_Chr5g0018111' => 'rch', 'RcHm_v2.0_Chr5g0021011' => 'rch', 'RcHm_v2.0_Chr5g0081171' => 'rch', 'RcHm_v2.0_Chr5g0081211' => 'rch', 'RcHm_v2.0_Chr6g0275871' => 'rch', 'RcHm_v2.0_Chr6g0276071' => 'rch', 'RcHm_v2.0_Chr6g0285591' => 'rch', 'RcHm_v2.0_Chr6g0291931' => 'rch', 'RcHm_v2.0_Chr6g0292091' => 'rch', 'RcHm_v2.0_Chr6g0292271' => 'rch', 'RcHm_v2.0_Chr7g0221261' => 'rch', 'Rhsim08G0219900' => 'rsi', 'Rhsim08G0220200' => 'rsi', 'Rhsim08G0237800' => 'rsi', 'Rhsim08G0238800' => 'rsi', 'Sabra09G0102700' => 'sbr', 'Sabra09G0127200' => 'sbr', 'Sabra11G0003700' => 'sbr', 'Sabra15G0014700' => 'sbr', 'Sc19g0000590' => 'sci', 'Sc19g0001870' => 'sci', 'SGA_v2.0_scaffold1G00346' => 'sas', 'SGA_v2.0_scaffold1G00575' => 'sas', 'SGA_v2.0_scaffold1G00761' => 'sas', 'SGA_v2.0_scaffold232G43501' => 'sas', 'TAR625G1137' => 'tar', 'Thecc.03G222100' => 'tca', 'TPR.G12691' => 'tpr', 'TWI34G0727' => 'twi', 'TWI36G0117' => 'twi', 'VMungo1309G0868' => 'vmu' ) $gf_id = 'HOM05D001729' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001729' ) $data_identifier = 'HOM05D001729' $data_type = 'gf_id' $species_gene_counts = array( 'amhyb' => (int) 1, 'cqu' => (int) 9, 'can' => (int) 1, 'cansat' => (int) 1, 'car' => (int) 1, 'col' => (int) 5, 'dca' => (int) 1, 'din' => (int) 2, 'dzi' => (int) 3, 'fan' => (int) 140, 'fve' => (int) 62, 'gma' => (int) 1, 'ghi' => (int) 2, 'gra' => (int) 1, 'han' => (int) 1, 'sun' => (int) 1, 'lonja' => (int) 6, 'lja' => (int) 1, 'lsa' => (int) 4, 'mes' => (int) 1, 'mdo' => (int) 14, 'mtr' => (int) 1, 'egut' => (int) 1, 'nta' => (int) 4, 'oeu' => (int) 1, 'stu' => (int) 2, 'pvu' => (int) 1, 'ptr' => (int) 4, 'ppe' => (int) 19, 'psa' => (int) 1, 'pso' => (int) 4, 'qlo' => (int) 36, 'rch' => (int) 23, 'rsi' => (int) 4, 'sbr' => (int) 4, 'sci' => (int) 2, 'sas' => (int) 4, 'tar' => (int) 1, 'tca' => (int) 1, 'tpr' => (int) 1, 'twi' => (int) 2, 'vmu' => (int) 1 ) $gf_gene_species = 'vmu' $gf_gene_id = 'VMungo1309G0868' $species_info = array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ) $local_species = 'rsi' $disabled = '' $selected = '' $num_hits = (int) 1
Warning (2): count(): Parameter must be an array or an object that implements Countable [APP/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp, line 33]Code Context $disabled = (!array_key_exists($local_species,$species_gene_counts))?"disabled":""; $selected = (isset($selected_species) && array_key_exists($local_species,$selected_species))?"checked='checked'":""; $num_hits = (array_key_exists($local_species,$species_gene_counts))?count($species_gene_counts[$local_species]):0; $viewFile = '/www/bioinformatics01_ro/plaza/_dev_instances/feedback/app/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp' $dataForView = array( 'sidebar_info' => array( 'gf_id' => 'HOM05D001729', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '375', 'num_species' => '42' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'Ah.07g204710' => 'amhyb', 'AUR62006001' => 'cqu', 'AUR62006002' => 'cqu', 'AUR62006003' => 'cqu', 'AUR62015641' => 'cqu', 'AUR62027174' => 'cqu', 'AUR62035623' => 'cqu', 'AUR62035624' => 'cqu', 'AUR62035625' => 'cqu', 'AUR62035626' => 'cqu', 'CAN.G1110.53' => 'can', 'CANSAT80G0415' => 'cansat', 'Ca_21364_v3' => 'car', 'COL.COLO4_30693' => 'col', 'COL.COLO4_30694' => 'col', 'COL.COLO4_30695' => 'col', 'COL.COLO4_30696' => 'col', 'COL.COLO4_34020' => 'col', 'DCAR_004585' => 'dca', 'Dinv04029' => 'din', 'Dinv34857' => 'din', 'Duzib147G0011' => 'dzi', 'Duzib170G0599' => 'dzi', 'Duzib192G1051' => 'dzi', 'FAN01G0708' => 'fan', 'FAN01G0742' => 'fan', 'FAN02G0048' => 'fan', 'FAN02G0583' => 'fan', 'FAN02G0688' => 'fan', 'FAN02G1588' => 'fan', 'FAN02G2194' => 'fan', 'FAN02G2750' => 'fan', 'FAN02G3094' => 'fan', 'FAN02G3887' => 'fan', 'FAN02G3911' => 'fan', 'FAN02G3994' => 'fan', 'FAN02G4432' => 'fan', 'FAN02G4556' => 'fan', 'FAN03G1977' => 'fan', 'FAN03G2781' => 'fan', 'FAN03G2850' => 'fan', 'FAN03G3155' => 'fan', 'FAN04G2487' => 'fan', 'FAN05G0208' => 'fan', 'FAN05G0656' => 'fan', 'FAN05G0696' => 'fan', 'FAN05G0810' => 'fan', 'FAN05G1447' => 'fan', 'FAN05G2640' => 'fan', 'FAN05G2911' => 'fan', 'FAN05G3901' => 'fan', 'FAN05G4859' => 'fan', 'FAN05G4861' => 'fan', 'FAN05G4988' => 'fan', 'FAN05G5187' => 'fan', 'FAN05G5452' => 'fan', 'FAN05G5500' => 'fan', 'FAN05G5688' => 'fan', 'FAN06G0177' => 'fan', 'FAN06G0675' => 'fan', 'FAN06G1290' => 'fan', 'FAN06G2191' => 'fan', 'FAN06G2405' => 'fan', 'FAN06G3231' => 'fan', 'FAN06G3932' => 'fan', 'FAN07G0163' => 'fan', 'FAN07G0471' => 'fan', 'FAN07G1354' => 'fan', 'FAN08G0338' => 'fan', 'FAN08G1373' => 'fan', 'FAN08G2539' => 'fan', 'FAN08G2728' => 'fan', 'FAN09G0608' => 'fan', 'FAN09G1136' => 'fan', 'FAN09G1958' => 'fan', 'FAN09G2508' => 'fan', 'FAN09G2597' => 'fan', 'FAN09G2658' => 'fan', 'FAN09G2757' => 'fan', 'FAN09G2983' => 'fan', 'FAN09G3130' => 'fan', 'FAN09G3565' => 'fan', 'FAN09G3613' => 'fan', 'FAN09G4011' => 'fan', 'FAN09G4239' => 'fan', 'FAN09G4277' => 'fan', 'FAN09G4720' => 'fan', 'FAN11G0139' => 'fan', 'FAN11G1727' => 'fan', 'FAN11G2672' => 'fan', 'FAN11G2795' => 'fan', 'FAN11G3238' => 'fan', 'FAN11G3734' => 'fan', 'FAN12G0631' => 'fan', 'FAN12G2239' => 'fan', 'FAN12G2308' => 'fan', 'FAN12G2569' => 'fan', 'FAN12G2623' => 'fan', 'FAN13G3182' => 'fan', 'FAN14G0053' => 'fan', 'FAN14G0370' => 'fan', 'FAN14G0382' => 'fan', 'FAN14G0421' => 'fan', 'FAN14G0866' => 'fan', 'FAN14G1187' => 'fan', 'FAN14G1727' => 'fan', 'FAN14G1791' => 'fan', 'FAN14G2361' => 'fan', 'FAN14G2668' => 'fan', 'FAN14G2770' => 'fan', 'FAN14G2874' => 'fan', 'FAN14G3193' => 'fan', 'FAN14G3624' => 'fan', 'FAN14G3676' => 'fan', 'FAN14G3807' => 'fan', 'FAN14G4082' => 'fan', 'FAN14G4342' => 'fan', 'FAN14G4985' => 'fan', 'FAN14G5126' => 'fan', 'FAN14G5781' => 'fan', 'FAN14G5808' => 'fan', 'FAN14G5949' => 'fan', 'FAN15G0828' => 'fan', 'FAN15G1054' => 'fan', 'FAN15G2023' => 'fan', 'FAN15G2506' => 'fan', 'FAN16G0128' => 'fan', 'FAN16G0249' => 'fan', 'FAN16G0429' => 'fan', 'FAN16G1493' => 'fan', 'FAN16G2210' => 'fan', 'FAN16G2506' => 'fan', 'FAN18G1542' => 'fan', 'FAN18G4057' => 'fan', 'FAN19G0745' => 'fan', 'FAN19G1216' => 'fan', 'FAN19G1733' => 'fan', 'FAN20G0258' => 'fan', 'FAN20G1095' => 'fan', 'FAN20G1557' => 'fan', 'FAN21G0302' => 'fan', 'FAN21G0519' => 'fan', 'FAN21G0970' => 'fan', 'FAN21G1159' => 'fan', 'FAN21G1312' => 'fan', 'FAN21G1440' => 'fan', 'FAN21G1715' => 'fan', 'FAN23G1584' => 'fan', 'FAN24G0045' => 'fan', 'FAN24G0053' => 'fan', 'FAN24G1500' => 'fan', 'FAN24G1817' => 'fan', 'FAN24G2147' => 'fan', 'FAN24G2236' => 'fan', 'FAN24G2446' => 'fan', 'FAN24G2684' => 'fan', 'FAN25G0187' => 'fan', 'FAN25G0505' => 'fan', 'FAN25G0589' => 'fan', 'FAN25G3663' => 'fan', 'FAN26G1025' => 'fan', 'FAN26G2860' => 'fan', 'FAN27G1329' => 'fan', 'FAN27G3392' => 'fan', 'FvH4_1g02011' => 'fve', 'FvH4_1g06511' => 'fve', 'FvH4_2g19900' => 'fve', 'FvH4_2g19920' => 'fve', 'FvH4_2g24261' => 'fve', 'FvH4_2g24270' => 'fve', 'FvH4_2g24631' => 'fve', 'FvH4_2g30622' => 'fve', 'FvH4_3g12920' => 'fve', 'FvH4_3g30171' => 'fve', 'FvH4_3g35490' => 'fve', 'FvH4_3g43682' => 'fve', 'FvH4_3g43730' => 'fve', 'FvH4_3g43732' => 'fve', 'FvH4_3g43751' => 'fve', 'FvH4_3g43752' => 'fve', 'FvH4_3g43770' => 'fve', 'FvH4_3g44471' => 'fve', 'FvH4_3g44510' => 'fve', 'FvH4_3g44582' => 'fve', 'FvH4_4g16921' => 'fve', 'FvH4_4g17121' => 'fve', 'FvH4_4g17782' => 'fve', 'FvH4_4g17783' => 'fve', 'FvH4_4g18120' => 'fve', 'FvH4_4g31310' => 'fve', 'FvH4_4g35052' => 'fve', 'FvH4_5g30862' => 'fve', 'FvH4_6g01541' => 'fve', 'FvH4_6g02021' => 'fve', 'FvH4_6g02041' => 'fve', 'FvH4_6g02071' => 'fve', 'FvH4_6g02171' => 'fve', 'FvH4_6g03181' => 'fve', 'FvH4_6g03182' => 'fve', 'FvH4_6g03221' => 'fve', 'FvH4_6g03380' => 'fve', 'FvH4_6g05201' => 'fve', 'FvH4_6g05203' => 'fve', 'FvH4_6g20231' => 'fve', 'FvH4_6g31981' => 'fve', 'FvH4_6g32061' => 'fve', 'FvH4_6g37041' => 'fve', 'FvH4_6g37932' => 'fve', 'FvH4_6g38731' => 'fve', 'FvH4_6g39370' => 'fve', 'FvH4_6g39371' => 'fve', 'FvH4_6g40891' => 'fve', 'FvH4_6g40892' => 'fve', 'FvH4_6g43143' => 'fve', 'FvH4_6g45251' => 'fve', 'FvH4_6g45260' => 'fve', 'FvH4_6g45291' => 'fve', 'FvH4_6g45890' => 'fve', 'FvH4_6g46240' => 'fve', 'FvH4_6g46241' => 'fve', 'FvH4_6g46242' => 'fve', 'FvH4_6g46260' => 'fve', 'FvH4_6g46280' => 'fve', 'FvH4_6g46380' => 'fve', 'FvH4_7g12841' => 'fve', 'FvH4_7g31431' => 'fve', 'Glyma.09G075900' => 'gma', 'Gohir.A09G096401' => 'ghi', 'Gohir.D09G096101' => 'ghi', 'Gorai.006G112800' => 'gra', 'HanXRQChr04g0121411' => 'han', 'Hund15878' => 'sun', 'Lj2A1107G68' => 'lonja', 'Lj2A630G63' => 'lonja', 'Lj2A946T25' => 'lonja', 'Lj2C714T1' => 'lonja', 'Lj2C966T3' => 'lonja', 'Lj2C966T4' => 'lonja', 'Lj4g0002979' => 'lja', 'Lsat_1_v5_gn_5_30901' => 'lsa', 'Lsat_1_v5_gn_5_31100' => 'lsa', 'Lsat_1_v5_gn_5_38600' => 'lsa', 'Lsat_1_v5_gn_6_92061' => 'lsa', 'Manes.05G071301' => 'mes', 'MD02G1008700' => 'mdo', 'MD02G1008900' => 'mdo', 'MD03G1256400' => 'mdo', 'MD04G1180900' => 'mdo', 'MD04G1181000' => 'mdo', 'MD04G1181200' => 'mdo', 'MD05G1244200' => 'mdo', 'MD05G1324200' => 'mdo', 'MD09G1201600' => 'mdo', 'MD10G1000600' => 'mdo', 'MD14G1026900' => 'mdo', 'MD14G1187900' => 'mdo', 'MD15G1017800' => 'mdo', 'MD15G1018100' => 'mdo', 'Medtr4g124160' => 'mtr', 'Migut.L01260' => 'egut', 'Nitab4.5_0000008g0440' => 'nta', 'Nitab4.5_0000207g0170' => 'nta', 'Nitab4.5_0007671g0030' => 'nta', 'Nitab4.5_0010853g0020' => 'nta', 'Oeu057656.1' => 'oeu', 'PGSC0003DMG400005638' => 'stu', 'PGSC0003DMG400005639' => 'stu', 'Phvul.009G222800' => 'pvu', 'Potri.009G132400' => 'ptr', 'Potri.009G163001' => 'ptr', 'Potri.011G000700' => 'ptr', 'Potri.011G004800' => 'ptr', 'Prupe.1G509300' => 'ppe', 'Prupe.1G509700' => 'ppe', 'Prupe.1G510400' => 'ppe', 'Prupe.1G510700' => 'ppe', 'Prupe.1G512600' => 'ppe', 'Prupe.2G073200' => 'ppe', 'Prupe.3G059500' => 'ppe', 'Prupe.3G059600' => 'ppe', 'Prupe.3G246100' => 'ppe', 'Prupe.3G265100' => 'ppe', 'Prupe.4G034700' => 'ppe', 'Prupe.4G052100' => 'ppe', 'Prupe.4G053600' => 'ppe', 'Prupe.5G068800' => 'ppe', 'Prupe.5G070600' => 'ppe', 'Prupe.6G075400' => 'ppe', 'Prupe.6G075500' => 'ppe', 'Prupe.6G076400' => 'ppe', 'Prupe.8G110700' => 'ppe', 'Psat4g020960' => 'psa', 'PSO135G0788' => 'pso', 'PSO210G6463' => 'pso', 'PSO384G0370' => 'pso', 'PSO386G0056' => 'pso', 'QL01p006048' => 'qlo', 'QL02p054283' => 'qlo', 'QL05p008000' => 'qlo', 'QL05p008212' => 'qlo', 'QL05p008950' => 'qlo', 'QL05p009042' => 'qlo', 'QL05p009518' => 'qlo', 'QL05p012589' => 'qlo', 'QL05p012608' => 'qlo', 'QL05p012650' => 'qlo', 'QL05p012667' => 'qlo', 'QL05p014501' => 'qlo', 'QL05p052800' => 'qlo', 'QL05p065010' => 'qlo', 'QL05p074156' => 'qlo', 'QL05p074160' => 'qlo', 'QL05p074174' => 'qlo', 'QL05p074178' => 'qlo', 'QL05p074214' => 'qlo', 'QL06p001050' => 'qlo', 'QL06p001056' => 'qlo', 'QL06p006093' => 'qlo', 'QL06p006111' => 'qlo', 'QL07p019784' => 'qlo', 'QL07p019801' => 'qlo', 'QL07p036110' => 'qlo', 'QL07p036134' => 'qlo', 'QL07p036147' => 'qlo', 'QL07p036156' => 'qlo', 'QL07p036300' => 'qlo', 'QL07p036320' => 'qlo', 'QL08p014547' => 'qlo', 'QL08p014551' => 'qlo', 'QL08p043319' => 'qlo', 'QL08p043324' => 'qlo', 'QL11p009094' => 'qlo', 'RcHm_v2.0_Chr1g0380481' => 'rch', 'RcHm_v2.0_Chr2g0089331' => 'rch', 'RcHm_v2.0_Chr2g0123691' => 'rch', 'RcHm_v2.0_Chr2g0151111' => 'rch', 'RcHm_v2.0_Chr2g0163011' => 'rch', 'RcHm_v2.0_Chr2g0163051' => 'rch', 'RcHm_v2.0_Chr2g0164671' => 'rch', 'RcHm_v2.0_Chr2g0164681' => 'rch', 'RcHm_v2.0_Chr2g0164721' => 'rch', 'RcHm_v2.0_Chr3g0449911' => 'rch', 'RcHm_v2.0_Chr3g0450211' => 'rch', 'RcHm_v2.0_Chr3g0457271' => 'rch', 'RcHm_v2.0_Chr5g0018111' => 'rch', 'RcHm_v2.0_Chr5g0021011' => 'rch', 'RcHm_v2.0_Chr5g0081171' => 'rch', 'RcHm_v2.0_Chr5g0081211' => 'rch', 'RcHm_v2.0_Chr6g0275871' => 'rch', 'RcHm_v2.0_Chr6g0276071' => 'rch', 'RcHm_v2.0_Chr6g0285591' => 'rch', 'RcHm_v2.0_Chr6g0291931' => 'rch', 'RcHm_v2.0_Chr6g0292091' => 'rch', 'RcHm_v2.0_Chr6g0292271' => 'rch', 'RcHm_v2.0_Chr7g0221261' => 'rch', 'Rhsim08G0219900' => 'rsi', 'Rhsim08G0220200' => 'rsi', 'Rhsim08G0237800' => 'rsi', 'Rhsim08G0238800' => 'rsi', 'Sabra09G0102700' => 'sbr', 'Sabra09G0127200' => 'sbr', 'Sabra11G0003700' => 'sbr', 'Sabra15G0014700' => 'sbr', 'Sc19g0000590' => 'sci', 'Sc19g0001870' => 'sci', 'SGA_v2.0_scaffold1G00346' => 'sas', 'SGA_v2.0_scaffold1G00575' => 'sas', 'SGA_v2.0_scaffold1G00761' => 'sas', 'SGA_v2.0_scaffold232G43501' => 'sas', 'TAR625G1137' => 'tar', 'Thecc.03G222100' => 'tca', 'TPR.G12691' => 'tpr', 'TWI34G0727' => 'twi', 'TWI36G0117' => 'twi', 'VMungo1309G0868' => 'vmu' ), 'gf_id' => 'HOM05D001729', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001729' ), 'data_identifier' => 'HOM05D001729', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001729', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '375', 'num_species' => '42' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'Ah.07g204710' => 'amhyb', 'AUR62006001' => 'cqu', 'AUR62006002' => 'cqu', 'AUR62006003' => 'cqu', 'AUR62015641' => 'cqu', 'AUR62027174' => 'cqu', 'AUR62035623' => 'cqu', 'AUR62035624' => 'cqu', 'AUR62035625' => 'cqu', 'AUR62035626' => 'cqu', 'CAN.G1110.53' => 'can', 'CANSAT80G0415' => 'cansat', 'Ca_21364_v3' => 'car', 'COL.COLO4_30693' => 'col', 'COL.COLO4_30694' => 'col', 'COL.COLO4_30695' => 'col', 'COL.COLO4_30696' => 'col', 'COL.COLO4_34020' => 'col', 'DCAR_004585' => 'dca', 'Dinv04029' => 'din', 'Dinv34857' => 'din', 'Duzib147G0011' => 'dzi', 'Duzib170G0599' => 'dzi', 'Duzib192G1051' => 'dzi', 'FAN01G0708' => 'fan', 'FAN01G0742' => 'fan', 'FAN02G0048' => 'fan', 'FAN02G0583' => 'fan', 'FAN02G0688' => 'fan', 'FAN02G1588' => 'fan', 'FAN02G2194' => 'fan', 'FAN02G2750' => 'fan', 'FAN02G3094' => 'fan', 'FAN02G3887' => 'fan', 'FAN02G3911' => 'fan', 'FAN02G3994' => 'fan', 'FAN02G4432' => 'fan', 'FAN02G4556' => 'fan', 'FAN03G1977' => 'fan', 'FAN03G2781' => 'fan', 'FAN03G2850' => 'fan', 'FAN03G3155' => 'fan', 'FAN04G2487' => 'fan', 'FAN05G0208' => 'fan', 'FAN05G0656' => 'fan', 'FAN05G0696' => 'fan', 'FAN05G0810' => 'fan', 'FAN05G1447' => 'fan', 'FAN05G2640' => 'fan', 'FAN05G2911' => 'fan', 'FAN05G3901' => 'fan', 'FAN05G4859' => 'fan', 'FAN05G4861' => 'fan', 'FAN05G4988' => 'fan', 'FAN05G5187' => 'fan', 'FAN05G5452' => 'fan', 'FAN05G5500' => 'fan', 'FAN05G5688' => 'fan', 'FAN06G0177' => 'fan', 'FAN06G0675' => 'fan', 'FAN06G1290' => 'fan', 'FAN06G2191' => 'fan', 'FAN06G2405' => 'fan', 'FAN06G3231' => 'fan', 'FAN06G3932' => 'fan', 'FAN07G0163' => 'fan', 'FAN07G0471' => 'fan', 'FAN07G1354' => 'fan', 'FAN08G0338' => 'fan', 'FAN08G1373' => 'fan', 'FAN08G2539' => 'fan', 'FAN08G2728' => 'fan', 'FAN09G0608' => 'fan', 'FAN09G1136' => 'fan', 'FAN09G1958' => 'fan', 'FAN09G2508' => 'fan', 'FAN09G2597' => 'fan', 'FAN09G2658' => 'fan', 'FAN09G2757' => 'fan', 'FAN09G2983' => 'fan', 'FAN09G3130' => 'fan', 'FAN09G3565' => 'fan', 'FAN09G3613' => 'fan', 'FAN09G4011' => 'fan', 'FAN09G4239' => 'fan', 'FAN09G4277' => 'fan', 'FAN09G4720' => 'fan', 'FAN11G0139' => 'fan', 'FAN11G1727' => 'fan', 'FAN11G2672' => 'fan', 'FAN11G2795' => 'fan', 'FAN11G3238' => 'fan', 'FAN11G3734' => 'fan', 'FAN12G0631' => 'fan', 'FAN12G2239' => 'fan', 'FAN12G2308' => 'fan', 'FAN12G2569' => 'fan', 'FAN12G2623' => 'fan', 'FAN13G3182' => 'fan', 'FAN14G0053' => 'fan', 'FAN14G0370' => 'fan', 'FAN14G0382' => 'fan', 'FAN14G0421' => 'fan', 'FAN14G0866' => 'fan', 'FAN14G1187' => 'fan', 'FAN14G1727' => 'fan', 'FAN14G1791' => 'fan', 'FAN14G2361' => 'fan', 'FAN14G2668' => 'fan', 'FAN14G2770' => 'fan', 'FAN14G2874' => 'fan', 'FAN14G3193' => 'fan', 'FAN14G3624' => 'fan', 'FAN14G3676' => 'fan', 'FAN14G3807' => 'fan', 'FAN14G4082' => 'fan', 'FAN14G4342' => 'fan', 'FAN14G4985' => 'fan', 'FAN14G5126' => 'fan', 'FAN14G5781' => 'fan', 'FAN14G5808' => 'fan', 'FAN14G5949' => 'fan', 'FAN15G0828' => 'fan', 'FAN15G1054' => 'fan', 'FAN15G2023' => 'fan', 'FAN15G2506' => 'fan', 'FAN16G0128' => 'fan', 'FAN16G0249' => 'fan', 'FAN16G0429' => 'fan', 'FAN16G1493' => 'fan', 'FAN16G2210' => 'fan', 'FAN16G2506' => 'fan', 'FAN18G1542' => 'fan', 'FAN18G4057' => 'fan', 'FAN19G0745' => 'fan', 'FAN19G1216' => 'fan', 'FAN19G1733' => 'fan', 'FAN20G0258' => 'fan', 'FAN20G1095' => 'fan', 'FAN20G1557' => 'fan', 'FAN21G0302' => 'fan', 'FAN21G0519' => 'fan', 'FAN21G0970' => 'fan', 'FAN21G1159' => 'fan', 'FAN21G1312' => 'fan', 'FAN21G1440' => 'fan', 'FAN21G1715' => 'fan', 'FAN23G1584' => 'fan', 'FAN24G0045' => 'fan', 'FAN24G0053' => 'fan', 'FAN24G1500' => 'fan', 'FAN24G1817' => 'fan', 'FAN24G2147' => 'fan', 'FAN24G2236' => 'fan', 'FAN24G2446' => 'fan', 'FAN24G2684' => 'fan', 'FAN25G0187' => 'fan', 'FAN25G0505' => 'fan', 'FAN25G0589' => 'fan', 'FAN25G3663' => 'fan', 'FAN26G1025' => 'fan', 'FAN26G2860' => 'fan', 'FAN27G1329' => 'fan', 'FAN27G3392' => 'fan', 'FvH4_1g02011' => 'fve', 'FvH4_1g06511' => 'fve', 'FvH4_2g19900' => 'fve', 'FvH4_2g19920' => 'fve', 'FvH4_2g24261' => 'fve', 'FvH4_2g24270' => 'fve', 'FvH4_2g24631' => 'fve', 'FvH4_2g30622' => 'fve', 'FvH4_3g12920' => 'fve', 'FvH4_3g30171' => 'fve', 'FvH4_3g35490' => 'fve', 'FvH4_3g43682' => 'fve', 'FvH4_3g43730' => 'fve', 'FvH4_3g43732' => 'fve', 'FvH4_3g43751' => 'fve', 'FvH4_3g43752' => 'fve', 'FvH4_3g43770' => 'fve', 'FvH4_3g44471' => 'fve', 'FvH4_3g44510' => 'fve', 'FvH4_3g44582' => 'fve', 'FvH4_4g16921' => 'fve', 'FvH4_4g17121' => 'fve', 'FvH4_4g17782' => 'fve', 'FvH4_4g17783' => 'fve', 'FvH4_4g18120' => 'fve', 'FvH4_4g31310' => 'fve', 'FvH4_4g35052' => 'fve', 'FvH4_5g30862' => 'fve', 'FvH4_6g01541' => 'fve', 'FvH4_6g02021' => 'fve', 'FvH4_6g02041' => 'fve', 'FvH4_6g02071' => 'fve', 'FvH4_6g02171' => 'fve', 'FvH4_6g03181' => 'fve', 'FvH4_6g03182' => 'fve', 'FvH4_6g03221' => 'fve', 'FvH4_6g03380' => 'fve', 'FvH4_6g05201' => 'fve', 'FvH4_6g05203' => 'fve', 'FvH4_6g20231' => 'fve', 'FvH4_6g31981' => 'fve', 'FvH4_6g32061' => 'fve', 'FvH4_6g37041' => 'fve', 'FvH4_6g37932' => 'fve', 'FvH4_6g38731' => 'fve', 'FvH4_6g39370' => 'fve', 'FvH4_6g39371' => 'fve', 'FvH4_6g40891' => 'fve', 'FvH4_6g40892' => 'fve', 'FvH4_6g43143' => 'fve', 'FvH4_6g45251' => 'fve', 'FvH4_6g45260' => 'fve', 'FvH4_6g45291' => 'fve', 'FvH4_6g45890' => 'fve', 'FvH4_6g46240' => 'fve', 'FvH4_6g46241' => 'fve', 'FvH4_6g46242' => 'fve', 'FvH4_6g46260' => 'fve', 'FvH4_6g46280' => 'fve', 'FvH4_6g46380' => 'fve', 'FvH4_7g12841' => 'fve', 'FvH4_7g31431' => 'fve', 'Glyma.09G075900' => 'gma', 'Gohir.A09G096401' => 'ghi', 'Gohir.D09G096101' => 'ghi', 'Gorai.006G112800' => 'gra', 'HanXRQChr04g0121411' => 'han', 'Hund15878' => 'sun', 'Lj2A1107G68' => 'lonja', 'Lj2A630G63' => 'lonja', 'Lj2A946T25' => 'lonja', 'Lj2C714T1' => 'lonja', 'Lj2C966T3' => 'lonja', 'Lj2C966T4' => 'lonja', 'Lj4g0002979' => 'lja', 'Lsat_1_v5_gn_5_30901' => 'lsa', 'Lsat_1_v5_gn_5_31100' => 'lsa', 'Lsat_1_v5_gn_5_38600' => 'lsa', 'Lsat_1_v5_gn_6_92061' => 'lsa', 'Manes.05G071301' => 'mes', 'MD02G1008700' => 'mdo', 'MD02G1008900' => 'mdo', 'MD03G1256400' => 'mdo', 'MD04G1180900' => 'mdo', 'MD04G1181000' => 'mdo', 'MD04G1181200' => 'mdo', 'MD05G1244200' => 'mdo', 'MD05G1324200' => 'mdo', 'MD09G1201600' => 'mdo', 'MD10G1000600' => 'mdo', 'MD14G1026900' => 'mdo', 'MD14G1187900' => 'mdo', 'MD15G1017800' => 'mdo', 'MD15G1018100' => 'mdo', 'Medtr4g124160' => 'mtr', 'Migut.L01260' => 'egut', 'Nitab4.5_0000008g0440' => 'nta', 'Nitab4.5_0000207g0170' => 'nta', 'Nitab4.5_0007671g0030' => 'nta', 'Nitab4.5_0010853g0020' => 'nta', 'Oeu057656.1' => 'oeu', 'PGSC0003DMG400005638' => 'stu', 'PGSC0003DMG400005639' => 'stu', 'Phvul.009G222800' => 'pvu', 'Potri.009G132400' => 'ptr', 'Potri.009G163001' => 'ptr', 'Potri.011G000700' => 'ptr', 'Potri.011G004800' => 'ptr', 'Prupe.1G509300' => 'ppe', 'Prupe.1G509700' => 'ppe', 'Prupe.1G510400' => 'ppe', 'Prupe.1G510700' => 'ppe', 'Prupe.1G512600' => 'ppe', 'Prupe.2G073200' => 'ppe', 'Prupe.3G059500' => 'ppe', 'Prupe.3G059600' => 'ppe', 'Prupe.3G246100' => 'ppe', 'Prupe.3G265100' => 'ppe', 'Prupe.4G034700' => 'ppe', 'Prupe.4G052100' => 'ppe', 'Prupe.4G053600' => 'ppe', 'Prupe.5G068800' => 'ppe', 'Prupe.5G070600' => 'ppe', 'Prupe.6G075400' => 'ppe', 'Prupe.6G075500' => 'ppe', 'Prupe.6G076400' => 'ppe', 'Prupe.8G110700' => 'ppe', 'Psat4g020960' => 'psa', 'PSO135G0788' => 'pso', 'PSO210G6463' => 'pso', 'PSO384G0370' => 'pso', 'PSO386G0056' => 'pso', 'QL01p006048' => 'qlo', 'QL02p054283' => 'qlo', 'QL05p008000' => 'qlo', 'QL05p008212' => 'qlo', 'QL05p008950' => 'qlo', 'QL05p009042' => 'qlo', 'QL05p009518' => 'qlo', 'QL05p012589' => 'qlo', 'QL05p012608' => 'qlo', 'QL05p012650' => 'qlo', 'QL05p012667' => 'qlo', 'QL05p014501' => 'qlo', 'QL05p052800' => 'qlo', 'QL05p065010' => 'qlo', 'QL05p074156' => 'qlo', 'QL05p074160' => 'qlo', 'QL05p074174' => 'qlo', 'QL05p074178' => 'qlo', 'QL05p074214' => 'qlo', 'QL06p001050' => 'qlo', 'QL06p001056' => 'qlo', 'QL06p006093' => 'qlo', 'QL06p006111' => 'qlo', 'QL07p019784' => 'qlo', 'QL07p019801' => 'qlo', 'QL07p036110' => 'qlo', 'QL07p036134' => 'qlo', 'QL07p036147' => 'qlo', 'QL07p036156' => 'qlo', 'QL07p036300' => 'qlo', 'QL07p036320' => 'qlo', 'QL08p014547' => 'qlo', 'QL08p014551' => 'qlo', 'QL08p043319' => 'qlo', 'QL08p043324' => 'qlo', 'QL11p009094' => 'qlo', 'RcHm_v2.0_Chr1g0380481' => 'rch', 'RcHm_v2.0_Chr2g0089331' => 'rch', 'RcHm_v2.0_Chr2g0123691' => 'rch', 'RcHm_v2.0_Chr2g0151111' => 'rch', 'RcHm_v2.0_Chr2g0163011' => 'rch', 'RcHm_v2.0_Chr2g0163051' => 'rch', 'RcHm_v2.0_Chr2g0164671' => 'rch', 'RcHm_v2.0_Chr2g0164681' => 'rch', 'RcHm_v2.0_Chr2g0164721' => 'rch', 'RcHm_v2.0_Chr3g0449911' => 'rch', 'RcHm_v2.0_Chr3g0450211' => 'rch', 'RcHm_v2.0_Chr3g0457271' => 'rch', 'RcHm_v2.0_Chr5g0018111' => 'rch', 'RcHm_v2.0_Chr5g0021011' => 'rch', 'RcHm_v2.0_Chr5g0081171' => 'rch', 'RcHm_v2.0_Chr5g0081211' => 'rch', 'RcHm_v2.0_Chr6g0275871' => 'rch', 'RcHm_v2.0_Chr6g0276071' => 'rch', 'RcHm_v2.0_Chr6g0285591' => 'rch', 'RcHm_v2.0_Chr6g0291931' => 'rch', 'RcHm_v2.0_Chr6g0292091' => 'rch', 'RcHm_v2.0_Chr6g0292271' => 'rch', 'RcHm_v2.0_Chr7g0221261' => 'rch', 'Rhsim08G0219900' => 'rsi', 'Rhsim08G0220200' => 'rsi', 'Rhsim08G0237800' => 'rsi', 'Rhsim08G0238800' => 'rsi', 'Sabra09G0102700' => 'sbr', 'Sabra09G0127200' => 'sbr', 'Sabra11G0003700' => 'sbr', 'Sabra15G0014700' => 'sbr', 'Sc19g0000590' => 'sci', 'Sc19g0001870' => 'sci', 'SGA_v2.0_scaffold1G00346' => 'sas', 'SGA_v2.0_scaffold1G00575' => 'sas', 'SGA_v2.0_scaffold1G00761' => 'sas', 'SGA_v2.0_scaffold232G43501' => 'sas', 'TAR625G1137' => 'tar', 'Thecc.03G222100' => 'tca', 'TPR.G12691' => 'tpr', 'TWI34G0727' => 'twi', 'TWI36G0117' => 'twi', 'VMungo1309G0868' => 'vmu' ) $gf_id = 'HOM05D001729' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001729' ) $data_identifier = 'HOM05D001729' $data_type = 'gf_id' $species_gene_counts = array( 'amhyb' => (int) 1, 'cqu' => (int) 9, 'can' => (int) 1, 'cansat' => (int) 1, 'car' => (int) 1, 'col' => (int) 5, 'dca' => (int) 1, 'din' => (int) 2, 'dzi' => (int) 3, 'fan' => (int) 140, 'fve' => (int) 62, 'gma' => (int) 1, 'ghi' => (int) 2, 'gra' => (int) 1, 'han' => (int) 1, 'sun' => (int) 1, 'lonja' => (int) 6, 'lja' => (int) 1, 'lsa' => (int) 4, 'mes' => (int) 1, 'mdo' => (int) 14, 'mtr' => (int) 1, 'egut' => (int) 1, 'nta' => (int) 4, 'oeu' => (int) 1, 'stu' => (int) 2, 'pvu' => (int) 1, 'ptr' => (int) 4, 'ppe' => (int) 19, 'psa' => (int) 1, 'pso' => (int) 4, 'qlo' => (int) 36, 'rch' => (int) 23, 'rsi' => (int) 4, 'sbr' => (int) 4, 'sci' => (int) 2, 'sas' => (int) 4, 'tar' => (int) 1, 'tca' => (int) 1, 'tpr' => (int) 1, 'twi' => (int) 2, 'vmu' => (int) 1 ) $gf_gene_species = 'vmu' $gf_gene_id = 'VMungo1309G0868' $species_info = array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ) $local_species = 'rch' $disabled = '' $selected = '' $num_hits = (int) 1include - APP/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp, line 33 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933 View::_renderElement() - CORE/Cake/View/View.php, line 1224 View::element() - CORE/Cake/View/View.php, line 418 include - APP/View/Elements/analysis/phylogenetics_module/gf_data_settings.ctp, line 37 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933 View::_renderElement() - CORE/Cake/View/View.php, line 1224 View::element() - CORE/Cake/View/View.php, line 418 include - APP/View/Elements/analysis/phylogenetics_module/parameter_selection.ctp, line 64 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933 View::_renderElement() - CORE/Cake/View/View.php, line 1224 View::element() - CORE/Cake/View/View.php, line 418 include - APP/View/Analysis/custom_tree_creation.ctp, line 27 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933
$viewFile = '/www/bioinformatics01_ro/plaza/_dev_instances/feedback/app/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp' $dataForView = array( 'sidebar_info' => array( 'gf_id' => 'HOM05D001729', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '375', 'num_species' => '42' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'Ah.07g204710' => 'amhyb', 'AUR62006001' => 'cqu', 'AUR62006002' => 'cqu', 'AUR62006003' => 'cqu', 'AUR62015641' => 'cqu', 'AUR62027174' => 'cqu', 'AUR62035623' => 'cqu', 'AUR62035624' => 'cqu', 'AUR62035625' => 'cqu', 'AUR62035626' => 'cqu', 'CAN.G1110.53' => 'can', 'CANSAT80G0415' => 'cansat', 'Ca_21364_v3' => 'car', 'COL.COLO4_30693' => 'col', 'COL.COLO4_30694' => 'col', 'COL.COLO4_30695' => 'col', 'COL.COLO4_30696' => 'col', 'COL.COLO4_34020' => 'col', 'DCAR_004585' => 'dca', 'Dinv04029' => 'din', 'Dinv34857' => 'din', 'Duzib147G0011' => 'dzi', 'Duzib170G0599' => 'dzi', 'Duzib192G1051' => 'dzi', 'FAN01G0708' => 'fan', 'FAN01G0742' => 'fan', 'FAN02G0048' => 'fan', 'FAN02G0583' => 'fan', 'FAN02G0688' => 'fan', 'FAN02G1588' => 'fan', 'FAN02G2194' => 'fan', 'FAN02G2750' => 'fan', 'FAN02G3094' => 'fan', 'FAN02G3887' => 'fan', 'FAN02G3911' => 'fan', 'FAN02G3994' => 'fan', 'FAN02G4432' => 'fan', 'FAN02G4556' => 'fan', 'FAN03G1977' => 'fan', 'FAN03G2781' => 'fan', 'FAN03G2850' => 'fan', 'FAN03G3155' => 'fan', 'FAN04G2487' => 'fan', 'FAN05G0208' => 'fan', 'FAN05G0656' => 'fan', 'FAN05G0696' => 'fan', 'FAN05G0810' => 'fan', 'FAN05G1447' => 'fan', 'FAN05G2640' => 'fan', 'FAN05G2911' => 'fan', 'FAN05G3901' => 'fan', 'FAN05G4859' => 'fan', 'FAN05G4861' => 'fan', 'FAN05G4988' => 'fan', 'FAN05G5187' => 'fan', 'FAN05G5452' => 'fan', 'FAN05G5500' => 'fan', 'FAN05G5688' => 'fan', 'FAN06G0177' => 'fan', 'FAN06G0675' => 'fan', 'FAN06G1290' => 'fan', 'FAN06G2191' => 'fan', 'FAN06G2405' => 'fan', 'FAN06G3231' => 'fan', 'FAN06G3932' => 'fan', 'FAN07G0163' => 'fan', 'FAN07G0471' => 'fan', 'FAN07G1354' => 'fan', 'FAN08G0338' => 'fan', 'FAN08G1373' => 'fan', 'FAN08G2539' => 'fan', 'FAN08G2728' => 'fan', 'FAN09G0608' => 'fan', 'FAN09G1136' => 'fan', 'FAN09G1958' => 'fan', 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'FAN14G5126' => 'fan', 'FAN14G5781' => 'fan', 'FAN14G5808' => 'fan', 'FAN14G5949' => 'fan', 'FAN15G0828' => 'fan', 'FAN15G1054' => 'fan', 'FAN15G2023' => 'fan', 'FAN15G2506' => 'fan', 'FAN16G0128' => 'fan', 'FAN16G0249' => 'fan', 'FAN16G0429' => 'fan', 'FAN16G1493' => 'fan', 'FAN16G2210' => 'fan', 'FAN16G2506' => 'fan', 'FAN18G1542' => 'fan', 'FAN18G4057' => 'fan', 'FAN19G0745' => 'fan', 'FAN19G1216' => 'fan', 'FAN19G1733' => 'fan', 'FAN20G0258' => 'fan', 'FAN20G1095' => 'fan', 'FAN20G1557' => 'fan', 'FAN21G0302' => 'fan', 'FAN21G0519' => 'fan', 'FAN21G0970' => 'fan', 'FAN21G1159' => 'fan', 'FAN21G1312' => 'fan', 'FAN21G1440' => 'fan', 'FAN21G1715' => 'fan', 'FAN23G1584' => 'fan', 'FAN24G0045' => 'fan', 'FAN24G0053' => 'fan', 'FAN24G1500' => 'fan', 'FAN24G1817' => 'fan', 'FAN24G2147' => 'fan', 'FAN24G2236' => 'fan', 'FAN24G2446' => 'fan', 'FAN24G2684' => 'fan', 'FAN25G0187' => 'fan', 'FAN25G0505' => 'fan', 'FAN25G0589' => 'fan', 'FAN25G3663' => 'fan', 'FAN26G1025' => 'fan', 'FAN26G2860' => 'fan', 'FAN27G1329' => 'fan', 'FAN27G3392' => 'fan', 'FvH4_1g02011' => 'fve', 'FvH4_1g06511' => 'fve', 'FvH4_2g19900' => 'fve', 'FvH4_2g19920' => 'fve', 'FvH4_2g24261' => 'fve', 'FvH4_2g24270' => 'fve', 'FvH4_2g24631' => 'fve', 'FvH4_2g30622' => 'fve', 'FvH4_3g12920' => 'fve', 'FvH4_3g30171' => 'fve', 'FvH4_3g35490' => 'fve', 'FvH4_3g43682' => 'fve', 'FvH4_3g43730' => 'fve', 'FvH4_3g43732' => 'fve', 'FvH4_3g43751' => 'fve', 'FvH4_3g43752' => 'fve', 'FvH4_3g43770' => 'fve', 'FvH4_3g44471' => 'fve', 'FvH4_3g44510' => 'fve', 'FvH4_3g44582' => 'fve', 'FvH4_4g16921' => 'fve', 'FvH4_4g17121' => 'fve', 'FvH4_4g17782' => 'fve', 'FvH4_4g17783' => 'fve', 'FvH4_4g18120' => 'fve', 'FvH4_4g31310' => 'fve', 'FvH4_4g35052' => 'fve', 'FvH4_5g30862' => 'fve', 'FvH4_6g01541' => 'fve', 'FvH4_6g02021' => 'fve', 'FvH4_6g02041' => 'fve', 'FvH4_6g02071' => 'fve', 'FvH4_6g02171' => 'fve', 'FvH4_6g03181' => 'fve', 'FvH4_6g03182' => 'fve', 'FvH4_6g03221' => 'fve', 'FvH4_6g03380' => 'fve', 'FvH4_6g05201' => 'fve', 'FvH4_6g05203' => 'fve', 'FvH4_6g20231' => 'fve', 'FvH4_6g31981' => 'fve', 'FvH4_6g32061' => 'fve', 'FvH4_6g37041' => 'fve', 'FvH4_6g37932' => 'fve', 'FvH4_6g38731' => 'fve', 'FvH4_6g39370' => 'fve', 'FvH4_6g39371' => 'fve', 'FvH4_6g40891' => 'fve', 'FvH4_6g40892' => 'fve', 'FvH4_6g43143' => 'fve', 'FvH4_6g45251' => 'fve', 'FvH4_6g45260' => 'fve', 'FvH4_6g45291' => 'fve', 'FvH4_6g45890' => 'fve', 'FvH4_6g46240' => 'fve', 'FvH4_6g46241' => 'fve', 'FvH4_6g46242' => 'fve', 'FvH4_6g46260' => 'fve', 'FvH4_6g46280' => 'fve', 'FvH4_6g46380' => 'fve', 'FvH4_7g12841' => 'fve', 'FvH4_7g31431' => 'fve', 'Glyma.09G075900' => 'gma', 'Gohir.A09G096401' => 'ghi', 'Gohir.D09G096101' => 'ghi', 'Gorai.006G112800' => 'gra', 'HanXRQChr04g0121411' => 'han', 'Hund15878' => 'sun', 'Lj2A1107G68' => 'lonja', 'Lj2A630G63' => 'lonja', 'Lj2A946T25' => 'lonja', 'Lj2C714T1' => 'lonja', 'Lj2C966T3' => 'lonja', 'Lj2C966T4' => 'lonja', 'Lj4g0002979' => 'lja', 'Lsat_1_v5_gn_5_30901' => 'lsa', 'Lsat_1_v5_gn_5_31100' => 'lsa', 'Lsat_1_v5_gn_5_38600' => 'lsa', 'Lsat_1_v5_gn_6_92061' => 'lsa', 'Manes.05G071301' => 'mes', 'MD02G1008700' => 'mdo', 'MD02G1008900' => 'mdo', 'MD03G1256400' => 'mdo', 'MD04G1180900' => 'mdo', 'MD04G1181000' => 'mdo', 'MD04G1181200' => 'mdo', 'MD05G1244200' => 'mdo', 'MD05G1324200' => 'mdo', 'MD09G1201600' => 'mdo', 'MD10G1000600' => 'mdo', 'MD14G1026900' => 'mdo', 'MD14G1187900' => 'mdo', 'MD15G1017800' => 'mdo', 'MD15G1018100' => 'mdo', 'Medtr4g124160' => 'mtr', 'Migut.L01260' => 'egut', 'Nitab4.5_0000008g0440' => 'nta', 'Nitab4.5_0000207g0170' => 'nta', 'Nitab4.5_0007671g0030' => 'nta', 'Nitab4.5_0010853g0020' => 'nta', 'Oeu057656.1' => 'oeu', 'PGSC0003DMG400005638' => 'stu', 'PGSC0003DMG400005639' => 'stu', 'Phvul.009G222800' => 'pvu', 'Potri.009G132400' => 'ptr', 'Potri.009G163001' => 'ptr', 'Potri.011G000700' => 'ptr', 'Potri.011G004800' => 'ptr', 'Prupe.1G509300' => 'ppe', 'Prupe.1G509700' => 'ppe', 'Prupe.1G510400' => 'ppe', 'Prupe.1G510700' => 'ppe', 'Prupe.1G512600' => 'ppe', 'Prupe.2G073200' => 'ppe', 'Prupe.3G059500' => 'ppe', 'Prupe.3G059600' => 'ppe', 'Prupe.3G246100' => 'ppe', 'Prupe.3G265100' => 'ppe', 'Prupe.4G034700' => 'ppe', 'Prupe.4G052100' => 'ppe', 'Prupe.4G053600' => 'ppe', 'Prupe.5G068800' => 'ppe', 'Prupe.5G070600' => 'ppe', 'Prupe.6G075400' => 'ppe', 'Prupe.6G075500' => 'ppe', 'Prupe.6G076400' => 'ppe', 'Prupe.8G110700' => 'ppe', 'Psat4g020960' => 'psa', 'PSO135G0788' => 'pso', 'PSO210G6463' => 'pso', 'PSO384G0370' => 'pso', 'PSO386G0056' => 'pso', 'QL01p006048' => 'qlo', 'QL02p054283' => 'qlo', 'QL05p008000' => 'qlo', 'QL05p008212' => 'qlo', 'QL05p008950' => 'qlo', 'QL05p009042' => 'qlo', 'QL05p009518' => 'qlo', 'QL05p012589' => 'qlo', 'QL05p012608' => 'qlo', 'QL05p012650' => 'qlo', 'QL05p012667' => 'qlo', 'QL05p014501' => 'qlo', 'QL05p052800' => 'qlo', 'QL05p065010' => 'qlo', 'QL05p074156' => 'qlo', 'QL05p074160' => 'qlo', 'QL05p074174' => 'qlo', 'QL05p074178' => 'qlo', 'QL05p074214' => 'qlo', 'QL06p001050' => 'qlo', 'QL06p001056' => 'qlo', 'QL06p006093' => 'qlo', 'QL06p006111' => 'qlo', 'QL07p019784' => 'qlo', 'QL07p019801' => 'qlo', 'QL07p036110' => 'qlo', 'QL07p036134' => 'qlo', 'QL07p036147' => 'qlo', 'QL07p036156' => 'qlo', 'QL07p036300' => 'qlo', 'QL07p036320' => 'qlo', 'QL08p014547' => 'qlo', 'QL08p014551' => 'qlo', 'QL08p043319' => 'qlo', 'QL08p043324' => 'qlo', 'QL11p009094' => 'qlo', 'RcHm_v2.0_Chr1g0380481' => 'rch', 'RcHm_v2.0_Chr2g0089331' => 'rch', 'RcHm_v2.0_Chr2g0123691' => 'rch', 'RcHm_v2.0_Chr2g0151111' => 'rch', 'RcHm_v2.0_Chr2g0163011' => 'rch', 'RcHm_v2.0_Chr2g0163051' => 'rch', 'RcHm_v2.0_Chr2g0164671' => 'rch', 'RcHm_v2.0_Chr2g0164681' => 'rch', 'RcHm_v2.0_Chr2g0164721' => 'rch', 'RcHm_v2.0_Chr3g0449911' => 'rch', 'RcHm_v2.0_Chr3g0450211' => 'rch', 'RcHm_v2.0_Chr3g0457271' => 'rch', 'RcHm_v2.0_Chr5g0018111' => 'rch', 'RcHm_v2.0_Chr5g0021011' => 'rch', 'RcHm_v2.0_Chr5g0081171' => 'rch', 'RcHm_v2.0_Chr5g0081211' => 'rch', 'RcHm_v2.0_Chr6g0275871' => 'rch', 'RcHm_v2.0_Chr6g0276071' => 'rch', 'RcHm_v2.0_Chr6g0285591' => 'rch', 'RcHm_v2.0_Chr6g0291931' => 'rch', 'RcHm_v2.0_Chr6g0292091' => 'rch', 'RcHm_v2.0_Chr6g0292271' => 'rch', 'RcHm_v2.0_Chr7g0221261' => 'rch', 'Rhsim08G0219900' => 'rsi', 'Rhsim08G0220200' => 'rsi', 'Rhsim08G0237800' => 'rsi', 'Rhsim08G0238800' => 'rsi', 'Sabra09G0102700' => 'sbr', 'Sabra09G0127200' => 'sbr', 'Sabra11G0003700' => 'sbr', 'Sabra15G0014700' => 'sbr', 'Sc19g0000590' => 'sci', 'Sc19g0001870' => 'sci', 'SGA_v2.0_scaffold1G00346' => 'sas', 'SGA_v2.0_scaffold1G00575' => 'sas', 'SGA_v2.0_scaffold1G00761' => 'sas', 'SGA_v2.0_scaffold232G43501' => 'sas', 'TAR625G1137' => 'tar', 'Thecc.03G222100' => 'tca', 'TPR.G12691' => 'tpr', 'TWI34G0727' => 'twi', 'TWI36G0117' => 'twi', 'VMungo1309G0868' => 'vmu' ), 'gf_id' => 'HOM05D001729', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001729' ), 'data_identifier' => 'HOM05D001729', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001729', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '375', 'num_species' => '42' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'Ah.07g204710' => 'amhyb', 'AUR62006001' => 'cqu', 'AUR62006002' => 'cqu', 'AUR62006003' => 'cqu', 'AUR62015641' => 'cqu', 'AUR62027174' => 'cqu', 'AUR62035623' => 'cqu', 'AUR62035624' => 'cqu', 'AUR62035625' => 'cqu', 'AUR62035626' => 'cqu', 'CAN.G1110.53' => 'can', 'CANSAT80G0415' => 'cansat', 'Ca_21364_v3' => 'car', 'COL.COLO4_30693' => 'col', 'COL.COLO4_30694' => 'col', 'COL.COLO4_30695' => 'col', 'COL.COLO4_30696' => 'col', 'COL.COLO4_34020' => 'col', 'DCAR_004585' => 'dca', 'Dinv04029' => 'din', 'Dinv34857' => 'din', 'Duzib147G0011' => 'dzi', 'Duzib170G0599' => 'dzi', 'Duzib192G1051' => 'dzi', 'FAN01G0708' => 'fan', 'FAN01G0742' => 'fan', 'FAN02G0048' => 'fan', 'FAN02G0583' => 'fan', 'FAN02G0688' => 'fan', 'FAN02G1588' => 'fan', 'FAN02G2194' => 'fan', 'FAN02G2750' => 'fan', 'FAN02G3094' => 'fan', 'FAN02G3887' => 'fan', 'FAN02G3911' => 'fan', 'FAN02G3994' => 'fan', 'FAN02G4432' => 'fan', 'FAN02G4556' => 'fan', 'FAN03G1977' => 'fan', 'FAN03G2781' => 'fan', 'FAN03G2850' => 'fan', 'FAN03G3155' => 'fan', 'FAN04G2487' => 'fan', 'FAN05G0208' => 'fan', 'FAN05G0656' => 'fan', 'FAN05G0696' => 'fan', 'FAN05G0810' => 'fan', 'FAN05G1447' => 'fan', 'FAN05G2640' => 'fan', 'FAN05G2911' => 'fan', 'FAN05G3901' => 'fan', 'FAN05G4859' => 'fan', 'FAN05G4861' => 'fan', 'FAN05G4988' => 'fan', 'FAN05G5187' => 'fan', 'FAN05G5452' => 'fan', 'FAN05G5500' => 'fan', 'FAN05G5688' => 'fan', 'FAN06G0177' => 'fan', 'FAN06G0675' => 'fan', 'FAN06G1290' => 'fan', 'FAN06G2191' => 'fan', 'FAN06G2405' => 'fan', 'FAN06G3231' => 'fan', 'FAN06G3932' => 'fan', 'FAN07G0163' => 'fan', 'FAN07G0471' => 'fan', 'FAN07G1354' => 'fan', 'FAN08G0338' => 'fan', 'FAN08G1373' => 'fan', 'FAN08G2539' => 'fan', 'FAN08G2728' => 'fan', 'FAN09G0608' => 'fan', 'FAN09G1136' => 'fan', 'FAN09G1958' => 'fan', 'FAN09G2508' => 'fan', 'FAN09G2597' => 'fan', 'FAN09G2658' => 'fan', 'FAN09G2757' => 'fan', 'FAN09G2983' => 'fan', 'FAN09G3130' => 'fan', 'FAN09G3565' => 'fan', 'FAN09G3613' => 'fan', 'FAN09G4011' => 'fan', 'FAN09G4239' => 'fan', 'FAN09G4277' => 'fan', 'FAN09G4720' => 'fan', 'FAN11G0139' => 'fan', 'FAN11G1727' => 'fan', 'FAN11G2672' => 'fan', 'FAN11G2795' => 'fan', 'FAN11G3238' => 'fan', 'FAN11G3734' => 'fan', 'FAN12G0631' => 'fan', 'FAN12G2239' => 'fan', 'FAN12G2308' => 'fan', 'FAN12G2569' => 'fan', 'FAN12G2623' => 'fan', 'FAN13G3182' => 'fan', 'FAN14G0053' => 'fan', 'FAN14G0370' => 'fan', 'FAN14G0382' => 'fan', 'FAN14G0421' => 'fan', 'FAN14G0866' => 'fan', 'FAN14G1187' => 'fan', 'FAN14G1727' => 'fan', 'FAN14G1791' => 'fan', 'FAN14G2361' => 'fan', 'FAN14G2668' => 'fan', 'FAN14G2770' => 'fan', 'FAN14G2874' => 'fan', 'FAN14G3193' => 'fan', 'FAN14G3624' => 'fan', 'FAN14G3676' => 'fan', 'FAN14G3807' => 'fan', 'FAN14G4082' => 'fan', 'FAN14G4342' => 'fan', 'FAN14G4985' => 'fan', 'FAN14G5126' => 'fan', 'FAN14G5781' => 'fan', 'FAN14G5808' => 'fan', 'FAN14G5949' => 'fan', 'FAN15G0828' => 'fan', 'FAN15G1054' => 'fan', 'FAN15G2023' => 'fan', 'FAN15G2506' => 'fan', 'FAN16G0128' => 'fan', 'FAN16G0249' => 'fan', 'FAN16G0429' => 'fan', 'FAN16G1493' => 'fan', 'FAN16G2210' => 'fan', 'FAN16G2506' => 'fan', 'FAN18G1542' => 'fan', 'FAN18G4057' => 'fan', 'FAN19G0745' => 'fan', 'FAN19G1216' => 'fan', 'FAN19G1733' => 'fan', 'FAN20G0258' => 'fan', 'FAN20G1095' => 'fan', 'FAN20G1557' => 'fan', 'FAN21G0302' => 'fan', 'FAN21G0519' => 'fan', 'FAN21G0970' => 'fan', 'FAN21G1159' => 'fan', 'FAN21G1312' => 'fan', 'FAN21G1440' => 'fan', 'FAN21G1715' => 'fan', 'FAN23G1584' => 'fan', 'FAN24G0045' => 'fan', 'FAN24G0053' => 'fan', 'FAN24G1500' => 'fan', 'FAN24G1817' => 'fan', 'FAN24G2147' => 'fan', 'FAN24G2236' => 'fan', 'FAN24G2446' => 'fan', 'FAN24G2684' => 'fan', 'FAN25G0187' => 'fan', 'FAN25G0505' => 'fan', 'FAN25G0589' => 'fan', 'FAN25G3663' => 'fan', 'FAN26G1025' => 'fan', 'FAN26G2860' => 'fan', 'FAN27G1329' => 'fan', 'FAN27G3392' => 'fan', 'FvH4_1g02011' => 'fve', 'FvH4_1g06511' => 'fve', 'FvH4_2g19900' => 'fve', 'FvH4_2g19920' => 'fve', 'FvH4_2g24261' => 'fve', 'FvH4_2g24270' => 'fve', 'FvH4_2g24631' => 'fve', 'FvH4_2g30622' => 'fve', 'FvH4_3g12920' => 'fve', 'FvH4_3g30171' => 'fve', 'FvH4_3g35490' => 'fve', 'FvH4_3g43682' => 'fve', 'FvH4_3g43730' => 'fve', 'FvH4_3g43732' => 'fve', 'FvH4_3g43751' => 'fve', 'FvH4_3g43752' => 'fve', 'FvH4_3g43770' => 'fve', 'FvH4_3g44471' => 'fve', 'FvH4_3g44510' => 'fve', 'FvH4_3g44582' => 'fve', 'FvH4_4g16921' => 'fve', 'FvH4_4g17121' => 'fve', 'FvH4_4g17782' => 'fve', 'FvH4_4g17783' => 'fve', 'FvH4_4g18120' => 'fve', 'FvH4_4g31310' => 'fve', 'FvH4_4g35052' => 'fve', 'FvH4_5g30862' => 'fve', 'FvH4_6g01541' => 'fve', 'FvH4_6g02021' => 'fve', 'FvH4_6g02041' => 'fve', 'FvH4_6g02071' => 'fve', 'FvH4_6g02171' => 'fve', 'FvH4_6g03181' => 'fve', 'FvH4_6g03182' => 'fve', 'FvH4_6g03221' => 'fve', 'FvH4_6g03380' => 'fve', 'FvH4_6g05201' => 'fve', 'FvH4_6g05203' => 'fve', 'FvH4_6g20231' => 'fve', 'FvH4_6g31981' => 'fve', 'FvH4_6g32061' => 'fve', 'FvH4_6g37041' => 'fve', 'FvH4_6g37932' => 'fve', 'FvH4_6g38731' => 'fve', 'FvH4_6g39370' => 'fve', 'FvH4_6g39371' => 'fve', 'FvH4_6g40891' => 'fve', 'FvH4_6g40892' => 'fve', 'FvH4_6g43143' => 'fve', 'FvH4_6g45251' => 'fve', 'FvH4_6g45260' => 'fve', 'FvH4_6g45291' => 'fve', 'FvH4_6g45890' => 'fve', 'FvH4_6g46240' => 'fve', 'FvH4_6g46241' => 'fve', 'FvH4_6g46242' => 'fve', 'FvH4_6g46260' => 'fve', 'FvH4_6g46280' => 'fve', 'FvH4_6g46380' => 'fve', 'FvH4_7g12841' => 'fve', 'FvH4_7g31431' => 'fve', 'Glyma.09G075900' => 'gma', 'Gohir.A09G096401' => 'ghi', 'Gohir.D09G096101' => 'ghi', 'Gorai.006G112800' => 'gra', 'HanXRQChr04g0121411' => 'han', 'Hund15878' => 'sun', 'Lj2A1107G68' => 'lonja', 'Lj2A630G63' => 'lonja', 'Lj2A946T25' => 'lonja', 'Lj2C714T1' => 'lonja', 'Lj2C966T3' => 'lonja', 'Lj2C966T4' => 'lonja', 'Lj4g0002979' => 'lja', 'Lsat_1_v5_gn_5_30901' => 'lsa', 'Lsat_1_v5_gn_5_31100' => 'lsa', 'Lsat_1_v5_gn_5_38600' => 'lsa', 'Lsat_1_v5_gn_6_92061' => 'lsa', 'Manes.05G071301' => 'mes', 'MD02G1008700' => 'mdo', 'MD02G1008900' => 'mdo', 'MD03G1256400' => 'mdo', 'MD04G1180900' => 'mdo', 'MD04G1181000' => 'mdo', 'MD04G1181200' => 'mdo', 'MD05G1244200' => 'mdo', 'MD05G1324200' => 'mdo', 'MD09G1201600' => 'mdo', 'MD10G1000600' => 'mdo', 'MD14G1026900' => 'mdo', 'MD14G1187900' => 'mdo', 'MD15G1017800' => 'mdo', 'MD15G1018100' => 'mdo', 'Medtr4g124160' => 'mtr', 'Migut.L01260' => 'egut', 'Nitab4.5_0000008g0440' => 'nta', 'Nitab4.5_0000207g0170' => 'nta', 'Nitab4.5_0007671g0030' => 'nta', 'Nitab4.5_0010853g0020' => 'nta', 'Oeu057656.1' => 'oeu', 'PGSC0003DMG400005638' => 'stu', 'PGSC0003DMG400005639' => 'stu', 'Phvul.009G222800' => 'pvu', 'Potri.009G132400' => 'ptr', 'Potri.009G163001' => 'ptr', 'Potri.011G000700' => 'ptr', 'Potri.011G004800' => 'ptr', 'Prupe.1G509300' => 'ppe', 'Prupe.1G509700' => 'ppe', 'Prupe.1G510400' => 'ppe', 'Prupe.1G510700' => 'ppe', 'Prupe.1G512600' => 'ppe', 'Prupe.2G073200' => 'ppe', 'Prupe.3G059500' => 'ppe', 'Prupe.3G059600' => 'ppe', 'Prupe.3G246100' => 'ppe', 'Prupe.3G265100' => 'ppe', 'Prupe.4G034700' => 'ppe', 'Prupe.4G052100' => 'ppe', 'Prupe.4G053600' => 'ppe', 'Prupe.5G068800' => 'ppe', 'Prupe.5G070600' => 'ppe', 'Prupe.6G075400' => 'ppe', 'Prupe.6G075500' => 'ppe', 'Prupe.6G076400' => 'ppe', 'Prupe.8G110700' => 'ppe', 'Psat4g020960' => 'psa', 'PSO135G0788' => 'pso', 'PSO210G6463' => 'pso', 'PSO384G0370' => 'pso', 'PSO386G0056' => 'pso', 'QL01p006048' => 'qlo', 'QL02p054283' => 'qlo', 'QL05p008000' => 'qlo', 'QL05p008212' => 'qlo', 'QL05p008950' => 'qlo', 'QL05p009042' => 'qlo', 'QL05p009518' => 'qlo', 'QL05p012589' => 'qlo', 'QL05p012608' => 'qlo', 'QL05p012650' => 'qlo', 'QL05p012667' => 'qlo', 'QL05p014501' => 'qlo', 'QL05p052800' => 'qlo', 'QL05p065010' => 'qlo', 'QL05p074156' => 'qlo', 'QL05p074160' => 'qlo', 'QL05p074174' => 'qlo', 'QL05p074178' => 'qlo', 'QL05p074214' => 'qlo', 'QL06p001050' => 'qlo', 'QL06p001056' => 'qlo', 'QL06p006093' => 'qlo', 'QL06p006111' => 'qlo', 'QL07p019784' => 'qlo', 'QL07p019801' => 'qlo', 'QL07p036110' => 'qlo', 'QL07p036134' => 'qlo', 'QL07p036147' => 'qlo', 'QL07p036156' => 'qlo', 'QL07p036300' => 'qlo', 'QL07p036320' => 'qlo', 'QL08p014547' => 'qlo', 'QL08p014551' => 'qlo', 'QL08p043319' => 'qlo', 'QL08p043324' => 'qlo', 'QL11p009094' => 'qlo', 'RcHm_v2.0_Chr1g0380481' => 'rch', 'RcHm_v2.0_Chr2g0089331' => 'rch', 'RcHm_v2.0_Chr2g0123691' => 'rch', 'RcHm_v2.0_Chr2g0151111' => 'rch', 'RcHm_v2.0_Chr2g0163011' => 'rch', 'RcHm_v2.0_Chr2g0163051' => 'rch', 'RcHm_v2.0_Chr2g0164671' => 'rch', 'RcHm_v2.0_Chr2g0164681' => 'rch', 'RcHm_v2.0_Chr2g0164721' => 'rch', 'RcHm_v2.0_Chr3g0449911' => 'rch', 'RcHm_v2.0_Chr3g0450211' => 'rch', 'RcHm_v2.0_Chr3g0457271' => 'rch', 'RcHm_v2.0_Chr5g0018111' => 'rch', 'RcHm_v2.0_Chr5g0021011' => 'rch', 'RcHm_v2.0_Chr5g0081171' => 'rch', 'RcHm_v2.0_Chr5g0081211' => 'rch', 'RcHm_v2.0_Chr6g0275871' => 'rch', 'RcHm_v2.0_Chr6g0276071' => 'rch', 'RcHm_v2.0_Chr6g0285591' => 'rch', 'RcHm_v2.0_Chr6g0291931' => 'rch', 'RcHm_v2.0_Chr6g0292091' => 'rch', 'RcHm_v2.0_Chr6g0292271' => 'rch', 'RcHm_v2.0_Chr7g0221261' => 'rch', 'Rhsim08G0219900' => 'rsi', 'Rhsim08G0220200' => 'rsi', 'Rhsim08G0237800' => 'rsi', 'Rhsim08G0238800' => 'rsi', 'Sabra09G0102700' => 'sbr', 'Sabra09G0127200' => 'sbr', 'Sabra11G0003700' => 'sbr', 'Sabra15G0014700' => 'sbr', 'Sc19g0000590' => 'sci', 'Sc19g0001870' => 'sci', 'SGA_v2.0_scaffold1G00346' => 'sas', 'SGA_v2.0_scaffold1G00575' => 'sas', 'SGA_v2.0_scaffold1G00761' => 'sas', 'SGA_v2.0_scaffold232G43501' => 'sas', 'TAR625G1137' => 'tar', 'Thecc.03G222100' => 'tca', 'TPR.G12691' => 'tpr', 'TWI34G0727' => 'twi', 'TWI36G0117' => 'twi', 'VMungo1309G0868' => 'vmu' ) $gf_id = 'HOM05D001729' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001729' ) $data_identifier = 'HOM05D001729' $data_type = 'gf_id' $species_gene_counts = array( 'amhyb' => (int) 1, 'cqu' => (int) 9, 'can' => (int) 1, 'cansat' => (int) 1, 'car' => (int) 1, 'col' => (int) 5, 'dca' => (int) 1, 'din' => (int) 2, 'dzi' => (int) 3, 'fan' => (int) 140, 'fve' => (int) 62, 'gma' => (int) 1, 'ghi' => (int) 2, 'gra' => (int) 1, 'han' => (int) 1, 'sun' => (int) 1, 'lonja' => (int) 6, 'lja' => (int) 1, 'lsa' => (int) 4, 'mes' => (int) 1, 'mdo' => (int) 14, 'mtr' => (int) 1, 'egut' => (int) 1, 'nta' => (int) 4, 'oeu' => (int) 1, 'stu' => (int) 2, 'pvu' => (int) 1, 'ptr' => (int) 4, 'ppe' => (int) 19, 'psa' => (int) 1, 'pso' => (int) 4, 'qlo' => (int) 36, 'rch' => (int) 23, 'rsi' => (int) 4, 'sbr' => (int) 4, 'sci' => (int) 2, 'sas' => (int) 4, 'tar' => (int) 1, 'tca' => (int) 1, 'tpr' => (int) 1, 'twi' => (int) 2, 'vmu' => (int) 1 ) $gf_gene_species = 'vmu' $gf_gene_id = 'VMungo1309G0868' $species_info = array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ) $local_species = 'rch' $disabled = '' $selected = '' $num_hits = (int) 1
Warning (2): count(): Parameter must be an array or an object that implements Countable [APP/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp, line 33]Code Context $disabled = (!array_key_exists($local_species,$species_gene_counts))?"disabled":""; $selected = (isset($selected_species) && array_key_exists($local_species,$selected_species))?"checked='checked'":""; $num_hits = (array_key_exists($local_species,$species_gene_counts))?count($species_gene_counts[$local_species]):0; $viewFile = '/www/bioinformatics01_ro/plaza/_dev_instances/feedback/app/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp' $dataForView = array( 'sidebar_info' => array( 'gf_id' => 'HOM05D001729', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '375', 'num_species' => '42' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'Ah.07g204710' => 'amhyb', 'AUR62006001' => 'cqu', 'AUR62006002' => 'cqu', 'AUR62006003' => 'cqu', 'AUR62015641' => 'cqu', 'AUR62027174' => 'cqu', 'AUR62035623' => 'cqu', 'AUR62035624' => 'cqu', 'AUR62035625' => 'cqu', 'AUR62035626' => 'cqu', 'CAN.G1110.53' => 'can', 'CANSAT80G0415' => 'cansat', 'Ca_21364_v3' => 'car', 'COL.COLO4_30693' => 'col', 'COL.COLO4_30694' => 'col', 'COL.COLO4_30695' => 'col', 'COL.COLO4_30696' => 'col', 'COL.COLO4_34020' => 'col', 'DCAR_004585' => 'dca', 'Dinv04029' => 'din', 'Dinv34857' => 'din', 'Duzib147G0011' => 'dzi', 'Duzib170G0599' => 'dzi', 'Duzib192G1051' => 'dzi', 'FAN01G0708' => 'fan', 'FAN01G0742' => 'fan', 'FAN02G0048' => 'fan', 'FAN02G0583' => 'fan', 'FAN02G0688' => 'fan', 'FAN02G1588' => 'fan', 'FAN02G2194' => 'fan', 'FAN02G2750' => 'fan', 'FAN02G3094' => 'fan', 'FAN02G3887' => 'fan', 'FAN02G3911' => 'fan', 'FAN02G3994' => 'fan', 'FAN02G4432' => 'fan', 'FAN02G4556' => 'fan', 'FAN03G1977' => 'fan', 'FAN03G2781' => 'fan', 'FAN03G2850' => 'fan', 'FAN03G3155' => 'fan', 'FAN04G2487' => 'fan', 'FAN05G0208' => 'fan', 'FAN05G0656' => 'fan', 'FAN05G0696' => 'fan', 'FAN05G0810' => 'fan', 'FAN05G1447' => 'fan', 'FAN05G2640' => 'fan', 'FAN05G2911' => 'fan', 'FAN05G3901' => 'fan', 'FAN05G4859' => 'fan', 'FAN05G4861' => 'fan', 'FAN05G4988' => 'fan', 'FAN05G5187' => 'fan', 'FAN05G5452' => 'fan', 'FAN05G5500' => 'fan', 'FAN05G5688' => 'fan', 'FAN06G0177' => 'fan', 'FAN06G0675' => 'fan', 'FAN06G1290' => 'fan', 'FAN06G2191' => 'fan', 'FAN06G2405' => 'fan', 'FAN06G3231' => 'fan', 'FAN06G3932' => 'fan', 'FAN07G0163' => 'fan', 'FAN07G0471' => 'fan', 'FAN07G1354' => 'fan', 'FAN08G0338' => 'fan', 'FAN08G1373' => 'fan', 'FAN08G2539' => 'fan', 'FAN08G2728' => 'fan', 'FAN09G0608' => 'fan', 'FAN09G1136' => 'fan', 'FAN09G1958' => 'fan', 'FAN09G2508' => 'fan', 'FAN09G2597' => 'fan', 'FAN09G2658' => 'fan', 'FAN09G2757' => 'fan', 'FAN09G2983' => 'fan', 'FAN09G3130' => 'fan', 'FAN09G3565' => 'fan', 'FAN09G3613' => 'fan', 'FAN09G4011' => 'fan', 'FAN09G4239' => 'fan', 'FAN09G4277' => 'fan', 'FAN09G4720' => 'fan', 'FAN11G0139' => 'fan', 'FAN11G1727' => 'fan', 'FAN11G2672' => 'fan', 'FAN11G2795' => 'fan', 'FAN11G3238' => 'fan', 'FAN11G3734' => 'fan', 'FAN12G0631' => 'fan', 'FAN12G2239' => 'fan', 'FAN12G2308' => 'fan', 'FAN12G2569' => 'fan', 'FAN12G2623' => 'fan', 'FAN13G3182' => 'fan', 'FAN14G0053' => 'fan', 'FAN14G0370' => 'fan', 'FAN14G0382' => 'fan', 'FAN14G0421' => 'fan', 'FAN14G0866' => 'fan', 'FAN14G1187' => 'fan', 'FAN14G1727' => 'fan', 'FAN14G1791' => 'fan', 'FAN14G2361' => 'fan', 'FAN14G2668' => 'fan', 'FAN14G2770' => 'fan', 'FAN14G2874' => 'fan', 'FAN14G3193' => 'fan', 'FAN14G3624' => 'fan', 'FAN14G3676' => 'fan', 'FAN14G3807' => 'fan', 'FAN14G4082' => 'fan', 'FAN14G4342' => 'fan', 'FAN14G4985' => 'fan', 'FAN14G5126' => 'fan', 'FAN14G5781' => 'fan', 'FAN14G5808' => 'fan', 'FAN14G5949' => 'fan', 'FAN15G0828' => 'fan', 'FAN15G1054' => 'fan', 'FAN15G2023' => 'fan', 'FAN15G2506' => 'fan', 'FAN16G0128' => 'fan', 'FAN16G0249' => 'fan', 'FAN16G0429' => 'fan', 'FAN16G1493' => 'fan', 'FAN16G2210' => 'fan', 'FAN16G2506' => 'fan', 'FAN18G1542' => 'fan', 'FAN18G4057' => 'fan', 'FAN19G0745' => 'fan', 'FAN19G1216' => 'fan', 'FAN19G1733' => 'fan', 'FAN20G0258' => 'fan', 'FAN20G1095' => 'fan', 'FAN20G1557' => 'fan', 'FAN21G0302' => 'fan', 'FAN21G0519' => 'fan', 'FAN21G0970' => 'fan', 'FAN21G1159' => 'fan', 'FAN21G1312' => 'fan', 'FAN21G1440' => 'fan', 'FAN21G1715' => 'fan', 'FAN23G1584' => 'fan', 'FAN24G0045' => 'fan', 'FAN24G0053' => 'fan', 'FAN24G1500' => 'fan', 'FAN24G1817' => 'fan', 'FAN24G2147' => 'fan', 'FAN24G2236' => 'fan', 'FAN24G2446' => 'fan', 'FAN24G2684' => 'fan', 'FAN25G0187' => 'fan', 'FAN25G0505' => 'fan', 'FAN25G0589' => 'fan', 'FAN25G3663' => 'fan', 'FAN26G1025' => 'fan', 'FAN26G2860' => 'fan', 'FAN27G1329' => 'fan', 'FAN27G3392' => 'fan', 'FvH4_1g02011' => 'fve', 'FvH4_1g06511' => 'fve', 'FvH4_2g19900' => 'fve', 'FvH4_2g19920' => 'fve', 'FvH4_2g24261' => 'fve', 'FvH4_2g24270' => 'fve', 'FvH4_2g24631' => 'fve', 'FvH4_2g30622' => 'fve', 'FvH4_3g12920' => 'fve', 'FvH4_3g30171' => 'fve', 'FvH4_3g35490' => 'fve', 'FvH4_3g43682' => 'fve', 'FvH4_3g43730' => 'fve', 'FvH4_3g43732' => 'fve', 'FvH4_3g43751' => 'fve', 'FvH4_3g43752' => 'fve', 'FvH4_3g43770' => 'fve', 'FvH4_3g44471' => 'fve', 'FvH4_3g44510' => 'fve', 'FvH4_3g44582' => 'fve', 'FvH4_4g16921' => 'fve', 'FvH4_4g17121' => 'fve', 'FvH4_4g17782' => 'fve', 'FvH4_4g17783' => 'fve', 'FvH4_4g18120' => 'fve', 'FvH4_4g31310' => 'fve', 'FvH4_4g35052' => 'fve', 'FvH4_5g30862' => 'fve', 'FvH4_6g01541' => 'fve', 'FvH4_6g02021' => 'fve', 'FvH4_6g02041' => 'fve', 'FvH4_6g02071' => 'fve', 'FvH4_6g02171' => 'fve', 'FvH4_6g03181' => 'fve', 'FvH4_6g03182' => 'fve', 'FvH4_6g03221' => 'fve', 'FvH4_6g03380' => 'fve', 'FvH4_6g05201' => 'fve', 'FvH4_6g05203' => 'fve', 'FvH4_6g20231' => 'fve', 'FvH4_6g31981' => 'fve', 'FvH4_6g32061' => 'fve', 'FvH4_6g37041' => 'fve', 'FvH4_6g37932' => 'fve', 'FvH4_6g38731' => 'fve', 'FvH4_6g39370' => 'fve', 'FvH4_6g39371' => 'fve', 'FvH4_6g40891' => 'fve', 'FvH4_6g40892' => 'fve', 'FvH4_6g43143' => 'fve', 'FvH4_6g45251' => 'fve', 'FvH4_6g45260' => 'fve', 'FvH4_6g45291' => 'fve', 'FvH4_6g45890' => 'fve', 'FvH4_6g46240' => 'fve', 'FvH4_6g46241' => 'fve', 'FvH4_6g46242' => 'fve', 'FvH4_6g46260' => 'fve', 'FvH4_6g46280' => 'fve', 'FvH4_6g46380' => 'fve', 'FvH4_7g12841' => 'fve', 'FvH4_7g31431' => 'fve', 'Glyma.09G075900' => 'gma', 'Gohir.A09G096401' => 'ghi', 'Gohir.D09G096101' => 'ghi', 'Gorai.006G112800' => 'gra', 'HanXRQChr04g0121411' => 'han', 'Hund15878' => 'sun', 'Lj2A1107G68' => 'lonja', 'Lj2A630G63' => 'lonja', 'Lj2A946T25' => 'lonja', 'Lj2C714T1' => 'lonja', 'Lj2C966T3' => 'lonja', 'Lj2C966T4' => 'lonja', 'Lj4g0002979' => 'lja', 'Lsat_1_v5_gn_5_30901' => 'lsa', 'Lsat_1_v5_gn_5_31100' => 'lsa', 'Lsat_1_v5_gn_5_38600' => 'lsa', 'Lsat_1_v5_gn_6_92061' => 'lsa', 'Manes.05G071301' => 'mes', 'MD02G1008700' => 'mdo', 'MD02G1008900' => 'mdo', 'MD03G1256400' => 'mdo', 'MD04G1180900' => 'mdo', 'MD04G1181000' => 'mdo', 'MD04G1181200' => 'mdo', 'MD05G1244200' => 'mdo', 'MD05G1324200' => 'mdo', 'MD09G1201600' => 'mdo', 'MD10G1000600' => 'mdo', 'MD14G1026900' => 'mdo', 'MD14G1187900' => 'mdo', 'MD15G1017800' => 'mdo', 'MD15G1018100' => 'mdo', 'Medtr4g124160' => 'mtr', 'Migut.L01260' => 'egut', 'Nitab4.5_0000008g0440' => 'nta', 'Nitab4.5_0000207g0170' => 'nta', 'Nitab4.5_0007671g0030' => 'nta', 'Nitab4.5_0010853g0020' => 'nta', 'Oeu057656.1' => 'oeu', 'PGSC0003DMG400005638' => 'stu', 'PGSC0003DMG400005639' => 'stu', 'Phvul.009G222800' => 'pvu', 'Potri.009G132400' => 'ptr', 'Potri.009G163001' => 'ptr', 'Potri.011G000700' => 'ptr', 'Potri.011G004800' => 'ptr', 'Prupe.1G509300' => 'ppe', 'Prupe.1G509700' => 'ppe', 'Prupe.1G510400' => 'ppe', 'Prupe.1G510700' => 'ppe', 'Prupe.1G512600' => 'ppe', 'Prupe.2G073200' => 'ppe', 'Prupe.3G059500' => 'ppe', 'Prupe.3G059600' => 'ppe', 'Prupe.3G246100' => 'ppe', 'Prupe.3G265100' => 'ppe', 'Prupe.4G034700' => 'ppe', 'Prupe.4G052100' => 'ppe', 'Prupe.4G053600' => 'ppe', 'Prupe.5G068800' => 'ppe', 'Prupe.5G070600' => 'ppe', 'Prupe.6G075400' => 'ppe', 'Prupe.6G075500' => 'ppe', 'Prupe.6G076400' => 'ppe', 'Prupe.8G110700' => 'ppe', 'Psat4g020960' => 'psa', 'PSO135G0788' => 'pso', 'PSO210G6463' => 'pso', 'PSO384G0370' => 'pso', 'PSO386G0056' => 'pso', 'QL01p006048' => 'qlo', 'QL02p054283' => 'qlo', 'QL05p008000' => 'qlo', 'QL05p008212' => 'qlo', 'QL05p008950' => 'qlo', 'QL05p009042' => 'qlo', 'QL05p009518' => 'qlo', 'QL05p012589' => 'qlo', 'QL05p012608' => 'qlo', 'QL05p012650' => 'qlo', 'QL05p012667' => 'qlo', 'QL05p014501' => 'qlo', 'QL05p052800' => 'qlo', 'QL05p065010' => 'qlo', 'QL05p074156' => 'qlo', 'QL05p074160' => 'qlo', 'QL05p074174' => 'qlo', 'QL05p074178' => 'qlo', 'QL05p074214' => 'qlo', 'QL06p001050' => 'qlo', 'QL06p001056' => 'qlo', 'QL06p006093' => 'qlo', 'QL06p006111' => 'qlo', 'QL07p019784' => 'qlo', 'QL07p019801' => 'qlo', 'QL07p036110' => 'qlo', 'QL07p036134' => 'qlo', 'QL07p036147' => 'qlo', 'QL07p036156' => 'qlo', 'QL07p036300' => 'qlo', 'QL07p036320' => 'qlo', 'QL08p014547' => 'qlo', 'QL08p014551' => 'qlo', 'QL08p043319' => 'qlo', 'QL08p043324' => 'qlo', 'QL11p009094' => 'qlo', 'RcHm_v2.0_Chr1g0380481' => 'rch', 'RcHm_v2.0_Chr2g0089331' => 'rch', 'RcHm_v2.0_Chr2g0123691' => 'rch', 'RcHm_v2.0_Chr2g0151111' => 'rch', 'RcHm_v2.0_Chr2g0163011' => 'rch', 'RcHm_v2.0_Chr2g0163051' => 'rch', 'RcHm_v2.0_Chr2g0164671' => 'rch', 'RcHm_v2.0_Chr2g0164681' => 'rch', 'RcHm_v2.0_Chr2g0164721' => 'rch', 'RcHm_v2.0_Chr3g0449911' => 'rch', 'RcHm_v2.0_Chr3g0450211' => 'rch', 'RcHm_v2.0_Chr3g0457271' => 'rch', 'RcHm_v2.0_Chr5g0018111' => 'rch', 'RcHm_v2.0_Chr5g0021011' => 'rch', 'RcHm_v2.0_Chr5g0081171' => 'rch', 'RcHm_v2.0_Chr5g0081211' => 'rch', 'RcHm_v2.0_Chr6g0275871' => 'rch', 'RcHm_v2.0_Chr6g0276071' => 'rch', 'RcHm_v2.0_Chr6g0285591' => 'rch', 'RcHm_v2.0_Chr6g0291931' => 'rch', 'RcHm_v2.0_Chr6g0292091' => 'rch', 'RcHm_v2.0_Chr6g0292271' => 'rch', 'RcHm_v2.0_Chr7g0221261' => 'rch', 'Rhsim08G0219900' => 'rsi', 'Rhsim08G0220200' => 'rsi', 'Rhsim08G0237800' => 'rsi', 'Rhsim08G0238800' => 'rsi', 'Sabra09G0102700' => 'sbr', 'Sabra09G0127200' => 'sbr', 'Sabra11G0003700' => 'sbr', 'Sabra15G0014700' => 'sbr', 'Sc19g0000590' => 'sci', 'Sc19g0001870' => 'sci', 'SGA_v2.0_scaffold1G00346' => 'sas', 'SGA_v2.0_scaffold1G00575' => 'sas', 'SGA_v2.0_scaffold1G00761' => 'sas', 'SGA_v2.0_scaffold232G43501' => 'sas', 'TAR625G1137' => 'tar', 'Thecc.03G222100' => 'tca', 'TPR.G12691' => 'tpr', 'TWI34G0727' => 'twi', 'TWI36G0117' => 'twi', 'VMungo1309G0868' => 'vmu' ), 'gf_id' => 'HOM05D001729', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001729' ), 'data_identifier' => 'HOM05D001729', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001729', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '375', 'num_species' => '42' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'Ah.07g204710' => 'amhyb', 'AUR62006001' => 'cqu', 'AUR62006002' => 'cqu', 'AUR62006003' => 'cqu', 'AUR62015641' => 'cqu', 'AUR62027174' => 'cqu', 'AUR62035623' => 'cqu', 'AUR62035624' => 'cqu', 'AUR62035625' => 'cqu', 'AUR62035626' => 'cqu', 'CAN.G1110.53' => 'can', 'CANSAT80G0415' => 'cansat', 'Ca_21364_v3' => 'car', 'COL.COLO4_30693' => 'col', 'COL.COLO4_30694' => 'col', 'COL.COLO4_30695' => 'col', 'COL.COLO4_30696' => 'col', 'COL.COLO4_34020' => 'col', 'DCAR_004585' => 'dca', 'Dinv04029' => 'din', 'Dinv34857' => 'din', 'Duzib147G0011' => 'dzi', 'Duzib170G0599' => 'dzi', 'Duzib192G1051' => 'dzi', 'FAN01G0708' => 'fan', 'FAN01G0742' => 'fan', 'FAN02G0048' => 'fan', 'FAN02G0583' => 'fan', 'FAN02G0688' => 'fan', 'FAN02G1588' => 'fan', 'FAN02G2194' => 'fan', 'FAN02G2750' => 'fan', 'FAN02G3094' => 'fan', 'FAN02G3887' => 'fan', 'FAN02G3911' => 'fan', 'FAN02G3994' => 'fan', 'FAN02G4432' => 'fan', 'FAN02G4556' => 'fan', 'FAN03G1977' => 'fan', 'FAN03G2781' => 'fan', 'FAN03G2850' => 'fan', 'FAN03G3155' => 'fan', 'FAN04G2487' => 'fan', 'FAN05G0208' => 'fan', 'FAN05G0656' => 'fan', 'FAN05G0696' => 'fan', 'FAN05G0810' => 'fan', 'FAN05G1447' => 'fan', 'FAN05G2640' => 'fan', 'FAN05G2911' => 'fan', 'FAN05G3901' => 'fan', 'FAN05G4859' => 'fan', 'FAN05G4861' => 'fan', 'FAN05G4988' => 'fan', 'FAN05G5187' => 'fan', 'FAN05G5452' => 'fan', 'FAN05G5500' => 'fan', 'FAN05G5688' => 'fan', 'FAN06G0177' => 'fan', 'FAN06G0675' => 'fan', 'FAN06G1290' => 'fan', 'FAN06G2191' => 'fan', 'FAN06G2405' => 'fan', 'FAN06G3231' => 'fan', 'FAN06G3932' => 'fan', 'FAN07G0163' => 'fan', 'FAN07G0471' => 'fan', 'FAN07G1354' => 'fan', 'FAN08G0338' => 'fan', 'FAN08G1373' => 'fan', 'FAN08G2539' => 'fan', 'FAN08G2728' => 'fan', 'FAN09G0608' => 'fan', 'FAN09G1136' => 'fan', 'FAN09G1958' => 'fan', 'FAN09G2508' => 'fan', 'FAN09G2597' => 'fan', 'FAN09G2658' => 'fan', 'FAN09G2757' => 'fan', 'FAN09G2983' => 'fan', 'FAN09G3130' => 'fan', 'FAN09G3565' => 'fan', 'FAN09G3613' => 'fan', 'FAN09G4011' => 'fan', 'FAN09G4239' => 'fan', 'FAN09G4277' => 'fan', 'FAN09G4720' => 'fan', 'FAN11G0139' => 'fan', 'FAN11G1727' => 'fan', 'FAN11G2672' => 'fan', 'FAN11G2795' => 'fan', 'FAN11G3238' => 'fan', 'FAN11G3734' => 'fan', 'FAN12G0631' => 'fan', 'FAN12G2239' => 'fan', 'FAN12G2308' => 'fan', 'FAN12G2569' => 'fan', 'FAN12G2623' => 'fan', 'FAN13G3182' => 'fan', 'FAN14G0053' => 'fan', 'FAN14G0370' => 'fan', 'FAN14G0382' => 'fan', 'FAN14G0421' => 'fan', 'FAN14G0866' => 'fan', 'FAN14G1187' => 'fan', 'FAN14G1727' => 'fan', 'FAN14G1791' => 'fan', 'FAN14G2361' => 'fan', 'FAN14G2668' => 'fan', 'FAN14G2770' => 'fan', 'FAN14G2874' => 'fan', 'FAN14G3193' => 'fan', 'FAN14G3624' => 'fan', 'FAN14G3676' => 'fan', 'FAN14G3807' => 'fan', 'FAN14G4082' => 'fan', 'FAN14G4342' => 'fan', 'FAN14G4985' => 'fan', 'FAN14G5126' => 'fan', 'FAN14G5781' => 'fan', 'FAN14G5808' => 'fan', 'FAN14G5949' => 'fan', 'FAN15G0828' => 'fan', 'FAN15G1054' => 'fan', 'FAN15G2023' => 'fan', 'FAN15G2506' => 'fan', 'FAN16G0128' => 'fan', 'FAN16G0249' => 'fan', 'FAN16G0429' => 'fan', 'FAN16G1493' => 'fan', 'FAN16G2210' => 'fan', 'FAN16G2506' => 'fan', 'FAN18G1542' => 'fan', 'FAN18G4057' => 'fan', 'FAN19G0745' => 'fan', 'FAN19G1216' => 'fan', 'FAN19G1733' => 'fan', 'FAN20G0258' => 'fan', 'FAN20G1095' => 'fan', 'FAN20G1557' => 'fan', 'FAN21G0302' => 'fan', 'FAN21G0519' => 'fan', 'FAN21G0970' => 'fan', 'FAN21G1159' => 'fan', 'FAN21G1312' => 'fan', 'FAN21G1440' => 'fan', 'FAN21G1715' => 'fan', 'FAN23G1584' => 'fan', 'FAN24G0045' => 'fan', 'FAN24G0053' => 'fan', 'FAN24G1500' => 'fan', 'FAN24G1817' => 'fan', 'FAN24G2147' => 'fan', 'FAN24G2236' => 'fan', 'FAN24G2446' => 'fan', 'FAN24G2684' => 'fan', 'FAN25G0187' => 'fan', 'FAN25G0505' => 'fan', 'FAN25G0589' => 'fan', 'FAN25G3663' => 'fan', 'FAN26G1025' => 'fan', 'FAN26G2860' => 'fan', 'FAN27G1329' => 'fan', 'FAN27G3392' => 'fan', 'FvH4_1g02011' => 'fve', 'FvH4_1g06511' => 'fve', 'FvH4_2g19900' => 'fve', 'FvH4_2g19920' => 'fve', 'FvH4_2g24261' => 'fve', 'FvH4_2g24270' => 'fve', 'FvH4_2g24631' => 'fve', 'FvH4_2g30622' => 'fve', 'FvH4_3g12920' => 'fve', 'FvH4_3g30171' => 'fve', 'FvH4_3g35490' => 'fve', 'FvH4_3g43682' => 'fve', 'FvH4_3g43730' => 'fve', 'FvH4_3g43732' => 'fve', 'FvH4_3g43751' => 'fve', 'FvH4_3g43752' => 'fve', 'FvH4_3g43770' => 'fve', 'FvH4_3g44471' => 'fve', 'FvH4_3g44510' => 'fve', 'FvH4_3g44582' => 'fve', 'FvH4_4g16921' => 'fve', 'FvH4_4g17121' => 'fve', 'FvH4_4g17782' => 'fve', 'FvH4_4g17783' => 'fve', 'FvH4_4g18120' => 'fve', 'FvH4_4g31310' => 'fve', 'FvH4_4g35052' => 'fve', 'FvH4_5g30862' => 'fve', 'FvH4_6g01541' => 'fve', 'FvH4_6g02021' => 'fve', 'FvH4_6g02041' => 'fve', 'FvH4_6g02071' => 'fve', 'FvH4_6g02171' => 'fve', 'FvH4_6g03181' => 'fve', 'FvH4_6g03182' => 'fve', 'FvH4_6g03221' => 'fve', 'FvH4_6g03380' => 'fve', 'FvH4_6g05201' => 'fve', 'FvH4_6g05203' => 'fve', 'FvH4_6g20231' => 'fve', 'FvH4_6g31981' => 'fve', 'FvH4_6g32061' => 'fve', 'FvH4_6g37041' => 'fve', 'FvH4_6g37932' => 'fve', 'FvH4_6g38731' => 'fve', 'FvH4_6g39370' => 'fve', 'FvH4_6g39371' => 'fve', 'FvH4_6g40891' => 'fve', 'FvH4_6g40892' => 'fve', 'FvH4_6g43143' => 'fve', 'FvH4_6g45251' => 'fve', 'FvH4_6g45260' => 'fve', 'FvH4_6g45291' => 'fve', 'FvH4_6g45890' => 'fve', 'FvH4_6g46240' => 'fve', 'FvH4_6g46241' => 'fve', 'FvH4_6g46242' => 'fve', 'FvH4_6g46260' => 'fve', 'FvH4_6g46280' => 'fve', 'FvH4_6g46380' => 'fve', 'FvH4_7g12841' => 'fve', 'FvH4_7g31431' => 'fve', 'Glyma.09G075900' => 'gma', 'Gohir.A09G096401' => 'ghi', 'Gohir.D09G096101' => 'ghi', 'Gorai.006G112800' => 'gra', 'HanXRQChr04g0121411' => 'han', 'Hund15878' => 'sun', 'Lj2A1107G68' => 'lonja', 'Lj2A630G63' => 'lonja', 'Lj2A946T25' => 'lonja', 'Lj2C714T1' => 'lonja', 'Lj2C966T3' => 'lonja', 'Lj2C966T4' => 'lonja', 'Lj4g0002979' => 'lja', 'Lsat_1_v5_gn_5_30901' => 'lsa', 'Lsat_1_v5_gn_5_31100' => 'lsa', 'Lsat_1_v5_gn_5_38600' => 'lsa', 'Lsat_1_v5_gn_6_92061' => 'lsa', 'Manes.05G071301' => 'mes', 'MD02G1008700' => 'mdo', 'MD02G1008900' => 'mdo', 'MD03G1256400' => 'mdo', 'MD04G1180900' => 'mdo', 'MD04G1181000' => 'mdo', 'MD04G1181200' => 'mdo', 'MD05G1244200' => 'mdo', 'MD05G1324200' => 'mdo', 'MD09G1201600' => 'mdo', 'MD10G1000600' => 'mdo', 'MD14G1026900' => 'mdo', 'MD14G1187900' => 'mdo', 'MD15G1017800' => 'mdo', 'MD15G1018100' => 'mdo', 'Medtr4g124160' => 'mtr', 'Migut.L01260' => 'egut', 'Nitab4.5_0000008g0440' => 'nta', 'Nitab4.5_0000207g0170' => 'nta', 'Nitab4.5_0007671g0030' => 'nta', 'Nitab4.5_0010853g0020' => 'nta', 'Oeu057656.1' => 'oeu', 'PGSC0003DMG400005638' => 'stu', 'PGSC0003DMG400005639' => 'stu', 'Phvul.009G222800' => 'pvu', 'Potri.009G132400' => 'ptr', 'Potri.009G163001' => 'ptr', 'Potri.011G000700' => 'ptr', 'Potri.011G004800' => 'ptr', 'Prupe.1G509300' => 'ppe', 'Prupe.1G509700' => 'ppe', 'Prupe.1G510400' => 'ppe', 'Prupe.1G510700' => 'ppe', 'Prupe.1G512600' => 'ppe', 'Prupe.2G073200' => 'ppe', 'Prupe.3G059500' => 'ppe', 'Prupe.3G059600' => 'ppe', 'Prupe.3G246100' => 'ppe', 'Prupe.3G265100' => 'ppe', 'Prupe.4G034700' => 'ppe', 'Prupe.4G052100' => 'ppe', 'Prupe.4G053600' => 'ppe', 'Prupe.5G068800' => 'ppe', 'Prupe.5G070600' => 'ppe', 'Prupe.6G075400' => 'ppe', 'Prupe.6G075500' => 'ppe', 'Prupe.6G076400' => 'ppe', 'Prupe.8G110700' => 'ppe', 'Psat4g020960' => 'psa', 'PSO135G0788' => 'pso', 'PSO210G6463' => 'pso', 'PSO384G0370' => 'pso', 'PSO386G0056' => 'pso', 'QL01p006048' => 'qlo', 'QL02p054283' => 'qlo', 'QL05p008000' => 'qlo', 'QL05p008212' => 'qlo', 'QL05p008950' => 'qlo', 'QL05p009042' => 'qlo', 'QL05p009518' => 'qlo', 'QL05p012589' => 'qlo', 'QL05p012608' => 'qlo', 'QL05p012650' => 'qlo', 'QL05p012667' => 'qlo', 'QL05p014501' => 'qlo', 'QL05p052800' => 'qlo', 'QL05p065010' => 'qlo', 'QL05p074156' => 'qlo', 'QL05p074160' => 'qlo', 'QL05p074174' => 'qlo', 'QL05p074178' => 'qlo', 'QL05p074214' => 'qlo', 'QL06p001050' => 'qlo', 'QL06p001056' => 'qlo', 'QL06p006093' => 'qlo', 'QL06p006111' => 'qlo', 'QL07p019784' => 'qlo', 'QL07p019801' => 'qlo', 'QL07p036110' => 'qlo', 'QL07p036134' => 'qlo', 'QL07p036147' => 'qlo', 'QL07p036156' => 'qlo', 'QL07p036300' => 'qlo', 'QL07p036320' => 'qlo', 'QL08p014547' => 'qlo', 'QL08p014551' => 'qlo', 'QL08p043319' => 'qlo', 'QL08p043324' => 'qlo', 'QL11p009094' => 'qlo', 'RcHm_v2.0_Chr1g0380481' => 'rch', 'RcHm_v2.0_Chr2g0089331' => 'rch', 'RcHm_v2.0_Chr2g0123691' => 'rch', 'RcHm_v2.0_Chr2g0151111' => 'rch', 'RcHm_v2.0_Chr2g0163011' => 'rch', 'RcHm_v2.0_Chr2g0163051' => 'rch', 'RcHm_v2.0_Chr2g0164671' => 'rch', 'RcHm_v2.0_Chr2g0164681' => 'rch', 'RcHm_v2.0_Chr2g0164721' => 'rch', 'RcHm_v2.0_Chr3g0449911' => 'rch', 'RcHm_v2.0_Chr3g0450211' => 'rch', 'RcHm_v2.0_Chr3g0457271' => 'rch', 'RcHm_v2.0_Chr5g0018111' => 'rch', 'RcHm_v2.0_Chr5g0021011' => 'rch', 'RcHm_v2.0_Chr5g0081171' => 'rch', 'RcHm_v2.0_Chr5g0081211' => 'rch', 'RcHm_v2.0_Chr6g0275871' => 'rch', 'RcHm_v2.0_Chr6g0276071' => 'rch', 'RcHm_v2.0_Chr6g0285591' => 'rch', 'RcHm_v2.0_Chr6g0291931' => 'rch', 'RcHm_v2.0_Chr6g0292091' => 'rch', 'RcHm_v2.0_Chr6g0292271' => 'rch', 'RcHm_v2.0_Chr7g0221261' => 'rch', 'Rhsim08G0219900' => 'rsi', 'Rhsim08G0220200' => 'rsi', 'Rhsim08G0237800' => 'rsi', 'Rhsim08G0238800' => 'rsi', 'Sabra09G0102700' => 'sbr', 'Sabra09G0127200' => 'sbr', 'Sabra11G0003700' => 'sbr', 'Sabra15G0014700' => 'sbr', 'Sc19g0000590' => 'sci', 'Sc19g0001870' => 'sci', 'SGA_v2.0_scaffold1G00346' => 'sas', 'SGA_v2.0_scaffold1G00575' => 'sas', 'SGA_v2.0_scaffold1G00761' => 'sas', 'SGA_v2.0_scaffold232G43501' => 'sas', 'TAR625G1137' => 'tar', 'Thecc.03G222100' => 'tca', 'TPR.G12691' => 'tpr', 'TWI34G0727' => 'twi', 'TWI36G0117' => 'twi', 'VMungo1309G0868' => 'vmu' ) $gf_id = 'HOM05D001729' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001729' ) $data_identifier = 'HOM05D001729' $data_type = 'gf_id' $species_gene_counts = array( 'amhyb' => (int) 1, 'cqu' => (int) 9, 'can' => (int) 1, 'cansat' => (int) 1, 'car' => (int) 1, 'col' => (int) 5, 'dca' => (int) 1, 'din' => (int) 2, 'dzi' => (int) 3, 'fan' => (int) 140, 'fve' => (int) 62, 'gma' => (int) 1, 'ghi' => (int) 2, 'gra' => (int) 1, 'han' => (int) 1, 'sun' => (int) 1, 'lonja' => (int) 6, 'lja' => (int) 1, 'lsa' => (int) 4, 'mes' => (int) 1, 'mdo' => (int) 14, 'mtr' => (int) 1, 'egut' => (int) 1, 'nta' => (int) 4, 'oeu' => (int) 1, 'stu' => (int) 2, 'pvu' => (int) 1, 'ptr' => (int) 4, 'ppe' => (int) 19, 'psa' => (int) 1, 'pso' => (int) 4, 'qlo' => (int) 36, 'rch' => (int) 23, 'rsi' => (int) 4, 'sbr' => (int) 4, 'sci' => (int) 2, 'sas' => (int) 4, 'tar' => (int) 1, 'tca' => (int) 1, 'tpr' => (int) 1, 'twi' => (int) 2, 'vmu' => (int) 1 ) $gf_gene_species = 'vmu' $gf_gene_id = 'VMungo1309G0868' $species_info = array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ) $local_species = 'sbr' $disabled = '' $selected = '' $num_hits = (int) 1include - APP/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp, line 33 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933 View::_renderElement() - CORE/Cake/View/View.php, line 1224 View::element() - CORE/Cake/View/View.php, line 418 include - APP/View/Elements/analysis/phylogenetics_module/gf_data_settings.ctp, line 37 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933 View::_renderElement() - CORE/Cake/View/View.php, line 1224 View::element() - CORE/Cake/View/View.php, line 418 include - APP/View/Elements/analysis/phylogenetics_module/parameter_selection.ctp, line 64 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933 View::_renderElement() - CORE/Cake/View/View.php, line 1224 View::element() - CORE/Cake/View/View.php, line 418 include - APP/View/Analysis/custom_tree_creation.ctp, line 27 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933
$viewFile = '/www/bioinformatics01_ro/plaza/_dev_instances/feedback/app/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp' $dataForView = array( 'sidebar_info' => array( 'gf_id' => 'HOM05D001729', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '375', 'num_species' => '42' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'Ah.07g204710' => 'amhyb', 'AUR62006001' => 'cqu', 'AUR62006002' => 'cqu', 'AUR62006003' => 'cqu', 'AUR62015641' => 'cqu', 'AUR62027174' => 'cqu', 'AUR62035623' => 'cqu', 'AUR62035624' => 'cqu', 'AUR62035625' => 'cqu', 'AUR62035626' => 'cqu', 'CAN.G1110.53' => 'can', 'CANSAT80G0415' => 'cansat', 'Ca_21364_v3' => 'car', 'COL.COLO4_30693' => 'col', 'COL.COLO4_30694' => 'col', 'COL.COLO4_30695' => 'col', 'COL.COLO4_30696' => 'col', 'COL.COLO4_34020' => 'col', 'DCAR_004585' => 'dca', 'Dinv04029' => 'din', 'Dinv34857' => 'din', 'Duzib147G0011' => 'dzi', 'Duzib170G0599' => 'dzi', 'Duzib192G1051' => 'dzi', 'FAN01G0708' => 'fan', 'FAN01G0742' => 'fan', 'FAN02G0048' => 'fan', 'FAN02G0583' => 'fan', 'FAN02G0688' => 'fan', 'FAN02G1588' => 'fan', 'FAN02G2194' => 'fan', 'FAN02G2750' => 'fan', 'FAN02G3094' => 'fan', 'FAN02G3887' => 'fan', 'FAN02G3911' => 'fan', 'FAN02G3994' => 'fan', 'FAN02G4432' => 'fan', 'FAN02G4556' => 'fan', 'FAN03G1977' => 'fan', 'FAN03G2781' => 'fan', 'FAN03G2850' => 'fan', 'FAN03G3155' => 'fan', 'FAN04G2487' => 'fan', 'FAN05G0208' => 'fan', 'FAN05G0656' => 'fan', 'FAN05G0696' => 'fan', 'FAN05G0810' => 'fan', 'FAN05G1447' => 'fan', 'FAN05G2640' => 'fan', 'FAN05G2911' => 'fan', 'FAN05G3901' => 'fan', 'FAN05G4859' => 'fan', 'FAN05G4861' => 'fan', 'FAN05G4988' => 'fan', 'FAN05G5187' => 'fan', 'FAN05G5452' => 'fan', 'FAN05G5500' => 'fan', 'FAN05G5688' => 'fan', 'FAN06G0177' => 'fan', 'FAN06G0675' => 'fan', 'FAN06G1290' => 'fan', 'FAN06G2191' => 'fan', 'FAN06G2405' => 'fan', 'FAN06G3231' => 'fan', 'FAN06G3932' => 'fan', 'FAN07G0163' => 'fan', 'FAN07G0471' => 'fan', 'FAN07G1354' => 'fan', 'FAN08G0338' => 'fan', 'FAN08G1373' => 'fan', 'FAN08G2539' => 'fan', 'FAN08G2728' => 'fan', 'FAN09G0608' => 'fan', 'FAN09G1136' => 'fan', 'FAN09G1958' => 'fan', 'FAN09G2508' => 'fan', 'FAN09G2597' => 'fan', 'FAN09G2658' => 'fan', 'FAN09G2757' => 'fan', 'FAN09G2983' => 'fan', 'FAN09G3130' => 'fan', 'FAN09G3565' => 'fan', 'FAN09G3613' => 'fan', 'FAN09G4011' => 'fan', 'FAN09G4239' => 'fan', 'FAN09G4277' => 'fan', 'FAN09G4720' => 'fan', 'FAN11G0139' => 'fan', 'FAN11G1727' => 'fan', 'FAN11G2672' => 'fan', 'FAN11G2795' => 'fan', 'FAN11G3238' => 'fan', 'FAN11G3734' => 'fan', 'FAN12G0631' => 'fan', 'FAN12G2239' => 'fan', 'FAN12G2308' => 'fan', 'FAN12G2569' => 'fan', 'FAN12G2623' => 'fan', 'FAN13G3182' => 'fan', 'FAN14G0053' => 'fan', 'FAN14G0370' => 'fan', 'FAN14G0382' => 'fan', 'FAN14G0421' => 'fan', 'FAN14G0866' => 'fan', 'FAN14G1187' => 'fan', 'FAN14G1727' => 'fan', 'FAN14G1791' => 'fan', 'FAN14G2361' => 'fan', 'FAN14G2668' => 'fan', 'FAN14G2770' => 'fan', 'FAN14G2874' => 'fan', 'FAN14G3193' => 'fan', 'FAN14G3624' => 'fan', 'FAN14G3676' => 'fan', 'FAN14G3807' => 'fan', 'FAN14G4082' => 'fan', 'FAN14G4342' => 'fan', 'FAN14G4985' => 'fan', 'FAN14G5126' => 'fan', 'FAN14G5781' => 'fan', 'FAN14G5808' => 'fan', 'FAN14G5949' => 'fan', 'FAN15G0828' => 'fan', 'FAN15G1054' => 'fan', 'FAN15G2023' => 'fan', 'FAN15G2506' => 'fan', 'FAN16G0128' => 'fan', 'FAN16G0249' => 'fan', 'FAN16G0429' => 'fan', 'FAN16G1493' => 'fan', 'FAN16G2210' => 'fan', 'FAN16G2506' => 'fan', 'FAN18G1542' => 'fan', 'FAN18G4057' => 'fan', 'FAN19G0745' => 'fan', 'FAN19G1216' => 'fan', 'FAN19G1733' => 'fan', 'FAN20G0258' => 'fan', 'FAN20G1095' => 'fan', 'FAN20G1557' => 'fan', 'FAN21G0302' => 'fan', 'FAN21G0519' => 'fan', 'FAN21G0970' => 'fan', 'FAN21G1159' => 'fan', 'FAN21G1312' => 'fan', 'FAN21G1440' => 'fan', 'FAN21G1715' => 'fan', 'FAN23G1584' => 'fan', 'FAN24G0045' => 'fan', 'FAN24G0053' => 'fan', 'FAN24G1500' => 'fan', 'FAN24G1817' => 'fan', 'FAN24G2147' => 'fan', 'FAN24G2236' => 'fan', 'FAN24G2446' => 'fan', 'FAN24G2684' => 'fan', 'FAN25G0187' => 'fan', 'FAN25G0505' => 'fan', 'FAN25G0589' => 'fan', 'FAN25G3663' => 'fan', 'FAN26G1025' => 'fan', 'FAN26G2860' => 'fan', 'FAN27G1329' => 'fan', 'FAN27G3392' => 'fan', 'FvH4_1g02011' => 'fve', 'FvH4_1g06511' => 'fve', 'FvH4_2g19900' => 'fve', 'FvH4_2g19920' => 'fve', 'FvH4_2g24261' => 'fve', 'FvH4_2g24270' => 'fve', 'FvH4_2g24631' => 'fve', 'FvH4_2g30622' => 'fve', 'FvH4_3g12920' => 'fve', 'FvH4_3g30171' => 'fve', 'FvH4_3g35490' => 'fve', 'FvH4_3g43682' => 'fve', 'FvH4_3g43730' => 'fve', 'FvH4_3g43732' => 'fve', 'FvH4_3g43751' => 'fve', 'FvH4_3g43752' => 'fve', 'FvH4_3g43770' => 'fve', 'FvH4_3g44471' => 'fve', 'FvH4_3g44510' => 'fve', 'FvH4_3g44582' => 'fve', 'FvH4_4g16921' => 'fve', 'FvH4_4g17121' => 'fve', 'FvH4_4g17782' => 'fve', 'FvH4_4g17783' => 'fve', 'FvH4_4g18120' => 'fve', 'FvH4_4g31310' => 'fve', 'FvH4_4g35052' => 'fve', 'FvH4_5g30862' => 'fve', 'FvH4_6g01541' => 'fve', 'FvH4_6g02021' => 'fve', 'FvH4_6g02041' => 'fve', 'FvH4_6g02071' => 'fve', 'FvH4_6g02171' => 'fve', 'FvH4_6g03181' => 'fve', 'FvH4_6g03182' => 'fve', 'FvH4_6g03221' => 'fve', 'FvH4_6g03380' => 'fve', 'FvH4_6g05201' => 'fve', 'FvH4_6g05203' => 'fve', 'FvH4_6g20231' => 'fve', 'FvH4_6g31981' => 'fve', 'FvH4_6g32061' => 'fve', 'FvH4_6g37041' => 'fve', 'FvH4_6g37932' => 'fve', 'FvH4_6g38731' => 'fve', 'FvH4_6g39370' => 'fve', 'FvH4_6g39371' => 'fve', 'FvH4_6g40891' => 'fve', 'FvH4_6g40892' => 'fve', 'FvH4_6g43143' => 'fve', 'FvH4_6g45251' => 'fve', 'FvH4_6g45260' => 'fve', 'FvH4_6g45291' => 'fve', 'FvH4_6g45890' => 'fve', 'FvH4_6g46240' => 'fve', 'FvH4_6g46241' => 'fve', 'FvH4_6g46242' => 'fve', 'FvH4_6g46260' => 'fve', 'FvH4_6g46280' => 'fve', 'FvH4_6g46380' => 'fve', 'FvH4_7g12841' => 'fve', 'FvH4_7g31431' => 'fve', 'Glyma.09G075900' => 'gma', 'Gohir.A09G096401' => 'ghi', 'Gohir.D09G096101' => 'ghi', 'Gorai.006G112800' => 'gra', 'HanXRQChr04g0121411' => 'han', 'Hund15878' => 'sun', 'Lj2A1107G68' => 'lonja', 'Lj2A630G63' => 'lonja', 'Lj2A946T25' => 'lonja', 'Lj2C714T1' => 'lonja', 'Lj2C966T3' => 'lonja', 'Lj2C966T4' => 'lonja', 'Lj4g0002979' => 'lja', 'Lsat_1_v5_gn_5_30901' => 'lsa', 'Lsat_1_v5_gn_5_31100' => 'lsa', 'Lsat_1_v5_gn_5_38600' => 'lsa', 'Lsat_1_v5_gn_6_92061' => 'lsa', 'Manes.05G071301' => 'mes', 'MD02G1008700' => 'mdo', 'MD02G1008900' => 'mdo', 'MD03G1256400' => 'mdo', 'MD04G1180900' => 'mdo', 'MD04G1181000' => 'mdo', 'MD04G1181200' => 'mdo', 'MD05G1244200' => 'mdo', 'MD05G1324200' => 'mdo', 'MD09G1201600' => 'mdo', 'MD10G1000600' => 'mdo', 'MD14G1026900' => 'mdo', 'MD14G1187900' => 'mdo', 'MD15G1017800' => 'mdo', 'MD15G1018100' => 'mdo', 'Medtr4g124160' => 'mtr', 'Migut.L01260' => 'egut', 'Nitab4.5_0000008g0440' => 'nta', 'Nitab4.5_0000207g0170' => 'nta', 'Nitab4.5_0007671g0030' => 'nta', 'Nitab4.5_0010853g0020' => 'nta', 'Oeu057656.1' => 'oeu', 'PGSC0003DMG400005638' => 'stu', 'PGSC0003DMG400005639' => 'stu', 'Phvul.009G222800' => 'pvu', 'Potri.009G132400' => 'ptr', 'Potri.009G163001' => 'ptr', 'Potri.011G000700' => 'ptr', 'Potri.011G004800' => 'ptr', 'Prupe.1G509300' => 'ppe', 'Prupe.1G509700' => 'ppe', 'Prupe.1G510400' => 'ppe', 'Prupe.1G510700' => 'ppe', 'Prupe.1G512600' => 'ppe', 'Prupe.2G073200' => 'ppe', 'Prupe.3G059500' => 'ppe', 'Prupe.3G059600' => 'ppe', 'Prupe.3G246100' => 'ppe', 'Prupe.3G265100' => 'ppe', 'Prupe.4G034700' => 'ppe', 'Prupe.4G052100' => 'ppe', 'Prupe.4G053600' => 'ppe', 'Prupe.5G068800' => 'ppe', 'Prupe.5G070600' => 'ppe', 'Prupe.6G075400' => 'ppe', 'Prupe.6G075500' => 'ppe', 'Prupe.6G076400' => 'ppe', 'Prupe.8G110700' => 'ppe', 'Psat4g020960' => 'psa', 'PSO135G0788' => 'pso', 'PSO210G6463' => 'pso', 'PSO384G0370' => 'pso', 'PSO386G0056' => 'pso', 'QL01p006048' => 'qlo', 'QL02p054283' => 'qlo', 'QL05p008000' => 'qlo', 'QL05p008212' => 'qlo', 'QL05p008950' => 'qlo', 'QL05p009042' => 'qlo', 'QL05p009518' => 'qlo', 'QL05p012589' => 'qlo', 'QL05p012608' => 'qlo', 'QL05p012650' => 'qlo', 'QL05p012667' => 'qlo', 'QL05p014501' => 'qlo', 'QL05p052800' => 'qlo', 'QL05p065010' => 'qlo', 'QL05p074156' => 'qlo', 'QL05p074160' => 'qlo', 'QL05p074174' => 'qlo', 'QL05p074178' => 'qlo', 'QL05p074214' => 'qlo', 'QL06p001050' => 'qlo', 'QL06p001056' => 'qlo', 'QL06p006093' => 'qlo', 'QL06p006111' => 'qlo', 'QL07p019784' => 'qlo', 'QL07p019801' => 'qlo', 'QL07p036110' => 'qlo', 'QL07p036134' => 'qlo', 'QL07p036147' => 'qlo', 'QL07p036156' => 'qlo', 'QL07p036300' => 'qlo', 'QL07p036320' => 'qlo', 'QL08p014547' => 'qlo', 'QL08p014551' => 'qlo', 'QL08p043319' => 'qlo', 'QL08p043324' => 'qlo', 'QL11p009094' => 'qlo', 'RcHm_v2.0_Chr1g0380481' => 'rch', 'RcHm_v2.0_Chr2g0089331' => 'rch', 'RcHm_v2.0_Chr2g0123691' => 'rch', 'RcHm_v2.0_Chr2g0151111' => 'rch', 'RcHm_v2.0_Chr2g0163011' => 'rch', 'RcHm_v2.0_Chr2g0163051' => 'rch', 'RcHm_v2.0_Chr2g0164671' => 'rch', 'RcHm_v2.0_Chr2g0164681' => 'rch', 'RcHm_v2.0_Chr2g0164721' => 'rch', 'RcHm_v2.0_Chr3g0449911' => 'rch', 'RcHm_v2.0_Chr3g0450211' => 'rch', 'RcHm_v2.0_Chr3g0457271' => 'rch', 'RcHm_v2.0_Chr5g0018111' => 'rch', 'RcHm_v2.0_Chr5g0021011' => 'rch', 'RcHm_v2.0_Chr5g0081171' => 'rch', 'RcHm_v2.0_Chr5g0081211' => 'rch', 'RcHm_v2.0_Chr6g0275871' => 'rch', 'RcHm_v2.0_Chr6g0276071' => 'rch', 'RcHm_v2.0_Chr6g0285591' => 'rch', 'RcHm_v2.0_Chr6g0291931' => 'rch', 'RcHm_v2.0_Chr6g0292091' => 'rch', 'RcHm_v2.0_Chr6g0292271' => 'rch', 'RcHm_v2.0_Chr7g0221261' => 'rch', 'Rhsim08G0219900' => 'rsi', 'Rhsim08G0220200' => 'rsi', 'Rhsim08G0237800' => 'rsi', 'Rhsim08G0238800' => 'rsi', 'Sabra09G0102700' => 'sbr', 'Sabra09G0127200' => 'sbr', 'Sabra11G0003700' => 'sbr', 'Sabra15G0014700' => 'sbr', 'Sc19g0000590' => 'sci', 'Sc19g0001870' => 'sci', 'SGA_v2.0_scaffold1G00346' => 'sas', 'SGA_v2.0_scaffold1G00575' => 'sas', 'SGA_v2.0_scaffold1G00761' => 'sas', 'SGA_v2.0_scaffold232G43501' => 'sas', 'TAR625G1137' => 'tar', 'Thecc.03G222100' => 'tca', 'TPR.G12691' => 'tpr', 'TWI34G0727' => 'twi', 'TWI36G0117' => 'twi', 'VMungo1309G0868' => 'vmu' ), 'gf_id' => 'HOM05D001729', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001729' ), 'data_identifier' => 'HOM05D001729', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001729', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '375', 'num_species' => '42' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'Ah.07g204710' => 'amhyb', 'AUR62006001' => 'cqu', 'AUR62006002' => 'cqu', 'AUR62006003' => 'cqu', 'AUR62015641' => 'cqu', 'AUR62027174' => 'cqu', 'AUR62035623' => 'cqu', 'AUR62035624' => 'cqu', 'AUR62035625' => 'cqu', 'AUR62035626' => 'cqu', 'CAN.G1110.53' => 'can', 'CANSAT80G0415' => 'cansat', 'Ca_21364_v3' => 'car', 'COL.COLO4_30693' => 'col', 'COL.COLO4_30694' => 'col', 'COL.COLO4_30695' => 'col', 'COL.COLO4_30696' => 'col', 'COL.COLO4_34020' => 'col', 'DCAR_004585' => 'dca', 'Dinv04029' => 'din', 'Dinv34857' => 'din', 'Duzib147G0011' => 'dzi', 'Duzib170G0599' => 'dzi', 'Duzib192G1051' => 'dzi', 'FAN01G0708' => 'fan', 'FAN01G0742' => 'fan', 'FAN02G0048' => 'fan', 'FAN02G0583' => 'fan', 'FAN02G0688' => 'fan', 'FAN02G1588' => 'fan', 'FAN02G2194' => 'fan', 'FAN02G2750' => 'fan', 'FAN02G3094' => 'fan', 'FAN02G3887' => 'fan', 'FAN02G3911' => 'fan', 'FAN02G3994' => 'fan', 'FAN02G4432' => 'fan', 'FAN02G4556' => 'fan', 'FAN03G1977' => 'fan', 'FAN03G2781' => 'fan', 'FAN03G2850' => 'fan', 'FAN03G3155' => 'fan', 'FAN04G2487' => 'fan', 'FAN05G0208' => 'fan', 'FAN05G0656' => 'fan', 'FAN05G0696' => 'fan', 'FAN05G0810' => 'fan', 'FAN05G1447' => 'fan', 'FAN05G2640' => 'fan', 'FAN05G2911' => 'fan', 'FAN05G3901' => 'fan', 'FAN05G4859' => 'fan', 'FAN05G4861' => 'fan', 'FAN05G4988' => 'fan', 'FAN05G5187' => 'fan', 'FAN05G5452' => 'fan', 'FAN05G5500' => 'fan', 'FAN05G5688' => 'fan', 'FAN06G0177' => 'fan', 'FAN06G0675' => 'fan', 'FAN06G1290' => 'fan', 'FAN06G2191' => 'fan', 'FAN06G2405' => 'fan', 'FAN06G3231' => 'fan', 'FAN06G3932' => 'fan', 'FAN07G0163' => 'fan', 'FAN07G0471' => 'fan', 'FAN07G1354' => 'fan', 'FAN08G0338' => 'fan', 'FAN08G1373' => 'fan', 'FAN08G2539' => 'fan', 'FAN08G2728' => 'fan', 'FAN09G0608' => 'fan', 'FAN09G1136' => 'fan', 'FAN09G1958' => 'fan', 'FAN09G2508' => 'fan', 'FAN09G2597' => 'fan', 'FAN09G2658' => 'fan', 'FAN09G2757' => 'fan', 'FAN09G2983' => 'fan', 'FAN09G3130' => 'fan', 'FAN09G3565' => 'fan', 'FAN09G3613' => 'fan', 'FAN09G4011' => 'fan', 'FAN09G4239' => 'fan', 'FAN09G4277' => 'fan', 'FAN09G4720' => 'fan', 'FAN11G0139' => 'fan', 'FAN11G1727' => 'fan', 'FAN11G2672' => 'fan', 'FAN11G2795' => 'fan', 'FAN11G3238' => 'fan', 'FAN11G3734' => 'fan', 'FAN12G0631' => 'fan', 'FAN12G2239' => 'fan', 'FAN12G2308' => 'fan', 'FAN12G2569' => 'fan', 'FAN12G2623' => 'fan', 'FAN13G3182' => 'fan', 'FAN14G0053' => 'fan', 'FAN14G0370' => 'fan', 'FAN14G0382' => 'fan', 'FAN14G0421' => 'fan', 'FAN14G0866' => 'fan', 'FAN14G1187' => 'fan', 'FAN14G1727' => 'fan', 'FAN14G1791' => 'fan', 'FAN14G2361' => 'fan', 'FAN14G2668' => 'fan', 'FAN14G2770' => 'fan', 'FAN14G2874' => 'fan', 'FAN14G3193' => 'fan', 'FAN14G3624' => 'fan', 'FAN14G3676' => 'fan', 'FAN14G3807' => 'fan', 'FAN14G4082' => 'fan', 'FAN14G4342' => 'fan', 'FAN14G4985' => 'fan', 'FAN14G5126' => 'fan', 'FAN14G5781' => 'fan', 'FAN14G5808' => 'fan', 'FAN14G5949' => 'fan', 'FAN15G0828' => 'fan', 'FAN15G1054' => 'fan', 'FAN15G2023' => 'fan', 'FAN15G2506' => 'fan', 'FAN16G0128' => 'fan', 'FAN16G0249' => 'fan', 'FAN16G0429' => 'fan', 'FAN16G1493' => 'fan', 'FAN16G2210' => 'fan', 'FAN16G2506' => 'fan', 'FAN18G1542' => 'fan', 'FAN18G4057' => 'fan', 'FAN19G0745' => 'fan', 'FAN19G1216' => 'fan', 'FAN19G1733' => 'fan', 'FAN20G0258' => 'fan', 'FAN20G1095' => 'fan', 'FAN20G1557' => 'fan', 'FAN21G0302' => 'fan', 'FAN21G0519' => 'fan', 'FAN21G0970' => 'fan', 'FAN21G1159' => 'fan', 'FAN21G1312' => 'fan', 'FAN21G1440' => 'fan', 'FAN21G1715' => 'fan', 'FAN23G1584' => 'fan', 'FAN24G0045' => 'fan', 'FAN24G0053' => 'fan', 'FAN24G1500' => 'fan', 'FAN24G1817' => 'fan', 'FAN24G2147' => 'fan', 'FAN24G2236' => 'fan', 'FAN24G2446' => 'fan', 'FAN24G2684' => 'fan', 'FAN25G0187' => 'fan', 'FAN25G0505' => 'fan', 'FAN25G0589' => 'fan', 'FAN25G3663' => 'fan', 'FAN26G1025' => 'fan', 'FAN26G2860' => 'fan', 'FAN27G1329' => 'fan', 'FAN27G3392' => 'fan', 'FvH4_1g02011' => 'fve', 'FvH4_1g06511' => 'fve', 'FvH4_2g19900' => 'fve', 'FvH4_2g19920' => 'fve', 'FvH4_2g24261' => 'fve', 'FvH4_2g24270' => 'fve', 'FvH4_2g24631' => 'fve', 'FvH4_2g30622' => 'fve', 'FvH4_3g12920' => 'fve', 'FvH4_3g30171' => 'fve', 'FvH4_3g35490' => 'fve', 'FvH4_3g43682' => 'fve', 'FvH4_3g43730' => 'fve', 'FvH4_3g43732' => 'fve', 'FvH4_3g43751' => 'fve', 'FvH4_3g43752' => 'fve', 'FvH4_3g43770' => 'fve', 'FvH4_3g44471' => 'fve', 'FvH4_3g44510' => 'fve', 'FvH4_3g44582' => 'fve', 'FvH4_4g16921' => 'fve', 'FvH4_4g17121' => 'fve', 'FvH4_4g17782' => 'fve', 'FvH4_4g17783' => 'fve', 'FvH4_4g18120' => 'fve', 'FvH4_4g31310' => 'fve', 'FvH4_4g35052' => 'fve', 'FvH4_5g30862' => 'fve', 'FvH4_6g01541' => 'fve', 'FvH4_6g02021' => 'fve', 'FvH4_6g02041' => 'fve', 'FvH4_6g02071' => 'fve', 'FvH4_6g02171' => 'fve', 'FvH4_6g03181' => 'fve', 'FvH4_6g03182' => 'fve', 'FvH4_6g03221' => 'fve', 'FvH4_6g03380' => 'fve', 'FvH4_6g05201' => 'fve', 'FvH4_6g05203' => 'fve', 'FvH4_6g20231' => 'fve', 'FvH4_6g31981' => 'fve', 'FvH4_6g32061' => 'fve', 'FvH4_6g37041' => 'fve', 'FvH4_6g37932' => 'fve', 'FvH4_6g38731' => 'fve', 'FvH4_6g39370' => 'fve', 'FvH4_6g39371' => 'fve', 'FvH4_6g40891' => 'fve', 'FvH4_6g40892' => 'fve', 'FvH4_6g43143' => 'fve', 'FvH4_6g45251' => 'fve', 'FvH4_6g45260' => 'fve', 'FvH4_6g45291' => 'fve', 'FvH4_6g45890' => 'fve', 'FvH4_6g46240' => 'fve', 'FvH4_6g46241' => 'fve', 'FvH4_6g46242' => 'fve', 'FvH4_6g46260' => 'fve', 'FvH4_6g46280' => 'fve', 'FvH4_6g46380' => 'fve', 'FvH4_7g12841' => 'fve', 'FvH4_7g31431' => 'fve', 'Glyma.09G075900' => 'gma', 'Gohir.A09G096401' => 'ghi', 'Gohir.D09G096101' => 'ghi', 'Gorai.006G112800' => 'gra', 'HanXRQChr04g0121411' => 'han', 'Hund15878' => 'sun', 'Lj2A1107G68' => 'lonja', 'Lj2A630G63' => 'lonja', 'Lj2A946T25' => 'lonja', 'Lj2C714T1' => 'lonja', 'Lj2C966T3' => 'lonja', 'Lj2C966T4' => 'lonja', 'Lj4g0002979' => 'lja', 'Lsat_1_v5_gn_5_30901' => 'lsa', 'Lsat_1_v5_gn_5_31100' => 'lsa', 'Lsat_1_v5_gn_5_38600' => 'lsa', 'Lsat_1_v5_gn_6_92061' => 'lsa', 'Manes.05G071301' => 'mes', 'MD02G1008700' => 'mdo', 'MD02G1008900' => 'mdo', 'MD03G1256400' => 'mdo', 'MD04G1180900' => 'mdo', 'MD04G1181000' => 'mdo', 'MD04G1181200' => 'mdo', 'MD05G1244200' => 'mdo', 'MD05G1324200' => 'mdo', 'MD09G1201600' => 'mdo', 'MD10G1000600' => 'mdo', 'MD14G1026900' => 'mdo', 'MD14G1187900' => 'mdo', 'MD15G1017800' => 'mdo', 'MD15G1018100' => 'mdo', 'Medtr4g124160' => 'mtr', 'Migut.L01260' => 'egut', 'Nitab4.5_0000008g0440' => 'nta', 'Nitab4.5_0000207g0170' => 'nta', 'Nitab4.5_0007671g0030' => 'nta', 'Nitab4.5_0010853g0020' => 'nta', 'Oeu057656.1' => 'oeu', 'PGSC0003DMG400005638' => 'stu', 'PGSC0003DMG400005639' => 'stu', 'Phvul.009G222800' => 'pvu', 'Potri.009G132400' => 'ptr', 'Potri.009G163001' => 'ptr', 'Potri.011G000700' => 'ptr', 'Potri.011G004800' => 'ptr', 'Prupe.1G509300' => 'ppe', 'Prupe.1G509700' => 'ppe', 'Prupe.1G510400' => 'ppe', 'Prupe.1G510700' => 'ppe', 'Prupe.1G512600' => 'ppe', 'Prupe.2G073200' => 'ppe', 'Prupe.3G059500' => 'ppe', 'Prupe.3G059600' => 'ppe', 'Prupe.3G246100' => 'ppe', 'Prupe.3G265100' => 'ppe', 'Prupe.4G034700' => 'ppe', 'Prupe.4G052100' => 'ppe', 'Prupe.4G053600' => 'ppe', 'Prupe.5G068800' => 'ppe', 'Prupe.5G070600' => 'ppe', 'Prupe.6G075400' => 'ppe', 'Prupe.6G075500' => 'ppe', 'Prupe.6G076400' => 'ppe', 'Prupe.8G110700' => 'ppe', 'Psat4g020960' => 'psa', 'PSO135G0788' => 'pso', 'PSO210G6463' => 'pso', 'PSO384G0370' => 'pso', 'PSO386G0056' => 'pso', 'QL01p006048' => 'qlo', 'QL02p054283' => 'qlo', 'QL05p008000' => 'qlo', 'QL05p008212' => 'qlo', 'QL05p008950' => 'qlo', 'QL05p009042' => 'qlo', 'QL05p009518' => 'qlo', 'QL05p012589' => 'qlo', 'QL05p012608' => 'qlo', 'QL05p012650' => 'qlo', 'QL05p012667' => 'qlo', 'QL05p014501' => 'qlo', 'QL05p052800' => 'qlo', 'QL05p065010' => 'qlo', 'QL05p074156' => 'qlo', 'QL05p074160' => 'qlo', 'QL05p074174' => 'qlo', 'QL05p074178' => 'qlo', 'QL05p074214' => 'qlo', 'QL06p001050' => 'qlo', 'QL06p001056' => 'qlo', 'QL06p006093' => 'qlo', 'QL06p006111' => 'qlo', 'QL07p019784' => 'qlo', 'QL07p019801' => 'qlo', 'QL07p036110' => 'qlo', 'QL07p036134' => 'qlo', 'QL07p036147' => 'qlo', 'QL07p036156' => 'qlo', 'QL07p036300' => 'qlo', 'QL07p036320' => 'qlo', 'QL08p014547' => 'qlo', 'QL08p014551' => 'qlo', 'QL08p043319' => 'qlo', 'QL08p043324' => 'qlo', 'QL11p009094' => 'qlo', 'RcHm_v2.0_Chr1g0380481' => 'rch', 'RcHm_v2.0_Chr2g0089331' => 'rch', 'RcHm_v2.0_Chr2g0123691' => 'rch', 'RcHm_v2.0_Chr2g0151111' => 'rch', 'RcHm_v2.0_Chr2g0163011' => 'rch', 'RcHm_v2.0_Chr2g0163051' => 'rch', 'RcHm_v2.0_Chr2g0164671' => 'rch', 'RcHm_v2.0_Chr2g0164681' => 'rch', 'RcHm_v2.0_Chr2g0164721' => 'rch', 'RcHm_v2.0_Chr3g0449911' => 'rch', 'RcHm_v2.0_Chr3g0450211' => 'rch', 'RcHm_v2.0_Chr3g0457271' => 'rch', 'RcHm_v2.0_Chr5g0018111' => 'rch', 'RcHm_v2.0_Chr5g0021011' => 'rch', 'RcHm_v2.0_Chr5g0081171' => 'rch', 'RcHm_v2.0_Chr5g0081211' => 'rch', 'RcHm_v2.0_Chr6g0275871' => 'rch', 'RcHm_v2.0_Chr6g0276071' => 'rch', 'RcHm_v2.0_Chr6g0285591' => 'rch', 'RcHm_v2.0_Chr6g0291931' => 'rch', 'RcHm_v2.0_Chr6g0292091' => 'rch', 'RcHm_v2.0_Chr6g0292271' => 'rch', 'RcHm_v2.0_Chr7g0221261' => 'rch', 'Rhsim08G0219900' => 'rsi', 'Rhsim08G0220200' => 'rsi', 'Rhsim08G0237800' => 'rsi', 'Rhsim08G0238800' => 'rsi', 'Sabra09G0102700' => 'sbr', 'Sabra09G0127200' => 'sbr', 'Sabra11G0003700' => 'sbr', 'Sabra15G0014700' => 'sbr', 'Sc19g0000590' => 'sci', 'Sc19g0001870' => 'sci', 'SGA_v2.0_scaffold1G00346' => 'sas', 'SGA_v2.0_scaffold1G00575' => 'sas', 'SGA_v2.0_scaffold1G00761' => 'sas', 'SGA_v2.0_scaffold232G43501' => 'sas', 'TAR625G1137' => 'tar', 'Thecc.03G222100' => 'tca', 'TPR.G12691' => 'tpr', 'TWI34G0727' => 'twi', 'TWI36G0117' => 'twi', 'VMungo1309G0868' => 'vmu' ) $gf_id = 'HOM05D001729' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001729' ) $data_identifier = 'HOM05D001729' $data_type = 'gf_id' $species_gene_counts = array( 'amhyb' => (int) 1, 'cqu' => (int) 9, 'can' => (int) 1, 'cansat' => (int) 1, 'car' => (int) 1, 'col' => (int) 5, 'dca' => (int) 1, 'din' => (int) 2, 'dzi' => (int) 3, 'fan' => (int) 140, 'fve' => (int) 62, 'gma' => (int) 1, 'ghi' => (int) 2, 'gra' => (int) 1, 'han' => (int) 1, 'sun' => (int) 1, 'lonja' => (int) 6, 'lja' => (int) 1, 'lsa' => (int) 4, 'mes' => (int) 1, 'mdo' => (int) 14, 'mtr' => (int) 1, 'egut' => (int) 1, 'nta' => (int) 4, 'oeu' => (int) 1, 'stu' => (int) 2, 'pvu' => (int) 1, 'ptr' => (int) 4, 'ppe' => (int) 19, 'psa' => (int) 1, 'pso' => (int) 4, 'qlo' => (int) 36, 'rch' => (int) 23, 'rsi' => (int) 4, 'sbr' => (int) 4, 'sci' => (int) 2, 'sas' => (int) 4, 'tar' => (int) 1, 'tca' => (int) 1, 'tpr' => (int) 1, 'twi' => (int) 2, 'vmu' => (int) 1 ) $gf_gene_species = 'vmu' $gf_gene_id = 'VMungo1309G0868' $species_info = array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ) $local_species = 'sbr' $disabled = '' $selected = '' $num_hits = (int) 1
Warning (2): count(): Parameter must be an array or an object that implements Countable [APP/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp, line 33]Code Context $disabled = (!array_key_exists($local_species,$species_gene_counts))?"disabled":""; $selected = (isset($selected_species) && array_key_exists($local_species,$selected_species))?"checked='checked'":""; $num_hits = (array_key_exists($local_species,$species_gene_counts))?count($species_gene_counts[$local_species]):0; $viewFile = '/www/bioinformatics01_ro/plaza/_dev_instances/feedback/app/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp' $dataForView = array( 'sidebar_info' => array( 'gf_id' => 'HOM05D001729', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '375', 'num_species' => '42' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'Ah.07g204710' => 'amhyb', 'AUR62006001' => 'cqu', 'AUR62006002' => 'cqu', 'AUR62006003' => 'cqu', 'AUR62015641' => 'cqu', 'AUR62027174' => 'cqu', 'AUR62035623' => 'cqu', 'AUR62035624' => 'cqu', 'AUR62035625' => 'cqu', 'AUR62035626' => 'cqu', 'CAN.G1110.53' => 'can', 'CANSAT80G0415' => 'cansat', 'Ca_21364_v3' => 'car', 'COL.COLO4_30693' => 'col', 'COL.COLO4_30694' => 'col', 'COL.COLO4_30695' => 'col', 'COL.COLO4_30696' => 'col', 'COL.COLO4_34020' => 'col', 'DCAR_004585' => 'dca', 'Dinv04029' => 'din', 'Dinv34857' => 'din', 'Duzib147G0011' => 'dzi', 'Duzib170G0599' => 'dzi', 'Duzib192G1051' => 'dzi', 'FAN01G0708' => 'fan', 'FAN01G0742' => 'fan', 'FAN02G0048' => 'fan', 'FAN02G0583' => 'fan', 'FAN02G0688' => 'fan', 'FAN02G1588' => 'fan', 'FAN02G2194' => 'fan', 'FAN02G2750' => 'fan', 'FAN02G3094' => 'fan', 'FAN02G3887' => 'fan', 'FAN02G3911' => 'fan', 'FAN02G3994' => 'fan', 'FAN02G4432' => 'fan', 'FAN02G4556' => 'fan', 'FAN03G1977' => 'fan', 'FAN03G2781' => 'fan', 'FAN03G2850' => 'fan', 'FAN03G3155' => 'fan', 'FAN04G2487' => 'fan', 'FAN05G0208' => 'fan', 'FAN05G0656' => 'fan', 'FAN05G0696' => 'fan', 'FAN05G0810' => 'fan', 'FAN05G1447' => 'fan', 'FAN05G2640' => 'fan', 'FAN05G2911' => 'fan', 'FAN05G3901' => 'fan', 'FAN05G4859' => 'fan', 'FAN05G4861' => 'fan', 'FAN05G4988' => 'fan', 'FAN05G5187' => 'fan', 'FAN05G5452' => 'fan', 'FAN05G5500' => 'fan', 'FAN05G5688' => 'fan', 'FAN06G0177' => 'fan', 'FAN06G0675' => 'fan', 'FAN06G1290' => 'fan', 'FAN06G2191' => 'fan', 'FAN06G2405' => 'fan', 'FAN06G3231' => 'fan', 'FAN06G3932' => 'fan', 'FAN07G0163' => 'fan', 'FAN07G0471' => 'fan', 'FAN07G1354' => 'fan', 'FAN08G0338' => 'fan', 'FAN08G1373' => 'fan', 'FAN08G2539' => 'fan', 'FAN08G2728' => 'fan', 'FAN09G0608' => 'fan', 'FAN09G1136' => 'fan', 'FAN09G1958' => 'fan', 'FAN09G2508' => 'fan', 'FAN09G2597' => 'fan', 'FAN09G2658' => 'fan', 'FAN09G2757' => 'fan', 'FAN09G2983' => 'fan', 'FAN09G3130' => 'fan', 'FAN09G3565' => 'fan', 'FAN09G3613' => 'fan', 'FAN09G4011' => 'fan', 'FAN09G4239' => 'fan', 'FAN09G4277' => 'fan', 'FAN09G4720' => 'fan', 'FAN11G0139' => 'fan', 'FAN11G1727' => 'fan', 'FAN11G2672' => 'fan', 'FAN11G2795' => 'fan', 'FAN11G3238' => 'fan', 'FAN11G3734' => 'fan', 'FAN12G0631' => 'fan', 'FAN12G2239' => 'fan', 'FAN12G2308' => 'fan', 'FAN12G2569' => 'fan', 'FAN12G2623' => 'fan', 'FAN13G3182' => 'fan', 'FAN14G0053' => 'fan', 'FAN14G0370' => 'fan', 'FAN14G0382' => 'fan', 'FAN14G0421' => 'fan', 'FAN14G0866' => 'fan', 'FAN14G1187' => 'fan', 'FAN14G1727' => 'fan', 'FAN14G1791' => 'fan', 'FAN14G2361' => 'fan', 'FAN14G2668' => 'fan', 'FAN14G2770' => 'fan', 'FAN14G2874' => 'fan', 'FAN14G3193' => 'fan', 'FAN14G3624' => 'fan', 'FAN14G3676' => 'fan', 'FAN14G3807' => 'fan', 'FAN14G4082' => 'fan', 'FAN14G4342' => 'fan', 'FAN14G4985' => 'fan', 'FAN14G5126' => 'fan', 'FAN14G5781' => 'fan', 'FAN14G5808' => 'fan', 'FAN14G5949' => 'fan', 'FAN15G0828' => 'fan', 'FAN15G1054' => 'fan', 'FAN15G2023' => 'fan', 'FAN15G2506' => 'fan', 'FAN16G0128' => 'fan', 'FAN16G0249' => 'fan', 'FAN16G0429' => 'fan', 'FAN16G1493' => 'fan', 'FAN16G2210' => 'fan', 'FAN16G2506' => 'fan', 'FAN18G1542' => 'fan', 'FAN18G4057' => 'fan', 'FAN19G0745' => 'fan', 'FAN19G1216' => 'fan', 'FAN19G1733' => 'fan', 'FAN20G0258' => 'fan', 'FAN20G1095' => 'fan', 'FAN20G1557' => 'fan', 'FAN21G0302' => 'fan', 'FAN21G0519' => 'fan', 'FAN21G0970' => 'fan', 'FAN21G1159' => 'fan', 'FAN21G1312' => 'fan', 'FAN21G1440' => 'fan', 'FAN21G1715' => 'fan', 'FAN23G1584' => 'fan', 'FAN24G0045' => 'fan', 'FAN24G0053' => 'fan', 'FAN24G1500' => 'fan', 'FAN24G1817' => 'fan', 'FAN24G2147' => 'fan', 'FAN24G2236' => 'fan', 'FAN24G2446' => 'fan', 'FAN24G2684' => 'fan', 'FAN25G0187' => 'fan', 'FAN25G0505' => 'fan', 'FAN25G0589' => 'fan', 'FAN25G3663' => 'fan', 'FAN26G1025' => 'fan', 'FAN26G2860' => 'fan', 'FAN27G1329' => 'fan', 'FAN27G3392' => 'fan', 'FvH4_1g02011' => 'fve', 'FvH4_1g06511' => 'fve', 'FvH4_2g19900' => 'fve', 'FvH4_2g19920' => 'fve', 'FvH4_2g24261' => 'fve', 'FvH4_2g24270' => 'fve', 'FvH4_2g24631' => 'fve', 'FvH4_2g30622' => 'fve', 'FvH4_3g12920' => 'fve', 'FvH4_3g30171' => 'fve', 'FvH4_3g35490' => 'fve', 'FvH4_3g43682' => 'fve', 'FvH4_3g43730' => 'fve', 'FvH4_3g43732' => 'fve', 'FvH4_3g43751' => 'fve', 'FvH4_3g43752' => 'fve', 'FvH4_3g43770' => 'fve', 'FvH4_3g44471' => 'fve', 'FvH4_3g44510' => 'fve', 'FvH4_3g44582' => 'fve', 'FvH4_4g16921' => 'fve', 'FvH4_4g17121' => 'fve', 'FvH4_4g17782' => 'fve', 'FvH4_4g17783' => 'fve', 'FvH4_4g18120' => 'fve', 'FvH4_4g31310' => 'fve', 'FvH4_4g35052' => 'fve', 'FvH4_5g30862' => 'fve', 'FvH4_6g01541' => 'fve', 'FvH4_6g02021' => 'fve', 'FvH4_6g02041' => 'fve', 'FvH4_6g02071' => 'fve', 'FvH4_6g02171' => 'fve', 'FvH4_6g03181' => 'fve', 'FvH4_6g03182' => 'fve', 'FvH4_6g03221' => 'fve', 'FvH4_6g03380' => 'fve', 'FvH4_6g05201' => 'fve', 'FvH4_6g05203' => 'fve', 'FvH4_6g20231' => 'fve', 'FvH4_6g31981' => 'fve', 'FvH4_6g32061' => 'fve', 'FvH4_6g37041' => 'fve', 'FvH4_6g37932' => 'fve', 'FvH4_6g38731' => 'fve', 'FvH4_6g39370' => 'fve', 'FvH4_6g39371' => 'fve', 'FvH4_6g40891' => 'fve', 'FvH4_6g40892' => 'fve', 'FvH4_6g43143' => 'fve', 'FvH4_6g45251' => 'fve', 'FvH4_6g45260' => 'fve', 'FvH4_6g45291' => 'fve', 'FvH4_6g45890' => 'fve', 'FvH4_6g46240' => 'fve', 'FvH4_6g46241' => 'fve', 'FvH4_6g46242' => 'fve', 'FvH4_6g46260' => 'fve', 'FvH4_6g46280' => 'fve', 'FvH4_6g46380' => 'fve', 'FvH4_7g12841' => 'fve', 'FvH4_7g31431' => 'fve', 'Glyma.09G075900' => 'gma', 'Gohir.A09G096401' => 'ghi', 'Gohir.D09G096101' => 'ghi', 'Gorai.006G112800' => 'gra', 'HanXRQChr04g0121411' => 'han', 'Hund15878' => 'sun', 'Lj2A1107G68' => 'lonja', 'Lj2A630G63' => 'lonja', 'Lj2A946T25' => 'lonja', 'Lj2C714T1' => 'lonja', 'Lj2C966T3' => 'lonja', 'Lj2C966T4' => 'lonja', 'Lj4g0002979' => 'lja', 'Lsat_1_v5_gn_5_30901' => 'lsa', 'Lsat_1_v5_gn_5_31100' => 'lsa', 'Lsat_1_v5_gn_5_38600' => 'lsa', 'Lsat_1_v5_gn_6_92061' => 'lsa', 'Manes.05G071301' => 'mes', 'MD02G1008700' => 'mdo', 'MD02G1008900' => 'mdo', 'MD03G1256400' => 'mdo', 'MD04G1180900' => 'mdo', 'MD04G1181000' => 'mdo', 'MD04G1181200' => 'mdo', 'MD05G1244200' => 'mdo', 'MD05G1324200' => 'mdo', 'MD09G1201600' => 'mdo', 'MD10G1000600' => 'mdo', 'MD14G1026900' => 'mdo', 'MD14G1187900' => 'mdo', 'MD15G1017800' => 'mdo', 'MD15G1018100' => 'mdo', 'Medtr4g124160' => 'mtr', 'Migut.L01260' => 'egut', 'Nitab4.5_0000008g0440' => 'nta', 'Nitab4.5_0000207g0170' => 'nta', 'Nitab4.5_0007671g0030' => 'nta', 'Nitab4.5_0010853g0020' => 'nta', 'Oeu057656.1' => 'oeu', 'PGSC0003DMG400005638' => 'stu', 'PGSC0003DMG400005639' => 'stu', 'Phvul.009G222800' => 'pvu', 'Potri.009G132400' => 'ptr', 'Potri.009G163001' => 'ptr', 'Potri.011G000700' => 'ptr', 'Potri.011G004800' => 'ptr', 'Prupe.1G509300' => 'ppe', 'Prupe.1G509700' => 'ppe', 'Prupe.1G510400' => 'ppe', 'Prupe.1G510700' => 'ppe', 'Prupe.1G512600' => 'ppe', 'Prupe.2G073200' => 'ppe', 'Prupe.3G059500' => 'ppe', 'Prupe.3G059600' => 'ppe', 'Prupe.3G246100' => 'ppe', 'Prupe.3G265100' => 'ppe', 'Prupe.4G034700' => 'ppe', 'Prupe.4G052100' => 'ppe', 'Prupe.4G053600' => 'ppe', 'Prupe.5G068800' => 'ppe', 'Prupe.5G070600' => 'ppe', 'Prupe.6G075400' => 'ppe', 'Prupe.6G075500' => 'ppe', 'Prupe.6G076400' => 'ppe', 'Prupe.8G110700' => 'ppe', 'Psat4g020960' => 'psa', 'PSO135G0788' => 'pso', 'PSO210G6463' => 'pso', 'PSO384G0370' => 'pso', 'PSO386G0056' => 'pso', 'QL01p006048' => 'qlo', 'QL02p054283' => 'qlo', 'QL05p008000' => 'qlo', 'QL05p008212' => 'qlo', 'QL05p008950' => 'qlo', 'QL05p009042' => 'qlo', 'QL05p009518' => 'qlo', 'QL05p012589' => 'qlo', 'QL05p012608' => 'qlo', 'QL05p012650' => 'qlo', 'QL05p012667' => 'qlo', 'QL05p014501' => 'qlo', 'QL05p052800' => 'qlo', 'QL05p065010' => 'qlo', 'QL05p074156' => 'qlo', 'QL05p074160' => 'qlo', 'QL05p074174' => 'qlo', 'QL05p074178' => 'qlo', 'QL05p074214' => 'qlo', 'QL06p001050' => 'qlo', 'QL06p001056' => 'qlo', 'QL06p006093' => 'qlo', 'QL06p006111' => 'qlo', 'QL07p019784' => 'qlo', 'QL07p019801' => 'qlo', 'QL07p036110' => 'qlo', 'QL07p036134' => 'qlo', 'QL07p036147' => 'qlo', 'QL07p036156' => 'qlo', 'QL07p036300' => 'qlo', 'QL07p036320' => 'qlo', 'QL08p014547' => 'qlo', 'QL08p014551' => 'qlo', 'QL08p043319' => 'qlo', 'QL08p043324' => 'qlo', 'QL11p009094' => 'qlo', 'RcHm_v2.0_Chr1g0380481' => 'rch', 'RcHm_v2.0_Chr2g0089331' => 'rch', 'RcHm_v2.0_Chr2g0123691' => 'rch', 'RcHm_v2.0_Chr2g0151111' => 'rch', 'RcHm_v2.0_Chr2g0163011' => 'rch', 'RcHm_v2.0_Chr2g0163051' => 'rch', 'RcHm_v2.0_Chr2g0164671' => 'rch', 'RcHm_v2.0_Chr2g0164681' => 'rch', 'RcHm_v2.0_Chr2g0164721' => 'rch', 'RcHm_v2.0_Chr3g0449911' => 'rch', 'RcHm_v2.0_Chr3g0450211' => 'rch', 'RcHm_v2.0_Chr3g0457271' => 'rch', 'RcHm_v2.0_Chr5g0018111' => 'rch', 'RcHm_v2.0_Chr5g0021011' => 'rch', 'RcHm_v2.0_Chr5g0081171' => 'rch', 'RcHm_v2.0_Chr5g0081211' => 'rch', 'RcHm_v2.0_Chr6g0275871' => 'rch', 'RcHm_v2.0_Chr6g0276071' => 'rch', 'RcHm_v2.0_Chr6g0285591' => 'rch', 'RcHm_v2.0_Chr6g0291931' => 'rch', 'RcHm_v2.0_Chr6g0292091' => 'rch', 'RcHm_v2.0_Chr6g0292271' => 'rch', 'RcHm_v2.0_Chr7g0221261' => 'rch', 'Rhsim08G0219900' => 'rsi', 'Rhsim08G0220200' => 'rsi', 'Rhsim08G0237800' => 'rsi', 'Rhsim08G0238800' => 'rsi', 'Sabra09G0102700' => 'sbr', 'Sabra09G0127200' => 'sbr', 'Sabra11G0003700' => 'sbr', 'Sabra15G0014700' => 'sbr', 'Sc19g0000590' => 'sci', 'Sc19g0001870' => 'sci', 'SGA_v2.0_scaffold1G00346' => 'sas', 'SGA_v2.0_scaffold1G00575' => 'sas', 'SGA_v2.0_scaffold1G00761' => 'sas', 'SGA_v2.0_scaffold232G43501' => 'sas', 'TAR625G1137' => 'tar', 'Thecc.03G222100' => 'tca', 'TPR.G12691' => 'tpr', 'TWI34G0727' => 'twi', 'TWI36G0117' => 'twi', 'VMungo1309G0868' => 'vmu' ), 'gf_id' => 'HOM05D001729', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001729' ), 'data_identifier' => 'HOM05D001729', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001729', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '375', 'num_species' => '42' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'Ah.07g204710' => 'amhyb', 'AUR62006001' => 'cqu', 'AUR62006002' => 'cqu', 'AUR62006003' => 'cqu', 'AUR62015641' => 'cqu', 'AUR62027174' => 'cqu', 'AUR62035623' => 'cqu', 'AUR62035624' => 'cqu', 'AUR62035625' => 'cqu', 'AUR62035626' => 'cqu', 'CAN.G1110.53' => 'can', 'CANSAT80G0415' => 'cansat', 'Ca_21364_v3' => 'car', 'COL.COLO4_30693' => 'col', 'COL.COLO4_30694' => 'col', 'COL.COLO4_30695' => 'col', 'COL.COLO4_30696' => 'col', 'COL.COLO4_34020' => 'col', 'DCAR_004585' => 'dca', 'Dinv04029' => 'din', 'Dinv34857' => 'din', 'Duzib147G0011' => 'dzi', 'Duzib170G0599' => 'dzi', 'Duzib192G1051' => 'dzi', 'FAN01G0708' => 'fan', 'FAN01G0742' => 'fan', 'FAN02G0048' => 'fan', 'FAN02G0583' => 'fan', 'FAN02G0688' => 'fan', 'FAN02G1588' => 'fan', 'FAN02G2194' => 'fan', 'FAN02G2750' => 'fan', 'FAN02G3094' => 'fan', 'FAN02G3887' => 'fan', 'FAN02G3911' => 'fan', 'FAN02G3994' => 'fan', 'FAN02G4432' => 'fan', 'FAN02G4556' => 'fan', 'FAN03G1977' => 'fan', 'FAN03G2781' => 'fan', 'FAN03G2850' => 'fan', 'FAN03G3155' => 'fan', 'FAN04G2487' => 'fan', 'FAN05G0208' => 'fan', 'FAN05G0656' => 'fan', 'FAN05G0696' => 'fan', 'FAN05G0810' => 'fan', 'FAN05G1447' => 'fan', 'FAN05G2640' => 'fan', 'FAN05G2911' => 'fan', 'FAN05G3901' => 'fan', 'FAN05G4859' => 'fan', 'FAN05G4861' => 'fan', 'FAN05G4988' => 'fan', 'FAN05G5187' => 'fan', 'FAN05G5452' => 'fan', 'FAN05G5500' => 'fan', 'FAN05G5688' => 'fan', 'FAN06G0177' => 'fan', 'FAN06G0675' => 'fan', 'FAN06G1290' => 'fan', 'FAN06G2191' => 'fan', 'FAN06G2405' => 'fan', 'FAN06G3231' => 'fan', 'FAN06G3932' => 'fan', 'FAN07G0163' => 'fan', 'FAN07G0471' => 'fan', 'FAN07G1354' => 'fan', 'FAN08G0338' => 'fan', 'FAN08G1373' => 'fan', 'FAN08G2539' => 'fan', 'FAN08G2728' => 'fan', 'FAN09G0608' => 'fan', 'FAN09G1136' => 'fan', 'FAN09G1958' => 'fan', 'FAN09G2508' => 'fan', 'FAN09G2597' => 'fan', 'FAN09G2658' => 'fan', 'FAN09G2757' => 'fan', 'FAN09G2983' => 'fan', 'FAN09G3130' => 'fan', 'FAN09G3565' => 'fan', 'FAN09G3613' => 'fan', 'FAN09G4011' => 'fan', 'FAN09G4239' => 'fan', 'FAN09G4277' => 'fan', 'FAN09G4720' => 'fan', 'FAN11G0139' => 'fan', 'FAN11G1727' => 'fan', 'FAN11G2672' => 'fan', 'FAN11G2795' => 'fan', 'FAN11G3238' => 'fan', 'FAN11G3734' => 'fan', 'FAN12G0631' => 'fan', 'FAN12G2239' => 'fan', 'FAN12G2308' => 'fan', 'FAN12G2569' => 'fan', 'FAN12G2623' => 'fan', 'FAN13G3182' => 'fan', 'FAN14G0053' => 'fan', 'FAN14G0370' => 'fan', 'FAN14G0382' => 'fan', 'FAN14G0421' => 'fan', 'FAN14G0866' => 'fan', 'FAN14G1187' => 'fan', 'FAN14G1727' => 'fan', 'FAN14G1791' => 'fan', 'FAN14G2361' => 'fan', 'FAN14G2668' => 'fan', 'FAN14G2770' => 'fan', 'FAN14G2874' => 'fan', 'FAN14G3193' => 'fan', 'FAN14G3624' => 'fan', 'FAN14G3676' => 'fan', 'FAN14G3807' => 'fan', 'FAN14G4082' => 'fan', 'FAN14G4342' => 'fan', 'FAN14G4985' => 'fan', 'FAN14G5126' => 'fan', 'FAN14G5781' => 'fan', 'FAN14G5808' => 'fan', 'FAN14G5949' => 'fan', 'FAN15G0828' => 'fan', 'FAN15G1054' => 'fan', 'FAN15G2023' => 'fan', 'FAN15G2506' => 'fan', 'FAN16G0128' => 'fan', 'FAN16G0249' => 'fan', 'FAN16G0429' => 'fan', 'FAN16G1493' => 'fan', 'FAN16G2210' => 'fan', 'FAN16G2506' => 'fan', 'FAN18G1542' => 'fan', 'FAN18G4057' => 'fan', 'FAN19G0745' => 'fan', 'FAN19G1216' => 'fan', 'FAN19G1733' => 'fan', 'FAN20G0258' => 'fan', 'FAN20G1095' => 'fan', 'FAN20G1557' => 'fan', 'FAN21G0302' => 'fan', 'FAN21G0519' => 'fan', 'FAN21G0970' => 'fan', 'FAN21G1159' => 'fan', 'FAN21G1312' => 'fan', 'FAN21G1440' => 'fan', 'FAN21G1715' => 'fan', 'FAN23G1584' => 'fan', 'FAN24G0045' => 'fan', 'FAN24G0053' => 'fan', 'FAN24G1500' => 'fan', 'FAN24G1817' => 'fan', 'FAN24G2147' => 'fan', 'FAN24G2236' => 'fan', 'FAN24G2446' => 'fan', 'FAN24G2684' => 'fan', 'FAN25G0187' => 'fan', 'FAN25G0505' => 'fan', 'FAN25G0589' => 'fan', 'FAN25G3663' => 'fan', 'FAN26G1025' => 'fan', 'FAN26G2860' => 'fan', 'FAN27G1329' => 'fan', 'FAN27G3392' => 'fan', 'FvH4_1g02011' => 'fve', 'FvH4_1g06511' => 'fve', 'FvH4_2g19900' => 'fve', 'FvH4_2g19920' => 'fve', 'FvH4_2g24261' => 'fve', 'FvH4_2g24270' => 'fve', 'FvH4_2g24631' => 'fve', 'FvH4_2g30622' => 'fve', 'FvH4_3g12920' => 'fve', 'FvH4_3g30171' => 'fve', 'FvH4_3g35490' => 'fve', 'FvH4_3g43682' => 'fve', 'FvH4_3g43730' => 'fve', 'FvH4_3g43732' => 'fve', 'FvH4_3g43751' => 'fve', 'FvH4_3g43752' => 'fve', 'FvH4_3g43770' => 'fve', 'FvH4_3g44471' => 'fve', 'FvH4_3g44510' => 'fve', 'FvH4_3g44582' => 'fve', 'FvH4_4g16921' => 'fve', 'FvH4_4g17121' => 'fve', 'FvH4_4g17782' => 'fve', 'FvH4_4g17783' => 'fve', 'FvH4_4g18120' => 'fve', 'FvH4_4g31310' => 'fve', 'FvH4_4g35052' => 'fve', 'FvH4_5g30862' => 'fve', 'FvH4_6g01541' => 'fve', 'FvH4_6g02021' => 'fve', 'FvH4_6g02041' => 'fve', 'FvH4_6g02071' => 'fve', 'FvH4_6g02171' => 'fve', 'FvH4_6g03181' => 'fve', 'FvH4_6g03182' => 'fve', 'FvH4_6g03221' => 'fve', 'FvH4_6g03380' => 'fve', 'FvH4_6g05201' => 'fve', 'FvH4_6g05203' => 'fve', 'FvH4_6g20231' => 'fve', 'FvH4_6g31981' => 'fve', 'FvH4_6g32061' => 'fve', 'FvH4_6g37041' => 'fve', 'FvH4_6g37932' => 'fve', 'FvH4_6g38731' => 'fve', 'FvH4_6g39370' => 'fve', 'FvH4_6g39371' => 'fve', 'FvH4_6g40891' => 'fve', 'FvH4_6g40892' => 'fve', 'FvH4_6g43143' => 'fve', 'FvH4_6g45251' => 'fve', 'FvH4_6g45260' => 'fve', 'FvH4_6g45291' => 'fve', 'FvH4_6g45890' => 'fve', 'FvH4_6g46240' => 'fve', 'FvH4_6g46241' => 'fve', 'FvH4_6g46242' => 'fve', 'FvH4_6g46260' => 'fve', 'FvH4_6g46280' => 'fve', 'FvH4_6g46380' => 'fve', 'FvH4_7g12841' => 'fve', 'FvH4_7g31431' => 'fve', 'Glyma.09G075900' => 'gma', 'Gohir.A09G096401' => 'ghi', 'Gohir.D09G096101' => 'ghi', 'Gorai.006G112800' => 'gra', 'HanXRQChr04g0121411' => 'han', 'Hund15878' => 'sun', 'Lj2A1107G68' => 'lonja', 'Lj2A630G63' => 'lonja', 'Lj2A946T25' => 'lonja', 'Lj2C714T1' => 'lonja', 'Lj2C966T3' => 'lonja', 'Lj2C966T4' => 'lonja', 'Lj4g0002979' => 'lja', 'Lsat_1_v5_gn_5_30901' => 'lsa', 'Lsat_1_v5_gn_5_31100' => 'lsa', 'Lsat_1_v5_gn_5_38600' => 'lsa', 'Lsat_1_v5_gn_6_92061' => 'lsa', 'Manes.05G071301' => 'mes', 'MD02G1008700' => 'mdo', 'MD02G1008900' => 'mdo', 'MD03G1256400' => 'mdo', 'MD04G1180900' => 'mdo', 'MD04G1181000' => 'mdo', 'MD04G1181200' => 'mdo', 'MD05G1244200' => 'mdo', 'MD05G1324200' => 'mdo', 'MD09G1201600' => 'mdo', 'MD10G1000600' => 'mdo', 'MD14G1026900' => 'mdo', 'MD14G1187900' => 'mdo', 'MD15G1017800' => 'mdo', 'MD15G1018100' => 'mdo', 'Medtr4g124160' => 'mtr', 'Migut.L01260' => 'egut', 'Nitab4.5_0000008g0440' => 'nta', 'Nitab4.5_0000207g0170' => 'nta', 'Nitab4.5_0007671g0030' => 'nta', 'Nitab4.5_0010853g0020' => 'nta', 'Oeu057656.1' => 'oeu', 'PGSC0003DMG400005638' => 'stu', 'PGSC0003DMG400005639' => 'stu', 'Phvul.009G222800' => 'pvu', 'Potri.009G132400' => 'ptr', 'Potri.009G163001' => 'ptr', 'Potri.011G000700' => 'ptr', 'Potri.011G004800' => 'ptr', 'Prupe.1G509300' => 'ppe', 'Prupe.1G509700' => 'ppe', 'Prupe.1G510400' => 'ppe', 'Prupe.1G510700' => 'ppe', 'Prupe.1G512600' => 'ppe', 'Prupe.2G073200' => 'ppe', 'Prupe.3G059500' => 'ppe', 'Prupe.3G059600' => 'ppe', 'Prupe.3G246100' => 'ppe', 'Prupe.3G265100' => 'ppe', 'Prupe.4G034700' => 'ppe', 'Prupe.4G052100' => 'ppe', 'Prupe.4G053600' => 'ppe', 'Prupe.5G068800' => 'ppe', 'Prupe.5G070600' => 'ppe', 'Prupe.6G075400' => 'ppe', 'Prupe.6G075500' => 'ppe', 'Prupe.6G076400' => 'ppe', 'Prupe.8G110700' => 'ppe', 'Psat4g020960' => 'psa', 'PSO135G0788' => 'pso', 'PSO210G6463' => 'pso', 'PSO384G0370' => 'pso', 'PSO386G0056' => 'pso', 'QL01p006048' => 'qlo', 'QL02p054283' => 'qlo', 'QL05p008000' => 'qlo', 'QL05p008212' => 'qlo', 'QL05p008950' => 'qlo', 'QL05p009042' => 'qlo', 'QL05p009518' => 'qlo', 'QL05p012589' => 'qlo', 'QL05p012608' => 'qlo', 'QL05p012650' => 'qlo', 'QL05p012667' => 'qlo', 'QL05p014501' => 'qlo', 'QL05p052800' => 'qlo', 'QL05p065010' => 'qlo', 'QL05p074156' => 'qlo', 'QL05p074160' => 'qlo', 'QL05p074174' => 'qlo', 'QL05p074178' => 'qlo', 'QL05p074214' => 'qlo', 'QL06p001050' => 'qlo', 'QL06p001056' => 'qlo', 'QL06p006093' => 'qlo', 'QL06p006111' => 'qlo', 'QL07p019784' => 'qlo', 'QL07p019801' => 'qlo', 'QL07p036110' => 'qlo', 'QL07p036134' => 'qlo', 'QL07p036147' => 'qlo', 'QL07p036156' => 'qlo', 'QL07p036300' => 'qlo', 'QL07p036320' => 'qlo', 'QL08p014547' => 'qlo', 'QL08p014551' => 'qlo', 'QL08p043319' => 'qlo', 'QL08p043324' => 'qlo', 'QL11p009094' => 'qlo', 'RcHm_v2.0_Chr1g0380481' => 'rch', 'RcHm_v2.0_Chr2g0089331' => 'rch', 'RcHm_v2.0_Chr2g0123691' => 'rch', 'RcHm_v2.0_Chr2g0151111' => 'rch', 'RcHm_v2.0_Chr2g0163011' => 'rch', 'RcHm_v2.0_Chr2g0163051' => 'rch', 'RcHm_v2.0_Chr2g0164671' => 'rch', 'RcHm_v2.0_Chr2g0164681' => 'rch', 'RcHm_v2.0_Chr2g0164721' => 'rch', 'RcHm_v2.0_Chr3g0449911' => 'rch', 'RcHm_v2.0_Chr3g0450211' => 'rch', 'RcHm_v2.0_Chr3g0457271' => 'rch', 'RcHm_v2.0_Chr5g0018111' => 'rch', 'RcHm_v2.0_Chr5g0021011' => 'rch', 'RcHm_v2.0_Chr5g0081171' => 'rch', 'RcHm_v2.0_Chr5g0081211' => 'rch', 'RcHm_v2.0_Chr6g0275871' => 'rch', 'RcHm_v2.0_Chr6g0276071' => 'rch', 'RcHm_v2.0_Chr6g0285591' => 'rch', 'RcHm_v2.0_Chr6g0291931' => 'rch', 'RcHm_v2.0_Chr6g0292091' => 'rch', 'RcHm_v2.0_Chr6g0292271' => 'rch', 'RcHm_v2.0_Chr7g0221261' => 'rch', 'Rhsim08G0219900' => 'rsi', 'Rhsim08G0220200' => 'rsi', 'Rhsim08G0237800' => 'rsi', 'Rhsim08G0238800' => 'rsi', 'Sabra09G0102700' => 'sbr', 'Sabra09G0127200' => 'sbr', 'Sabra11G0003700' => 'sbr', 'Sabra15G0014700' => 'sbr', 'Sc19g0000590' => 'sci', 'Sc19g0001870' => 'sci', 'SGA_v2.0_scaffold1G00346' => 'sas', 'SGA_v2.0_scaffold1G00575' => 'sas', 'SGA_v2.0_scaffold1G00761' => 'sas', 'SGA_v2.0_scaffold232G43501' => 'sas', 'TAR625G1137' => 'tar', 'Thecc.03G222100' => 'tca', 'TPR.G12691' => 'tpr', 'TWI34G0727' => 'twi', 'TWI36G0117' => 'twi', 'VMungo1309G0868' => 'vmu' ) $gf_id = 'HOM05D001729' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001729' ) $data_identifier = 'HOM05D001729' $data_type = 'gf_id' $species_gene_counts = array( 'amhyb' => (int) 1, 'cqu' => (int) 9, 'can' => (int) 1, 'cansat' => (int) 1, 'car' => (int) 1, 'col' => (int) 5, 'dca' => (int) 1, 'din' => (int) 2, 'dzi' => (int) 3, 'fan' => (int) 140, 'fve' => (int) 62, 'gma' => (int) 1, 'ghi' => (int) 2, 'gra' => (int) 1, 'han' => (int) 1, 'sun' => (int) 1, 'lonja' => (int) 6, 'lja' => (int) 1, 'lsa' => (int) 4, 'mes' => (int) 1, 'mdo' => (int) 14, 'mtr' => (int) 1, 'egut' => (int) 1, 'nta' => (int) 4, 'oeu' => (int) 1, 'stu' => (int) 2, 'pvu' => (int) 1, 'ptr' => (int) 4, 'ppe' => (int) 19, 'psa' => (int) 1, 'pso' => (int) 4, 'qlo' => (int) 36, 'rch' => (int) 23, 'rsi' => (int) 4, 'sbr' => (int) 4, 'sci' => (int) 2, 'sas' => (int) 4, 'tar' => (int) 1, 'tca' => (int) 1, 'tpr' => (int) 1, 'twi' => (int) 2, 'vmu' => (int) 1 ) $gf_gene_species = 'vmu' $gf_gene_id = 'VMungo1309G0868' $species_info = array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ) $local_species = 'sun' $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' => 'HOM05D001729', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '375', 'num_species' => '42' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'Ah.07g204710' => 'amhyb', 'AUR62006001' => 'cqu', 'AUR62006002' => 'cqu', 'AUR62006003' => 'cqu', 'AUR62015641' => 'cqu', 'AUR62027174' => 'cqu', 'AUR62035623' => 'cqu', 'AUR62035624' => 'cqu', 'AUR62035625' => 'cqu', 'AUR62035626' => 'cqu', 'CAN.G1110.53' => 'can', 'CANSAT80G0415' => 'cansat', 'Ca_21364_v3' => 'car', 'COL.COLO4_30693' => 'col', 'COL.COLO4_30694' => 'col', 'COL.COLO4_30695' => 'col', 'COL.COLO4_30696' => 'col', 'COL.COLO4_34020' => 'col', 'DCAR_004585' => 'dca', 'Dinv04029' => 'din', 'Dinv34857' => 'din', 'Duzib147G0011' => 'dzi', 'Duzib170G0599' => 'dzi', 'Duzib192G1051' => 'dzi', 'FAN01G0708' => 'fan', 'FAN01G0742' => 'fan', 'FAN02G0048' => 'fan', 'FAN02G0583' => 'fan', 'FAN02G0688' => 'fan', 'FAN02G1588' => 'fan', 'FAN02G2194' => 'fan', 'FAN02G2750' => 'fan', 'FAN02G3094' => 'fan', 'FAN02G3887' => 'fan', 'FAN02G3911' => 'fan', 'FAN02G3994' => 'fan', 'FAN02G4432' => 'fan', 'FAN02G4556' => 'fan', 'FAN03G1977' => 'fan', 'FAN03G2781' => 'fan', 'FAN03G2850' => 'fan', 'FAN03G3155' => 'fan', 'FAN04G2487' => 'fan', 'FAN05G0208' => 'fan', 'FAN05G0656' => 'fan', 'FAN05G0696' => 'fan', 'FAN05G0810' => 'fan', 'FAN05G1447' => 'fan', 'FAN05G2640' => 'fan', 'FAN05G2911' => 'fan', 'FAN05G3901' => 'fan', 'FAN05G4859' => 'fan', 'FAN05G4861' => 'fan', 'FAN05G4988' => 'fan', 'FAN05G5187' => 'fan', 'FAN05G5452' => 'fan', 'FAN05G5500' => 'fan', 'FAN05G5688' => 'fan', 'FAN06G0177' => 'fan', 'FAN06G0675' => 'fan', 'FAN06G1290' => 'fan', 'FAN06G2191' => 'fan', 'FAN06G2405' => 'fan', 'FAN06G3231' => 'fan', 'FAN06G3932' => 'fan', 'FAN07G0163' => 'fan', 'FAN07G0471' => 'fan', 'FAN07G1354' => 'fan', 'FAN08G0338' => 'fan', 'FAN08G1373' => 'fan', 'FAN08G2539' => 'fan', 'FAN08G2728' => 'fan', 'FAN09G0608' => 'fan', 'FAN09G1136' => 'fan', 'FAN09G1958' => 'fan', 'FAN09G2508' => 'fan', 'FAN09G2597' => 'fan', 'FAN09G2658' => 'fan', 'FAN09G2757' => 'fan', 'FAN09G2983' => 'fan', 'FAN09G3130' => 'fan', 'FAN09G3565' => 'fan', 'FAN09G3613' => 'fan', 'FAN09G4011' => 'fan', 'FAN09G4239' => 'fan', 'FAN09G4277' => 'fan', 'FAN09G4720' => 'fan', 'FAN11G0139' => 'fan', 'FAN11G1727' => 'fan', 'FAN11G2672' => 'fan', 'FAN11G2795' => 'fan', 'FAN11G3238' => 'fan', 'FAN11G3734' => 'fan', 'FAN12G0631' => 'fan', 'FAN12G2239' => 'fan', 'FAN12G2308' => 'fan', 'FAN12G2569' => 'fan', 'FAN12G2623' => 'fan', 'FAN13G3182' => 'fan', 'FAN14G0053' => 'fan', 'FAN14G0370' => 'fan', 'FAN14G0382' => 'fan', 'FAN14G0421' => 'fan', 'FAN14G0866' => 'fan', 'FAN14G1187' => 'fan', 'FAN14G1727' => 'fan', 'FAN14G1791' => 'fan', 'FAN14G2361' => 'fan', 'FAN14G2668' => 'fan', 'FAN14G2770' => 'fan', 'FAN14G2874' => 'fan', 'FAN14G3193' => 'fan', 'FAN14G3624' => 'fan', 'FAN14G3676' => 'fan', 'FAN14G3807' => 'fan', 'FAN14G4082' => 'fan', 'FAN14G4342' => 'fan', 'FAN14G4985' => 'fan', 'FAN14G5126' => 'fan', 'FAN14G5781' => 'fan', 'FAN14G5808' => 'fan', 'FAN14G5949' => 'fan', 'FAN15G0828' => 'fan', 'FAN15G1054' => 'fan', 'FAN15G2023' => 'fan', 'FAN15G2506' => 'fan', 'FAN16G0128' => 'fan', 'FAN16G0249' => 'fan', 'FAN16G0429' => 'fan', 'FAN16G1493' => 'fan', 'FAN16G2210' => 'fan', 'FAN16G2506' => 'fan', 'FAN18G1542' => 'fan', 'FAN18G4057' => 'fan', 'FAN19G0745' => 'fan', 'FAN19G1216' => 'fan', 'FAN19G1733' => 'fan', 'FAN20G0258' => 'fan', 'FAN20G1095' => 'fan', 'FAN20G1557' => 'fan', 'FAN21G0302' => 'fan', 'FAN21G0519' => 'fan', 'FAN21G0970' => 'fan', 'FAN21G1159' => 'fan', 'FAN21G1312' => 'fan', 'FAN21G1440' => 'fan', 'FAN21G1715' => 'fan', 'FAN23G1584' => 'fan', 'FAN24G0045' => 'fan', 'FAN24G0053' => 'fan', 'FAN24G1500' => 'fan', 'FAN24G1817' => 'fan', 'FAN24G2147' => 'fan', 'FAN24G2236' => 'fan', 'FAN24G2446' => 'fan', 'FAN24G2684' => 'fan', 'FAN25G0187' => 'fan', 'FAN25G0505' => 'fan', 'FAN25G0589' => 'fan', 'FAN25G3663' => 'fan', 'FAN26G1025' => 'fan', 'FAN26G2860' => 'fan', 'FAN27G1329' => 'fan', 'FAN27G3392' => 'fan', 'FvH4_1g02011' => 'fve', 'FvH4_1g06511' => 'fve', 'FvH4_2g19900' => 'fve', 'FvH4_2g19920' => 'fve', 'FvH4_2g24261' => 'fve', 'FvH4_2g24270' => 'fve', 'FvH4_2g24631' => 'fve', 'FvH4_2g30622' => 'fve', 'FvH4_3g12920' => 'fve', 'FvH4_3g30171' => 'fve', 'FvH4_3g35490' => 'fve', 'FvH4_3g43682' => 'fve', 'FvH4_3g43730' => 'fve', 'FvH4_3g43732' => 'fve', 'FvH4_3g43751' => 'fve', 'FvH4_3g43752' => 'fve', 'FvH4_3g43770' => 'fve', 'FvH4_3g44471' => 'fve', 'FvH4_3g44510' => 'fve', 'FvH4_3g44582' => 'fve', 'FvH4_4g16921' => 'fve', 'FvH4_4g17121' => 'fve', 'FvH4_4g17782' => 'fve', 'FvH4_4g17783' => 'fve', 'FvH4_4g18120' => 'fve', 'FvH4_4g31310' => 'fve', 'FvH4_4g35052' => 'fve', 'FvH4_5g30862' => 'fve', 'FvH4_6g01541' => 'fve', 'FvH4_6g02021' => 'fve', 'FvH4_6g02041' => 'fve', 'FvH4_6g02071' => 'fve', 'FvH4_6g02171' => 'fve', 'FvH4_6g03181' => 'fve', 'FvH4_6g03182' => 'fve', 'FvH4_6g03221' => 'fve', 'FvH4_6g03380' => 'fve', 'FvH4_6g05201' => 'fve', 'FvH4_6g05203' => 'fve', 'FvH4_6g20231' => 'fve', 'FvH4_6g31981' => 'fve', 'FvH4_6g32061' => 'fve', 'FvH4_6g37041' => 'fve', 'FvH4_6g37932' => 'fve', 'FvH4_6g38731' => 'fve', 'FvH4_6g39370' => 'fve', 'FvH4_6g39371' => 'fve', 'FvH4_6g40891' => 'fve', 'FvH4_6g40892' => 'fve', 'FvH4_6g43143' => 'fve', 'FvH4_6g45251' => 'fve', 'FvH4_6g45260' => 'fve', 'FvH4_6g45291' => 'fve', 'FvH4_6g45890' => 'fve', 'FvH4_6g46240' => 'fve', 'FvH4_6g46241' => 'fve', 'FvH4_6g46242' => 'fve', 'FvH4_6g46260' => 'fve', 'FvH4_6g46280' => 'fve', 'FvH4_6g46380' => 'fve', 'FvH4_7g12841' => 'fve', 'FvH4_7g31431' => 'fve', 'Glyma.09G075900' => 'gma', 'Gohir.A09G096401' => 'ghi', 'Gohir.D09G096101' => 'ghi', 'Gorai.006G112800' => 'gra', 'HanXRQChr04g0121411' => 'han', 'Hund15878' => 'sun', 'Lj2A1107G68' => 'lonja', 'Lj2A630G63' => 'lonja', 'Lj2A946T25' => 'lonja', 'Lj2C714T1' => 'lonja', 'Lj2C966T3' => 'lonja', 'Lj2C966T4' => 'lonja', 'Lj4g0002979' => 'lja', 'Lsat_1_v5_gn_5_30901' => 'lsa', 'Lsat_1_v5_gn_5_31100' => 'lsa', 'Lsat_1_v5_gn_5_38600' => 'lsa', 'Lsat_1_v5_gn_6_92061' => 'lsa', 'Manes.05G071301' => 'mes', 'MD02G1008700' => 'mdo', 'MD02G1008900' => 'mdo', 'MD03G1256400' => 'mdo', 'MD04G1180900' => 'mdo', 'MD04G1181000' => 'mdo', 'MD04G1181200' => 'mdo', 'MD05G1244200' => 'mdo', 'MD05G1324200' => 'mdo', 'MD09G1201600' => 'mdo', 'MD10G1000600' => 'mdo', 'MD14G1026900' => 'mdo', 'MD14G1187900' => 'mdo', 'MD15G1017800' => 'mdo', 'MD15G1018100' => 'mdo', 'Medtr4g124160' => 'mtr', 'Migut.L01260' => 'egut', 'Nitab4.5_0000008g0440' => 'nta', 'Nitab4.5_0000207g0170' => 'nta', 'Nitab4.5_0007671g0030' => 'nta', 'Nitab4.5_0010853g0020' => 'nta', 'Oeu057656.1' => 'oeu', 'PGSC0003DMG400005638' => 'stu', 'PGSC0003DMG400005639' => 'stu', 'Phvul.009G222800' => 'pvu', 'Potri.009G132400' => 'ptr', 'Potri.009G163001' => 'ptr', 'Potri.011G000700' => 'ptr', 'Potri.011G004800' => 'ptr', 'Prupe.1G509300' => 'ppe', 'Prupe.1G509700' => 'ppe', 'Prupe.1G510400' => 'ppe', 'Prupe.1G510700' => 'ppe', 'Prupe.1G512600' => 'ppe', 'Prupe.2G073200' => 'ppe', 'Prupe.3G059500' => 'ppe', 'Prupe.3G059600' => 'ppe', 'Prupe.3G246100' => 'ppe', 'Prupe.3G265100' => 'ppe', 'Prupe.4G034700' => 'ppe', 'Prupe.4G052100' => 'ppe', 'Prupe.4G053600' => 'ppe', 'Prupe.5G068800' => 'ppe', 'Prupe.5G070600' => 'ppe', 'Prupe.6G075400' => 'ppe', 'Prupe.6G075500' => 'ppe', 'Prupe.6G076400' => 'ppe', 'Prupe.8G110700' => 'ppe', 'Psat4g020960' => 'psa', 'PSO135G0788' => 'pso', 'PSO210G6463' => 'pso', 'PSO384G0370' => 'pso', 'PSO386G0056' => 'pso', 'QL01p006048' => 'qlo', 'QL02p054283' => 'qlo', 'QL05p008000' => 'qlo', 'QL05p008212' => 'qlo', 'QL05p008950' => 'qlo', 'QL05p009042' => 'qlo', 'QL05p009518' => 'qlo', 'QL05p012589' => 'qlo', 'QL05p012608' => 'qlo', 'QL05p012650' => 'qlo', 'QL05p012667' => 'qlo', 'QL05p014501' => 'qlo', 'QL05p052800' => 'qlo', 'QL05p065010' => 'qlo', 'QL05p074156' => 'qlo', 'QL05p074160' => 'qlo', 'QL05p074174' => 'qlo', 'QL05p074178' => 'qlo', 'QL05p074214' => 'qlo', 'QL06p001050' => 'qlo', 'QL06p001056' => 'qlo', 'QL06p006093' => 'qlo', 'QL06p006111' => 'qlo', 'QL07p019784' => 'qlo', 'QL07p019801' => 'qlo', 'QL07p036110' => 'qlo', 'QL07p036134' => 'qlo', 'QL07p036147' => 'qlo', 'QL07p036156' => 'qlo', 'QL07p036300' => 'qlo', 'QL07p036320' => 'qlo', 'QL08p014547' => 'qlo', 'QL08p014551' => 'qlo', 'QL08p043319' => 'qlo', 'QL08p043324' => 'qlo', 'QL11p009094' => 'qlo', 'RcHm_v2.0_Chr1g0380481' => 'rch', 'RcHm_v2.0_Chr2g0089331' => 'rch', 'RcHm_v2.0_Chr2g0123691' => 'rch', 'RcHm_v2.0_Chr2g0151111' => 'rch', 'RcHm_v2.0_Chr2g0163011' => 'rch', 'RcHm_v2.0_Chr2g0163051' => 'rch', 'RcHm_v2.0_Chr2g0164671' => 'rch', 'RcHm_v2.0_Chr2g0164681' => 'rch', 'RcHm_v2.0_Chr2g0164721' => 'rch', 'RcHm_v2.0_Chr3g0449911' => 'rch', 'RcHm_v2.0_Chr3g0450211' => 'rch', 'RcHm_v2.0_Chr3g0457271' => 'rch', 'RcHm_v2.0_Chr5g0018111' => 'rch', 'RcHm_v2.0_Chr5g0021011' => 'rch', 'RcHm_v2.0_Chr5g0081171' => 'rch', 'RcHm_v2.0_Chr5g0081211' => 'rch', 'RcHm_v2.0_Chr6g0275871' => 'rch', 'RcHm_v2.0_Chr6g0276071' => 'rch', 'RcHm_v2.0_Chr6g0285591' => 'rch', 'RcHm_v2.0_Chr6g0291931' => 'rch', 'RcHm_v2.0_Chr6g0292091' => 'rch', 'RcHm_v2.0_Chr6g0292271' => 'rch', 'RcHm_v2.0_Chr7g0221261' => 'rch', 'Rhsim08G0219900' => 'rsi', 'Rhsim08G0220200' => 'rsi', 'Rhsim08G0237800' => 'rsi', 'Rhsim08G0238800' => 'rsi', 'Sabra09G0102700' => 'sbr', 'Sabra09G0127200' => 'sbr', 'Sabra11G0003700' => 'sbr', 'Sabra15G0014700' => 'sbr', 'Sc19g0000590' => 'sci', 'Sc19g0001870' => 'sci', 'SGA_v2.0_scaffold1G00346' => 'sas', 'SGA_v2.0_scaffold1G00575' => 'sas', 'SGA_v2.0_scaffold1G00761' => 'sas', 'SGA_v2.0_scaffold232G43501' => 'sas', 'TAR625G1137' => 'tar', 'Thecc.03G222100' => 'tca', 'TPR.G12691' => 'tpr', 'TWI34G0727' => 'twi', 'TWI36G0117' => 'twi', 'VMungo1309G0868' => 'vmu' ), 'gf_id' => 'HOM05D001729', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001729' ), 'data_identifier' => 'HOM05D001729', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001729', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '375', 'num_species' => '42' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'Ah.07g204710' => 'amhyb', 'AUR62006001' => 'cqu', 'AUR62006002' => 'cqu', 'AUR62006003' => 'cqu', 'AUR62015641' => 'cqu', 'AUR62027174' => 'cqu', 'AUR62035623' => 'cqu', 'AUR62035624' => 'cqu', 'AUR62035625' => 'cqu', 'AUR62035626' => 'cqu', 'CAN.G1110.53' => 'can', 'CANSAT80G0415' => 'cansat', 'Ca_21364_v3' => 'car', 'COL.COLO4_30693' => 'col', 'COL.COLO4_30694' => 'col', 'COL.COLO4_30695' => 'col', 'COL.COLO4_30696' => 'col', 'COL.COLO4_34020' => 'col', 'DCAR_004585' => 'dca', 'Dinv04029' => 'din', 'Dinv34857' => 'din', 'Duzib147G0011' => 'dzi', 'Duzib170G0599' => 'dzi', 'Duzib192G1051' => 'dzi', 'FAN01G0708' => 'fan', 'FAN01G0742' => 'fan', 'FAN02G0048' => 'fan', 'FAN02G0583' => 'fan', 'FAN02G0688' => 'fan', 'FAN02G1588' => 'fan', 'FAN02G2194' => 'fan', 'FAN02G2750' => 'fan', 'FAN02G3094' => 'fan', 'FAN02G3887' => 'fan', 'FAN02G3911' => 'fan', 'FAN02G3994' => 'fan', 'FAN02G4432' => 'fan', 'FAN02G4556' => 'fan', 'FAN03G1977' => 'fan', 'FAN03G2781' => 'fan', 'FAN03G2850' => 'fan', 'FAN03G3155' => 'fan', 'FAN04G2487' => 'fan', 'FAN05G0208' => 'fan', 'FAN05G0656' => 'fan', 'FAN05G0696' => 'fan', 'FAN05G0810' => 'fan', 'FAN05G1447' => 'fan', 'FAN05G2640' => 'fan', 'FAN05G2911' => 'fan', 'FAN05G3901' => 'fan', 'FAN05G4859' => 'fan', 'FAN05G4861' => 'fan', 'FAN05G4988' => 'fan', 'FAN05G5187' => 'fan', 'FAN05G5452' => 'fan', 'FAN05G5500' => 'fan', 'FAN05G5688' => 'fan', 'FAN06G0177' => 'fan', 'FAN06G0675' => 'fan', 'FAN06G1290' => 'fan', 'FAN06G2191' => 'fan', 'FAN06G2405' => 'fan', 'FAN06G3231' => 'fan', 'FAN06G3932' => 'fan', 'FAN07G0163' => 'fan', 'FAN07G0471' => 'fan', 'FAN07G1354' => 'fan', 'FAN08G0338' => 'fan', 'FAN08G1373' => 'fan', 'FAN08G2539' => 'fan', 'FAN08G2728' => 'fan', 'FAN09G0608' => 'fan', 'FAN09G1136' => 'fan', 'FAN09G1958' => 'fan', 'FAN09G2508' => 'fan', 'FAN09G2597' => 'fan', 'FAN09G2658' => 'fan', 'FAN09G2757' => 'fan', 'FAN09G2983' => 'fan', 'FAN09G3130' => 'fan', 'FAN09G3565' => 'fan', 'FAN09G3613' => 'fan', 'FAN09G4011' => 'fan', 'FAN09G4239' => 'fan', 'FAN09G4277' => 'fan', 'FAN09G4720' => 'fan', 'FAN11G0139' => 'fan', 'FAN11G1727' => 'fan', 'FAN11G2672' => 'fan', 'FAN11G2795' => 'fan', 'FAN11G3238' => 'fan', 'FAN11G3734' => 'fan', 'FAN12G0631' => 'fan', 'FAN12G2239' => 'fan', 'FAN12G2308' => 'fan', 'FAN12G2569' => 'fan', 'FAN12G2623' => 'fan', 'FAN13G3182' => 'fan', 'FAN14G0053' => 'fan', 'FAN14G0370' => 'fan', 'FAN14G0382' => 'fan', 'FAN14G0421' => 'fan', 'FAN14G0866' => 'fan', 'FAN14G1187' => 'fan', 'FAN14G1727' => 'fan', 'FAN14G1791' => 'fan', 'FAN14G2361' => 'fan', 'FAN14G2668' => 'fan', 'FAN14G2770' => 'fan', 'FAN14G2874' => 'fan', 'FAN14G3193' => 'fan', 'FAN14G3624' => 'fan', 'FAN14G3676' => 'fan', 'FAN14G3807' => 'fan', 'FAN14G4082' => 'fan', 'FAN14G4342' => 'fan', 'FAN14G4985' => 'fan', 'FAN14G5126' => 'fan', 'FAN14G5781' => 'fan', 'FAN14G5808' => 'fan', 'FAN14G5949' => 'fan', 'FAN15G0828' => 'fan', 'FAN15G1054' => 'fan', 'FAN15G2023' => 'fan', 'FAN15G2506' => 'fan', 'FAN16G0128' => 'fan', 'FAN16G0249' => 'fan', 'FAN16G0429' => 'fan', 'FAN16G1493' => 'fan', 'FAN16G2210' => 'fan', 'FAN16G2506' => 'fan', 'FAN18G1542' => 'fan', 'FAN18G4057' => 'fan', 'FAN19G0745' => 'fan', 'FAN19G1216' => 'fan', 'FAN19G1733' => 'fan', 'FAN20G0258' => 'fan', 'FAN20G1095' => 'fan', 'FAN20G1557' => 'fan', 'FAN21G0302' => 'fan', 'FAN21G0519' => 'fan', 'FAN21G0970' => 'fan', 'FAN21G1159' => 'fan', 'FAN21G1312' => 'fan', 'FAN21G1440' => 'fan', 'FAN21G1715' => 'fan', 'FAN23G1584' => 'fan', 'FAN24G0045' => 'fan', 'FAN24G0053' => 'fan', 'FAN24G1500' => 'fan', 'FAN24G1817' => 'fan', 'FAN24G2147' => 'fan', 'FAN24G2236' => 'fan', 'FAN24G2446' => 'fan', 'FAN24G2684' => 'fan', 'FAN25G0187' => 'fan', 'FAN25G0505' => 'fan', 'FAN25G0589' => 'fan', 'FAN25G3663' => 'fan', 'FAN26G1025' => 'fan', 'FAN26G2860' => 'fan', 'FAN27G1329' => 'fan', 'FAN27G3392' => 'fan', 'FvH4_1g02011' => 'fve', 'FvH4_1g06511' => 'fve', 'FvH4_2g19900' => 'fve', 'FvH4_2g19920' => 'fve', 'FvH4_2g24261' => 'fve', 'FvH4_2g24270' => 'fve', 'FvH4_2g24631' => 'fve', 'FvH4_2g30622' => 'fve', 'FvH4_3g12920' => 'fve', 'FvH4_3g30171' => 'fve', 'FvH4_3g35490' => 'fve', 'FvH4_3g43682' => 'fve', 'FvH4_3g43730' => 'fve', 'FvH4_3g43732' => 'fve', 'FvH4_3g43751' => 'fve', 'FvH4_3g43752' => 'fve', 'FvH4_3g43770' => 'fve', 'FvH4_3g44471' => 'fve', 'FvH4_3g44510' => 'fve', 'FvH4_3g44582' => 'fve', 'FvH4_4g16921' => 'fve', 'FvH4_4g17121' => 'fve', 'FvH4_4g17782' => 'fve', 'FvH4_4g17783' => 'fve', 'FvH4_4g18120' => 'fve', 'FvH4_4g31310' => 'fve', 'FvH4_4g35052' => 'fve', 'FvH4_5g30862' => 'fve', 'FvH4_6g01541' => 'fve', 'FvH4_6g02021' => 'fve', 'FvH4_6g02041' => 'fve', 'FvH4_6g02071' => 'fve', 'FvH4_6g02171' => 'fve', 'FvH4_6g03181' => 'fve', 'FvH4_6g03182' => 'fve', 'FvH4_6g03221' => 'fve', 'FvH4_6g03380' => 'fve', 'FvH4_6g05201' => 'fve', 'FvH4_6g05203' => 'fve', 'FvH4_6g20231' => 'fve', 'FvH4_6g31981' => 'fve', 'FvH4_6g32061' => 'fve', 'FvH4_6g37041' => 'fve', 'FvH4_6g37932' => 'fve', 'FvH4_6g38731' => 'fve', 'FvH4_6g39370' => 'fve', 'FvH4_6g39371' => 'fve', 'FvH4_6g40891' => 'fve', 'FvH4_6g40892' => 'fve', 'FvH4_6g43143' => 'fve', 'FvH4_6g45251' => 'fve', 'FvH4_6g45260' => 'fve', 'FvH4_6g45291' => 'fve', 'FvH4_6g45890' => 'fve', 'FvH4_6g46240' => 'fve', 'FvH4_6g46241' => 'fve', 'FvH4_6g46242' => 'fve', 'FvH4_6g46260' => 'fve', 'FvH4_6g46280' => 'fve', 'FvH4_6g46380' => 'fve', 'FvH4_7g12841' => 'fve', 'FvH4_7g31431' => 'fve', 'Glyma.09G075900' => 'gma', 'Gohir.A09G096401' => 'ghi', 'Gohir.D09G096101' => 'ghi', 'Gorai.006G112800' => 'gra', 'HanXRQChr04g0121411' => 'han', 'Hund15878' => 'sun', 'Lj2A1107G68' => 'lonja', 'Lj2A630G63' => 'lonja', 'Lj2A946T25' => 'lonja', 'Lj2C714T1' => 'lonja', 'Lj2C966T3' => 'lonja', 'Lj2C966T4' => 'lonja', 'Lj4g0002979' => 'lja', 'Lsat_1_v5_gn_5_30901' => 'lsa', 'Lsat_1_v5_gn_5_31100' => 'lsa', 'Lsat_1_v5_gn_5_38600' => 'lsa', 'Lsat_1_v5_gn_6_92061' => 'lsa', 'Manes.05G071301' => 'mes', 'MD02G1008700' => 'mdo', 'MD02G1008900' => 'mdo', 'MD03G1256400' => 'mdo', 'MD04G1180900' => 'mdo', 'MD04G1181000' => 'mdo', 'MD04G1181200' => 'mdo', 'MD05G1244200' => 'mdo', 'MD05G1324200' => 'mdo', 'MD09G1201600' => 'mdo', 'MD10G1000600' => 'mdo', 'MD14G1026900' => 'mdo', 'MD14G1187900' => 'mdo', 'MD15G1017800' => 'mdo', 'MD15G1018100' => 'mdo', 'Medtr4g124160' => 'mtr', 'Migut.L01260' => 'egut', 'Nitab4.5_0000008g0440' => 'nta', 'Nitab4.5_0000207g0170' => 'nta', 'Nitab4.5_0007671g0030' => 'nta', 'Nitab4.5_0010853g0020' => 'nta', 'Oeu057656.1' => 'oeu', 'PGSC0003DMG400005638' => 'stu', 'PGSC0003DMG400005639' => 'stu', 'Phvul.009G222800' => 'pvu', 'Potri.009G132400' => 'ptr', 'Potri.009G163001' => 'ptr', 'Potri.011G000700' => 'ptr', 'Potri.011G004800' => 'ptr', 'Prupe.1G509300' => 'ppe', 'Prupe.1G509700' => 'ppe', 'Prupe.1G510400' => 'ppe', 'Prupe.1G510700' => 'ppe', 'Prupe.1G512600' => 'ppe', 'Prupe.2G073200' => 'ppe', 'Prupe.3G059500' => 'ppe', 'Prupe.3G059600' => 'ppe', 'Prupe.3G246100' => 'ppe', 'Prupe.3G265100' => 'ppe', 'Prupe.4G034700' => 'ppe', 'Prupe.4G052100' => 'ppe', 'Prupe.4G053600' => 'ppe', 'Prupe.5G068800' => 'ppe', 'Prupe.5G070600' => 'ppe', 'Prupe.6G075400' => 'ppe', 'Prupe.6G075500' => 'ppe', 'Prupe.6G076400' => 'ppe', 'Prupe.8G110700' => 'ppe', 'Psat4g020960' => 'psa', 'PSO135G0788' => 'pso', 'PSO210G6463' => 'pso', 'PSO384G0370' => 'pso', 'PSO386G0056' => 'pso', 'QL01p006048' => 'qlo', 'QL02p054283' => 'qlo', 'QL05p008000' => 'qlo', 'QL05p008212' => 'qlo', 'QL05p008950' => 'qlo', 'QL05p009042' => 'qlo', 'QL05p009518' => 'qlo', 'QL05p012589' => 'qlo', 'QL05p012608' => 'qlo', 'QL05p012650' => 'qlo', 'QL05p012667' => 'qlo', 'QL05p014501' => 'qlo', 'QL05p052800' => 'qlo', 'QL05p065010' => 'qlo', 'QL05p074156' => 'qlo', 'QL05p074160' => 'qlo', 'QL05p074174' => 'qlo', 'QL05p074178' => 'qlo', 'QL05p074214' => 'qlo', 'QL06p001050' => 'qlo', 'QL06p001056' => 'qlo', 'QL06p006093' => 'qlo', 'QL06p006111' => 'qlo', 'QL07p019784' => 'qlo', 'QL07p019801' => 'qlo', 'QL07p036110' => 'qlo', 'QL07p036134' => 'qlo', 'QL07p036147' => 'qlo', 'QL07p036156' => 'qlo', 'QL07p036300' => 'qlo', 'QL07p036320' => 'qlo', 'QL08p014547' => 'qlo', 'QL08p014551' => 'qlo', 'QL08p043319' => 'qlo', 'QL08p043324' => 'qlo', 'QL11p009094' => 'qlo', 'RcHm_v2.0_Chr1g0380481' => 'rch', 'RcHm_v2.0_Chr2g0089331' => 'rch', 'RcHm_v2.0_Chr2g0123691' => 'rch', 'RcHm_v2.0_Chr2g0151111' => 'rch', 'RcHm_v2.0_Chr2g0163011' => 'rch', 'RcHm_v2.0_Chr2g0163051' => 'rch', 'RcHm_v2.0_Chr2g0164671' => 'rch', 'RcHm_v2.0_Chr2g0164681' => 'rch', 'RcHm_v2.0_Chr2g0164721' => 'rch', 'RcHm_v2.0_Chr3g0449911' => 'rch', 'RcHm_v2.0_Chr3g0450211' => 'rch', 'RcHm_v2.0_Chr3g0457271' => 'rch', 'RcHm_v2.0_Chr5g0018111' => 'rch', 'RcHm_v2.0_Chr5g0021011' => 'rch', 'RcHm_v2.0_Chr5g0081171' => 'rch', 'RcHm_v2.0_Chr5g0081211' => 'rch', 'RcHm_v2.0_Chr6g0275871' => 'rch', 'RcHm_v2.0_Chr6g0276071' => 'rch', 'RcHm_v2.0_Chr6g0285591' => 'rch', 'RcHm_v2.0_Chr6g0291931' => 'rch', 'RcHm_v2.0_Chr6g0292091' => 'rch', 'RcHm_v2.0_Chr6g0292271' => 'rch', 'RcHm_v2.0_Chr7g0221261' => 'rch', 'Rhsim08G0219900' => 'rsi', 'Rhsim08G0220200' => 'rsi', 'Rhsim08G0237800' => 'rsi', 'Rhsim08G0238800' => 'rsi', 'Sabra09G0102700' => 'sbr', 'Sabra09G0127200' => 'sbr', 'Sabra11G0003700' => 'sbr', 'Sabra15G0014700' => 'sbr', 'Sc19g0000590' => 'sci', 'Sc19g0001870' => 'sci', 'SGA_v2.0_scaffold1G00346' => 'sas', 'SGA_v2.0_scaffold1G00575' => 'sas', 'SGA_v2.0_scaffold1G00761' => 'sas', 'SGA_v2.0_scaffold232G43501' => 'sas', 'TAR625G1137' => 'tar', 'Thecc.03G222100' => 'tca', 'TPR.G12691' => 'tpr', 'TWI34G0727' => 'twi', 'TWI36G0117' => 'twi', 'VMungo1309G0868' => 'vmu' ) $gf_id = 'HOM05D001729' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001729' ) $data_identifier = 'HOM05D001729' $data_type = 'gf_id' $species_gene_counts = array( 'amhyb' => (int) 1, 'cqu' => (int) 9, 'can' => (int) 1, 'cansat' => (int) 1, 'car' => (int) 1, 'col' => (int) 5, 'dca' => (int) 1, 'din' => (int) 2, 'dzi' => (int) 3, 'fan' => (int) 140, 'fve' => (int) 62, 'gma' => (int) 1, 'ghi' => (int) 2, 'gra' => (int) 1, 'han' => (int) 1, 'sun' => (int) 1, 'lonja' => (int) 6, 'lja' => (int) 1, 'lsa' => (int) 4, 'mes' => (int) 1, 'mdo' => (int) 14, 'mtr' => (int) 1, 'egut' => (int) 1, 'nta' => (int) 4, 'oeu' => (int) 1, 'stu' => (int) 2, 'pvu' => (int) 1, 'ptr' => (int) 4, 'ppe' => (int) 19, 'psa' => (int) 1, 'pso' => (int) 4, 'qlo' => (int) 36, 'rch' => (int) 23, 'rsi' => (int) 4, 'sbr' => (int) 4, 'sci' => (int) 2, 'sas' => (int) 4, 'tar' => (int) 1, 'tca' => (int) 1, 'tpr' => (int) 1, 'twi' => (int) 2, 'vmu' => (int) 1 ) $gf_gene_species = 'vmu' $gf_gene_id = 'VMungo1309G0868' $species_info = array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ) $local_species = 'sun' $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' => 'HOM05D001729', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '375', 'num_species' => '42' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'Ah.07g204710' => 'amhyb', 'AUR62006001' => 'cqu', 'AUR62006002' => 'cqu', 'AUR62006003' => 'cqu', 'AUR62015641' => 'cqu', 'AUR62027174' => 'cqu', 'AUR62035623' => 'cqu', 'AUR62035624' => 'cqu', 'AUR62035625' => 'cqu', 'AUR62035626' => 'cqu', 'CAN.G1110.53' => 'can', 'CANSAT80G0415' => 'cansat', 'Ca_21364_v3' => 'car', 'COL.COLO4_30693' => 'col', 'COL.COLO4_30694' => 'col', 'COL.COLO4_30695' => 'col', 'COL.COLO4_30696' => 'col', 'COL.COLO4_34020' => 'col', 'DCAR_004585' => 'dca', 'Dinv04029' => 'din', 'Dinv34857' => 'din', 'Duzib147G0011' => 'dzi', 'Duzib170G0599' => 'dzi', 'Duzib192G1051' => 'dzi', 'FAN01G0708' => 'fan', 'FAN01G0742' => 'fan', 'FAN02G0048' => 'fan', 'FAN02G0583' => 'fan', 'FAN02G0688' => 'fan', 'FAN02G1588' => 'fan', 'FAN02G2194' => 'fan', 'FAN02G2750' => 'fan', 'FAN02G3094' => 'fan', 'FAN02G3887' => 'fan', 'FAN02G3911' => 'fan', 'FAN02G3994' => 'fan', 'FAN02G4432' => 'fan', 'FAN02G4556' => 'fan', 'FAN03G1977' => 'fan', 'FAN03G2781' => 'fan', 'FAN03G2850' => 'fan', 'FAN03G3155' => 'fan', 'FAN04G2487' => 'fan', 'FAN05G0208' => 'fan', 'FAN05G0656' => 'fan', 'FAN05G0696' => 'fan', 'FAN05G0810' => 'fan', 'FAN05G1447' => 'fan', 'FAN05G2640' => 'fan', 'FAN05G2911' => 'fan', 'FAN05G3901' => 'fan', 'FAN05G4859' => 'fan', 'FAN05G4861' => 'fan', 'FAN05G4988' => 'fan', 'FAN05G5187' => 'fan', 'FAN05G5452' => 'fan', 'FAN05G5500' => 'fan', 'FAN05G5688' => 'fan', 'FAN06G0177' => 'fan', 'FAN06G0675' => 'fan', 'FAN06G1290' => 'fan', 'FAN06G2191' => 'fan', 'FAN06G2405' => 'fan', 'FAN06G3231' => 'fan', 'FAN06G3932' => 'fan', 'FAN07G0163' => 'fan', 'FAN07G0471' => 'fan', 'FAN07G1354' => 'fan', 'FAN08G0338' => 'fan', 'FAN08G1373' => 'fan', 'FAN08G2539' => 'fan', 'FAN08G2728' => 'fan', 'FAN09G0608' => 'fan', 'FAN09G1136' => 'fan', 'FAN09G1958' => 'fan', 'FAN09G2508' => 'fan', 'FAN09G2597' => 'fan', 'FAN09G2658' => 'fan', 'FAN09G2757' => 'fan', 'FAN09G2983' => 'fan', 'FAN09G3130' => 'fan', 'FAN09G3565' => 'fan', 'FAN09G3613' => 'fan', 'FAN09G4011' => 'fan', 'FAN09G4239' => 'fan', 'FAN09G4277' => 'fan', 'FAN09G4720' => 'fan', 'FAN11G0139' => 'fan', 'FAN11G1727' => 'fan', 'FAN11G2672' => 'fan', 'FAN11G2795' => 'fan', 'FAN11G3238' => 'fan', 'FAN11G3734' => 'fan', 'FAN12G0631' => 'fan', 'FAN12G2239' => 'fan', 'FAN12G2308' => 'fan', 'FAN12G2569' => 'fan', 'FAN12G2623' => 'fan', 'FAN13G3182' => 'fan', 'FAN14G0053' => 'fan', 'FAN14G0370' => 'fan', 'FAN14G0382' => 'fan', 'FAN14G0421' => 'fan', 'FAN14G0866' => 'fan', 'FAN14G1187' => 'fan', 'FAN14G1727' => 'fan', 'FAN14G1791' => 'fan', 'FAN14G2361' => 'fan', 'FAN14G2668' => 'fan', 'FAN14G2770' => 'fan', 'FAN14G2874' => 'fan', 'FAN14G3193' => 'fan', 'FAN14G3624' => 'fan', 'FAN14G3676' => 'fan', 'FAN14G3807' => 'fan', 'FAN14G4082' => 'fan', 'FAN14G4342' => 'fan', 'FAN14G4985' => 'fan', 'FAN14G5126' => 'fan', 'FAN14G5781' => 'fan', 'FAN14G5808' => 'fan', 'FAN14G5949' => 'fan', 'FAN15G0828' => 'fan', 'FAN15G1054' => 'fan', 'FAN15G2023' => 'fan', 'FAN15G2506' => 'fan', 'FAN16G0128' => 'fan', 'FAN16G0249' => 'fan', 'FAN16G0429' => 'fan', 'FAN16G1493' => 'fan', 'FAN16G2210' => 'fan', 'FAN16G2506' => 'fan', 'FAN18G1542' => 'fan', 'FAN18G4057' => 'fan', 'FAN19G0745' => 'fan', 'FAN19G1216' => 'fan', 'FAN19G1733' => 'fan', 'FAN20G0258' => 'fan', 'FAN20G1095' => 'fan', 'FAN20G1557' => 'fan', 'FAN21G0302' => 'fan', 'FAN21G0519' => 'fan', 'FAN21G0970' => 'fan', 'FAN21G1159' => 'fan', 'FAN21G1312' => 'fan', 'FAN21G1440' => 'fan', 'FAN21G1715' => 'fan', 'FAN23G1584' => 'fan', 'FAN24G0045' => 'fan', 'FAN24G0053' => 'fan', 'FAN24G1500' => 'fan', 'FAN24G1817' => 'fan', 'FAN24G2147' => 'fan', 'FAN24G2236' => 'fan', 'FAN24G2446' => 'fan', 'FAN24G2684' => 'fan', 'FAN25G0187' => 'fan', 'FAN25G0505' => 'fan', 'FAN25G0589' => 'fan', 'FAN25G3663' => 'fan', 'FAN26G1025' => 'fan', 'FAN26G2860' => 'fan', 'FAN27G1329' => 'fan', 'FAN27G3392' => 'fan', 'FvH4_1g02011' => 'fve', 'FvH4_1g06511' => 'fve', 'FvH4_2g19900' => 'fve', 'FvH4_2g19920' => 'fve', 'FvH4_2g24261' => 'fve', 'FvH4_2g24270' => 'fve', 'FvH4_2g24631' => 'fve', 'FvH4_2g30622' => 'fve', 'FvH4_3g12920' => 'fve', 'FvH4_3g30171' => 'fve', 'FvH4_3g35490' => 'fve', 'FvH4_3g43682' => 'fve', 'FvH4_3g43730' => 'fve', 'FvH4_3g43732' => 'fve', 'FvH4_3g43751' => 'fve', 'FvH4_3g43752' => 'fve', 'FvH4_3g43770' => 'fve', 'FvH4_3g44471' => 'fve', 'FvH4_3g44510' => 'fve', 'FvH4_3g44582' => 'fve', 'FvH4_4g16921' => 'fve', 'FvH4_4g17121' => 'fve', 'FvH4_4g17782' => 'fve', 'FvH4_4g17783' => 'fve', 'FvH4_4g18120' => 'fve', 'FvH4_4g31310' => 'fve', 'FvH4_4g35052' => 'fve', 'FvH4_5g30862' => 'fve', 'FvH4_6g01541' => 'fve', 'FvH4_6g02021' => 'fve', 'FvH4_6g02041' => 'fve', 'FvH4_6g02071' => 'fve', 'FvH4_6g02171' => 'fve', 'FvH4_6g03181' => 'fve', 'FvH4_6g03182' => 'fve', 'FvH4_6g03221' => 'fve', 'FvH4_6g03380' => 'fve', 'FvH4_6g05201' => 'fve', 'FvH4_6g05203' => 'fve', 'FvH4_6g20231' => 'fve', 'FvH4_6g31981' => 'fve', 'FvH4_6g32061' => 'fve', 'FvH4_6g37041' => 'fve', 'FvH4_6g37932' => 'fve', 'FvH4_6g38731' => 'fve', 'FvH4_6g39370' => 'fve', 'FvH4_6g39371' => 'fve', 'FvH4_6g40891' => 'fve', 'FvH4_6g40892' => 'fve', 'FvH4_6g43143' => 'fve', 'FvH4_6g45251' => 'fve', 'FvH4_6g45260' => 'fve', 'FvH4_6g45291' => 'fve', 'FvH4_6g45890' => 'fve', 'FvH4_6g46240' => 'fve', 'FvH4_6g46241' => 'fve', 'FvH4_6g46242' => 'fve', 'FvH4_6g46260' => 'fve', 'FvH4_6g46280' => 'fve', 'FvH4_6g46380' => 'fve', 'FvH4_7g12841' => 'fve', 'FvH4_7g31431' => 'fve', 'Glyma.09G075900' => 'gma', 'Gohir.A09G096401' => 'ghi', 'Gohir.D09G096101' => 'ghi', 'Gorai.006G112800' => 'gra', 'HanXRQChr04g0121411' => 'han', 'Hund15878' => 'sun', 'Lj2A1107G68' => 'lonja', 'Lj2A630G63' => 'lonja', 'Lj2A946T25' => 'lonja', 'Lj2C714T1' => 'lonja', 'Lj2C966T3' => 'lonja', 'Lj2C966T4' => 'lonja', 'Lj4g0002979' => 'lja', 'Lsat_1_v5_gn_5_30901' => 'lsa', 'Lsat_1_v5_gn_5_31100' => 'lsa', 'Lsat_1_v5_gn_5_38600' => 'lsa', 'Lsat_1_v5_gn_6_92061' => 'lsa', 'Manes.05G071301' => 'mes', 'MD02G1008700' => 'mdo', 'MD02G1008900' => 'mdo', 'MD03G1256400' => 'mdo', 'MD04G1180900' => 'mdo', 'MD04G1181000' => 'mdo', 'MD04G1181200' => 'mdo', 'MD05G1244200' => 'mdo', 'MD05G1324200' => 'mdo', 'MD09G1201600' => 'mdo', 'MD10G1000600' => 'mdo', 'MD14G1026900' => 'mdo', 'MD14G1187900' => 'mdo', 'MD15G1017800' => 'mdo', 'MD15G1018100' => 'mdo', 'Medtr4g124160' => 'mtr', 'Migut.L01260' => 'egut', 'Nitab4.5_0000008g0440' => 'nta', 'Nitab4.5_0000207g0170' => 'nta', 'Nitab4.5_0007671g0030' => 'nta', 'Nitab4.5_0010853g0020' => 'nta', 'Oeu057656.1' => 'oeu', 'PGSC0003DMG400005638' => 'stu', 'PGSC0003DMG400005639' => 'stu', 'Phvul.009G222800' => 'pvu', 'Potri.009G132400' => 'ptr', 'Potri.009G163001' => 'ptr', 'Potri.011G000700' => 'ptr', 'Potri.011G004800' => 'ptr', 'Prupe.1G509300' => 'ppe', 'Prupe.1G509700' => 'ppe', 'Prupe.1G510400' => 'ppe', 'Prupe.1G510700' => 'ppe', 'Prupe.1G512600' => 'ppe', 'Prupe.2G073200' => 'ppe', 'Prupe.3G059500' => 'ppe', 'Prupe.3G059600' => 'ppe', 'Prupe.3G246100' => 'ppe', 'Prupe.3G265100' => 'ppe', 'Prupe.4G034700' => 'ppe', 'Prupe.4G052100' => 'ppe', 'Prupe.4G053600' => 'ppe', 'Prupe.5G068800' => 'ppe', 'Prupe.5G070600' => 'ppe', 'Prupe.6G075400' => 'ppe', 'Prupe.6G075500' => 'ppe', 'Prupe.6G076400' => 'ppe', 'Prupe.8G110700' => 'ppe', 'Psat4g020960' => 'psa', 'PSO135G0788' => 'pso', 'PSO210G6463' => 'pso', 'PSO384G0370' => 'pso', 'PSO386G0056' => 'pso', 'QL01p006048' => 'qlo', 'QL02p054283' => 'qlo', 'QL05p008000' => 'qlo', 'QL05p008212' => 'qlo', 'QL05p008950' => 'qlo', 'QL05p009042' => 'qlo', 'QL05p009518' => 'qlo', 'QL05p012589' => 'qlo', 'QL05p012608' => 'qlo', 'QL05p012650' => 'qlo', 'QL05p012667' => 'qlo', 'QL05p014501' => 'qlo', 'QL05p052800' => 'qlo', 'QL05p065010' => 'qlo', 'QL05p074156' => 'qlo', 'QL05p074160' => 'qlo', 'QL05p074174' => 'qlo', 'QL05p074178' => 'qlo', 'QL05p074214' => 'qlo', 'QL06p001050' => 'qlo', 'QL06p001056' => 'qlo', 'QL06p006093' => 'qlo', 'QL06p006111' => 'qlo', 'QL07p019784' => 'qlo', 'QL07p019801' => 'qlo', 'QL07p036110' => 'qlo', 'QL07p036134' => 'qlo', 'QL07p036147' => 'qlo', 'QL07p036156' => 'qlo', 'QL07p036300' => 'qlo', 'QL07p036320' => 'qlo', 'QL08p014547' => 'qlo', 'QL08p014551' => 'qlo', 'QL08p043319' => 'qlo', 'QL08p043324' => 'qlo', 'QL11p009094' => 'qlo', 'RcHm_v2.0_Chr1g0380481' => 'rch', 'RcHm_v2.0_Chr2g0089331' => 'rch', 'RcHm_v2.0_Chr2g0123691' => 'rch', 'RcHm_v2.0_Chr2g0151111' => 'rch', 'RcHm_v2.0_Chr2g0163011' => 'rch', 'RcHm_v2.0_Chr2g0163051' => 'rch', 'RcHm_v2.0_Chr2g0164671' => 'rch', 'RcHm_v2.0_Chr2g0164681' => 'rch', 'RcHm_v2.0_Chr2g0164721' => 'rch', 'RcHm_v2.0_Chr3g0449911' => 'rch', 'RcHm_v2.0_Chr3g0450211' => 'rch', 'RcHm_v2.0_Chr3g0457271' => 'rch', 'RcHm_v2.0_Chr5g0018111' => 'rch', 'RcHm_v2.0_Chr5g0021011' => 'rch', 'RcHm_v2.0_Chr5g0081171' => 'rch', 'RcHm_v2.0_Chr5g0081211' => 'rch', 'RcHm_v2.0_Chr6g0275871' => 'rch', 'RcHm_v2.0_Chr6g0276071' => 'rch', 'RcHm_v2.0_Chr6g0285591' => 'rch', 'RcHm_v2.0_Chr6g0291931' => 'rch', 'RcHm_v2.0_Chr6g0292091' => 'rch', 'RcHm_v2.0_Chr6g0292271' => 'rch', 'RcHm_v2.0_Chr7g0221261' => 'rch', 'Rhsim08G0219900' => 'rsi', 'Rhsim08G0220200' => 'rsi', 'Rhsim08G0237800' => 'rsi', 'Rhsim08G0238800' => 'rsi', 'Sabra09G0102700' => 'sbr', 'Sabra09G0127200' => 'sbr', 'Sabra11G0003700' => 'sbr', 'Sabra15G0014700' => 'sbr', 'Sc19g0000590' => 'sci', 'Sc19g0001870' => 'sci', 'SGA_v2.0_scaffold1G00346' => 'sas', 'SGA_v2.0_scaffold1G00575' => 'sas', 'SGA_v2.0_scaffold1G00761' => 'sas', 'SGA_v2.0_scaffold232G43501' => 'sas', 'TAR625G1137' => 'tar', 'Thecc.03G222100' => 'tca', 'TPR.G12691' => 'tpr', 'TWI34G0727' => 'twi', 'TWI36G0117' => 'twi', 'VMungo1309G0868' => 'vmu' ), 'gf_id' => 'HOM05D001729', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001729' ), 'data_identifier' => 'HOM05D001729', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001729', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '375', 'num_species' => '42' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'Ah.07g204710' => 'amhyb', 'AUR62006001' => 'cqu', 'AUR62006002' => 'cqu', 'AUR62006003' => 'cqu', 'AUR62015641' => 'cqu', 'AUR62027174' => 'cqu', 'AUR62035623' => 'cqu', 'AUR62035624' => 'cqu', 'AUR62035625' => 'cqu', 'AUR62035626' => 'cqu', 'CAN.G1110.53' => 'can', 'CANSAT80G0415' => 'cansat', 'Ca_21364_v3' => 'car', 'COL.COLO4_30693' => 'col', 'COL.COLO4_30694' => 'col', 'COL.COLO4_30695' => 'col', 'COL.COLO4_30696' => 'col', 'COL.COLO4_34020' => 'col', 'DCAR_004585' => 'dca', 'Dinv04029' => 'din', 'Dinv34857' => 'din', 'Duzib147G0011' => 'dzi', 'Duzib170G0599' => 'dzi', 'Duzib192G1051' => 'dzi', 'FAN01G0708' => 'fan', 'FAN01G0742' => 'fan', 'FAN02G0048' => 'fan', 'FAN02G0583' => 'fan', 'FAN02G0688' => 'fan', 'FAN02G1588' => 'fan', 'FAN02G2194' => 'fan', 'FAN02G2750' => 'fan', 'FAN02G3094' => 'fan', 'FAN02G3887' => 'fan', 'FAN02G3911' => 'fan', 'FAN02G3994' => 'fan', 'FAN02G4432' => 'fan', 'FAN02G4556' => 'fan', 'FAN03G1977' => 'fan', 'FAN03G2781' => 'fan', 'FAN03G2850' => 'fan', 'FAN03G3155' => 'fan', 'FAN04G2487' => 'fan', 'FAN05G0208' => 'fan', 'FAN05G0656' => 'fan', 'FAN05G0696' => 'fan', 'FAN05G0810' => 'fan', 'FAN05G1447' => 'fan', 'FAN05G2640' => 'fan', 'FAN05G2911' => 'fan', 'FAN05G3901' => 'fan', 'FAN05G4859' => 'fan', 'FAN05G4861' => 'fan', 'FAN05G4988' => 'fan', 'FAN05G5187' => 'fan', 'FAN05G5452' => 'fan', 'FAN05G5500' => 'fan', 'FAN05G5688' => 'fan', 'FAN06G0177' => 'fan', 'FAN06G0675' => 'fan', 'FAN06G1290' => 'fan', 'FAN06G2191' => 'fan', 'FAN06G2405' => 'fan', 'FAN06G3231' => 'fan', 'FAN06G3932' => 'fan', 'FAN07G0163' => 'fan', 'FAN07G0471' => 'fan', 'FAN07G1354' => 'fan', 'FAN08G0338' => 'fan', 'FAN08G1373' => 'fan', 'FAN08G2539' => 'fan', 'FAN08G2728' => 'fan', 'FAN09G0608' => 'fan', 'FAN09G1136' => 'fan', 'FAN09G1958' => 'fan', 'FAN09G2508' => 'fan', 'FAN09G2597' => 'fan', 'FAN09G2658' => 'fan', 'FAN09G2757' => 'fan', 'FAN09G2983' => 'fan', 'FAN09G3130' => 'fan', 'FAN09G3565' => 'fan', 'FAN09G3613' => 'fan', 'FAN09G4011' => 'fan', 'FAN09G4239' => 'fan', 'FAN09G4277' => 'fan', 'FAN09G4720' => 'fan', 'FAN11G0139' => 'fan', 'FAN11G1727' => 'fan', 'FAN11G2672' => 'fan', 'FAN11G2795' => 'fan', 'FAN11G3238' => 'fan', 'FAN11G3734' => 'fan', 'FAN12G0631' => 'fan', 'FAN12G2239' => 'fan', 'FAN12G2308' => 'fan', 'FAN12G2569' => 'fan', 'FAN12G2623' => 'fan', 'FAN13G3182' => 'fan', 'FAN14G0053' => 'fan', 'FAN14G0370' => 'fan', 'FAN14G0382' => 'fan', 'FAN14G0421' => 'fan', 'FAN14G0866' => 'fan', 'FAN14G1187' => 'fan', 'FAN14G1727' => 'fan', 'FAN14G1791' => 'fan', 'FAN14G2361' => 'fan', 'FAN14G2668' => 'fan', 'FAN14G2770' => 'fan', 'FAN14G2874' => 'fan', 'FAN14G3193' => 'fan', 'FAN14G3624' => 'fan', 'FAN14G3676' => 'fan', 'FAN14G3807' => 'fan', 'FAN14G4082' => 'fan', 'FAN14G4342' => 'fan', 'FAN14G4985' => 'fan', 'FAN14G5126' => 'fan', 'FAN14G5781' => 'fan', 'FAN14G5808' => 'fan', 'FAN14G5949' => 'fan', 'FAN15G0828' => 'fan', 'FAN15G1054' => 'fan', 'FAN15G2023' => 'fan', 'FAN15G2506' => 'fan', 'FAN16G0128' => 'fan', 'FAN16G0249' => 'fan', 'FAN16G0429' => 'fan', 'FAN16G1493' => 'fan', 'FAN16G2210' => 'fan', 'FAN16G2506' => 'fan', 'FAN18G1542' => 'fan', 'FAN18G4057' => 'fan', 'FAN19G0745' => 'fan', 'FAN19G1216' => 'fan', 'FAN19G1733' => 'fan', 'FAN20G0258' => 'fan', 'FAN20G1095' => 'fan', 'FAN20G1557' => 'fan', 'FAN21G0302' => 'fan', 'FAN21G0519' => 'fan', 'FAN21G0970' => 'fan', 'FAN21G1159' => 'fan', 'FAN21G1312' => 'fan', 'FAN21G1440' => 'fan', 'FAN21G1715' => 'fan', 'FAN23G1584' => 'fan', 'FAN24G0045' => 'fan', 'FAN24G0053' => 'fan', 'FAN24G1500' => 'fan', 'FAN24G1817' => 'fan', 'FAN24G2147' => 'fan', 'FAN24G2236' => 'fan', 'FAN24G2446' => 'fan', 'FAN24G2684' => 'fan', 'FAN25G0187' => 'fan', 'FAN25G0505' => 'fan', 'FAN25G0589' => 'fan', 'FAN25G3663' => 'fan', 'FAN26G1025' => 'fan', 'FAN26G2860' => 'fan', 'FAN27G1329' => 'fan', 'FAN27G3392' => 'fan', 'FvH4_1g02011' => 'fve', 'FvH4_1g06511' => 'fve', 'FvH4_2g19900' => 'fve', 'FvH4_2g19920' => 'fve', 'FvH4_2g24261' => 'fve', 'FvH4_2g24270' => 'fve', 'FvH4_2g24631' => 'fve', 'FvH4_2g30622' => 'fve', 'FvH4_3g12920' => 'fve', 'FvH4_3g30171' => 'fve', 'FvH4_3g35490' => 'fve', 'FvH4_3g43682' => 'fve', 'FvH4_3g43730' => 'fve', 'FvH4_3g43732' => 'fve', 'FvH4_3g43751' => 'fve', 'FvH4_3g43752' => 'fve', 'FvH4_3g43770' => 'fve', 'FvH4_3g44471' => 'fve', 'FvH4_3g44510' => 'fve', 'FvH4_3g44582' => 'fve', 'FvH4_4g16921' => 'fve', 'FvH4_4g17121' => 'fve', 'FvH4_4g17782' => 'fve', 'FvH4_4g17783' => 'fve', 'FvH4_4g18120' => 'fve', 'FvH4_4g31310' => 'fve', 'FvH4_4g35052' => 'fve', 'FvH4_5g30862' => 'fve', 'FvH4_6g01541' => 'fve', 'FvH4_6g02021' => 'fve', 'FvH4_6g02041' => 'fve', 'FvH4_6g02071' => 'fve', 'FvH4_6g02171' => 'fve', 'FvH4_6g03181' => 'fve', 'FvH4_6g03182' => 'fve', 'FvH4_6g03221' => 'fve', 'FvH4_6g03380' => 'fve', 'FvH4_6g05201' => 'fve', 'FvH4_6g05203' => 'fve', 'FvH4_6g20231' => 'fve', 'FvH4_6g31981' => 'fve', 'FvH4_6g32061' => 'fve', 'FvH4_6g37041' => 'fve', 'FvH4_6g37932' => 'fve', 'FvH4_6g38731' => 'fve', 'FvH4_6g39370' => 'fve', 'FvH4_6g39371' => 'fve', 'FvH4_6g40891' => 'fve', 'FvH4_6g40892' => 'fve', 'FvH4_6g43143' => 'fve', 'FvH4_6g45251' => 'fve', 'FvH4_6g45260' => 'fve', 'FvH4_6g45291' => 'fve', 'FvH4_6g45890' => 'fve', 'FvH4_6g46240' => 'fve', 'FvH4_6g46241' => 'fve', 'FvH4_6g46242' => 'fve', 'FvH4_6g46260' => 'fve', 'FvH4_6g46280' => 'fve', 'FvH4_6g46380' => 'fve', 'FvH4_7g12841' => 'fve', 'FvH4_7g31431' => 'fve', 'Glyma.09G075900' => 'gma', 'Gohir.A09G096401' => 'ghi', 'Gohir.D09G096101' => 'ghi', 'Gorai.006G112800' => 'gra', 'HanXRQChr04g0121411' => 'han', 'Hund15878' => 'sun', 'Lj2A1107G68' => 'lonja', 'Lj2A630G63' => 'lonja', 'Lj2A946T25' => 'lonja', 'Lj2C714T1' => 'lonja', 'Lj2C966T3' => 'lonja', 'Lj2C966T4' => 'lonja', 'Lj4g0002979' => 'lja', 'Lsat_1_v5_gn_5_30901' => 'lsa', 'Lsat_1_v5_gn_5_31100' => 'lsa', 'Lsat_1_v5_gn_5_38600' => 'lsa', 'Lsat_1_v5_gn_6_92061' => 'lsa', 'Manes.05G071301' => 'mes', 'MD02G1008700' => 'mdo', 'MD02G1008900' => 'mdo', 'MD03G1256400' => 'mdo', 'MD04G1180900' => 'mdo', 'MD04G1181000' => 'mdo', 'MD04G1181200' => 'mdo', 'MD05G1244200' => 'mdo', 'MD05G1324200' => 'mdo', 'MD09G1201600' => 'mdo', 'MD10G1000600' => 'mdo', 'MD14G1026900' => 'mdo', 'MD14G1187900' => 'mdo', 'MD15G1017800' => 'mdo', 'MD15G1018100' => 'mdo', 'Medtr4g124160' => 'mtr', 'Migut.L01260' => 'egut', 'Nitab4.5_0000008g0440' => 'nta', 'Nitab4.5_0000207g0170' => 'nta', 'Nitab4.5_0007671g0030' => 'nta', 'Nitab4.5_0010853g0020' => 'nta', 'Oeu057656.1' => 'oeu', 'PGSC0003DMG400005638' => 'stu', 'PGSC0003DMG400005639' => 'stu', 'Phvul.009G222800' => 'pvu', 'Potri.009G132400' => 'ptr', 'Potri.009G163001' => 'ptr', 'Potri.011G000700' => 'ptr', 'Potri.011G004800' => 'ptr', 'Prupe.1G509300' => 'ppe', 'Prupe.1G509700' => 'ppe', 'Prupe.1G510400' => 'ppe', 'Prupe.1G510700' => 'ppe', 'Prupe.1G512600' => 'ppe', 'Prupe.2G073200' => 'ppe', 'Prupe.3G059500' => 'ppe', 'Prupe.3G059600' => 'ppe', 'Prupe.3G246100' => 'ppe', 'Prupe.3G265100' => 'ppe', 'Prupe.4G034700' => 'ppe', 'Prupe.4G052100' => 'ppe', 'Prupe.4G053600' => 'ppe', 'Prupe.5G068800' => 'ppe', 'Prupe.5G070600' => 'ppe', 'Prupe.6G075400' => 'ppe', 'Prupe.6G075500' => 'ppe', 'Prupe.6G076400' => 'ppe', 'Prupe.8G110700' => 'ppe', 'Psat4g020960' => 'psa', 'PSO135G0788' => 'pso', 'PSO210G6463' => 'pso', 'PSO384G0370' => 'pso', 'PSO386G0056' => 'pso', 'QL01p006048' => 'qlo', 'QL02p054283' => 'qlo', 'QL05p008000' => 'qlo', 'QL05p008212' => 'qlo', 'QL05p008950' => 'qlo', 'QL05p009042' => 'qlo', 'QL05p009518' => 'qlo', 'QL05p012589' => 'qlo', 'QL05p012608' => 'qlo', 'QL05p012650' => 'qlo', 'QL05p012667' => 'qlo', 'QL05p014501' => 'qlo', 'QL05p052800' => 'qlo', 'QL05p065010' => 'qlo', 'QL05p074156' => 'qlo', 'QL05p074160' => 'qlo', 'QL05p074174' => 'qlo', 'QL05p074178' => 'qlo', 'QL05p074214' => 'qlo', 'QL06p001050' => 'qlo', 'QL06p001056' => 'qlo', 'QL06p006093' => 'qlo', 'QL06p006111' => 'qlo', 'QL07p019784' => 'qlo', 'QL07p019801' => 'qlo', 'QL07p036110' => 'qlo', 'QL07p036134' => 'qlo', 'QL07p036147' => 'qlo', 'QL07p036156' => 'qlo', 'QL07p036300' => 'qlo', 'QL07p036320' => 'qlo', 'QL08p014547' => 'qlo', 'QL08p014551' => 'qlo', 'QL08p043319' => 'qlo', 'QL08p043324' => 'qlo', 'QL11p009094' => 'qlo', 'RcHm_v2.0_Chr1g0380481' => 'rch', 'RcHm_v2.0_Chr2g0089331' => 'rch', 'RcHm_v2.0_Chr2g0123691' => 'rch', 'RcHm_v2.0_Chr2g0151111' => 'rch', 'RcHm_v2.0_Chr2g0163011' => 'rch', 'RcHm_v2.0_Chr2g0163051' => 'rch', 'RcHm_v2.0_Chr2g0164671' => 'rch', 'RcHm_v2.0_Chr2g0164681' => 'rch', 'RcHm_v2.0_Chr2g0164721' => 'rch', 'RcHm_v2.0_Chr3g0449911' => 'rch', 'RcHm_v2.0_Chr3g0450211' => 'rch', 'RcHm_v2.0_Chr3g0457271' => 'rch', 'RcHm_v2.0_Chr5g0018111' => 'rch', 'RcHm_v2.0_Chr5g0021011' => 'rch', 'RcHm_v2.0_Chr5g0081171' => 'rch', 'RcHm_v2.0_Chr5g0081211' => 'rch', 'RcHm_v2.0_Chr6g0275871' => 'rch', 'RcHm_v2.0_Chr6g0276071' => 'rch', 'RcHm_v2.0_Chr6g0285591' => 'rch', 'RcHm_v2.0_Chr6g0291931' => 'rch', 'RcHm_v2.0_Chr6g0292091' => 'rch', 'RcHm_v2.0_Chr6g0292271' => 'rch', 'RcHm_v2.0_Chr7g0221261' => 'rch', 'Rhsim08G0219900' => 'rsi', 'Rhsim08G0220200' => 'rsi', 'Rhsim08G0237800' => 'rsi', 'Rhsim08G0238800' => 'rsi', 'Sabra09G0102700' => 'sbr', 'Sabra09G0127200' => 'sbr', 'Sabra11G0003700' => 'sbr', 'Sabra15G0014700' => 'sbr', 'Sc19g0000590' => 'sci', 'Sc19g0001870' => 'sci', 'SGA_v2.0_scaffold1G00346' => 'sas', 'SGA_v2.0_scaffold1G00575' => 'sas', 'SGA_v2.0_scaffold1G00761' => 'sas', 'SGA_v2.0_scaffold232G43501' => 'sas', 'TAR625G1137' => 'tar', 'Thecc.03G222100' => 'tca', 'TPR.G12691' => 'tpr', 'TWI34G0727' => 'twi', 'TWI36G0117' => 'twi', 'VMungo1309G0868' => 'vmu' ) $gf_id = 'HOM05D001729' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001729' ) $data_identifier = 'HOM05D001729' $data_type = 'gf_id' $species_gene_counts = array( 'amhyb' => (int) 1, 'cqu' => (int) 9, 'can' => (int) 1, 'cansat' => (int) 1, 'car' => (int) 1, 'col' => (int) 5, 'dca' => (int) 1, 'din' => (int) 2, 'dzi' => (int) 3, 'fan' => (int) 140, 'fve' => (int) 62, 'gma' => (int) 1, 'ghi' => (int) 2, 'gra' => (int) 1, 'han' => (int) 1, 'sun' => (int) 1, 'lonja' => (int) 6, 'lja' => (int) 1, 'lsa' => (int) 4, 'mes' => (int) 1, 'mdo' => (int) 14, 'mtr' => (int) 1, 'egut' => (int) 1, 'nta' => (int) 4, 'oeu' => (int) 1, 'stu' => (int) 2, 'pvu' => (int) 1, 'ptr' => (int) 4, 'ppe' => (int) 19, 'psa' => (int) 1, 'pso' => (int) 4, 'qlo' => (int) 36, 'rch' => (int) 23, 'rsi' => (int) 4, 'sbr' => (int) 4, 'sci' => (int) 2, 'sas' => (int) 4, 'tar' => (int) 1, 'tca' => (int) 1, 'tpr' => (int) 1, 'twi' => (int) 2, 'vmu' => (int) 1 ) $gf_gene_species = 'vmu' $gf_gene_id = 'VMungo1309G0868' $species_info = array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ) $local_species = 'sci' $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' => 'HOM05D001729', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '375', 'num_species' => '42' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'Ah.07g204710' => 'amhyb', 'AUR62006001' => 'cqu', 'AUR62006002' => 'cqu', 'AUR62006003' => 'cqu', 'AUR62015641' => 'cqu', 'AUR62027174' => 'cqu', 'AUR62035623' => 'cqu', 'AUR62035624' => 'cqu', 'AUR62035625' => 'cqu', 'AUR62035626' => 'cqu', 'CAN.G1110.53' => 'can', 'CANSAT80G0415' => 'cansat', 'Ca_21364_v3' => 'car', 'COL.COLO4_30693' => 'col', 'COL.COLO4_30694' => 'col', 'COL.COLO4_30695' => 'col', 'COL.COLO4_30696' => 'col', 'COL.COLO4_34020' => 'col', 'DCAR_004585' => 'dca', 'Dinv04029' => 'din', 'Dinv34857' => 'din', 'Duzib147G0011' => 'dzi', 'Duzib170G0599' => 'dzi', 'Duzib192G1051' => 'dzi', 'FAN01G0708' => 'fan', 'FAN01G0742' => 'fan', 'FAN02G0048' => 'fan', 'FAN02G0583' => 'fan', 'FAN02G0688' => 'fan', 'FAN02G1588' => 'fan', 'FAN02G2194' => 'fan', 'FAN02G2750' => 'fan', 'FAN02G3094' => 'fan', 'FAN02G3887' => 'fan', 'FAN02G3911' => 'fan', 'FAN02G3994' => 'fan', 'FAN02G4432' => 'fan', 'FAN02G4556' => 'fan', 'FAN03G1977' => 'fan', 'FAN03G2781' => 'fan', 'FAN03G2850' => 'fan', 'FAN03G3155' => 'fan', 'FAN04G2487' => 'fan', 'FAN05G0208' => 'fan', 'FAN05G0656' => 'fan', 'FAN05G0696' => 'fan', 'FAN05G0810' => 'fan', 'FAN05G1447' => 'fan', 'FAN05G2640' => 'fan', 'FAN05G2911' => 'fan', 'FAN05G3901' => 'fan', 'FAN05G4859' => 'fan', 'FAN05G4861' => 'fan', 'FAN05G4988' => 'fan', 'FAN05G5187' => 'fan', 'FAN05G5452' => 'fan', 'FAN05G5500' => 'fan', 'FAN05G5688' => 'fan', 'FAN06G0177' => 'fan', 'FAN06G0675' => 'fan', 'FAN06G1290' => 'fan', 'FAN06G2191' => 'fan', 'FAN06G2405' => 'fan', 'FAN06G3231' => 'fan', 'FAN06G3932' => 'fan', 'FAN07G0163' => 'fan', 'FAN07G0471' => 'fan', 'FAN07G1354' => 'fan', 'FAN08G0338' => 'fan', 'FAN08G1373' => 'fan', 'FAN08G2539' => 'fan', 'FAN08G2728' => 'fan', 'FAN09G0608' => 'fan', 'FAN09G1136' => 'fan', 'FAN09G1958' => 'fan', 'FAN09G2508' => 'fan', 'FAN09G2597' => 'fan', 'FAN09G2658' => 'fan', 'FAN09G2757' => 'fan', 'FAN09G2983' => 'fan', 'FAN09G3130' => 'fan', 'FAN09G3565' => 'fan', 'FAN09G3613' => 'fan', 'FAN09G4011' => 'fan', 'FAN09G4239' => 'fan', 'FAN09G4277' => 'fan', 'FAN09G4720' => 'fan', 'FAN11G0139' => 'fan', 'FAN11G1727' => 'fan', 'FAN11G2672' => 'fan', 'FAN11G2795' => 'fan', 'FAN11G3238' => 'fan', 'FAN11G3734' => 'fan', 'FAN12G0631' => 'fan', 'FAN12G2239' => 'fan', 'FAN12G2308' => 'fan', 'FAN12G2569' => 'fan', 'FAN12G2623' => 'fan', 'FAN13G3182' => 'fan', 'FAN14G0053' => 'fan', 'FAN14G0370' => 'fan', 'FAN14G0382' => 'fan', 'FAN14G0421' => 'fan', 'FAN14G0866' => 'fan', 'FAN14G1187' => 'fan', 'FAN14G1727' => 'fan', 'FAN14G1791' => 'fan', 'FAN14G2361' => 'fan', 'FAN14G2668' => 'fan', 'FAN14G2770' => 'fan', 'FAN14G2874' => 'fan', 'FAN14G3193' => 'fan', 'FAN14G3624' => 'fan', 'FAN14G3676' => 'fan', 'FAN14G3807' => 'fan', 'FAN14G4082' => 'fan', 'FAN14G4342' => 'fan', 'FAN14G4985' => 'fan', 'FAN14G5126' => 'fan', 'FAN14G5781' => 'fan', 'FAN14G5808' => 'fan', 'FAN14G5949' => 'fan', 'FAN15G0828' => 'fan', 'FAN15G1054' => 'fan', 'FAN15G2023' => 'fan', 'FAN15G2506' => 'fan', 'FAN16G0128' => 'fan', 'FAN16G0249' => 'fan', 'FAN16G0429' => 'fan', 'FAN16G1493' => 'fan', 'FAN16G2210' => 'fan', 'FAN16G2506' => 'fan', 'FAN18G1542' => 'fan', 'FAN18G4057' => 'fan', 'FAN19G0745' => 'fan', 'FAN19G1216' => 'fan', 'FAN19G1733' => 'fan', 'FAN20G0258' => 'fan', 'FAN20G1095' => 'fan', 'FAN20G1557' => 'fan', 'FAN21G0302' => 'fan', 'FAN21G0519' => 'fan', 'FAN21G0970' => 'fan', 'FAN21G1159' => 'fan', 'FAN21G1312' => 'fan', 'FAN21G1440' => 'fan', 'FAN21G1715' => 'fan', 'FAN23G1584' => 'fan', 'FAN24G0045' => 'fan', 'FAN24G0053' => 'fan', 'FAN24G1500' => 'fan', 'FAN24G1817' => 'fan', 'FAN24G2147' => 'fan', 'FAN24G2236' => 'fan', 'FAN24G2446' => 'fan', 'FAN24G2684' => 'fan', 'FAN25G0187' => 'fan', 'FAN25G0505' => 'fan', 'FAN25G0589' => 'fan', 'FAN25G3663' => 'fan', 'FAN26G1025' => 'fan', 'FAN26G2860' => 'fan', 'FAN27G1329' => 'fan', 'FAN27G3392' => 'fan', 'FvH4_1g02011' => 'fve', 'FvH4_1g06511' => 'fve', 'FvH4_2g19900' => 'fve', 'FvH4_2g19920' => 'fve', 'FvH4_2g24261' => 'fve', 'FvH4_2g24270' => 'fve', 'FvH4_2g24631' => 'fve', 'FvH4_2g30622' => 'fve', 'FvH4_3g12920' => 'fve', 'FvH4_3g30171' => 'fve', 'FvH4_3g35490' => 'fve', 'FvH4_3g43682' => 'fve', 'FvH4_3g43730' => 'fve', 'FvH4_3g43732' => 'fve', 'FvH4_3g43751' => 'fve', 'FvH4_3g43752' => 'fve', 'FvH4_3g43770' => 'fve', 'FvH4_3g44471' => 'fve', 'FvH4_3g44510' => 'fve', 'FvH4_3g44582' => 'fve', 'FvH4_4g16921' => 'fve', 'FvH4_4g17121' => 'fve', 'FvH4_4g17782' => 'fve', 'FvH4_4g17783' => 'fve', 'FvH4_4g18120' => 'fve', 'FvH4_4g31310' => 'fve', 'FvH4_4g35052' => 'fve', 'FvH4_5g30862' => 'fve', 'FvH4_6g01541' => 'fve', 'FvH4_6g02021' => 'fve', 'FvH4_6g02041' => 'fve', 'FvH4_6g02071' => 'fve', 'FvH4_6g02171' => 'fve', 'FvH4_6g03181' => 'fve', 'FvH4_6g03182' => 'fve', 'FvH4_6g03221' => 'fve', 'FvH4_6g03380' => 'fve', 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'ppe', 'Prupe.1G512600' => 'ppe', 'Prupe.2G073200' => 'ppe', 'Prupe.3G059500' => 'ppe', 'Prupe.3G059600' => 'ppe', 'Prupe.3G246100' => 'ppe', 'Prupe.3G265100' => 'ppe', 'Prupe.4G034700' => 'ppe', 'Prupe.4G052100' => 'ppe', 'Prupe.4G053600' => 'ppe', 'Prupe.5G068800' => 'ppe', 'Prupe.5G070600' => 'ppe', 'Prupe.6G075400' => 'ppe', 'Prupe.6G075500' => 'ppe', 'Prupe.6G076400' => 'ppe', 'Prupe.8G110700' => 'ppe', 'Psat4g020960' => 'psa', 'PSO135G0788' => 'pso', 'PSO210G6463' => 'pso', 'PSO384G0370' => 'pso', 'PSO386G0056' => 'pso', 'QL01p006048' => 'qlo', 'QL02p054283' => 'qlo', 'QL05p008000' => 'qlo', 'QL05p008212' => 'qlo', 'QL05p008950' => 'qlo', 'QL05p009042' => 'qlo', 'QL05p009518' => 'qlo', 'QL05p012589' => 'qlo', 'QL05p012608' => 'qlo', 'QL05p012650' => 'qlo', 'QL05p012667' => 'qlo', 'QL05p014501' => 'qlo', 'QL05p052800' => 'qlo', 'QL05p065010' => 'qlo', 'QL05p074156' => 'qlo', 'QL05p074160' => 'qlo', 'QL05p074174' => 'qlo', 'QL05p074178' => 'qlo', 'QL05p074214' => 'qlo', 'QL06p001050' => 'qlo', 'QL06p001056' => 'qlo', 'QL06p006093' => 'qlo', 'QL06p006111' => 'qlo', 'QL07p019784' => 'qlo', 'QL07p019801' => 'qlo', 'QL07p036110' => 'qlo', 'QL07p036134' => 'qlo', 'QL07p036147' => 'qlo', 'QL07p036156' => 'qlo', 'QL07p036300' => 'qlo', 'QL07p036320' => 'qlo', 'QL08p014547' => 'qlo', 'QL08p014551' => 'qlo', 'QL08p043319' => 'qlo', 'QL08p043324' => 'qlo', 'QL11p009094' => 'qlo', 'RcHm_v2.0_Chr1g0380481' => 'rch', 'RcHm_v2.0_Chr2g0089331' => 'rch', 'RcHm_v2.0_Chr2g0123691' => 'rch', 'RcHm_v2.0_Chr2g0151111' => 'rch', 'RcHm_v2.0_Chr2g0163011' => 'rch', 'RcHm_v2.0_Chr2g0163051' => 'rch', 'RcHm_v2.0_Chr2g0164671' => 'rch', 'RcHm_v2.0_Chr2g0164681' => 'rch', 'RcHm_v2.0_Chr2g0164721' => 'rch', 'RcHm_v2.0_Chr3g0449911' => 'rch', 'RcHm_v2.0_Chr3g0450211' => 'rch', 'RcHm_v2.0_Chr3g0457271' => 'rch', 'RcHm_v2.0_Chr5g0018111' => 'rch', 'RcHm_v2.0_Chr5g0021011' => 'rch', 'RcHm_v2.0_Chr5g0081171' => 'rch', 'RcHm_v2.0_Chr5g0081211' => 'rch', 'RcHm_v2.0_Chr6g0275871' => 'rch', 'RcHm_v2.0_Chr6g0276071' => 'rch', 'RcHm_v2.0_Chr6g0285591' => 'rch', 'RcHm_v2.0_Chr6g0291931' => 'rch', 'RcHm_v2.0_Chr6g0292091' => 'rch', 'RcHm_v2.0_Chr6g0292271' => 'rch', 'RcHm_v2.0_Chr7g0221261' => 'rch', 'Rhsim08G0219900' => 'rsi', 'Rhsim08G0220200' => 'rsi', 'Rhsim08G0237800' => 'rsi', 'Rhsim08G0238800' => 'rsi', 'Sabra09G0102700' => 'sbr', 'Sabra09G0127200' => 'sbr', 'Sabra11G0003700' => 'sbr', 'Sabra15G0014700' => 'sbr', 'Sc19g0000590' => 'sci', 'Sc19g0001870' => 'sci', 'SGA_v2.0_scaffold1G00346' => 'sas', 'SGA_v2.0_scaffold1G00575' => 'sas', 'SGA_v2.0_scaffold1G00761' => 'sas', 'SGA_v2.0_scaffold232G43501' => 'sas', 'TAR625G1137' => 'tar', 'Thecc.03G222100' => 'tca', 'TPR.G12691' => 'tpr', 'TWI34G0727' => 'twi', 'TWI36G0117' => 'twi', 'VMungo1309G0868' => 'vmu' ), 'gf_id' => 'HOM05D001729', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001729' ), 'data_identifier' => 'HOM05D001729', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001729', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '375', 'num_species' => '42' ) 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'AUR62035624' => 'cqu', 'AUR62035625' => 'cqu', 'AUR62035626' => 'cqu', 'CAN.G1110.53' => 'can', 'CANSAT80G0415' => 'cansat', 'Ca_21364_v3' => 'car', 'COL.COLO4_30693' => 'col', 'COL.COLO4_30694' => 'col', 'COL.COLO4_30695' => 'col', 'COL.COLO4_30696' => 'col', 'COL.COLO4_34020' => 'col', 'DCAR_004585' => 'dca', 'Dinv04029' => 'din', 'Dinv34857' => 'din', 'Duzib147G0011' => 'dzi', 'Duzib170G0599' => 'dzi', 'Duzib192G1051' => 'dzi', 'FAN01G0708' => 'fan', 'FAN01G0742' => 'fan', 'FAN02G0048' => 'fan', 'FAN02G0583' => 'fan', 'FAN02G0688' => 'fan', 'FAN02G1588' => 'fan', 'FAN02G2194' => 'fan', 'FAN02G2750' => 'fan', 'FAN02G3094' => 'fan', 'FAN02G3887' => 'fan', 'FAN02G3911' => 'fan', 'FAN02G3994' => 'fan', 'FAN02G4432' => 'fan', 'FAN02G4556' => 'fan', 'FAN03G1977' => 'fan', 'FAN03G2781' => 'fan', 'FAN03G2850' => 'fan', 'FAN03G3155' => 'fan', 'FAN04G2487' => 'fan', 'FAN05G0208' => 'fan', 'FAN05G0656' => 'fan', 'FAN05G0696' => 'fan', 'FAN05G0810' => 'fan', 'FAN05G1447' => 'fan', 'FAN05G2640' => 'fan', 'FAN05G2911' => 'fan', 'FAN05G3901' => 'fan', 'FAN05G4859' => 'fan', 'FAN05G4861' => 'fan', 'FAN05G4988' => 'fan', 'FAN05G5187' => 'fan', 'FAN05G5452' => 'fan', 'FAN05G5500' => 'fan', 'FAN05G5688' => 'fan', 'FAN06G0177' => 'fan', 'FAN06G0675' => 'fan', 'FAN06G1290' => 'fan', 'FAN06G2191' => 'fan', 'FAN06G2405' => 'fan', 'FAN06G3231' => 'fan', 'FAN06G3932' => 'fan', 'FAN07G0163' => 'fan', 'FAN07G0471' => 'fan', 'FAN07G1354' => 'fan', 'FAN08G0338' => 'fan', 'FAN08G1373' => 'fan', 'FAN08G2539' => 'fan', 'FAN08G2728' => 'fan', 'FAN09G0608' => 'fan', 'FAN09G1136' => 'fan', 'FAN09G1958' => 'fan', 'FAN09G2508' => 'fan', 'FAN09G2597' => 'fan', 'FAN09G2658' => 'fan', 'FAN09G2757' => 'fan', 'FAN09G2983' => 'fan', 'FAN09G3130' => 'fan', 'FAN09G3565' => 'fan', 'FAN09G3613' => 'fan', 'FAN09G4011' => 'fan', 'FAN09G4239' => 'fan', 'FAN09G4277' => 'fan', 'FAN09G4720' => 'fan', 'FAN11G0139' => 'fan', 'FAN11G1727' => 'fan', 'FAN11G2672' => 'fan', 'FAN11G2795' => 'fan', 'FAN11G3238' => 'fan', 'FAN11G3734' => 'fan', 'FAN12G0631' => 'fan', 'FAN12G2239' => 'fan', 'FAN12G2308' => 'fan', 'FAN12G2569' => 'fan', 'FAN12G2623' => 'fan', 'FAN13G3182' => 'fan', 'FAN14G0053' => 'fan', 'FAN14G0370' => 'fan', 'FAN14G0382' => 'fan', 'FAN14G0421' => 'fan', 'FAN14G0866' => 'fan', 'FAN14G1187' => 'fan', 'FAN14G1727' => 'fan', 'FAN14G1791' => 'fan', 'FAN14G2361' => 'fan', 'FAN14G2668' => 'fan', 'FAN14G2770' => 'fan', 'FAN14G2874' => 'fan', 'FAN14G3193' => 'fan', 'FAN14G3624' => 'fan', 'FAN14G3676' => 'fan', 'FAN14G3807' => 'fan', 'FAN14G4082' => 'fan', 'FAN14G4342' => 'fan', 'FAN14G4985' => 'fan', 'FAN14G5126' => 'fan', 'FAN14G5781' => 'fan', 'FAN14G5808' => 'fan', 'FAN14G5949' => 'fan', 'FAN15G0828' => 'fan', 'FAN15G1054' => 'fan', 'FAN15G2023' => 'fan', 'FAN15G2506' => 'fan', 'FAN16G0128' => 'fan', 'FAN16G0249' => 'fan', 'FAN16G0429' => 'fan', 'FAN16G1493' => 'fan', 'FAN16G2210' => 'fan', 'FAN16G2506' => 'fan', 'FAN18G1542' => 'fan', 'FAN18G4057' => 'fan', 'FAN19G0745' => 'fan', 'FAN19G1216' => 'fan', 'FAN19G1733' => 'fan', 'FAN20G0258' => 'fan', 'FAN20G1095' => 'fan', 'FAN20G1557' => 'fan', 'FAN21G0302' => 'fan', 'FAN21G0519' => 'fan', 'FAN21G0970' => 'fan', 'FAN21G1159' => 'fan', 'FAN21G1312' => 'fan', 'FAN21G1440' => 'fan', 'FAN21G1715' => 'fan', 'FAN23G1584' => 'fan', 'FAN24G0045' => 'fan', 'FAN24G0053' => 'fan', 'FAN24G1500' => 'fan', 'FAN24G1817' => 'fan', 'FAN24G2147' => 'fan', 'FAN24G2236' => 'fan', 'FAN24G2446' => 'fan', 'FAN24G2684' => 'fan', 'FAN25G0187' => 'fan', 'FAN25G0505' => 'fan', 'FAN25G0589' => 'fan', 'FAN25G3663' => 'fan', 'FAN26G1025' => 'fan', 'FAN26G2860' => 'fan', 'FAN27G1329' => 'fan', 'FAN27G3392' => 'fan', 'FvH4_1g02011' => 'fve', 'FvH4_1g06511' => 'fve', 'FvH4_2g19900' => 'fve', 'FvH4_2g19920' => 'fve', 'FvH4_2g24261' => 'fve', 'FvH4_2g24270' => 'fve', 'FvH4_2g24631' => 'fve', 'FvH4_2g30622' => 'fve', 'FvH4_3g12920' => 'fve', 'FvH4_3g30171' => 'fve', 'FvH4_3g35490' => 'fve', 'FvH4_3g43682' => 'fve', 'FvH4_3g43730' => 'fve', 'FvH4_3g43732' => 'fve', 'FvH4_3g43751' => 'fve', 'FvH4_3g43752' => 'fve', 'FvH4_3g43770' => 'fve', 'FvH4_3g44471' => 'fve', 'FvH4_3g44510' => 'fve', 'FvH4_3g44582' => 'fve', 'FvH4_4g16921' => 'fve', 'FvH4_4g17121' => 'fve', 'FvH4_4g17782' => 'fve', 'FvH4_4g17783' => 'fve', 'FvH4_4g18120' => 'fve', 'FvH4_4g31310' => 'fve', 'FvH4_4g35052' => 'fve', 'FvH4_5g30862' => 'fve', 'FvH4_6g01541' => 'fve', 'FvH4_6g02021' => 'fve', 'FvH4_6g02041' => 'fve', 'FvH4_6g02071' => 'fve', 'FvH4_6g02171' => 'fve', 'FvH4_6g03181' => 'fve', 'FvH4_6g03182' => 'fve', 'FvH4_6g03221' => 'fve', 'FvH4_6g03380' => 'fve', 'FvH4_6g05201' => 'fve', 'FvH4_6g05203' => 'fve', 'FvH4_6g20231' => 'fve', 'FvH4_6g31981' => 'fve', 'FvH4_6g32061' => 'fve', 'FvH4_6g37041' => 'fve', 'FvH4_6g37932' => 'fve', 'FvH4_6g38731' => 'fve', 'FvH4_6g39370' => 'fve', 'FvH4_6g39371' => 'fve', 'FvH4_6g40891' => 'fve', 'FvH4_6g40892' => 'fve', 'FvH4_6g43143' => 'fve', 'FvH4_6g45251' => 'fve', 'FvH4_6g45260' => 'fve', 'FvH4_6g45291' => 'fve', 'FvH4_6g45890' => 'fve', 'FvH4_6g46240' => 'fve', 'FvH4_6g46241' => 'fve', 'FvH4_6g46242' => 'fve', 'FvH4_6g46260' => 'fve', 'FvH4_6g46280' => 'fve', 'FvH4_6g46380' => 'fve', 'FvH4_7g12841' => 'fve', 'FvH4_7g31431' => 'fve', 'Glyma.09G075900' => 'gma', 'Gohir.A09G096401' => 'ghi', 'Gohir.D09G096101' => 'ghi', 'Gorai.006G112800' => 'gra', 'HanXRQChr04g0121411' => 'han', 'Hund15878' => 'sun', 'Lj2A1107G68' => 'lonja', 'Lj2A630G63' => 'lonja', 'Lj2A946T25' => 'lonja', 'Lj2C714T1' => 'lonja', 'Lj2C966T3' => 'lonja', 'Lj2C966T4' => 'lonja', 'Lj4g0002979' => 'lja', 'Lsat_1_v5_gn_5_30901' => 'lsa', 'Lsat_1_v5_gn_5_31100' => 'lsa', 'Lsat_1_v5_gn_5_38600' => 'lsa', 'Lsat_1_v5_gn_6_92061' => 'lsa', 'Manes.05G071301' => 'mes', 'MD02G1008700' => 'mdo', 'MD02G1008900' => 'mdo', 'MD03G1256400' => 'mdo', 'MD04G1180900' => 'mdo', 'MD04G1181000' => 'mdo', 'MD04G1181200' => 'mdo', 'MD05G1244200' => 'mdo', 'MD05G1324200' => 'mdo', 'MD09G1201600' => 'mdo', 'MD10G1000600' => 'mdo', 'MD14G1026900' => 'mdo', 'MD14G1187900' => 'mdo', 'MD15G1017800' => 'mdo', 'MD15G1018100' => 'mdo', 'Medtr4g124160' => 'mtr', 'Migut.L01260' => 'egut', 'Nitab4.5_0000008g0440' => 'nta', 'Nitab4.5_0000207g0170' => 'nta', 'Nitab4.5_0007671g0030' => 'nta', 'Nitab4.5_0010853g0020' => 'nta', 'Oeu057656.1' => 'oeu', 'PGSC0003DMG400005638' => 'stu', 'PGSC0003DMG400005639' => 'stu', 'Phvul.009G222800' => 'pvu', 'Potri.009G132400' => 'ptr', 'Potri.009G163001' => 'ptr', 'Potri.011G000700' => 'ptr', 'Potri.011G004800' => 'ptr', 'Prupe.1G509300' => 'ppe', 'Prupe.1G509700' => 'ppe', 'Prupe.1G510400' => 'ppe', 'Prupe.1G510700' => 'ppe', 'Prupe.1G512600' => 'ppe', 'Prupe.2G073200' => 'ppe', 'Prupe.3G059500' => 'ppe', 'Prupe.3G059600' => 'ppe', 'Prupe.3G246100' => 'ppe', 'Prupe.3G265100' => 'ppe', 'Prupe.4G034700' => 'ppe', 'Prupe.4G052100' => 'ppe', 'Prupe.4G053600' => 'ppe', 'Prupe.5G068800' => 'ppe', 'Prupe.5G070600' => 'ppe', 'Prupe.6G075400' => 'ppe', 'Prupe.6G075500' => 'ppe', 'Prupe.6G076400' => 'ppe', 'Prupe.8G110700' => 'ppe', 'Psat4g020960' => 'psa', 'PSO135G0788' => 'pso', 'PSO210G6463' => 'pso', 'PSO384G0370' => 'pso', 'PSO386G0056' => 'pso', 'QL01p006048' => 'qlo', 'QL02p054283' => 'qlo', 'QL05p008000' => 'qlo', 'QL05p008212' => 'qlo', 'QL05p008950' => 'qlo', 'QL05p009042' => 'qlo', 'QL05p009518' => 'qlo', 'QL05p012589' => 'qlo', 'QL05p012608' => 'qlo', 'QL05p012650' => 'qlo', 'QL05p012667' => 'qlo', 'QL05p014501' => 'qlo', 'QL05p052800' => 'qlo', 'QL05p065010' => 'qlo', 'QL05p074156' => 'qlo', 'QL05p074160' => 'qlo', 'QL05p074174' => 'qlo', 'QL05p074178' => 'qlo', 'QL05p074214' => 'qlo', 'QL06p001050' => 'qlo', 'QL06p001056' => 'qlo', 'QL06p006093' => 'qlo', 'QL06p006111' => 'qlo', 'QL07p019784' => 'qlo', 'QL07p019801' => 'qlo', 'QL07p036110' => 'qlo', 'QL07p036134' => 'qlo', 'QL07p036147' => 'qlo', 'QL07p036156' => 'qlo', 'QL07p036300' => 'qlo', 'QL07p036320' => 'qlo', 'QL08p014547' => 'qlo', 'QL08p014551' => 'qlo', 'QL08p043319' => 'qlo', 'QL08p043324' => 'qlo', 'QL11p009094' => 'qlo', 'RcHm_v2.0_Chr1g0380481' => 'rch', 'RcHm_v2.0_Chr2g0089331' => 'rch', 'RcHm_v2.0_Chr2g0123691' => 'rch', 'RcHm_v2.0_Chr2g0151111' => 'rch', 'RcHm_v2.0_Chr2g0163011' => 'rch', 'RcHm_v2.0_Chr2g0163051' => 'rch', 'RcHm_v2.0_Chr2g0164671' => 'rch', 'RcHm_v2.0_Chr2g0164681' => 'rch', 'RcHm_v2.0_Chr2g0164721' => 'rch', 'RcHm_v2.0_Chr3g0449911' => 'rch', 'RcHm_v2.0_Chr3g0450211' => 'rch', 'RcHm_v2.0_Chr3g0457271' => 'rch', 'RcHm_v2.0_Chr5g0018111' => 'rch', 'RcHm_v2.0_Chr5g0021011' => 'rch', 'RcHm_v2.0_Chr5g0081171' => 'rch', 'RcHm_v2.0_Chr5g0081211' => 'rch', 'RcHm_v2.0_Chr6g0275871' => 'rch', 'RcHm_v2.0_Chr6g0276071' => 'rch', 'RcHm_v2.0_Chr6g0285591' => 'rch', 'RcHm_v2.0_Chr6g0291931' => 'rch', 'RcHm_v2.0_Chr6g0292091' => 'rch', 'RcHm_v2.0_Chr6g0292271' => 'rch', 'RcHm_v2.0_Chr7g0221261' => 'rch', 'Rhsim08G0219900' => 'rsi', 'Rhsim08G0220200' => 'rsi', 'Rhsim08G0237800' => 'rsi', 'Rhsim08G0238800' => 'rsi', 'Sabra09G0102700' => 'sbr', 'Sabra09G0127200' => 'sbr', 'Sabra11G0003700' => 'sbr', 'Sabra15G0014700' => 'sbr', 'Sc19g0000590' => 'sci', 'Sc19g0001870' => 'sci', 'SGA_v2.0_scaffold1G00346' => 'sas', 'SGA_v2.0_scaffold1G00575' => 'sas', 'SGA_v2.0_scaffold1G00761' => 'sas', 'SGA_v2.0_scaffold232G43501' => 'sas', 'TAR625G1137' => 'tar', 'Thecc.03G222100' => 'tca', 'TPR.G12691' => 'tpr', 'TWI34G0727' => 'twi', 'TWI36G0117' => 'twi', 'VMungo1309G0868' => 'vmu' ) $gf_id = 'HOM05D001729' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001729' ) $data_identifier = 'HOM05D001729' $data_type = 'gf_id' $species_gene_counts = array( 'amhyb' => (int) 1, 'cqu' => (int) 9, 'can' => (int) 1, 'cansat' => (int) 1, 'car' => (int) 1, 'col' => (int) 5, 'dca' => (int) 1, 'din' => (int) 2, 'dzi' => (int) 3, 'fan' => (int) 140, 'fve' => (int) 62, 'gma' => (int) 1, 'ghi' => (int) 2, 'gra' => (int) 1, 'han' => (int) 1, 'sun' => (int) 1, 'lonja' => (int) 6, 'lja' => (int) 1, 'lsa' => (int) 4, 'mes' => (int) 1, 'mdo' => (int) 14, 'mtr' => (int) 1, 'egut' => (int) 1, 'nta' => (int) 4, 'oeu' => (int) 1, 'stu' => (int) 2, 'pvu' => (int) 1, 'ptr' => (int) 4, 'ppe' => (int) 19, 'psa' => (int) 1, 'pso' => (int) 4, 'qlo' => (int) 36, 'rch' => (int) 23, 'rsi' => (int) 4, 'sbr' => (int) 4, 'sci' => (int) 2, 'sas' => (int) 4, 'tar' => (int) 1, 'tca' => (int) 1, 'tpr' => (int) 1, 'twi' => (int) 2, 'vmu' => (int) 1 ) $gf_gene_species = 'vmu' $gf_gene_id = 'VMungo1309G0868' $species_info = array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ) $local_species = 'sci' $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' => 'HOM05D001729', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '375', 'num_species' => '42' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'Ah.07g204710' => 'amhyb', 'AUR62006001' => 'cqu', 'AUR62006002' => 'cqu', 'AUR62006003' => 'cqu', 'AUR62015641' => 'cqu', 'AUR62027174' => 'cqu', 'AUR62035623' => 'cqu', 'AUR62035624' => 'cqu', 'AUR62035625' => 'cqu', 'AUR62035626' => 'cqu', 'CAN.G1110.53' => 'can', 'CANSAT80G0415' => 'cansat', 'Ca_21364_v3' => 'car', 'COL.COLO4_30693' => 'col', 'COL.COLO4_30694' => 'col', 'COL.COLO4_30695' => 'col', 'COL.COLO4_30696' => 'col', 'COL.COLO4_34020' => 'col', 'DCAR_004585' => 'dca', 'Dinv04029' => 'din', 'Dinv34857' => 'din', 'Duzib147G0011' => 'dzi', 'Duzib170G0599' => 'dzi', 'Duzib192G1051' => 'dzi', 'FAN01G0708' => 'fan', 'FAN01G0742' => 'fan', 'FAN02G0048' => 'fan', 'FAN02G0583' => 'fan', 'FAN02G0688' => 'fan', 'FAN02G1588' => 'fan', 'FAN02G2194' => 'fan', 'FAN02G2750' => 'fan', 'FAN02G3094' => 'fan', 'FAN02G3887' => 'fan', 'FAN02G3911' => 'fan', 'FAN02G3994' => 'fan', 'FAN02G4432' => 'fan', 'FAN02G4556' => 'fan', 'FAN03G1977' => 'fan', 'FAN03G2781' => 'fan', 'FAN03G2850' => 'fan', 'FAN03G3155' => 'fan', 'FAN04G2487' => 'fan', 'FAN05G0208' => 'fan', 'FAN05G0656' => 'fan', 'FAN05G0696' => 'fan', 'FAN05G0810' => 'fan', 'FAN05G1447' => 'fan', 'FAN05G2640' => 'fan', 'FAN05G2911' => 'fan', 'FAN05G3901' => 'fan', 'FAN05G4859' => 'fan', 'FAN05G4861' => 'fan', 'FAN05G4988' => 'fan', 'FAN05G5187' => 'fan', 'FAN05G5452' => 'fan', 'FAN05G5500' => 'fan', 'FAN05G5688' => 'fan', 'FAN06G0177' => 'fan', 'FAN06G0675' => 'fan', 'FAN06G1290' => 'fan', 'FAN06G2191' => 'fan', 'FAN06G2405' => 'fan', 'FAN06G3231' => 'fan', 'FAN06G3932' => 'fan', 'FAN07G0163' => 'fan', 'FAN07G0471' => 'fan', 'FAN07G1354' => 'fan', 'FAN08G0338' => 'fan', 'FAN08G1373' => 'fan', 'FAN08G2539' => 'fan', 'FAN08G2728' => 'fan', 'FAN09G0608' => 'fan', 'FAN09G1136' => 'fan', 'FAN09G1958' => 'fan', 'FAN09G2508' => 'fan', 'FAN09G2597' => 'fan', 'FAN09G2658' => 'fan', 'FAN09G2757' => 'fan', 'FAN09G2983' => 'fan', 'FAN09G3130' => 'fan', 'FAN09G3565' => 'fan', 'FAN09G3613' => 'fan', 'FAN09G4011' => 'fan', 'FAN09G4239' => 'fan', 'FAN09G4277' => 'fan', 'FAN09G4720' => 'fan', 'FAN11G0139' => 'fan', 'FAN11G1727' => 'fan', 'FAN11G2672' => 'fan', 'FAN11G2795' => 'fan', 'FAN11G3238' => 'fan', 'FAN11G3734' => 'fan', 'FAN12G0631' => 'fan', 'FAN12G2239' => 'fan', 'FAN12G2308' => 'fan', 'FAN12G2569' => 'fan', 'FAN12G2623' => 'fan', 'FAN13G3182' => 'fan', 'FAN14G0053' => 'fan', 'FAN14G0370' => 'fan', 'FAN14G0382' => 'fan', 'FAN14G0421' => 'fan', 'FAN14G0866' => 'fan', 'FAN14G1187' => 'fan', 'FAN14G1727' => 'fan', 'FAN14G1791' => 'fan', 'FAN14G2361' => 'fan', 'FAN14G2668' => 'fan', 'FAN14G2770' => 'fan', 'FAN14G2874' => 'fan', 'FAN14G3193' => 'fan', 'FAN14G3624' => 'fan', 'FAN14G3676' => 'fan', 'FAN14G3807' => 'fan', 'FAN14G4082' => 'fan', 'FAN14G4342' => 'fan', 'FAN14G4985' => 'fan', 'FAN14G5126' => 'fan', 'FAN14G5781' => 'fan', 'FAN14G5808' => 'fan', 'FAN14G5949' => 'fan', 'FAN15G0828' => 'fan', 'FAN15G1054' => 'fan', 'FAN15G2023' => 'fan', 'FAN15G2506' => 'fan', 'FAN16G0128' => 'fan', 'FAN16G0249' => 'fan', 'FAN16G0429' => 'fan', 'FAN16G1493' => 'fan', 'FAN16G2210' => 'fan', 'FAN16G2506' => 'fan', 'FAN18G1542' => 'fan', 'FAN18G4057' => 'fan', 'FAN19G0745' => 'fan', 'FAN19G1216' => 'fan', 'FAN19G1733' => 'fan', 'FAN20G0258' => 'fan', 'FAN20G1095' => 'fan', 'FAN20G1557' => 'fan', 'FAN21G0302' => 'fan', 'FAN21G0519' => 'fan', 'FAN21G0970' => 'fan', 'FAN21G1159' => 'fan', 'FAN21G1312' => 'fan', 'FAN21G1440' => 'fan', 'FAN21G1715' => 'fan', 'FAN23G1584' => 'fan', 'FAN24G0045' => 'fan', 'FAN24G0053' => 'fan', 'FAN24G1500' => 'fan', 'FAN24G1817' => 'fan', 'FAN24G2147' => 'fan', 'FAN24G2236' => 'fan', 'FAN24G2446' => 'fan', 'FAN24G2684' => 'fan', 'FAN25G0187' => 'fan', 'FAN25G0505' => 'fan', 'FAN25G0589' => 'fan', 'FAN25G3663' => 'fan', 'FAN26G1025' => 'fan', 'FAN26G2860' => 'fan', 'FAN27G1329' => 'fan', 'FAN27G3392' => 'fan', 'FvH4_1g02011' => 'fve', 'FvH4_1g06511' => 'fve', 'FvH4_2g19900' => 'fve', 'FvH4_2g19920' => 'fve', 'FvH4_2g24261' => 'fve', 'FvH4_2g24270' => 'fve', 'FvH4_2g24631' => 'fve', 'FvH4_2g30622' => 'fve', 'FvH4_3g12920' => 'fve', 'FvH4_3g30171' => 'fve', 'FvH4_3g35490' => 'fve', 'FvH4_3g43682' => 'fve', 'FvH4_3g43730' => 'fve', 'FvH4_3g43732' => 'fve', 'FvH4_3g43751' => 'fve', 'FvH4_3g43752' => 'fve', 'FvH4_3g43770' => 'fve', 'FvH4_3g44471' => 'fve', 'FvH4_3g44510' => 'fve', 'FvH4_3g44582' => 'fve', 'FvH4_4g16921' => 'fve', 'FvH4_4g17121' => 'fve', 'FvH4_4g17782' => 'fve', 'FvH4_4g17783' => 'fve', 'FvH4_4g18120' => 'fve', 'FvH4_4g31310' => 'fve', 'FvH4_4g35052' => 'fve', 'FvH4_5g30862' => 'fve', 'FvH4_6g01541' => 'fve', 'FvH4_6g02021' => 'fve', 'FvH4_6g02041' => 'fve', 'FvH4_6g02071' => 'fve', 'FvH4_6g02171' => 'fve', 'FvH4_6g03181' => 'fve', 'FvH4_6g03182' => 'fve', 'FvH4_6g03221' => 'fve', 'FvH4_6g03380' => 'fve', 'FvH4_6g05201' => 'fve', 'FvH4_6g05203' => 'fve', 'FvH4_6g20231' => 'fve', 'FvH4_6g31981' => 'fve', 'FvH4_6g32061' => 'fve', 'FvH4_6g37041' => 'fve', 'FvH4_6g37932' => 'fve', 'FvH4_6g38731' => 'fve', 'FvH4_6g39370' => 'fve', 'FvH4_6g39371' => 'fve', 'FvH4_6g40891' => 'fve', 'FvH4_6g40892' => 'fve', 'FvH4_6g43143' => 'fve', 'FvH4_6g45251' => 'fve', 'FvH4_6g45260' => 'fve', 'FvH4_6g45291' => 'fve', 'FvH4_6g45890' => 'fve', 'FvH4_6g46240' => 'fve', 'FvH4_6g46241' => 'fve', 'FvH4_6g46242' => 'fve', 'FvH4_6g46260' => 'fve', 'FvH4_6g46280' => 'fve', 'FvH4_6g46380' => 'fve', 'FvH4_7g12841' => 'fve', 'FvH4_7g31431' => 'fve', 'Glyma.09G075900' => 'gma', 'Gohir.A09G096401' => 'ghi', 'Gohir.D09G096101' => 'ghi', 'Gorai.006G112800' => 'gra', 'HanXRQChr04g0121411' => 'han', 'Hund15878' => 'sun', 'Lj2A1107G68' => 'lonja', 'Lj2A630G63' => 'lonja', 'Lj2A946T25' => 'lonja', 'Lj2C714T1' => 'lonja', 'Lj2C966T3' => 'lonja', 'Lj2C966T4' => 'lonja', 'Lj4g0002979' => 'lja', 'Lsat_1_v5_gn_5_30901' => 'lsa', 'Lsat_1_v5_gn_5_31100' => 'lsa', 'Lsat_1_v5_gn_5_38600' => 'lsa', 'Lsat_1_v5_gn_6_92061' => 'lsa', 'Manes.05G071301' => 'mes', 'MD02G1008700' => 'mdo', 'MD02G1008900' => 'mdo', 'MD03G1256400' => 'mdo', 'MD04G1180900' => 'mdo', 'MD04G1181000' => 'mdo', 'MD04G1181200' => 'mdo', 'MD05G1244200' => 'mdo', 'MD05G1324200' => 'mdo', 'MD09G1201600' => 'mdo', 'MD10G1000600' => 'mdo', 'MD14G1026900' => 'mdo', 'MD14G1187900' => 'mdo', 'MD15G1017800' => 'mdo', 'MD15G1018100' => 'mdo', 'Medtr4g124160' => 'mtr', 'Migut.L01260' => 'egut', 'Nitab4.5_0000008g0440' => 'nta', 'Nitab4.5_0000207g0170' => 'nta', 'Nitab4.5_0007671g0030' => 'nta', 'Nitab4.5_0010853g0020' => 'nta', 'Oeu057656.1' => 'oeu', 'PGSC0003DMG400005638' => 'stu', 'PGSC0003DMG400005639' => 'stu', 'Phvul.009G222800' => 'pvu', 'Potri.009G132400' => 'ptr', 'Potri.009G163001' => 'ptr', 'Potri.011G000700' => 'ptr', 'Potri.011G004800' => 'ptr', 'Prupe.1G509300' => 'ppe', 'Prupe.1G509700' => 'ppe', 'Prupe.1G510400' => 'ppe', 'Prupe.1G510700' => 'ppe', 'Prupe.1G512600' => 'ppe', 'Prupe.2G073200' => 'ppe', 'Prupe.3G059500' => 'ppe', 'Prupe.3G059600' => 'ppe', 'Prupe.3G246100' => 'ppe', 'Prupe.3G265100' => 'ppe', 'Prupe.4G034700' => 'ppe', 'Prupe.4G052100' => 'ppe', 'Prupe.4G053600' => 'ppe', 'Prupe.5G068800' => 'ppe', 'Prupe.5G070600' => 'ppe', 'Prupe.6G075400' => 'ppe', 'Prupe.6G075500' => 'ppe', 'Prupe.6G076400' => 'ppe', 'Prupe.8G110700' => 'ppe', 'Psat4g020960' => 'psa', 'PSO135G0788' => 'pso', 'PSO210G6463' => 'pso', 'PSO384G0370' => 'pso', 'PSO386G0056' => 'pso', 'QL01p006048' => 'qlo', 'QL02p054283' => 'qlo', 'QL05p008000' => 'qlo', 'QL05p008212' => 'qlo', 'QL05p008950' => 'qlo', 'QL05p009042' => 'qlo', 'QL05p009518' => 'qlo', 'QL05p012589' => 'qlo', 'QL05p012608' => 'qlo', 'QL05p012650' => 'qlo', 'QL05p012667' => 'qlo', 'QL05p014501' => 'qlo', 'QL05p052800' => 'qlo', 'QL05p065010' => 'qlo', 'QL05p074156' => 'qlo', 'QL05p074160' => 'qlo', 'QL05p074174' => 'qlo', 'QL05p074178' => 'qlo', 'QL05p074214' => 'qlo', 'QL06p001050' => 'qlo', 'QL06p001056' => 'qlo', 'QL06p006093' => 'qlo', 'QL06p006111' => 'qlo', 'QL07p019784' => 'qlo', 'QL07p019801' => 'qlo', 'QL07p036110' => 'qlo', 'QL07p036134' => 'qlo', 'QL07p036147' => 'qlo', 'QL07p036156' => 'qlo', 'QL07p036300' => 'qlo', 'QL07p036320' => 'qlo', 'QL08p014547' => 'qlo', 'QL08p014551' => 'qlo', 'QL08p043319' => 'qlo', 'QL08p043324' => 'qlo', 'QL11p009094' => 'qlo', 'RcHm_v2.0_Chr1g0380481' => 'rch', 'RcHm_v2.0_Chr2g0089331' => 'rch', 'RcHm_v2.0_Chr2g0123691' => 'rch', 'RcHm_v2.0_Chr2g0151111' => 'rch', 'RcHm_v2.0_Chr2g0163011' => 'rch', 'RcHm_v2.0_Chr2g0163051' => 'rch', 'RcHm_v2.0_Chr2g0164671' => 'rch', 'RcHm_v2.0_Chr2g0164681' => 'rch', 'RcHm_v2.0_Chr2g0164721' => 'rch', 'RcHm_v2.0_Chr3g0449911' => 'rch', 'RcHm_v2.0_Chr3g0450211' => 'rch', 'RcHm_v2.0_Chr3g0457271' => 'rch', 'RcHm_v2.0_Chr5g0018111' => 'rch', 'RcHm_v2.0_Chr5g0021011' => 'rch', 'RcHm_v2.0_Chr5g0081171' => 'rch', 'RcHm_v2.0_Chr5g0081211' => 'rch', 'RcHm_v2.0_Chr6g0275871' => 'rch', 'RcHm_v2.0_Chr6g0276071' => 'rch', 'RcHm_v2.0_Chr6g0285591' => 'rch', 'RcHm_v2.0_Chr6g0291931' => 'rch', 'RcHm_v2.0_Chr6g0292091' => 'rch', 'RcHm_v2.0_Chr6g0292271' => 'rch', 'RcHm_v2.0_Chr7g0221261' => 'rch', 'Rhsim08G0219900' => 'rsi', 'Rhsim08G0220200' => 'rsi', 'Rhsim08G0237800' => 'rsi', 'Rhsim08G0238800' => 'rsi', 'Sabra09G0102700' => 'sbr', 'Sabra09G0127200' => 'sbr', 'Sabra11G0003700' => 'sbr', 'Sabra15G0014700' => 'sbr', 'Sc19g0000590' => 'sci', 'Sc19g0001870' => 'sci', 'SGA_v2.0_scaffold1G00346' => 'sas', 'SGA_v2.0_scaffold1G00575' => 'sas', 'SGA_v2.0_scaffold1G00761' => 'sas', 'SGA_v2.0_scaffold232G43501' => 'sas', 'TAR625G1137' => 'tar', 'Thecc.03G222100' => 'tca', 'TPR.G12691' => 'tpr', 'TWI34G0727' => 'twi', 'TWI36G0117' => 'twi', 'VMungo1309G0868' => 'vmu' ), 'gf_id' => 'HOM05D001729', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001729' ), 'data_identifier' => 'HOM05D001729', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001729', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '375', 'num_species' => '42' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'Ah.07g204710' => 'amhyb', 'AUR62006001' => 'cqu', 'AUR62006002' => 'cqu', 'AUR62006003' => 'cqu', 'AUR62015641' => 'cqu', 'AUR62027174' => 'cqu', 'AUR62035623' => 'cqu', 'AUR62035624' => 'cqu', 'AUR62035625' => 'cqu', 'AUR62035626' => 'cqu', 'CAN.G1110.53' => 'can', 'CANSAT80G0415' => 'cansat', 'Ca_21364_v3' => 'car', 'COL.COLO4_30693' => 'col', 'COL.COLO4_30694' => 'col', 'COL.COLO4_30695' => 'col', 'COL.COLO4_30696' => 'col', 'COL.COLO4_34020' => 'col', 'DCAR_004585' => 'dca', 'Dinv04029' => 'din', 'Dinv34857' => 'din', 'Duzib147G0011' => 'dzi', 'Duzib170G0599' => 'dzi', 'Duzib192G1051' => 'dzi', 'FAN01G0708' => 'fan', 'FAN01G0742' => 'fan', 'FAN02G0048' => 'fan', 'FAN02G0583' => 'fan', 'FAN02G0688' => 'fan', 'FAN02G1588' => 'fan', 'FAN02G2194' => 'fan', 'FAN02G2750' => 'fan', 'FAN02G3094' => 'fan', 'FAN02G3887' => 'fan', 'FAN02G3911' => 'fan', 'FAN02G3994' => 'fan', 'FAN02G4432' => 'fan', 'FAN02G4556' => 'fan', 'FAN03G1977' => 'fan', 'FAN03G2781' => 'fan', 'FAN03G2850' => 'fan', 'FAN03G3155' => 'fan', 'FAN04G2487' => 'fan', 'FAN05G0208' => 'fan', 'FAN05G0656' => 'fan', 'FAN05G0696' => 'fan', 'FAN05G0810' => 'fan', 'FAN05G1447' => 'fan', 'FAN05G2640' => 'fan', 'FAN05G2911' => 'fan', 'FAN05G3901' => 'fan', 'FAN05G4859' => 'fan', 'FAN05G4861' => 'fan', 'FAN05G4988' => 'fan', 'FAN05G5187' => 'fan', 'FAN05G5452' => 'fan', 'FAN05G5500' => 'fan', 'FAN05G5688' => 'fan', 'FAN06G0177' => 'fan', 'FAN06G0675' => 'fan', 'FAN06G1290' => 'fan', 'FAN06G2191' => 'fan', 'FAN06G2405' => 'fan', 'FAN06G3231' => 'fan', 'FAN06G3932' => 'fan', 'FAN07G0163' => 'fan', 'FAN07G0471' => 'fan', 'FAN07G1354' => 'fan', 'FAN08G0338' => 'fan', 'FAN08G1373' => 'fan', 'FAN08G2539' => 'fan', 'FAN08G2728' => 'fan', 'FAN09G0608' => 'fan', 'FAN09G1136' => 'fan', 'FAN09G1958' => 'fan', 'FAN09G2508' => 'fan', 'FAN09G2597' => 'fan', 'FAN09G2658' => 'fan', 'FAN09G2757' => 'fan', 'FAN09G2983' => 'fan', 'FAN09G3130' => 'fan', 'FAN09G3565' => 'fan', 'FAN09G3613' => 'fan', 'FAN09G4011' => 'fan', 'FAN09G4239' => 'fan', 'FAN09G4277' => 'fan', 'FAN09G4720' => 'fan', 'FAN11G0139' => 'fan', 'FAN11G1727' => 'fan', 'FAN11G2672' => 'fan', 'FAN11G2795' => 'fan', 'FAN11G3238' => 'fan', 'FAN11G3734' => 'fan', 'FAN12G0631' => 'fan', 'FAN12G2239' => 'fan', 'FAN12G2308' => 'fan', 'FAN12G2569' => 'fan', 'FAN12G2623' => 'fan', 'FAN13G3182' => 'fan', 'FAN14G0053' => 'fan', 'FAN14G0370' => 'fan', 'FAN14G0382' => 'fan', 'FAN14G0421' => 'fan', 'FAN14G0866' => 'fan', 'FAN14G1187' => 'fan', 'FAN14G1727' => 'fan', 'FAN14G1791' => 'fan', 'FAN14G2361' => 'fan', 'FAN14G2668' => 'fan', 'FAN14G2770' => 'fan', 'FAN14G2874' => 'fan', 'FAN14G3193' => 'fan', 'FAN14G3624' => 'fan', 'FAN14G3676' => 'fan', 'FAN14G3807' => 'fan', 'FAN14G4082' => 'fan', 'FAN14G4342' => 'fan', 'FAN14G4985' => 'fan', 'FAN14G5126' => 'fan', 'FAN14G5781' => 'fan', 'FAN14G5808' => 'fan', 'FAN14G5949' => 'fan', 'FAN15G0828' => 'fan', 'FAN15G1054' => 'fan', 'FAN15G2023' => 'fan', 'FAN15G2506' => 'fan', 'FAN16G0128' => 'fan', 'FAN16G0249' => 'fan', 'FAN16G0429' => 'fan', 'FAN16G1493' => 'fan', 'FAN16G2210' => 'fan', 'FAN16G2506' => 'fan', 'FAN18G1542' => 'fan', 'FAN18G4057' => 'fan', 'FAN19G0745' => 'fan', 'FAN19G1216' => 'fan', 'FAN19G1733' => 'fan', 'FAN20G0258' => 'fan', 'FAN20G1095' => 'fan', 'FAN20G1557' => 'fan', 'FAN21G0302' => 'fan', 'FAN21G0519' => 'fan', 'FAN21G0970' => 'fan', 'FAN21G1159' => 'fan', 'FAN21G1312' => 'fan', 'FAN21G1440' => 'fan', 'FAN21G1715' => 'fan', 'FAN23G1584' => 'fan', 'FAN24G0045' => 'fan', 'FAN24G0053' => 'fan', 'FAN24G1500' => 'fan', 'FAN24G1817' => 'fan', 'FAN24G2147' => 'fan', 'FAN24G2236' => 'fan', 'FAN24G2446' => 'fan', 'FAN24G2684' => 'fan', 'FAN25G0187' => 'fan', 'FAN25G0505' => 'fan', 'FAN25G0589' => 'fan', 'FAN25G3663' => 'fan', 'FAN26G1025' => 'fan', 'FAN26G2860' => 'fan', 'FAN27G1329' => 'fan', 'FAN27G3392' => 'fan', 'FvH4_1g02011' => 'fve', 'FvH4_1g06511' => 'fve', 'FvH4_2g19900' => 'fve', 'FvH4_2g19920' => 'fve', 'FvH4_2g24261' => 'fve', 'FvH4_2g24270' => 'fve', 'FvH4_2g24631' => 'fve', 'FvH4_2g30622' => 'fve', 'FvH4_3g12920' => 'fve', 'FvH4_3g30171' => 'fve', 'FvH4_3g35490' => 'fve', 'FvH4_3g43682' => 'fve', 'FvH4_3g43730' => 'fve', 'FvH4_3g43732' => 'fve', 'FvH4_3g43751' => 'fve', 'FvH4_3g43752' => 'fve', 'FvH4_3g43770' => 'fve', 'FvH4_3g44471' => 'fve', 'FvH4_3g44510' => 'fve', 'FvH4_3g44582' => 'fve', 'FvH4_4g16921' => 'fve', 'FvH4_4g17121' => 'fve', 'FvH4_4g17782' => 'fve', 'FvH4_4g17783' => 'fve', 'FvH4_4g18120' => 'fve', 'FvH4_4g31310' => 'fve', 'FvH4_4g35052' => 'fve', 'FvH4_5g30862' => 'fve', 'FvH4_6g01541' => 'fve', 'FvH4_6g02021' => 'fve', 'FvH4_6g02041' => 'fve', 'FvH4_6g02071' => 'fve', 'FvH4_6g02171' => 'fve', 'FvH4_6g03181' => 'fve', 'FvH4_6g03182' => 'fve', 'FvH4_6g03221' => 'fve', 'FvH4_6g03380' => 'fve', 'FvH4_6g05201' => 'fve', 'FvH4_6g05203' => 'fve', 'FvH4_6g20231' => 'fve', 'FvH4_6g31981' => 'fve', 'FvH4_6g32061' => 'fve', 'FvH4_6g37041' => 'fve', 'FvH4_6g37932' => 'fve', 'FvH4_6g38731' => 'fve', 'FvH4_6g39370' => 'fve', 'FvH4_6g39371' => 'fve', 'FvH4_6g40891' => 'fve', 'FvH4_6g40892' => 'fve', 'FvH4_6g43143' => 'fve', 'FvH4_6g45251' => 'fve', 'FvH4_6g45260' => 'fve', 'FvH4_6g45291' => 'fve', 'FvH4_6g45890' => 'fve', 'FvH4_6g46240' => 'fve', 'FvH4_6g46241' => 'fve', 'FvH4_6g46242' => 'fve', 'FvH4_6g46260' => 'fve', 'FvH4_6g46280' => 'fve', 'FvH4_6g46380' => 'fve', 'FvH4_7g12841' => 'fve', 'FvH4_7g31431' => 'fve', 'Glyma.09G075900' => 'gma', 'Gohir.A09G096401' => 'ghi', 'Gohir.D09G096101' => 'ghi', 'Gorai.006G112800' => 'gra', 'HanXRQChr04g0121411' => 'han', 'Hund15878' => 'sun', 'Lj2A1107G68' => 'lonja', 'Lj2A630G63' => 'lonja', 'Lj2A946T25' => 'lonja', 'Lj2C714T1' => 'lonja', 'Lj2C966T3' => 'lonja', 'Lj2C966T4' => 'lonja', 'Lj4g0002979' => 'lja', 'Lsat_1_v5_gn_5_30901' => 'lsa', 'Lsat_1_v5_gn_5_31100' => 'lsa', 'Lsat_1_v5_gn_5_38600' => 'lsa', 'Lsat_1_v5_gn_6_92061' => 'lsa', 'Manes.05G071301' => 'mes', 'MD02G1008700' => 'mdo', 'MD02G1008900' => 'mdo', 'MD03G1256400' => 'mdo', 'MD04G1180900' => 'mdo', 'MD04G1181000' => 'mdo', 'MD04G1181200' => 'mdo', 'MD05G1244200' => 'mdo', 'MD05G1324200' => 'mdo', 'MD09G1201600' => 'mdo', 'MD10G1000600' => 'mdo', 'MD14G1026900' => 'mdo', 'MD14G1187900' => 'mdo', 'MD15G1017800' => 'mdo', 'MD15G1018100' => 'mdo', 'Medtr4g124160' => 'mtr', 'Migut.L01260' => 'egut', 'Nitab4.5_0000008g0440' => 'nta', 'Nitab4.5_0000207g0170' => 'nta', 'Nitab4.5_0007671g0030' => 'nta', 'Nitab4.5_0010853g0020' => 'nta', 'Oeu057656.1' => 'oeu', 'PGSC0003DMG400005638' => 'stu', 'PGSC0003DMG400005639' => 'stu', 'Phvul.009G222800' => 'pvu', 'Potri.009G132400' => 'ptr', 'Potri.009G163001' => 'ptr', 'Potri.011G000700' => 'ptr', 'Potri.011G004800' => 'ptr', 'Prupe.1G509300' => 'ppe', 'Prupe.1G509700' => 'ppe', 'Prupe.1G510400' => 'ppe', 'Prupe.1G510700' => 'ppe', 'Prupe.1G512600' => 'ppe', 'Prupe.2G073200' => 'ppe', 'Prupe.3G059500' => 'ppe', 'Prupe.3G059600' => 'ppe', 'Prupe.3G246100' => 'ppe', 'Prupe.3G265100' => 'ppe', 'Prupe.4G034700' => 'ppe', 'Prupe.4G052100' => 'ppe', 'Prupe.4G053600' => 'ppe', 'Prupe.5G068800' => 'ppe', 'Prupe.5G070600' => 'ppe', 'Prupe.6G075400' => 'ppe', 'Prupe.6G075500' => 'ppe', 'Prupe.6G076400' => 'ppe', 'Prupe.8G110700' => 'ppe', 'Psat4g020960' => 'psa', 'PSO135G0788' => 'pso', 'PSO210G6463' => 'pso', 'PSO384G0370' => 'pso', 'PSO386G0056' => 'pso', 'QL01p006048' => 'qlo', 'QL02p054283' => 'qlo', 'QL05p008000' => 'qlo', 'QL05p008212' => 'qlo', 'QL05p008950' => 'qlo', 'QL05p009042' => 'qlo', 'QL05p009518' => 'qlo', 'QL05p012589' => 'qlo', 'QL05p012608' => 'qlo', 'QL05p012650' => 'qlo', 'QL05p012667' => 'qlo', 'QL05p014501' => 'qlo', 'QL05p052800' => 'qlo', 'QL05p065010' => 'qlo', 'QL05p074156' => 'qlo', 'QL05p074160' => 'qlo', 'QL05p074174' => 'qlo', 'QL05p074178' => 'qlo', 'QL05p074214' => 'qlo', 'QL06p001050' => 'qlo', 'QL06p001056' => 'qlo', 'QL06p006093' => 'qlo', 'QL06p006111' => 'qlo', 'QL07p019784' => 'qlo', 'QL07p019801' => 'qlo', 'QL07p036110' => 'qlo', 'QL07p036134' => 'qlo', 'QL07p036147' => 'qlo', 'QL07p036156' => 'qlo', 'QL07p036300' => 'qlo', 'QL07p036320' => 'qlo', 'QL08p014547' => 'qlo', 'QL08p014551' => 'qlo', 'QL08p043319' => 'qlo', 'QL08p043324' => 'qlo', 'QL11p009094' => 'qlo', 'RcHm_v2.0_Chr1g0380481' => 'rch', 'RcHm_v2.0_Chr2g0089331' => 'rch', 'RcHm_v2.0_Chr2g0123691' => 'rch', 'RcHm_v2.0_Chr2g0151111' => 'rch', 'RcHm_v2.0_Chr2g0163011' => 'rch', 'RcHm_v2.0_Chr2g0163051' => 'rch', 'RcHm_v2.0_Chr2g0164671' => 'rch', 'RcHm_v2.0_Chr2g0164681' => 'rch', 'RcHm_v2.0_Chr2g0164721' => 'rch', 'RcHm_v2.0_Chr3g0449911' => 'rch', 'RcHm_v2.0_Chr3g0450211' => 'rch', 'RcHm_v2.0_Chr3g0457271' => 'rch', 'RcHm_v2.0_Chr5g0018111' => 'rch', 'RcHm_v2.0_Chr5g0021011' => 'rch', 'RcHm_v2.0_Chr5g0081171' => 'rch', 'RcHm_v2.0_Chr5g0081211' => 'rch', 'RcHm_v2.0_Chr6g0275871' => 'rch', 'RcHm_v2.0_Chr6g0276071' => 'rch', 'RcHm_v2.0_Chr6g0285591' => 'rch', 'RcHm_v2.0_Chr6g0291931' => 'rch', 'RcHm_v2.0_Chr6g0292091' => 'rch', 'RcHm_v2.0_Chr6g0292271' => 'rch', 'RcHm_v2.0_Chr7g0221261' => 'rch', 'Rhsim08G0219900' => 'rsi', 'Rhsim08G0220200' => 'rsi', 'Rhsim08G0237800' => 'rsi', 'Rhsim08G0238800' => 'rsi', 'Sabra09G0102700' => 'sbr', 'Sabra09G0127200' => 'sbr', 'Sabra11G0003700' => 'sbr', 'Sabra15G0014700' => 'sbr', 'Sc19g0000590' => 'sci', 'Sc19g0001870' => 'sci', 'SGA_v2.0_scaffold1G00346' => 'sas', 'SGA_v2.0_scaffold1G00575' => 'sas', 'SGA_v2.0_scaffold1G00761' => 'sas', 'SGA_v2.0_scaffold232G43501' => 'sas', 'TAR625G1137' => 'tar', 'Thecc.03G222100' => 'tca', 'TPR.G12691' => 'tpr', 'TWI34G0727' => 'twi', 'TWI36G0117' => 'twi', 'VMungo1309G0868' => 'vmu' ) $gf_id = 'HOM05D001729' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001729' ) $data_identifier = 'HOM05D001729' $data_type = 'gf_id' $species_gene_counts = array( 'amhyb' => (int) 1, 'cqu' => (int) 9, 'can' => (int) 1, 'cansat' => (int) 1, 'car' => (int) 1, 'col' => (int) 5, 'dca' => (int) 1, 'din' => (int) 2, 'dzi' => (int) 3, 'fan' => (int) 140, 'fve' => (int) 62, 'gma' => (int) 1, 'ghi' => (int) 2, 'gra' => (int) 1, 'han' => (int) 1, 'sun' => (int) 1, 'lonja' => (int) 6, 'lja' => (int) 1, 'lsa' => (int) 4, 'mes' => (int) 1, 'mdo' => (int) 14, 'mtr' => (int) 1, 'egut' => (int) 1, 'nta' => (int) 4, 'oeu' => (int) 1, 'stu' => (int) 2, 'pvu' => (int) 1, 'ptr' => (int) 4, 'ppe' => (int) 19, 'psa' => (int) 1, 'pso' => (int) 4, 'qlo' => (int) 36, 'rch' => (int) 23, 'rsi' => (int) 4, 'sbr' => (int) 4, 'sci' => (int) 2, 'sas' => (int) 4, 'tar' => (int) 1, 'tca' => (int) 1, 'tpr' => (int) 1, 'twi' => (int) 2, 'vmu' => (int) 1 ) $gf_gene_species = 'vmu' $gf_gene_id = 'VMungo1309G0868' $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' => 'HOM05D001729', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '375', 'num_species' => '42' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'Ah.07g204710' => 'amhyb', 'AUR62006001' => 'cqu', 'AUR62006002' => 'cqu', 'AUR62006003' => 'cqu', 'AUR62015641' => 'cqu', 'AUR62027174' => 'cqu', 'AUR62035623' => 'cqu', 'AUR62035624' => 'cqu', 'AUR62035625' => 'cqu', 'AUR62035626' => 'cqu', 'CAN.G1110.53' => 'can', 'CANSAT80G0415' => 'cansat', 'Ca_21364_v3' => 'car', 'COL.COLO4_30693' => 'col', 'COL.COLO4_30694' => 'col', 'COL.COLO4_30695' => 'col', 'COL.COLO4_30696' => 'col', 'COL.COLO4_34020' => 'col', 'DCAR_004585' => 'dca', 'Dinv04029' => 'din', 'Dinv34857' => 'din', 'Duzib147G0011' => 'dzi', 'Duzib170G0599' => 'dzi', 'Duzib192G1051' => 'dzi', 'FAN01G0708' => 'fan', 'FAN01G0742' => 'fan', 'FAN02G0048' => 'fan', 'FAN02G0583' => 'fan', 'FAN02G0688' => 'fan', 'FAN02G1588' => 'fan', 'FAN02G2194' => 'fan', 'FAN02G2750' => 'fan', 'FAN02G3094' => 'fan', 'FAN02G3887' => 'fan', 'FAN02G3911' => 'fan', 'FAN02G3994' => 'fan', 'FAN02G4432' => 'fan', 'FAN02G4556' => 'fan', 'FAN03G1977' => 'fan', 'FAN03G2781' => 'fan', 'FAN03G2850' => 'fan', 'FAN03G3155' => 'fan', 'FAN04G2487' => 'fan', 'FAN05G0208' => 'fan', 'FAN05G0656' => 'fan', 'FAN05G0696' => 'fan', 'FAN05G0810' => 'fan', 'FAN05G1447' => 'fan', 'FAN05G2640' => 'fan', 'FAN05G2911' => 'fan', 'FAN05G3901' => 'fan', 'FAN05G4859' => 'fan', 'FAN05G4861' => 'fan', 'FAN05G4988' => 'fan', 'FAN05G5187' => 'fan', 'FAN05G5452' => 'fan', 'FAN05G5500' => 'fan', 'FAN05G5688' => 'fan', 'FAN06G0177' => 'fan', 'FAN06G0675' => 'fan', 'FAN06G1290' => 'fan', 'FAN06G2191' => 'fan', 'FAN06G2405' => 'fan', 'FAN06G3231' => 'fan', 'FAN06G3932' => 'fan', 'FAN07G0163' => 'fan', 'FAN07G0471' => 'fan', 'FAN07G1354' => 'fan', 'FAN08G0338' => 'fan', 'FAN08G1373' => 'fan', 'FAN08G2539' => 'fan', 'FAN08G2728' => 'fan', 'FAN09G0608' => 'fan', 'FAN09G1136' => 'fan', 'FAN09G1958' => 'fan', 'FAN09G2508' => 'fan', 'FAN09G2597' => 'fan', 'FAN09G2658' => 'fan', 'FAN09G2757' => 'fan', 'FAN09G2983' => 'fan', 'FAN09G3130' => 'fan', 'FAN09G3565' => 'fan', 'FAN09G3613' => 'fan', 'FAN09G4011' => 'fan', 'FAN09G4239' => 'fan', 'FAN09G4277' => 'fan', 'FAN09G4720' => 'fan', 'FAN11G0139' => 'fan', 'FAN11G1727' => 'fan', 'FAN11G2672' => 'fan', 'FAN11G2795' => 'fan', 'FAN11G3238' => 'fan', 'FAN11G3734' => 'fan', 'FAN12G0631' => 'fan', 'FAN12G2239' => 'fan', 'FAN12G2308' => 'fan', 'FAN12G2569' => 'fan', 'FAN12G2623' => 'fan', 'FAN13G3182' => 'fan', 'FAN14G0053' => 'fan', 'FAN14G0370' => 'fan', 'FAN14G0382' => 'fan', 'FAN14G0421' => 'fan', 'FAN14G0866' => 'fan', 'FAN14G1187' => 'fan', 'FAN14G1727' => 'fan', 'FAN14G1791' => 'fan', 'FAN14G2361' => 'fan', 'FAN14G2668' => 'fan', 'FAN14G2770' => 'fan', 'FAN14G2874' => 'fan', 'FAN14G3193' => 'fan', 'FAN14G3624' => 'fan', 'FAN14G3676' => 'fan', 'FAN14G3807' => 'fan', 'FAN14G4082' => 'fan', 'FAN14G4342' => 'fan', 'FAN14G4985' => 'fan', 'FAN14G5126' => 'fan', 'FAN14G5781' => 'fan', 'FAN14G5808' => 'fan', 'FAN14G5949' => 'fan', 'FAN15G0828' => 'fan', 'FAN15G1054' => 'fan', 'FAN15G2023' => 'fan', 'FAN15G2506' => 'fan', 'FAN16G0128' => 'fan', 'FAN16G0249' => 'fan', 'FAN16G0429' => 'fan', 'FAN16G1493' => 'fan', 'FAN16G2210' => 'fan', 'FAN16G2506' => 'fan', 'FAN18G1542' => 'fan', 'FAN18G4057' => 'fan', 'FAN19G0745' => 'fan', 'FAN19G1216' => 'fan', 'FAN19G1733' => 'fan', 'FAN20G0258' => 'fan', 'FAN20G1095' => 'fan', 'FAN20G1557' => 'fan', 'FAN21G0302' => 'fan', 'FAN21G0519' => 'fan', 'FAN21G0970' => 'fan', 'FAN21G1159' => 'fan', 'FAN21G1312' => 'fan', 'FAN21G1440' => 'fan', 'FAN21G1715' => 'fan', 'FAN23G1584' => 'fan', 'FAN24G0045' => 'fan', 'FAN24G0053' => 'fan', 'FAN24G1500' => 'fan', 'FAN24G1817' => 'fan', 'FAN24G2147' => 'fan', 'FAN24G2236' => 'fan', 'FAN24G2446' => 'fan', 'FAN24G2684' => 'fan', 'FAN25G0187' => 'fan', 'FAN25G0505' => 'fan', 'FAN25G0589' => 'fan', 'FAN25G3663' => 'fan', 'FAN26G1025' => 'fan', 'FAN26G2860' => 'fan', 'FAN27G1329' => 'fan', 'FAN27G3392' => 'fan', 'FvH4_1g02011' => 'fve', 'FvH4_1g06511' => 'fve', 'FvH4_2g19900' => 'fve', 'FvH4_2g19920' => 'fve', 'FvH4_2g24261' => 'fve', 'FvH4_2g24270' => 'fve', 'FvH4_2g24631' => 'fve', 'FvH4_2g30622' => 'fve', 'FvH4_3g12920' => 'fve', 'FvH4_3g30171' => 'fve', 'FvH4_3g35490' => 'fve', 'FvH4_3g43682' => 'fve', 'FvH4_3g43730' => 'fve', 'FvH4_3g43732' => 'fve', 'FvH4_3g43751' => 'fve', 'FvH4_3g43752' => 'fve', 'FvH4_3g43770' => 'fve', 'FvH4_3g44471' => 'fve', 'FvH4_3g44510' => 'fve', 'FvH4_3g44582' => 'fve', 'FvH4_4g16921' => 'fve', 'FvH4_4g17121' => 'fve', 'FvH4_4g17782' => 'fve', 'FvH4_4g17783' => 'fve', 'FvH4_4g18120' => 'fve', 'FvH4_4g31310' => 'fve', 'FvH4_4g35052' => 'fve', 'FvH4_5g30862' => 'fve', 'FvH4_6g01541' => 'fve', 'FvH4_6g02021' => 'fve', 'FvH4_6g02041' => 'fve', 'FvH4_6g02071' => 'fve', 'FvH4_6g02171' => 'fve', 'FvH4_6g03181' => 'fve', 'FvH4_6g03182' => 'fve', 'FvH4_6g03221' => 'fve', 'FvH4_6g03380' => 'fve', 'FvH4_6g05201' => 'fve', 'FvH4_6g05203' => 'fve', 'FvH4_6g20231' => 'fve', 'FvH4_6g31981' => 'fve', 'FvH4_6g32061' => 'fve', 'FvH4_6g37041' => 'fve', 'FvH4_6g37932' => 'fve', 'FvH4_6g38731' => 'fve', 'FvH4_6g39370' => 'fve', 'FvH4_6g39371' => 'fve', 'FvH4_6g40891' => 'fve', 'FvH4_6g40892' => 'fve', 'FvH4_6g43143' => 'fve', 'FvH4_6g45251' => 'fve', 'FvH4_6g45260' => 'fve', 'FvH4_6g45291' => 'fve', 'FvH4_6g45890' => 'fve', 'FvH4_6g46240' => 'fve', 'FvH4_6g46241' => 'fve', 'FvH4_6g46242' => 'fve', 'FvH4_6g46260' => 'fve', 'FvH4_6g46280' => 'fve', 'FvH4_6g46380' => 'fve', 'FvH4_7g12841' => 'fve', 'FvH4_7g31431' => 'fve', 'Glyma.09G075900' => 'gma', 'Gohir.A09G096401' => 'ghi', 'Gohir.D09G096101' => 'ghi', 'Gorai.006G112800' => 'gra', 'HanXRQChr04g0121411' => 'han', 'Hund15878' => 'sun', 'Lj2A1107G68' => 'lonja', 'Lj2A630G63' => 'lonja', 'Lj2A946T25' => 'lonja', 'Lj2C714T1' => 'lonja', 'Lj2C966T3' => 'lonja', 'Lj2C966T4' => 'lonja', 'Lj4g0002979' => 'lja', 'Lsat_1_v5_gn_5_30901' => 'lsa', 'Lsat_1_v5_gn_5_31100' => 'lsa', 'Lsat_1_v5_gn_5_38600' => 'lsa', 'Lsat_1_v5_gn_6_92061' => 'lsa', 'Manes.05G071301' => 'mes', 'MD02G1008700' => 'mdo', 'MD02G1008900' => 'mdo', 'MD03G1256400' => 'mdo', 'MD04G1180900' => 'mdo', 'MD04G1181000' => 'mdo', 'MD04G1181200' => 'mdo', 'MD05G1244200' => 'mdo', 'MD05G1324200' => 'mdo', 'MD09G1201600' => 'mdo', 'MD10G1000600' => 'mdo', 'MD14G1026900' => 'mdo', 'MD14G1187900' => 'mdo', 'MD15G1017800' => 'mdo', 'MD15G1018100' => 'mdo', 'Medtr4g124160' => 'mtr', 'Migut.L01260' => 'egut', 'Nitab4.5_0000008g0440' => 'nta', 'Nitab4.5_0000207g0170' => 'nta', 'Nitab4.5_0007671g0030' => 'nta', 'Nitab4.5_0010853g0020' => 'nta', 'Oeu057656.1' => 'oeu', 'PGSC0003DMG400005638' => 'stu', 'PGSC0003DMG400005639' => 'stu', 'Phvul.009G222800' => 'pvu', 'Potri.009G132400' => 'ptr', 'Potri.009G163001' => 'ptr', 'Potri.011G000700' => 'ptr', 'Potri.011G004800' => 'ptr', 'Prupe.1G509300' => 'ppe', 'Prupe.1G509700' => 'ppe', 'Prupe.1G510400' => 'ppe', 'Prupe.1G510700' => 'ppe', 'Prupe.1G512600' => 'ppe', 'Prupe.2G073200' => 'ppe', 'Prupe.3G059500' => 'ppe', 'Prupe.3G059600' => 'ppe', 'Prupe.3G246100' => 'ppe', 'Prupe.3G265100' => 'ppe', 'Prupe.4G034700' => 'ppe', 'Prupe.4G052100' => 'ppe', 'Prupe.4G053600' => 'ppe', 'Prupe.5G068800' => 'ppe', 'Prupe.5G070600' => 'ppe', 'Prupe.6G075400' => 'ppe', 'Prupe.6G075500' => 'ppe', 'Prupe.6G076400' => 'ppe', 'Prupe.8G110700' => 'ppe', 'Psat4g020960' => 'psa', 'PSO135G0788' => 'pso', 'PSO210G6463' => 'pso', 'PSO384G0370' => 'pso', 'PSO386G0056' => 'pso', 'QL01p006048' => 'qlo', 'QL02p054283' => 'qlo', 'QL05p008000' => 'qlo', 'QL05p008212' => 'qlo', 'QL05p008950' => 'qlo', 'QL05p009042' => 'qlo', 'QL05p009518' => 'qlo', 'QL05p012589' => 'qlo', 'QL05p012608' => 'qlo', 'QL05p012650' => 'qlo', 'QL05p012667' => 'qlo', 'QL05p014501' => 'qlo', 'QL05p052800' => 'qlo', 'QL05p065010' => 'qlo', 'QL05p074156' => 'qlo', 'QL05p074160' => 'qlo', 'QL05p074174' => 'qlo', 'QL05p074178' => 'qlo', 'QL05p074214' => 'qlo', 'QL06p001050' => 'qlo', 'QL06p001056' => 'qlo', 'QL06p006093' => 'qlo', 'QL06p006111' => 'qlo', 'QL07p019784' => 'qlo', 'QL07p019801' => 'qlo', 'QL07p036110' => 'qlo', 'QL07p036134' => 'qlo', 'QL07p036147' => 'qlo', 'QL07p036156' => 'qlo', 'QL07p036300' => 'qlo', 'QL07p036320' => 'qlo', 'QL08p014547' => 'qlo', 'QL08p014551' => 'qlo', 'QL08p043319' => 'qlo', 'QL08p043324' => 'qlo', 'QL11p009094' => 'qlo', 'RcHm_v2.0_Chr1g0380481' => 'rch', 'RcHm_v2.0_Chr2g0089331' => 'rch', 'RcHm_v2.0_Chr2g0123691' => 'rch', 'RcHm_v2.0_Chr2g0151111' => 'rch', 'RcHm_v2.0_Chr2g0163011' => 'rch', 'RcHm_v2.0_Chr2g0163051' => 'rch', 'RcHm_v2.0_Chr2g0164671' => 'rch', 'RcHm_v2.0_Chr2g0164681' => 'rch', 'RcHm_v2.0_Chr2g0164721' => 'rch', 'RcHm_v2.0_Chr3g0449911' => 'rch', 'RcHm_v2.0_Chr3g0450211' => 'rch', 'RcHm_v2.0_Chr3g0457271' => 'rch', 'RcHm_v2.0_Chr5g0018111' => 'rch', 'RcHm_v2.0_Chr5g0021011' => 'rch', 'RcHm_v2.0_Chr5g0081171' => 'rch', 'RcHm_v2.0_Chr5g0081211' => 'rch', 'RcHm_v2.0_Chr6g0275871' => 'rch', 'RcHm_v2.0_Chr6g0276071' => 'rch', 'RcHm_v2.0_Chr6g0285591' => 'rch', 'RcHm_v2.0_Chr6g0291931' => 'rch', 'RcHm_v2.0_Chr6g0292091' => 'rch', 'RcHm_v2.0_Chr6g0292271' => 'rch', 'RcHm_v2.0_Chr7g0221261' => 'rch', 'Rhsim08G0219900' => 'rsi', 'Rhsim08G0220200' => 'rsi', 'Rhsim08G0237800' => 'rsi', 'Rhsim08G0238800' => 'rsi', 'Sabra09G0102700' => 'sbr', 'Sabra09G0127200' => 'sbr', 'Sabra11G0003700' => 'sbr', 'Sabra15G0014700' => 'sbr', 'Sc19g0000590' => 'sci', 'Sc19g0001870' => 'sci', 'SGA_v2.0_scaffold1G00346' => 'sas', 'SGA_v2.0_scaffold1G00575' => 'sas', 'SGA_v2.0_scaffold1G00761' => 'sas', 'SGA_v2.0_scaffold232G43501' => 'sas', 'TAR625G1137' => 'tar', 'Thecc.03G222100' => 'tca', 'TPR.G12691' => 'tpr', 'TWI34G0727' => 'twi', 'TWI36G0117' => 'twi', 'VMungo1309G0868' => 'vmu' ), 'gf_id' => 'HOM05D001729', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001729' ), 'data_identifier' => 'HOM05D001729', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001729', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '375', 'num_species' => '42' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'Ah.07g204710' => 'amhyb', 'AUR62006001' => 'cqu', 'AUR62006002' => 'cqu', 'AUR62006003' => 'cqu', 'AUR62015641' => 'cqu', 'AUR62027174' => 'cqu', 'AUR62035623' => 'cqu', 'AUR62035624' => 'cqu', 'AUR62035625' => 'cqu', 'AUR62035626' => 'cqu', 'CAN.G1110.53' => 'can', 'CANSAT80G0415' => 'cansat', 'Ca_21364_v3' => 'car', 'COL.COLO4_30693' => 'col', 'COL.COLO4_30694' => 'col', 'COL.COLO4_30695' => 'col', 'COL.COLO4_30696' => 'col', 'COL.COLO4_34020' => 'col', 'DCAR_004585' => 'dca', 'Dinv04029' => 'din', 'Dinv34857' => 'din', 'Duzib147G0011' => 'dzi', 'Duzib170G0599' => 'dzi', 'Duzib192G1051' => 'dzi', 'FAN01G0708' => 'fan', 'FAN01G0742' => 'fan', 'FAN02G0048' => 'fan', 'FAN02G0583' => 'fan', 'FAN02G0688' => 'fan', 'FAN02G1588' => 'fan', 'FAN02G2194' => 'fan', 'FAN02G2750' => 'fan', 'FAN02G3094' => 'fan', 'FAN02G3887' => 'fan', 'FAN02G3911' => 'fan', 'FAN02G3994' => 'fan', 'FAN02G4432' => 'fan', 'FAN02G4556' => 'fan', 'FAN03G1977' => 'fan', 'FAN03G2781' => 'fan', 'FAN03G2850' => 'fan', 'FAN03G3155' => 'fan', 'FAN04G2487' => 'fan', 'FAN05G0208' => 'fan', 'FAN05G0656' => 'fan', 'FAN05G0696' => 'fan', 'FAN05G0810' => 'fan', 'FAN05G1447' => 'fan', 'FAN05G2640' => 'fan', 'FAN05G2911' => 'fan', 'FAN05G3901' => 'fan', 'FAN05G4859' => 'fan', 'FAN05G4861' => 'fan', 'FAN05G4988' => 'fan', 'FAN05G5187' => 'fan', 'FAN05G5452' => 'fan', 'FAN05G5500' => 'fan', 'FAN05G5688' => 'fan', 'FAN06G0177' => 'fan', 'FAN06G0675' => 'fan', 'FAN06G1290' => 'fan', 'FAN06G2191' => 'fan', 'FAN06G2405' => 'fan', 'FAN06G3231' => 'fan', 'FAN06G3932' => 'fan', 'FAN07G0163' => 'fan', 'FAN07G0471' => 'fan', 'FAN07G1354' => 'fan', 'FAN08G0338' => 'fan', 'FAN08G1373' => 'fan', 'FAN08G2539' => 'fan', 'FAN08G2728' => 'fan', 'FAN09G0608' => 'fan', 'FAN09G1136' => 'fan', 'FAN09G1958' => 'fan', 'FAN09G2508' => 'fan', 'FAN09G2597' => 'fan', 'FAN09G2658' => 'fan', 'FAN09G2757' => 'fan', 'FAN09G2983' => 'fan', 'FAN09G3130' => 'fan', 'FAN09G3565' => 'fan', 'FAN09G3613' => 'fan', 'FAN09G4011' => 'fan', 'FAN09G4239' => 'fan', 'FAN09G4277' => 'fan', 'FAN09G4720' => 'fan', 'FAN11G0139' => 'fan', 'FAN11G1727' => 'fan', 'FAN11G2672' => 'fan', 'FAN11G2795' => 'fan', 'FAN11G3238' => 'fan', 'FAN11G3734' => 'fan', 'FAN12G0631' => 'fan', 'FAN12G2239' => 'fan', 'FAN12G2308' => 'fan', 'FAN12G2569' => 'fan', 'FAN12G2623' => 'fan', 'FAN13G3182' => 'fan', 'FAN14G0053' => 'fan', 'FAN14G0370' => 'fan', 'FAN14G0382' => 'fan', 'FAN14G0421' => 'fan', 'FAN14G0866' => 'fan', 'FAN14G1187' => 'fan', 'FAN14G1727' => 'fan', 'FAN14G1791' => 'fan', 'FAN14G2361' => 'fan', 'FAN14G2668' => 'fan', 'FAN14G2770' => 'fan', 'FAN14G2874' => 'fan', 'FAN14G3193' => 'fan', 'FAN14G3624' => 'fan', 'FAN14G3676' => 'fan', 'FAN14G3807' => 'fan', 'FAN14G4082' => 'fan', 'FAN14G4342' => 'fan', 'FAN14G4985' => 'fan', 'FAN14G5126' => 'fan', 'FAN14G5781' => 'fan', 'FAN14G5808' => 'fan', 'FAN14G5949' => 'fan', 'FAN15G0828' => 'fan', 'FAN15G1054' => 'fan', 'FAN15G2023' => 'fan', 'FAN15G2506' => 'fan', 'FAN16G0128' => 'fan', 'FAN16G0249' => 'fan', 'FAN16G0429' => 'fan', 'FAN16G1493' => 'fan', 'FAN16G2210' => 'fan', 'FAN16G2506' => 'fan', 'FAN18G1542' => 'fan', 'FAN18G4057' => 'fan', 'FAN19G0745' => 'fan', 'FAN19G1216' => 'fan', 'FAN19G1733' => 'fan', 'FAN20G0258' => 'fan', 'FAN20G1095' => 'fan', 'FAN20G1557' => 'fan', 'FAN21G0302' => 'fan', 'FAN21G0519' => 'fan', 'FAN21G0970' => 'fan', 'FAN21G1159' => 'fan', 'FAN21G1312' => 'fan', 'FAN21G1440' => 'fan', 'FAN21G1715' => 'fan', 'FAN23G1584' => 'fan', 'FAN24G0045' => 'fan', 'FAN24G0053' => 'fan', 'FAN24G1500' => 'fan', 'FAN24G1817' => 'fan', 'FAN24G2147' => 'fan', 'FAN24G2236' => 'fan', 'FAN24G2446' => 'fan', 'FAN24G2684' => 'fan', 'FAN25G0187' => 'fan', 'FAN25G0505' => 'fan', 'FAN25G0589' => 'fan', 'FAN25G3663' => 'fan', 'FAN26G1025' => 'fan', 'FAN26G2860' => 'fan', 'FAN27G1329' => 'fan', 'FAN27G3392' => 'fan', 'FvH4_1g02011' => 'fve', 'FvH4_1g06511' => 'fve', 'FvH4_2g19900' => 'fve', 'FvH4_2g19920' => 'fve', 'FvH4_2g24261' => 'fve', 'FvH4_2g24270' => 'fve', 'FvH4_2g24631' => 'fve', 'FvH4_2g30622' => 'fve', 'FvH4_3g12920' => 'fve', 'FvH4_3g30171' => 'fve', 'FvH4_3g35490' => 'fve', 'FvH4_3g43682' => 'fve', 'FvH4_3g43730' => 'fve', 'FvH4_3g43732' => 'fve', 'FvH4_3g43751' => 'fve', 'FvH4_3g43752' => 'fve', 'FvH4_3g43770' => 'fve', 'FvH4_3g44471' => 'fve', 'FvH4_3g44510' => 'fve', 'FvH4_3g44582' => 'fve', 'FvH4_4g16921' => 'fve', 'FvH4_4g17121' => 'fve', 'FvH4_4g17782' => 'fve', 'FvH4_4g17783' => 'fve', 'FvH4_4g18120' => 'fve', 'FvH4_4g31310' => 'fve', 'FvH4_4g35052' => 'fve', 'FvH4_5g30862' => 'fve', 'FvH4_6g01541' => 'fve', 'FvH4_6g02021' => 'fve', 'FvH4_6g02041' => 'fve', 'FvH4_6g02071' => 'fve', 'FvH4_6g02171' => 'fve', 'FvH4_6g03181' => 'fve', 'FvH4_6g03182' => 'fve', 'FvH4_6g03221' => 'fve', 'FvH4_6g03380' => 'fve', 'FvH4_6g05201' => 'fve', 'FvH4_6g05203' => 'fve', 'FvH4_6g20231' => 'fve', 'FvH4_6g31981' => 'fve', 'FvH4_6g32061' => 'fve', 'FvH4_6g37041' => 'fve', 'FvH4_6g37932' => 'fve', 'FvH4_6g38731' => 'fve', 'FvH4_6g39370' => 'fve', 'FvH4_6g39371' => 'fve', 'FvH4_6g40891' => 'fve', 'FvH4_6g40892' => 'fve', 'FvH4_6g43143' => 'fve', 'FvH4_6g45251' => 'fve', 'FvH4_6g45260' => 'fve', 'FvH4_6g45291' => 'fve', 'FvH4_6g45890' => 'fve', 'FvH4_6g46240' => 'fve', 'FvH4_6g46241' => 'fve', 'FvH4_6g46242' => 'fve', 'FvH4_6g46260' => 'fve', 'FvH4_6g46280' => 'fve', 'FvH4_6g46380' => 'fve', 'FvH4_7g12841' => 'fve', 'FvH4_7g31431' => 'fve', 'Glyma.09G075900' => 'gma', 'Gohir.A09G096401' => 'ghi', 'Gohir.D09G096101' => 'ghi', 'Gorai.006G112800' => 'gra', 'HanXRQChr04g0121411' => 'han', 'Hund15878' => 'sun', 'Lj2A1107G68' => 'lonja', 'Lj2A630G63' => 'lonja', 'Lj2A946T25' => 'lonja', 'Lj2C714T1' => 'lonja', 'Lj2C966T3' => 'lonja', 'Lj2C966T4' => 'lonja', 'Lj4g0002979' => 'lja', 'Lsat_1_v5_gn_5_30901' => 'lsa', 'Lsat_1_v5_gn_5_31100' => 'lsa', 'Lsat_1_v5_gn_5_38600' => 'lsa', 'Lsat_1_v5_gn_6_92061' => 'lsa', 'Manes.05G071301' => 'mes', 'MD02G1008700' => 'mdo', 'MD02G1008900' => 'mdo', 'MD03G1256400' => 'mdo', 'MD04G1180900' => 'mdo', 'MD04G1181000' => 'mdo', 'MD04G1181200' => 'mdo', 'MD05G1244200' => 'mdo', 'MD05G1324200' => 'mdo', 'MD09G1201600' => 'mdo', 'MD10G1000600' => 'mdo', 'MD14G1026900' => 'mdo', 'MD14G1187900' => 'mdo', 'MD15G1017800' => 'mdo', 'MD15G1018100' => 'mdo', 'Medtr4g124160' => 'mtr', 'Migut.L01260' => 'egut', 'Nitab4.5_0000008g0440' => 'nta', 'Nitab4.5_0000207g0170' => 'nta', 'Nitab4.5_0007671g0030' => 'nta', 'Nitab4.5_0010853g0020' => 'nta', 'Oeu057656.1' => 'oeu', 'PGSC0003DMG400005638' => 'stu', 'PGSC0003DMG400005639' => 'stu', 'Phvul.009G222800' => 'pvu', 'Potri.009G132400' => 'ptr', 'Potri.009G163001' => 'ptr', 'Potri.011G000700' => 'ptr', 'Potri.011G004800' => 'ptr', 'Prupe.1G509300' => 'ppe', 'Prupe.1G509700' => 'ppe', 'Prupe.1G510400' => 'ppe', 'Prupe.1G510700' => 'ppe', 'Prupe.1G512600' => 'ppe', 'Prupe.2G073200' => 'ppe', 'Prupe.3G059500' => 'ppe', 'Prupe.3G059600' => 'ppe', 'Prupe.3G246100' => 'ppe', 'Prupe.3G265100' => 'ppe', 'Prupe.4G034700' => 'ppe', 'Prupe.4G052100' => 'ppe', 'Prupe.4G053600' => 'ppe', 'Prupe.5G068800' => 'ppe', 'Prupe.5G070600' => 'ppe', 'Prupe.6G075400' => 'ppe', 'Prupe.6G075500' => 'ppe', 'Prupe.6G076400' => 'ppe', 'Prupe.8G110700' => 'ppe', 'Psat4g020960' => 'psa', 'PSO135G0788' => 'pso', 'PSO210G6463' => 'pso', 'PSO384G0370' => 'pso', 'PSO386G0056' => 'pso', 'QL01p006048' => 'qlo', 'QL02p054283' => 'qlo', 'QL05p008000' => 'qlo', 'QL05p008212' => 'qlo', 'QL05p008950' => 'qlo', 'QL05p009042' => 'qlo', 'QL05p009518' => 'qlo', 'QL05p012589' => 'qlo', 'QL05p012608' => 'qlo', 'QL05p012650' => 'qlo', 'QL05p012667' => 'qlo', 'QL05p014501' => 'qlo', 'QL05p052800' => 'qlo', 'QL05p065010' => 'qlo', 'QL05p074156' => 'qlo', 'QL05p074160' => 'qlo', 'QL05p074174' => 'qlo', 'QL05p074178' => 'qlo', 'QL05p074214' => 'qlo', 'QL06p001050' => 'qlo', 'QL06p001056' => 'qlo', 'QL06p006093' => 'qlo', 'QL06p006111' => 'qlo', 'QL07p019784' => 'qlo', 'QL07p019801' => 'qlo', 'QL07p036110' => 'qlo', 'QL07p036134' => 'qlo', 'QL07p036147' => 'qlo', 'QL07p036156' => 'qlo', 'QL07p036300' => 'qlo', 'QL07p036320' => 'qlo', 'QL08p014547' => 'qlo', 'QL08p014551' => 'qlo', 'QL08p043319' => 'qlo', 'QL08p043324' => 'qlo', 'QL11p009094' => 'qlo', 'RcHm_v2.0_Chr1g0380481' => 'rch', 'RcHm_v2.0_Chr2g0089331' => 'rch', 'RcHm_v2.0_Chr2g0123691' => 'rch', 'RcHm_v2.0_Chr2g0151111' => 'rch', 'RcHm_v2.0_Chr2g0163011' => 'rch', 'RcHm_v2.0_Chr2g0163051' => 'rch', 'RcHm_v2.0_Chr2g0164671' => 'rch', 'RcHm_v2.0_Chr2g0164681' => 'rch', 'RcHm_v2.0_Chr2g0164721' => 'rch', 'RcHm_v2.0_Chr3g0449911' => 'rch', 'RcHm_v2.0_Chr3g0450211' => 'rch', 'RcHm_v2.0_Chr3g0457271' => 'rch', 'RcHm_v2.0_Chr5g0018111' => 'rch', 'RcHm_v2.0_Chr5g0021011' => 'rch', 'RcHm_v2.0_Chr5g0081171' => 'rch', 'RcHm_v2.0_Chr5g0081211' => 'rch', 'RcHm_v2.0_Chr6g0275871' => 'rch', 'RcHm_v2.0_Chr6g0276071' => 'rch', 'RcHm_v2.0_Chr6g0285591' => 'rch', 'RcHm_v2.0_Chr6g0291931' => 'rch', 'RcHm_v2.0_Chr6g0292091' => 'rch', 'RcHm_v2.0_Chr6g0292271' => 'rch', 'RcHm_v2.0_Chr7g0221261' => 'rch', 'Rhsim08G0219900' => 'rsi', 'Rhsim08G0220200' => 'rsi', 'Rhsim08G0237800' => 'rsi', 'Rhsim08G0238800' => 'rsi', 'Sabra09G0102700' => 'sbr', 'Sabra09G0127200' => 'sbr', 'Sabra11G0003700' => 'sbr', 'Sabra15G0014700' => 'sbr', 'Sc19g0000590' => 'sci', 'Sc19g0001870' => 'sci', 'SGA_v2.0_scaffold1G00346' => 'sas', 'SGA_v2.0_scaffold1G00575' => 'sas', 'SGA_v2.0_scaffold1G00761' => 'sas', 'SGA_v2.0_scaffold232G43501' => 'sas', 'TAR625G1137' => 'tar', 'Thecc.03G222100' => 'tca', 'TPR.G12691' => 'tpr', 'TWI34G0727' => 'twi', 'TWI36G0117' => 'twi', 'VMungo1309G0868' => 'vmu' ) $gf_id = 'HOM05D001729' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001729' ) $data_identifier = 'HOM05D001729' $data_type = 'gf_id' $species_gene_counts = array( 'amhyb' => (int) 1, 'cqu' => (int) 9, 'can' => (int) 1, 'cansat' => (int) 1, 'car' => (int) 1, 'col' => (int) 5, 'dca' => (int) 1, 'din' => (int) 2, 'dzi' => (int) 3, 'fan' => (int) 140, 'fve' => (int) 62, 'gma' => (int) 1, 'ghi' => (int) 2, 'gra' => (int) 1, 'han' => (int) 1, 'sun' => (int) 1, 'lonja' => (int) 6, 'lja' => (int) 1, 'lsa' => (int) 4, 'mes' => (int) 1, 'mdo' => (int) 14, 'mtr' => (int) 1, 'egut' => (int) 1, 'nta' => (int) 4, 'oeu' => (int) 1, 'stu' => (int) 2, 'pvu' => (int) 1, 'ptr' => (int) 4, 'ppe' => (int) 19, 'psa' => (int) 1, 'pso' => (int) 4, 'qlo' => (int) 36, 'rch' => (int) 23, 'rsi' => (int) 4, 'sbr' => (int) 4, 'sci' => (int) 2, 'sas' => (int) 4, 'tar' => (int) 1, 'tca' => (int) 1, 'tpr' => (int) 1, 'twi' => (int) 2, 'vmu' => (int) 1 ) $gf_gene_species = 'vmu' $gf_gene_id = 'VMungo1309G0868' $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' => 'HOM05D001729', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '375', 'num_species' => '42' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'Ah.07g204710' => 'amhyb', 'AUR62006001' => 'cqu', 'AUR62006002' => 'cqu', 'AUR62006003' => 'cqu', 'AUR62015641' => 'cqu', 'AUR62027174' => 'cqu', 'AUR62035623' => 'cqu', 'AUR62035624' => 'cqu', 'AUR62035625' => 'cqu', 'AUR62035626' => 'cqu', 'CAN.G1110.53' => 'can', 'CANSAT80G0415' => 'cansat', 'Ca_21364_v3' => 'car', 'COL.COLO4_30693' => 'col', 'COL.COLO4_30694' => 'col', 'COL.COLO4_30695' => 'col', 'COL.COLO4_30696' => 'col', 'COL.COLO4_34020' => 'col', 'DCAR_004585' => 'dca', 'Dinv04029' => 'din', 'Dinv34857' => 'din', 'Duzib147G0011' => 'dzi', 'Duzib170G0599' => 'dzi', 'Duzib192G1051' => 'dzi', 'FAN01G0708' => 'fan', 'FAN01G0742' => 'fan', 'FAN02G0048' => 'fan', 'FAN02G0583' => 'fan', 'FAN02G0688' => 'fan', 'FAN02G1588' => 'fan', 'FAN02G2194' => 'fan', 'FAN02G2750' => 'fan', 'FAN02G3094' => 'fan', 'FAN02G3887' => 'fan', 'FAN02G3911' => 'fan', 'FAN02G3994' => 'fan', 'FAN02G4432' => 'fan', 'FAN02G4556' => 'fan', 'FAN03G1977' => 'fan', 'FAN03G2781' => 'fan', 'FAN03G2850' => 'fan', 'FAN03G3155' => 'fan', 'FAN04G2487' => 'fan', 'FAN05G0208' => 'fan', 'FAN05G0656' => 'fan', 'FAN05G0696' => 'fan', 'FAN05G0810' => 'fan', 'FAN05G1447' => 'fan', 'FAN05G2640' => 'fan', 'FAN05G2911' => 'fan', 'FAN05G3901' => 'fan', 'FAN05G4859' => 'fan', 'FAN05G4861' => 'fan', 'FAN05G4988' => 'fan', 'FAN05G5187' => 'fan', 'FAN05G5452' => 'fan', 'FAN05G5500' => 'fan', 'FAN05G5688' => 'fan', 'FAN06G0177' => 'fan', 'FAN06G0675' => 'fan', 'FAN06G1290' => 'fan', 'FAN06G2191' => 'fan', 'FAN06G2405' => 'fan', 'FAN06G3231' => 'fan', 'FAN06G3932' => 'fan', 'FAN07G0163' => 'fan', 'FAN07G0471' => 'fan', 'FAN07G1354' => 'fan', 'FAN08G0338' => 'fan', 'FAN08G1373' => 'fan', 'FAN08G2539' => 'fan', 'FAN08G2728' => 'fan', 'FAN09G0608' => 'fan', 'FAN09G1136' => 'fan', 'FAN09G1958' => 'fan', 'FAN09G2508' => 'fan', 'FAN09G2597' => 'fan', 'FAN09G2658' => 'fan', 'FAN09G2757' => 'fan', 'FAN09G2983' => 'fan', 'FAN09G3130' => 'fan', 'FAN09G3565' => 'fan', 'FAN09G3613' => 'fan', 'FAN09G4011' => 'fan', 'FAN09G4239' => 'fan', 'FAN09G4277' => 'fan', 'FAN09G4720' => 'fan', 'FAN11G0139' => 'fan', 'FAN11G1727' => 'fan', 'FAN11G2672' => 'fan', 'FAN11G2795' => 'fan', 'FAN11G3238' => 'fan', 'FAN11G3734' => 'fan', 'FAN12G0631' => 'fan', 'FAN12G2239' => 'fan', 'FAN12G2308' => 'fan', 'FAN12G2569' => 'fan', 'FAN12G2623' => 'fan', 'FAN13G3182' => 'fan', 'FAN14G0053' => 'fan', 'FAN14G0370' => 'fan', 'FAN14G0382' => 'fan', 'FAN14G0421' => 'fan', 'FAN14G0866' => 'fan', 'FAN14G1187' => 'fan', 'FAN14G1727' => 'fan', 'FAN14G1791' => 'fan', 'FAN14G2361' => 'fan', 'FAN14G2668' => 'fan', 'FAN14G2770' => 'fan', 'FAN14G2874' => 'fan', 'FAN14G3193' => 'fan', 'FAN14G3624' => 'fan', 'FAN14G3676' => 'fan', 'FAN14G3807' => 'fan', 'FAN14G4082' => 'fan', 'FAN14G4342' => 'fan', 'FAN14G4985' => 'fan', 'FAN14G5126' => 'fan', 'FAN14G5781' => 'fan', 'FAN14G5808' => 'fan', 'FAN14G5949' => 'fan', 'FAN15G0828' => 'fan', 'FAN15G1054' => 'fan', 'FAN15G2023' => 'fan', 'FAN15G2506' => 'fan', 'FAN16G0128' => 'fan', 'FAN16G0249' => 'fan', 'FAN16G0429' => 'fan', 'FAN16G1493' => 'fan', 'FAN16G2210' => 'fan', 'FAN16G2506' => 'fan', 'FAN18G1542' => 'fan', 'FAN18G4057' => 'fan', 'FAN19G0745' => 'fan', 'FAN19G1216' => 'fan', 'FAN19G1733' => 'fan', 'FAN20G0258' => 'fan', 'FAN20G1095' => 'fan', 'FAN20G1557' => 'fan', 'FAN21G0302' => 'fan', 'FAN21G0519' => 'fan', 'FAN21G0970' => 'fan', 'FAN21G1159' => 'fan', 'FAN21G1312' => 'fan', 'FAN21G1440' => 'fan', 'FAN21G1715' => 'fan', 'FAN23G1584' => 'fan', 'FAN24G0045' => 'fan', 'FAN24G0053' => 'fan', 'FAN24G1500' => 'fan', 'FAN24G1817' => 'fan', 'FAN24G2147' => 'fan', 'FAN24G2236' => 'fan', 'FAN24G2446' => 'fan', 'FAN24G2684' => 'fan', 'FAN25G0187' => 'fan', 'FAN25G0505' => 'fan', 'FAN25G0589' => 'fan', 'FAN25G3663' => 'fan', 'FAN26G1025' => 'fan', 'FAN26G2860' => 'fan', 'FAN27G1329' => 'fan', 'FAN27G3392' => 'fan', 'FvH4_1g02011' => 'fve', 'FvH4_1g06511' => 'fve', 'FvH4_2g19900' => 'fve', 'FvH4_2g19920' => 'fve', 'FvH4_2g24261' => 'fve', 'FvH4_2g24270' => 'fve', 'FvH4_2g24631' => 'fve', 'FvH4_2g30622' => 'fve', 'FvH4_3g12920' => 'fve', 'FvH4_3g30171' => 'fve', 'FvH4_3g35490' => 'fve', 'FvH4_3g43682' => 'fve', 'FvH4_3g43730' => 'fve', 'FvH4_3g43732' => 'fve', 'FvH4_3g43751' => 'fve', 'FvH4_3g43752' => 'fve', 'FvH4_3g43770' => 'fve', 'FvH4_3g44471' => 'fve', 'FvH4_3g44510' => 'fve', 'FvH4_3g44582' => 'fve', 'FvH4_4g16921' => 'fve', 'FvH4_4g17121' => 'fve', 'FvH4_4g17782' => 'fve', 'FvH4_4g17783' => 'fve', 'FvH4_4g18120' => 'fve', 'FvH4_4g31310' => 'fve', 'FvH4_4g35052' => 'fve', 'FvH4_5g30862' => 'fve', 'FvH4_6g01541' => 'fve', 'FvH4_6g02021' => 'fve', 'FvH4_6g02041' => 'fve', 'FvH4_6g02071' => 'fve', 'FvH4_6g02171' => 'fve', 'FvH4_6g03181' => 'fve', 'FvH4_6g03182' => 'fve', 'FvH4_6g03221' => 'fve', 'FvH4_6g03380' => 'fve', 'FvH4_6g05201' => 'fve', 'FvH4_6g05203' => 'fve', 'FvH4_6g20231' => 'fve', 'FvH4_6g31981' => 'fve', 'FvH4_6g32061' => 'fve', 'FvH4_6g37041' => 'fve', 'FvH4_6g37932' => 'fve', 'FvH4_6g38731' => 'fve', 'FvH4_6g39370' => 'fve', 'FvH4_6g39371' => 'fve', 'FvH4_6g40891' => 'fve', 'FvH4_6g40892' => 'fve', 'FvH4_6g43143' => 'fve', 'FvH4_6g45251' => 'fve', 'FvH4_6g45260' => 'fve', 'FvH4_6g45291' => 'fve', 'FvH4_6g45890' => 'fve', 'FvH4_6g46240' => 'fve', 'FvH4_6g46241' => 'fve', 'FvH4_6g46242' => 'fve', 'FvH4_6g46260' => 'fve', 'FvH4_6g46280' => 'fve', 'FvH4_6g46380' => 'fve', 'FvH4_7g12841' => 'fve', 'FvH4_7g31431' => 'fve', 'Glyma.09G075900' => 'gma', 'Gohir.A09G096401' => 'ghi', 'Gohir.D09G096101' => 'ghi', 'Gorai.006G112800' => 'gra', 'HanXRQChr04g0121411' => 'han', 'Hund15878' => 'sun', 'Lj2A1107G68' => 'lonja', 'Lj2A630G63' => 'lonja', 'Lj2A946T25' => 'lonja', 'Lj2C714T1' => 'lonja', 'Lj2C966T3' => 'lonja', 'Lj2C966T4' => 'lonja', 'Lj4g0002979' => 'lja', 'Lsat_1_v5_gn_5_30901' => 'lsa', 'Lsat_1_v5_gn_5_31100' => 'lsa', 'Lsat_1_v5_gn_5_38600' => 'lsa', 'Lsat_1_v5_gn_6_92061' => 'lsa', 'Manes.05G071301' => 'mes', 'MD02G1008700' => 'mdo', 'MD02G1008900' => 'mdo', 'MD03G1256400' => 'mdo', 'MD04G1180900' => 'mdo', 'MD04G1181000' => 'mdo', 'MD04G1181200' => 'mdo', 'MD05G1244200' => 'mdo', 'MD05G1324200' => 'mdo', 'MD09G1201600' => 'mdo', 'MD10G1000600' => 'mdo', 'MD14G1026900' => 'mdo', 'MD14G1187900' => 'mdo', 'MD15G1017800' => 'mdo', 'MD15G1018100' => 'mdo', 'Medtr4g124160' => 'mtr', 'Migut.L01260' => 'egut', 'Nitab4.5_0000008g0440' => 'nta', 'Nitab4.5_0000207g0170' => 'nta', 'Nitab4.5_0007671g0030' => 'nta', 'Nitab4.5_0010853g0020' => 'nta', 'Oeu057656.1' => 'oeu', 'PGSC0003DMG400005638' => 'stu', 'PGSC0003DMG400005639' => 'stu', 'Phvul.009G222800' => 'pvu', 'Potri.009G132400' => 'ptr', 'Potri.009G163001' => 'ptr', 'Potri.011G000700' => 'ptr', 'Potri.011G004800' => 'ptr', 'Prupe.1G509300' => 'ppe', 'Prupe.1G509700' => 'ppe', 'Prupe.1G510400' => 'ppe', 'Prupe.1G510700' => 'ppe', 'Prupe.1G512600' => 'ppe', 'Prupe.2G073200' => 'ppe', 'Prupe.3G059500' => 'ppe', 'Prupe.3G059600' => 'ppe', 'Prupe.3G246100' => 'ppe', 'Prupe.3G265100' => 'ppe', 'Prupe.4G034700' => 'ppe', 'Prupe.4G052100' => 'ppe', 'Prupe.4G053600' => 'ppe', 'Prupe.5G068800' => 'ppe', 'Prupe.5G070600' => 'ppe', 'Prupe.6G075400' => 'ppe', 'Prupe.6G075500' => 'ppe', 'Prupe.6G076400' => 'ppe', 'Prupe.8G110700' => 'ppe', 'Psat4g020960' => 'psa', 'PSO135G0788' => 'pso', 'PSO210G6463' => 'pso', 'PSO384G0370' => 'pso', 'PSO386G0056' => 'pso', 'QL01p006048' => 'qlo', 'QL02p054283' => 'qlo', 'QL05p008000' => 'qlo', 'QL05p008212' => 'qlo', 'QL05p008950' => 'qlo', 'QL05p009042' => 'qlo', 'QL05p009518' => 'qlo', 'QL05p012589' => 'qlo', 'QL05p012608' => 'qlo', 'QL05p012650' => 'qlo', 'QL05p012667' => 'qlo', 'QL05p014501' => 'qlo', 'QL05p052800' => 'qlo', 'QL05p065010' => 'qlo', 'QL05p074156' => 'qlo', 'QL05p074160' => 'qlo', 'QL05p074174' => 'qlo', 'QL05p074178' => 'qlo', 'QL05p074214' => 'qlo', 'QL06p001050' => 'qlo', 'QL06p001056' => 'qlo', 'QL06p006093' => 'qlo', 'QL06p006111' => 'qlo', 'QL07p019784' => 'qlo', 'QL07p019801' => 'qlo', 'QL07p036110' => 'qlo', 'QL07p036134' => 'qlo', 'QL07p036147' => 'qlo', 'QL07p036156' => 'qlo', 'QL07p036300' => 'qlo', 'QL07p036320' => 'qlo', 'QL08p014547' => 'qlo', 'QL08p014551' => 'qlo', 'QL08p043319' => 'qlo', 'QL08p043324' => 'qlo', 'QL11p009094' => 'qlo', 'RcHm_v2.0_Chr1g0380481' => 'rch', 'RcHm_v2.0_Chr2g0089331' => 'rch', 'RcHm_v2.0_Chr2g0123691' => 'rch', 'RcHm_v2.0_Chr2g0151111' => 'rch', 'RcHm_v2.0_Chr2g0163011' => 'rch', 'RcHm_v2.0_Chr2g0163051' => 'rch', 'RcHm_v2.0_Chr2g0164671' => 'rch', 'RcHm_v2.0_Chr2g0164681' => 'rch', 'RcHm_v2.0_Chr2g0164721' => 'rch', 'RcHm_v2.0_Chr3g0449911' => 'rch', 'RcHm_v2.0_Chr3g0450211' => 'rch', 'RcHm_v2.0_Chr3g0457271' => 'rch', 'RcHm_v2.0_Chr5g0018111' => 'rch', 'RcHm_v2.0_Chr5g0021011' => 'rch', 'RcHm_v2.0_Chr5g0081171' => 'rch', 'RcHm_v2.0_Chr5g0081211' => 'rch', 'RcHm_v2.0_Chr6g0275871' => 'rch', 'RcHm_v2.0_Chr6g0276071' => 'rch', 'RcHm_v2.0_Chr6g0285591' => 'rch', 'RcHm_v2.0_Chr6g0291931' => 'rch', 'RcHm_v2.0_Chr6g0292091' => 'rch', 'RcHm_v2.0_Chr6g0292271' => 'rch', 'RcHm_v2.0_Chr7g0221261' => 'rch', 'Rhsim08G0219900' => 'rsi', 'Rhsim08G0220200' => 'rsi', 'Rhsim08G0237800' => 'rsi', 'Rhsim08G0238800' => 'rsi', 'Sabra09G0102700' => 'sbr', 'Sabra09G0127200' => 'sbr', 'Sabra11G0003700' => 'sbr', 'Sabra15G0014700' => 'sbr', 'Sc19g0000590' => 'sci', 'Sc19g0001870' => 'sci', 'SGA_v2.0_scaffold1G00346' => 'sas', 'SGA_v2.0_scaffold1G00575' => 'sas', 'SGA_v2.0_scaffold1G00761' => 'sas', 'SGA_v2.0_scaffold232G43501' => 'sas', 'TAR625G1137' => 'tar', 'Thecc.03G222100' => 'tca', 'TPR.G12691' => 'tpr', 'TWI34G0727' => 'twi', 'TWI36G0117' => 'twi', 'VMungo1309G0868' => 'vmu' ), 'gf_id' => 'HOM05D001729', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001729' ), 'data_identifier' => 'HOM05D001729', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001729', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '375', 'num_species' => '42' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'Ah.07g204710' => 'amhyb', 'AUR62006001' => 'cqu', 'AUR62006002' => 'cqu', 'AUR62006003' => 'cqu', 'AUR62015641' => 'cqu', 'AUR62027174' => 'cqu', 'AUR62035623' => 'cqu', 'AUR62035624' => 'cqu', 'AUR62035625' => 'cqu', 'AUR62035626' => 'cqu', 'CAN.G1110.53' => 'can', 'CANSAT80G0415' => 'cansat', 'Ca_21364_v3' => 'car', 'COL.COLO4_30693' => 'col', 'COL.COLO4_30694' => 'col', 'COL.COLO4_30695' => 'col', 'COL.COLO4_30696' => 'col', 'COL.COLO4_34020' => 'col', 'DCAR_004585' => 'dca', 'Dinv04029' => 'din', 'Dinv34857' => 'din', 'Duzib147G0011' => 'dzi', 'Duzib170G0599' => 'dzi', 'Duzib192G1051' => 'dzi', 'FAN01G0708' => 'fan', 'FAN01G0742' => 'fan', 'FAN02G0048' => 'fan', 'FAN02G0583' => 'fan', 'FAN02G0688' => 'fan', 'FAN02G1588' => 'fan', 'FAN02G2194' => 'fan', 'FAN02G2750' => 'fan', 'FAN02G3094' => 'fan', 'FAN02G3887' => 'fan', 'FAN02G3911' => 'fan', 'FAN02G3994' => 'fan', 'FAN02G4432' => 'fan', 'FAN02G4556' => 'fan', 'FAN03G1977' => 'fan', 'FAN03G2781' => 'fan', 'FAN03G2850' => 'fan', 'FAN03G3155' => 'fan', 'FAN04G2487' => 'fan', 'FAN05G0208' => 'fan', 'FAN05G0656' => 'fan', 'FAN05G0696' => 'fan', 'FAN05G0810' => 'fan', 'FAN05G1447' => 'fan', 'FAN05G2640' => 'fan', 'FAN05G2911' => 'fan', 'FAN05G3901' => 'fan', 'FAN05G4859' => 'fan', 'FAN05G4861' => 'fan', 'FAN05G4988' => 'fan', 'FAN05G5187' => 'fan', 'FAN05G5452' => 'fan', 'FAN05G5500' => 'fan', 'FAN05G5688' => 'fan', 'FAN06G0177' => 'fan', 'FAN06G0675' => 'fan', 'FAN06G1290' => 'fan', 'FAN06G2191' => 'fan', 'FAN06G2405' => 'fan', 'FAN06G3231' => 'fan', 'FAN06G3932' => 'fan', 'FAN07G0163' => 'fan', 'FAN07G0471' => 'fan', 'FAN07G1354' => 'fan', 'FAN08G0338' => 'fan', 'FAN08G1373' => 'fan', 'FAN08G2539' => 'fan', 'FAN08G2728' => 'fan', 'FAN09G0608' => 'fan', 'FAN09G1136' => 'fan', 'FAN09G1958' => 'fan', 'FAN09G2508' => 'fan', 'FAN09G2597' => 'fan', 'FAN09G2658' => 'fan', 'FAN09G2757' => 'fan', 'FAN09G2983' => 'fan', 'FAN09G3130' => 'fan', 'FAN09G3565' => 'fan', 'FAN09G3613' => 'fan', 'FAN09G4011' => 'fan', 'FAN09G4239' => 'fan', 'FAN09G4277' => 'fan', 'FAN09G4720' => 'fan', 'FAN11G0139' => 'fan', 'FAN11G1727' => 'fan', 'FAN11G2672' => 'fan', 'FAN11G2795' => 'fan', 'FAN11G3238' => 'fan', 'FAN11G3734' => 'fan', 'FAN12G0631' => 'fan', 'FAN12G2239' => 'fan', 'FAN12G2308' => 'fan', 'FAN12G2569' => 'fan', 'FAN12G2623' => 'fan', 'FAN13G3182' => 'fan', 'FAN14G0053' => 'fan', 'FAN14G0370' => 'fan', 'FAN14G0382' => 'fan', 'FAN14G0421' => 'fan', 'FAN14G0866' => 'fan', 'FAN14G1187' => 'fan', 'FAN14G1727' => 'fan', 'FAN14G1791' => 'fan', 'FAN14G2361' => 'fan', 'FAN14G2668' => 'fan', 'FAN14G2770' => 'fan', 'FAN14G2874' => 'fan', 'FAN14G3193' => 'fan', 'FAN14G3624' => 'fan', 'FAN14G3676' => 'fan', 'FAN14G3807' => 'fan', 'FAN14G4082' => 'fan', 'FAN14G4342' => 'fan', 'FAN14G4985' => 'fan', 'FAN14G5126' => 'fan', 'FAN14G5781' => 'fan', 'FAN14G5808' => 'fan', 'FAN14G5949' => 'fan', 'FAN15G0828' => 'fan', 'FAN15G1054' => 'fan', 'FAN15G2023' => 'fan', 'FAN15G2506' => 'fan', 'FAN16G0128' => 'fan', 'FAN16G0249' => 'fan', 'FAN16G0429' => 'fan', 'FAN16G1493' => 'fan', 'FAN16G2210' => 'fan', 'FAN16G2506' => 'fan', 'FAN18G1542' => 'fan', 'FAN18G4057' => 'fan', 'FAN19G0745' => 'fan', 'FAN19G1216' => 'fan', 'FAN19G1733' => 'fan', 'FAN20G0258' => 'fan', 'FAN20G1095' => 'fan', 'FAN20G1557' => 'fan', 'FAN21G0302' => 'fan', 'FAN21G0519' => 'fan', 'FAN21G0970' => 'fan', 'FAN21G1159' => 'fan', 'FAN21G1312' => 'fan', 'FAN21G1440' => 'fan', 'FAN21G1715' => 'fan', 'FAN23G1584' => 'fan', 'FAN24G0045' => 'fan', 'FAN24G0053' => 'fan', 'FAN24G1500' => 'fan', 'FAN24G1817' => 'fan', 'FAN24G2147' => 'fan', 'FAN24G2236' => 'fan', 'FAN24G2446' => 'fan', 'FAN24G2684' => 'fan', 'FAN25G0187' => 'fan', 'FAN25G0505' => 'fan', 'FAN25G0589' => 'fan', 'FAN25G3663' => 'fan', 'FAN26G1025' => 'fan', 'FAN26G2860' => 'fan', 'FAN27G1329' => 'fan', 'FAN27G3392' => 'fan', 'FvH4_1g02011' => 'fve', 'FvH4_1g06511' => 'fve', 'FvH4_2g19900' => 'fve', 'FvH4_2g19920' => 'fve', 'FvH4_2g24261' => 'fve', 'FvH4_2g24270' => 'fve', 'FvH4_2g24631' => 'fve', 'FvH4_2g30622' => 'fve', 'FvH4_3g12920' => 'fve', 'FvH4_3g30171' => 'fve', 'FvH4_3g35490' => 'fve', 'FvH4_3g43682' => 'fve', 'FvH4_3g43730' => 'fve', 'FvH4_3g43732' => 'fve', 'FvH4_3g43751' => 'fve', 'FvH4_3g43752' => 'fve', 'FvH4_3g43770' => 'fve', 'FvH4_3g44471' => 'fve', 'FvH4_3g44510' => 'fve', 'FvH4_3g44582' => 'fve', 'FvH4_4g16921' => 'fve', 'FvH4_4g17121' => 'fve', 'FvH4_4g17782' => 'fve', 'FvH4_4g17783' => 'fve', 'FvH4_4g18120' => 'fve', 'FvH4_4g31310' => 'fve', 'FvH4_4g35052' => 'fve', 'FvH4_5g30862' => 'fve', 'FvH4_6g01541' => 'fve', 'FvH4_6g02021' => 'fve', 'FvH4_6g02041' => 'fve', 'FvH4_6g02071' => 'fve', 'FvH4_6g02171' => 'fve', 'FvH4_6g03181' => 'fve', 'FvH4_6g03182' => 'fve', 'FvH4_6g03221' => 'fve', 'FvH4_6g03380' => 'fve', 'FvH4_6g05201' => 'fve', 'FvH4_6g05203' => 'fve', 'FvH4_6g20231' => 'fve', 'FvH4_6g31981' => 'fve', 'FvH4_6g32061' => 'fve', 'FvH4_6g37041' => 'fve', 'FvH4_6g37932' => 'fve', 'FvH4_6g38731' => 'fve', 'FvH4_6g39370' => 'fve', 'FvH4_6g39371' => 'fve', 'FvH4_6g40891' => 'fve', 'FvH4_6g40892' => 'fve', 'FvH4_6g43143' => 'fve', 'FvH4_6g45251' => 'fve', 'FvH4_6g45260' => 'fve', 'FvH4_6g45291' => 'fve', 'FvH4_6g45890' => 'fve', 'FvH4_6g46240' => 'fve', 'FvH4_6g46241' => 'fve', 'FvH4_6g46242' => 'fve', 'FvH4_6g46260' => 'fve', 'FvH4_6g46280' => 'fve', 'FvH4_6g46380' => 'fve', 'FvH4_7g12841' => 'fve', 'FvH4_7g31431' => 'fve', 'Glyma.09G075900' => 'gma', 'Gohir.A09G096401' => 'ghi', 'Gohir.D09G096101' => 'ghi', 'Gorai.006G112800' => 'gra', 'HanXRQChr04g0121411' => 'han', 'Hund15878' => 'sun', 'Lj2A1107G68' => 'lonja', 'Lj2A630G63' => 'lonja', 'Lj2A946T25' => 'lonja', 'Lj2C714T1' => 'lonja', 'Lj2C966T3' => 'lonja', 'Lj2C966T4' => 'lonja', 'Lj4g0002979' => 'lja', 'Lsat_1_v5_gn_5_30901' => 'lsa', 'Lsat_1_v5_gn_5_31100' => 'lsa', 'Lsat_1_v5_gn_5_38600' => 'lsa', 'Lsat_1_v5_gn_6_92061' => 'lsa', 'Manes.05G071301' => 'mes', 'MD02G1008700' => 'mdo', 'MD02G1008900' => 'mdo', 'MD03G1256400' => 'mdo', 'MD04G1180900' => 'mdo', 'MD04G1181000' => 'mdo', 'MD04G1181200' => 'mdo', 'MD05G1244200' => 'mdo', 'MD05G1324200' => 'mdo', 'MD09G1201600' => 'mdo', 'MD10G1000600' => 'mdo', 'MD14G1026900' => 'mdo', 'MD14G1187900' => 'mdo', 'MD15G1017800' => 'mdo', 'MD15G1018100' => 'mdo', 'Medtr4g124160' => 'mtr', 'Migut.L01260' => 'egut', 'Nitab4.5_0000008g0440' => 'nta', 'Nitab4.5_0000207g0170' => 'nta', 'Nitab4.5_0007671g0030' => 'nta', 'Nitab4.5_0010853g0020' => 'nta', 'Oeu057656.1' => 'oeu', 'PGSC0003DMG400005638' => 'stu', 'PGSC0003DMG400005639' => 'stu', 'Phvul.009G222800' => 'pvu', 'Potri.009G132400' => 'ptr', 'Potri.009G163001' => 'ptr', 'Potri.011G000700' => 'ptr', 'Potri.011G004800' => 'ptr', 'Prupe.1G509300' => 'ppe', 'Prupe.1G509700' => 'ppe', 'Prupe.1G510400' => 'ppe', 'Prupe.1G510700' => 'ppe', 'Prupe.1G512600' => 'ppe', 'Prupe.2G073200' => 'ppe', 'Prupe.3G059500' => 'ppe', 'Prupe.3G059600' => 'ppe', 'Prupe.3G246100' => 'ppe', 'Prupe.3G265100' => 'ppe', 'Prupe.4G034700' => 'ppe', 'Prupe.4G052100' => 'ppe', 'Prupe.4G053600' => 'ppe', 'Prupe.5G068800' => 'ppe', 'Prupe.5G070600' => 'ppe', 'Prupe.6G075400' => 'ppe', 'Prupe.6G075500' => 'ppe', 'Prupe.6G076400' => 'ppe', 'Prupe.8G110700' => 'ppe', 'Psat4g020960' => 'psa', 'PSO135G0788' => 'pso', 'PSO210G6463' => 'pso', 'PSO384G0370' => 'pso', 'PSO386G0056' => 'pso', 'QL01p006048' => 'qlo', 'QL02p054283' => 'qlo', 'QL05p008000' => 'qlo', 'QL05p008212' => 'qlo', 'QL05p008950' => 'qlo', 'QL05p009042' => 'qlo', 'QL05p009518' => 'qlo', 'QL05p012589' => 'qlo', 'QL05p012608' => 'qlo', 'QL05p012650' => 'qlo', 'QL05p012667' => 'qlo', 'QL05p014501' => 'qlo', 'QL05p052800' => 'qlo', 'QL05p065010' => 'qlo', 'QL05p074156' => 'qlo', 'QL05p074160' => 'qlo', 'QL05p074174' => 'qlo', 'QL05p074178' => 'qlo', 'QL05p074214' => 'qlo', 'QL06p001050' => 'qlo', 'QL06p001056' => 'qlo', 'QL06p006093' => 'qlo', 'QL06p006111' => 'qlo', 'QL07p019784' => 'qlo', 'QL07p019801' => 'qlo', 'QL07p036110' => 'qlo', 'QL07p036134' => 'qlo', 'QL07p036147' => 'qlo', 'QL07p036156' => 'qlo', 'QL07p036300' => 'qlo', 'QL07p036320' => 'qlo', 'QL08p014547' => 'qlo', 'QL08p014551' => 'qlo', 'QL08p043319' => 'qlo', 'QL08p043324' => 'qlo', 'QL11p009094' => 'qlo', 'RcHm_v2.0_Chr1g0380481' => 'rch', 'RcHm_v2.0_Chr2g0089331' => 'rch', 'RcHm_v2.0_Chr2g0123691' => 'rch', 'RcHm_v2.0_Chr2g0151111' => 'rch', 'RcHm_v2.0_Chr2g0163011' => 'rch', 'RcHm_v2.0_Chr2g0163051' => 'rch', 'RcHm_v2.0_Chr2g0164671' => 'rch', 'RcHm_v2.0_Chr2g0164681' => 'rch', 'RcHm_v2.0_Chr2g0164721' => 'rch', 'RcHm_v2.0_Chr3g0449911' => 'rch', 'RcHm_v2.0_Chr3g0450211' => 'rch', 'RcHm_v2.0_Chr3g0457271' => 'rch', 'RcHm_v2.0_Chr5g0018111' => 'rch', 'RcHm_v2.0_Chr5g0021011' => 'rch', 'RcHm_v2.0_Chr5g0081171' => 'rch', 'RcHm_v2.0_Chr5g0081211' => 'rch', 'RcHm_v2.0_Chr6g0275871' => 'rch', 'RcHm_v2.0_Chr6g0276071' => 'rch', 'RcHm_v2.0_Chr6g0285591' => 'rch', 'RcHm_v2.0_Chr6g0291931' => 'rch', 'RcHm_v2.0_Chr6g0292091' => 'rch', 'RcHm_v2.0_Chr6g0292271' => 'rch', 'RcHm_v2.0_Chr7g0221261' => 'rch', 'Rhsim08G0219900' => 'rsi', 'Rhsim08G0220200' => 'rsi', 'Rhsim08G0237800' => 'rsi', 'Rhsim08G0238800' => 'rsi', 'Sabra09G0102700' => 'sbr', 'Sabra09G0127200' => 'sbr', 'Sabra11G0003700' => 'sbr', 'Sabra15G0014700' => 'sbr', 'Sc19g0000590' => 'sci', 'Sc19g0001870' => 'sci', 'SGA_v2.0_scaffold1G00346' => 'sas', 'SGA_v2.0_scaffold1G00575' => 'sas', 'SGA_v2.0_scaffold1G00761' => 'sas', 'SGA_v2.0_scaffold232G43501' => 'sas', 'TAR625G1137' => 'tar', 'Thecc.03G222100' => 'tca', 'TPR.G12691' => 'tpr', 'TWI34G0727' => 'twi', 'TWI36G0117' => 'twi', 'VMungo1309G0868' => 'vmu' ) $gf_id = 'HOM05D001729' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001729' ) $data_identifier = 'HOM05D001729' $data_type = 'gf_id' $species_gene_counts = array( 'amhyb' => (int) 1, 'cqu' => (int) 9, 'can' => (int) 1, 'cansat' => (int) 1, 'car' => (int) 1, 'col' => (int) 5, 'dca' => (int) 1, 'din' => (int) 2, 'dzi' => (int) 3, 'fan' => (int) 140, 'fve' => (int) 62, 'gma' => (int) 1, 'ghi' => (int) 2, 'gra' => (int) 1, 'han' => (int) 1, 'sun' => (int) 1, 'lonja' => (int) 6, 'lja' => (int) 1, 'lsa' => (int) 4, 'mes' => (int) 1, 'mdo' => (int) 14, 'mtr' => (int) 1, 'egut' => (int) 1, 'nta' => (int) 4, 'oeu' => (int) 1, 'stu' => (int) 2, 'pvu' => (int) 1, 'ptr' => (int) 4, 'ppe' => (int) 19, 'psa' => (int) 1, 'pso' => (int) 4, 'qlo' => (int) 36, 'rch' => (int) 23, 'rsi' => (int) 4, 'sbr' => (int) 4, 'sci' => (int) 2, 'sas' => (int) 4, 'tar' => (int) 1, 'tca' => (int) 1, 'tpr' => (int) 1, 'twi' => (int) 2, 'vmu' => (int) 1 ) $gf_gene_species = 'vmu' $gf_gene_id = 'VMungo1309G0868' $species_info = array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ) $local_species = 'sas' $disabled = '' $selected = '' $num_hits = (int) 1include - APP/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp, line 33 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933 View::_renderElement() - CORE/Cake/View/View.php, line 1224 View::element() - CORE/Cake/View/View.php, line 418 include - APP/View/Elements/analysis/phylogenetics_module/gf_data_settings.ctp, line 37 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933 View::_renderElement() - CORE/Cake/View/View.php, line 1224 View::element() - CORE/Cake/View/View.php, line 418 include - APP/View/Elements/analysis/phylogenetics_module/parameter_selection.ctp, line 64 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933 View::_renderElement() - CORE/Cake/View/View.php, line 1224 View::element() - CORE/Cake/View/View.php, line 418 include - APP/View/Analysis/custom_tree_creation.ctp, line 27 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933
$viewFile = '/www/bioinformatics01_ro/plaza/_dev_instances/feedback/app/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp' $dataForView = array( 'sidebar_info' => array( 'gf_id' => 'HOM05D001729', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '375', 'num_species' => '42' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'Ah.07g204710' => 'amhyb', 'AUR62006001' => 'cqu', 'AUR62006002' => 'cqu', 'AUR62006003' => 'cqu', 'AUR62015641' => 'cqu', 'AUR62027174' => 'cqu', 'AUR62035623' => 'cqu', 'AUR62035624' => 'cqu', 'AUR62035625' => 'cqu', 'AUR62035626' => 'cqu', 'CAN.G1110.53' => 'can', 'CANSAT80G0415' => 'cansat', 'Ca_21364_v3' => 'car', 'COL.COLO4_30693' => 'col', 'COL.COLO4_30694' => 'col', 'COL.COLO4_30695' => 'col', 'COL.COLO4_30696' => 'col', 'COL.COLO4_34020' => 'col', 'DCAR_004585' => 'dca', 'Dinv04029' => 'din', 'Dinv34857' => 'din', 'Duzib147G0011' => 'dzi', 'Duzib170G0599' => 'dzi', 'Duzib192G1051' => 'dzi', 'FAN01G0708' => 'fan', 'FAN01G0742' => 'fan', 'FAN02G0048' => 'fan', 'FAN02G0583' => 'fan', 'FAN02G0688' => 'fan', 'FAN02G1588' => 'fan', 'FAN02G2194' => 'fan', 'FAN02G2750' => 'fan', 'FAN02G3094' => 'fan', 'FAN02G3887' => 'fan', 'FAN02G3911' => 'fan', 'FAN02G3994' => 'fan', 'FAN02G4432' => 'fan', 'FAN02G4556' => 'fan', 'FAN03G1977' => 'fan', 'FAN03G2781' => 'fan', 'FAN03G2850' => 'fan', 'FAN03G3155' => 'fan', 'FAN04G2487' => 'fan', 'FAN05G0208' => 'fan', 'FAN05G0656' => 'fan', 'FAN05G0696' => 'fan', 'FAN05G0810' => 'fan', 'FAN05G1447' => 'fan', 'FAN05G2640' => 'fan', 'FAN05G2911' => 'fan', 'FAN05G3901' => 'fan', 'FAN05G4859' => 'fan', 'FAN05G4861' => 'fan', 'FAN05G4988' => 'fan', 'FAN05G5187' => 'fan', 'FAN05G5452' => 'fan', 'FAN05G5500' => 'fan', 'FAN05G5688' => 'fan', 'FAN06G0177' => 'fan', 'FAN06G0675' => 'fan', 'FAN06G1290' => 'fan', 'FAN06G2191' => 'fan', 'FAN06G2405' => 'fan', 'FAN06G3231' => 'fan', 'FAN06G3932' => 'fan', 'FAN07G0163' => 'fan', 'FAN07G0471' => 'fan', 'FAN07G1354' => 'fan', 'FAN08G0338' => 'fan', 'FAN08G1373' => 'fan', 'FAN08G2539' => 'fan', 'FAN08G2728' => 'fan', 'FAN09G0608' => 'fan', 'FAN09G1136' => 'fan', 'FAN09G1958' => 'fan', 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'FAN14G5126' => 'fan', 'FAN14G5781' => 'fan', 'FAN14G5808' => 'fan', 'FAN14G5949' => 'fan', 'FAN15G0828' => 'fan', 'FAN15G1054' => 'fan', 'FAN15G2023' => 'fan', 'FAN15G2506' => 'fan', 'FAN16G0128' => 'fan', 'FAN16G0249' => 'fan', 'FAN16G0429' => 'fan', 'FAN16G1493' => 'fan', 'FAN16G2210' => 'fan', 'FAN16G2506' => 'fan', 'FAN18G1542' => 'fan', 'FAN18G4057' => 'fan', 'FAN19G0745' => 'fan', 'FAN19G1216' => 'fan', 'FAN19G1733' => 'fan', 'FAN20G0258' => 'fan', 'FAN20G1095' => 'fan', 'FAN20G1557' => 'fan', 'FAN21G0302' => 'fan', 'FAN21G0519' => 'fan', 'FAN21G0970' => 'fan', 'FAN21G1159' => 'fan', 'FAN21G1312' => 'fan', 'FAN21G1440' => 'fan', 'FAN21G1715' => 'fan', 'FAN23G1584' => 'fan', 'FAN24G0045' => 'fan', 'FAN24G0053' => 'fan', 'FAN24G1500' => 'fan', 'FAN24G1817' => 'fan', 'FAN24G2147' => 'fan', 'FAN24G2236' => 'fan', 'FAN24G2446' => 'fan', 'FAN24G2684' => 'fan', 'FAN25G0187' => 'fan', 'FAN25G0505' => 'fan', 'FAN25G0589' => 'fan', 'FAN25G3663' => 'fan', 'FAN26G1025' => 'fan', 'FAN26G2860' => 'fan', 'FAN27G1329' => 'fan', 'FAN27G3392' => 'fan', 'FvH4_1g02011' => 'fve', 'FvH4_1g06511' => 'fve', 'FvH4_2g19900' => 'fve', 'FvH4_2g19920' => 'fve', 'FvH4_2g24261' => 'fve', 'FvH4_2g24270' => 'fve', 'FvH4_2g24631' => 'fve', 'FvH4_2g30622' => 'fve', 'FvH4_3g12920' => 'fve', 'FvH4_3g30171' => 'fve', 'FvH4_3g35490' => 'fve', 'FvH4_3g43682' => 'fve', 'FvH4_3g43730' => 'fve', 'FvH4_3g43732' => 'fve', 'FvH4_3g43751' => 'fve', 'FvH4_3g43752' => 'fve', 'FvH4_3g43770' => 'fve', 'FvH4_3g44471' => 'fve', 'FvH4_3g44510' => 'fve', 'FvH4_3g44582' => 'fve', 'FvH4_4g16921' => 'fve', 'FvH4_4g17121' => 'fve', 'FvH4_4g17782' => 'fve', 'FvH4_4g17783' => 'fve', 'FvH4_4g18120' => 'fve', 'FvH4_4g31310' => 'fve', 'FvH4_4g35052' => 'fve', 'FvH4_5g30862' => 'fve', 'FvH4_6g01541' => 'fve', 'FvH4_6g02021' => 'fve', 'FvH4_6g02041' => 'fve', 'FvH4_6g02071' => 'fve', 'FvH4_6g02171' => 'fve', 'FvH4_6g03181' => 'fve', 'FvH4_6g03182' => 'fve', 'FvH4_6g03221' => 'fve', 'FvH4_6g03380' => 'fve', 'FvH4_6g05201' => 'fve', 'FvH4_6g05203' => 'fve', 'FvH4_6g20231' => 'fve', 'FvH4_6g31981' => 'fve', 'FvH4_6g32061' => 'fve', 'FvH4_6g37041' => 'fve', 'FvH4_6g37932' => 'fve', 'FvH4_6g38731' => 'fve', 'FvH4_6g39370' => 'fve', 'FvH4_6g39371' => 'fve', 'FvH4_6g40891' => 'fve', 'FvH4_6g40892' => 'fve', 'FvH4_6g43143' => 'fve', 'FvH4_6g45251' => 'fve', 'FvH4_6g45260' => 'fve', 'FvH4_6g45291' => 'fve', 'FvH4_6g45890' => 'fve', 'FvH4_6g46240' => 'fve', 'FvH4_6g46241' => 'fve', 'FvH4_6g46242' => 'fve', 'FvH4_6g46260' => 'fve', 'FvH4_6g46280' => 'fve', 'FvH4_6g46380' => 'fve', 'FvH4_7g12841' => 'fve', 'FvH4_7g31431' => 'fve', 'Glyma.09G075900' => 'gma', 'Gohir.A09G096401' => 'ghi', 'Gohir.D09G096101' => 'ghi', 'Gorai.006G112800' => 'gra', 'HanXRQChr04g0121411' => 'han', 'Hund15878' => 'sun', 'Lj2A1107G68' => 'lonja', 'Lj2A630G63' => 'lonja', 'Lj2A946T25' => 'lonja', 'Lj2C714T1' => 'lonja', 'Lj2C966T3' => 'lonja', 'Lj2C966T4' => 'lonja', 'Lj4g0002979' => 'lja', 'Lsat_1_v5_gn_5_30901' => 'lsa', 'Lsat_1_v5_gn_5_31100' => 'lsa', 'Lsat_1_v5_gn_5_38600' => 'lsa', 'Lsat_1_v5_gn_6_92061' => 'lsa', 'Manes.05G071301' => 'mes', 'MD02G1008700' => 'mdo', 'MD02G1008900' => 'mdo', 'MD03G1256400' => 'mdo', 'MD04G1180900' => 'mdo', 'MD04G1181000' => 'mdo', 'MD04G1181200' => 'mdo', 'MD05G1244200' => 'mdo', 'MD05G1324200' => 'mdo', 'MD09G1201600' => 'mdo', 'MD10G1000600' => 'mdo', 'MD14G1026900' => 'mdo', 'MD14G1187900' => 'mdo', 'MD15G1017800' => 'mdo', 'MD15G1018100' => 'mdo', 'Medtr4g124160' => 'mtr', 'Migut.L01260' => 'egut', 'Nitab4.5_0000008g0440' => 'nta', 'Nitab4.5_0000207g0170' => 'nta', 'Nitab4.5_0007671g0030' => 'nta', 'Nitab4.5_0010853g0020' => 'nta', 'Oeu057656.1' => 'oeu', 'PGSC0003DMG400005638' => 'stu', 'PGSC0003DMG400005639' => 'stu', 'Phvul.009G222800' => 'pvu', 'Potri.009G132400' => 'ptr', 'Potri.009G163001' => 'ptr', 'Potri.011G000700' => 'ptr', 'Potri.011G004800' => 'ptr', 'Prupe.1G509300' => 'ppe', 'Prupe.1G509700' => 'ppe', 'Prupe.1G510400' => 'ppe', 'Prupe.1G510700' => 'ppe', 'Prupe.1G512600' => 'ppe', 'Prupe.2G073200' => 'ppe', 'Prupe.3G059500' => 'ppe', 'Prupe.3G059600' => 'ppe', 'Prupe.3G246100' => 'ppe', 'Prupe.3G265100' => 'ppe', 'Prupe.4G034700' => 'ppe', 'Prupe.4G052100' => 'ppe', 'Prupe.4G053600' => 'ppe', 'Prupe.5G068800' => 'ppe', 'Prupe.5G070600' => 'ppe', 'Prupe.6G075400' => 'ppe', 'Prupe.6G075500' => 'ppe', 'Prupe.6G076400' => 'ppe', 'Prupe.8G110700' => 'ppe', 'Psat4g020960' => 'psa', 'PSO135G0788' => 'pso', 'PSO210G6463' => 'pso', 'PSO384G0370' => 'pso', 'PSO386G0056' => 'pso', 'QL01p006048' => 'qlo', 'QL02p054283' => 'qlo', 'QL05p008000' => 'qlo', 'QL05p008212' => 'qlo', 'QL05p008950' => 'qlo', 'QL05p009042' => 'qlo', 'QL05p009518' => 'qlo', 'QL05p012589' => 'qlo', 'QL05p012608' => 'qlo', 'QL05p012650' => 'qlo', 'QL05p012667' => 'qlo', 'QL05p014501' => 'qlo', 'QL05p052800' => 'qlo', 'QL05p065010' => 'qlo', 'QL05p074156' => 'qlo', 'QL05p074160' => 'qlo', 'QL05p074174' => 'qlo', 'QL05p074178' => 'qlo', 'QL05p074214' => 'qlo', 'QL06p001050' => 'qlo', 'QL06p001056' => 'qlo', 'QL06p006093' => 'qlo', 'QL06p006111' => 'qlo', 'QL07p019784' => 'qlo', 'QL07p019801' => 'qlo', 'QL07p036110' => 'qlo', 'QL07p036134' => 'qlo', 'QL07p036147' => 'qlo', 'QL07p036156' => 'qlo', 'QL07p036300' => 'qlo', 'QL07p036320' => 'qlo', 'QL08p014547' => 'qlo', 'QL08p014551' => 'qlo', 'QL08p043319' => 'qlo', 'QL08p043324' => 'qlo', 'QL11p009094' => 'qlo', 'RcHm_v2.0_Chr1g0380481' => 'rch', 'RcHm_v2.0_Chr2g0089331' => 'rch', 'RcHm_v2.0_Chr2g0123691' => 'rch', 'RcHm_v2.0_Chr2g0151111' => 'rch', 'RcHm_v2.0_Chr2g0163011' => 'rch', 'RcHm_v2.0_Chr2g0163051' => 'rch', 'RcHm_v2.0_Chr2g0164671' => 'rch', 'RcHm_v2.0_Chr2g0164681' => 'rch', 'RcHm_v2.0_Chr2g0164721' => 'rch', 'RcHm_v2.0_Chr3g0449911' => 'rch', 'RcHm_v2.0_Chr3g0450211' => 'rch', 'RcHm_v2.0_Chr3g0457271' => 'rch', 'RcHm_v2.0_Chr5g0018111' => 'rch', 'RcHm_v2.0_Chr5g0021011' => 'rch', 'RcHm_v2.0_Chr5g0081171' => 'rch', 'RcHm_v2.0_Chr5g0081211' => 'rch', 'RcHm_v2.0_Chr6g0275871' => 'rch', 'RcHm_v2.0_Chr6g0276071' => 'rch', 'RcHm_v2.0_Chr6g0285591' => 'rch', 'RcHm_v2.0_Chr6g0291931' => 'rch', 'RcHm_v2.0_Chr6g0292091' => 'rch', 'RcHm_v2.0_Chr6g0292271' => 'rch', 'RcHm_v2.0_Chr7g0221261' => 'rch', 'Rhsim08G0219900' => 'rsi', 'Rhsim08G0220200' => 'rsi', 'Rhsim08G0237800' => 'rsi', 'Rhsim08G0238800' => 'rsi', 'Sabra09G0102700' => 'sbr', 'Sabra09G0127200' => 'sbr', 'Sabra11G0003700' => 'sbr', 'Sabra15G0014700' => 'sbr', 'Sc19g0000590' => 'sci', 'Sc19g0001870' => 'sci', 'SGA_v2.0_scaffold1G00346' => 'sas', 'SGA_v2.0_scaffold1G00575' => 'sas', 'SGA_v2.0_scaffold1G00761' => 'sas', 'SGA_v2.0_scaffold232G43501' => 'sas', 'TAR625G1137' => 'tar', 'Thecc.03G222100' => 'tca', 'TPR.G12691' => 'tpr', 'TWI34G0727' => 'twi', 'TWI36G0117' => 'twi', 'VMungo1309G0868' => 'vmu' ), 'gf_id' => 'HOM05D001729', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001729' ), 'data_identifier' => 'HOM05D001729', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001729', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '375', 'num_species' => '42' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'Ah.07g204710' => 'amhyb', 'AUR62006001' => 'cqu', 'AUR62006002' => 'cqu', 'AUR62006003' => 'cqu', 'AUR62015641' => 'cqu', 'AUR62027174' => 'cqu', 'AUR62035623' => 'cqu', 'AUR62035624' => 'cqu', 'AUR62035625' => 'cqu', 'AUR62035626' => 'cqu', 'CAN.G1110.53' => 'can', 'CANSAT80G0415' => 'cansat', 'Ca_21364_v3' => 'car', 'COL.COLO4_30693' => 'col', 'COL.COLO4_30694' => 'col', 'COL.COLO4_30695' => 'col', 'COL.COLO4_30696' => 'col', 'COL.COLO4_34020' => 'col', 'DCAR_004585' => 'dca', 'Dinv04029' => 'din', 'Dinv34857' => 'din', 'Duzib147G0011' => 'dzi', 'Duzib170G0599' => 'dzi', 'Duzib192G1051' => 'dzi', 'FAN01G0708' => 'fan', 'FAN01G0742' => 'fan', 'FAN02G0048' => 'fan', 'FAN02G0583' => 'fan', 'FAN02G0688' => 'fan', 'FAN02G1588' => 'fan', 'FAN02G2194' => 'fan', 'FAN02G2750' => 'fan', 'FAN02G3094' => 'fan', 'FAN02G3887' => 'fan', 'FAN02G3911' => 'fan', 'FAN02G3994' => 'fan', 'FAN02G4432' => 'fan', 'FAN02G4556' => 'fan', 'FAN03G1977' => 'fan', 'FAN03G2781' => 'fan', 'FAN03G2850' => 'fan', 'FAN03G3155' => 'fan', 'FAN04G2487' => 'fan', 'FAN05G0208' => 'fan', 'FAN05G0656' => 'fan', 'FAN05G0696' => 'fan', 'FAN05G0810' => 'fan', 'FAN05G1447' => 'fan', 'FAN05G2640' => 'fan', 'FAN05G2911' => 'fan', 'FAN05G3901' => 'fan', 'FAN05G4859' => 'fan', 'FAN05G4861' => 'fan', 'FAN05G4988' => 'fan', 'FAN05G5187' => 'fan', 'FAN05G5452' => 'fan', 'FAN05G5500' => 'fan', 'FAN05G5688' => 'fan', 'FAN06G0177' => 'fan', 'FAN06G0675' => 'fan', 'FAN06G1290' => 'fan', 'FAN06G2191' => 'fan', 'FAN06G2405' => 'fan', 'FAN06G3231' => 'fan', 'FAN06G3932' => 'fan', 'FAN07G0163' => 'fan', 'FAN07G0471' => 'fan', 'FAN07G1354' => 'fan', 'FAN08G0338' => 'fan', 'FAN08G1373' => 'fan', 'FAN08G2539' => 'fan', 'FAN08G2728' => 'fan', 'FAN09G0608' => 'fan', 'FAN09G1136' => 'fan', 'FAN09G1958' => 'fan', 'FAN09G2508' => 'fan', 'FAN09G2597' => 'fan', 'FAN09G2658' => 'fan', 'FAN09G2757' => 'fan', 'FAN09G2983' => 'fan', 'FAN09G3130' => 'fan', 'FAN09G3565' => 'fan', 'FAN09G3613' => 'fan', 'FAN09G4011' => 'fan', 'FAN09G4239' => 'fan', 'FAN09G4277' => 'fan', 'FAN09G4720' => 'fan', 'FAN11G0139' => 'fan', 'FAN11G1727' => 'fan', 'FAN11G2672' => 'fan', 'FAN11G2795' => 'fan', 'FAN11G3238' => 'fan', 'FAN11G3734' => 'fan', 'FAN12G0631' => 'fan', 'FAN12G2239' => 'fan', 'FAN12G2308' => 'fan', 'FAN12G2569' => 'fan', 'FAN12G2623' => 'fan', 'FAN13G3182' => 'fan', 'FAN14G0053' => 'fan', 'FAN14G0370' => 'fan', 'FAN14G0382' => 'fan', 'FAN14G0421' => 'fan', 'FAN14G0866' => 'fan', 'FAN14G1187' => 'fan', 'FAN14G1727' => 'fan', 'FAN14G1791' => 'fan', 'FAN14G2361' => 'fan', 'FAN14G2668' => 'fan', 'FAN14G2770' => 'fan', 'FAN14G2874' => 'fan', 'FAN14G3193' => 'fan', 'FAN14G3624' => 'fan', 'FAN14G3676' => 'fan', 'FAN14G3807' => 'fan', 'FAN14G4082' => 'fan', 'FAN14G4342' => 'fan', 'FAN14G4985' => 'fan', 'FAN14G5126' => 'fan', 'FAN14G5781' => 'fan', 'FAN14G5808' => 'fan', 'FAN14G5949' => 'fan', 'FAN15G0828' => 'fan', 'FAN15G1054' => 'fan', 'FAN15G2023' => 'fan', 'FAN15G2506' => 'fan', 'FAN16G0128' => 'fan', 'FAN16G0249' => 'fan', 'FAN16G0429' => 'fan', 'FAN16G1493' => 'fan', 'FAN16G2210' => 'fan', 'FAN16G2506' => 'fan', 'FAN18G1542' => 'fan', 'FAN18G4057' => 'fan', 'FAN19G0745' => 'fan', 'FAN19G1216' => 'fan', 'FAN19G1733' => 'fan', 'FAN20G0258' => 'fan', 'FAN20G1095' => 'fan', 'FAN20G1557' => 'fan', 'FAN21G0302' => 'fan', 'FAN21G0519' => 'fan', 'FAN21G0970' => 'fan', 'FAN21G1159' => 'fan', 'FAN21G1312' => 'fan', 'FAN21G1440' => 'fan', 'FAN21G1715' => 'fan', 'FAN23G1584' => 'fan', 'FAN24G0045' => 'fan', 'FAN24G0053' => 'fan', 'FAN24G1500' => 'fan', 'FAN24G1817' => 'fan', 'FAN24G2147' => 'fan', 'FAN24G2236' => 'fan', 'FAN24G2446' => 'fan', 'FAN24G2684' => 'fan', 'FAN25G0187' => 'fan', 'FAN25G0505' => 'fan', 'FAN25G0589' => 'fan', 'FAN25G3663' => 'fan', 'FAN26G1025' => 'fan', 'FAN26G2860' => 'fan', 'FAN27G1329' => 'fan', 'FAN27G3392' => 'fan', 'FvH4_1g02011' => 'fve', 'FvH4_1g06511' => 'fve', 'FvH4_2g19900' => 'fve', 'FvH4_2g19920' => 'fve', 'FvH4_2g24261' => 'fve', 'FvH4_2g24270' => 'fve', 'FvH4_2g24631' => 'fve', 'FvH4_2g30622' => 'fve', 'FvH4_3g12920' => 'fve', 'FvH4_3g30171' => 'fve', 'FvH4_3g35490' => 'fve', 'FvH4_3g43682' => 'fve', 'FvH4_3g43730' => 'fve', 'FvH4_3g43732' => 'fve', 'FvH4_3g43751' => 'fve', 'FvH4_3g43752' => 'fve', 'FvH4_3g43770' => 'fve', 'FvH4_3g44471' => 'fve', 'FvH4_3g44510' => 'fve', 'FvH4_3g44582' => 'fve', 'FvH4_4g16921' => 'fve', 'FvH4_4g17121' => 'fve', 'FvH4_4g17782' => 'fve', 'FvH4_4g17783' => 'fve', 'FvH4_4g18120' => 'fve', 'FvH4_4g31310' => 'fve', 'FvH4_4g35052' => 'fve', 'FvH4_5g30862' => 'fve', 'FvH4_6g01541' => 'fve', 'FvH4_6g02021' => 'fve', 'FvH4_6g02041' => 'fve', 'FvH4_6g02071' => 'fve', 'FvH4_6g02171' => 'fve', 'FvH4_6g03181' => 'fve', 'FvH4_6g03182' => 'fve', 'FvH4_6g03221' => 'fve', 'FvH4_6g03380' => 'fve', 'FvH4_6g05201' => 'fve', 'FvH4_6g05203' => 'fve', 'FvH4_6g20231' => 'fve', 'FvH4_6g31981' => 'fve', 'FvH4_6g32061' => 'fve', 'FvH4_6g37041' => 'fve', 'FvH4_6g37932' => 'fve', 'FvH4_6g38731' => 'fve', 'FvH4_6g39370' => 'fve', 'FvH4_6g39371' => 'fve', 'FvH4_6g40891' => 'fve', 'FvH4_6g40892' => 'fve', 'FvH4_6g43143' => 'fve', 'FvH4_6g45251' => 'fve', 'FvH4_6g45260' => 'fve', 'FvH4_6g45291' => 'fve', 'FvH4_6g45890' => 'fve', 'FvH4_6g46240' => 'fve', 'FvH4_6g46241' => 'fve', 'FvH4_6g46242' => 'fve', 'FvH4_6g46260' => 'fve', 'FvH4_6g46280' => 'fve', 'FvH4_6g46380' => 'fve', 'FvH4_7g12841' => 'fve', 'FvH4_7g31431' => 'fve', 'Glyma.09G075900' => 'gma', 'Gohir.A09G096401' => 'ghi', 'Gohir.D09G096101' => 'ghi', 'Gorai.006G112800' => 'gra', 'HanXRQChr04g0121411' => 'han', 'Hund15878' => 'sun', 'Lj2A1107G68' => 'lonja', 'Lj2A630G63' => 'lonja', 'Lj2A946T25' => 'lonja', 'Lj2C714T1' => 'lonja', 'Lj2C966T3' => 'lonja', 'Lj2C966T4' => 'lonja', 'Lj4g0002979' => 'lja', 'Lsat_1_v5_gn_5_30901' => 'lsa', 'Lsat_1_v5_gn_5_31100' => 'lsa', 'Lsat_1_v5_gn_5_38600' => 'lsa', 'Lsat_1_v5_gn_6_92061' => 'lsa', 'Manes.05G071301' => 'mes', 'MD02G1008700' => 'mdo', 'MD02G1008900' => 'mdo', 'MD03G1256400' => 'mdo', 'MD04G1180900' => 'mdo', 'MD04G1181000' => 'mdo', 'MD04G1181200' => 'mdo', 'MD05G1244200' => 'mdo', 'MD05G1324200' => 'mdo', 'MD09G1201600' => 'mdo', 'MD10G1000600' => 'mdo', 'MD14G1026900' => 'mdo', 'MD14G1187900' => 'mdo', 'MD15G1017800' => 'mdo', 'MD15G1018100' => 'mdo', 'Medtr4g124160' => 'mtr', 'Migut.L01260' => 'egut', 'Nitab4.5_0000008g0440' => 'nta', 'Nitab4.5_0000207g0170' => 'nta', 'Nitab4.5_0007671g0030' => 'nta', 'Nitab4.5_0010853g0020' => 'nta', 'Oeu057656.1' => 'oeu', 'PGSC0003DMG400005638' => 'stu', 'PGSC0003DMG400005639' => 'stu', 'Phvul.009G222800' => 'pvu', 'Potri.009G132400' => 'ptr', 'Potri.009G163001' => 'ptr', 'Potri.011G000700' => 'ptr', 'Potri.011G004800' => 'ptr', 'Prupe.1G509300' => 'ppe', 'Prupe.1G509700' => 'ppe', 'Prupe.1G510400' => 'ppe', 'Prupe.1G510700' => 'ppe', 'Prupe.1G512600' => 'ppe', 'Prupe.2G073200' => 'ppe', 'Prupe.3G059500' => 'ppe', 'Prupe.3G059600' => 'ppe', 'Prupe.3G246100' => 'ppe', 'Prupe.3G265100' => 'ppe', 'Prupe.4G034700' => 'ppe', 'Prupe.4G052100' => 'ppe', 'Prupe.4G053600' => 'ppe', 'Prupe.5G068800' => 'ppe', 'Prupe.5G070600' => 'ppe', 'Prupe.6G075400' => 'ppe', 'Prupe.6G075500' => 'ppe', 'Prupe.6G076400' => 'ppe', 'Prupe.8G110700' => 'ppe', 'Psat4g020960' => 'psa', 'PSO135G0788' => 'pso', 'PSO210G6463' => 'pso', 'PSO384G0370' => 'pso', 'PSO386G0056' => 'pso', 'QL01p006048' => 'qlo', 'QL02p054283' => 'qlo', 'QL05p008000' => 'qlo', 'QL05p008212' => 'qlo', 'QL05p008950' => 'qlo', 'QL05p009042' => 'qlo', 'QL05p009518' => 'qlo', 'QL05p012589' => 'qlo', 'QL05p012608' => 'qlo', 'QL05p012650' => 'qlo', 'QL05p012667' => 'qlo', 'QL05p014501' => 'qlo', 'QL05p052800' => 'qlo', 'QL05p065010' => 'qlo', 'QL05p074156' => 'qlo', 'QL05p074160' => 'qlo', 'QL05p074174' => 'qlo', 'QL05p074178' => 'qlo', 'QL05p074214' => 'qlo', 'QL06p001050' => 'qlo', 'QL06p001056' => 'qlo', 'QL06p006093' => 'qlo', 'QL06p006111' => 'qlo', 'QL07p019784' => 'qlo', 'QL07p019801' => 'qlo', 'QL07p036110' => 'qlo', 'QL07p036134' => 'qlo', 'QL07p036147' => 'qlo', 'QL07p036156' => 'qlo', 'QL07p036300' => 'qlo', 'QL07p036320' => 'qlo', 'QL08p014547' => 'qlo', 'QL08p014551' => 'qlo', 'QL08p043319' => 'qlo', 'QL08p043324' => 'qlo', 'QL11p009094' => 'qlo', 'RcHm_v2.0_Chr1g0380481' => 'rch', 'RcHm_v2.0_Chr2g0089331' => 'rch', 'RcHm_v2.0_Chr2g0123691' => 'rch', 'RcHm_v2.0_Chr2g0151111' => 'rch', 'RcHm_v2.0_Chr2g0163011' => 'rch', 'RcHm_v2.0_Chr2g0163051' => 'rch', 'RcHm_v2.0_Chr2g0164671' => 'rch', 'RcHm_v2.0_Chr2g0164681' => 'rch', 'RcHm_v2.0_Chr2g0164721' => 'rch', 'RcHm_v2.0_Chr3g0449911' => 'rch', 'RcHm_v2.0_Chr3g0450211' => 'rch', 'RcHm_v2.0_Chr3g0457271' => 'rch', 'RcHm_v2.0_Chr5g0018111' => 'rch', 'RcHm_v2.0_Chr5g0021011' => 'rch', 'RcHm_v2.0_Chr5g0081171' => 'rch', 'RcHm_v2.0_Chr5g0081211' => 'rch', 'RcHm_v2.0_Chr6g0275871' => 'rch', 'RcHm_v2.0_Chr6g0276071' => 'rch', 'RcHm_v2.0_Chr6g0285591' => 'rch', 'RcHm_v2.0_Chr6g0291931' => 'rch', 'RcHm_v2.0_Chr6g0292091' => 'rch', 'RcHm_v2.0_Chr6g0292271' => 'rch', 'RcHm_v2.0_Chr7g0221261' => 'rch', 'Rhsim08G0219900' => 'rsi', 'Rhsim08G0220200' => 'rsi', 'Rhsim08G0237800' => 'rsi', 'Rhsim08G0238800' => 'rsi', 'Sabra09G0102700' => 'sbr', 'Sabra09G0127200' => 'sbr', 'Sabra11G0003700' => 'sbr', 'Sabra15G0014700' => 'sbr', 'Sc19g0000590' => 'sci', 'Sc19g0001870' => 'sci', 'SGA_v2.0_scaffold1G00346' => 'sas', 'SGA_v2.0_scaffold1G00575' => 'sas', 'SGA_v2.0_scaffold1G00761' => 'sas', 'SGA_v2.0_scaffold232G43501' => 'sas', 'TAR625G1137' => 'tar', 'Thecc.03G222100' => 'tca', 'TPR.G12691' => 'tpr', 'TWI34G0727' => 'twi', 'TWI36G0117' => 'twi', 'VMungo1309G0868' => 'vmu' ) $gf_id = 'HOM05D001729' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001729' ) $data_identifier = 'HOM05D001729' $data_type = 'gf_id' $species_gene_counts = array( 'amhyb' => (int) 1, 'cqu' => (int) 9, 'can' => (int) 1, 'cansat' => (int) 1, 'car' => (int) 1, 'col' => (int) 5, 'dca' => (int) 1, 'din' => (int) 2, 'dzi' => (int) 3, 'fan' => (int) 140, 'fve' => (int) 62, 'gma' => (int) 1, 'ghi' => (int) 2, 'gra' => (int) 1, 'han' => (int) 1, 'sun' => (int) 1, 'lonja' => (int) 6, 'lja' => (int) 1, 'lsa' => (int) 4, 'mes' => (int) 1, 'mdo' => (int) 14, 'mtr' => (int) 1, 'egut' => (int) 1, 'nta' => (int) 4, 'oeu' => (int) 1, 'stu' => (int) 2, 'pvu' => (int) 1, 'ptr' => (int) 4, 'ppe' => (int) 19, 'psa' => (int) 1, 'pso' => (int) 4, 'qlo' => (int) 36, 'rch' => (int) 23, 'rsi' => (int) 4, 'sbr' => (int) 4, 'sci' => (int) 2, 'sas' => (int) 4, 'tar' => (int) 1, 'tca' => (int) 1, 'tpr' => (int) 1, 'twi' => (int) 2, 'vmu' => (int) 1 ) $gf_gene_species = 'vmu' $gf_gene_id = 'VMungo1309G0868' $species_info = array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ) $local_species = 'sas' $disabled = '' $selected = '' $num_hits = (int) 1
Warning (2): count(): Parameter must be an array or an object that implements Countable [APP/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp, line 33]Code Context $disabled = (!array_key_exists($local_species,$species_gene_counts))?"disabled":""; $selected = (isset($selected_species) && array_key_exists($local_species,$selected_species))?"checked='checked'":""; $num_hits = (array_key_exists($local_species,$species_gene_counts))?count($species_gene_counts[$local_species]):0; $viewFile = '/www/bioinformatics01_ro/plaza/_dev_instances/feedback/app/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp' $dataForView = array( 'sidebar_info' => array( 'gf_id' => 'HOM05D001729', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '375', 'num_species' => '42' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'Ah.07g204710' => 'amhyb', 'AUR62006001' => 'cqu', 'AUR62006002' => 'cqu', 'AUR62006003' => 'cqu', 'AUR62015641' => 'cqu', 'AUR62027174' => 'cqu', 'AUR62035623' => 'cqu', 'AUR62035624' => 'cqu', 'AUR62035625' => 'cqu', 'AUR62035626' => 'cqu', 'CAN.G1110.53' => 'can', 'CANSAT80G0415' => 'cansat', 'Ca_21364_v3' => 'car', 'COL.COLO4_30693' => 'col', 'COL.COLO4_30694' => 'col', 'COL.COLO4_30695' => 'col', 'COL.COLO4_30696' => 'col', 'COL.COLO4_34020' => 'col', 'DCAR_004585' => 'dca', 'Dinv04029' => 'din', 'Dinv34857' => 'din', 'Duzib147G0011' => 'dzi', 'Duzib170G0599' => 'dzi', 'Duzib192G1051' => 'dzi', 'FAN01G0708' => 'fan', 'FAN01G0742' => 'fan', 'FAN02G0048' => 'fan', 'FAN02G0583' => 'fan', 'FAN02G0688' => 'fan', 'FAN02G1588' => 'fan', 'FAN02G2194' => 'fan', 'FAN02G2750' => 'fan', 'FAN02G3094' => 'fan', 'FAN02G3887' => 'fan', 'FAN02G3911' => 'fan', 'FAN02G3994' => 'fan', 'FAN02G4432' => 'fan', 'FAN02G4556' => 'fan', 'FAN03G1977' => 'fan', 'FAN03G2781' => 'fan', 'FAN03G2850' => 'fan', 'FAN03G3155' => 'fan', 'FAN04G2487' => 'fan', 'FAN05G0208' => 'fan', 'FAN05G0656' => 'fan', 'FAN05G0696' => 'fan', 'FAN05G0810' => 'fan', 'FAN05G1447' => 'fan', 'FAN05G2640' => 'fan', 'FAN05G2911' => 'fan', 'FAN05G3901' => 'fan', 'FAN05G4859' => 'fan', 'FAN05G4861' => 'fan', 'FAN05G4988' => 'fan', 'FAN05G5187' => 'fan', 'FAN05G5452' => 'fan', 'FAN05G5500' => 'fan', 'FAN05G5688' => 'fan', 'FAN06G0177' => 'fan', 'FAN06G0675' => 'fan', 'FAN06G1290' => 'fan', 'FAN06G2191' => 'fan', 'FAN06G2405' => 'fan', 'FAN06G3231' => 'fan', 'FAN06G3932' => 'fan', 'FAN07G0163' => 'fan', 'FAN07G0471' => 'fan', 'FAN07G1354' => 'fan', 'FAN08G0338' => 'fan', 'FAN08G1373' => 'fan', 'FAN08G2539' => 'fan', 'FAN08G2728' => 'fan', 'FAN09G0608' => 'fan', 'FAN09G1136' => 'fan', 'FAN09G1958' => 'fan', 'FAN09G2508' => 'fan', 'FAN09G2597' => 'fan', 'FAN09G2658' => 'fan', 'FAN09G2757' => 'fan', 'FAN09G2983' => 'fan', 'FAN09G3130' => 'fan', 'FAN09G3565' => 'fan', 'FAN09G3613' => 'fan', 'FAN09G4011' => 'fan', 'FAN09G4239' => 'fan', 'FAN09G4277' => 'fan', 'FAN09G4720' => 'fan', 'FAN11G0139' => 'fan', 'FAN11G1727' => 'fan', 'FAN11G2672' => 'fan', 'FAN11G2795' => 'fan', 'FAN11G3238' => 'fan', 'FAN11G3734' => 'fan', 'FAN12G0631' => 'fan', 'FAN12G2239' => 'fan', 'FAN12G2308' => 'fan', 'FAN12G2569' => 'fan', 'FAN12G2623' => 'fan', 'FAN13G3182' => 'fan', 'FAN14G0053' => 'fan', 'FAN14G0370' => 'fan', 'FAN14G0382' => 'fan', 'FAN14G0421' => 'fan', 'FAN14G0866' => 'fan', 'FAN14G1187' => 'fan', 'FAN14G1727' => 'fan', 'FAN14G1791' => 'fan', 'FAN14G2361' => 'fan', 'FAN14G2668' => 'fan', 'FAN14G2770' => 'fan', 'FAN14G2874' => 'fan', 'FAN14G3193' => 'fan', 'FAN14G3624' => 'fan', 'FAN14G3676' => 'fan', 'FAN14G3807' => 'fan', 'FAN14G4082' => 'fan', 'FAN14G4342' => 'fan', 'FAN14G4985' => 'fan', 'FAN14G5126' => 'fan', 'FAN14G5781' => 'fan', 'FAN14G5808' => 'fan', 'FAN14G5949' => 'fan', 'FAN15G0828' => 'fan', 'FAN15G1054' => 'fan', 'FAN15G2023' => 'fan', 'FAN15G2506' => 'fan', 'FAN16G0128' => 'fan', 'FAN16G0249' => 'fan', 'FAN16G0429' => 'fan', 'FAN16G1493' => 'fan', 'FAN16G2210' => 'fan', 'FAN16G2506' => 'fan', 'FAN18G1542' => 'fan', 'FAN18G4057' => 'fan', 'FAN19G0745' => 'fan', 'FAN19G1216' => 'fan', 'FAN19G1733' => 'fan', 'FAN20G0258' => 'fan', 'FAN20G1095' => 'fan', 'FAN20G1557' => 'fan', 'FAN21G0302' => 'fan', 'FAN21G0519' => 'fan', 'FAN21G0970' => 'fan', 'FAN21G1159' => 'fan', 'FAN21G1312' => 'fan', 'FAN21G1440' => 'fan', 'FAN21G1715' => 'fan', 'FAN23G1584' => 'fan', 'FAN24G0045' => 'fan', 'FAN24G0053' => 'fan', 'FAN24G1500' => 'fan', 'FAN24G1817' => 'fan', 'FAN24G2147' => 'fan', 'FAN24G2236' => 'fan', 'FAN24G2446' => 'fan', 'FAN24G2684' => 'fan', 'FAN25G0187' => 'fan', 'FAN25G0505' => 'fan', 'FAN25G0589' => 'fan', 'FAN25G3663' => 'fan', 'FAN26G1025' => 'fan', 'FAN26G2860' => 'fan', 'FAN27G1329' => 'fan', 'FAN27G3392' => 'fan', 'FvH4_1g02011' => 'fve', 'FvH4_1g06511' => 'fve', 'FvH4_2g19900' => 'fve', 'FvH4_2g19920' => 'fve', 'FvH4_2g24261' => 'fve', 'FvH4_2g24270' => 'fve', 'FvH4_2g24631' => 'fve', 'FvH4_2g30622' => 'fve', 'FvH4_3g12920' => 'fve', 'FvH4_3g30171' => 'fve', 'FvH4_3g35490' => 'fve', 'FvH4_3g43682' => 'fve', 'FvH4_3g43730' => 'fve', 'FvH4_3g43732' => 'fve', 'FvH4_3g43751' => 'fve', 'FvH4_3g43752' => 'fve', 'FvH4_3g43770' => 'fve', 'FvH4_3g44471' => 'fve', 'FvH4_3g44510' => 'fve', 'FvH4_3g44582' => 'fve', 'FvH4_4g16921' => 'fve', 'FvH4_4g17121' => 'fve', 'FvH4_4g17782' => 'fve', 'FvH4_4g17783' => 'fve', 'FvH4_4g18120' => 'fve', 'FvH4_4g31310' => 'fve', 'FvH4_4g35052' => 'fve', 'FvH4_5g30862' => 'fve', 'FvH4_6g01541' => 'fve', 'FvH4_6g02021' => 'fve', 'FvH4_6g02041' => 'fve', 'FvH4_6g02071' => 'fve', 'FvH4_6g02171' => 'fve', 'FvH4_6g03181' => 'fve', 'FvH4_6g03182' => 'fve', 'FvH4_6g03221' => 'fve', 'FvH4_6g03380' => 'fve', 'FvH4_6g05201' => 'fve', 'FvH4_6g05203' => 'fve', 'FvH4_6g20231' => 'fve', 'FvH4_6g31981' => 'fve', 'FvH4_6g32061' => 'fve', 'FvH4_6g37041' => 'fve', 'FvH4_6g37932' => 'fve', 'FvH4_6g38731' => 'fve', 'FvH4_6g39370' => 'fve', 'FvH4_6g39371' => 'fve', 'FvH4_6g40891' => 'fve', 'FvH4_6g40892' => 'fve', 'FvH4_6g43143' => 'fve', 'FvH4_6g45251' => 'fve', 'FvH4_6g45260' => 'fve', 'FvH4_6g45291' => 'fve', 'FvH4_6g45890' => 'fve', 'FvH4_6g46240' => 'fve', 'FvH4_6g46241' => 'fve', 'FvH4_6g46242' => 'fve', 'FvH4_6g46260' => 'fve', 'FvH4_6g46280' => 'fve', 'FvH4_6g46380' => 'fve', 'FvH4_7g12841' => 'fve', 'FvH4_7g31431' => 'fve', 'Glyma.09G075900' => 'gma', 'Gohir.A09G096401' => 'ghi', 'Gohir.D09G096101' => 'ghi', 'Gorai.006G112800' => 'gra', 'HanXRQChr04g0121411' => 'han', 'Hund15878' => 'sun', 'Lj2A1107G68' => 'lonja', 'Lj2A630G63' => 'lonja', 'Lj2A946T25' => 'lonja', 'Lj2C714T1' => 'lonja', 'Lj2C966T3' => 'lonja', 'Lj2C966T4' => 'lonja', 'Lj4g0002979' => 'lja', 'Lsat_1_v5_gn_5_30901' => 'lsa', 'Lsat_1_v5_gn_5_31100' => 'lsa', 'Lsat_1_v5_gn_5_38600' => 'lsa', 'Lsat_1_v5_gn_6_92061' => 'lsa', 'Manes.05G071301' => 'mes', 'MD02G1008700' => 'mdo', 'MD02G1008900' => 'mdo', 'MD03G1256400' => 'mdo', 'MD04G1180900' => 'mdo', 'MD04G1181000' => 'mdo', 'MD04G1181200' => 'mdo', 'MD05G1244200' => 'mdo', 'MD05G1324200' => 'mdo', 'MD09G1201600' => 'mdo', 'MD10G1000600' => 'mdo', 'MD14G1026900' => 'mdo', 'MD14G1187900' => 'mdo', 'MD15G1017800' => 'mdo', 'MD15G1018100' => 'mdo', 'Medtr4g124160' => 'mtr', 'Migut.L01260' => 'egut', 'Nitab4.5_0000008g0440' => 'nta', 'Nitab4.5_0000207g0170' => 'nta', 'Nitab4.5_0007671g0030' => 'nta', 'Nitab4.5_0010853g0020' => 'nta', 'Oeu057656.1' => 'oeu', 'PGSC0003DMG400005638' => 'stu', 'PGSC0003DMG400005639' => 'stu', 'Phvul.009G222800' => 'pvu', 'Potri.009G132400' => 'ptr', 'Potri.009G163001' => 'ptr', 'Potri.011G000700' => 'ptr', 'Potri.011G004800' => 'ptr', 'Prupe.1G509300' => 'ppe', 'Prupe.1G509700' => 'ppe', 'Prupe.1G510400' => 'ppe', 'Prupe.1G510700' => 'ppe', 'Prupe.1G512600' => 'ppe', 'Prupe.2G073200' => 'ppe', 'Prupe.3G059500' => 'ppe', 'Prupe.3G059600' => 'ppe', 'Prupe.3G246100' => 'ppe', 'Prupe.3G265100' => 'ppe', 'Prupe.4G034700' => 'ppe', 'Prupe.4G052100' => 'ppe', 'Prupe.4G053600' => 'ppe', 'Prupe.5G068800' => 'ppe', 'Prupe.5G070600' => 'ppe', 'Prupe.6G075400' => 'ppe', 'Prupe.6G075500' => 'ppe', 'Prupe.6G076400' => 'ppe', 'Prupe.8G110700' => 'ppe', 'Psat4g020960' => 'psa', 'PSO135G0788' => 'pso', 'PSO210G6463' => 'pso', 'PSO384G0370' => 'pso', 'PSO386G0056' => 'pso', 'QL01p006048' => 'qlo', 'QL02p054283' => 'qlo', 'QL05p008000' => 'qlo', 'QL05p008212' => 'qlo', 'QL05p008950' => 'qlo', 'QL05p009042' => 'qlo', 'QL05p009518' => 'qlo', 'QL05p012589' => 'qlo', 'QL05p012608' => 'qlo', 'QL05p012650' => 'qlo', 'QL05p012667' => 'qlo', 'QL05p014501' => 'qlo', 'QL05p052800' => 'qlo', 'QL05p065010' => 'qlo', 'QL05p074156' => 'qlo', 'QL05p074160' => 'qlo', 'QL05p074174' => 'qlo', 'QL05p074178' => 'qlo', 'QL05p074214' => 'qlo', 'QL06p001050' => 'qlo', 'QL06p001056' => 'qlo', 'QL06p006093' => 'qlo', 'QL06p006111' => 'qlo', 'QL07p019784' => 'qlo', 'QL07p019801' => 'qlo', 'QL07p036110' => 'qlo', 'QL07p036134' => 'qlo', 'QL07p036147' => 'qlo', 'QL07p036156' => 'qlo', 'QL07p036300' => 'qlo', 'QL07p036320' => 'qlo', 'QL08p014547' => 'qlo', 'QL08p014551' => 'qlo', 'QL08p043319' => 'qlo', 'QL08p043324' => 'qlo', 'QL11p009094' => 'qlo', 'RcHm_v2.0_Chr1g0380481' => 'rch', 'RcHm_v2.0_Chr2g0089331' => 'rch', 'RcHm_v2.0_Chr2g0123691' => 'rch', 'RcHm_v2.0_Chr2g0151111' => 'rch', 'RcHm_v2.0_Chr2g0163011' => 'rch', 'RcHm_v2.0_Chr2g0163051' => 'rch', 'RcHm_v2.0_Chr2g0164671' => 'rch', 'RcHm_v2.0_Chr2g0164681' => 'rch', 'RcHm_v2.0_Chr2g0164721' => 'rch', 'RcHm_v2.0_Chr3g0449911' => 'rch', 'RcHm_v2.0_Chr3g0450211' => 'rch', 'RcHm_v2.0_Chr3g0457271' => 'rch', 'RcHm_v2.0_Chr5g0018111' => 'rch', 'RcHm_v2.0_Chr5g0021011' => 'rch', 'RcHm_v2.0_Chr5g0081171' => 'rch', 'RcHm_v2.0_Chr5g0081211' => 'rch', 'RcHm_v2.0_Chr6g0275871' => 'rch', 'RcHm_v2.0_Chr6g0276071' => 'rch', 'RcHm_v2.0_Chr6g0285591' => 'rch', 'RcHm_v2.0_Chr6g0291931' => 'rch', 'RcHm_v2.0_Chr6g0292091' => 'rch', 'RcHm_v2.0_Chr6g0292271' => 'rch', 'RcHm_v2.0_Chr7g0221261' => 'rch', 'Rhsim08G0219900' => 'rsi', 'Rhsim08G0220200' => 'rsi', 'Rhsim08G0237800' => 'rsi', 'Rhsim08G0238800' => 'rsi', 'Sabra09G0102700' => 'sbr', 'Sabra09G0127200' => 'sbr', 'Sabra11G0003700' => 'sbr', 'Sabra15G0014700' => 'sbr', 'Sc19g0000590' => 'sci', 'Sc19g0001870' => 'sci', 'SGA_v2.0_scaffold1G00346' => 'sas', 'SGA_v2.0_scaffold1G00575' => 'sas', 'SGA_v2.0_scaffold1G00761' => 'sas', 'SGA_v2.0_scaffold232G43501' => 'sas', 'TAR625G1137' => 'tar', 'Thecc.03G222100' => 'tca', 'TPR.G12691' => 'tpr', 'TWI34G0727' => 'twi', 'TWI36G0117' => 'twi', 'VMungo1309G0868' => 'vmu' ), 'gf_id' => 'HOM05D001729', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001729' ), 'data_identifier' => 'HOM05D001729', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001729', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '375', 'num_species' => '42' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'Ah.07g204710' => 'amhyb', 'AUR62006001' => 'cqu', 'AUR62006002' => 'cqu', 'AUR62006003' => 'cqu', 'AUR62015641' => 'cqu', 'AUR62027174' => 'cqu', 'AUR62035623' => 'cqu', 'AUR62035624' => 'cqu', 'AUR62035625' => 'cqu', 'AUR62035626' => 'cqu', 'CAN.G1110.53' => 'can', 'CANSAT80G0415' => 'cansat', 'Ca_21364_v3' => 'car', 'COL.COLO4_30693' => 'col', 'COL.COLO4_30694' => 'col', 'COL.COLO4_30695' => 'col', 'COL.COLO4_30696' => 'col', 'COL.COLO4_34020' => 'col', 'DCAR_004585' => 'dca', 'Dinv04029' => 'din', 'Dinv34857' => 'din', 'Duzib147G0011' => 'dzi', 'Duzib170G0599' => 'dzi', 'Duzib192G1051' => 'dzi', 'FAN01G0708' => 'fan', 'FAN01G0742' => 'fan', 'FAN02G0048' => 'fan', 'FAN02G0583' => 'fan', 'FAN02G0688' => 'fan', 'FAN02G1588' => 'fan', 'FAN02G2194' => 'fan', 'FAN02G2750' => 'fan', 'FAN02G3094' => 'fan', 'FAN02G3887' => 'fan', 'FAN02G3911' => 'fan', 'FAN02G3994' => 'fan', 'FAN02G4432' => 'fan', 'FAN02G4556' => 'fan', 'FAN03G1977' => 'fan', 'FAN03G2781' => 'fan', 'FAN03G2850' => 'fan', 'FAN03G3155' => 'fan', 'FAN04G2487' => 'fan', 'FAN05G0208' => 'fan', 'FAN05G0656' => 'fan', 'FAN05G0696' => 'fan', 'FAN05G0810' => 'fan', 'FAN05G1447' => 'fan', 'FAN05G2640' => 'fan', 'FAN05G2911' => 'fan', 'FAN05G3901' => 'fan', 'FAN05G4859' => 'fan', 'FAN05G4861' => 'fan', 'FAN05G4988' => 'fan', 'FAN05G5187' => 'fan', 'FAN05G5452' => 'fan', 'FAN05G5500' => 'fan', 'FAN05G5688' => 'fan', 'FAN06G0177' => 'fan', 'FAN06G0675' => 'fan', 'FAN06G1290' => 'fan', 'FAN06G2191' => 'fan', 'FAN06G2405' => 'fan', 'FAN06G3231' => 'fan', 'FAN06G3932' => 'fan', 'FAN07G0163' => 'fan', 'FAN07G0471' => 'fan', 'FAN07G1354' => 'fan', 'FAN08G0338' => 'fan', 'FAN08G1373' => 'fan', 'FAN08G2539' => 'fan', 'FAN08G2728' => 'fan', 'FAN09G0608' => 'fan', 'FAN09G1136' => 'fan', 'FAN09G1958' => 'fan', 'FAN09G2508' => 'fan', 'FAN09G2597' => 'fan', 'FAN09G2658' => 'fan', 'FAN09G2757' => 'fan', 'FAN09G2983' => 'fan', 'FAN09G3130' => 'fan', 'FAN09G3565' => 'fan', 'FAN09G3613' => 'fan', 'FAN09G4011' => 'fan', 'FAN09G4239' => 'fan', 'FAN09G4277' => 'fan', 'FAN09G4720' => 'fan', 'FAN11G0139' => 'fan', 'FAN11G1727' => 'fan', 'FAN11G2672' => 'fan', 'FAN11G2795' => 'fan', 'FAN11G3238' => 'fan', 'FAN11G3734' => 'fan', 'FAN12G0631' => 'fan', 'FAN12G2239' => 'fan', 'FAN12G2308' => 'fan', 'FAN12G2569' => 'fan', 'FAN12G2623' => 'fan', 'FAN13G3182' => 'fan', 'FAN14G0053' => 'fan', 'FAN14G0370' => 'fan', 'FAN14G0382' => 'fan', 'FAN14G0421' => 'fan', 'FAN14G0866' => 'fan', 'FAN14G1187' => 'fan', 'FAN14G1727' => 'fan', 'FAN14G1791' => 'fan', 'FAN14G2361' => 'fan', 'FAN14G2668' => 'fan', 'FAN14G2770' => 'fan', 'FAN14G2874' => 'fan', 'FAN14G3193' => 'fan', 'FAN14G3624' => 'fan', 'FAN14G3676' => 'fan', 'FAN14G3807' => 'fan', 'FAN14G4082' => 'fan', 'FAN14G4342' => 'fan', 'FAN14G4985' => 'fan', 'FAN14G5126' => 'fan', 'FAN14G5781' => 'fan', 'FAN14G5808' => 'fan', 'FAN14G5949' => 'fan', 'FAN15G0828' => 'fan', 'FAN15G1054' => 'fan', 'FAN15G2023' => 'fan', 'FAN15G2506' => 'fan', 'FAN16G0128' => 'fan', 'FAN16G0249' => 'fan', 'FAN16G0429' => 'fan', 'FAN16G1493' => 'fan', 'FAN16G2210' => 'fan', 'FAN16G2506' => 'fan', 'FAN18G1542' => 'fan', 'FAN18G4057' => 'fan', 'FAN19G0745' => 'fan', 'FAN19G1216' => 'fan', 'FAN19G1733' => 'fan', 'FAN20G0258' => 'fan', 'FAN20G1095' => 'fan', 'FAN20G1557' => 'fan', 'FAN21G0302' => 'fan', 'FAN21G0519' => 'fan', 'FAN21G0970' => 'fan', 'FAN21G1159' => 'fan', 'FAN21G1312' => 'fan', 'FAN21G1440' => 'fan', 'FAN21G1715' => 'fan', 'FAN23G1584' => 'fan', 'FAN24G0045' => 'fan', 'FAN24G0053' => 'fan', 'FAN24G1500' => 'fan', 'FAN24G1817' => 'fan', 'FAN24G2147' => 'fan', 'FAN24G2236' => 'fan', 'FAN24G2446' => 'fan', 'FAN24G2684' => 'fan', 'FAN25G0187' => 'fan', 'FAN25G0505' => 'fan', 'FAN25G0589' => 'fan', 'FAN25G3663' => 'fan', 'FAN26G1025' => 'fan', 'FAN26G2860' => 'fan', 'FAN27G1329' => 'fan', 'FAN27G3392' => 'fan', 'FvH4_1g02011' => 'fve', 'FvH4_1g06511' => 'fve', 'FvH4_2g19900' => 'fve', 'FvH4_2g19920' => 'fve', 'FvH4_2g24261' => 'fve', 'FvH4_2g24270' => 'fve', 'FvH4_2g24631' => 'fve', 'FvH4_2g30622' => 'fve', 'FvH4_3g12920' => 'fve', 'FvH4_3g30171' => 'fve', 'FvH4_3g35490' => 'fve', 'FvH4_3g43682' => 'fve', 'FvH4_3g43730' => 'fve', 'FvH4_3g43732' => 'fve', 'FvH4_3g43751' => 'fve', 'FvH4_3g43752' => 'fve', 'FvH4_3g43770' => 'fve', 'FvH4_3g44471' => 'fve', 'FvH4_3g44510' => 'fve', 'FvH4_3g44582' => 'fve', 'FvH4_4g16921' => 'fve', 'FvH4_4g17121' => 'fve', 'FvH4_4g17782' => 'fve', 'FvH4_4g17783' => 'fve', 'FvH4_4g18120' => 'fve', 'FvH4_4g31310' => 'fve', 'FvH4_4g35052' => 'fve', 'FvH4_5g30862' => 'fve', 'FvH4_6g01541' => 'fve', 'FvH4_6g02021' => 'fve', 'FvH4_6g02041' => 'fve', 'FvH4_6g02071' => 'fve', 'FvH4_6g02171' => 'fve', 'FvH4_6g03181' => 'fve', 'FvH4_6g03182' => 'fve', 'FvH4_6g03221' => 'fve', 'FvH4_6g03380' => 'fve', 'FvH4_6g05201' => 'fve', 'FvH4_6g05203' => 'fve', 'FvH4_6g20231' => 'fve', 'FvH4_6g31981' => 'fve', 'FvH4_6g32061' => 'fve', 'FvH4_6g37041' => 'fve', 'FvH4_6g37932' => 'fve', 'FvH4_6g38731' => 'fve', 'FvH4_6g39370' => 'fve', 'FvH4_6g39371' => 'fve', 'FvH4_6g40891' => 'fve', 'FvH4_6g40892' => 'fve', 'FvH4_6g43143' => 'fve', 'FvH4_6g45251' => 'fve', 'FvH4_6g45260' => 'fve', 'FvH4_6g45291' => 'fve', 'FvH4_6g45890' => 'fve', 'FvH4_6g46240' => 'fve', 'FvH4_6g46241' => 'fve', 'FvH4_6g46242' => 'fve', 'FvH4_6g46260' => 'fve', 'FvH4_6g46280' => 'fve', 'FvH4_6g46380' => 'fve', 'FvH4_7g12841' => 'fve', 'FvH4_7g31431' => 'fve', 'Glyma.09G075900' => 'gma', 'Gohir.A09G096401' => 'ghi', 'Gohir.D09G096101' => 'ghi', 'Gorai.006G112800' => 'gra', 'HanXRQChr04g0121411' => 'han', 'Hund15878' => 'sun', 'Lj2A1107G68' => 'lonja', 'Lj2A630G63' => 'lonja', 'Lj2A946T25' => 'lonja', 'Lj2C714T1' => 'lonja', 'Lj2C966T3' => 'lonja', 'Lj2C966T4' => 'lonja', 'Lj4g0002979' => 'lja', 'Lsat_1_v5_gn_5_30901' => 'lsa', 'Lsat_1_v5_gn_5_31100' => 'lsa', 'Lsat_1_v5_gn_5_38600' => 'lsa', 'Lsat_1_v5_gn_6_92061' => 'lsa', 'Manes.05G071301' => 'mes', 'MD02G1008700' => 'mdo', 'MD02G1008900' => 'mdo', 'MD03G1256400' => 'mdo', 'MD04G1180900' => 'mdo', 'MD04G1181000' => 'mdo', 'MD04G1181200' => 'mdo', 'MD05G1244200' => 'mdo', 'MD05G1324200' => 'mdo', 'MD09G1201600' => 'mdo', 'MD10G1000600' => 'mdo', 'MD14G1026900' => 'mdo', 'MD14G1187900' => 'mdo', 'MD15G1017800' => 'mdo', 'MD15G1018100' => 'mdo', 'Medtr4g124160' => 'mtr', 'Migut.L01260' => 'egut', 'Nitab4.5_0000008g0440' => 'nta', 'Nitab4.5_0000207g0170' => 'nta', 'Nitab4.5_0007671g0030' => 'nta', 'Nitab4.5_0010853g0020' => 'nta', 'Oeu057656.1' => 'oeu', 'PGSC0003DMG400005638' => 'stu', 'PGSC0003DMG400005639' => 'stu', 'Phvul.009G222800' => 'pvu', 'Potri.009G132400' => 'ptr', 'Potri.009G163001' => 'ptr', 'Potri.011G000700' => 'ptr', 'Potri.011G004800' => 'ptr', 'Prupe.1G509300' => 'ppe', 'Prupe.1G509700' => 'ppe', 'Prupe.1G510400' => 'ppe', 'Prupe.1G510700' => 'ppe', 'Prupe.1G512600' => 'ppe', 'Prupe.2G073200' => 'ppe', 'Prupe.3G059500' => 'ppe', 'Prupe.3G059600' => 'ppe', 'Prupe.3G246100' => 'ppe', 'Prupe.3G265100' => 'ppe', 'Prupe.4G034700' => 'ppe', 'Prupe.4G052100' => 'ppe', 'Prupe.4G053600' => 'ppe', 'Prupe.5G068800' => 'ppe', 'Prupe.5G070600' => 'ppe', 'Prupe.6G075400' => 'ppe', 'Prupe.6G075500' => 'ppe', 'Prupe.6G076400' => 'ppe', 'Prupe.8G110700' => 'ppe', 'Psat4g020960' => 'psa', 'PSO135G0788' => 'pso', 'PSO210G6463' => 'pso', 'PSO384G0370' => 'pso', 'PSO386G0056' => 'pso', 'QL01p006048' => 'qlo', 'QL02p054283' => 'qlo', 'QL05p008000' => 'qlo', 'QL05p008212' => 'qlo', 'QL05p008950' => 'qlo', 'QL05p009042' => 'qlo', 'QL05p009518' => 'qlo', 'QL05p012589' => 'qlo', 'QL05p012608' => 'qlo', 'QL05p012650' => 'qlo', 'QL05p012667' => 'qlo', 'QL05p014501' => 'qlo', 'QL05p052800' => 'qlo', 'QL05p065010' => 'qlo', 'QL05p074156' => 'qlo', 'QL05p074160' => 'qlo', 'QL05p074174' => 'qlo', 'QL05p074178' => 'qlo', 'QL05p074214' => 'qlo', 'QL06p001050' => 'qlo', 'QL06p001056' => 'qlo', 'QL06p006093' => 'qlo', 'QL06p006111' => 'qlo', 'QL07p019784' => 'qlo', 'QL07p019801' => 'qlo', 'QL07p036110' => 'qlo', 'QL07p036134' => 'qlo', 'QL07p036147' => 'qlo', 'QL07p036156' => 'qlo', 'QL07p036300' => 'qlo', 'QL07p036320' => 'qlo', 'QL08p014547' => 'qlo', 'QL08p014551' => 'qlo', 'QL08p043319' => 'qlo', 'QL08p043324' => 'qlo', 'QL11p009094' => 'qlo', 'RcHm_v2.0_Chr1g0380481' => 'rch', 'RcHm_v2.0_Chr2g0089331' => 'rch', 'RcHm_v2.0_Chr2g0123691' => 'rch', 'RcHm_v2.0_Chr2g0151111' => 'rch', 'RcHm_v2.0_Chr2g0163011' => 'rch', 'RcHm_v2.0_Chr2g0163051' => 'rch', 'RcHm_v2.0_Chr2g0164671' => 'rch', 'RcHm_v2.0_Chr2g0164681' => 'rch', 'RcHm_v2.0_Chr2g0164721' => 'rch', 'RcHm_v2.0_Chr3g0449911' => 'rch', 'RcHm_v2.0_Chr3g0450211' => 'rch', 'RcHm_v2.0_Chr3g0457271' => 'rch', 'RcHm_v2.0_Chr5g0018111' => 'rch', 'RcHm_v2.0_Chr5g0021011' => 'rch', 'RcHm_v2.0_Chr5g0081171' => 'rch', 'RcHm_v2.0_Chr5g0081211' => 'rch', 'RcHm_v2.0_Chr6g0275871' => 'rch', 'RcHm_v2.0_Chr6g0276071' => 'rch', 'RcHm_v2.0_Chr6g0285591' => 'rch', 'RcHm_v2.0_Chr6g0291931' => 'rch', 'RcHm_v2.0_Chr6g0292091' => 'rch', 'RcHm_v2.0_Chr6g0292271' => 'rch', 'RcHm_v2.0_Chr7g0221261' => 'rch', 'Rhsim08G0219900' => 'rsi', 'Rhsim08G0220200' => 'rsi', 'Rhsim08G0237800' => 'rsi', 'Rhsim08G0238800' => 'rsi', 'Sabra09G0102700' => 'sbr', 'Sabra09G0127200' => 'sbr', 'Sabra11G0003700' => 'sbr', 'Sabra15G0014700' => 'sbr', 'Sc19g0000590' => 'sci', 'Sc19g0001870' => 'sci', 'SGA_v2.0_scaffold1G00346' => 'sas', 'SGA_v2.0_scaffold1G00575' => 'sas', 'SGA_v2.0_scaffold1G00761' => 'sas', 'SGA_v2.0_scaffold232G43501' => 'sas', 'TAR625G1137' => 'tar', 'Thecc.03G222100' => 'tca', 'TPR.G12691' => 'tpr', 'TWI34G0727' => 'twi', 'TWI36G0117' => 'twi', 'VMungo1309G0868' => 'vmu' ) $gf_id = 'HOM05D001729' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001729' ) $data_identifier = 'HOM05D001729' $data_type = 'gf_id' $species_gene_counts = array( 'amhyb' => (int) 1, 'cqu' => (int) 9, 'can' => (int) 1, 'cansat' => (int) 1, 'car' => (int) 1, 'col' => (int) 5, 'dca' => (int) 1, 'din' => (int) 2, 'dzi' => (int) 3, 'fan' => (int) 140, 'fve' => (int) 62, 'gma' => (int) 1, 'ghi' => (int) 2, 'gra' => (int) 1, 'han' => (int) 1, 'sun' => (int) 1, 'lonja' => (int) 6, 'lja' => (int) 1, 'lsa' => (int) 4, 'mes' => (int) 1, 'mdo' => (int) 14, 'mtr' => (int) 1, 'egut' => (int) 1, 'nta' => (int) 4, 'oeu' => (int) 1, 'stu' => (int) 2, 'pvu' => (int) 1, 'ptr' => (int) 4, 'ppe' => (int) 19, 'psa' => (int) 1, 'pso' => (int) 4, 'qlo' => (int) 36, 'rch' => (int) 23, 'rsi' => (int) 4, 'sbr' => (int) 4, 'sci' => (int) 2, 'sas' => (int) 4, 'tar' => (int) 1, 'tca' => (int) 1, 'tpr' => (int) 1, 'twi' => (int) 2, 'vmu' => (int) 1 ) $gf_gene_species = 'vmu' $gf_gene_id = 'VMungo1309G0868' $species_info = array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ) $local_species = 'tca' $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' => 'HOM05D001729', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '375', 'num_species' => '42' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'Ah.07g204710' => 'amhyb', 'AUR62006001' => 'cqu', 'AUR62006002' => 'cqu', 'AUR62006003' => 'cqu', 'AUR62015641' => 'cqu', 'AUR62027174' => 'cqu', 'AUR62035623' => 'cqu', 'AUR62035624' => 'cqu', 'AUR62035625' => 'cqu', 'AUR62035626' => 'cqu', 'CAN.G1110.53' => 'can', 'CANSAT80G0415' => 'cansat', 'Ca_21364_v3' => 'car', 'COL.COLO4_30693' => 'col', 'COL.COLO4_30694' => 'col', 'COL.COLO4_30695' => 'col', 'COL.COLO4_30696' => 'col', 'COL.COLO4_34020' => 'col', 'DCAR_004585' => 'dca', 'Dinv04029' => 'din', 'Dinv34857' => 'din', 'Duzib147G0011' => 'dzi', 'Duzib170G0599' => 'dzi', 'Duzib192G1051' => 'dzi', 'FAN01G0708' => 'fan', 'FAN01G0742' => 'fan', 'FAN02G0048' => 'fan', 'FAN02G0583' => 'fan', 'FAN02G0688' => 'fan', 'FAN02G1588' => 'fan', 'FAN02G2194' => 'fan', 'FAN02G2750' => 'fan', 'FAN02G3094' => 'fan', 'FAN02G3887' => 'fan', 'FAN02G3911' => 'fan', 'FAN02G3994' => 'fan', 'FAN02G4432' => 'fan', 'FAN02G4556' => 'fan', 'FAN03G1977' => 'fan', 'FAN03G2781' => 'fan', 'FAN03G2850' => 'fan', 'FAN03G3155' => 'fan', 'FAN04G2487' => 'fan', 'FAN05G0208' => 'fan', 'FAN05G0656' => 'fan', 'FAN05G0696' => 'fan', 'FAN05G0810' => 'fan', 'FAN05G1447' => 'fan', 'FAN05G2640' => 'fan', 'FAN05G2911' => 'fan', 'FAN05G3901' => 'fan', 'FAN05G4859' => 'fan', 'FAN05G4861' => 'fan', 'FAN05G4988' => 'fan', 'FAN05G5187' => 'fan', 'FAN05G5452' => 'fan', 'FAN05G5500' => 'fan', 'FAN05G5688' => 'fan', 'FAN06G0177' => 'fan', 'FAN06G0675' => 'fan', 'FAN06G1290' => 'fan', 'FAN06G2191' => 'fan', 'FAN06G2405' => 'fan', 'FAN06G3231' => 'fan', 'FAN06G3932' => 'fan', 'FAN07G0163' => 'fan', 'FAN07G0471' => 'fan', 'FAN07G1354' => 'fan', 'FAN08G0338' => 'fan', 'FAN08G1373' => 'fan', 'FAN08G2539' => 'fan', 'FAN08G2728' => 'fan', 'FAN09G0608' => 'fan', 'FAN09G1136' => 'fan', 'FAN09G1958' => 'fan', 'FAN09G2508' => 'fan', 'FAN09G2597' => 'fan', 'FAN09G2658' => 'fan', 'FAN09G2757' => 'fan', 'FAN09G2983' => 'fan', 'FAN09G3130' => 'fan', 'FAN09G3565' => 'fan', 'FAN09G3613' => 'fan', 'FAN09G4011' => 'fan', 'FAN09G4239' => 'fan', 'FAN09G4277' => 'fan', 'FAN09G4720' => 'fan', 'FAN11G0139' => 'fan', 'FAN11G1727' => 'fan', 'FAN11G2672' => 'fan', 'FAN11G2795' => 'fan', 'FAN11G3238' => 'fan', 'FAN11G3734' => 'fan', 'FAN12G0631' => 'fan', 'FAN12G2239' => 'fan', 'FAN12G2308' => 'fan', 'FAN12G2569' => 'fan', 'FAN12G2623' => 'fan', 'FAN13G3182' => 'fan', 'FAN14G0053' => 'fan', 'FAN14G0370' => 'fan', 'FAN14G0382' => 'fan', 'FAN14G0421' => 'fan', 'FAN14G0866' => 'fan', 'FAN14G1187' => 'fan', 'FAN14G1727' => 'fan', 'FAN14G1791' => 'fan', 'FAN14G2361' => 'fan', 'FAN14G2668' => 'fan', 'FAN14G2770' => 'fan', 'FAN14G2874' => 'fan', 'FAN14G3193' => 'fan', 'FAN14G3624' => 'fan', 'FAN14G3676' => 'fan', 'FAN14G3807' => 'fan', 'FAN14G4082' => 'fan', 'FAN14G4342' => 'fan', 'FAN14G4985' => 'fan', 'FAN14G5126' => 'fan', 'FAN14G5781' => 'fan', 'FAN14G5808' => 'fan', 'FAN14G5949' => 'fan', 'FAN15G0828' => 'fan', 'FAN15G1054' => 'fan', 'FAN15G2023' => 'fan', 'FAN15G2506' => 'fan', 'FAN16G0128' => 'fan', 'FAN16G0249' => 'fan', 'FAN16G0429' => 'fan', 'FAN16G1493' => 'fan', 'FAN16G2210' => 'fan', 'FAN16G2506' => 'fan', 'FAN18G1542' => 'fan', 'FAN18G4057' => 'fan', 'FAN19G0745' => 'fan', 'FAN19G1216' => 'fan', 'FAN19G1733' => 'fan', 'FAN20G0258' => 'fan', 'FAN20G1095' => 'fan', 'FAN20G1557' => 'fan', 'FAN21G0302' => 'fan', 'FAN21G0519' => 'fan', 'FAN21G0970' => 'fan', 'FAN21G1159' => 'fan', 'FAN21G1312' => 'fan', 'FAN21G1440' => 'fan', 'FAN21G1715' => 'fan', 'FAN23G1584' => 'fan', 'FAN24G0045' => 'fan', 'FAN24G0053' => 'fan', 'FAN24G1500' => 'fan', 'FAN24G1817' => 'fan', 'FAN24G2147' => 'fan', 'FAN24G2236' => 'fan', 'FAN24G2446' => 'fan', 'FAN24G2684' => 'fan', 'FAN25G0187' => 'fan', 'FAN25G0505' => 'fan', 'FAN25G0589' => 'fan', 'FAN25G3663' => 'fan', 'FAN26G1025' => 'fan', 'FAN26G2860' => 'fan', 'FAN27G1329' => 'fan', 'FAN27G3392' => 'fan', 'FvH4_1g02011' => 'fve', 'FvH4_1g06511' => 'fve', 'FvH4_2g19900' => 'fve', 'FvH4_2g19920' => 'fve', 'FvH4_2g24261' => 'fve', 'FvH4_2g24270' => 'fve', 'FvH4_2g24631' => 'fve', 'FvH4_2g30622' => 'fve', 'FvH4_3g12920' => 'fve', 'FvH4_3g30171' => 'fve', 'FvH4_3g35490' => 'fve', 'FvH4_3g43682' => 'fve', 'FvH4_3g43730' => 'fve', 'FvH4_3g43732' => 'fve', 'FvH4_3g43751' => 'fve', 'FvH4_3g43752' => 'fve', 'FvH4_3g43770' => 'fve', 'FvH4_3g44471' => 'fve', 'FvH4_3g44510' => 'fve', 'FvH4_3g44582' => 'fve', 'FvH4_4g16921' => 'fve', 'FvH4_4g17121' => 'fve', 'FvH4_4g17782' => 'fve', 'FvH4_4g17783' => 'fve', 'FvH4_4g18120' => 'fve', 'FvH4_4g31310' => 'fve', 'FvH4_4g35052' => 'fve', 'FvH4_5g30862' => 'fve', 'FvH4_6g01541' => 'fve', 'FvH4_6g02021' => 'fve', 'FvH4_6g02041' => 'fve', 'FvH4_6g02071' => 'fve', 'FvH4_6g02171' => 'fve', 'FvH4_6g03181' => 'fve', 'FvH4_6g03182' => 'fve', 'FvH4_6g03221' => 'fve', 'FvH4_6g03380' => 'fve', 'FvH4_6g05201' => 'fve', 'FvH4_6g05203' => 'fve', 'FvH4_6g20231' => 'fve', 'FvH4_6g31981' => 'fve', 'FvH4_6g32061' => 'fve', 'FvH4_6g37041' => 'fve', 'FvH4_6g37932' => 'fve', 'FvH4_6g38731' => 'fve', 'FvH4_6g39370' => 'fve', 'FvH4_6g39371' => 'fve', 'FvH4_6g40891' => 'fve', 'FvH4_6g40892' => 'fve', 'FvH4_6g43143' => 'fve', 'FvH4_6g45251' => 'fve', 'FvH4_6g45260' => 'fve', 'FvH4_6g45291' => 'fve', 'FvH4_6g45890' => 'fve', 'FvH4_6g46240' => 'fve', 'FvH4_6g46241' => 'fve', 'FvH4_6g46242' => 'fve', 'FvH4_6g46260' => 'fve', 'FvH4_6g46280' => 'fve', 'FvH4_6g46380' => 'fve', 'FvH4_7g12841' => 'fve', 'FvH4_7g31431' => 'fve', 'Glyma.09G075900' => 'gma', 'Gohir.A09G096401' => 'ghi', 'Gohir.D09G096101' => 'ghi', 'Gorai.006G112800' => 'gra', 'HanXRQChr04g0121411' => 'han', 'Hund15878' => 'sun', 'Lj2A1107G68' => 'lonja', 'Lj2A630G63' => 'lonja', 'Lj2A946T25' => 'lonja', 'Lj2C714T1' => 'lonja', 'Lj2C966T3' => 'lonja', 'Lj2C966T4' => 'lonja', 'Lj4g0002979' => 'lja', 'Lsat_1_v5_gn_5_30901' => 'lsa', 'Lsat_1_v5_gn_5_31100' => 'lsa', 'Lsat_1_v5_gn_5_38600' => 'lsa', 'Lsat_1_v5_gn_6_92061' => 'lsa', 'Manes.05G071301' => 'mes', 'MD02G1008700' => 'mdo', 'MD02G1008900' => 'mdo', 'MD03G1256400' => 'mdo', 'MD04G1180900' => 'mdo', 'MD04G1181000' => 'mdo', 'MD04G1181200' => 'mdo', 'MD05G1244200' => 'mdo', 'MD05G1324200' => 'mdo', 'MD09G1201600' => 'mdo', 'MD10G1000600' => 'mdo', 'MD14G1026900' => 'mdo', 'MD14G1187900' => 'mdo', 'MD15G1017800' => 'mdo', 'MD15G1018100' => 'mdo', 'Medtr4g124160' => 'mtr', 'Migut.L01260' => 'egut', 'Nitab4.5_0000008g0440' => 'nta', 'Nitab4.5_0000207g0170' => 'nta', 'Nitab4.5_0007671g0030' => 'nta', 'Nitab4.5_0010853g0020' => 'nta', 'Oeu057656.1' => 'oeu', 'PGSC0003DMG400005638' => 'stu', 'PGSC0003DMG400005639' => 'stu', 'Phvul.009G222800' => 'pvu', 'Potri.009G132400' => 'ptr', 'Potri.009G163001' => 'ptr', 'Potri.011G000700' => 'ptr', 'Potri.011G004800' => 'ptr', 'Prupe.1G509300' => 'ppe', 'Prupe.1G509700' => 'ppe', 'Prupe.1G510400' => 'ppe', 'Prupe.1G510700' => 'ppe', 'Prupe.1G512600' => 'ppe', 'Prupe.2G073200' => 'ppe', 'Prupe.3G059500' => 'ppe', 'Prupe.3G059600' => 'ppe', 'Prupe.3G246100' => 'ppe', 'Prupe.3G265100' => 'ppe', 'Prupe.4G034700' => 'ppe', 'Prupe.4G052100' => 'ppe', 'Prupe.4G053600' => 'ppe', 'Prupe.5G068800' => 'ppe', 'Prupe.5G070600' => 'ppe', 'Prupe.6G075400' => 'ppe', 'Prupe.6G075500' => 'ppe', 'Prupe.6G076400' => 'ppe', 'Prupe.8G110700' => 'ppe', 'Psat4g020960' => 'psa', 'PSO135G0788' => 'pso', 'PSO210G6463' => 'pso', 'PSO384G0370' => 'pso', 'PSO386G0056' => 'pso', 'QL01p006048' => 'qlo', 'QL02p054283' => 'qlo', 'QL05p008000' => 'qlo', 'QL05p008212' => 'qlo', 'QL05p008950' => 'qlo', 'QL05p009042' => 'qlo', 'QL05p009518' => 'qlo', 'QL05p012589' => 'qlo', 'QL05p012608' => 'qlo', 'QL05p012650' => 'qlo', 'QL05p012667' => 'qlo', 'QL05p014501' => 'qlo', 'QL05p052800' => 'qlo', 'QL05p065010' => 'qlo', 'QL05p074156' => 'qlo', 'QL05p074160' => 'qlo', 'QL05p074174' => 'qlo', 'QL05p074178' => 'qlo', 'QL05p074214' => 'qlo', 'QL06p001050' => 'qlo', 'QL06p001056' => 'qlo', 'QL06p006093' => 'qlo', 'QL06p006111' => 'qlo', 'QL07p019784' => 'qlo', 'QL07p019801' => 'qlo', 'QL07p036110' => 'qlo', 'QL07p036134' => 'qlo', 'QL07p036147' => 'qlo', 'QL07p036156' => 'qlo', 'QL07p036300' => 'qlo', 'QL07p036320' => 'qlo', 'QL08p014547' => 'qlo', 'QL08p014551' => 'qlo', 'QL08p043319' => 'qlo', 'QL08p043324' => 'qlo', 'QL11p009094' => 'qlo', 'RcHm_v2.0_Chr1g0380481' => 'rch', 'RcHm_v2.0_Chr2g0089331' => 'rch', 'RcHm_v2.0_Chr2g0123691' => 'rch', 'RcHm_v2.0_Chr2g0151111' => 'rch', 'RcHm_v2.0_Chr2g0163011' => 'rch', 'RcHm_v2.0_Chr2g0163051' => 'rch', 'RcHm_v2.0_Chr2g0164671' => 'rch', 'RcHm_v2.0_Chr2g0164681' => 'rch', 'RcHm_v2.0_Chr2g0164721' => 'rch', 'RcHm_v2.0_Chr3g0449911' => 'rch', 'RcHm_v2.0_Chr3g0450211' => 'rch', 'RcHm_v2.0_Chr3g0457271' => 'rch', 'RcHm_v2.0_Chr5g0018111' => 'rch', 'RcHm_v2.0_Chr5g0021011' => 'rch', 'RcHm_v2.0_Chr5g0081171' => 'rch', 'RcHm_v2.0_Chr5g0081211' => 'rch', 'RcHm_v2.0_Chr6g0275871' => 'rch', 'RcHm_v2.0_Chr6g0276071' => 'rch', 'RcHm_v2.0_Chr6g0285591' => 'rch', 'RcHm_v2.0_Chr6g0291931' => 'rch', 'RcHm_v2.0_Chr6g0292091' => 'rch', 'RcHm_v2.0_Chr6g0292271' => 'rch', 'RcHm_v2.0_Chr7g0221261' => 'rch', 'Rhsim08G0219900' => 'rsi', 'Rhsim08G0220200' => 'rsi', 'Rhsim08G0237800' => 'rsi', 'Rhsim08G0238800' => 'rsi', 'Sabra09G0102700' => 'sbr', 'Sabra09G0127200' => 'sbr', 'Sabra11G0003700' => 'sbr', 'Sabra15G0014700' => 'sbr', 'Sc19g0000590' => 'sci', 'Sc19g0001870' => 'sci', 'SGA_v2.0_scaffold1G00346' => 'sas', 'SGA_v2.0_scaffold1G00575' => 'sas', 'SGA_v2.0_scaffold1G00761' => 'sas', 'SGA_v2.0_scaffold232G43501' => 'sas', 'TAR625G1137' => 'tar', 'Thecc.03G222100' => 'tca', 'TPR.G12691' => 'tpr', 'TWI34G0727' => 'twi', 'TWI36G0117' => 'twi', 'VMungo1309G0868' => 'vmu' ), 'gf_id' => 'HOM05D001729', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001729' ), 'data_identifier' => 'HOM05D001729', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001729', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '375', 'num_species' => '42' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'Ah.07g204710' => 'amhyb', 'AUR62006001' => 'cqu', 'AUR62006002' => 'cqu', 'AUR62006003' => 'cqu', 'AUR62015641' => 'cqu', 'AUR62027174' => 'cqu', 'AUR62035623' => 'cqu', 'AUR62035624' => 'cqu', 'AUR62035625' => 'cqu', 'AUR62035626' => 'cqu', 'CAN.G1110.53' => 'can', 'CANSAT80G0415' => 'cansat', 'Ca_21364_v3' => 'car', 'COL.COLO4_30693' => 'col', 'COL.COLO4_30694' => 'col', 'COL.COLO4_30695' => 'col', 'COL.COLO4_30696' => 'col', 'COL.COLO4_34020' => 'col', 'DCAR_004585' => 'dca', 'Dinv04029' => 'din', 'Dinv34857' => 'din', 'Duzib147G0011' => 'dzi', 'Duzib170G0599' => 'dzi', 'Duzib192G1051' => 'dzi', 'FAN01G0708' => 'fan', 'FAN01G0742' => 'fan', 'FAN02G0048' => 'fan', 'FAN02G0583' => 'fan', 'FAN02G0688' => 'fan', 'FAN02G1588' => 'fan', 'FAN02G2194' => 'fan', 'FAN02G2750' => 'fan', 'FAN02G3094' => 'fan', 'FAN02G3887' => 'fan', 'FAN02G3911' => 'fan', 'FAN02G3994' => 'fan', 'FAN02G4432' => 'fan', 'FAN02G4556' => 'fan', 'FAN03G1977' => 'fan', 'FAN03G2781' => 'fan', 'FAN03G2850' => 'fan', 'FAN03G3155' => 'fan', 'FAN04G2487' => 'fan', 'FAN05G0208' => 'fan', 'FAN05G0656' => 'fan', 'FAN05G0696' => 'fan', 'FAN05G0810' => 'fan', 'FAN05G1447' => 'fan', 'FAN05G2640' => 'fan', 'FAN05G2911' => 'fan', 'FAN05G3901' => 'fan', 'FAN05G4859' => 'fan', 'FAN05G4861' => 'fan', 'FAN05G4988' => 'fan', 'FAN05G5187' => 'fan', 'FAN05G5452' => 'fan', 'FAN05G5500' => 'fan', 'FAN05G5688' => 'fan', 'FAN06G0177' => 'fan', 'FAN06G0675' => 'fan', 'FAN06G1290' => 'fan', 'FAN06G2191' => 'fan', 'FAN06G2405' => 'fan', 'FAN06G3231' => 'fan', 'FAN06G3932' => 'fan', 'FAN07G0163' => 'fan', 'FAN07G0471' => 'fan', 'FAN07G1354' => 'fan', 'FAN08G0338' => 'fan', 'FAN08G1373' => 'fan', 'FAN08G2539' => 'fan', 'FAN08G2728' => 'fan', 'FAN09G0608' => 'fan', 'FAN09G1136' => 'fan', 'FAN09G1958' => 'fan', 'FAN09G2508' => 'fan', 'FAN09G2597' => 'fan', 'FAN09G2658' => 'fan', 'FAN09G2757' => 'fan', 'FAN09G2983' => 'fan', 'FAN09G3130' => 'fan', 'FAN09G3565' => 'fan', 'FAN09G3613' => 'fan', 'FAN09G4011' => 'fan', 'FAN09G4239' => 'fan', 'FAN09G4277' => 'fan', 'FAN09G4720' => 'fan', 'FAN11G0139' => 'fan', 'FAN11G1727' => 'fan', 'FAN11G2672' => 'fan', 'FAN11G2795' => 'fan', 'FAN11G3238' => 'fan', 'FAN11G3734' => 'fan', 'FAN12G0631' => 'fan', 'FAN12G2239' => 'fan', 'FAN12G2308' => 'fan', 'FAN12G2569' => 'fan', 'FAN12G2623' => 'fan', 'FAN13G3182' => 'fan', 'FAN14G0053' => 'fan', 'FAN14G0370' => 'fan', 'FAN14G0382' => 'fan', 'FAN14G0421' => 'fan', 'FAN14G0866' => 'fan', 'FAN14G1187' => 'fan', 'FAN14G1727' => 'fan', 'FAN14G1791' => 'fan', 'FAN14G2361' => 'fan', 'FAN14G2668' => 'fan', 'FAN14G2770' => 'fan', 'FAN14G2874' => 'fan', 'FAN14G3193' => 'fan', 'FAN14G3624' => 'fan', 'FAN14G3676' => 'fan', 'FAN14G3807' => 'fan', 'FAN14G4082' => 'fan', 'FAN14G4342' => 'fan', 'FAN14G4985' => 'fan', 'FAN14G5126' => 'fan', 'FAN14G5781' => 'fan', 'FAN14G5808' => 'fan', 'FAN14G5949' => 'fan', 'FAN15G0828' => 'fan', 'FAN15G1054' => 'fan', 'FAN15G2023' => 'fan', 'FAN15G2506' => 'fan', 'FAN16G0128' => 'fan', 'FAN16G0249' => 'fan', 'FAN16G0429' => 'fan', 'FAN16G1493' => 'fan', 'FAN16G2210' => 'fan', 'FAN16G2506' => 'fan', 'FAN18G1542' => 'fan', 'FAN18G4057' => 'fan', 'FAN19G0745' => 'fan', 'FAN19G1216' => 'fan', 'FAN19G1733' => 'fan', 'FAN20G0258' => 'fan', 'FAN20G1095' => 'fan', 'FAN20G1557' => 'fan', 'FAN21G0302' => 'fan', 'FAN21G0519' => 'fan', 'FAN21G0970' => 'fan', 'FAN21G1159' => 'fan', 'FAN21G1312' => 'fan', 'FAN21G1440' => 'fan', 'FAN21G1715' => 'fan', 'FAN23G1584' => 'fan', 'FAN24G0045' => 'fan', 'FAN24G0053' => 'fan', 'FAN24G1500' => 'fan', 'FAN24G1817' => 'fan', 'FAN24G2147' => 'fan', 'FAN24G2236' => 'fan', 'FAN24G2446' => 'fan', 'FAN24G2684' => 'fan', 'FAN25G0187' => 'fan', 'FAN25G0505' => 'fan', 'FAN25G0589' => 'fan', 'FAN25G3663' => 'fan', 'FAN26G1025' => 'fan', 'FAN26G2860' => 'fan', 'FAN27G1329' => 'fan', 'FAN27G3392' => 'fan', 'FvH4_1g02011' => 'fve', 'FvH4_1g06511' => 'fve', 'FvH4_2g19900' => 'fve', 'FvH4_2g19920' => 'fve', 'FvH4_2g24261' => 'fve', 'FvH4_2g24270' => 'fve', 'FvH4_2g24631' => 'fve', 'FvH4_2g30622' => 'fve', 'FvH4_3g12920' => 'fve', 'FvH4_3g30171' => 'fve', 'FvH4_3g35490' => 'fve', 'FvH4_3g43682' => 'fve', 'FvH4_3g43730' => 'fve', 'FvH4_3g43732' => 'fve', 'FvH4_3g43751' => 'fve', 'FvH4_3g43752' => 'fve', 'FvH4_3g43770' => 'fve', 'FvH4_3g44471' => 'fve', 'FvH4_3g44510' => 'fve', 'FvH4_3g44582' => 'fve', 'FvH4_4g16921' => 'fve', 'FvH4_4g17121' => 'fve', 'FvH4_4g17782' => 'fve', 'FvH4_4g17783' => 'fve', 'FvH4_4g18120' => 'fve', 'FvH4_4g31310' => 'fve', 'FvH4_4g35052' => 'fve', 'FvH4_5g30862' => 'fve', 'FvH4_6g01541' => 'fve', 'FvH4_6g02021' => 'fve', 'FvH4_6g02041' => 'fve', 'FvH4_6g02071' => 'fve', 'FvH4_6g02171' => 'fve', 'FvH4_6g03181' => 'fve', 'FvH4_6g03182' => 'fve', 'FvH4_6g03221' => 'fve', 'FvH4_6g03380' => 'fve', 'FvH4_6g05201' => 'fve', 'FvH4_6g05203' => 'fve', 'FvH4_6g20231' => 'fve', 'FvH4_6g31981' => 'fve', 'FvH4_6g32061' => 'fve', 'FvH4_6g37041' => 'fve', 'FvH4_6g37932' => 'fve', 'FvH4_6g38731' => 'fve', 'FvH4_6g39370' => 'fve', 'FvH4_6g39371' => 'fve', 'FvH4_6g40891' => 'fve', 'FvH4_6g40892' => 'fve', 'FvH4_6g43143' => 'fve', 'FvH4_6g45251' => 'fve', 'FvH4_6g45260' => 'fve', 'FvH4_6g45291' => 'fve', 'FvH4_6g45890' => 'fve', 'FvH4_6g46240' => 'fve', 'FvH4_6g46241' => 'fve', 'FvH4_6g46242' => 'fve', 'FvH4_6g46260' => 'fve', 'FvH4_6g46280' => 'fve', 'FvH4_6g46380' => 'fve', 'FvH4_7g12841' => 'fve', 'FvH4_7g31431' => 'fve', 'Glyma.09G075900' => 'gma', 'Gohir.A09G096401' => 'ghi', 'Gohir.D09G096101' => 'ghi', 'Gorai.006G112800' => 'gra', 'HanXRQChr04g0121411' => 'han', 'Hund15878' => 'sun', 'Lj2A1107G68' => 'lonja', 'Lj2A630G63' => 'lonja', 'Lj2A946T25' => 'lonja', 'Lj2C714T1' => 'lonja', 'Lj2C966T3' => 'lonja', 'Lj2C966T4' => 'lonja', 'Lj4g0002979' => 'lja', 'Lsat_1_v5_gn_5_30901' => 'lsa', 'Lsat_1_v5_gn_5_31100' => 'lsa', 'Lsat_1_v5_gn_5_38600' => 'lsa', 'Lsat_1_v5_gn_6_92061' => 'lsa', 'Manes.05G071301' => 'mes', 'MD02G1008700' => 'mdo', 'MD02G1008900' => 'mdo', 'MD03G1256400' => 'mdo', 'MD04G1180900' => 'mdo', 'MD04G1181000' => 'mdo', 'MD04G1181200' => 'mdo', 'MD05G1244200' => 'mdo', 'MD05G1324200' => 'mdo', 'MD09G1201600' => 'mdo', 'MD10G1000600' => 'mdo', 'MD14G1026900' => 'mdo', 'MD14G1187900' => 'mdo', 'MD15G1017800' => 'mdo', 'MD15G1018100' => 'mdo', 'Medtr4g124160' => 'mtr', 'Migut.L01260' => 'egut', 'Nitab4.5_0000008g0440' => 'nta', 'Nitab4.5_0000207g0170' => 'nta', 'Nitab4.5_0007671g0030' => 'nta', 'Nitab4.5_0010853g0020' => 'nta', 'Oeu057656.1' => 'oeu', 'PGSC0003DMG400005638' => 'stu', 'PGSC0003DMG400005639' => 'stu', 'Phvul.009G222800' => 'pvu', 'Potri.009G132400' => 'ptr', 'Potri.009G163001' => 'ptr', 'Potri.011G000700' => 'ptr', 'Potri.011G004800' => 'ptr', 'Prupe.1G509300' => 'ppe', 'Prupe.1G509700' => 'ppe', 'Prupe.1G510400' => 'ppe', 'Prupe.1G510700' => 'ppe', 'Prupe.1G512600' => 'ppe', 'Prupe.2G073200' => 'ppe', 'Prupe.3G059500' => 'ppe', 'Prupe.3G059600' => 'ppe', 'Prupe.3G246100' => 'ppe', 'Prupe.3G265100' => 'ppe', 'Prupe.4G034700' => 'ppe', 'Prupe.4G052100' => 'ppe', 'Prupe.4G053600' => 'ppe', 'Prupe.5G068800' => 'ppe', 'Prupe.5G070600' => 'ppe', 'Prupe.6G075400' => 'ppe', 'Prupe.6G075500' => 'ppe', 'Prupe.6G076400' => 'ppe', 'Prupe.8G110700' => 'ppe', 'Psat4g020960' => 'psa', 'PSO135G0788' => 'pso', 'PSO210G6463' => 'pso', 'PSO384G0370' => 'pso', 'PSO386G0056' => 'pso', 'QL01p006048' => 'qlo', 'QL02p054283' => 'qlo', 'QL05p008000' => 'qlo', 'QL05p008212' => 'qlo', 'QL05p008950' => 'qlo', 'QL05p009042' => 'qlo', 'QL05p009518' => 'qlo', 'QL05p012589' => 'qlo', 'QL05p012608' => 'qlo', 'QL05p012650' => 'qlo', 'QL05p012667' => 'qlo', 'QL05p014501' => 'qlo', 'QL05p052800' => 'qlo', 'QL05p065010' => 'qlo', 'QL05p074156' => 'qlo', 'QL05p074160' => 'qlo', 'QL05p074174' => 'qlo', 'QL05p074178' => 'qlo', 'QL05p074214' => 'qlo', 'QL06p001050' => 'qlo', 'QL06p001056' => 'qlo', 'QL06p006093' => 'qlo', 'QL06p006111' => 'qlo', 'QL07p019784' => 'qlo', 'QL07p019801' => 'qlo', 'QL07p036110' => 'qlo', 'QL07p036134' => 'qlo', 'QL07p036147' => 'qlo', 'QL07p036156' => 'qlo', 'QL07p036300' => 'qlo', 'QL07p036320' => 'qlo', 'QL08p014547' => 'qlo', 'QL08p014551' => 'qlo', 'QL08p043319' => 'qlo', 'QL08p043324' => 'qlo', 'QL11p009094' => 'qlo', 'RcHm_v2.0_Chr1g0380481' => 'rch', 'RcHm_v2.0_Chr2g0089331' => 'rch', 'RcHm_v2.0_Chr2g0123691' => 'rch', 'RcHm_v2.0_Chr2g0151111' => 'rch', 'RcHm_v2.0_Chr2g0163011' => 'rch', 'RcHm_v2.0_Chr2g0163051' => 'rch', 'RcHm_v2.0_Chr2g0164671' => 'rch', 'RcHm_v2.0_Chr2g0164681' => 'rch', 'RcHm_v2.0_Chr2g0164721' => 'rch', 'RcHm_v2.0_Chr3g0449911' => 'rch', 'RcHm_v2.0_Chr3g0450211' => 'rch', 'RcHm_v2.0_Chr3g0457271' => 'rch', 'RcHm_v2.0_Chr5g0018111' => 'rch', 'RcHm_v2.0_Chr5g0021011' => 'rch', 'RcHm_v2.0_Chr5g0081171' => 'rch', 'RcHm_v2.0_Chr5g0081211' => 'rch', 'RcHm_v2.0_Chr6g0275871' => 'rch', 'RcHm_v2.0_Chr6g0276071' => 'rch', 'RcHm_v2.0_Chr6g0285591' => 'rch', 'RcHm_v2.0_Chr6g0291931' => 'rch', 'RcHm_v2.0_Chr6g0292091' => 'rch', 'RcHm_v2.0_Chr6g0292271' => 'rch', 'RcHm_v2.0_Chr7g0221261' => 'rch', 'Rhsim08G0219900' => 'rsi', 'Rhsim08G0220200' => 'rsi', 'Rhsim08G0237800' => 'rsi', 'Rhsim08G0238800' => 'rsi', 'Sabra09G0102700' => 'sbr', 'Sabra09G0127200' => 'sbr', 'Sabra11G0003700' => 'sbr', 'Sabra15G0014700' => 'sbr', 'Sc19g0000590' => 'sci', 'Sc19g0001870' => 'sci', 'SGA_v2.0_scaffold1G00346' => 'sas', 'SGA_v2.0_scaffold1G00575' => 'sas', 'SGA_v2.0_scaffold1G00761' => 'sas', 'SGA_v2.0_scaffold232G43501' => 'sas', 'TAR625G1137' => 'tar', 'Thecc.03G222100' => 'tca', 'TPR.G12691' => 'tpr', 'TWI34G0727' => 'twi', 'TWI36G0117' => 'twi', 'VMungo1309G0868' => 'vmu' ) $gf_id = 'HOM05D001729' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001729' ) $data_identifier = 'HOM05D001729' $data_type = 'gf_id' $species_gene_counts = array( 'amhyb' => (int) 1, 'cqu' => (int) 9, 'can' => (int) 1, 'cansat' => (int) 1, 'car' => (int) 1, 'col' => (int) 5, 'dca' => (int) 1, 'din' => (int) 2, 'dzi' => (int) 3, 'fan' => (int) 140, 'fve' => (int) 62, 'gma' => (int) 1, 'ghi' => (int) 2, 'gra' => (int) 1, 'han' => (int) 1, 'sun' => (int) 1, 'lonja' => (int) 6, 'lja' => (int) 1, 'lsa' => (int) 4, 'mes' => (int) 1, 'mdo' => (int) 14, 'mtr' => (int) 1, 'egut' => (int) 1, 'nta' => (int) 4, 'oeu' => (int) 1, 'stu' => (int) 2, 'pvu' => (int) 1, 'ptr' => (int) 4, 'ppe' => (int) 19, 'psa' => (int) 1, 'pso' => (int) 4, 'qlo' => (int) 36, 'rch' => (int) 23, 'rsi' => (int) 4, 'sbr' => (int) 4, 'sci' => (int) 2, 'sas' => (int) 4, 'tar' => (int) 1, 'tca' => (int) 1, 'tpr' => (int) 1, 'twi' => (int) 2, 'vmu' => (int) 1 ) $gf_gene_species = 'vmu' $gf_gene_id = 'VMungo1309G0868' $species_info = array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ) $local_species = 'tca' $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' => 'HOM05D001729', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '375', 'num_species' => '42' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'Ah.07g204710' => 'amhyb', 'AUR62006001' => 'cqu', 'AUR62006002' => 'cqu', 'AUR62006003' => 'cqu', 'AUR62015641' => 'cqu', 'AUR62027174' => 'cqu', 'AUR62035623' => 'cqu', 'AUR62035624' => 'cqu', 'AUR62035625' => 'cqu', 'AUR62035626' => 'cqu', 'CAN.G1110.53' => 'can', 'CANSAT80G0415' => 'cansat', 'Ca_21364_v3' => 'car', 'COL.COLO4_30693' => 'col', 'COL.COLO4_30694' => 'col', 'COL.COLO4_30695' => 'col', 'COL.COLO4_30696' => 'col', 'COL.COLO4_34020' => 'col', 'DCAR_004585' => 'dca', 'Dinv04029' => 'din', 'Dinv34857' => 'din', 'Duzib147G0011' => 'dzi', 'Duzib170G0599' => 'dzi', 'Duzib192G1051' => 'dzi', 'FAN01G0708' => 'fan', 'FAN01G0742' => 'fan', 'FAN02G0048' => 'fan', 'FAN02G0583' => 'fan', 'FAN02G0688' => 'fan', 'FAN02G1588' => 'fan', 'FAN02G2194' => 'fan', 'FAN02G2750' => 'fan', 'FAN02G3094' => 'fan', 'FAN02G3887' => 'fan', 'FAN02G3911' => 'fan', 'FAN02G3994' => 'fan', 'FAN02G4432' => 'fan', 'FAN02G4556' => 'fan', 'FAN03G1977' => 'fan', 'FAN03G2781' => 'fan', 'FAN03G2850' => 'fan', 'FAN03G3155' => 'fan', 'FAN04G2487' => 'fan', 'FAN05G0208' => 'fan', 'FAN05G0656' => 'fan', 'FAN05G0696' => 'fan', 'FAN05G0810' => 'fan', 'FAN05G1447' => 'fan', 'FAN05G2640' => 'fan', 'FAN05G2911' => 'fan', 'FAN05G3901' => 'fan', 'FAN05G4859' => 'fan', 'FAN05G4861' => 'fan', 'FAN05G4988' => 'fan', 'FAN05G5187' => 'fan', 'FAN05G5452' => 'fan', 'FAN05G5500' => 'fan', 'FAN05G5688' => 'fan', 'FAN06G0177' => 'fan', 'FAN06G0675' => 'fan', 'FAN06G1290' => 'fan', 'FAN06G2191' => 'fan', 'FAN06G2405' => 'fan', 'FAN06G3231' => 'fan', 'FAN06G3932' => 'fan', 'FAN07G0163' => 'fan', 'FAN07G0471' => 'fan', 'FAN07G1354' => 'fan', 'FAN08G0338' => 'fan', 'FAN08G1373' => 'fan', 'FAN08G2539' => 'fan', 'FAN08G2728' => 'fan', 'FAN09G0608' => 'fan', 'FAN09G1136' => 'fan', 'FAN09G1958' => 'fan', 'FAN09G2508' => 'fan', 'FAN09G2597' => 'fan', 'FAN09G2658' => 'fan', 'FAN09G2757' => 'fan', 'FAN09G2983' => 'fan', 'FAN09G3130' => 'fan', 'FAN09G3565' => 'fan', 'FAN09G3613' => 'fan', 'FAN09G4011' => 'fan', 'FAN09G4239' => 'fan', 'FAN09G4277' => 'fan', 'FAN09G4720' => 'fan', 'FAN11G0139' => 'fan', 'FAN11G1727' => 'fan', 'FAN11G2672' => 'fan', 'FAN11G2795' => 'fan', 'FAN11G3238' => 'fan', 'FAN11G3734' => 'fan', 'FAN12G0631' => 'fan', 'FAN12G2239' => 'fan', 'FAN12G2308' => 'fan', 'FAN12G2569' => 'fan', 'FAN12G2623' => 'fan', 'FAN13G3182' => 'fan', 'FAN14G0053' => 'fan', 'FAN14G0370' => 'fan', 'FAN14G0382' => 'fan', 'FAN14G0421' => 'fan', 'FAN14G0866' => 'fan', 'FAN14G1187' => 'fan', 'FAN14G1727' => 'fan', 'FAN14G1791' => 'fan', 'FAN14G2361' => 'fan', 'FAN14G2668' => 'fan', 'FAN14G2770' => 'fan', 'FAN14G2874' => 'fan', 'FAN14G3193' => 'fan', 'FAN14G3624' => 'fan', 'FAN14G3676' => 'fan', 'FAN14G3807' => 'fan', 'FAN14G4082' => 'fan', 'FAN14G4342' => 'fan', 'FAN14G4985' => 'fan', 'FAN14G5126' => 'fan', 'FAN14G5781' => 'fan', 'FAN14G5808' => 'fan', 'FAN14G5949' => 'fan', 'FAN15G0828' => 'fan', 'FAN15G1054' => 'fan', 'FAN15G2023' => 'fan', 'FAN15G2506' => 'fan', 'FAN16G0128' => 'fan', 'FAN16G0249' => 'fan', 'FAN16G0429' => 'fan', 'FAN16G1493' => 'fan', 'FAN16G2210' => 'fan', 'FAN16G2506' => 'fan', 'FAN18G1542' => 'fan', 'FAN18G4057' => 'fan', 'FAN19G0745' => 'fan', 'FAN19G1216' => 'fan', 'FAN19G1733' => 'fan', 'FAN20G0258' => 'fan', 'FAN20G1095' => 'fan', 'FAN20G1557' => 'fan', 'FAN21G0302' => 'fan', 'FAN21G0519' => 'fan', 'FAN21G0970' => 'fan', 'FAN21G1159' => 'fan', 'FAN21G1312' => 'fan', 'FAN21G1440' => 'fan', 'FAN21G1715' => 'fan', 'FAN23G1584' => 'fan', 'FAN24G0045' => 'fan', 'FAN24G0053' => 'fan', 'FAN24G1500' => 'fan', 'FAN24G1817' => 'fan', 'FAN24G2147' => 'fan', 'FAN24G2236' => 'fan', 'FAN24G2446' => 'fan', 'FAN24G2684' => 'fan', 'FAN25G0187' => 'fan', 'FAN25G0505' => 'fan', 'FAN25G0589' => 'fan', 'FAN25G3663' => 'fan', 'FAN26G1025' => 'fan', 'FAN26G2860' => 'fan', 'FAN27G1329' => 'fan', 'FAN27G3392' => 'fan', 'FvH4_1g02011' => 'fve', 'FvH4_1g06511' => 'fve', 'FvH4_2g19900' => 'fve', 'FvH4_2g19920' => 'fve', 'FvH4_2g24261' => 'fve', 'FvH4_2g24270' => 'fve', 'FvH4_2g24631' => 'fve', 'FvH4_2g30622' => 'fve', 'FvH4_3g12920' => 'fve', 'FvH4_3g30171' => 'fve', 'FvH4_3g35490' => 'fve', 'FvH4_3g43682' => 'fve', 'FvH4_3g43730' => 'fve', 'FvH4_3g43732' => 'fve', 'FvH4_3g43751' => 'fve', 'FvH4_3g43752' => 'fve', 'FvH4_3g43770' => 'fve', 'FvH4_3g44471' => 'fve', 'FvH4_3g44510' => 'fve', 'FvH4_3g44582' => 'fve', 'FvH4_4g16921' => 'fve', 'FvH4_4g17121' => 'fve', 'FvH4_4g17782' => 'fve', 'FvH4_4g17783' => 'fve', 'FvH4_4g18120' => 'fve', 'FvH4_4g31310' => 'fve', 'FvH4_4g35052' => 'fve', 'FvH4_5g30862' => 'fve', 'FvH4_6g01541' => 'fve', 'FvH4_6g02021' => 'fve', 'FvH4_6g02041' => 'fve', 'FvH4_6g02071' => 'fve', 'FvH4_6g02171' => 'fve', 'FvH4_6g03181' => 'fve', 'FvH4_6g03182' => 'fve', 'FvH4_6g03221' => 'fve', 'FvH4_6g03380' => 'fve', 'FvH4_6g05201' => 'fve', 'FvH4_6g05203' => 'fve', 'FvH4_6g20231' => 'fve', 'FvH4_6g31981' => 'fve', 'FvH4_6g32061' => 'fve', 'FvH4_6g37041' => 'fve', 'FvH4_6g37932' => 'fve', 'FvH4_6g38731' => 'fve', 'FvH4_6g39370' => 'fve', 'FvH4_6g39371' => 'fve', 'FvH4_6g40891' => 'fve', 'FvH4_6g40892' => 'fve', 'FvH4_6g43143' => 'fve', 'FvH4_6g45251' => 'fve', 'FvH4_6g45260' => 'fve', 'FvH4_6g45291' => 'fve', 'FvH4_6g45890' => 'fve', 'FvH4_6g46240' => 'fve', 'FvH4_6g46241' => 'fve', 'FvH4_6g46242' => 'fve', 'FvH4_6g46260' => 'fve', 'FvH4_6g46280' => 'fve', 'FvH4_6g46380' => 'fve', 'FvH4_7g12841' => 'fve', 'FvH4_7g31431' => 'fve', 'Glyma.09G075900' => 'gma', 'Gohir.A09G096401' => 'ghi', 'Gohir.D09G096101' => 'ghi', 'Gorai.006G112800' => 'gra', 'HanXRQChr04g0121411' => 'han', 'Hund15878' => 'sun', 'Lj2A1107G68' => 'lonja', 'Lj2A630G63' => 'lonja', 'Lj2A946T25' => 'lonja', 'Lj2C714T1' => 'lonja', 'Lj2C966T3' => 'lonja', 'Lj2C966T4' => 'lonja', 'Lj4g0002979' => 'lja', 'Lsat_1_v5_gn_5_30901' => 'lsa', 'Lsat_1_v5_gn_5_31100' => 'lsa', 'Lsat_1_v5_gn_5_38600' => 'lsa', 'Lsat_1_v5_gn_6_92061' => 'lsa', 'Manes.05G071301' => 'mes', 'MD02G1008700' => 'mdo', 'MD02G1008900' => 'mdo', 'MD03G1256400' => 'mdo', 'MD04G1180900' => 'mdo', 'MD04G1181000' => 'mdo', 'MD04G1181200' => 'mdo', 'MD05G1244200' => 'mdo', 'MD05G1324200' => 'mdo', 'MD09G1201600' => 'mdo', 'MD10G1000600' => 'mdo', 'MD14G1026900' => 'mdo', 'MD14G1187900' => 'mdo', 'MD15G1017800' => 'mdo', 'MD15G1018100' => 'mdo', 'Medtr4g124160' => 'mtr', 'Migut.L01260' => 'egut', 'Nitab4.5_0000008g0440' => 'nta', 'Nitab4.5_0000207g0170' => 'nta', 'Nitab4.5_0007671g0030' => 'nta', 'Nitab4.5_0010853g0020' => 'nta', 'Oeu057656.1' => 'oeu', 'PGSC0003DMG400005638' => 'stu', 'PGSC0003DMG400005639' => 'stu', 'Phvul.009G222800' => 'pvu', 'Potri.009G132400' => 'ptr', 'Potri.009G163001' => 'ptr', 'Potri.011G000700' => 'ptr', 'Potri.011G004800' => 'ptr', 'Prupe.1G509300' => 'ppe', 'Prupe.1G509700' => 'ppe', 'Prupe.1G510400' => 'ppe', 'Prupe.1G510700' => 'ppe', 'Prupe.1G512600' => 'ppe', 'Prupe.2G073200' => 'ppe', 'Prupe.3G059500' => 'ppe', 'Prupe.3G059600' => 'ppe', 'Prupe.3G246100' => 'ppe', 'Prupe.3G265100' => 'ppe', 'Prupe.4G034700' => 'ppe', 'Prupe.4G052100' => 'ppe', 'Prupe.4G053600' => 'ppe', 'Prupe.5G068800' => 'ppe', 'Prupe.5G070600' => 'ppe', 'Prupe.6G075400' => 'ppe', 'Prupe.6G075500' => 'ppe', 'Prupe.6G076400' => 'ppe', 'Prupe.8G110700' => 'ppe', 'Psat4g020960' => 'psa', 'PSO135G0788' => 'pso', 'PSO210G6463' => 'pso', 'PSO384G0370' => 'pso', 'PSO386G0056' => 'pso', 'QL01p006048' => 'qlo', 'QL02p054283' => 'qlo', 'QL05p008000' => 'qlo', 'QL05p008212' => 'qlo', 'QL05p008950' => 'qlo', 'QL05p009042' => 'qlo', 'QL05p009518' => 'qlo', 'QL05p012589' => 'qlo', 'QL05p012608' => 'qlo', 'QL05p012650' => 'qlo', 'QL05p012667' => 'qlo', 'QL05p014501' => 'qlo', 'QL05p052800' => 'qlo', 'QL05p065010' => 'qlo', 'QL05p074156' => 'qlo', 'QL05p074160' => 'qlo', 'QL05p074174' => 'qlo', 'QL05p074178' => 'qlo', 'QL05p074214' => 'qlo', 'QL06p001050' => 'qlo', 'QL06p001056' => 'qlo', 'QL06p006093' => 'qlo', 'QL06p006111' => 'qlo', 'QL07p019784' => 'qlo', 'QL07p019801' => 'qlo', 'QL07p036110' => 'qlo', 'QL07p036134' => 'qlo', 'QL07p036147' => 'qlo', 'QL07p036156' => 'qlo', 'QL07p036300' => 'qlo', 'QL07p036320' => 'qlo', 'QL08p014547' => 'qlo', 'QL08p014551' => 'qlo', 'QL08p043319' => 'qlo', 'QL08p043324' => 'qlo', 'QL11p009094' => 'qlo', 'RcHm_v2.0_Chr1g0380481' => 'rch', 'RcHm_v2.0_Chr2g0089331' => 'rch', 'RcHm_v2.0_Chr2g0123691' => 'rch', 'RcHm_v2.0_Chr2g0151111' => 'rch', 'RcHm_v2.0_Chr2g0163011' => 'rch', 'RcHm_v2.0_Chr2g0163051' => 'rch', 'RcHm_v2.0_Chr2g0164671' => 'rch', 'RcHm_v2.0_Chr2g0164681' => 'rch', 'RcHm_v2.0_Chr2g0164721' => 'rch', 'RcHm_v2.0_Chr3g0449911' => 'rch', 'RcHm_v2.0_Chr3g0450211' => 'rch', 'RcHm_v2.0_Chr3g0457271' => 'rch', 'RcHm_v2.0_Chr5g0018111' => 'rch', 'RcHm_v2.0_Chr5g0021011' => 'rch', 'RcHm_v2.0_Chr5g0081171' => 'rch', 'RcHm_v2.0_Chr5g0081211' => 'rch', 'RcHm_v2.0_Chr6g0275871' => 'rch', 'RcHm_v2.0_Chr6g0276071' => 'rch', 'RcHm_v2.0_Chr6g0285591' => 'rch', 'RcHm_v2.0_Chr6g0291931' => 'rch', 'RcHm_v2.0_Chr6g0292091' => 'rch', 'RcHm_v2.0_Chr6g0292271' => 'rch', 'RcHm_v2.0_Chr7g0221261' => 'rch', 'Rhsim08G0219900' => 'rsi', 'Rhsim08G0220200' => 'rsi', 'Rhsim08G0237800' => 'rsi', 'Rhsim08G0238800' => 'rsi', 'Sabra09G0102700' => 'sbr', 'Sabra09G0127200' => 'sbr', 'Sabra11G0003700' => 'sbr', 'Sabra15G0014700' => 'sbr', 'Sc19g0000590' => 'sci', 'Sc19g0001870' => 'sci', 'SGA_v2.0_scaffold1G00346' => 'sas', 'SGA_v2.0_scaffold1G00575' => 'sas', 'SGA_v2.0_scaffold1G00761' => 'sas', 'SGA_v2.0_scaffold232G43501' => 'sas', 'TAR625G1137' => 'tar', 'Thecc.03G222100' => 'tca', 'TPR.G12691' => 'tpr', 'TWI34G0727' => 'twi', 'TWI36G0117' => 'twi', 'VMungo1309G0868' => 'vmu' ), 'gf_id' => 'HOM05D001729', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001729' ), 'data_identifier' => 'HOM05D001729', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001729', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '375', 'num_species' => '42' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'Ah.07g204710' => 'amhyb', 'AUR62006001' => 'cqu', 'AUR62006002' => 'cqu', 'AUR62006003' => 'cqu', 'AUR62015641' => 'cqu', 'AUR62027174' => 'cqu', 'AUR62035623' => 'cqu', 'AUR62035624' => 'cqu', 'AUR62035625' => 'cqu', 'AUR62035626' => 'cqu', 'CAN.G1110.53' => 'can', 'CANSAT80G0415' => 'cansat', 'Ca_21364_v3' => 'car', 'COL.COLO4_30693' => 'col', 'COL.COLO4_30694' => 'col', 'COL.COLO4_30695' => 'col', 'COL.COLO4_30696' => 'col', 'COL.COLO4_34020' => 'col', 'DCAR_004585' => 'dca', 'Dinv04029' => 'din', 'Dinv34857' => 'din', 'Duzib147G0011' => 'dzi', 'Duzib170G0599' => 'dzi', 'Duzib192G1051' => 'dzi', 'FAN01G0708' => 'fan', 'FAN01G0742' => 'fan', 'FAN02G0048' => 'fan', 'FAN02G0583' => 'fan', 'FAN02G0688' => 'fan', 'FAN02G1588' => 'fan', 'FAN02G2194' => 'fan', 'FAN02G2750' => 'fan', 'FAN02G3094' => 'fan', 'FAN02G3887' => 'fan', 'FAN02G3911' => 'fan', 'FAN02G3994' => 'fan', 'FAN02G4432' => 'fan', 'FAN02G4556' => 'fan', 'FAN03G1977' => 'fan', 'FAN03G2781' => 'fan', 'FAN03G2850' => 'fan', 'FAN03G3155' => 'fan', 'FAN04G2487' => 'fan', 'FAN05G0208' => 'fan', 'FAN05G0656' => 'fan', 'FAN05G0696' => 'fan', 'FAN05G0810' => 'fan', 'FAN05G1447' => 'fan', 'FAN05G2640' => 'fan', 'FAN05G2911' => 'fan', 'FAN05G3901' => 'fan', 'FAN05G4859' => 'fan', 'FAN05G4861' => 'fan', 'FAN05G4988' => 'fan', 'FAN05G5187' => 'fan', 'FAN05G5452' => 'fan', 'FAN05G5500' => 'fan', 'FAN05G5688' => 'fan', 'FAN06G0177' => 'fan', 'FAN06G0675' => 'fan', 'FAN06G1290' => 'fan', 'FAN06G2191' => 'fan', 'FAN06G2405' => 'fan', 'FAN06G3231' => 'fan', 'FAN06G3932' => 'fan', 'FAN07G0163' => 'fan', 'FAN07G0471' => 'fan', 'FAN07G1354' => 'fan', 'FAN08G0338' => 'fan', 'FAN08G1373' => 'fan', 'FAN08G2539' => 'fan', 'FAN08G2728' => 'fan', 'FAN09G0608' => 'fan', 'FAN09G1136' => 'fan', 'FAN09G1958' => 'fan', 'FAN09G2508' => 'fan', 'FAN09G2597' => 'fan', 'FAN09G2658' => 'fan', 'FAN09G2757' => 'fan', 'FAN09G2983' => 'fan', 'FAN09G3130' => 'fan', 'FAN09G3565' => 'fan', 'FAN09G3613' => 'fan', 'FAN09G4011' => 'fan', 'FAN09G4239' => 'fan', 'FAN09G4277' => 'fan', 'FAN09G4720' => 'fan', 'FAN11G0139' => 'fan', 'FAN11G1727' => 'fan', 'FAN11G2672' => 'fan', 'FAN11G2795' => 'fan', 'FAN11G3238' => 'fan', 'FAN11G3734' => 'fan', 'FAN12G0631' => 'fan', 'FAN12G2239' => 'fan', 'FAN12G2308' => 'fan', 'FAN12G2569' => 'fan', 'FAN12G2623' => 'fan', 'FAN13G3182' => 'fan', 'FAN14G0053' => 'fan', 'FAN14G0370' => 'fan', 'FAN14G0382' => 'fan', 'FAN14G0421' => 'fan', 'FAN14G0866' => 'fan', 'FAN14G1187' => 'fan', 'FAN14G1727' => 'fan', 'FAN14G1791' => 'fan', 'FAN14G2361' => 'fan', 'FAN14G2668' => 'fan', 'FAN14G2770' => 'fan', 'FAN14G2874' => 'fan', 'FAN14G3193' => 'fan', 'FAN14G3624' => 'fan', 'FAN14G3676' => 'fan', 'FAN14G3807' => 'fan', 'FAN14G4082' => 'fan', 'FAN14G4342' => 'fan', 'FAN14G4985' => 'fan', 'FAN14G5126' => 'fan', 'FAN14G5781' => 'fan', 'FAN14G5808' => 'fan', 'FAN14G5949' => 'fan', 'FAN15G0828' => 'fan', 'FAN15G1054' => 'fan', 'FAN15G2023' => 'fan', 'FAN15G2506' => 'fan', 'FAN16G0128' => 'fan', 'FAN16G0249' => 'fan', 'FAN16G0429' => 'fan', 'FAN16G1493' => 'fan', 'FAN16G2210' => 'fan', 'FAN16G2506' => 'fan', 'FAN18G1542' => 'fan', 'FAN18G4057' => 'fan', 'FAN19G0745' => 'fan', 'FAN19G1216' => 'fan', 'FAN19G1733' => 'fan', 'FAN20G0258' => 'fan', 'FAN20G1095' => 'fan', 'FAN20G1557' => 'fan', 'FAN21G0302' => 'fan', 'FAN21G0519' => 'fan', 'FAN21G0970' => 'fan', 'FAN21G1159' => 'fan', 'FAN21G1312' => 'fan', 'FAN21G1440' => 'fan', 'FAN21G1715' => 'fan', 'FAN23G1584' => 'fan', 'FAN24G0045' => 'fan', 'FAN24G0053' => 'fan', 'FAN24G1500' => 'fan', 'FAN24G1817' => 'fan', 'FAN24G2147' => 'fan', 'FAN24G2236' => 'fan', 'FAN24G2446' => 'fan', 'FAN24G2684' => 'fan', 'FAN25G0187' => 'fan', 'FAN25G0505' => 'fan', 'FAN25G0589' => 'fan', 'FAN25G3663' => 'fan', 'FAN26G1025' => 'fan', 'FAN26G2860' => 'fan', 'FAN27G1329' => 'fan', 'FAN27G3392' => 'fan', 'FvH4_1g02011' => 'fve', 'FvH4_1g06511' => 'fve', 'FvH4_2g19900' => 'fve', 'FvH4_2g19920' => 'fve', 'FvH4_2g24261' => 'fve', 'FvH4_2g24270' => 'fve', 'FvH4_2g24631' => 'fve', 'FvH4_2g30622' => 'fve', 'FvH4_3g12920' => 'fve', 'FvH4_3g30171' => 'fve', 'FvH4_3g35490' => 'fve', 'FvH4_3g43682' => 'fve', 'FvH4_3g43730' => 'fve', 'FvH4_3g43732' => 'fve', 'FvH4_3g43751' => 'fve', 'FvH4_3g43752' => 'fve', 'FvH4_3g43770' => 'fve', 'FvH4_3g44471' => 'fve', 'FvH4_3g44510' => 'fve', 'FvH4_3g44582' => 'fve', 'FvH4_4g16921' => 'fve', 'FvH4_4g17121' => 'fve', 'FvH4_4g17782' => 'fve', 'FvH4_4g17783' => 'fve', 'FvH4_4g18120' => 'fve', 'FvH4_4g31310' => 'fve', 'FvH4_4g35052' => 'fve', 'FvH4_5g30862' => 'fve', 'FvH4_6g01541' => 'fve', 'FvH4_6g02021' => 'fve', 'FvH4_6g02041' => 'fve', 'FvH4_6g02071' => 'fve', 'FvH4_6g02171' => 'fve', 'FvH4_6g03181' => 'fve', 'FvH4_6g03182' => 'fve', 'FvH4_6g03221' => 'fve', 'FvH4_6g03380' => 'fve', 'FvH4_6g05201' => 'fve', 'FvH4_6g05203' => 'fve', 'FvH4_6g20231' => 'fve', 'FvH4_6g31981' => 'fve', 'FvH4_6g32061' => 'fve', 'FvH4_6g37041' => 'fve', 'FvH4_6g37932' => 'fve', 'FvH4_6g38731' => 'fve', 'FvH4_6g39370' => 'fve', 'FvH4_6g39371' => 'fve', 'FvH4_6g40891' => 'fve', 'FvH4_6g40892' => 'fve', 'FvH4_6g43143' => 'fve', 'FvH4_6g45251' => 'fve', 'FvH4_6g45260' => 'fve', 'FvH4_6g45291' => 'fve', 'FvH4_6g45890' => 'fve', 'FvH4_6g46240' => 'fve', 'FvH4_6g46241' => 'fve', 'FvH4_6g46242' => 'fve', 'FvH4_6g46260' => 'fve', 'FvH4_6g46280' => 'fve', 'FvH4_6g46380' => 'fve', 'FvH4_7g12841' => 'fve', 'FvH4_7g31431' => 'fve', 'Glyma.09G075900' => 'gma', 'Gohir.A09G096401' => 'ghi', 'Gohir.D09G096101' => 'ghi', 'Gorai.006G112800' => 'gra', 'HanXRQChr04g0121411' => 'han', 'Hund15878' => 'sun', 'Lj2A1107G68' => 'lonja', 'Lj2A630G63' => 'lonja', 'Lj2A946T25' => 'lonja', 'Lj2C714T1' => 'lonja', 'Lj2C966T3' => 'lonja', 'Lj2C966T4' => 'lonja', 'Lj4g0002979' => 'lja', 'Lsat_1_v5_gn_5_30901' => 'lsa', 'Lsat_1_v5_gn_5_31100' => 'lsa', 'Lsat_1_v5_gn_5_38600' => 'lsa', 'Lsat_1_v5_gn_6_92061' => 'lsa', 'Manes.05G071301' => 'mes', 'MD02G1008700' => 'mdo', 'MD02G1008900' => 'mdo', 'MD03G1256400' => 'mdo', 'MD04G1180900' => 'mdo', 'MD04G1181000' => 'mdo', 'MD04G1181200' => 'mdo', 'MD05G1244200' => 'mdo', 'MD05G1324200' => 'mdo', 'MD09G1201600' => 'mdo', 'MD10G1000600' => 'mdo', 'MD14G1026900' => 'mdo', 'MD14G1187900' => 'mdo', 'MD15G1017800' => 'mdo', 'MD15G1018100' => 'mdo', 'Medtr4g124160' => 'mtr', 'Migut.L01260' => 'egut', 'Nitab4.5_0000008g0440' => 'nta', 'Nitab4.5_0000207g0170' => 'nta', 'Nitab4.5_0007671g0030' => 'nta', 'Nitab4.5_0010853g0020' => 'nta', 'Oeu057656.1' => 'oeu', 'PGSC0003DMG400005638' => 'stu', 'PGSC0003DMG400005639' => 'stu', 'Phvul.009G222800' => 'pvu', 'Potri.009G132400' => 'ptr', 'Potri.009G163001' => 'ptr', 'Potri.011G000700' => 'ptr', 'Potri.011G004800' => 'ptr', 'Prupe.1G509300' => 'ppe', 'Prupe.1G509700' => 'ppe', 'Prupe.1G510400' => 'ppe', 'Prupe.1G510700' => 'ppe', 'Prupe.1G512600' => 'ppe', 'Prupe.2G073200' => 'ppe', 'Prupe.3G059500' => 'ppe', 'Prupe.3G059600' => 'ppe', 'Prupe.3G246100' => 'ppe', 'Prupe.3G265100' => 'ppe', 'Prupe.4G034700' => 'ppe', 'Prupe.4G052100' => 'ppe', 'Prupe.4G053600' => 'ppe', 'Prupe.5G068800' => 'ppe', 'Prupe.5G070600' => 'ppe', 'Prupe.6G075400' => 'ppe', 'Prupe.6G075500' => 'ppe', 'Prupe.6G076400' => 'ppe', 'Prupe.8G110700' => 'ppe', 'Psat4g020960' => 'psa', 'PSO135G0788' => 'pso', 'PSO210G6463' => 'pso', 'PSO384G0370' => 'pso', 'PSO386G0056' => 'pso', 'QL01p006048' => 'qlo', 'QL02p054283' => 'qlo', 'QL05p008000' => 'qlo', 'QL05p008212' => 'qlo', 'QL05p008950' => 'qlo', 'QL05p009042' => 'qlo', 'QL05p009518' => 'qlo', 'QL05p012589' => 'qlo', 'QL05p012608' => 'qlo', 'QL05p012650' => 'qlo', 'QL05p012667' => 'qlo', 'QL05p014501' => 'qlo', 'QL05p052800' => 'qlo', 'QL05p065010' => 'qlo', 'QL05p074156' => 'qlo', 'QL05p074160' => 'qlo', 'QL05p074174' => 'qlo', 'QL05p074178' => 'qlo', 'QL05p074214' => 'qlo', 'QL06p001050' => 'qlo', 'QL06p001056' => 'qlo', 'QL06p006093' => 'qlo', 'QL06p006111' => 'qlo', 'QL07p019784' => 'qlo', 'QL07p019801' => 'qlo', 'QL07p036110' => 'qlo', 'QL07p036134' => 'qlo', 'QL07p036147' => 'qlo', 'QL07p036156' => 'qlo', 'QL07p036300' => 'qlo', 'QL07p036320' => 'qlo', 'QL08p014547' => 'qlo', 'QL08p014551' => 'qlo', 'QL08p043319' => 'qlo', 'QL08p043324' => 'qlo', 'QL11p009094' => 'qlo', 'RcHm_v2.0_Chr1g0380481' => 'rch', 'RcHm_v2.0_Chr2g0089331' => 'rch', 'RcHm_v2.0_Chr2g0123691' => 'rch', 'RcHm_v2.0_Chr2g0151111' => 'rch', 'RcHm_v2.0_Chr2g0163011' => 'rch', 'RcHm_v2.0_Chr2g0163051' => 'rch', 'RcHm_v2.0_Chr2g0164671' => 'rch', 'RcHm_v2.0_Chr2g0164681' => 'rch', 'RcHm_v2.0_Chr2g0164721' => 'rch', 'RcHm_v2.0_Chr3g0449911' => 'rch', 'RcHm_v2.0_Chr3g0450211' => 'rch', 'RcHm_v2.0_Chr3g0457271' => 'rch', 'RcHm_v2.0_Chr5g0018111' => 'rch', 'RcHm_v2.0_Chr5g0021011' => 'rch', 'RcHm_v2.0_Chr5g0081171' => 'rch', 'RcHm_v2.0_Chr5g0081211' => 'rch', 'RcHm_v2.0_Chr6g0275871' => 'rch', 'RcHm_v2.0_Chr6g0276071' => 'rch', 'RcHm_v2.0_Chr6g0285591' => 'rch', 'RcHm_v2.0_Chr6g0291931' => 'rch', 'RcHm_v2.0_Chr6g0292091' => 'rch', 'RcHm_v2.0_Chr6g0292271' => 'rch', 'RcHm_v2.0_Chr7g0221261' => 'rch', 'Rhsim08G0219900' => 'rsi', 'Rhsim08G0220200' => 'rsi', 'Rhsim08G0237800' => 'rsi', 'Rhsim08G0238800' => 'rsi', 'Sabra09G0102700' => 'sbr', 'Sabra09G0127200' => 'sbr', 'Sabra11G0003700' => 'sbr', 'Sabra15G0014700' => 'sbr', 'Sc19g0000590' => 'sci', 'Sc19g0001870' => 'sci', 'SGA_v2.0_scaffold1G00346' => 'sas', 'SGA_v2.0_scaffold1G00575' => 'sas', 'SGA_v2.0_scaffold1G00761' => 'sas', 'SGA_v2.0_scaffold232G43501' => 'sas', 'TAR625G1137' => 'tar', 'Thecc.03G222100' => 'tca', 'TPR.G12691' => 'tpr', 'TWI34G0727' => 'twi', 'TWI36G0117' => 'twi', 'VMungo1309G0868' => 'vmu' ) $gf_id = 'HOM05D001729' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001729' ) $data_identifier = 'HOM05D001729' $data_type = 'gf_id' $species_gene_counts = array( 'amhyb' => (int) 1, 'cqu' => (int) 9, 'can' => (int) 1, 'cansat' => (int) 1, 'car' => (int) 1, 'col' => (int) 5, 'dca' => (int) 1, 'din' => (int) 2, 'dzi' => (int) 3, 'fan' => (int) 140, 'fve' => (int) 62, 'gma' => (int) 1, 'ghi' => (int) 2, 'gra' => (int) 1, 'han' => (int) 1, 'sun' => (int) 1, 'lonja' => (int) 6, 'lja' => (int) 1, 'lsa' => (int) 4, 'mes' => (int) 1, 'mdo' => (int) 14, 'mtr' => (int) 1, 'egut' => (int) 1, 'nta' => (int) 4, 'oeu' => (int) 1, 'stu' => (int) 2, 'pvu' => (int) 1, 'ptr' => (int) 4, 'ppe' => (int) 19, 'psa' => (int) 1, 'pso' => (int) 4, 'qlo' => (int) 36, 'rch' => (int) 23, 'rsi' => (int) 4, 'sbr' => (int) 4, 'sci' => (int) 2, 'sas' => (int) 4, 'tar' => (int) 1, 'tca' => (int) 1, 'tpr' => (int) 1, 'twi' => (int) 2, 'vmu' => (int) 1 ) $gf_gene_species = 'vmu' $gf_gene_id = 'VMungo1309G0868' $species_info = array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ) $local_species = 'tpr' $disabled = '' $selected = '' $num_hits = (int) 1include - APP/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp, line 33 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933 View::_renderElement() - CORE/Cake/View/View.php, line 1224 View::element() - CORE/Cake/View/View.php, line 418 include - APP/View/Elements/analysis/phylogenetics_module/gf_data_settings.ctp, line 37 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933 View::_renderElement() - CORE/Cake/View/View.php, line 1224 View::element() - CORE/Cake/View/View.php, line 418 include - APP/View/Elements/analysis/phylogenetics_module/parameter_selection.ctp, line 64 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933 View::_renderElement() - CORE/Cake/View/View.php, line 1224 View::element() - CORE/Cake/View/View.php, line 418 include - APP/View/Analysis/custom_tree_creation.ctp, line 27 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933
$viewFile = '/www/bioinformatics01_ro/plaza/_dev_instances/feedback/app/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp' $dataForView = array( 'sidebar_info' => array( 'gf_id' => 'HOM05D001729', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '375', 'num_species' => '42' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'Ah.07g204710' => 'amhyb', 'AUR62006001' => 'cqu', 'AUR62006002' => 'cqu', 'AUR62006003' => 'cqu', 'AUR62015641' => 'cqu', 'AUR62027174' => 'cqu', 'AUR62035623' => 'cqu', 'AUR62035624' => 'cqu', 'AUR62035625' => 'cqu', 'AUR62035626' => 'cqu', 'CAN.G1110.53' => 'can', 'CANSAT80G0415' => 'cansat', 'Ca_21364_v3' => 'car', 'COL.COLO4_30693' => 'col', 'COL.COLO4_30694' => 'col', 'COL.COLO4_30695' => 'col', 'COL.COLO4_30696' => 'col', 'COL.COLO4_34020' => 'col', 'DCAR_004585' => 'dca', 'Dinv04029' => 'din', 'Dinv34857' => 'din', 'Duzib147G0011' => 'dzi', 'Duzib170G0599' => 'dzi', 'Duzib192G1051' => 'dzi', 'FAN01G0708' => 'fan', 'FAN01G0742' => 'fan', 'FAN02G0048' => 'fan', 'FAN02G0583' => 'fan', 'FAN02G0688' => 'fan', 'FAN02G1588' => 'fan', 'FAN02G2194' => 'fan', 'FAN02G2750' => 'fan', 'FAN02G3094' => 'fan', 'FAN02G3887' => 'fan', 'FAN02G3911' => 'fan', 'FAN02G3994' => 'fan', 'FAN02G4432' => 'fan', 'FAN02G4556' => 'fan', 'FAN03G1977' => 'fan', 'FAN03G2781' => 'fan', 'FAN03G2850' => 'fan', 'FAN03G3155' => 'fan', 'FAN04G2487' => 'fan', 'FAN05G0208' => 'fan', 'FAN05G0656' => 'fan', 'FAN05G0696' => 'fan', 'FAN05G0810' => 'fan', 'FAN05G1447' => 'fan', 'FAN05G2640' => 'fan', 'FAN05G2911' => 'fan', 'FAN05G3901' => 'fan', 'FAN05G4859' => 'fan', 'FAN05G4861' => 'fan', 'FAN05G4988' => 'fan', 'FAN05G5187' => 'fan', 'FAN05G5452' => 'fan', 'FAN05G5500' => 'fan', 'FAN05G5688' => 'fan', 'FAN06G0177' => 'fan', 'FAN06G0675' => 'fan', 'FAN06G1290' => 'fan', 'FAN06G2191' => 'fan', 'FAN06G2405' => 'fan', 'FAN06G3231' => 'fan', 'FAN06G3932' => 'fan', 'FAN07G0163' => 'fan', 'FAN07G0471' => 'fan', 'FAN07G1354' => 'fan', 'FAN08G0338' => 'fan', 'FAN08G1373' => 'fan', 'FAN08G2539' => 'fan', 'FAN08G2728' => 'fan', 'FAN09G0608' => 'fan', 'FAN09G1136' => 'fan', 'FAN09G1958' => 'fan', 'FAN09G2508' => 'fan', 'FAN09G2597' => 'fan', 'FAN09G2658' => 'fan', 'FAN09G2757' => 'fan', 'FAN09G2983' => 'fan', 'FAN09G3130' => 'fan', 'FAN09G3565' => 'fan', 'FAN09G3613' => 'fan', 'FAN09G4011' => 'fan', 'FAN09G4239' => 'fan', 'FAN09G4277' => 'fan', 'FAN09G4720' => 'fan', 'FAN11G0139' => 'fan', 'FAN11G1727' => 'fan', 'FAN11G2672' => 'fan', 'FAN11G2795' => 'fan', 'FAN11G3238' => 'fan', 'FAN11G3734' => 'fan', 'FAN12G0631' => 'fan', 'FAN12G2239' => 'fan', 'FAN12G2308' => 'fan', 'FAN12G2569' => 'fan', 'FAN12G2623' => 'fan', 'FAN13G3182' => 'fan', 'FAN14G0053' => 'fan', 'FAN14G0370' => 'fan', 'FAN14G0382' => 'fan', 'FAN14G0421' => 'fan', 'FAN14G0866' => 'fan', 'FAN14G1187' => 'fan', 'FAN14G1727' => 'fan', 'FAN14G1791' => 'fan', 'FAN14G2361' => 'fan', 'FAN14G2668' => 'fan', 'FAN14G2770' => 'fan', 'FAN14G2874' => 'fan', 'FAN14G3193' => 'fan', 'FAN14G3624' => 'fan', 'FAN14G3676' => 'fan', 'FAN14G3807' => 'fan', 'FAN14G4082' => 'fan', 'FAN14G4342' => 'fan', 'FAN14G4985' => 'fan', 'FAN14G5126' => 'fan', 'FAN14G5781' => 'fan', 'FAN14G5808' => 'fan', 'FAN14G5949' => 'fan', 'FAN15G0828' => 'fan', 'FAN15G1054' => 'fan', 'FAN15G2023' => 'fan', 'FAN15G2506' => 'fan', 'FAN16G0128' => 'fan', 'FAN16G0249' => 'fan', 'FAN16G0429' => 'fan', 'FAN16G1493' => 'fan', 'FAN16G2210' => 'fan', 'FAN16G2506' => 'fan', 'FAN18G1542' => 'fan', 'FAN18G4057' => 'fan', 'FAN19G0745' => 'fan', 'FAN19G1216' => 'fan', 'FAN19G1733' => 'fan', 'FAN20G0258' => 'fan', 'FAN20G1095' => 'fan', 'FAN20G1557' => 'fan', 'FAN21G0302' => 'fan', 'FAN21G0519' => 'fan', 'FAN21G0970' => 'fan', 'FAN21G1159' => 'fan', 'FAN21G1312' => 'fan', 'FAN21G1440' => 'fan', 'FAN21G1715' => 'fan', 'FAN23G1584' => 'fan', 'FAN24G0045' => 'fan', 'FAN24G0053' => 'fan', 'FAN24G1500' => 'fan', 'FAN24G1817' => 'fan', 'FAN24G2147' => 'fan', 'FAN24G2236' => 'fan', 'FAN24G2446' => 'fan', 'FAN24G2684' => 'fan', 'FAN25G0187' => 'fan', 'FAN25G0505' => 'fan', 'FAN25G0589' => 'fan', 'FAN25G3663' => 'fan', 'FAN26G1025' => 'fan', 'FAN26G2860' => 'fan', 'FAN27G1329' => 'fan', 'FAN27G3392' => 'fan', 'FvH4_1g02011' => 'fve', 'FvH4_1g06511' => 'fve', 'FvH4_2g19900' => 'fve', 'FvH4_2g19920' => 'fve', 'FvH4_2g24261' => 'fve', 'FvH4_2g24270' => 'fve', 'FvH4_2g24631' => 'fve', 'FvH4_2g30622' => 'fve', 'FvH4_3g12920' => 'fve', 'FvH4_3g30171' => 'fve', 'FvH4_3g35490' => 'fve', 'FvH4_3g43682' => 'fve', 'FvH4_3g43730' => 'fve', 'FvH4_3g43732' => 'fve', 'FvH4_3g43751' => 'fve', 'FvH4_3g43752' => 'fve', 'FvH4_3g43770' => 'fve', 'FvH4_3g44471' => 'fve', 'FvH4_3g44510' => 'fve', 'FvH4_3g44582' => 'fve', 'FvH4_4g16921' => 'fve', 'FvH4_4g17121' => 'fve', 'FvH4_4g17782' => 'fve', 'FvH4_4g17783' => 'fve', 'FvH4_4g18120' => 'fve', 'FvH4_4g31310' => 'fve', 'FvH4_4g35052' => 'fve', 'FvH4_5g30862' => 'fve', 'FvH4_6g01541' => 'fve', 'FvH4_6g02021' => 'fve', 'FvH4_6g02041' => 'fve', 'FvH4_6g02071' => 'fve', 'FvH4_6g02171' => 'fve', 'FvH4_6g03181' => 'fve', 'FvH4_6g03182' => 'fve', 'FvH4_6g03221' => 'fve', 'FvH4_6g03380' => 'fve', 'FvH4_6g05201' => 'fve', 'FvH4_6g05203' => 'fve', 'FvH4_6g20231' => 'fve', 'FvH4_6g31981' => 'fve', 'FvH4_6g32061' => 'fve', 'FvH4_6g37041' => 'fve', 'FvH4_6g37932' => 'fve', 'FvH4_6g38731' => 'fve', 'FvH4_6g39370' => 'fve', 'FvH4_6g39371' => 'fve', 'FvH4_6g40891' => 'fve', 'FvH4_6g40892' => 'fve', 'FvH4_6g43143' => 'fve', 'FvH4_6g45251' => 'fve', 'FvH4_6g45260' => 'fve', 'FvH4_6g45291' => 'fve', 'FvH4_6g45890' => 'fve', 'FvH4_6g46240' => 'fve', 'FvH4_6g46241' => 'fve', 'FvH4_6g46242' => 'fve', 'FvH4_6g46260' => 'fve', 'FvH4_6g46280' => 'fve', 'FvH4_6g46380' => 'fve', 'FvH4_7g12841' => 'fve', 'FvH4_7g31431' => 'fve', 'Glyma.09G075900' => 'gma', 'Gohir.A09G096401' => 'ghi', 'Gohir.D09G096101' => 'ghi', 'Gorai.006G112800' => 'gra', 'HanXRQChr04g0121411' => 'han', 'Hund15878' => 'sun', 'Lj2A1107G68' => 'lonja', 'Lj2A630G63' => 'lonja', 'Lj2A946T25' => 'lonja', 'Lj2C714T1' => 'lonja', 'Lj2C966T3' => 'lonja', 'Lj2C966T4' => 'lonja', 'Lj4g0002979' => 'lja', 'Lsat_1_v5_gn_5_30901' => 'lsa', 'Lsat_1_v5_gn_5_31100' => 'lsa', 'Lsat_1_v5_gn_5_38600' => 'lsa', 'Lsat_1_v5_gn_6_92061' => 'lsa', 'Manes.05G071301' => 'mes', 'MD02G1008700' => 'mdo', 'MD02G1008900' => 'mdo', 'MD03G1256400' => 'mdo', 'MD04G1180900' => 'mdo', 'MD04G1181000' => 'mdo', 'MD04G1181200' => 'mdo', 'MD05G1244200' => 'mdo', 'MD05G1324200' => 'mdo', 'MD09G1201600' => 'mdo', 'MD10G1000600' => 'mdo', 'MD14G1026900' => 'mdo', 'MD14G1187900' => 'mdo', 'MD15G1017800' => 'mdo', 'MD15G1018100' => 'mdo', 'Medtr4g124160' => 'mtr', 'Migut.L01260' => 'egut', 'Nitab4.5_0000008g0440' => 'nta', 'Nitab4.5_0000207g0170' => 'nta', 'Nitab4.5_0007671g0030' => 'nta', 'Nitab4.5_0010853g0020' => 'nta', 'Oeu057656.1' => 'oeu', 'PGSC0003DMG400005638' => 'stu', 'PGSC0003DMG400005639' => 'stu', 'Phvul.009G222800' => 'pvu', 'Potri.009G132400' => 'ptr', 'Potri.009G163001' => 'ptr', 'Potri.011G000700' => 'ptr', 'Potri.011G004800' => 'ptr', 'Prupe.1G509300' => 'ppe', 'Prupe.1G509700' => 'ppe', 'Prupe.1G510400' => 'ppe', 'Prupe.1G510700' => 'ppe', 'Prupe.1G512600' => 'ppe', 'Prupe.2G073200' => 'ppe', 'Prupe.3G059500' => 'ppe', 'Prupe.3G059600' => 'ppe', 'Prupe.3G246100' => 'ppe', 'Prupe.3G265100' => 'ppe', 'Prupe.4G034700' => 'ppe', 'Prupe.4G052100' => 'ppe', 'Prupe.4G053600' => 'ppe', 'Prupe.5G068800' => 'ppe', 'Prupe.5G070600' => 'ppe', 'Prupe.6G075400' => 'ppe', 'Prupe.6G075500' => 'ppe', 'Prupe.6G076400' => 'ppe', 'Prupe.8G110700' => 'ppe', 'Psat4g020960' => 'psa', 'PSO135G0788' => 'pso', 'PSO210G6463' => 'pso', 'PSO384G0370' => 'pso', 'PSO386G0056' => 'pso', 'QL01p006048' => 'qlo', 'QL02p054283' => 'qlo', 'QL05p008000' => 'qlo', 'QL05p008212' => 'qlo', 'QL05p008950' => 'qlo', 'QL05p009042' => 'qlo', 'QL05p009518' => 'qlo', 'QL05p012589' => 'qlo', 'QL05p012608' => 'qlo', 'QL05p012650' => 'qlo', 'QL05p012667' => 'qlo', 'QL05p014501' => 'qlo', 'QL05p052800' => 'qlo', 'QL05p065010' => 'qlo', 'QL05p074156' => 'qlo', 'QL05p074160' => 'qlo', 'QL05p074174' => 'qlo', 'QL05p074178' => 'qlo', 'QL05p074214' => 'qlo', 'QL06p001050' => 'qlo', 'QL06p001056' => 'qlo', 'QL06p006093' => 'qlo', 'QL06p006111' => 'qlo', 'QL07p019784' => 'qlo', 'QL07p019801' => 'qlo', 'QL07p036110' => 'qlo', 'QL07p036134' => 'qlo', 'QL07p036147' => 'qlo', 'QL07p036156' => 'qlo', 'QL07p036300' => 'qlo', 'QL07p036320' => 'qlo', 'QL08p014547' => 'qlo', 'QL08p014551' => 'qlo', 'QL08p043319' => 'qlo', 'QL08p043324' => 'qlo', 'QL11p009094' => 'qlo', 'RcHm_v2.0_Chr1g0380481' => 'rch', 'RcHm_v2.0_Chr2g0089331' => 'rch', 'RcHm_v2.0_Chr2g0123691' => 'rch', 'RcHm_v2.0_Chr2g0151111' => 'rch', 'RcHm_v2.0_Chr2g0163011' => 'rch', 'RcHm_v2.0_Chr2g0163051' => 'rch', 'RcHm_v2.0_Chr2g0164671' => 'rch', 'RcHm_v2.0_Chr2g0164681' => 'rch', 'RcHm_v2.0_Chr2g0164721' => 'rch', 'RcHm_v2.0_Chr3g0449911' => 'rch', 'RcHm_v2.0_Chr3g0450211' => 'rch', 'RcHm_v2.0_Chr3g0457271' => 'rch', 'RcHm_v2.0_Chr5g0018111' => 'rch', 'RcHm_v2.0_Chr5g0021011' => 'rch', 'RcHm_v2.0_Chr5g0081171' => 'rch', 'RcHm_v2.0_Chr5g0081211' => 'rch', 'RcHm_v2.0_Chr6g0275871' => 'rch', 'RcHm_v2.0_Chr6g0276071' => 'rch', 'RcHm_v2.0_Chr6g0285591' => 'rch', 'RcHm_v2.0_Chr6g0291931' => 'rch', 'RcHm_v2.0_Chr6g0292091' => 'rch', 'RcHm_v2.0_Chr6g0292271' => 'rch', 'RcHm_v2.0_Chr7g0221261' => 'rch', 'Rhsim08G0219900' => 'rsi', 'Rhsim08G0220200' => 'rsi', 'Rhsim08G0237800' => 'rsi', 'Rhsim08G0238800' => 'rsi', 'Sabra09G0102700' => 'sbr', 'Sabra09G0127200' => 'sbr', 'Sabra11G0003700' => 'sbr', 'Sabra15G0014700' => 'sbr', 'Sc19g0000590' => 'sci', 'Sc19g0001870' => 'sci', 'SGA_v2.0_scaffold1G00346' => 'sas', 'SGA_v2.0_scaffold1G00575' => 'sas', 'SGA_v2.0_scaffold1G00761' => 'sas', 'SGA_v2.0_scaffold232G43501' => 'sas', 'TAR625G1137' => 'tar', 'Thecc.03G222100' => 'tca', 'TPR.G12691' => 'tpr', 'TWI34G0727' => 'twi', 'TWI36G0117' => 'twi', 'VMungo1309G0868' => 'vmu' ), 'gf_id' => 'HOM05D001729', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001729' ), 'data_identifier' => 'HOM05D001729', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001729', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '375', 'num_species' => '42' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'Ah.07g204710' => 'amhyb', 'AUR62006001' => 'cqu', 'AUR62006002' => 'cqu', 'AUR62006003' => 'cqu', 'AUR62015641' => 'cqu', 'AUR62027174' => 'cqu', 'AUR62035623' => 'cqu', 'AUR62035624' => 'cqu', 'AUR62035625' => 'cqu', 'AUR62035626' => 'cqu', 'CAN.G1110.53' => 'can', 'CANSAT80G0415' => 'cansat', 'Ca_21364_v3' => 'car', 'COL.COLO4_30693' => 'col', 'COL.COLO4_30694' => 'col', 'COL.COLO4_30695' => 'col', 'COL.COLO4_30696' => 'col', 'COL.COLO4_34020' => 'col', 'DCAR_004585' => 'dca', 'Dinv04029' => 'din', 'Dinv34857' => 'din', 'Duzib147G0011' => 'dzi', 'Duzib170G0599' => 'dzi', 'Duzib192G1051' => 'dzi', 'FAN01G0708' => 'fan', 'FAN01G0742' => 'fan', 'FAN02G0048' => 'fan', 'FAN02G0583' => 'fan', 'FAN02G0688' => 'fan', 'FAN02G1588' => 'fan', 'FAN02G2194' => 'fan', 'FAN02G2750' => 'fan', 'FAN02G3094' => 'fan', 'FAN02G3887' => 'fan', 'FAN02G3911' => 'fan', 'FAN02G3994' => 'fan', 'FAN02G4432' => 'fan', 'FAN02G4556' => 'fan', 'FAN03G1977' => 'fan', 'FAN03G2781' => 'fan', 'FAN03G2850' => 'fan', 'FAN03G3155' => 'fan', 'FAN04G2487' => 'fan', 'FAN05G0208' => 'fan', 'FAN05G0656' => 'fan', 'FAN05G0696' => 'fan', 'FAN05G0810' => 'fan', 'FAN05G1447' => 'fan', 'FAN05G2640' => 'fan', 'FAN05G2911' => 'fan', 'FAN05G3901' => 'fan', 'FAN05G4859' => 'fan', 'FAN05G4861' => 'fan', 'FAN05G4988' => 'fan', 'FAN05G5187' => 'fan', 'FAN05G5452' => 'fan', 'FAN05G5500' => 'fan', 'FAN05G5688' => 'fan', 'FAN06G0177' => 'fan', 'FAN06G0675' => 'fan', 'FAN06G1290' => 'fan', 'FAN06G2191' => 'fan', 'FAN06G2405' => 'fan', 'FAN06G3231' => 'fan', 'FAN06G3932' => 'fan', 'FAN07G0163' => 'fan', 'FAN07G0471' => 'fan', 'FAN07G1354' => 'fan', 'FAN08G0338' => 'fan', 'FAN08G1373' => 'fan', 'FAN08G2539' => 'fan', 'FAN08G2728' => 'fan', 'FAN09G0608' => 'fan', 'FAN09G1136' => 'fan', 'FAN09G1958' => 'fan', 'FAN09G2508' => 'fan', 'FAN09G2597' => 'fan', 'FAN09G2658' => 'fan', 'FAN09G2757' => 'fan', 'FAN09G2983' => 'fan', 'FAN09G3130' => 'fan', 'FAN09G3565' => 'fan', 'FAN09G3613' => 'fan', 'FAN09G4011' => 'fan', 'FAN09G4239' => 'fan', 'FAN09G4277' => 'fan', 'FAN09G4720' => 'fan', 'FAN11G0139' => 'fan', 'FAN11G1727' => 'fan', 'FAN11G2672' => 'fan', 'FAN11G2795' => 'fan', 'FAN11G3238' => 'fan', 'FAN11G3734' => 'fan', 'FAN12G0631' => 'fan', 'FAN12G2239' => 'fan', 'FAN12G2308' => 'fan', 'FAN12G2569' => 'fan', 'FAN12G2623' => 'fan', 'FAN13G3182' => 'fan', 'FAN14G0053' => 'fan', 'FAN14G0370' => 'fan', 'FAN14G0382' => 'fan', 'FAN14G0421' => 'fan', 'FAN14G0866' => 'fan', 'FAN14G1187' => 'fan', 'FAN14G1727' => 'fan', 'FAN14G1791' => 'fan', 'FAN14G2361' => 'fan', 'FAN14G2668' => 'fan', 'FAN14G2770' => 'fan', 'FAN14G2874' => 'fan', 'FAN14G3193' => 'fan', 'FAN14G3624' => 'fan', 'FAN14G3676' => 'fan', 'FAN14G3807' => 'fan', 'FAN14G4082' => 'fan', 'FAN14G4342' => 'fan', 'FAN14G4985' => 'fan', 'FAN14G5126' => 'fan', 'FAN14G5781' => 'fan', 'FAN14G5808' => 'fan', 'FAN14G5949' => 'fan', 'FAN15G0828' => 'fan', 'FAN15G1054' => 'fan', 'FAN15G2023' => 'fan', 'FAN15G2506' => 'fan', 'FAN16G0128' => 'fan', 'FAN16G0249' => 'fan', 'FAN16G0429' => 'fan', 'FAN16G1493' => 'fan', 'FAN16G2210' => 'fan', 'FAN16G2506' => 'fan', 'FAN18G1542' => 'fan', 'FAN18G4057' => 'fan', 'FAN19G0745' => 'fan', 'FAN19G1216' => 'fan', 'FAN19G1733' => 'fan', 'FAN20G0258' => 'fan', 'FAN20G1095' => 'fan', 'FAN20G1557' => 'fan', 'FAN21G0302' => 'fan', 'FAN21G0519' => 'fan', 'FAN21G0970' => 'fan', 'FAN21G1159' => 'fan', 'FAN21G1312' => 'fan', 'FAN21G1440' => 'fan', 'FAN21G1715' => 'fan', 'FAN23G1584' => 'fan', 'FAN24G0045' => 'fan', 'FAN24G0053' => 'fan', 'FAN24G1500' => 'fan', 'FAN24G1817' => 'fan', 'FAN24G2147' => 'fan', 'FAN24G2236' => 'fan', 'FAN24G2446' => 'fan', 'FAN24G2684' => 'fan', 'FAN25G0187' => 'fan', 'FAN25G0505' => 'fan', 'FAN25G0589' => 'fan', 'FAN25G3663' => 'fan', 'FAN26G1025' => 'fan', 'FAN26G2860' => 'fan', 'FAN27G1329' => 'fan', 'FAN27G3392' => 'fan', 'FvH4_1g02011' => 'fve', 'FvH4_1g06511' => 'fve', 'FvH4_2g19900' => 'fve', 'FvH4_2g19920' => 'fve', 'FvH4_2g24261' => 'fve', 'FvH4_2g24270' => 'fve', 'FvH4_2g24631' => 'fve', 'FvH4_2g30622' => 'fve', 'FvH4_3g12920' => 'fve', 'FvH4_3g30171' => 'fve', 'FvH4_3g35490' => 'fve', 'FvH4_3g43682' => 'fve', 'FvH4_3g43730' => 'fve', 'FvH4_3g43732' => 'fve', 'FvH4_3g43751' => 'fve', 'FvH4_3g43752' => 'fve', 'FvH4_3g43770' => 'fve', 'FvH4_3g44471' => 'fve', 'FvH4_3g44510' => 'fve', 'FvH4_3g44582' => 'fve', 'FvH4_4g16921' => 'fve', 'FvH4_4g17121' => 'fve', 'FvH4_4g17782' => 'fve', 'FvH4_4g17783' => 'fve', 'FvH4_4g18120' => 'fve', 'FvH4_4g31310' => 'fve', 'FvH4_4g35052' => 'fve', 'FvH4_5g30862' => 'fve', 'FvH4_6g01541' => 'fve', 'FvH4_6g02021' => 'fve', 'FvH4_6g02041' => 'fve', 'FvH4_6g02071' => 'fve', 'FvH4_6g02171' => 'fve', 'FvH4_6g03181' => 'fve', 'FvH4_6g03182' => 'fve', 'FvH4_6g03221' => 'fve', 'FvH4_6g03380' => 'fve', 'FvH4_6g05201' => 'fve', 'FvH4_6g05203' => 'fve', 'FvH4_6g20231' => 'fve', 'FvH4_6g31981' => 'fve', 'FvH4_6g32061' => 'fve', 'FvH4_6g37041' => 'fve', 'FvH4_6g37932' => 'fve', 'FvH4_6g38731' => 'fve', 'FvH4_6g39370' => 'fve', 'FvH4_6g39371' => 'fve', 'FvH4_6g40891' => 'fve', 'FvH4_6g40892' => 'fve', 'FvH4_6g43143' => 'fve', 'FvH4_6g45251' => 'fve', 'FvH4_6g45260' => 'fve', 'FvH4_6g45291' => 'fve', 'FvH4_6g45890' => 'fve', 'FvH4_6g46240' => 'fve', 'FvH4_6g46241' => 'fve', 'FvH4_6g46242' => 'fve', 'FvH4_6g46260' => 'fve', 'FvH4_6g46280' => 'fve', 'FvH4_6g46380' => 'fve', 'FvH4_7g12841' => 'fve', 'FvH4_7g31431' => 'fve', 'Glyma.09G075900' => 'gma', 'Gohir.A09G096401' => 'ghi', 'Gohir.D09G096101' => 'ghi', 'Gorai.006G112800' => 'gra', 'HanXRQChr04g0121411' => 'han', 'Hund15878' => 'sun', 'Lj2A1107G68' => 'lonja', 'Lj2A630G63' => 'lonja', 'Lj2A946T25' => 'lonja', 'Lj2C714T1' => 'lonja', 'Lj2C966T3' => 'lonja', 'Lj2C966T4' => 'lonja', 'Lj4g0002979' => 'lja', 'Lsat_1_v5_gn_5_30901' => 'lsa', 'Lsat_1_v5_gn_5_31100' => 'lsa', 'Lsat_1_v5_gn_5_38600' => 'lsa', 'Lsat_1_v5_gn_6_92061' => 'lsa', 'Manes.05G071301' => 'mes', 'MD02G1008700' => 'mdo', 'MD02G1008900' => 'mdo', 'MD03G1256400' => 'mdo', 'MD04G1180900' => 'mdo', 'MD04G1181000' => 'mdo', 'MD04G1181200' => 'mdo', 'MD05G1244200' => 'mdo', 'MD05G1324200' => 'mdo', 'MD09G1201600' => 'mdo', 'MD10G1000600' => 'mdo', 'MD14G1026900' => 'mdo', 'MD14G1187900' => 'mdo', 'MD15G1017800' => 'mdo', 'MD15G1018100' => 'mdo', 'Medtr4g124160' => 'mtr', 'Migut.L01260' => 'egut', 'Nitab4.5_0000008g0440' => 'nta', 'Nitab4.5_0000207g0170' => 'nta', 'Nitab4.5_0007671g0030' => 'nta', 'Nitab4.5_0010853g0020' => 'nta', 'Oeu057656.1' => 'oeu', 'PGSC0003DMG400005638' => 'stu', 'PGSC0003DMG400005639' => 'stu', 'Phvul.009G222800' => 'pvu', 'Potri.009G132400' => 'ptr', 'Potri.009G163001' => 'ptr', 'Potri.011G000700' => 'ptr', 'Potri.011G004800' => 'ptr', 'Prupe.1G509300' => 'ppe', 'Prupe.1G509700' => 'ppe', 'Prupe.1G510400' => 'ppe', 'Prupe.1G510700' => 'ppe', 'Prupe.1G512600' => 'ppe', 'Prupe.2G073200' => 'ppe', 'Prupe.3G059500' => 'ppe', 'Prupe.3G059600' => 'ppe', 'Prupe.3G246100' => 'ppe', 'Prupe.3G265100' => 'ppe', 'Prupe.4G034700' => 'ppe', 'Prupe.4G052100' => 'ppe', 'Prupe.4G053600' => 'ppe', 'Prupe.5G068800' => 'ppe', 'Prupe.5G070600' => 'ppe', 'Prupe.6G075400' => 'ppe', 'Prupe.6G075500' => 'ppe', 'Prupe.6G076400' => 'ppe', 'Prupe.8G110700' => 'ppe', 'Psat4g020960' => 'psa', 'PSO135G0788' => 'pso', 'PSO210G6463' => 'pso', 'PSO384G0370' => 'pso', 'PSO386G0056' => 'pso', 'QL01p006048' => 'qlo', 'QL02p054283' => 'qlo', 'QL05p008000' => 'qlo', 'QL05p008212' => 'qlo', 'QL05p008950' => 'qlo', 'QL05p009042' => 'qlo', 'QL05p009518' => 'qlo', 'QL05p012589' => 'qlo', 'QL05p012608' => 'qlo', 'QL05p012650' => 'qlo', 'QL05p012667' => 'qlo', 'QL05p014501' => 'qlo', 'QL05p052800' => 'qlo', 'QL05p065010' => 'qlo', 'QL05p074156' => 'qlo', 'QL05p074160' => 'qlo', 'QL05p074174' => 'qlo', 'QL05p074178' => 'qlo', 'QL05p074214' => 'qlo', 'QL06p001050' => 'qlo', 'QL06p001056' => 'qlo', 'QL06p006093' => 'qlo', 'QL06p006111' => 'qlo', 'QL07p019784' => 'qlo', 'QL07p019801' => 'qlo', 'QL07p036110' => 'qlo', 'QL07p036134' => 'qlo', 'QL07p036147' => 'qlo', 'QL07p036156' => 'qlo', 'QL07p036300' => 'qlo', 'QL07p036320' => 'qlo', 'QL08p014547' => 'qlo', 'QL08p014551' => 'qlo', 'QL08p043319' => 'qlo', 'QL08p043324' => 'qlo', 'QL11p009094' => 'qlo', 'RcHm_v2.0_Chr1g0380481' => 'rch', 'RcHm_v2.0_Chr2g0089331' => 'rch', 'RcHm_v2.0_Chr2g0123691' => 'rch', 'RcHm_v2.0_Chr2g0151111' => 'rch', 'RcHm_v2.0_Chr2g0163011' => 'rch', 'RcHm_v2.0_Chr2g0163051' => 'rch', 'RcHm_v2.0_Chr2g0164671' => 'rch', 'RcHm_v2.0_Chr2g0164681' => 'rch', 'RcHm_v2.0_Chr2g0164721' => 'rch', 'RcHm_v2.0_Chr3g0449911' => 'rch', 'RcHm_v2.0_Chr3g0450211' => 'rch', 'RcHm_v2.0_Chr3g0457271' => 'rch', 'RcHm_v2.0_Chr5g0018111' => 'rch', 'RcHm_v2.0_Chr5g0021011' => 'rch', 'RcHm_v2.0_Chr5g0081171' => 'rch', 'RcHm_v2.0_Chr5g0081211' => 'rch', 'RcHm_v2.0_Chr6g0275871' => 'rch', 'RcHm_v2.0_Chr6g0276071' => 'rch', 'RcHm_v2.0_Chr6g0285591' => 'rch', 'RcHm_v2.0_Chr6g0291931' => 'rch', 'RcHm_v2.0_Chr6g0292091' => 'rch', 'RcHm_v2.0_Chr6g0292271' => 'rch', 'RcHm_v2.0_Chr7g0221261' => 'rch', 'Rhsim08G0219900' => 'rsi', 'Rhsim08G0220200' => 'rsi', 'Rhsim08G0237800' => 'rsi', 'Rhsim08G0238800' => 'rsi', 'Sabra09G0102700' => 'sbr', 'Sabra09G0127200' => 'sbr', 'Sabra11G0003700' => 'sbr', 'Sabra15G0014700' => 'sbr', 'Sc19g0000590' => 'sci', 'Sc19g0001870' => 'sci', 'SGA_v2.0_scaffold1G00346' => 'sas', 'SGA_v2.0_scaffold1G00575' => 'sas', 'SGA_v2.0_scaffold1G00761' => 'sas', 'SGA_v2.0_scaffold232G43501' => 'sas', 'TAR625G1137' => 'tar', 'Thecc.03G222100' => 'tca', 'TPR.G12691' => 'tpr', 'TWI34G0727' => 'twi', 'TWI36G0117' => 'twi', 'VMungo1309G0868' => 'vmu' ) $gf_id = 'HOM05D001729' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001729' ) $data_identifier = 'HOM05D001729' $data_type = 'gf_id' $species_gene_counts = array( 'amhyb' => (int) 1, 'cqu' => (int) 9, 'can' => (int) 1, 'cansat' => (int) 1, 'car' => (int) 1, 'col' => (int) 5, 'dca' => (int) 1, 'din' => (int) 2, 'dzi' => (int) 3, 'fan' => (int) 140, 'fve' => (int) 62, 'gma' => (int) 1, 'ghi' => (int) 2, 'gra' => (int) 1, 'han' => (int) 1, 'sun' => (int) 1, 'lonja' => (int) 6, 'lja' => (int) 1, 'lsa' => (int) 4, 'mes' => (int) 1, 'mdo' => (int) 14, 'mtr' => (int) 1, 'egut' => (int) 1, 'nta' => (int) 4, 'oeu' => (int) 1, 'stu' => (int) 2, 'pvu' => (int) 1, 'ptr' => (int) 4, 'ppe' => (int) 19, 'psa' => (int) 1, 'pso' => (int) 4, 'qlo' => (int) 36, 'rch' => (int) 23, 'rsi' => (int) 4, 'sbr' => (int) 4, 'sci' => (int) 2, 'sas' => (int) 4, 'tar' => (int) 1, 'tca' => (int) 1, 'tpr' => (int) 1, 'twi' => (int) 2, 'vmu' => (int) 1 ) $gf_gene_species = 'vmu' $gf_gene_id = 'VMungo1309G0868' $species_info = array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ) $local_species = 'tpr' $disabled = '' $selected = '' $num_hits = (int) 1
Warning (2): count(): Parameter must be an array or an object that implements Countable [APP/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp, line 33]Code Context $disabled = (!array_key_exists($local_species,$species_gene_counts))?"disabled":""; $selected = (isset($selected_species) && array_key_exists($local_species,$selected_species))?"checked='checked'":""; $num_hits = (array_key_exists($local_species,$species_gene_counts))?count($species_gene_counts[$local_species]):0; $viewFile = '/www/bioinformatics01_ro/plaza/_dev_instances/feedback/app/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp' $dataForView = array( 'sidebar_info' => array( 'gf_id' => 'HOM05D001729', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '375', 'num_species' => '42' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'Ah.07g204710' => 'amhyb', 'AUR62006001' => 'cqu', 'AUR62006002' => 'cqu', 'AUR62006003' => 'cqu', 'AUR62015641' => 'cqu', 'AUR62027174' => 'cqu', 'AUR62035623' => 'cqu', 'AUR62035624' => 'cqu', 'AUR62035625' => 'cqu', 'AUR62035626' => 'cqu', 'CAN.G1110.53' => 'can', 'CANSAT80G0415' => 'cansat', 'Ca_21364_v3' => 'car', 'COL.COLO4_30693' => 'col', 'COL.COLO4_30694' => 'col', 'COL.COLO4_30695' => 'col', 'COL.COLO4_30696' => 'col', 'COL.COLO4_34020' => 'col', 'DCAR_004585' => 'dca', 'Dinv04029' => 'din', 'Dinv34857' => 'din', 'Duzib147G0011' => 'dzi', 'Duzib170G0599' => 'dzi', 'Duzib192G1051' => 'dzi', 'FAN01G0708' => 'fan', 'FAN01G0742' => 'fan', 'FAN02G0048' => 'fan', 'FAN02G0583' => 'fan', 'FAN02G0688' => 'fan', 'FAN02G1588' => 'fan', 'FAN02G2194' => 'fan', 'FAN02G2750' => 'fan', 'FAN02G3094' => 'fan', 'FAN02G3887' => 'fan', 'FAN02G3911' => 'fan', 'FAN02G3994' => 'fan', 'FAN02G4432' => 'fan', 'FAN02G4556' => 'fan', 'FAN03G1977' => 'fan', 'FAN03G2781' => 'fan', 'FAN03G2850' => 'fan', 'FAN03G3155' => 'fan', 'FAN04G2487' => 'fan', 'FAN05G0208' => 'fan', 'FAN05G0656' => 'fan', 'FAN05G0696' => 'fan', 'FAN05G0810' => 'fan', 'FAN05G1447' => 'fan', 'FAN05G2640' => 'fan', 'FAN05G2911' => 'fan', 'FAN05G3901' => 'fan', 'FAN05G4859' => 'fan', 'FAN05G4861' => 'fan', 'FAN05G4988' => 'fan', 'FAN05G5187' => 'fan', 'FAN05G5452' => 'fan', 'FAN05G5500' => 'fan', 'FAN05G5688' => 'fan', 'FAN06G0177' => 'fan', 'FAN06G0675' => 'fan', 'FAN06G1290' => 'fan', 'FAN06G2191' => 'fan', 'FAN06G2405' => 'fan', 'FAN06G3231' => 'fan', 'FAN06G3932' => 'fan', 'FAN07G0163' => 'fan', 'FAN07G0471' => 'fan', 'FAN07G1354' => 'fan', 'FAN08G0338' => 'fan', 'FAN08G1373' => 'fan', 'FAN08G2539' => 'fan', 'FAN08G2728' => 'fan', 'FAN09G0608' => 'fan', 'FAN09G1136' => 'fan', 'FAN09G1958' => 'fan', 'FAN09G2508' => 'fan', 'FAN09G2597' => 'fan', 'FAN09G2658' => 'fan', 'FAN09G2757' => 'fan', 'FAN09G2983' => 'fan', 'FAN09G3130' => 'fan', 'FAN09G3565' => 'fan', 'FAN09G3613' => 'fan', 'FAN09G4011' => 'fan', 'FAN09G4239' => 'fan', 'FAN09G4277' => 'fan', 'FAN09G4720' => 'fan', 'FAN11G0139' => 'fan', 'FAN11G1727' => 'fan', 'FAN11G2672' => 'fan', 'FAN11G2795' => 'fan', 'FAN11G3238' => 'fan', 'FAN11G3734' => 'fan', 'FAN12G0631' => 'fan', 'FAN12G2239' => 'fan', 'FAN12G2308' => 'fan', 'FAN12G2569' => 'fan', 'FAN12G2623' => 'fan', 'FAN13G3182' => 'fan', 'FAN14G0053' => 'fan', 'FAN14G0370' => 'fan', 'FAN14G0382' => 'fan', 'FAN14G0421' => 'fan', 'FAN14G0866' => 'fan', 'FAN14G1187' => 'fan', 'FAN14G1727' => 'fan', 'FAN14G1791' => 'fan', 'FAN14G2361' => 'fan', 'FAN14G2668' => 'fan', 'FAN14G2770' => 'fan', 'FAN14G2874' => 'fan', 'FAN14G3193' => 'fan', 'FAN14G3624' => 'fan', 'FAN14G3676' => 'fan', 'FAN14G3807' => 'fan', 'FAN14G4082' => 'fan', 'FAN14G4342' => 'fan', 'FAN14G4985' => 'fan', 'FAN14G5126' => 'fan', 'FAN14G5781' => 'fan', 'FAN14G5808' => 'fan', 'FAN14G5949' => 'fan', 'FAN15G0828' => 'fan', 'FAN15G1054' => 'fan', 'FAN15G2023' => 'fan', 'FAN15G2506' => 'fan', 'FAN16G0128' => 'fan', 'FAN16G0249' => 'fan', 'FAN16G0429' => 'fan', 'FAN16G1493' => 'fan', 'FAN16G2210' => 'fan', 'FAN16G2506' => 'fan', 'FAN18G1542' => 'fan', 'FAN18G4057' => 'fan', 'FAN19G0745' => 'fan', 'FAN19G1216' => 'fan', 'FAN19G1733' => 'fan', 'FAN20G0258' => 'fan', 'FAN20G1095' => 'fan', 'FAN20G1557' => 'fan', 'FAN21G0302' => 'fan', 'FAN21G0519' => 'fan', 'FAN21G0970' => 'fan', 'FAN21G1159' => 'fan', 'FAN21G1312' => 'fan', 'FAN21G1440' => 'fan', 'FAN21G1715' => 'fan', 'FAN23G1584' => 'fan', 'FAN24G0045' => 'fan', 'FAN24G0053' => 'fan', 'FAN24G1500' => 'fan', 'FAN24G1817' => 'fan', 'FAN24G2147' => 'fan', 'FAN24G2236' => 'fan', 'FAN24G2446' => 'fan', 'FAN24G2684' => 'fan', 'FAN25G0187' => 'fan', 'FAN25G0505' => 'fan', 'FAN25G0589' => 'fan', 'FAN25G3663' => 'fan', 'FAN26G1025' => 'fan', 'FAN26G2860' => 'fan', 'FAN27G1329' => 'fan', 'FAN27G3392' => 'fan', 'FvH4_1g02011' => 'fve', 'FvH4_1g06511' => 'fve', 'FvH4_2g19900' => 'fve', 'FvH4_2g19920' => 'fve', 'FvH4_2g24261' => 'fve', 'FvH4_2g24270' => 'fve', 'FvH4_2g24631' => 'fve', 'FvH4_2g30622' => 'fve', 'FvH4_3g12920' => 'fve', 'FvH4_3g30171' => 'fve', 'FvH4_3g35490' => 'fve', 'FvH4_3g43682' => 'fve', 'FvH4_3g43730' => 'fve', 'FvH4_3g43732' => 'fve', 'FvH4_3g43751' => 'fve', 'FvH4_3g43752' => 'fve', 'FvH4_3g43770' => 'fve', 'FvH4_3g44471' => 'fve', 'FvH4_3g44510' => 'fve', 'FvH4_3g44582' => 'fve', 'FvH4_4g16921' => 'fve', 'FvH4_4g17121' => 'fve', 'FvH4_4g17782' => 'fve', 'FvH4_4g17783' => 'fve', 'FvH4_4g18120' => 'fve', 'FvH4_4g31310' => 'fve', 'FvH4_4g35052' => 'fve', 'FvH4_5g30862' => 'fve', 'FvH4_6g01541' => 'fve', 'FvH4_6g02021' => 'fve', 'FvH4_6g02041' => 'fve', 'FvH4_6g02071' => 'fve', 'FvH4_6g02171' => 'fve', 'FvH4_6g03181' => 'fve', 'FvH4_6g03182' => 'fve', 'FvH4_6g03221' => 'fve', 'FvH4_6g03380' => 'fve', 'FvH4_6g05201' => 'fve', 'FvH4_6g05203' => 'fve', 'FvH4_6g20231' => 'fve', 'FvH4_6g31981' => 'fve', 'FvH4_6g32061' => 'fve', 'FvH4_6g37041' => 'fve', 'FvH4_6g37932' => 'fve', 'FvH4_6g38731' => 'fve', 'FvH4_6g39370' => 'fve', 'FvH4_6g39371' => 'fve', 'FvH4_6g40891' => 'fve', 'FvH4_6g40892' => 'fve', 'FvH4_6g43143' => 'fve', 'FvH4_6g45251' => 'fve', 'FvH4_6g45260' => 'fve', 'FvH4_6g45291' => 'fve', 'FvH4_6g45890' => 'fve', 'FvH4_6g46240' => 'fve', 'FvH4_6g46241' => 'fve', 'FvH4_6g46242' => 'fve', 'FvH4_6g46260' => 'fve', 'FvH4_6g46280' => 'fve', 'FvH4_6g46380' => 'fve', 'FvH4_7g12841' => 'fve', 'FvH4_7g31431' => 'fve', 'Glyma.09G075900' => 'gma', 'Gohir.A09G096401' => 'ghi', 'Gohir.D09G096101' => 'ghi', 'Gorai.006G112800' => 'gra', 'HanXRQChr04g0121411' => 'han', 'Hund15878' => 'sun', 'Lj2A1107G68' => 'lonja', 'Lj2A630G63' => 'lonja', 'Lj2A946T25' => 'lonja', 'Lj2C714T1' => 'lonja', 'Lj2C966T3' => 'lonja', 'Lj2C966T4' => 'lonja', 'Lj4g0002979' => 'lja', 'Lsat_1_v5_gn_5_30901' => 'lsa', 'Lsat_1_v5_gn_5_31100' => 'lsa', 'Lsat_1_v5_gn_5_38600' => 'lsa', 'Lsat_1_v5_gn_6_92061' => 'lsa', 'Manes.05G071301' => 'mes', 'MD02G1008700' => 'mdo', 'MD02G1008900' => 'mdo', 'MD03G1256400' => 'mdo', 'MD04G1180900' => 'mdo', 'MD04G1181000' => 'mdo', 'MD04G1181200' => 'mdo', 'MD05G1244200' => 'mdo', 'MD05G1324200' => 'mdo', 'MD09G1201600' => 'mdo', 'MD10G1000600' => 'mdo', 'MD14G1026900' => 'mdo', 'MD14G1187900' => 'mdo', 'MD15G1017800' => 'mdo', 'MD15G1018100' => 'mdo', 'Medtr4g124160' => 'mtr', 'Migut.L01260' => 'egut', 'Nitab4.5_0000008g0440' => 'nta', 'Nitab4.5_0000207g0170' => 'nta', 'Nitab4.5_0007671g0030' => 'nta', 'Nitab4.5_0010853g0020' => 'nta', 'Oeu057656.1' => 'oeu', 'PGSC0003DMG400005638' => 'stu', 'PGSC0003DMG400005639' => 'stu', 'Phvul.009G222800' => 'pvu', 'Potri.009G132400' => 'ptr', 'Potri.009G163001' => 'ptr', 'Potri.011G000700' => 'ptr', 'Potri.011G004800' => 'ptr', 'Prupe.1G509300' => 'ppe', 'Prupe.1G509700' => 'ppe', 'Prupe.1G510400' => 'ppe', 'Prupe.1G510700' => 'ppe', 'Prupe.1G512600' => 'ppe', 'Prupe.2G073200' => 'ppe', 'Prupe.3G059500' => 'ppe', 'Prupe.3G059600' => 'ppe', 'Prupe.3G246100' => 'ppe', 'Prupe.3G265100' => 'ppe', 'Prupe.4G034700' => 'ppe', 'Prupe.4G052100' => 'ppe', 'Prupe.4G053600' => 'ppe', 'Prupe.5G068800' => 'ppe', 'Prupe.5G070600' => 'ppe', 'Prupe.6G075400' => 'ppe', 'Prupe.6G075500' => 'ppe', 'Prupe.6G076400' => 'ppe', 'Prupe.8G110700' => 'ppe', 'Psat4g020960' => 'psa', 'PSO135G0788' => 'pso', 'PSO210G6463' => 'pso', 'PSO384G0370' => 'pso', 'PSO386G0056' => 'pso', 'QL01p006048' => 'qlo', 'QL02p054283' => 'qlo', 'QL05p008000' => 'qlo', 'QL05p008212' => 'qlo', 'QL05p008950' => 'qlo', 'QL05p009042' => 'qlo', 'QL05p009518' => 'qlo', 'QL05p012589' => 'qlo', 'QL05p012608' => 'qlo', 'QL05p012650' => 'qlo', 'QL05p012667' => 'qlo', 'QL05p014501' => 'qlo', 'QL05p052800' => 'qlo', 'QL05p065010' => 'qlo', 'QL05p074156' => 'qlo', 'QL05p074160' => 'qlo', 'QL05p074174' => 'qlo', 'QL05p074178' => 'qlo', 'QL05p074214' => 'qlo', 'QL06p001050' => 'qlo', 'QL06p001056' => 'qlo', 'QL06p006093' => 'qlo', 'QL06p006111' => 'qlo', 'QL07p019784' => 'qlo', 'QL07p019801' => 'qlo', 'QL07p036110' => 'qlo', 'QL07p036134' => 'qlo', 'QL07p036147' => 'qlo', 'QL07p036156' => 'qlo', 'QL07p036300' => 'qlo', 'QL07p036320' => 'qlo', 'QL08p014547' => 'qlo', 'QL08p014551' => 'qlo', 'QL08p043319' => 'qlo', 'QL08p043324' => 'qlo', 'QL11p009094' => 'qlo', 'RcHm_v2.0_Chr1g0380481' => 'rch', 'RcHm_v2.0_Chr2g0089331' => 'rch', 'RcHm_v2.0_Chr2g0123691' => 'rch', 'RcHm_v2.0_Chr2g0151111' => 'rch', 'RcHm_v2.0_Chr2g0163011' => 'rch', 'RcHm_v2.0_Chr2g0163051' => 'rch', 'RcHm_v2.0_Chr2g0164671' => 'rch', 'RcHm_v2.0_Chr2g0164681' => 'rch', 'RcHm_v2.0_Chr2g0164721' => 'rch', 'RcHm_v2.0_Chr3g0449911' => 'rch', 'RcHm_v2.0_Chr3g0450211' => 'rch', 'RcHm_v2.0_Chr3g0457271' => 'rch', 'RcHm_v2.0_Chr5g0018111' => 'rch', 'RcHm_v2.0_Chr5g0021011' => 'rch', 'RcHm_v2.0_Chr5g0081171' => 'rch', 'RcHm_v2.0_Chr5g0081211' => 'rch', 'RcHm_v2.0_Chr6g0275871' => 'rch', 'RcHm_v2.0_Chr6g0276071' => 'rch', 'RcHm_v2.0_Chr6g0285591' => 'rch', 'RcHm_v2.0_Chr6g0291931' => 'rch', 'RcHm_v2.0_Chr6g0292091' => 'rch', 'RcHm_v2.0_Chr6g0292271' => 'rch', 'RcHm_v2.0_Chr7g0221261' => 'rch', 'Rhsim08G0219900' => 'rsi', 'Rhsim08G0220200' => 'rsi', 'Rhsim08G0237800' => 'rsi', 'Rhsim08G0238800' => 'rsi', 'Sabra09G0102700' => 'sbr', 'Sabra09G0127200' => 'sbr', 'Sabra11G0003700' => 'sbr', 'Sabra15G0014700' => 'sbr', 'Sc19g0000590' => 'sci', 'Sc19g0001870' => 'sci', 'SGA_v2.0_scaffold1G00346' => 'sas', 'SGA_v2.0_scaffold1G00575' => 'sas', 'SGA_v2.0_scaffold1G00761' => 'sas', 'SGA_v2.0_scaffold232G43501' => 'sas', 'TAR625G1137' => 'tar', 'Thecc.03G222100' => 'tca', 'TPR.G12691' => 'tpr', 'TWI34G0727' => 'twi', 'TWI36G0117' => 'twi', 'VMungo1309G0868' => 'vmu' ), 'gf_id' => 'HOM05D001729', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001729' ), 'data_identifier' => 'HOM05D001729', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001729', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '375', 'num_species' => '42' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'Ah.07g204710' => 'amhyb', 'AUR62006001' => 'cqu', 'AUR62006002' => 'cqu', 'AUR62006003' => 'cqu', 'AUR62015641' => 'cqu', 'AUR62027174' => 'cqu', 'AUR62035623' => 'cqu', 'AUR62035624' => 'cqu', 'AUR62035625' => 'cqu', 'AUR62035626' => 'cqu', 'CAN.G1110.53' => 'can', 'CANSAT80G0415' => 'cansat', 'Ca_21364_v3' => 'car', 'COL.COLO4_30693' => 'col', 'COL.COLO4_30694' => 'col', 'COL.COLO4_30695' => 'col', 'COL.COLO4_30696' => 'col', 'COL.COLO4_34020' => 'col', 'DCAR_004585' => 'dca', 'Dinv04029' => 'din', 'Dinv34857' => 'din', 'Duzib147G0011' => 'dzi', 'Duzib170G0599' => 'dzi', 'Duzib192G1051' => 'dzi', 'FAN01G0708' => 'fan', 'FAN01G0742' => 'fan', 'FAN02G0048' => 'fan', 'FAN02G0583' => 'fan', 'FAN02G0688' => 'fan', 'FAN02G1588' => 'fan', 'FAN02G2194' => 'fan', 'FAN02G2750' => 'fan', 'FAN02G3094' => 'fan', 'FAN02G3887' => 'fan', 'FAN02G3911' => 'fan', 'FAN02G3994' => 'fan', 'FAN02G4432' => 'fan', 'FAN02G4556' => 'fan', 'FAN03G1977' => 'fan', 'FAN03G2781' => 'fan', 'FAN03G2850' => 'fan', 'FAN03G3155' => 'fan', 'FAN04G2487' => 'fan', 'FAN05G0208' => 'fan', 'FAN05G0656' => 'fan', 'FAN05G0696' => 'fan', 'FAN05G0810' => 'fan', 'FAN05G1447' => 'fan', 'FAN05G2640' => 'fan', 'FAN05G2911' => 'fan', 'FAN05G3901' => 'fan', 'FAN05G4859' => 'fan', 'FAN05G4861' => 'fan', 'FAN05G4988' => 'fan', 'FAN05G5187' => 'fan', 'FAN05G5452' => 'fan', 'FAN05G5500' => 'fan', 'FAN05G5688' => 'fan', 'FAN06G0177' => 'fan', 'FAN06G0675' => 'fan', 'FAN06G1290' => 'fan', 'FAN06G2191' => 'fan', 'FAN06G2405' => 'fan', 'FAN06G3231' => 'fan', 'FAN06G3932' => 'fan', 'FAN07G0163' => 'fan', 'FAN07G0471' => 'fan', 'FAN07G1354' => 'fan', 'FAN08G0338' => 'fan', 'FAN08G1373' => 'fan', 'FAN08G2539' => 'fan', 'FAN08G2728' => 'fan', 'FAN09G0608' => 'fan', 'FAN09G1136' => 'fan', 'FAN09G1958' => 'fan', 'FAN09G2508' => 'fan', 'FAN09G2597' => 'fan', 'FAN09G2658' => 'fan', 'FAN09G2757' => 'fan', 'FAN09G2983' => 'fan', 'FAN09G3130' => 'fan', 'FAN09G3565' => 'fan', 'FAN09G3613' => 'fan', 'FAN09G4011' => 'fan', 'FAN09G4239' => 'fan', 'FAN09G4277' => 'fan', 'FAN09G4720' => 'fan', 'FAN11G0139' => 'fan', 'FAN11G1727' => 'fan', 'FAN11G2672' => 'fan', 'FAN11G2795' => 'fan', 'FAN11G3238' => 'fan', 'FAN11G3734' => 'fan', 'FAN12G0631' => 'fan', 'FAN12G2239' => 'fan', 'FAN12G2308' => 'fan', 'FAN12G2569' => 'fan', 'FAN12G2623' => 'fan', 'FAN13G3182' => 'fan', 'FAN14G0053' => 'fan', 'FAN14G0370' => 'fan', 'FAN14G0382' => 'fan', 'FAN14G0421' => 'fan', 'FAN14G0866' => 'fan', 'FAN14G1187' => 'fan', 'FAN14G1727' => 'fan', 'FAN14G1791' => 'fan', 'FAN14G2361' => 'fan', 'FAN14G2668' => 'fan', 'FAN14G2770' => 'fan', 'FAN14G2874' => 'fan', 'FAN14G3193' => 'fan', 'FAN14G3624' => 'fan', 'FAN14G3676' => 'fan', 'FAN14G3807' => 'fan', 'FAN14G4082' => 'fan', 'FAN14G4342' => 'fan', 'FAN14G4985' => 'fan', 'FAN14G5126' => 'fan', 'FAN14G5781' => 'fan', 'FAN14G5808' => 'fan', 'FAN14G5949' => 'fan', 'FAN15G0828' => 'fan', 'FAN15G1054' => 'fan', 'FAN15G2023' => 'fan', 'FAN15G2506' => 'fan', 'FAN16G0128' => 'fan', 'FAN16G0249' => 'fan', 'FAN16G0429' => 'fan', 'FAN16G1493' => 'fan', 'FAN16G2210' => 'fan', 'FAN16G2506' => 'fan', 'FAN18G1542' => 'fan', 'FAN18G4057' => 'fan', 'FAN19G0745' => 'fan', 'FAN19G1216' => 'fan', 'FAN19G1733' => 'fan', 'FAN20G0258' => 'fan', 'FAN20G1095' => 'fan', 'FAN20G1557' => 'fan', 'FAN21G0302' => 'fan', 'FAN21G0519' => 'fan', 'FAN21G0970' => 'fan', 'FAN21G1159' => 'fan', 'FAN21G1312' => 'fan', 'FAN21G1440' => 'fan', 'FAN21G1715' => 'fan', 'FAN23G1584' => 'fan', 'FAN24G0045' => 'fan', 'FAN24G0053' => 'fan', 'FAN24G1500' => 'fan', 'FAN24G1817' => 'fan', 'FAN24G2147' => 'fan', 'FAN24G2236' => 'fan', 'FAN24G2446' => 'fan', 'FAN24G2684' => 'fan', 'FAN25G0187' => 'fan', 'FAN25G0505' => 'fan', 'FAN25G0589' => 'fan', 'FAN25G3663' => 'fan', 'FAN26G1025' => 'fan', 'FAN26G2860' => 'fan', 'FAN27G1329' => 'fan', 'FAN27G3392' => 'fan', 'FvH4_1g02011' => 'fve', 'FvH4_1g06511' => 'fve', 'FvH4_2g19900' => 'fve', 'FvH4_2g19920' => 'fve', 'FvH4_2g24261' => 'fve', 'FvH4_2g24270' => 'fve', 'FvH4_2g24631' => 'fve', 'FvH4_2g30622' => 'fve', 'FvH4_3g12920' => 'fve', 'FvH4_3g30171' => 'fve', 'FvH4_3g35490' => 'fve', 'FvH4_3g43682' => 'fve', 'FvH4_3g43730' => 'fve', 'FvH4_3g43732' => 'fve', 'FvH4_3g43751' => 'fve', 'FvH4_3g43752' => 'fve', 'FvH4_3g43770' => 'fve', 'FvH4_3g44471' => 'fve', 'FvH4_3g44510' => 'fve', 'FvH4_3g44582' => 'fve', 'FvH4_4g16921' => 'fve', 'FvH4_4g17121' => 'fve', 'FvH4_4g17782' => 'fve', 'FvH4_4g17783' => 'fve', 'FvH4_4g18120' => 'fve', 'FvH4_4g31310' => 'fve', 'FvH4_4g35052' => 'fve', 'FvH4_5g30862' => 'fve', 'FvH4_6g01541' => 'fve', 'FvH4_6g02021' => 'fve', 'FvH4_6g02041' => 'fve', 'FvH4_6g02071' => 'fve', 'FvH4_6g02171' => 'fve', 'FvH4_6g03181' => 'fve', 'FvH4_6g03182' => 'fve', 'FvH4_6g03221' => 'fve', 'FvH4_6g03380' => 'fve', 'FvH4_6g05201' => 'fve', 'FvH4_6g05203' => 'fve', 'FvH4_6g20231' => 'fve', 'FvH4_6g31981' => 'fve', 'FvH4_6g32061' => 'fve', 'FvH4_6g37041' => 'fve', 'FvH4_6g37932' => 'fve', 'FvH4_6g38731' => 'fve', 'FvH4_6g39370' => 'fve', 'FvH4_6g39371' => 'fve', 'FvH4_6g40891' => 'fve', 'FvH4_6g40892' => 'fve', 'FvH4_6g43143' => 'fve', 'FvH4_6g45251' => 'fve', 'FvH4_6g45260' => 'fve', 'FvH4_6g45291' => 'fve', 'FvH4_6g45890' => 'fve', 'FvH4_6g46240' => 'fve', 'FvH4_6g46241' => 'fve', 'FvH4_6g46242' => 'fve', 'FvH4_6g46260' => 'fve', 'FvH4_6g46280' => 'fve', 'FvH4_6g46380' => 'fve', 'FvH4_7g12841' => 'fve', 'FvH4_7g31431' => 'fve', 'Glyma.09G075900' => 'gma', 'Gohir.A09G096401' => 'ghi', 'Gohir.D09G096101' => 'ghi', 'Gorai.006G112800' => 'gra', 'HanXRQChr04g0121411' => 'han', 'Hund15878' => 'sun', 'Lj2A1107G68' => 'lonja', 'Lj2A630G63' => 'lonja', 'Lj2A946T25' => 'lonja', 'Lj2C714T1' => 'lonja', 'Lj2C966T3' => 'lonja', 'Lj2C966T4' => 'lonja', 'Lj4g0002979' => 'lja', 'Lsat_1_v5_gn_5_30901' => 'lsa', 'Lsat_1_v5_gn_5_31100' => 'lsa', 'Lsat_1_v5_gn_5_38600' => 'lsa', 'Lsat_1_v5_gn_6_92061' => 'lsa', 'Manes.05G071301' => 'mes', 'MD02G1008700' => 'mdo', 'MD02G1008900' => 'mdo', 'MD03G1256400' => 'mdo', 'MD04G1180900' => 'mdo', 'MD04G1181000' => 'mdo', 'MD04G1181200' => 'mdo', 'MD05G1244200' => 'mdo', 'MD05G1324200' => 'mdo', 'MD09G1201600' => 'mdo', 'MD10G1000600' => 'mdo', 'MD14G1026900' => 'mdo', 'MD14G1187900' => 'mdo', 'MD15G1017800' => 'mdo', 'MD15G1018100' => 'mdo', 'Medtr4g124160' => 'mtr', 'Migut.L01260' => 'egut', 'Nitab4.5_0000008g0440' => 'nta', 'Nitab4.5_0000207g0170' => 'nta', 'Nitab4.5_0007671g0030' => 'nta', 'Nitab4.5_0010853g0020' => 'nta', 'Oeu057656.1' => 'oeu', 'PGSC0003DMG400005638' => 'stu', 'PGSC0003DMG400005639' => 'stu', 'Phvul.009G222800' => 'pvu', 'Potri.009G132400' => 'ptr', 'Potri.009G163001' => 'ptr', 'Potri.011G000700' => 'ptr', 'Potri.011G004800' => 'ptr', 'Prupe.1G509300' => 'ppe', 'Prupe.1G509700' => 'ppe', 'Prupe.1G510400' => 'ppe', 'Prupe.1G510700' => 'ppe', 'Prupe.1G512600' => 'ppe', 'Prupe.2G073200' => 'ppe', 'Prupe.3G059500' => 'ppe', 'Prupe.3G059600' => 'ppe', 'Prupe.3G246100' => 'ppe', 'Prupe.3G265100' => 'ppe', 'Prupe.4G034700' => 'ppe', 'Prupe.4G052100' => 'ppe', 'Prupe.4G053600' => 'ppe', 'Prupe.5G068800' => 'ppe', 'Prupe.5G070600' => 'ppe', 'Prupe.6G075400' => 'ppe', 'Prupe.6G075500' => 'ppe', 'Prupe.6G076400' => 'ppe', 'Prupe.8G110700' => 'ppe', 'Psat4g020960' => 'psa', 'PSO135G0788' => 'pso', 'PSO210G6463' => 'pso', 'PSO384G0370' => 'pso', 'PSO386G0056' => 'pso', 'QL01p006048' => 'qlo', 'QL02p054283' => 'qlo', 'QL05p008000' => 'qlo', 'QL05p008212' => 'qlo', 'QL05p008950' => 'qlo', 'QL05p009042' => 'qlo', 'QL05p009518' => 'qlo', 'QL05p012589' => 'qlo', 'QL05p012608' => 'qlo', 'QL05p012650' => 'qlo', 'QL05p012667' => 'qlo', 'QL05p014501' => 'qlo', 'QL05p052800' => 'qlo', 'QL05p065010' => 'qlo', 'QL05p074156' => 'qlo', 'QL05p074160' => 'qlo', 'QL05p074174' => 'qlo', 'QL05p074178' => 'qlo', 'QL05p074214' => 'qlo', 'QL06p001050' => 'qlo', 'QL06p001056' => 'qlo', 'QL06p006093' => 'qlo', 'QL06p006111' => 'qlo', 'QL07p019784' => 'qlo', 'QL07p019801' => 'qlo', 'QL07p036110' => 'qlo', 'QL07p036134' => 'qlo', 'QL07p036147' => 'qlo', 'QL07p036156' => 'qlo', 'QL07p036300' => 'qlo', 'QL07p036320' => 'qlo', 'QL08p014547' => 'qlo', 'QL08p014551' => 'qlo', 'QL08p043319' => 'qlo', 'QL08p043324' => 'qlo', 'QL11p009094' => 'qlo', 'RcHm_v2.0_Chr1g0380481' => 'rch', 'RcHm_v2.0_Chr2g0089331' => 'rch', 'RcHm_v2.0_Chr2g0123691' => 'rch', 'RcHm_v2.0_Chr2g0151111' => 'rch', 'RcHm_v2.0_Chr2g0163011' => 'rch', 'RcHm_v2.0_Chr2g0163051' => 'rch', 'RcHm_v2.0_Chr2g0164671' => 'rch', 'RcHm_v2.0_Chr2g0164681' => 'rch', 'RcHm_v2.0_Chr2g0164721' => 'rch', 'RcHm_v2.0_Chr3g0449911' => 'rch', 'RcHm_v2.0_Chr3g0450211' => 'rch', 'RcHm_v2.0_Chr3g0457271' => 'rch', 'RcHm_v2.0_Chr5g0018111' => 'rch', 'RcHm_v2.0_Chr5g0021011' => 'rch', 'RcHm_v2.0_Chr5g0081171' => 'rch', 'RcHm_v2.0_Chr5g0081211' => 'rch', 'RcHm_v2.0_Chr6g0275871' => 'rch', 'RcHm_v2.0_Chr6g0276071' => 'rch', 'RcHm_v2.0_Chr6g0285591' => 'rch', 'RcHm_v2.0_Chr6g0291931' => 'rch', 'RcHm_v2.0_Chr6g0292091' => 'rch', 'RcHm_v2.0_Chr6g0292271' => 'rch', 'RcHm_v2.0_Chr7g0221261' => 'rch', 'Rhsim08G0219900' => 'rsi', 'Rhsim08G0220200' => 'rsi', 'Rhsim08G0237800' => 'rsi', 'Rhsim08G0238800' => 'rsi', 'Sabra09G0102700' => 'sbr', 'Sabra09G0127200' => 'sbr', 'Sabra11G0003700' => 'sbr', 'Sabra15G0014700' => 'sbr', 'Sc19g0000590' => 'sci', 'Sc19g0001870' => 'sci', 'SGA_v2.0_scaffold1G00346' => 'sas', 'SGA_v2.0_scaffold1G00575' => 'sas', 'SGA_v2.0_scaffold1G00761' => 'sas', 'SGA_v2.0_scaffold232G43501' => 'sas', 'TAR625G1137' => 'tar', 'Thecc.03G222100' => 'tca', 'TPR.G12691' => 'tpr', 'TWI34G0727' => 'twi', 'TWI36G0117' => 'twi', 'VMungo1309G0868' => 'vmu' ) $gf_id = 'HOM05D001729' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001729' ) $data_identifier = 'HOM05D001729' $data_type = 'gf_id' $species_gene_counts = array( 'amhyb' => (int) 1, 'cqu' => (int) 9, 'can' => (int) 1, 'cansat' => (int) 1, 'car' => (int) 1, 'col' => (int) 5, 'dca' => (int) 1, 'din' => (int) 2, 'dzi' => (int) 3, 'fan' => (int) 140, 'fve' => (int) 62, 'gma' => (int) 1, 'ghi' => (int) 2, 'gra' => (int) 1, 'han' => (int) 1, 'sun' => (int) 1, 'lonja' => (int) 6, 'lja' => (int) 1, 'lsa' => (int) 4, 'mes' => (int) 1, 'mdo' => (int) 14, 'mtr' => (int) 1, 'egut' => (int) 1, 'nta' => (int) 4, 'oeu' => (int) 1, 'stu' => (int) 2, 'pvu' => (int) 1, 'ptr' => (int) 4, 'ppe' => (int) 19, 'psa' => (int) 1, 'pso' => (int) 4, 'qlo' => (int) 36, 'rch' => (int) 23, 'rsi' => (int) 4, 'sbr' => (int) 4, 'sci' => (int) 2, 'sas' => (int) 4, 'tar' => (int) 1, 'tca' => (int) 1, 'tpr' => (int) 1, 'twi' => (int) 2, 'vmu' => (int) 1 ) $gf_gene_species = 'vmu' $gf_gene_id = 'VMungo1309G0868' $species_info = array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ) $local_species = 'twi' $disabled = '' $selected = '' $num_hits = (int) 1include - APP/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp, line 33 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933 View::_renderElement() - CORE/Cake/View/View.php, line 1224 View::element() - CORE/Cake/View/View.php, line 418 include - APP/View/Elements/analysis/phylogenetics_module/gf_data_settings.ctp, line 37 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933 View::_renderElement() - CORE/Cake/View/View.php, line 1224 View::element() - CORE/Cake/View/View.php, line 418 include - APP/View/Elements/analysis/phylogenetics_module/parameter_selection.ctp, line 64 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933 View::_renderElement() - CORE/Cake/View/View.php, line 1224 View::element() - CORE/Cake/View/View.php, line 418 include - APP/View/Analysis/custom_tree_creation.ctp, line 27 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933
$viewFile = '/www/bioinformatics01_ro/plaza/_dev_instances/feedback/app/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp' $dataForView = array( 'sidebar_info' => array( 'gf_id' => 'HOM05D001729', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '375', 'num_species' => '42' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'Ah.07g204710' => 'amhyb', 'AUR62006001' => 'cqu', 'AUR62006002' => 'cqu', 'AUR62006003' => 'cqu', 'AUR62015641' => 'cqu', 'AUR62027174' => 'cqu', 'AUR62035623' => 'cqu', 'AUR62035624' => 'cqu', 'AUR62035625' => 'cqu', 'AUR62035626' => 'cqu', 'CAN.G1110.53' => 'can', 'CANSAT80G0415' => 'cansat', 'Ca_21364_v3' => 'car', 'COL.COLO4_30693' => 'col', 'COL.COLO4_30694' => 'col', 'COL.COLO4_30695' => 'col', 'COL.COLO4_30696' => 'col', 'COL.COLO4_34020' => 'col', 'DCAR_004585' => 'dca', 'Dinv04029' => 'din', 'Dinv34857' => 'din', 'Duzib147G0011' => 'dzi', 'Duzib170G0599' => 'dzi', 'Duzib192G1051' => 'dzi', 'FAN01G0708' => 'fan', 'FAN01G0742' => 'fan', 'FAN02G0048' => 'fan', 'FAN02G0583' => 'fan', 'FAN02G0688' => 'fan', 'FAN02G1588' => 'fan', 'FAN02G2194' => 'fan', 'FAN02G2750' => 'fan', 'FAN02G3094' => 'fan', 'FAN02G3887' => 'fan', 'FAN02G3911' => 'fan', 'FAN02G3994' => 'fan', 'FAN02G4432' => 'fan', 'FAN02G4556' => 'fan', 'FAN03G1977' => 'fan', 'FAN03G2781' => 'fan', 'FAN03G2850' => 'fan', 'FAN03G3155' => 'fan', 'FAN04G2487' => 'fan', 'FAN05G0208' => 'fan', 'FAN05G0656' => 'fan', 'FAN05G0696' => 'fan', 'FAN05G0810' => 'fan', 'FAN05G1447' => 'fan', 'FAN05G2640' => 'fan', 'FAN05G2911' => 'fan', 'FAN05G3901' => 'fan', 'FAN05G4859' => 'fan', 'FAN05G4861' => 'fan', 'FAN05G4988' => 'fan', 'FAN05G5187' => 'fan', 'FAN05G5452' => 'fan', 'FAN05G5500' => 'fan', 'FAN05G5688' => 'fan', 'FAN06G0177' => 'fan', 'FAN06G0675' => 'fan', 'FAN06G1290' => 'fan', 'FAN06G2191' => 'fan', 'FAN06G2405' => 'fan', 'FAN06G3231' => 'fan', 'FAN06G3932' => 'fan', 'FAN07G0163' => 'fan', 'FAN07G0471' => 'fan', 'FAN07G1354' => 'fan', 'FAN08G0338' => 'fan', 'FAN08G1373' => 'fan', 'FAN08G2539' => 'fan', 'FAN08G2728' => 'fan', 'FAN09G0608' => 'fan', 'FAN09G1136' => 'fan', 'FAN09G1958' => 'fan', 'FAN09G2508' => 'fan', 'FAN09G2597' => 'fan', 'FAN09G2658' => 'fan', 'FAN09G2757' => 'fan', 'FAN09G2983' => 'fan', 'FAN09G3130' => 'fan', 'FAN09G3565' => 'fan', 'FAN09G3613' => 'fan', 'FAN09G4011' => 'fan', 'FAN09G4239' => 'fan', 'FAN09G4277' => 'fan', 'FAN09G4720' => 'fan', 'FAN11G0139' => 'fan', 'FAN11G1727' => 'fan', 'FAN11G2672' => 'fan', 'FAN11G2795' => 'fan', 'FAN11G3238' => 'fan', 'FAN11G3734' => 'fan', 'FAN12G0631' => 'fan', 'FAN12G2239' => 'fan', 'FAN12G2308' => 'fan', 'FAN12G2569' => 'fan', 'FAN12G2623' => 'fan', 'FAN13G3182' => 'fan', 'FAN14G0053' => 'fan', 'FAN14G0370' => 'fan', 'FAN14G0382' => 'fan', 'FAN14G0421' => 'fan', 'FAN14G0866' => 'fan', 'FAN14G1187' => 'fan', 'FAN14G1727' => 'fan', 'FAN14G1791' => 'fan', 'FAN14G2361' => 'fan', 'FAN14G2668' => 'fan', 'FAN14G2770' => 'fan', 'FAN14G2874' => 'fan', 'FAN14G3193' => 'fan', 'FAN14G3624' => 'fan', 'FAN14G3676' => 'fan', 'FAN14G3807' => 'fan', 'FAN14G4082' => 'fan', 'FAN14G4342' => 'fan', 'FAN14G4985' => 'fan', 'FAN14G5126' => 'fan', 'FAN14G5781' => 'fan', 'FAN14G5808' => 'fan', 'FAN14G5949' => 'fan', 'FAN15G0828' => 'fan', 'FAN15G1054' => 'fan', 'FAN15G2023' => 'fan', 'FAN15G2506' => 'fan', 'FAN16G0128' => 'fan', 'FAN16G0249' => 'fan', 'FAN16G0429' => 'fan', 'FAN16G1493' => 'fan', 'FAN16G2210' => 'fan', 'FAN16G2506' => 'fan', 'FAN18G1542' => 'fan', 'FAN18G4057' => 'fan', 'FAN19G0745' => 'fan', 'FAN19G1216' => 'fan', 'FAN19G1733' => 'fan', 'FAN20G0258' => 'fan', 'FAN20G1095' => 'fan', 'FAN20G1557' => 'fan', 'FAN21G0302' => 'fan', 'FAN21G0519' => 'fan', 'FAN21G0970' => 'fan', 'FAN21G1159' => 'fan', 'FAN21G1312' => 'fan', 'FAN21G1440' => 'fan', 'FAN21G1715' => 'fan', 'FAN23G1584' => 'fan', 'FAN24G0045' => 'fan', 'FAN24G0053' => 'fan', 'FAN24G1500' => 'fan', 'FAN24G1817' => 'fan', 'FAN24G2147' => 'fan', 'FAN24G2236' => 'fan', 'FAN24G2446' => 'fan', 'FAN24G2684' => 'fan', 'FAN25G0187' => 'fan', 'FAN25G0505' => 'fan', 'FAN25G0589' => 'fan', 'FAN25G3663' => 'fan', 'FAN26G1025' => 'fan', 'FAN26G2860' => 'fan', 'FAN27G1329' => 'fan', 'FAN27G3392' => 'fan', 'FvH4_1g02011' => 'fve', 'FvH4_1g06511' => 'fve', 'FvH4_2g19900' => 'fve', 'FvH4_2g19920' => 'fve', 'FvH4_2g24261' => 'fve', 'FvH4_2g24270' => 'fve', 'FvH4_2g24631' => 'fve', 'FvH4_2g30622' => 'fve', 'FvH4_3g12920' => 'fve', 'FvH4_3g30171' => 'fve', 'FvH4_3g35490' => 'fve', 'FvH4_3g43682' => 'fve', 'FvH4_3g43730' => 'fve', 'FvH4_3g43732' => 'fve', 'FvH4_3g43751' => 'fve', 'FvH4_3g43752' => 'fve', 'FvH4_3g43770' => 'fve', 'FvH4_3g44471' => 'fve', 'FvH4_3g44510' => 'fve', 'FvH4_3g44582' => 'fve', 'FvH4_4g16921' => 'fve', 'FvH4_4g17121' => 'fve', 'FvH4_4g17782' => 'fve', 'FvH4_4g17783' => 'fve', 'FvH4_4g18120' => 'fve', 'FvH4_4g31310' => 'fve', 'FvH4_4g35052' => 'fve', 'FvH4_5g30862' => 'fve', 'FvH4_6g01541' => 'fve', 'FvH4_6g02021' => 'fve', 'FvH4_6g02041' => 'fve', 'FvH4_6g02071' => 'fve', 'FvH4_6g02171' => 'fve', 'FvH4_6g03181' => 'fve', 'FvH4_6g03182' => 'fve', 'FvH4_6g03221' => 'fve', 'FvH4_6g03380' => 'fve', 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'ppe', 'Prupe.1G512600' => 'ppe', 'Prupe.2G073200' => 'ppe', 'Prupe.3G059500' => 'ppe', 'Prupe.3G059600' => 'ppe', 'Prupe.3G246100' => 'ppe', 'Prupe.3G265100' => 'ppe', 'Prupe.4G034700' => 'ppe', 'Prupe.4G052100' => 'ppe', 'Prupe.4G053600' => 'ppe', 'Prupe.5G068800' => 'ppe', 'Prupe.5G070600' => 'ppe', 'Prupe.6G075400' => 'ppe', 'Prupe.6G075500' => 'ppe', 'Prupe.6G076400' => 'ppe', 'Prupe.8G110700' => 'ppe', 'Psat4g020960' => 'psa', 'PSO135G0788' => 'pso', 'PSO210G6463' => 'pso', 'PSO384G0370' => 'pso', 'PSO386G0056' => 'pso', 'QL01p006048' => 'qlo', 'QL02p054283' => 'qlo', 'QL05p008000' => 'qlo', 'QL05p008212' => 'qlo', 'QL05p008950' => 'qlo', 'QL05p009042' => 'qlo', 'QL05p009518' => 'qlo', 'QL05p012589' => 'qlo', 'QL05p012608' => 'qlo', 'QL05p012650' => 'qlo', 'QL05p012667' => 'qlo', 'QL05p014501' => 'qlo', 'QL05p052800' => 'qlo', 'QL05p065010' => 'qlo', 'QL05p074156' => 'qlo', 'QL05p074160' => 'qlo', 'QL05p074174' => 'qlo', 'QL05p074178' => 'qlo', 'QL05p074214' => 'qlo', 'QL06p001050' => 'qlo', 'QL06p001056' => 'qlo', 'QL06p006093' => 'qlo', 'QL06p006111' => 'qlo', 'QL07p019784' => 'qlo', 'QL07p019801' => 'qlo', 'QL07p036110' => 'qlo', 'QL07p036134' => 'qlo', 'QL07p036147' => 'qlo', 'QL07p036156' => 'qlo', 'QL07p036300' => 'qlo', 'QL07p036320' => 'qlo', 'QL08p014547' => 'qlo', 'QL08p014551' => 'qlo', 'QL08p043319' => 'qlo', 'QL08p043324' => 'qlo', 'QL11p009094' => 'qlo', 'RcHm_v2.0_Chr1g0380481' => 'rch', 'RcHm_v2.0_Chr2g0089331' => 'rch', 'RcHm_v2.0_Chr2g0123691' => 'rch', 'RcHm_v2.0_Chr2g0151111' => 'rch', 'RcHm_v2.0_Chr2g0163011' => 'rch', 'RcHm_v2.0_Chr2g0163051' => 'rch', 'RcHm_v2.0_Chr2g0164671' => 'rch', 'RcHm_v2.0_Chr2g0164681' => 'rch', 'RcHm_v2.0_Chr2g0164721' => 'rch', 'RcHm_v2.0_Chr3g0449911' => 'rch', 'RcHm_v2.0_Chr3g0450211' => 'rch', 'RcHm_v2.0_Chr3g0457271' => 'rch', 'RcHm_v2.0_Chr5g0018111' => 'rch', 'RcHm_v2.0_Chr5g0021011' => 'rch', 'RcHm_v2.0_Chr5g0081171' => 'rch', 'RcHm_v2.0_Chr5g0081211' => 'rch', 'RcHm_v2.0_Chr6g0275871' => 'rch', 'RcHm_v2.0_Chr6g0276071' => 'rch', 'RcHm_v2.0_Chr6g0285591' => 'rch', 'RcHm_v2.0_Chr6g0291931' => 'rch', 'RcHm_v2.0_Chr6g0292091' => 'rch', 'RcHm_v2.0_Chr6g0292271' => 'rch', 'RcHm_v2.0_Chr7g0221261' => 'rch', 'Rhsim08G0219900' => 'rsi', 'Rhsim08G0220200' => 'rsi', 'Rhsim08G0237800' => 'rsi', 'Rhsim08G0238800' => 'rsi', 'Sabra09G0102700' => 'sbr', 'Sabra09G0127200' => 'sbr', 'Sabra11G0003700' => 'sbr', 'Sabra15G0014700' => 'sbr', 'Sc19g0000590' => 'sci', 'Sc19g0001870' => 'sci', 'SGA_v2.0_scaffold1G00346' => 'sas', 'SGA_v2.0_scaffold1G00575' => 'sas', 'SGA_v2.0_scaffold1G00761' => 'sas', 'SGA_v2.0_scaffold232G43501' => 'sas', 'TAR625G1137' => 'tar', 'Thecc.03G222100' => 'tca', 'TPR.G12691' => 'tpr', 'TWI34G0727' => 'twi', 'TWI36G0117' => 'twi', 'VMungo1309G0868' => 'vmu' ), 'gf_id' => 'HOM05D001729', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001729' ), 'data_identifier' => 'HOM05D001729', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001729', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '375', 'num_species' => '42' ) 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'AUR62035624' => 'cqu', 'AUR62035625' => 'cqu', 'AUR62035626' => 'cqu', 'CAN.G1110.53' => 'can', 'CANSAT80G0415' => 'cansat', 'Ca_21364_v3' => 'car', 'COL.COLO4_30693' => 'col', 'COL.COLO4_30694' => 'col', 'COL.COLO4_30695' => 'col', 'COL.COLO4_30696' => 'col', 'COL.COLO4_34020' => 'col', 'DCAR_004585' => 'dca', 'Dinv04029' => 'din', 'Dinv34857' => 'din', 'Duzib147G0011' => 'dzi', 'Duzib170G0599' => 'dzi', 'Duzib192G1051' => 'dzi', 'FAN01G0708' => 'fan', 'FAN01G0742' => 'fan', 'FAN02G0048' => 'fan', 'FAN02G0583' => 'fan', 'FAN02G0688' => 'fan', 'FAN02G1588' => 'fan', 'FAN02G2194' => 'fan', 'FAN02G2750' => 'fan', 'FAN02G3094' => 'fan', 'FAN02G3887' => 'fan', 'FAN02G3911' => 'fan', 'FAN02G3994' => 'fan', 'FAN02G4432' => 'fan', 'FAN02G4556' => 'fan', 'FAN03G1977' => 'fan', 'FAN03G2781' => 'fan', 'FAN03G2850' => 'fan', 'FAN03G3155' => 'fan', 'FAN04G2487' => 'fan', 'FAN05G0208' => 'fan', 'FAN05G0656' => 'fan', 'FAN05G0696' => 'fan', 'FAN05G0810' => 'fan', 'FAN05G1447' => 'fan', 'FAN05G2640' => 'fan', 'FAN05G2911' => 'fan', 'FAN05G3901' => 'fan', 'FAN05G4859' => 'fan', 'FAN05G4861' => 'fan', 'FAN05G4988' => 'fan', 'FAN05G5187' => 'fan', 'FAN05G5452' => 'fan', 'FAN05G5500' => 'fan', 'FAN05G5688' => 'fan', 'FAN06G0177' => 'fan', 'FAN06G0675' => 'fan', 'FAN06G1290' => 'fan', 'FAN06G2191' => 'fan', 'FAN06G2405' => 'fan', 'FAN06G3231' => 'fan', 'FAN06G3932' => 'fan', 'FAN07G0163' => 'fan', 'FAN07G0471' => 'fan', 'FAN07G1354' => 'fan', 'FAN08G0338' => 'fan', 'FAN08G1373' => 'fan', 'FAN08G2539' => 'fan', 'FAN08G2728' => 'fan', 'FAN09G0608' => 'fan', 'FAN09G1136' => 'fan', 'FAN09G1958' => 'fan', 'FAN09G2508' => 'fan', 'FAN09G2597' => 'fan', 'FAN09G2658' => 'fan', 'FAN09G2757' => 'fan', 'FAN09G2983' => 'fan', 'FAN09G3130' => 'fan', 'FAN09G3565' => 'fan', 'FAN09G3613' => 'fan', 'FAN09G4011' => 'fan', 'FAN09G4239' => 'fan', 'FAN09G4277' => 'fan', 'FAN09G4720' => 'fan', 'FAN11G0139' => 'fan', 'FAN11G1727' => 'fan', 'FAN11G2672' => 'fan', 'FAN11G2795' => 'fan', 'FAN11G3238' => 'fan', 'FAN11G3734' => 'fan', 'FAN12G0631' => 'fan', 'FAN12G2239' => 'fan', 'FAN12G2308' => 'fan', 'FAN12G2569' => 'fan', 'FAN12G2623' => 'fan', 'FAN13G3182' => 'fan', 'FAN14G0053' => 'fan', 'FAN14G0370' => 'fan', 'FAN14G0382' => 'fan', 'FAN14G0421' => 'fan', 'FAN14G0866' => 'fan', 'FAN14G1187' => 'fan', 'FAN14G1727' => 'fan', 'FAN14G1791' => 'fan', 'FAN14G2361' => 'fan', 'FAN14G2668' => 'fan', 'FAN14G2770' => 'fan', 'FAN14G2874' => 'fan', 'FAN14G3193' => 'fan', 'FAN14G3624' => 'fan', 'FAN14G3676' => 'fan', 'FAN14G3807' => 'fan', 'FAN14G4082' => 'fan', 'FAN14G4342' => 'fan', 'FAN14G4985' => 'fan', 'FAN14G5126' => 'fan', 'FAN14G5781' => 'fan', 'FAN14G5808' => 'fan', 'FAN14G5949' => 'fan', 'FAN15G0828' => 'fan', 'FAN15G1054' => 'fan', 'FAN15G2023' => 'fan', 'FAN15G2506' => 'fan', 'FAN16G0128' => 'fan', 'FAN16G0249' => 'fan', 'FAN16G0429' => 'fan', 'FAN16G1493' => 'fan', 'FAN16G2210' => 'fan', 'FAN16G2506' => 'fan', 'FAN18G1542' => 'fan', 'FAN18G4057' => 'fan', 'FAN19G0745' => 'fan', 'FAN19G1216' => 'fan', 'FAN19G1733' => 'fan', 'FAN20G0258' => 'fan', 'FAN20G1095' => 'fan', 'FAN20G1557' => 'fan', 'FAN21G0302' => 'fan', 'FAN21G0519' => 'fan', 'FAN21G0970' => 'fan', 'FAN21G1159' => 'fan', 'FAN21G1312' => 'fan', 'FAN21G1440' => 'fan', 'FAN21G1715' => 'fan', 'FAN23G1584' => 'fan', 'FAN24G0045' => 'fan', 'FAN24G0053' => 'fan', 'FAN24G1500' => 'fan', 'FAN24G1817' => 'fan', 'FAN24G2147' => 'fan', 'FAN24G2236' => 'fan', 'FAN24G2446' => 'fan', 'FAN24G2684' => 'fan', 'FAN25G0187' => 'fan', 'FAN25G0505' => 'fan', 'FAN25G0589' => 'fan', 'FAN25G3663' => 'fan', 'FAN26G1025' => 'fan', 'FAN26G2860' => 'fan', 'FAN27G1329' => 'fan', 'FAN27G3392' => 'fan', 'FvH4_1g02011' => 'fve', 'FvH4_1g06511' => 'fve', 'FvH4_2g19900' => 'fve', 'FvH4_2g19920' => 'fve', 'FvH4_2g24261' => 'fve', 'FvH4_2g24270' => 'fve', 'FvH4_2g24631' => 'fve', 'FvH4_2g30622' => 'fve', 'FvH4_3g12920' => 'fve', 'FvH4_3g30171' => 'fve', 'FvH4_3g35490' => 'fve', 'FvH4_3g43682' => 'fve', 'FvH4_3g43730' => 'fve', 'FvH4_3g43732' => 'fve', 'FvH4_3g43751' => 'fve', 'FvH4_3g43752' => 'fve', 'FvH4_3g43770' => 'fve', 'FvH4_3g44471' => 'fve', 'FvH4_3g44510' => 'fve', 'FvH4_3g44582' => 'fve', 'FvH4_4g16921' => 'fve', 'FvH4_4g17121' => 'fve', 'FvH4_4g17782' => 'fve', 'FvH4_4g17783' => 'fve', 'FvH4_4g18120' => 'fve', 'FvH4_4g31310' => 'fve', 'FvH4_4g35052' => 'fve', 'FvH4_5g30862' => 'fve', 'FvH4_6g01541' => 'fve', 'FvH4_6g02021' => 'fve', 'FvH4_6g02041' => 'fve', 'FvH4_6g02071' => 'fve', 'FvH4_6g02171' => 'fve', 'FvH4_6g03181' => 'fve', 'FvH4_6g03182' => 'fve', 'FvH4_6g03221' => 'fve', 'FvH4_6g03380' => 'fve', 'FvH4_6g05201' => 'fve', 'FvH4_6g05203' => 'fve', 'FvH4_6g20231' => 'fve', 'FvH4_6g31981' => 'fve', 'FvH4_6g32061' => 'fve', 'FvH4_6g37041' => 'fve', 'FvH4_6g37932' => 'fve', 'FvH4_6g38731' => 'fve', 'FvH4_6g39370' => 'fve', 'FvH4_6g39371' => 'fve', 'FvH4_6g40891' => 'fve', 'FvH4_6g40892' => 'fve', 'FvH4_6g43143' => 'fve', 'FvH4_6g45251' => 'fve', 'FvH4_6g45260' => 'fve', 'FvH4_6g45291' => 'fve', 'FvH4_6g45890' => 'fve', 'FvH4_6g46240' => 'fve', 'FvH4_6g46241' => 'fve', 'FvH4_6g46242' => 'fve', 'FvH4_6g46260' => 'fve', 'FvH4_6g46280' => 'fve', 'FvH4_6g46380' => 'fve', 'FvH4_7g12841' => 'fve', 'FvH4_7g31431' => 'fve', 'Glyma.09G075900' => 'gma', 'Gohir.A09G096401' => 'ghi', 'Gohir.D09G096101' => 'ghi', 'Gorai.006G112800' => 'gra', 'HanXRQChr04g0121411' => 'han', 'Hund15878' => 'sun', 'Lj2A1107G68' => 'lonja', 'Lj2A630G63' => 'lonja', 'Lj2A946T25' => 'lonja', 'Lj2C714T1' => 'lonja', 'Lj2C966T3' => 'lonja', 'Lj2C966T4' => 'lonja', 'Lj4g0002979' => 'lja', 'Lsat_1_v5_gn_5_30901' => 'lsa', 'Lsat_1_v5_gn_5_31100' => 'lsa', 'Lsat_1_v5_gn_5_38600' => 'lsa', 'Lsat_1_v5_gn_6_92061' => 'lsa', 'Manes.05G071301' => 'mes', 'MD02G1008700' => 'mdo', 'MD02G1008900' => 'mdo', 'MD03G1256400' => 'mdo', 'MD04G1180900' => 'mdo', 'MD04G1181000' => 'mdo', 'MD04G1181200' => 'mdo', 'MD05G1244200' => 'mdo', 'MD05G1324200' => 'mdo', 'MD09G1201600' => 'mdo', 'MD10G1000600' => 'mdo', 'MD14G1026900' => 'mdo', 'MD14G1187900' => 'mdo', 'MD15G1017800' => 'mdo', 'MD15G1018100' => 'mdo', 'Medtr4g124160' => 'mtr', 'Migut.L01260' => 'egut', 'Nitab4.5_0000008g0440' => 'nta', 'Nitab4.5_0000207g0170' => 'nta', 'Nitab4.5_0007671g0030' => 'nta', 'Nitab4.5_0010853g0020' => 'nta', 'Oeu057656.1' => 'oeu', 'PGSC0003DMG400005638' => 'stu', 'PGSC0003DMG400005639' => 'stu', 'Phvul.009G222800' => 'pvu', 'Potri.009G132400' => 'ptr', 'Potri.009G163001' => 'ptr', 'Potri.011G000700' => 'ptr', 'Potri.011G004800' => 'ptr', 'Prupe.1G509300' => 'ppe', 'Prupe.1G509700' => 'ppe', 'Prupe.1G510400' => 'ppe', 'Prupe.1G510700' => 'ppe', 'Prupe.1G512600' => 'ppe', 'Prupe.2G073200' => 'ppe', 'Prupe.3G059500' => 'ppe', 'Prupe.3G059600' => 'ppe', 'Prupe.3G246100' => 'ppe', 'Prupe.3G265100' => 'ppe', 'Prupe.4G034700' => 'ppe', 'Prupe.4G052100' => 'ppe', 'Prupe.4G053600' => 'ppe', 'Prupe.5G068800' => 'ppe', 'Prupe.5G070600' => 'ppe', 'Prupe.6G075400' => 'ppe', 'Prupe.6G075500' => 'ppe', 'Prupe.6G076400' => 'ppe', 'Prupe.8G110700' => 'ppe', 'Psat4g020960' => 'psa', 'PSO135G0788' => 'pso', 'PSO210G6463' => 'pso', 'PSO384G0370' => 'pso', 'PSO386G0056' => 'pso', 'QL01p006048' => 'qlo', 'QL02p054283' => 'qlo', 'QL05p008000' => 'qlo', 'QL05p008212' => 'qlo', 'QL05p008950' => 'qlo', 'QL05p009042' => 'qlo', 'QL05p009518' => 'qlo', 'QL05p012589' => 'qlo', 'QL05p012608' => 'qlo', 'QL05p012650' => 'qlo', 'QL05p012667' => 'qlo', 'QL05p014501' => 'qlo', 'QL05p052800' => 'qlo', 'QL05p065010' => 'qlo', 'QL05p074156' => 'qlo', 'QL05p074160' => 'qlo', 'QL05p074174' => 'qlo', 'QL05p074178' => 'qlo', 'QL05p074214' => 'qlo', 'QL06p001050' => 'qlo', 'QL06p001056' => 'qlo', 'QL06p006093' => 'qlo', 'QL06p006111' => 'qlo', 'QL07p019784' => 'qlo', 'QL07p019801' => 'qlo', 'QL07p036110' => 'qlo', 'QL07p036134' => 'qlo', 'QL07p036147' => 'qlo', 'QL07p036156' => 'qlo', 'QL07p036300' => 'qlo', 'QL07p036320' => 'qlo', 'QL08p014547' => 'qlo', 'QL08p014551' => 'qlo', 'QL08p043319' => 'qlo', 'QL08p043324' => 'qlo', 'QL11p009094' => 'qlo', 'RcHm_v2.0_Chr1g0380481' => 'rch', 'RcHm_v2.0_Chr2g0089331' => 'rch', 'RcHm_v2.0_Chr2g0123691' => 'rch', 'RcHm_v2.0_Chr2g0151111' => 'rch', 'RcHm_v2.0_Chr2g0163011' => 'rch', 'RcHm_v2.0_Chr2g0163051' => 'rch', 'RcHm_v2.0_Chr2g0164671' => 'rch', 'RcHm_v2.0_Chr2g0164681' => 'rch', 'RcHm_v2.0_Chr2g0164721' => 'rch', 'RcHm_v2.0_Chr3g0449911' => 'rch', 'RcHm_v2.0_Chr3g0450211' => 'rch', 'RcHm_v2.0_Chr3g0457271' => 'rch', 'RcHm_v2.0_Chr5g0018111' => 'rch', 'RcHm_v2.0_Chr5g0021011' => 'rch', 'RcHm_v2.0_Chr5g0081171' => 'rch', 'RcHm_v2.0_Chr5g0081211' => 'rch', 'RcHm_v2.0_Chr6g0275871' => 'rch', 'RcHm_v2.0_Chr6g0276071' => 'rch', 'RcHm_v2.0_Chr6g0285591' => 'rch', 'RcHm_v2.0_Chr6g0291931' => 'rch', 'RcHm_v2.0_Chr6g0292091' => 'rch', 'RcHm_v2.0_Chr6g0292271' => 'rch', 'RcHm_v2.0_Chr7g0221261' => 'rch', 'Rhsim08G0219900' => 'rsi', 'Rhsim08G0220200' => 'rsi', 'Rhsim08G0237800' => 'rsi', 'Rhsim08G0238800' => 'rsi', 'Sabra09G0102700' => 'sbr', 'Sabra09G0127200' => 'sbr', 'Sabra11G0003700' => 'sbr', 'Sabra15G0014700' => 'sbr', 'Sc19g0000590' => 'sci', 'Sc19g0001870' => 'sci', 'SGA_v2.0_scaffold1G00346' => 'sas', 'SGA_v2.0_scaffold1G00575' => 'sas', 'SGA_v2.0_scaffold1G00761' => 'sas', 'SGA_v2.0_scaffold232G43501' => 'sas', 'TAR625G1137' => 'tar', 'Thecc.03G222100' => 'tca', 'TPR.G12691' => 'tpr', 'TWI34G0727' => 'twi', 'TWI36G0117' => 'twi', 'VMungo1309G0868' => 'vmu' ) $gf_id = 'HOM05D001729' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001729' ) $data_identifier = 'HOM05D001729' $data_type = 'gf_id' $species_gene_counts = array( 'amhyb' => (int) 1, 'cqu' => (int) 9, 'can' => (int) 1, 'cansat' => (int) 1, 'car' => (int) 1, 'col' => (int) 5, 'dca' => (int) 1, 'din' => (int) 2, 'dzi' => (int) 3, 'fan' => (int) 140, 'fve' => (int) 62, 'gma' => (int) 1, 'ghi' => (int) 2, 'gra' => (int) 1, 'han' => (int) 1, 'sun' => (int) 1, 'lonja' => (int) 6, 'lja' => (int) 1, 'lsa' => (int) 4, 'mes' => (int) 1, 'mdo' => (int) 14, 'mtr' => (int) 1, 'egut' => (int) 1, 'nta' => (int) 4, 'oeu' => (int) 1, 'stu' => (int) 2, 'pvu' => (int) 1, 'ptr' => (int) 4, 'ppe' => (int) 19, 'psa' => (int) 1, 'pso' => (int) 4, 'qlo' => (int) 36, 'rch' => (int) 23, 'rsi' => (int) 4, 'sbr' => (int) 4, 'sci' => (int) 2, 'sas' => (int) 4, 'tar' => (int) 1, 'tca' => (int) 1, 'tpr' => (int) 1, 'twi' => (int) 2, 'vmu' => (int) 1 ) $gf_gene_species = 'vmu' $gf_gene_id = 'VMungo1309G0868' $species_info = array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ) $local_species = 'twi' $disabled = '' $selected = '' $num_hits = (int) 1
Warning (2): count(): Parameter must be an array or an object that implements Countable [APP/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp, line 33]Code Context $disabled = (!array_key_exists($local_species,$species_gene_counts))?"disabled":""; $selected = (isset($selected_species) && array_key_exists($local_species,$selected_species))?"checked='checked'":""; $num_hits = (array_key_exists($local_species,$species_gene_counts))?count($species_gene_counts[$local_species]):0; $viewFile = '/www/bioinformatics01_ro/plaza/_dev_instances/feedback/app/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp' $dataForView = array( 'sidebar_info' => array( 'gf_id' => 'HOM05D001729', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '375', 'num_species' => '42' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'Ah.07g204710' => 'amhyb', 'AUR62006001' => 'cqu', 'AUR62006002' => 'cqu', 'AUR62006003' => 'cqu', 'AUR62015641' => 'cqu', 'AUR62027174' => 'cqu', 'AUR62035623' => 'cqu', 'AUR62035624' => 'cqu', 'AUR62035625' => 'cqu', 'AUR62035626' => 'cqu', 'CAN.G1110.53' => 'can', 'CANSAT80G0415' => 'cansat', 'Ca_21364_v3' => 'car', 'COL.COLO4_30693' => 'col', 'COL.COLO4_30694' => 'col', 'COL.COLO4_30695' => 'col', 'COL.COLO4_30696' => 'col', 'COL.COLO4_34020' => 'col', 'DCAR_004585' => 'dca', 'Dinv04029' => 'din', 'Dinv34857' => 'din', 'Duzib147G0011' => 'dzi', 'Duzib170G0599' => 'dzi', 'Duzib192G1051' => 'dzi', 'FAN01G0708' => 'fan', 'FAN01G0742' => 'fan', 'FAN02G0048' => 'fan', 'FAN02G0583' => 'fan', 'FAN02G0688' => 'fan', 'FAN02G1588' => 'fan', 'FAN02G2194' => 'fan', 'FAN02G2750' => 'fan', 'FAN02G3094' => 'fan', 'FAN02G3887' => 'fan', 'FAN02G3911' => 'fan', 'FAN02G3994' => 'fan', 'FAN02G4432' => 'fan', 'FAN02G4556' => 'fan', 'FAN03G1977' => 'fan', 'FAN03G2781' => 'fan', 'FAN03G2850' => 'fan', 'FAN03G3155' => 'fan', 'FAN04G2487' => 'fan', 'FAN05G0208' => 'fan', 'FAN05G0656' => 'fan', 'FAN05G0696' => 'fan', 'FAN05G0810' => 'fan', 'FAN05G1447' => 'fan', 'FAN05G2640' => 'fan', 'FAN05G2911' => 'fan', 'FAN05G3901' => 'fan', 'FAN05G4859' => 'fan', 'FAN05G4861' => 'fan', 'FAN05G4988' => 'fan', 'FAN05G5187' => 'fan', 'FAN05G5452' => 'fan', 'FAN05G5500' => 'fan', 'FAN05G5688' => 'fan', 'FAN06G0177' => 'fan', 'FAN06G0675' => 'fan', 'FAN06G1290' => 'fan', 'FAN06G2191' => 'fan', 'FAN06G2405' => 'fan', 'FAN06G3231' => 'fan', 'FAN06G3932' => 'fan', 'FAN07G0163' => 'fan', 'FAN07G0471' => 'fan', 'FAN07G1354' => 'fan', 'FAN08G0338' => 'fan', 'FAN08G1373' => 'fan', 'FAN08G2539' => 'fan', 'FAN08G2728' => 'fan', 'FAN09G0608' => 'fan', 'FAN09G1136' => 'fan', 'FAN09G1958' => 'fan', 'FAN09G2508' => 'fan', 'FAN09G2597' => 'fan', 'FAN09G2658' => 'fan', 'FAN09G2757' => 'fan', 'FAN09G2983' => 'fan', 'FAN09G3130' => 'fan', 'FAN09G3565' => 'fan', 'FAN09G3613' => 'fan', 'FAN09G4011' => 'fan', 'FAN09G4239' => 'fan', 'FAN09G4277' => 'fan', 'FAN09G4720' => 'fan', 'FAN11G0139' => 'fan', 'FAN11G1727' => 'fan', 'FAN11G2672' => 'fan', 'FAN11G2795' => 'fan', 'FAN11G3238' => 'fan', 'FAN11G3734' => 'fan', 'FAN12G0631' => 'fan', 'FAN12G2239' => 'fan', 'FAN12G2308' => 'fan', 'FAN12G2569' => 'fan', 'FAN12G2623' => 'fan', 'FAN13G3182' => 'fan', 'FAN14G0053' => 'fan', 'FAN14G0370' => 'fan', 'FAN14G0382' => 'fan', 'FAN14G0421' => 'fan', 'FAN14G0866' => 'fan', 'FAN14G1187' => 'fan', 'FAN14G1727' => 'fan', 'FAN14G1791' => 'fan', 'FAN14G2361' => 'fan', 'FAN14G2668' => 'fan', 'FAN14G2770' => 'fan', 'FAN14G2874' => 'fan', 'FAN14G3193' => 'fan', 'FAN14G3624' => 'fan', 'FAN14G3676' => 'fan', 'FAN14G3807' => 'fan', 'FAN14G4082' => 'fan', 'FAN14G4342' => 'fan', 'FAN14G4985' => 'fan', 'FAN14G5126' => 'fan', 'FAN14G5781' => 'fan', 'FAN14G5808' => 'fan', 'FAN14G5949' => 'fan', 'FAN15G0828' => 'fan', 'FAN15G1054' => 'fan', 'FAN15G2023' => 'fan', 'FAN15G2506' => 'fan', 'FAN16G0128' => 'fan', 'FAN16G0249' => 'fan', 'FAN16G0429' => 'fan', 'FAN16G1493' => 'fan', 'FAN16G2210' => 'fan', 'FAN16G2506' => 'fan', 'FAN18G1542' => 'fan', 'FAN18G4057' => 'fan', 'FAN19G0745' => 'fan', 'FAN19G1216' => 'fan', 'FAN19G1733' => 'fan', 'FAN20G0258' => 'fan', 'FAN20G1095' => 'fan', 'FAN20G1557' => 'fan', 'FAN21G0302' => 'fan', 'FAN21G0519' => 'fan', 'FAN21G0970' => 'fan', 'FAN21G1159' => 'fan', 'FAN21G1312' => 'fan', 'FAN21G1440' => 'fan', 'FAN21G1715' => 'fan', 'FAN23G1584' => 'fan', 'FAN24G0045' => 'fan', 'FAN24G0053' => 'fan', 'FAN24G1500' => 'fan', 'FAN24G1817' => 'fan', 'FAN24G2147' => 'fan', 'FAN24G2236' => 'fan', 'FAN24G2446' => 'fan', 'FAN24G2684' => 'fan', 'FAN25G0187' => 'fan', 'FAN25G0505' => 'fan', 'FAN25G0589' => 'fan', 'FAN25G3663' => 'fan', 'FAN26G1025' => 'fan', 'FAN26G2860' => 'fan', 'FAN27G1329' => 'fan', 'FAN27G3392' => 'fan', 'FvH4_1g02011' => 'fve', 'FvH4_1g06511' => 'fve', 'FvH4_2g19900' => 'fve', 'FvH4_2g19920' => 'fve', 'FvH4_2g24261' => 'fve', 'FvH4_2g24270' => 'fve', 'FvH4_2g24631' => 'fve', 'FvH4_2g30622' => 'fve', 'FvH4_3g12920' => 'fve', 'FvH4_3g30171' => 'fve', 'FvH4_3g35490' => 'fve', 'FvH4_3g43682' => 'fve', 'FvH4_3g43730' => 'fve', 'FvH4_3g43732' => 'fve', 'FvH4_3g43751' => 'fve', 'FvH4_3g43752' => 'fve', 'FvH4_3g43770' => 'fve', 'FvH4_3g44471' => 'fve', 'FvH4_3g44510' => 'fve', 'FvH4_3g44582' => 'fve', 'FvH4_4g16921' => 'fve', 'FvH4_4g17121' => 'fve', 'FvH4_4g17782' => 'fve', 'FvH4_4g17783' => 'fve', 'FvH4_4g18120' => 'fve', 'FvH4_4g31310' => 'fve', 'FvH4_4g35052' => 'fve', 'FvH4_5g30862' => 'fve', 'FvH4_6g01541' => 'fve', 'FvH4_6g02021' => 'fve', 'FvH4_6g02041' => 'fve', 'FvH4_6g02071' => 'fve', 'FvH4_6g02171' => 'fve', 'FvH4_6g03181' => 'fve', 'FvH4_6g03182' => 'fve', 'FvH4_6g03221' => 'fve', 'FvH4_6g03380' => 'fve', 'FvH4_6g05201' => 'fve', 'FvH4_6g05203' => 'fve', 'FvH4_6g20231' => 'fve', 'FvH4_6g31981' => 'fve', 'FvH4_6g32061' => 'fve', 'FvH4_6g37041' => 'fve', 'FvH4_6g37932' => 'fve', 'FvH4_6g38731' => 'fve', 'FvH4_6g39370' => 'fve', 'FvH4_6g39371' => 'fve', 'FvH4_6g40891' => 'fve', 'FvH4_6g40892' => 'fve', 'FvH4_6g43143' => 'fve', 'FvH4_6g45251' => 'fve', 'FvH4_6g45260' => 'fve', 'FvH4_6g45291' => 'fve', 'FvH4_6g45890' => 'fve', 'FvH4_6g46240' => 'fve', 'FvH4_6g46241' => 'fve', 'FvH4_6g46242' => 'fve', 'FvH4_6g46260' => 'fve', 'FvH4_6g46280' => 'fve', 'FvH4_6g46380' => 'fve', 'FvH4_7g12841' => 'fve', 'FvH4_7g31431' => 'fve', 'Glyma.09G075900' => 'gma', 'Gohir.A09G096401' => 'ghi', 'Gohir.D09G096101' => 'ghi', 'Gorai.006G112800' => 'gra', 'HanXRQChr04g0121411' => 'han', 'Hund15878' => 'sun', 'Lj2A1107G68' => 'lonja', 'Lj2A630G63' => 'lonja', 'Lj2A946T25' => 'lonja', 'Lj2C714T1' => 'lonja', 'Lj2C966T3' => 'lonja', 'Lj2C966T4' => 'lonja', 'Lj4g0002979' => 'lja', 'Lsat_1_v5_gn_5_30901' => 'lsa', 'Lsat_1_v5_gn_5_31100' => 'lsa', 'Lsat_1_v5_gn_5_38600' => 'lsa', 'Lsat_1_v5_gn_6_92061' => 'lsa', 'Manes.05G071301' => 'mes', 'MD02G1008700' => 'mdo', 'MD02G1008900' => 'mdo', 'MD03G1256400' => 'mdo', 'MD04G1180900' => 'mdo', 'MD04G1181000' => 'mdo', 'MD04G1181200' => 'mdo', 'MD05G1244200' => 'mdo', 'MD05G1324200' => 'mdo', 'MD09G1201600' => 'mdo', 'MD10G1000600' => 'mdo', 'MD14G1026900' => 'mdo', 'MD14G1187900' => 'mdo', 'MD15G1017800' => 'mdo', 'MD15G1018100' => 'mdo', 'Medtr4g124160' => 'mtr', 'Migut.L01260' => 'egut', 'Nitab4.5_0000008g0440' => 'nta', 'Nitab4.5_0000207g0170' => 'nta', 'Nitab4.5_0007671g0030' => 'nta', 'Nitab4.5_0010853g0020' => 'nta', 'Oeu057656.1' => 'oeu', 'PGSC0003DMG400005638' => 'stu', 'PGSC0003DMG400005639' => 'stu', 'Phvul.009G222800' => 'pvu', 'Potri.009G132400' => 'ptr', 'Potri.009G163001' => 'ptr', 'Potri.011G000700' => 'ptr', 'Potri.011G004800' => 'ptr', 'Prupe.1G509300' => 'ppe', 'Prupe.1G509700' => 'ppe', 'Prupe.1G510400' => 'ppe', 'Prupe.1G510700' => 'ppe', 'Prupe.1G512600' => 'ppe', 'Prupe.2G073200' => 'ppe', 'Prupe.3G059500' => 'ppe', 'Prupe.3G059600' => 'ppe', 'Prupe.3G246100' => 'ppe', 'Prupe.3G265100' => 'ppe', 'Prupe.4G034700' => 'ppe', 'Prupe.4G052100' => 'ppe', 'Prupe.4G053600' => 'ppe', 'Prupe.5G068800' => 'ppe', 'Prupe.5G070600' => 'ppe', 'Prupe.6G075400' => 'ppe', 'Prupe.6G075500' => 'ppe', 'Prupe.6G076400' => 'ppe', 'Prupe.8G110700' => 'ppe', 'Psat4g020960' => 'psa', 'PSO135G0788' => 'pso', 'PSO210G6463' => 'pso', 'PSO384G0370' => 'pso', 'PSO386G0056' => 'pso', 'QL01p006048' => 'qlo', 'QL02p054283' => 'qlo', 'QL05p008000' => 'qlo', 'QL05p008212' => 'qlo', 'QL05p008950' => 'qlo', 'QL05p009042' => 'qlo', 'QL05p009518' => 'qlo', 'QL05p012589' => 'qlo', 'QL05p012608' => 'qlo', 'QL05p012650' => 'qlo', 'QL05p012667' => 'qlo', 'QL05p014501' => 'qlo', 'QL05p052800' => 'qlo', 'QL05p065010' => 'qlo', 'QL05p074156' => 'qlo', 'QL05p074160' => 'qlo', 'QL05p074174' => 'qlo', 'QL05p074178' => 'qlo', 'QL05p074214' => 'qlo', 'QL06p001050' => 'qlo', 'QL06p001056' => 'qlo', 'QL06p006093' => 'qlo', 'QL06p006111' => 'qlo', 'QL07p019784' => 'qlo', 'QL07p019801' => 'qlo', 'QL07p036110' => 'qlo', 'QL07p036134' => 'qlo', 'QL07p036147' => 'qlo', 'QL07p036156' => 'qlo', 'QL07p036300' => 'qlo', 'QL07p036320' => 'qlo', 'QL08p014547' => 'qlo', 'QL08p014551' => 'qlo', 'QL08p043319' => 'qlo', 'QL08p043324' => 'qlo', 'QL11p009094' => 'qlo', 'RcHm_v2.0_Chr1g0380481' => 'rch', 'RcHm_v2.0_Chr2g0089331' => 'rch', 'RcHm_v2.0_Chr2g0123691' => 'rch', 'RcHm_v2.0_Chr2g0151111' => 'rch', 'RcHm_v2.0_Chr2g0163011' => 'rch', 'RcHm_v2.0_Chr2g0163051' => 'rch', 'RcHm_v2.0_Chr2g0164671' => 'rch', 'RcHm_v2.0_Chr2g0164681' => 'rch', 'RcHm_v2.0_Chr2g0164721' => 'rch', 'RcHm_v2.0_Chr3g0449911' => 'rch', 'RcHm_v2.0_Chr3g0450211' => 'rch', 'RcHm_v2.0_Chr3g0457271' => 'rch', 'RcHm_v2.0_Chr5g0018111' => 'rch', 'RcHm_v2.0_Chr5g0021011' => 'rch', 'RcHm_v2.0_Chr5g0081171' => 'rch', 'RcHm_v2.0_Chr5g0081211' => 'rch', 'RcHm_v2.0_Chr6g0275871' => 'rch', 'RcHm_v2.0_Chr6g0276071' => 'rch', 'RcHm_v2.0_Chr6g0285591' => 'rch', 'RcHm_v2.0_Chr6g0291931' => 'rch', 'RcHm_v2.0_Chr6g0292091' => 'rch', 'RcHm_v2.0_Chr6g0292271' => 'rch', 'RcHm_v2.0_Chr7g0221261' => 'rch', 'Rhsim08G0219900' => 'rsi', 'Rhsim08G0220200' => 'rsi', 'Rhsim08G0237800' => 'rsi', 'Rhsim08G0238800' => 'rsi', 'Sabra09G0102700' => 'sbr', 'Sabra09G0127200' => 'sbr', 'Sabra11G0003700' => 'sbr', 'Sabra15G0014700' => 'sbr', 'Sc19g0000590' => 'sci', 'Sc19g0001870' => 'sci', 'SGA_v2.0_scaffold1G00346' => 'sas', 'SGA_v2.0_scaffold1G00575' => 'sas', 'SGA_v2.0_scaffold1G00761' => 'sas', 'SGA_v2.0_scaffold232G43501' => 'sas', 'TAR625G1137' => 'tar', 'Thecc.03G222100' => 'tca', 'TPR.G12691' => 'tpr', 'TWI34G0727' => 'twi', 'TWI36G0117' => 'twi', 'VMungo1309G0868' => 'vmu' ), 'gf_id' => 'HOM05D001729', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001729' ), 'data_identifier' => 'HOM05D001729', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001729', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '375', 'num_species' => '42' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'Ah.07g204710' => 'amhyb', 'AUR62006001' => 'cqu', 'AUR62006002' => 'cqu', 'AUR62006003' => 'cqu', 'AUR62015641' => 'cqu', 'AUR62027174' => 'cqu', 'AUR62035623' => 'cqu', 'AUR62035624' => 'cqu', 'AUR62035625' => 'cqu', 'AUR62035626' => 'cqu', 'CAN.G1110.53' => 'can', 'CANSAT80G0415' => 'cansat', 'Ca_21364_v3' => 'car', 'COL.COLO4_30693' => 'col', 'COL.COLO4_30694' => 'col', 'COL.COLO4_30695' => 'col', 'COL.COLO4_30696' => 'col', 'COL.COLO4_34020' => 'col', 'DCAR_004585' => 'dca', 'Dinv04029' => 'din', 'Dinv34857' => 'din', 'Duzib147G0011' => 'dzi', 'Duzib170G0599' => 'dzi', 'Duzib192G1051' => 'dzi', 'FAN01G0708' => 'fan', 'FAN01G0742' => 'fan', 'FAN02G0048' => 'fan', 'FAN02G0583' => 'fan', 'FAN02G0688' => 'fan', 'FAN02G1588' => 'fan', 'FAN02G2194' => 'fan', 'FAN02G2750' => 'fan', 'FAN02G3094' => 'fan', 'FAN02G3887' => 'fan', 'FAN02G3911' => 'fan', 'FAN02G3994' => 'fan', 'FAN02G4432' => 'fan', 'FAN02G4556' => 'fan', 'FAN03G1977' => 'fan', 'FAN03G2781' => 'fan', 'FAN03G2850' => 'fan', 'FAN03G3155' => 'fan', 'FAN04G2487' => 'fan', 'FAN05G0208' => 'fan', 'FAN05G0656' => 'fan', 'FAN05G0696' => 'fan', 'FAN05G0810' => 'fan', 'FAN05G1447' => 'fan', 'FAN05G2640' => 'fan', 'FAN05G2911' => 'fan', 'FAN05G3901' => 'fan', 'FAN05G4859' => 'fan', 'FAN05G4861' => 'fan', 'FAN05G4988' => 'fan', 'FAN05G5187' => 'fan', 'FAN05G5452' => 'fan', 'FAN05G5500' => 'fan', 'FAN05G5688' => 'fan', 'FAN06G0177' => 'fan', 'FAN06G0675' => 'fan', 'FAN06G1290' => 'fan', 'FAN06G2191' => 'fan', 'FAN06G2405' => 'fan', 'FAN06G3231' => 'fan', 'FAN06G3932' => 'fan', 'FAN07G0163' => 'fan', 'FAN07G0471' => 'fan', 'FAN07G1354' => 'fan', 'FAN08G0338' => 'fan', 'FAN08G1373' => 'fan', 'FAN08G2539' => 'fan', 'FAN08G2728' => 'fan', 'FAN09G0608' => 'fan', 'FAN09G1136' => 'fan', 'FAN09G1958' => 'fan', 'FAN09G2508' => 'fan', 'FAN09G2597' => 'fan', 'FAN09G2658' => 'fan', 'FAN09G2757' => 'fan', 'FAN09G2983' => 'fan', 'FAN09G3130' => 'fan', 'FAN09G3565' => 'fan', 'FAN09G3613' => 'fan', 'FAN09G4011' => 'fan', 'FAN09G4239' => 'fan', 'FAN09G4277' => 'fan', 'FAN09G4720' => 'fan', 'FAN11G0139' => 'fan', 'FAN11G1727' => 'fan', 'FAN11G2672' => 'fan', 'FAN11G2795' => 'fan', 'FAN11G3238' => 'fan', 'FAN11G3734' => 'fan', 'FAN12G0631' => 'fan', 'FAN12G2239' => 'fan', 'FAN12G2308' => 'fan', 'FAN12G2569' => 'fan', 'FAN12G2623' => 'fan', 'FAN13G3182' => 'fan', 'FAN14G0053' => 'fan', 'FAN14G0370' => 'fan', 'FAN14G0382' => 'fan', 'FAN14G0421' => 'fan', 'FAN14G0866' => 'fan', 'FAN14G1187' => 'fan', 'FAN14G1727' => 'fan', 'FAN14G1791' => 'fan', 'FAN14G2361' => 'fan', 'FAN14G2668' => 'fan', 'FAN14G2770' => 'fan', 'FAN14G2874' => 'fan', 'FAN14G3193' => 'fan', 'FAN14G3624' => 'fan', 'FAN14G3676' => 'fan', 'FAN14G3807' => 'fan', 'FAN14G4082' => 'fan', 'FAN14G4342' => 'fan', 'FAN14G4985' => 'fan', 'FAN14G5126' => 'fan', 'FAN14G5781' => 'fan', 'FAN14G5808' => 'fan', 'FAN14G5949' => 'fan', 'FAN15G0828' => 'fan', 'FAN15G1054' => 'fan', 'FAN15G2023' => 'fan', 'FAN15G2506' => 'fan', 'FAN16G0128' => 'fan', 'FAN16G0249' => 'fan', 'FAN16G0429' => 'fan', 'FAN16G1493' => 'fan', 'FAN16G2210' => 'fan', 'FAN16G2506' => 'fan', 'FAN18G1542' => 'fan', 'FAN18G4057' => 'fan', 'FAN19G0745' => 'fan', 'FAN19G1216' => 'fan', 'FAN19G1733' => 'fan', 'FAN20G0258' => 'fan', 'FAN20G1095' => 'fan', 'FAN20G1557' => 'fan', 'FAN21G0302' => 'fan', 'FAN21G0519' => 'fan', 'FAN21G0970' => 'fan', 'FAN21G1159' => 'fan', 'FAN21G1312' => 'fan', 'FAN21G1440' => 'fan', 'FAN21G1715' => 'fan', 'FAN23G1584' => 'fan', 'FAN24G0045' => 'fan', 'FAN24G0053' => 'fan', 'FAN24G1500' => 'fan', 'FAN24G1817' => 'fan', 'FAN24G2147' => 'fan', 'FAN24G2236' => 'fan', 'FAN24G2446' => 'fan', 'FAN24G2684' => 'fan', 'FAN25G0187' => 'fan', 'FAN25G0505' => 'fan', 'FAN25G0589' => 'fan', 'FAN25G3663' => 'fan', 'FAN26G1025' => 'fan', 'FAN26G2860' => 'fan', 'FAN27G1329' => 'fan', 'FAN27G3392' => 'fan', 'FvH4_1g02011' => 'fve', 'FvH4_1g06511' => 'fve', 'FvH4_2g19900' => 'fve', 'FvH4_2g19920' => 'fve', 'FvH4_2g24261' => 'fve', 'FvH4_2g24270' => 'fve', 'FvH4_2g24631' => 'fve', 'FvH4_2g30622' => 'fve', 'FvH4_3g12920' => 'fve', 'FvH4_3g30171' => 'fve', 'FvH4_3g35490' => 'fve', 'FvH4_3g43682' => 'fve', 'FvH4_3g43730' => 'fve', 'FvH4_3g43732' => 'fve', 'FvH4_3g43751' => 'fve', 'FvH4_3g43752' => 'fve', 'FvH4_3g43770' => 'fve', 'FvH4_3g44471' => 'fve', 'FvH4_3g44510' => 'fve', 'FvH4_3g44582' => 'fve', 'FvH4_4g16921' => 'fve', 'FvH4_4g17121' => 'fve', 'FvH4_4g17782' => 'fve', 'FvH4_4g17783' => 'fve', 'FvH4_4g18120' => 'fve', 'FvH4_4g31310' => 'fve', 'FvH4_4g35052' => 'fve', 'FvH4_5g30862' => 'fve', 'FvH4_6g01541' => 'fve', 'FvH4_6g02021' => 'fve', 'FvH4_6g02041' => 'fve', 'FvH4_6g02071' => 'fve', 'FvH4_6g02171' => 'fve', 'FvH4_6g03181' => 'fve', 'FvH4_6g03182' => 'fve', 'FvH4_6g03221' => 'fve', 'FvH4_6g03380' => 'fve', 'FvH4_6g05201' => 'fve', 'FvH4_6g05203' => 'fve', 'FvH4_6g20231' => 'fve', 'FvH4_6g31981' => 'fve', 'FvH4_6g32061' => 'fve', 'FvH4_6g37041' => 'fve', 'FvH4_6g37932' => 'fve', 'FvH4_6g38731' => 'fve', 'FvH4_6g39370' => 'fve', 'FvH4_6g39371' => 'fve', 'FvH4_6g40891' => 'fve', 'FvH4_6g40892' => 'fve', 'FvH4_6g43143' => 'fve', 'FvH4_6g45251' => 'fve', 'FvH4_6g45260' => 'fve', 'FvH4_6g45291' => 'fve', 'FvH4_6g45890' => 'fve', 'FvH4_6g46240' => 'fve', 'FvH4_6g46241' => 'fve', 'FvH4_6g46242' => 'fve', 'FvH4_6g46260' => 'fve', 'FvH4_6g46280' => 'fve', 'FvH4_6g46380' => 'fve', 'FvH4_7g12841' => 'fve', 'FvH4_7g31431' => 'fve', 'Glyma.09G075900' => 'gma', 'Gohir.A09G096401' => 'ghi', 'Gohir.D09G096101' => 'ghi', 'Gorai.006G112800' => 'gra', 'HanXRQChr04g0121411' => 'han', 'Hund15878' => 'sun', 'Lj2A1107G68' => 'lonja', 'Lj2A630G63' => 'lonja', 'Lj2A946T25' => 'lonja', 'Lj2C714T1' => 'lonja', 'Lj2C966T3' => 'lonja', 'Lj2C966T4' => 'lonja', 'Lj4g0002979' => 'lja', 'Lsat_1_v5_gn_5_30901' => 'lsa', 'Lsat_1_v5_gn_5_31100' => 'lsa', 'Lsat_1_v5_gn_5_38600' => 'lsa', 'Lsat_1_v5_gn_6_92061' => 'lsa', 'Manes.05G071301' => 'mes', 'MD02G1008700' => 'mdo', 'MD02G1008900' => 'mdo', 'MD03G1256400' => 'mdo', 'MD04G1180900' => 'mdo', 'MD04G1181000' => 'mdo', 'MD04G1181200' => 'mdo', 'MD05G1244200' => 'mdo', 'MD05G1324200' => 'mdo', 'MD09G1201600' => 'mdo', 'MD10G1000600' => 'mdo', 'MD14G1026900' => 'mdo', 'MD14G1187900' => 'mdo', 'MD15G1017800' => 'mdo', 'MD15G1018100' => 'mdo', 'Medtr4g124160' => 'mtr', 'Migut.L01260' => 'egut', 'Nitab4.5_0000008g0440' => 'nta', 'Nitab4.5_0000207g0170' => 'nta', 'Nitab4.5_0007671g0030' => 'nta', 'Nitab4.5_0010853g0020' => 'nta', 'Oeu057656.1' => 'oeu', 'PGSC0003DMG400005638' => 'stu', 'PGSC0003DMG400005639' => 'stu', 'Phvul.009G222800' => 'pvu', 'Potri.009G132400' => 'ptr', 'Potri.009G163001' => 'ptr', 'Potri.011G000700' => 'ptr', 'Potri.011G004800' => 'ptr', 'Prupe.1G509300' => 'ppe', 'Prupe.1G509700' => 'ppe', 'Prupe.1G510400' => 'ppe', 'Prupe.1G510700' => 'ppe', 'Prupe.1G512600' => 'ppe', 'Prupe.2G073200' => 'ppe', 'Prupe.3G059500' => 'ppe', 'Prupe.3G059600' => 'ppe', 'Prupe.3G246100' => 'ppe', 'Prupe.3G265100' => 'ppe', 'Prupe.4G034700' => 'ppe', 'Prupe.4G052100' => 'ppe', 'Prupe.4G053600' => 'ppe', 'Prupe.5G068800' => 'ppe', 'Prupe.5G070600' => 'ppe', 'Prupe.6G075400' => 'ppe', 'Prupe.6G075500' => 'ppe', 'Prupe.6G076400' => 'ppe', 'Prupe.8G110700' => 'ppe', 'Psat4g020960' => 'psa', 'PSO135G0788' => 'pso', 'PSO210G6463' => 'pso', 'PSO384G0370' => 'pso', 'PSO386G0056' => 'pso', 'QL01p006048' => 'qlo', 'QL02p054283' => 'qlo', 'QL05p008000' => 'qlo', 'QL05p008212' => 'qlo', 'QL05p008950' => 'qlo', 'QL05p009042' => 'qlo', 'QL05p009518' => 'qlo', 'QL05p012589' => 'qlo', 'QL05p012608' => 'qlo', 'QL05p012650' => 'qlo', 'QL05p012667' => 'qlo', 'QL05p014501' => 'qlo', 'QL05p052800' => 'qlo', 'QL05p065010' => 'qlo', 'QL05p074156' => 'qlo', 'QL05p074160' => 'qlo', 'QL05p074174' => 'qlo', 'QL05p074178' => 'qlo', 'QL05p074214' => 'qlo', 'QL06p001050' => 'qlo', 'QL06p001056' => 'qlo', 'QL06p006093' => 'qlo', 'QL06p006111' => 'qlo', 'QL07p019784' => 'qlo', 'QL07p019801' => 'qlo', 'QL07p036110' => 'qlo', 'QL07p036134' => 'qlo', 'QL07p036147' => 'qlo', 'QL07p036156' => 'qlo', 'QL07p036300' => 'qlo', 'QL07p036320' => 'qlo', 'QL08p014547' => 'qlo', 'QL08p014551' => 'qlo', 'QL08p043319' => 'qlo', 'QL08p043324' => 'qlo', 'QL11p009094' => 'qlo', 'RcHm_v2.0_Chr1g0380481' => 'rch', 'RcHm_v2.0_Chr2g0089331' => 'rch', 'RcHm_v2.0_Chr2g0123691' => 'rch', 'RcHm_v2.0_Chr2g0151111' => 'rch', 'RcHm_v2.0_Chr2g0163011' => 'rch', 'RcHm_v2.0_Chr2g0163051' => 'rch', 'RcHm_v2.0_Chr2g0164671' => 'rch', 'RcHm_v2.0_Chr2g0164681' => 'rch', 'RcHm_v2.0_Chr2g0164721' => 'rch', 'RcHm_v2.0_Chr3g0449911' => 'rch', 'RcHm_v2.0_Chr3g0450211' => 'rch', 'RcHm_v2.0_Chr3g0457271' => 'rch', 'RcHm_v2.0_Chr5g0018111' => 'rch', 'RcHm_v2.0_Chr5g0021011' => 'rch', 'RcHm_v2.0_Chr5g0081171' => 'rch', 'RcHm_v2.0_Chr5g0081211' => 'rch', 'RcHm_v2.0_Chr6g0275871' => 'rch', 'RcHm_v2.0_Chr6g0276071' => 'rch', 'RcHm_v2.0_Chr6g0285591' => 'rch', 'RcHm_v2.0_Chr6g0291931' => 'rch', 'RcHm_v2.0_Chr6g0292091' => 'rch', 'RcHm_v2.0_Chr6g0292271' => 'rch', 'RcHm_v2.0_Chr7g0221261' => 'rch', 'Rhsim08G0219900' => 'rsi', 'Rhsim08G0220200' => 'rsi', 'Rhsim08G0237800' => 'rsi', 'Rhsim08G0238800' => 'rsi', 'Sabra09G0102700' => 'sbr', 'Sabra09G0127200' => 'sbr', 'Sabra11G0003700' => 'sbr', 'Sabra15G0014700' => 'sbr', 'Sc19g0000590' => 'sci', 'Sc19g0001870' => 'sci', 'SGA_v2.0_scaffold1G00346' => 'sas', 'SGA_v2.0_scaffold1G00575' => 'sas', 'SGA_v2.0_scaffold1G00761' => 'sas', 'SGA_v2.0_scaffold232G43501' => 'sas', 'TAR625G1137' => 'tar', 'Thecc.03G222100' => 'tca', 'TPR.G12691' => 'tpr', 'TWI34G0727' => 'twi', 'TWI36G0117' => 'twi', 'VMungo1309G0868' => 'vmu' ) $gf_id = 'HOM05D001729' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001729' ) $data_identifier = 'HOM05D001729' $data_type = 'gf_id' $species_gene_counts = array( 'amhyb' => (int) 1, 'cqu' => (int) 9, 'can' => (int) 1, 'cansat' => (int) 1, 'car' => (int) 1, 'col' => (int) 5, 'dca' => (int) 1, 'din' => (int) 2, 'dzi' => (int) 3, 'fan' => (int) 140, 'fve' => (int) 62, 'gma' => (int) 1, 'ghi' => (int) 2, 'gra' => (int) 1, 'han' => (int) 1, 'sun' => (int) 1, 'lonja' => (int) 6, 'lja' => (int) 1, 'lsa' => (int) 4, 'mes' => (int) 1, 'mdo' => (int) 14, 'mtr' => (int) 1, 'egut' => (int) 1, 'nta' => (int) 4, 'oeu' => (int) 1, 'stu' => (int) 2, 'pvu' => (int) 1, 'ptr' => (int) 4, 'ppe' => (int) 19, 'psa' => (int) 1, 'pso' => (int) 4, 'qlo' => (int) 36, 'rch' => (int) 23, 'rsi' => (int) 4, 'sbr' => (int) 4, 'sci' => (int) 2, 'sas' => (int) 4, 'tar' => (int) 1, 'tca' => (int) 1, 'tpr' => (int) 1, 'twi' => (int) 2, 'vmu' => (int) 1 ) $gf_gene_species = 'vmu' $gf_gene_id = 'VMungo1309G0868' $species_info = array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ) $local_species = 'tar' $disabled = '' $selected = '' $num_hits = (int) 1include - APP/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp, line 33 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933 View::_renderElement() - CORE/Cake/View/View.php, line 1224 View::element() - CORE/Cake/View/View.php, line 418 include - APP/View/Elements/analysis/phylogenetics_module/gf_data_settings.ctp, line 37 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933 View::_renderElement() - CORE/Cake/View/View.php, line 1224 View::element() - CORE/Cake/View/View.php, line 418 include - APP/View/Elements/analysis/phylogenetics_module/parameter_selection.ctp, line 64 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933 View::_renderElement() - CORE/Cake/View/View.php, line 1224 View::element() - CORE/Cake/View/View.php, line 418 include - APP/View/Analysis/custom_tree_creation.ctp, line 27 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933
$viewFile = '/www/bioinformatics01_ro/plaza/_dev_instances/feedback/app/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp' $dataForView = array( 'sidebar_info' => array( 'gf_id' => 'HOM05D001729', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '375', 'num_species' => '42' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'Ah.07g204710' => 'amhyb', 'AUR62006001' => 'cqu', 'AUR62006002' => 'cqu', 'AUR62006003' => 'cqu', 'AUR62015641' => 'cqu', 'AUR62027174' => 'cqu', 'AUR62035623' => 'cqu', 'AUR62035624' => 'cqu', 'AUR62035625' => 'cqu', 'AUR62035626' => 'cqu', 'CAN.G1110.53' => 'can', 'CANSAT80G0415' => 'cansat', 'Ca_21364_v3' => 'car', 'COL.COLO4_30693' => 'col', 'COL.COLO4_30694' => 'col', 'COL.COLO4_30695' => 'col', 'COL.COLO4_30696' => 'col', 'COL.COLO4_34020' => 'col', 'DCAR_004585' => 'dca', 'Dinv04029' => 'din', 'Dinv34857' => 'din', 'Duzib147G0011' => 'dzi', 'Duzib170G0599' => 'dzi', 'Duzib192G1051' => 'dzi', 'FAN01G0708' => 'fan', 'FAN01G0742' => 'fan', 'FAN02G0048' => 'fan', 'FAN02G0583' => 'fan', 'FAN02G0688' => 'fan', 'FAN02G1588' => 'fan', 'FAN02G2194' => 'fan', 'FAN02G2750' => 'fan', 'FAN02G3094' => 'fan', 'FAN02G3887' => 'fan', 'FAN02G3911' => 'fan', 'FAN02G3994' => 'fan', 'FAN02G4432' => 'fan', 'FAN02G4556' => 'fan', 'FAN03G1977' => 'fan', 'FAN03G2781' => 'fan', 'FAN03G2850' => 'fan', 'FAN03G3155' => 'fan', 'FAN04G2487' => 'fan', 'FAN05G0208' => 'fan', 'FAN05G0656' => 'fan', 'FAN05G0696' => 'fan', 'FAN05G0810' => 'fan', 'FAN05G1447' => 'fan', 'FAN05G2640' => 'fan', 'FAN05G2911' => 'fan', 'FAN05G3901' => 'fan', 'FAN05G4859' => 'fan', 'FAN05G4861' => 'fan', 'FAN05G4988' => 'fan', 'FAN05G5187' => 'fan', 'FAN05G5452' => 'fan', 'FAN05G5500' => 'fan', 'FAN05G5688' => 'fan', 'FAN06G0177' => 'fan', 'FAN06G0675' => 'fan', 'FAN06G1290' => 'fan', 'FAN06G2191' => 'fan', 'FAN06G2405' => 'fan', 'FAN06G3231' => 'fan', 'FAN06G3932' => 'fan', 'FAN07G0163' => 'fan', 'FAN07G0471' => 'fan', 'FAN07G1354' => 'fan', 'FAN08G0338' => 'fan', 'FAN08G1373' => 'fan', 'FAN08G2539' => 'fan', 'FAN08G2728' => 'fan', 'FAN09G0608' => 'fan', 'FAN09G1136' => 'fan', 'FAN09G1958' => 'fan', 'FAN09G2508' => 'fan', 'FAN09G2597' => 'fan', 'FAN09G2658' => 'fan', 'FAN09G2757' => 'fan', 'FAN09G2983' => 'fan', 'FAN09G3130' => 'fan', 'FAN09G3565' => 'fan', 'FAN09G3613' => 'fan', 'FAN09G4011' => 'fan', 'FAN09G4239' => 'fan', 'FAN09G4277' => 'fan', 'FAN09G4720' => 'fan', 'FAN11G0139' => 'fan', 'FAN11G1727' => 'fan', 'FAN11G2672' => 'fan', 'FAN11G2795' => 'fan', 'FAN11G3238' => 'fan', 'FAN11G3734' => 'fan', 'FAN12G0631' => 'fan', 'FAN12G2239' => 'fan', 'FAN12G2308' => 'fan', 'FAN12G2569' => 'fan', 'FAN12G2623' => 'fan', 'FAN13G3182' => 'fan', 'FAN14G0053' => 'fan', 'FAN14G0370' => 'fan', 'FAN14G0382' => 'fan', 'FAN14G0421' => 'fan', 'FAN14G0866' => 'fan', 'FAN14G1187' => 'fan', 'FAN14G1727' => 'fan', 'FAN14G1791' => 'fan', 'FAN14G2361' => 'fan', 'FAN14G2668' => 'fan', 'FAN14G2770' => 'fan', 'FAN14G2874' => 'fan', 'FAN14G3193' => 'fan', 'FAN14G3624' => 'fan', 'FAN14G3676' => 'fan', 'FAN14G3807' => 'fan', 'FAN14G4082' => 'fan', 'FAN14G4342' => 'fan', 'FAN14G4985' => 'fan', 'FAN14G5126' => 'fan', 'FAN14G5781' => 'fan', 'FAN14G5808' => 'fan', 'FAN14G5949' => 'fan', 'FAN15G0828' => 'fan', 'FAN15G1054' => 'fan', 'FAN15G2023' => 'fan', 'FAN15G2506' => 'fan', 'FAN16G0128' => 'fan', 'FAN16G0249' => 'fan', 'FAN16G0429' => 'fan', 'FAN16G1493' => 'fan', 'FAN16G2210' => 'fan', 'FAN16G2506' => 'fan', 'FAN18G1542' => 'fan', 'FAN18G4057' => 'fan', 'FAN19G0745' => 'fan', 'FAN19G1216' => 'fan', 'FAN19G1733' => 'fan', 'FAN20G0258' => 'fan', 'FAN20G1095' => 'fan', 'FAN20G1557' => 'fan', 'FAN21G0302' => 'fan', 'FAN21G0519' => 'fan', 'FAN21G0970' => 'fan', 'FAN21G1159' => 'fan', 'FAN21G1312' => 'fan', 'FAN21G1440' => 'fan', 'FAN21G1715' => 'fan', 'FAN23G1584' => 'fan', 'FAN24G0045' => 'fan', 'FAN24G0053' => 'fan', 'FAN24G1500' => 'fan', 'FAN24G1817' => 'fan', 'FAN24G2147' => 'fan', 'FAN24G2236' => 'fan', 'FAN24G2446' => 'fan', 'FAN24G2684' => 'fan', 'FAN25G0187' => 'fan', 'FAN25G0505' => 'fan', 'FAN25G0589' => 'fan', 'FAN25G3663' => 'fan', 'FAN26G1025' => 'fan', 'FAN26G2860' => 'fan', 'FAN27G1329' => 'fan', 'FAN27G3392' => 'fan', 'FvH4_1g02011' => 'fve', 'FvH4_1g06511' => 'fve', 'FvH4_2g19900' => 'fve', 'FvH4_2g19920' => 'fve', 'FvH4_2g24261' => 'fve', 'FvH4_2g24270' => 'fve', 'FvH4_2g24631' => 'fve', 'FvH4_2g30622' => 'fve', 'FvH4_3g12920' => 'fve', 'FvH4_3g30171' => 'fve', 'FvH4_3g35490' => 'fve', 'FvH4_3g43682' => 'fve', 'FvH4_3g43730' => 'fve', 'FvH4_3g43732' => 'fve', 'FvH4_3g43751' => 'fve', 'FvH4_3g43752' => 'fve', 'FvH4_3g43770' => 'fve', 'FvH4_3g44471' => 'fve', 'FvH4_3g44510' => 'fve', 'FvH4_3g44582' => 'fve', 'FvH4_4g16921' => 'fve', 'FvH4_4g17121' => 'fve', 'FvH4_4g17782' => 'fve', 'FvH4_4g17783' => 'fve', 'FvH4_4g18120' => 'fve', 'FvH4_4g31310' => 'fve', 'FvH4_4g35052' => 'fve', 'FvH4_5g30862' => 'fve', 'FvH4_6g01541' => 'fve', 'FvH4_6g02021' => 'fve', 'FvH4_6g02041' => 'fve', 'FvH4_6g02071' => 'fve', 'FvH4_6g02171' => 'fve', 'FvH4_6g03181' => 'fve', 'FvH4_6g03182' => 'fve', 'FvH4_6g03221' => 'fve', 'FvH4_6g03380' => 'fve', 'FvH4_6g05201' => 'fve', 'FvH4_6g05203' => 'fve', 'FvH4_6g20231' => 'fve', 'FvH4_6g31981' => 'fve', 'FvH4_6g32061' => 'fve', 'FvH4_6g37041' => 'fve', 'FvH4_6g37932' => 'fve', 'FvH4_6g38731' => 'fve', 'FvH4_6g39370' => 'fve', 'FvH4_6g39371' => 'fve', 'FvH4_6g40891' => 'fve', 'FvH4_6g40892' => 'fve', 'FvH4_6g43143' => 'fve', 'FvH4_6g45251' => 'fve', 'FvH4_6g45260' => 'fve', 'FvH4_6g45291' => 'fve', 'FvH4_6g45890' => 'fve', 'FvH4_6g46240' => 'fve', 'FvH4_6g46241' => 'fve', 'FvH4_6g46242' => 'fve', 'FvH4_6g46260' => 'fve', 'FvH4_6g46280' => 'fve', 'FvH4_6g46380' => 'fve', 'FvH4_7g12841' => 'fve', 'FvH4_7g31431' => 'fve', 'Glyma.09G075900' => 'gma', 'Gohir.A09G096401' => 'ghi', 'Gohir.D09G096101' => 'ghi', 'Gorai.006G112800' => 'gra', 'HanXRQChr04g0121411' => 'han', 'Hund15878' => 'sun', 'Lj2A1107G68' => 'lonja', 'Lj2A630G63' => 'lonja', 'Lj2A946T25' => 'lonja', 'Lj2C714T1' => 'lonja', 'Lj2C966T3' => 'lonja', 'Lj2C966T4' => 'lonja', 'Lj4g0002979' => 'lja', 'Lsat_1_v5_gn_5_30901' => 'lsa', 'Lsat_1_v5_gn_5_31100' => 'lsa', 'Lsat_1_v5_gn_5_38600' => 'lsa', 'Lsat_1_v5_gn_6_92061' => 'lsa', 'Manes.05G071301' => 'mes', 'MD02G1008700' => 'mdo', 'MD02G1008900' => 'mdo', 'MD03G1256400' => 'mdo', 'MD04G1180900' => 'mdo', 'MD04G1181000' => 'mdo', 'MD04G1181200' => 'mdo', 'MD05G1244200' => 'mdo', 'MD05G1324200' => 'mdo', 'MD09G1201600' => 'mdo', 'MD10G1000600' => 'mdo', 'MD14G1026900' => 'mdo', 'MD14G1187900' => 'mdo', 'MD15G1017800' => 'mdo', 'MD15G1018100' => 'mdo', 'Medtr4g124160' => 'mtr', 'Migut.L01260' => 'egut', 'Nitab4.5_0000008g0440' => 'nta', 'Nitab4.5_0000207g0170' => 'nta', 'Nitab4.5_0007671g0030' => 'nta', 'Nitab4.5_0010853g0020' => 'nta', 'Oeu057656.1' => 'oeu', 'PGSC0003DMG400005638' => 'stu', 'PGSC0003DMG400005639' => 'stu', 'Phvul.009G222800' => 'pvu', 'Potri.009G132400' => 'ptr', 'Potri.009G163001' => 'ptr', 'Potri.011G000700' => 'ptr', 'Potri.011G004800' => 'ptr', 'Prupe.1G509300' => 'ppe', 'Prupe.1G509700' => 'ppe', 'Prupe.1G510400' => 'ppe', 'Prupe.1G510700' => 'ppe', 'Prupe.1G512600' => 'ppe', 'Prupe.2G073200' => 'ppe', 'Prupe.3G059500' => 'ppe', 'Prupe.3G059600' => 'ppe', 'Prupe.3G246100' => 'ppe', 'Prupe.3G265100' => 'ppe', 'Prupe.4G034700' => 'ppe', 'Prupe.4G052100' => 'ppe', 'Prupe.4G053600' => 'ppe', 'Prupe.5G068800' => 'ppe', 'Prupe.5G070600' => 'ppe', 'Prupe.6G075400' => 'ppe', 'Prupe.6G075500' => 'ppe', 'Prupe.6G076400' => 'ppe', 'Prupe.8G110700' => 'ppe', 'Psat4g020960' => 'psa', 'PSO135G0788' => 'pso', 'PSO210G6463' => 'pso', 'PSO384G0370' => 'pso', 'PSO386G0056' => 'pso', 'QL01p006048' => 'qlo', 'QL02p054283' => 'qlo', 'QL05p008000' => 'qlo', 'QL05p008212' => 'qlo', 'QL05p008950' => 'qlo', 'QL05p009042' => 'qlo', 'QL05p009518' => 'qlo', 'QL05p012589' => 'qlo', 'QL05p012608' => 'qlo', 'QL05p012650' => 'qlo', 'QL05p012667' => 'qlo', 'QL05p014501' => 'qlo', 'QL05p052800' => 'qlo', 'QL05p065010' => 'qlo', 'QL05p074156' => 'qlo', 'QL05p074160' => 'qlo', 'QL05p074174' => 'qlo', 'QL05p074178' => 'qlo', 'QL05p074214' => 'qlo', 'QL06p001050' => 'qlo', 'QL06p001056' => 'qlo', 'QL06p006093' => 'qlo', 'QL06p006111' => 'qlo', 'QL07p019784' => 'qlo', 'QL07p019801' => 'qlo', 'QL07p036110' => 'qlo', 'QL07p036134' => 'qlo', 'QL07p036147' => 'qlo', 'QL07p036156' => 'qlo', 'QL07p036300' => 'qlo', 'QL07p036320' => 'qlo', 'QL08p014547' => 'qlo', 'QL08p014551' => 'qlo', 'QL08p043319' => 'qlo', 'QL08p043324' => 'qlo', 'QL11p009094' => 'qlo', 'RcHm_v2.0_Chr1g0380481' => 'rch', 'RcHm_v2.0_Chr2g0089331' => 'rch', 'RcHm_v2.0_Chr2g0123691' => 'rch', 'RcHm_v2.0_Chr2g0151111' => 'rch', 'RcHm_v2.0_Chr2g0163011' => 'rch', 'RcHm_v2.0_Chr2g0163051' => 'rch', 'RcHm_v2.0_Chr2g0164671' => 'rch', 'RcHm_v2.0_Chr2g0164681' => 'rch', 'RcHm_v2.0_Chr2g0164721' => 'rch', 'RcHm_v2.0_Chr3g0449911' => 'rch', 'RcHm_v2.0_Chr3g0450211' => 'rch', 'RcHm_v2.0_Chr3g0457271' => 'rch', 'RcHm_v2.0_Chr5g0018111' => 'rch', 'RcHm_v2.0_Chr5g0021011' => 'rch', 'RcHm_v2.0_Chr5g0081171' => 'rch', 'RcHm_v2.0_Chr5g0081211' => 'rch', 'RcHm_v2.0_Chr6g0275871' => 'rch', 'RcHm_v2.0_Chr6g0276071' => 'rch', 'RcHm_v2.0_Chr6g0285591' => 'rch', 'RcHm_v2.0_Chr6g0291931' => 'rch', 'RcHm_v2.0_Chr6g0292091' => 'rch', 'RcHm_v2.0_Chr6g0292271' => 'rch', 'RcHm_v2.0_Chr7g0221261' => 'rch', 'Rhsim08G0219900' => 'rsi', 'Rhsim08G0220200' => 'rsi', 'Rhsim08G0237800' => 'rsi', 'Rhsim08G0238800' => 'rsi', 'Sabra09G0102700' => 'sbr', 'Sabra09G0127200' => 'sbr', 'Sabra11G0003700' => 'sbr', 'Sabra15G0014700' => 'sbr', 'Sc19g0000590' => 'sci', 'Sc19g0001870' => 'sci', 'SGA_v2.0_scaffold1G00346' => 'sas', 'SGA_v2.0_scaffold1G00575' => 'sas', 'SGA_v2.0_scaffold1G00761' => 'sas', 'SGA_v2.0_scaffold232G43501' => 'sas', 'TAR625G1137' => 'tar', 'Thecc.03G222100' => 'tca', 'TPR.G12691' => 'tpr', 'TWI34G0727' => 'twi', 'TWI36G0117' => 'twi', 'VMungo1309G0868' => 'vmu' ), 'gf_id' => 'HOM05D001729', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001729' ), 'data_identifier' => 'HOM05D001729', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001729', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '375', 'num_species' => '42' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'Ah.07g204710' => 'amhyb', 'AUR62006001' => 'cqu', 'AUR62006002' => 'cqu', 'AUR62006003' => 'cqu', 'AUR62015641' => 'cqu', 'AUR62027174' => 'cqu', 'AUR62035623' => 'cqu', 'AUR62035624' => 'cqu', 'AUR62035625' => 'cqu', 'AUR62035626' => 'cqu', 'CAN.G1110.53' => 'can', 'CANSAT80G0415' => 'cansat', 'Ca_21364_v3' => 'car', 'COL.COLO4_30693' => 'col', 'COL.COLO4_30694' => 'col', 'COL.COLO4_30695' => 'col', 'COL.COLO4_30696' => 'col', 'COL.COLO4_34020' => 'col', 'DCAR_004585' => 'dca', 'Dinv04029' => 'din', 'Dinv34857' => 'din', 'Duzib147G0011' => 'dzi', 'Duzib170G0599' => 'dzi', 'Duzib192G1051' => 'dzi', 'FAN01G0708' => 'fan', 'FAN01G0742' => 'fan', 'FAN02G0048' => 'fan', 'FAN02G0583' => 'fan', 'FAN02G0688' => 'fan', 'FAN02G1588' => 'fan', 'FAN02G2194' => 'fan', 'FAN02G2750' => 'fan', 'FAN02G3094' => 'fan', 'FAN02G3887' => 'fan', 'FAN02G3911' => 'fan', 'FAN02G3994' => 'fan', 'FAN02G4432' => 'fan', 'FAN02G4556' => 'fan', 'FAN03G1977' => 'fan', 'FAN03G2781' => 'fan', 'FAN03G2850' => 'fan', 'FAN03G3155' => 'fan', 'FAN04G2487' => 'fan', 'FAN05G0208' => 'fan', 'FAN05G0656' => 'fan', 'FAN05G0696' => 'fan', 'FAN05G0810' => 'fan', 'FAN05G1447' => 'fan', 'FAN05G2640' => 'fan', 'FAN05G2911' => 'fan', 'FAN05G3901' => 'fan', 'FAN05G4859' => 'fan', 'FAN05G4861' => 'fan', 'FAN05G4988' => 'fan', 'FAN05G5187' => 'fan', 'FAN05G5452' => 'fan', 'FAN05G5500' => 'fan', 'FAN05G5688' => 'fan', 'FAN06G0177' => 'fan', 'FAN06G0675' => 'fan', 'FAN06G1290' => 'fan', 'FAN06G2191' => 'fan', 'FAN06G2405' => 'fan', 'FAN06G3231' => 'fan', 'FAN06G3932' => 'fan', 'FAN07G0163' => 'fan', 'FAN07G0471' => 'fan', 'FAN07G1354' => 'fan', 'FAN08G0338' => 'fan', 'FAN08G1373' => 'fan', 'FAN08G2539' => 'fan', 'FAN08G2728' => 'fan', 'FAN09G0608' => 'fan', 'FAN09G1136' => 'fan', 'FAN09G1958' => 'fan', 'FAN09G2508' => 'fan', 'FAN09G2597' => 'fan', 'FAN09G2658' => 'fan', 'FAN09G2757' => 'fan', 'FAN09G2983' => 'fan', 'FAN09G3130' => 'fan', 'FAN09G3565' => 'fan', 'FAN09G3613' => 'fan', 'FAN09G4011' => 'fan', 'FAN09G4239' => 'fan', 'FAN09G4277' => 'fan', 'FAN09G4720' => 'fan', 'FAN11G0139' => 'fan', 'FAN11G1727' => 'fan', 'FAN11G2672' => 'fan', 'FAN11G2795' => 'fan', 'FAN11G3238' => 'fan', 'FAN11G3734' => 'fan', 'FAN12G0631' => 'fan', 'FAN12G2239' => 'fan', 'FAN12G2308' => 'fan', 'FAN12G2569' => 'fan', 'FAN12G2623' => 'fan', 'FAN13G3182' => 'fan', 'FAN14G0053' => 'fan', 'FAN14G0370' => 'fan', 'FAN14G0382' => 'fan', 'FAN14G0421' => 'fan', 'FAN14G0866' => 'fan', 'FAN14G1187' => 'fan', 'FAN14G1727' => 'fan', 'FAN14G1791' => 'fan', 'FAN14G2361' => 'fan', 'FAN14G2668' => 'fan', 'FAN14G2770' => 'fan', 'FAN14G2874' => 'fan', 'FAN14G3193' => 'fan', 'FAN14G3624' => 'fan', 'FAN14G3676' => 'fan', 'FAN14G3807' => 'fan', 'FAN14G4082' => 'fan', 'FAN14G4342' => 'fan', 'FAN14G4985' => 'fan', 'FAN14G5126' => 'fan', 'FAN14G5781' => 'fan', 'FAN14G5808' => 'fan', 'FAN14G5949' => 'fan', 'FAN15G0828' => 'fan', 'FAN15G1054' => 'fan', 'FAN15G2023' => 'fan', 'FAN15G2506' => 'fan', 'FAN16G0128' => 'fan', 'FAN16G0249' => 'fan', 'FAN16G0429' => 'fan', 'FAN16G1493' => 'fan', 'FAN16G2210' => 'fan', 'FAN16G2506' => 'fan', 'FAN18G1542' => 'fan', 'FAN18G4057' => 'fan', 'FAN19G0745' => 'fan', 'FAN19G1216' => 'fan', 'FAN19G1733' => 'fan', 'FAN20G0258' => 'fan', 'FAN20G1095' => 'fan', 'FAN20G1557' => 'fan', 'FAN21G0302' => 'fan', 'FAN21G0519' => 'fan', 'FAN21G0970' => 'fan', 'FAN21G1159' => 'fan', 'FAN21G1312' => 'fan', 'FAN21G1440' => 'fan', 'FAN21G1715' => 'fan', 'FAN23G1584' => 'fan', 'FAN24G0045' => 'fan', 'FAN24G0053' => 'fan', 'FAN24G1500' => 'fan', 'FAN24G1817' => 'fan', 'FAN24G2147' => 'fan', 'FAN24G2236' => 'fan', 'FAN24G2446' => 'fan', 'FAN24G2684' => 'fan', 'FAN25G0187' => 'fan', 'FAN25G0505' => 'fan', 'FAN25G0589' => 'fan', 'FAN25G3663' => 'fan', 'FAN26G1025' => 'fan', 'FAN26G2860' => 'fan', 'FAN27G1329' => 'fan', 'FAN27G3392' => 'fan', 'FvH4_1g02011' => 'fve', 'FvH4_1g06511' => 'fve', 'FvH4_2g19900' => 'fve', 'FvH4_2g19920' => 'fve', 'FvH4_2g24261' => 'fve', 'FvH4_2g24270' => 'fve', 'FvH4_2g24631' => 'fve', 'FvH4_2g30622' => 'fve', 'FvH4_3g12920' => 'fve', 'FvH4_3g30171' => 'fve', 'FvH4_3g35490' => 'fve', 'FvH4_3g43682' => 'fve', 'FvH4_3g43730' => 'fve', 'FvH4_3g43732' => 'fve', 'FvH4_3g43751' => 'fve', 'FvH4_3g43752' => 'fve', 'FvH4_3g43770' => 'fve', 'FvH4_3g44471' => 'fve', 'FvH4_3g44510' => 'fve', 'FvH4_3g44582' => 'fve', 'FvH4_4g16921' => 'fve', 'FvH4_4g17121' => 'fve', 'FvH4_4g17782' => 'fve', 'FvH4_4g17783' => 'fve', 'FvH4_4g18120' => 'fve', 'FvH4_4g31310' => 'fve', 'FvH4_4g35052' => 'fve', 'FvH4_5g30862' => 'fve', 'FvH4_6g01541' => 'fve', 'FvH4_6g02021' => 'fve', 'FvH4_6g02041' => 'fve', 'FvH4_6g02071' => 'fve', 'FvH4_6g02171' => 'fve', 'FvH4_6g03181' => 'fve', 'FvH4_6g03182' => 'fve', 'FvH4_6g03221' => 'fve', 'FvH4_6g03380' => 'fve', 'FvH4_6g05201' => 'fve', 'FvH4_6g05203' => 'fve', 'FvH4_6g20231' => 'fve', 'FvH4_6g31981' => 'fve', 'FvH4_6g32061' => 'fve', 'FvH4_6g37041' => 'fve', 'FvH4_6g37932' => 'fve', 'FvH4_6g38731' => 'fve', 'FvH4_6g39370' => 'fve', 'FvH4_6g39371' => 'fve', 'FvH4_6g40891' => 'fve', 'FvH4_6g40892' => 'fve', 'FvH4_6g43143' => 'fve', 'FvH4_6g45251' => 'fve', 'FvH4_6g45260' => 'fve', 'FvH4_6g45291' => 'fve', 'FvH4_6g45890' => 'fve', 'FvH4_6g46240' => 'fve', 'FvH4_6g46241' => 'fve', 'FvH4_6g46242' => 'fve', 'FvH4_6g46260' => 'fve', 'FvH4_6g46280' => 'fve', 'FvH4_6g46380' => 'fve', 'FvH4_7g12841' => 'fve', 'FvH4_7g31431' => 'fve', 'Glyma.09G075900' => 'gma', 'Gohir.A09G096401' => 'ghi', 'Gohir.D09G096101' => 'ghi', 'Gorai.006G112800' => 'gra', 'HanXRQChr04g0121411' => 'han', 'Hund15878' => 'sun', 'Lj2A1107G68' => 'lonja', 'Lj2A630G63' => 'lonja', 'Lj2A946T25' => 'lonja', 'Lj2C714T1' => 'lonja', 'Lj2C966T3' => 'lonja', 'Lj2C966T4' => 'lonja', 'Lj4g0002979' => 'lja', 'Lsat_1_v5_gn_5_30901' => 'lsa', 'Lsat_1_v5_gn_5_31100' => 'lsa', 'Lsat_1_v5_gn_5_38600' => 'lsa', 'Lsat_1_v5_gn_6_92061' => 'lsa', 'Manes.05G071301' => 'mes', 'MD02G1008700' => 'mdo', 'MD02G1008900' => 'mdo', 'MD03G1256400' => 'mdo', 'MD04G1180900' => 'mdo', 'MD04G1181000' => 'mdo', 'MD04G1181200' => 'mdo', 'MD05G1244200' => 'mdo', 'MD05G1324200' => 'mdo', 'MD09G1201600' => 'mdo', 'MD10G1000600' => 'mdo', 'MD14G1026900' => 'mdo', 'MD14G1187900' => 'mdo', 'MD15G1017800' => 'mdo', 'MD15G1018100' => 'mdo', 'Medtr4g124160' => 'mtr', 'Migut.L01260' => 'egut', 'Nitab4.5_0000008g0440' => 'nta', 'Nitab4.5_0000207g0170' => 'nta', 'Nitab4.5_0007671g0030' => 'nta', 'Nitab4.5_0010853g0020' => 'nta', 'Oeu057656.1' => 'oeu', 'PGSC0003DMG400005638' => 'stu', 'PGSC0003DMG400005639' => 'stu', 'Phvul.009G222800' => 'pvu', 'Potri.009G132400' => 'ptr', 'Potri.009G163001' => 'ptr', 'Potri.011G000700' => 'ptr', 'Potri.011G004800' => 'ptr', 'Prupe.1G509300' => 'ppe', 'Prupe.1G509700' => 'ppe', 'Prupe.1G510400' => 'ppe', 'Prupe.1G510700' => 'ppe', 'Prupe.1G512600' => 'ppe', 'Prupe.2G073200' => 'ppe', 'Prupe.3G059500' => 'ppe', 'Prupe.3G059600' => 'ppe', 'Prupe.3G246100' => 'ppe', 'Prupe.3G265100' => 'ppe', 'Prupe.4G034700' => 'ppe', 'Prupe.4G052100' => 'ppe', 'Prupe.4G053600' => 'ppe', 'Prupe.5G068800' => 'ppe', 'Prupe.5G070600' => 'ppe', 'Prupe.6G075400' => 'ppe', 'Prupe.6G075500' => 'ppe', 'Prupe.6G076400' => 'ppe', 'Prupe.8G110700' => 'ppe', 'Psat4g020960' => 'psa', 'PSO135G0788' => 'pso', 'PSO210G6463' => 'pso', 'PSO384G0370' => 'pso', 'PSO386G0056' => 'pso', 'QL01p006048' => 'qlo', 'QL02p054283' => 'qlo', 'QL05p008000' => 'qlo', 'QL05p008212' => 'qlo', 'QL05p008950' => 'qlo', 'QL05p009042' => 'qlo', 'QL05p009518' => 'qlo', 'QL05p012589' => 'qlo', 'QL05p012608' => 'qlo', 'QL05p012650' => 'qlo', 'QL05p012667' => 'qlo', 'QL05p014501' => 'qlo', 'QL05p052800' => 'qlo', 'QL05p065010' => 'qlo', 'QL05p074156' => 'qlo', 'QL05p074160' => 'qlo', 'QL05p074174' => 'qlo', 'QL05p074178' => 'qlo', 'QL05p074214' => 'qlo', 'QL06p001050' => 'qlo', 'QL06p001056' => 'qlo', 'QL06p006093' => 'qlo', 'QL06p006111' => 'qlo', 'QL07p019784' => 'qlo', 'QL07p019801' => 'qlo', 'QL07p036110' => 'qlo', 'QL07p036134' => 'qlo', 'QL07p036147' => 'qlo', 'QL07p036156' => 'qlo', 'QL07p036300' => 'qlo', 'QL07p036320' => 'qlo', 'QL08p014547' => 'qlo', 'QL08p014551' => 'qlo', 'QL08p043319' => 'qlo', 'QL08p043324' => 'qlo', 'QL11p009094' => 'qlo', 'RcHm_v2.0_Chr1g0380481' => 'rch', 'RcHm_v2.0_Chr2g0089331' => 'rch', 'RcHm_v2.0_Chr2g0123691' => 'rch', 'RcHm_v2.0_Chr2g0151111' => 'rch', 'RcHm_v2.0_Chr2g0163011' => 'rch', 'RcHm_v2.0_Chr2g0163051' => 'rch', 'RcHm_v2.0_Chr2g0164671' => 'rch', 'RcHm_v2.0_Chr2g0164681' => 'rch', 'RcHm_v2.0_Chr2g0164721' => 'rch', 'RcHm_v2.0_Chr3g0449911' => 'rch', 'RcHm_v2.0_Chr3g0450211' => 'rch', 'RcHm_v2.0_Chr3g0457271' => 'rch', 'RcHm_v2.0_Chr5g0018111' => 'rch', 'RcHm_v2.0_Chr5g0021011' => 'rch', 'RcHm_v2.0_Chr5g0081171' => 'rch', 'RcHm_v2.0_Chr5g0081211' => 'rch', 'RcHm_v2.0_Chr6g0275871' => 'rch', 'RcHm_v2.0_Chr6g0276071' => 'rch', 'RcHm_v2.0_Chr6g0285591' => 'rch', 'RcHm_v2.0_Chr6g0291931' => 'rch', 'RcHm_v2.0_Chr6g0292091' => 'rch', 'RcHm_v2.0_Chr6g0292271' => 'rch', 'RcHm_v2.0_Chr7g0221261' => 'rch', 'Rhsim08G0219900' => 'rsi', 'Rhsim08G0220200' => 'rsi', 'Rhsim08G0237800' => 'rsi', 'Rhsim08G0238800' => 'rsi', 'Sabra09G0102700' => 'sbr', 'Sabra09G0127200' => 'sbr', 'Sabra11G0003700' => 'sbr', 'Sabra15G0014700' => 'sbr', 'Sc19g0000590' => 'sci', 'Sc19g0001870' => 'sci', 'SGA_v2.0_scaffold1G00346' => 'sas', 'SGA_v2.0_scaffold1G00575' => 'sas', 'SGA_v2.0_scaffold1G00761' => 'sas', 'SGA_v2.0_scaffold232G43501' => 'sas', 'TAR625G1137' => 'tar', 'Thecc.03G222100' => 'tca', 'TPR.G12691' => 'tpr', 'TWI34G0727' => 'twi', 'TWI36G0117' => 'twi', 'VMungo1309G0868' => 'vmu' ) $gf_id = 'HOM05D001729' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001729' ) $data_identifier = 'HOM05D001729' $data_type = 'gf_id' $species_gene_counts = array( 'amhyb' => (int) 1, 'cqu' => (int) 9, 'can' => (int) 1, 'cansat' => (int) 1, 'car' => (int) 1, 'col' => (int) 5, 'dca' => (int) 1, 'din' => (int) 2, 'dzi' => (int) 3, 'fan' => (int) 140, 'fve' => (int) 62, 'gma' => (int) 1, 'ghi' => (int) 2, 'gra' => (int) 1, 'han' => (int) 1, 'sun' => (int) 1, 'lonja' => (int) 6, 'lja' => (int) 1, 'lsa' => (int) 4, 'mes' => (int) 1, 'mdo' => (int) 14, 'mtr' => (int) 1, 'egut' => (int) 1, 'nta' => (int) 4, 'oeu' => (int) 1, 'stu' => (int) 2, 'pvu' => (int) 1, 'ptr' => (int) 4, 'ppe' => (int) 19, 'psa' => (int) 1, 'pso' => (int) 4, 'qlo' => (int) 36, 'rch' => (int) 23, 'rsi' => (int) 4, 'sbr' => (int) 4, 'sci' => (int) 2, 'sas' => (int) 4, 'tar' => (int) 1, 'tca' => (int) 1, 'tpr' => (int) 1, 'twi' => (int) 2, 'vmu' => (int) 1 ) $gf_gene_species = 'vmu' $gf_gene_id = 'VMungo1309G0868' $species_info = array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ) $local_species = 'tar' $disabled = '' $selected = '' $num_hits = (int) 1
Warning (2): count(): Parameter must be an array or an object that implements Countable [APP/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp, line 33]Code Context $disabled = (!array_key_exists($local_species,$species_gene_counts))?"disabled":""; $selected = (isset($selected_species) && array_key_exists($local_species,$selected_species))?"checked='checked'":""; $num_hits = (array_key_exists($local_species,$species_gene_counts))?count($species_gene_counts[$local_species]):0; $viewFile = '/www/bioinformatics01_ro/plaza/_dev_instances/feedback/app/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp' $dataForView = array( 'sidebar_info' => array( 'gf_id' => 'HOM05D001729', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '375', 'num_species' => '42' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'Ah.07g204710' => 'amhyb', 'AUR62006001' => 'cqu', 'AUR62006002' => 'cqu', 'AUR62006003' => 'cqu', 'AUR62015641' => 'cqu', 'AUR62027174' => 'cqu', 'AUR62035623' => 'cqu', 'AUR62035624' => 'cqu', 'AUR62035625' => 'cqu', 'AUR62035626' => 'cqu', 'CAN.G1110.53' => 'can', 'CANSAT80G0415' => 'cansat', 'Ca_21364_v3' => 'car', 'COL.COLO4_30693' => 'col', 'COL.COLO4_30694' => 'col', 'COL.COLO4_30695' => 'col', 'COL.COLO4_30696' => 'col', 'COL.COLO4_34020' => 'col', 'DCAR_004585' => 'dca', 'Dinv04029' => 'din', 'Dinv34857' => 'din', 'Duzib147G0011' => 'dzi', 'Duzib170G0599' => 'dzi', 'Duzib192G1051' => 'dzi', 'FAN01G0708' => 'fan', 'FAN01G0742' => 'fan', 'FAN02G0048' => 'fan', 'FAN02G0583' => 'fan', 'FAN02G0688' => 'fan', 'FAN02G1588' => 'fan', 'FAN02G2194' => 'fan', 'FAN02G2750' => 'fan', 'FAN02G3094' => 'fan', 'FAN02G3887' => 'fan', 'FAN02G3911' => 'fan', 'FAN02G3994' => 'fan', 'FAN02G4432' => 'fan', 'FAN02G4556' => 'fan', 'FAN03G1977' => 'fan', 'FAN03G2781' => 'fan', 'FAN03G2850' => 'fan', 'FAN03G3155' => 'fan', 'FAN04G2487' => 'fan', 'FAN05G0208' => 'fan', 'FAN05G0656' => 'fan', 'FAN05G0696' => 'fan', 'FAN05G0810' => 'fan', 'FAN05G1447' => 'fan', 'FAN05G2640' => 'fan', 'FAN05G2911' => 'fan', 'FAN05G3901' => 'fan', 'FAN05G4859' => 'fan', 'FAN05G4861' => 'fan', 'FAN05G4988' => 'fan', 'FAN05G5187' => 'fan', 'FAN05G5452' => 'fan', 'FAN05G5500' => 'fan', 'FAN05G5688' => 'fan', 'FAN06G0177' => 'fan', 'FAN06G0675' => 'fan', 'FAN06G1290' => 'fan', 'FAN06G2191' => 'fan', 'FAN06G2405' => 'fan', 'FAN06G3231' => 'fan', 'FAN06G3932' => 'fan', 'FAN07G0163' => 'fan', 'FAN07G0471' => 'fan', 'FAN07G1354' => 'fan', 'FAN08G0338' => 'fan', 'FAN08G1373' => 'fan', 'FAN08G2539' => 'fan', 'FAN08G2728' => 'fan', 'FAN09G0608' => 'fan', 'FAN09G1136' => 'fan', 'FAN09G1958' => 'fan', 'FAN09G2508' => 'fan', 'FAN09G2597' => 'fan', 'FAN09G2658' => 'fan', 'FAN09G2757' => 'fan', 'FAN09G2983' => 'fan', 'FAN09G3130' => 'fan', 'FAN09G3565' => 'fan', 'FAN09G3613' => 'fan', 'FAN09G4011' => 'fan', 'FAN09G4239' => 'fan', 'FAN09G4277' => 'fan', 'FAN09G4720' => 'fan', 'FAN11G0139' => 'fan', 'FAN11G1727' => 'fan', 'FAN11G2672' => 'fan', 'FAN11G2795' => 'fan', 'FAN11G3238' => 'fan', 'FAN11G3734' => 'fan', 'FAN12G0631' => 'fan', 'FAN12G2239' => 'fan', 'FAN12G2308' => 'fan', 'FAN12G2569' => 'fan', 'FAN12G2623' => 'fan', 'FAN13G3182' => 'fan', 'FAN14G0053' => 'fan', 'FAN14G0370' => 'fan', 'FAN14G0382' => 'fan', 'FAN14G0421' => 'fan', 'FAN14G0866' => 'fan', 'FAN14G1187' => 'fan', 'FAN14G1727' => 'fan', 'FAN14G1791' => 'fan', 'FAN14G2361' => 'fan', 'FAN14G2668' => 'fan', 'FAN14G2770' => 'fan', 'FAN14G2874' => 'fan', 'FAN14G3193' => 'fan', 'FAN14G3624' => 'fan', 'FAN14G3676' => 'fan', 'FAN14G3807' => 'fan', 'FAN14G4082' => 'fan', 'FAN14G4342' => 'fan', 'FAN14G4985' => 'fan', 'FAN14G5126' => 'fan', 'FAN14G5781' => 'fan', 'FAN14G5808' => 'fan', 'FAN14G5949' => 'fan', 'FAN15G0828' => 'fan', 'FAN15G1054' => 'fan', 'FAN15G2023' => 'fan', 'FAN15G2506' => 'fan', 'FAN16G0128' => 'fan', 'FAN16G0249' => 'fan', 'FAN16G0429' => 'fan', 'FAN16G1493' => 'fan', 'FAN16G2210' => 'fan', 'FAN16G2506' => 'fan', 'FAN18G1542' => 'fan', 'FAN18G4057' => 'fan', 'FAN19G0745' => 'fan', 'FAN19G1216' => 'fan', 'FAN19G1733' => 'fan', 'FAN20G0258' => 'fan', 'FAN20G1095' => 'fan', 'FAN20G1557' => 'fan', 'FAN21G0302' => 'fan', 'FAN21G0519' => 'fan', 'FAN21G0970' => 'fan', 'FAN21G1159' => 'fan', 'FAN21G1312' => 'fan', 'FAN21G1440' => 'fan', 'FAN21G1715' => 'fan', 'FAN23G1584' => 'fan', 'FAN24G0045' => 'fan', 'FAN24G0053' => 'fan', 'FAN24G1500' => 'fan', 'FAN24G1817' => 'fan', 'FAN24G2147' => 'fan', 'FAN24G2236' => 'fan', 'FAN24G2446' => 'fan', 'FAN24G2684' => 'fan', 'FAN25G0187' => 'fan', 'FAN25G0505' => 'fan', 'FAN25G0589' => 'fan', 'FAN25G3663' => 'fan', 'FAN26G1025' => 'fan', 'FAN26G2860' => 'fan', 'FAN27G1329' => 'fan', 'FAN27G3392' => 'fan', 'FvH4_1g02011' => 'fve', 'FvH4_1g06511' => 'fve', 'FvH4_2g19900' => 'fve', 'FvH4_2g19920' => 'fve', 'FvH4_2g24261' => 'fve', 'FvH4_2g24270' => 'fve', 'FvH4_2g24631' => 'fve', 'FvH4_2g30622' => 'fve', 'FvH4_3g12920' => 'fve', 'FvH4_3g30171' => 'fve', 'FvH4_3g35490' => 'fve', 'FvH4_3g43682' => 'fve', 'FvH4_3g43730' => 'fve', 'FvH4_3g43732' => 'fve', 'FvH4_3g43751' => 'fve', 'FvH4_3g43752' => 'fve', 'FvH4_3g43770' => 'fve', 'FvH4_3g44471' => 'fve', 'FvH4_3g44510' => 'fve', 'FvH4_3g44582' => 'fve', 'FvH4_4g16921' => 'fve', 'FvH4_4g17121' => 'fve', 'FvH4_4g17782' => 'fve', 'FvH4_4g17783' => 'fve', 'FvH4_4g18120' => 'fve', 'FvH4_4g31310' => 'fve', 'FvH4_4g35052' => 'fve', 'FvH4_5g30862' => 'fve', 'FvH4_6g01541' => 'fve', 'FvH4_6g02021' => 'fve', 'FvH4_6g02041' => 'fve', 'FvH4_6g02071' => 'fve', 'FvH4_6g02171' => 'fve', 'FvH4_6g03181' => 'fve', 'FvH4_6g03182' => 'fve', 'FvH4_6g03221' => 'fve', 'FvH4_6g03380' => 'fve', 'FvH4_6g05201' => 'fve', 'FvH4_6g05203' => 'fve', 'FvH4_6g20231' => 'fve', 'FvH4_6g31981' => 'fve', 'FvH4_6g32061' => 'fve', 'FvH4_6g37041' => 'fve', 'FvH4_6g37932' => 'fve', 'FvH4_6g38731' => 'fve', 'FvH4_6g39370' => 'fve', 'FvH4_6g39371' => 'fve', 'FvH4_6g40891' => 'fve', 'FvH4_6g40892' => 'fve', 'FvH4_6g43143' => 'fve', 'FvH4_6g45251' => 'fve', 'FvH4_6g45260' => 'fve', 'FvH4_6g45291' => 'fve', 'FvH4_6g45890' => 'fve', 'FvH4_6g46240' => 'fve', 'FvH4_6g46241' => 'fve', 'FvH4_6g46242' => 'fve', 'FvH4_6g46260' => 'fve', 'FvH4_6g46280' => 'fve', 'FvH4_6g46380' => 'fve', 'FvH4_7g12841' => 'fve', 'FvH4_7g31431' => 'fve', 'Glyma.09G075900' => 'gma', 'Gohir.A09G096401' => 'ghi', 'Gohir.D09G096101' => 'ghi', 'Gorai.006G112800' => 'gra', 'HanXRQChr04g0121411' => 'han', 'Hund15878' => 'sun', 'Lj2A1107G68' => 'lonja', 'Lj2A630G63' => 'lonja', 'Lj2A946T25' => 'lonja', 'Lj2C714T1' => 'lonja', 'Lj2C966T3' => 'lonja', 'Lj2C966T4' => 'lonja', 'Lj4g0002979' => 'lja', 'Lsat_1_v5_gn_5_30901' => 'lsa', 'Lsat_1_v5_gn_5_31100' => 'lsa', 'Lsat_1_v5_gn_5_38600' => 'lsa', 'Lsat_1_v5_gn_6_92061' => 'lsa', 'Manes.05G071301' => 'mes', 'MD02G1008700' => 'mdo', 'MD02G1008900' => 'mdo', 'MD03G1256400' => 'mdo', 'MD04G1180900' => 'mdo', 'MD04G1181000' => 'mdo', 'MD04G1181200' => 'mdo', 'MD05G1244200' => 'mdo', 'MD05G1324200' => 'mdo', 'MD09G1201600' => 'mdo', 'MD10G1000600' => 'mdo', 'MD14G1026900' => 'mdo', 'MD14G1187900' => 'mdo', 'MD15G1017800' => 'mdo', 'MD15G1018100' => 'mdo', 'Medtr4g124160' => 'mtr', 'Migut.L01260' => 'egut', 'Nitab4.5_0000008g0440' => 'nta', 'Nitab4.5_0000207g0170' => 'nta', 'Nitab4.5_0007671g0030' => 'nta', 'Nitab4.5_0010853g0020' => 'nta', 'Oeu057656.1' => 'oeu', 'PGSC0003DMG400005638' => 'stu', 'PGSC0003DMG400005639' => 'stu', 'Phvul.009G222800' => 'pvu', 'Potri.009G132400' => 'ptr', 'Potri.009G163001' => 'ptr', 'Potri.011G000700' => 'ptr', 'Potri.011G004800' => 'ptr', 'Prupe.1G509300' => 'ppe', 'Prupe.1G509700' => 'ppe', 'Prupe.1G510400' => 'ppe', 'Prupe.1G510700' => 'ppe', 'Prupe.1G512600' => 'ppe', 'Prupe.2G073200' => 'ppe', 'Prupe.3G059500' => 'ppe', 'Prupe.3G059600' => 'ppe', 'Prupe.3G246100' => 'ppe', 'Prupe.3G265100' => 'ppe', 'Prupe.4G034700' => 'ppe', 'Prupe.4G052100' => 'ppe', 'Prupe.4G053600' => 'ppe', 'Prupe.5G068800' => 'ppe', 'Prupe.5G070600' => 'ppe', 'Prupe.6G075400' => 'ppe', 'Prupe.6G075500' => 'ppe', 'Prupe.6G076400' => 'ppe', 'Prupe.8G110700' => 'ppe', 'Psat4g020960' => 'psa', 'PSO135G0788' => 'pso', 'PSO210G6463' => 'pso', 'PSO384G0370' => 'pso', 'PSO386G0056' => 'pso', 'QL01p006048' => 'qlo', 'QL02p054283' => 'qlo', 'QL05p008000' => 'qlo', 'QL05p008212' => 'qlo', 'QL05p008950' => 'qlo', 'QL05p009042' => 'qlo', 'QL05p009518' => 'qlo', 'QL05p012589' => 'qlo', 'QL05p012608' => 'qlo', 'QL05p012650' => 'qlo', 'QL05p012667' => 'qlo', 'QL05p014501' => 'qlo', 'QL05p052800' => 'qlo', 'QL05p065010' => 'qlo', 'QL05p074156' => 'qlo', 'QL05p074160' => 'qlo', 'QL05p074174' => 'qlo', 'QL05p074178' => 'qlo', 'QL05p074214' => 'qlo', 'QL06p001050' => 'qlo', 'QL06p001056' => 'qlo', 'QL06p006093' => 'qlo', 'QL06p006111' => 'qlo', 'QL07p019784' => 'qlo', 'QL07p019801' => 'qlo', 'QL07p036110' => 'qlo', 'QL07p036134' => 'qlo', 'QL07p036147' => 'qlo', 'QL07p036156' => 'qlo', 'QL07p036300' => 'qlo', 'QL07p036320' => 'qlo', 'QL08p014547' => 'qlo', 'QL08p014551' => 'qlo', 'QL08p043319' => 'qlo', 'QL08p043324' => 'qlo', 'QL11p009094' => 'qlo', 'RcHm_v2.0_Chr1g0380481' => 'rch', 'RcHm_v2.0_Chr2g0089331' => 'rch', 'RcHm_v2.0_Chr2g0123691' => 'rch', 'RcHm_v2.0_Chr2g0151111' => 'rch', 'RcHm_v2.0_Chr2g0163011' => 'rch', 'RcHm_v2.0_Chr2g0163051' => 'rch', 'RcHm_v2.0_Chr2g0164671' => 'rch', 'RcHm_v2.0_Chr2g0164681' => 'rch', 'RcHm_v2.0_Chr2g0164721' => 'rch', 'RcHm_v2.0_Chr3g0449911' => 'rch', 'RcHm_v2.0_Chr3g0450211' => 'rch', 'RcHm_v2.0_Chr3g0457271' => 'rch', 'RcHm_v2.0_Chr5g0018111' => 'rch', 'RcHm_v2.0_Chr5g0021011' => 'rch', 'RcHm_v2.0_Chr5g0081171' => 'rch', 'RcHm_v2.0_Chr5g0081211' => 'rch', 'RcHm_v2.0_Chr6g0275871' => 'rch', 'RcHm_v2.0_Chr6g0276071' => 'rch', 'RcHm_v2.0_Chr6g0285591' => 'rch', 'RcHm_v2.0_Chr6g0291931' => 'rch', 'RcHm_v2.0_Chr6g0292091' => 'rch', 'RcHm_v2.0_Chr6g0292271' => 'rch', 'RcHm_v2.0_Chr7g0221261' => 'rch', 'Rhsim08G0219900' => 'rsi', 'Rhsim08G0220200' => 'rsi', 'Rhsim08G0237800' => 'rsi', 'Rhsim08G0238800' => 'rsi', 'Sabra09G0102700' => 'sbr', 'Sabra09G0127200' => 'sbr', 'Sabra11G0003700' => 'sbr', 'Sabra15G0014700' => 'sbr', 'Sc19g0000590' => 'sci', 'Sc19g0001870' => 'sci', 'SGA_v2.0_scaffold1G00346' => 'sas', 'SGA_v2.0_scaffold1G00575' => 'sas', 'SGA_v2.0_scaffold1G00761' => 'sas', 'SGA_v2.0_scaffold232G43501' => 'sas', 'TAR625G1137' => 'tar', 'Thecc.03G222100' => 'tca', 'TPR.G12691' => 'tpr', 'TWI34G0727' => 'twi', 'TWI36G0117' => 'twi', 'VMungo1309G0868' => 'vmu' ), 'gf_id' => 'HOM05D001729', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001729' ), 'data_identifier' => 'HOM05D001729', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001729', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '375', 'num_species' => '42' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'Ah.07g204710' => 'amhyb', 'AUR62006001' => 'cqu', 'AUR62006002' => 'cqu', 'AUR62006003' => 'cqu', 'AUR62015641' => 'cqu', 'AUR62027174' => 'cqu', 'AUR62035623' => 'cqu', 'AUR62035624' => 'cqu', 'AUR62035625' => 'cqu', 'AUR62035626' => 'cqu', 'CAN.G1110.53' => 'can', 'CANSAT80G0415' => 'cansat', 'Ca_21364_v3' => 'car', 'COL.COLO4_30693' => 'col', 'COL.COLO4_30694' => 'col', 'COL.COLO4_30695' => 'col', 'COL.COLO4_30696' => 'col', 'COL.COLO4_34020' => 'col', 'DCAR_004585' => 'dca', 'Dinv04029' => 'din', 'Dinv34857' => 'din', 'Duzib147G0011' => 'dzi', 'Duzib170G0599' => 'dzi', 'Duzib192G1051' => 'dzi', 'FAN01G0708' => 'fan', 'FAN01G0742' => 'fan', 'FAN02G0048' => 'fan', 'FAN02G0583' => 'fan', 'FAN02G0688' => 'fan', 'FAN02G1588' => 'fan', 'FAN02G2194' => 'fan', 'FAN02G2750' => 'fan', 'FAN02G3094' => 'fan', 'FAN02G3887' => 'fan', 'FAN02G3911' => 'fan', 'FAN02G3994' => 'fan', 'FAN02G4432' => 'fan', 'FAN02G4556' => 'fan', 'FAN03G1977' => 'fan', 'FAN03G2781' => 'fan', 'FAN03G2850' => 'fan', 'FAN03G3155' => 'fan', 'FAN04G2487' => 'fan', 'FAN05G0208' => 'fan', 'FAN05G0656' => 'fan', 'FAN05G0696' => 'fan', 'FAN05G0810' => 'fan', 'FAN05G1447' => 'fan', 'FAN05G2640' => 'fan', 'FAN05G2911' => 'fan', 'FAN05G3901' => 'fan', 'FAN05G4859' => 'fan', 'FAN05G4861' => 'fan', 'FAN05G4988' => 'fan', 'FAN05G5187' => 'fan', 'FAN05G5452' => 'fan', 'FAN05G5500' => 'fan', 'FAN05G5688' => 'fan', 'FAN06G0177' => 'fan', 'FAN06G0675' => 'fan', 'FAN06G1290' => 'fan', 'FAN06G2191' => 'fan', 'FAN06G2405' => 'fan', 'FAN06G3231' => 'fan', 'FAN06G3932' => 'fan', 'FAN07G0163' => 'fan', 'FAN07G0471' => 'fan', 'FAN07G1354' => 'fan', 'FAN08G0338' => 'fan', 'FAN08G1373' => 'fan', 'FAN08G2539' => 'fan', 'FAN08G2728' => 'fan', 'FAN09G0608' => 'fan', 'FAN09G1136' => 'fan', 'FAN09G1958' => 'fan', 'FAN09G2508' => 'fan', 'FAN09G2597' => 'fan', 'FAN09G2658' => 'fan', 'FAN09G2757' => 'fan', 'FAN09G2983' => 'fan', 'FAN09G3130' => 'fan', 'FAN09G3565' => 'fan', 'FAN09G3613' => 'fan', 'FAN09G4011' => 'fan', 'FAN09G4239' => 'fan', 'FAN09G4277' => 'fan', 'FAN09G4720' => 'fan', 'FAN11G0139' => 'fan', 'FAN11G1727' => 'fan', 'FAN11G2672' => 'fan', 'FAN11G2795' => 'fan', 'FAN11G3238' => 'fan', 'FAN11G3734' => 'fan', 'FAN12G0631' => 'fan', 'FAN12G2239' => 'fan', 'FAN12G2308' => 'fan', 'FAN12G2569' => 'fan', 'FAN12G2623' => 'fan', 'FAN13G3182' => 'fan', 'FAN14G0053' => 'fan', 'FAN14G0370' => 'fan', 'FAN14G0382' => 'fan', 'FAN14G0421' => 'fan', 'FAN14G0866' => 'fan', 'FAN14G1187' => 'fan', 'FAN14G1727' => 'fan', 'FAN14G1791' => 'fan', 'FAN14G2361' => 'fan', 'FAN14G2668' => 'fan', 'FAN14G2770' => 'fan', 'FAN14G2874' => 'fan', 'FAN14G3193' => 'fan', 'FAN14G3624' => 'fan', 'FAN14G3676' => 'fan', 'FAN14G3807' => 'fan', 'FAN14G4082' => 'fan', 'FAN14G4342' => 'fan', 'FAN14G4985' => 'fan', 'FAN14G5126' => 'fan', 'FAN14G5781' => 'fan', 'FAN14G5808' => 'fan', 'FAN14G5949' => 'fan', 'FAN15G0828' => 'fan', 'FAN15G1054' => 'fan', 'FAN15G2023' => 'fan', 'FAN15G2506' => 'fan', 'FAN16G0128' => 'fan', 'FAN16G0249' => 'fan', 'FAN16G0429' => 'fan', 'FAN16G1493' => 'fan', 'FAN16G2210' => 'fan', 'FAN16G2506' => 'fan', 'FAN18G1542' => 'fan', 'FAN18G4057' => 'fan', 'FAN19G0745' => 'fan', 'FAN19G1216' => 'fan', 'FAN19G1733' => 'fan', 'FAN20G0258' => 'fan', 'FAN20G1095' => 'fan', 'FAN20G1557' => 'fan', 'FAN21G0302' => 'fan', 'FAN21G0519' => 'fan', 'FAN21G0970' => 'fan', 'FAN21G1159' => 'fan', 'FAN21G1312' => 'fan', 'FAN21G1440' => 'fan', 'FAN21G1715' => 'fan', 'FAN23G1584' => 'fan', 'FAN24G0045' => 'fan', 'FAN24G0053' => 'fan', 'FAN24G1500' => 'fan', 'FAN24G1817' => 'fan', 'FAN24G2147' => 'fan', 'FAN24G2236' => 'fan', 'FAN24G2446' => 'fan', 'FAN24G2684' => 'fan', 'FAN25G0187' => 'fan', 'FAN25G0505' => 'fan', 'FAN25G0589' => 'fan', 'FAN25G3663' => 'fan', 'FAN26G1025' => 'fan', 'FAN26G2860' => 'fan', 'FAN27G1329' => 'fan', 'FAN27G3392' => 'fan', 'FvH4_1g02011' => 'fve', 'FvH4_1g06511' => 'fve', 'FvH4_2g19900' => 'fve', 'FvH4_2g19920' => 'fve', 'FvH4_2g24261' => 'fve', 'FvH4_2g24270' => 'fve', 'FvH4_2g24631' => 'fve', 'FvH4_2g30622' => 'fve', 'FvH4_3g12920' => 'fve', 'FvH4_3g30171' => 'fve', 'FvH4_3g35490' => 'fve', 'FvH4_3g43682' => 'fve', 'FvH4_3g43730' => 'fve', 'FvH4_3g43732' => 'fve', 'FvH4_3g43751' => 'fve', 'FvH4_3g43752' => 'fve', 'FvH4_3g43770' => 'fve', 'FvH4_3g44471' => 'fve', 'FvH4_3g44510' => 'fve', 'FvH4_3g44582' => 'fve', 'FvH4_4g16921' => 'fve', 'FvH4_4g17121' => 'fve', 'FvH4_4g17782' => 'fve', 'FvH4_4g17783' => 'fve', 'FvH4_4g18120' => 'fve', 'FvH4_4g31310' => 'fve', 'FvH4_4g35052' => 'fve', 'FvH4_5g30862' => 'fve', 'FvH4_6g01541' => 'fve', 'FvH4_6g02021' => 'fve', 'FvH4_6g02041' => 'fve', 'FvH4_6g02071' => 'fve', 'FvH4_6g02171' => 'fve', 'FvH4_6g03181' => 'fve', 'FvH4_6g03182' => 'fve', 'FvH4_6g03221' => 'fve', 'FvH4_6g03380' => 'fve', 'FvH4_6g05201' => 'fve', 'FvH4_6g05203' => 'fve', 'FvH4_6g20231' => 'fve', 'FvH4_6g31981' => 'fve', 'FvH4_6g32061' => 'fve', 'FvH4_6g37041' => 'fve', 'FvH4_6g37932' => 'fve', 'FvH4_6g38731' => 'fve', 'FvH4_6g39370' => 'fve', 'FvH4_6g39371' => 'fve', 'FvH4_6g40891' => 'fve', 'FvH4_6g40892' => 'fve', 'FvH4_6g43143' => 'fve', 'FvH4_6g45251' => 'fve', 'FvH4_6g45260' => 'fve', 'FvH4_6g45291' => 'fve', 'FvH4_6g45890' => 'fve', 'FvH4_6g46240' => 'fve', 'FvH4_6g46241' => 'fve', 'FvH4_6g46242' => 'fve', 'FvH4_6g46260' => 'fve', 'FvH4_6g46280' => 'fve', 'FvH4_6g46380' => 'fve', 'FvH4_7g12841' => 'fve', 'FvH4_7g31431' => 'fve', 'Glyma.09G075900' => 'gma', 'Gohir.A09G096401' => 'ghi', 'Gohir.D09G096101' => 'ghi', 'Gorai.006G112800' => 'gra', 'HanXRQChr04g0121411' => 'han', 'Hund15878' => 'sun', 'Lj2A1107G68' => 'lonja', 'Lj2A630G63' => 'lonja', 'Lj2A946T25' => 'lonja', 'Lj2C714T1' => 'lonja', 'Lj2C966T3' => 'lonja', 'Lj2C966T4' => 'lonja', 'Lj4g0002979' => 'lja', 'Lsat_1_v5_gn_5_30901' => 'lsa', 'Lsat_1_v5_gn_5_31100' => 'lsa', 'Lsat_1_v5_gn_5_38600' => 'lsa', 'Lsat_1_v5_gn_6_92061' => 'lsa', 'Manes.05G071301' => 'mes', 'MD02G1008700' => 'mdo', 'MD02G1008900' => 'mdo', 'MD03G1256400' => 'mdo', 'MD04G1180900' => 'mdo', 'MD04G1181000' => 'mdo', 'MD04G1181200' => 'mdo', 'MD05G1244200' => 'mdo', 'MD05G1324200' => 'mdo', 'MD09G1201600' => 'mdo', 'MD10G1000600' => 'mdo', 'MD14G1026900' => 'mdo', 'MD14G1187900' => 'mdo', 'MD15G1017800' => 'mdo', 'MD15G1018100' => 'mdo', 'Medtr4g124160' => 'mtr', 'Migut.L01260' => 'egut', 'Nitab4.5_0000008g0440' => 'nta', 'Nitab4.5_0000207g0170' => 'nta', 'Nitab4.5_0007671g0030' => 'nta', 'Nitab4.5_0010853g0020' => 'nta', 'Oeu057656.1' => 'oeu', 'PGSC0003DMG400005638' => 'stu', 'PGSC0003DMG400005639' => 'stu', 'Phvul.009G222800' => 'pvu', 'Potri.009G132400' => 'ptr', 'Potri.009G163001' => 'ptr', 'Potri.011G000700' => 'ptr', 'Potri.011G004800' => 'ptr', 'Prupe.1G509300' => 'ppe', 'Prupe.1G509700' => 'ppe', 'Prupe.1G510400' => 'ppe', 'Prupe.1G510700' => 'ppe', 'Prupe.1G512600' => 'ppe', 'Prupe.2G073200' => 'ppe', 'Prupe.3G059500' => 'ppe', 'Prupe.3G059600' => 'ppe', 'Prupe.3G246100' => 'ppe', 'Prupe.3G265100' => 'ppe', 'Prupe.4G034700' => 'ppe', 'Prupe.4G052100' => 'ppe', 'Prupe.4G053600' => 'ppe', 'Prupe.5G068800' => 'ppe', 'Prupe.5G070600' => 'ppe', 'Prupe.6G075400' => 'ppe', 'Prupe.6G075500' => 'ppe', 'Prupe.6G076400' => 'ppe', 'Prupe.8G110700' => 'ppe', 'Psat4g020960' => 'psa', 'PSO135G0788' => 'pso', 'PSO210G6463' => 'pso', 'PSO384G0370' => 'pso', 'PSO386G0056' => 'pso', 'QL01p006048' => 'qlo', 'QL02p054283' => 'qlo', 'QL05p008000' => 'qlo', 'QL05p008212' => 'qlo', 'QL05p008950' => 'qlo', 'QL05p009042' => 'qlo', 'QL05p009518' => 'qlo', 'QL05p012589' => 'qlo', 'QL05p012608' => 'qlo', 'QL05p012650' => 'qlo', 'QL05p012667' => 'qlo', 'QL05p014501' => 'qlo', 'QL05p052800' => 'qlo', 'QL05p065010' => 'qlo', 'QL05p074156' => 'qlo', 'QL05p074160' => 'qlo', 'QL05p074174' => 'qlo', 'QL05p074178' => 'qlo', 'QL05p074214' => 'qlo', 'QL06p001050' => 'qlo', 'QL06p001056' => 'qlo', 'QL06p006093' => 'qlo', 'QL06p006111' => 'qlo', 'QL07p019784' => 'qlo', 'QL07p019801' => 'qlo', 'QL07p036110' => 'qlo', 'QL07p036134' => 'qlo', 'QL07p036147' => 'qlo', 'QL07p036156' => 'qlo', 'QL07p036300' => 'qlo', 'QL07p036320' => 'qlo', 'QL08p014547' => 'qlo', 'QL08p014551' => 'qlo', 'QL08p043319' => 'qlo', 'QL08p043324' => 'qlo', 'QL11p009094' => 'qlo', 'RcHm_v2.0_Chr1g0380481' => 'rch', 'RcHm_v2.0_Chr2g0089331' => 'rch', 'RcHm_v2.0_Chr2g0123691' => 'rch', 'RcHm_v2.0_Chr2g0151111' => 'rch', 'RcHm_v2.0_Chr2g0163011' => 'rch', 'RcHm_v2.0_Chr2g0163051' => 'rch', 'RcHm_v2.0_Chr2g0164671' => 'rch', 'RcHm_v2.0_Chr2g0164681' => 'rch', 'RcHm_v2.0_Chr2g0164721' => 'rch', 'RcHm_v2.0_Chr3g0449911' => 'rch', 'RcHm_v2.0_Chr3g0450211' => 'rch', 'RcHm_v2.0_Chr3g0457271' => 'rch', 'RcHm_v2.0_Chr5g0018111' => 'rch', 'RcHm_v2.0_Chr5g0021011' => 'rch', 'RcHm_v2.0_Chr5g0081171' => 'rch', 'RcHm_v2.0_Chr5g0081211' => 'rch', 'RcHm_v2.0_Chr6g0275871' => 'rch', 'RcHm_v2.0_Chr6g0276071' => 'rch', 'RcHm_v2.0_Chr6g0285591' => 'rch', 'RcHm_v2.0_Chr6g0291931' => 'rch', 'RcHm_v2.0_Chr6g0292091' => 'rch', 'RcHm_v2.0_Chr6g0292271' => 'rch', 'RcHm_v2.0_Chr7g0221261' => 'rch', 'Rhsim08G0219900' => 'rsi', 'Rhsim08G0220200' => 'rsi', 'Rhsim08G0237800' => 'rsi', 'Rhsim08G0238800' => 'rsi', 'Sabra09G0102700' => 'sbr', 'Sabra09G0127200' => 'sbr', 'Sabra11G0003700' => 'sbr', 'Sabra15G0014700' => 'sbr', 'Sc19g0000590' => 'sci', 'Sc19g0001870' => 'sci', 'SGA_v2.0_scaffold1G00346' => 'sas', 'SGA_v2.0_scaffold1G00575' => 'sas', 'SGA_v2.0_scaffold1G00761' => 'sas', 'SGA_v2.0_scaffold232G43501' => 'sas', 'TAR625G1137' => 'tar', 'Thecc.03G222100' => 'tca', 'TPR.G12691' => 'tpr', 'TWI34G0727' => 'twi', 'TWI36G0117' => 'twi', 'VMungo1309G0868' => 'vmu' ) $gf_id = 'HOM05D001729' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001729' ) $data_identifier = 'HOM05D001729' $data_type = 'gf_id' $species_gene_counts = array( 'amhyb' => (int) 1, 'cqu' => (int) 9, 'can' => (int) 1, 'cansat' => (int) 1, 'car' => (int) 1, 'col' => (int) 5, 'dca' => (int) 1, 'din' => (int) 2, 'dzi' => (int) 3, 'fan' => (int) 140, 'fve' => (int) 62, 'gma' => (int) 1, 'ghi' => (int) 2, 'gra' => (int) 1, 'han' => (int) 1, 'sun' => (int) 1, 'lonja' => (int) 6, 'lja' => (int) 1, 'lsa' => (int) 4, 'mes' => (int) 1, 'mdo' => (int) 14, 'mtr' => (int) 1, 'egut' => (int) 1, 'nta' => (int) 4, 'oeu' => (int) 1, 'stu' => (int) 2, 'pvu' => (int) 1, 'ptr' => (int) 4, 'ppe' => (int) 19, 'psa' => (int) 1, 'pso' => (int) 4, 'qlo' => (int) 36, 'rch' => (int) 23, 'rsi' => (int) 4, 'sbr' => (int) 4, 'sci' => (int) 2, 'sas' => (int) 4, 'tar' => (int) 1, 'tca' => (int) 1, 'tpr' => (int) 1, 'twi' => (int) 2, 'vmu' => (int) 1 ) $gf_gene_species = 'vmu' $gf_gene_id = 'VMungo1309G0868' $species_info = array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ) $local_species = 'vmu' $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' => 'HOM05D001729', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '375', 'num_species' => '42' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'Ah.07g204710' => 'amhyb', 'AUR62006001' => 'cqu', 'AUR62006002' => 'cqu', 'AUR62006003' => 'cqu', 'AUR62015641' => 'cqu', 'AUR62027174' => 'cqu', 'AUR62035623' => 'cqu', 'AUR62035624' => 'cqu', 'AUR62035625' => 'cqu', 'AUR62035626' => 'cqu', 'CAN.G1110.53' => 'can', 'CANSAT80G0415' => 'cansat', 'Ca_21364_v3' => 'car', 'COL.COLO4_30693' => 'col', 'COL.COLO4_30694' => 'col', 'COL.COLO4_30695' => 'col', 'COL.COLO4_30696' => 'col', 'COL.COLO4_34020' => 'col', 'DCAR_004585' => 'dca', 'Dinv04029' => 'din', 'Dinv34857' => 'din', 'Duzib147G0011' => 'dzi', 'Duzib170G0599' => 'dzi', 'Duzib192G1051' => 'dzi', 'FAN01G0708' => 'fan', 'FAN01G0742' => 'fan', 'FAN02G0048' => 'fan', 'FAN02G0583' => 'fan', 'FAN02G0688' => 'fan', 'FAN02G1588' => 'fan', 'FAN02G2194' => 'fan', 'FAN02G2750' => 'fan', 'FAN02G3094' => 'fan', 'FAN02G3887' => 'fan', 'FAN02G3911' => 'fan', 'FAN02G3994' => 'fan', 'FAN02G4432' => 'fan', 'FAN02G4556' => 'fan', 'FAN03G1977' => 'fan', 'FAN03G2781' => 'fan', 'FAN03G2850' => 'fan', 'FAN03G3155' => 'fan', 'FAN04G2487' => 'fan', 'FAN05G0208' => 'fan', 'FAN05G0656' => 'fan', 'FAN05G0696' => 'fan', 'FAN05G0810' => 'fan', 'FAN05G1447' => 'fan', 'FAN05G2640' => 'fan', 'FAN05G2911' => 'fan', 'FAN05G3901' => 'fan', 'FAN05G4859' => 'fan', 'FAN05G4861' => 'fan', 'FAN05G4988' => 'fan', 'FAN05G5187' => 'fan', 'FAN05G5452' => 'fan', 'FAN05G5500' => 'fan', 'FAN05G5688' => 'fan', 'FAN06G0177' => 'fan', 'FAN06G0675' => 'fan', 'FAN06G1290' => 'fan', 'FAN06G2191' => 'fan', 'FAN06G2405' => 'fan', 'FAN06G3231' => 'fan', 'FAN06G3932' => 'fan', 'FAN07G0163' => 'fan', 'FAN07G0471' => 'fan', 'FAN07G1354' => 'fan', 'FAN08G0338' => 'fan', 'FAN08G1373' => 'fan', 'FAN08G2539' => 'fan', 'FAN08G2728' => 'fan', 'FAN09G0608' => 'fan', 'FAN09G1136' => 'fan', 'FAN09G1958' => 'fan', 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'FAN14G5126' => 'fan', 'FAN14G5781' => 'fan', 'FAN14G5808' => 'fan', 'FAN14G5949' => 'fan', 'FAN15G0828' => 'fan', 'FAN15G1054' => 'fan', 'FAN15G2023' => 'fan', 'FAN15G2506' => 'fan', 'FAN16G0128' => 'fan', 'FAN16G0249' => 'fan', 'FAN16G0429' => 'fan', 'FAN16G1493' => 'fan', 'FAN16G2210' => 'fan', 'FAN16G2506' => 'fan', 'FAN18G1542' => 'fan', 'FAN18G4057' => 'fan', 'FAN19G0745' => 'fan', 'FAN19G1216' => 'fan', 'FAN19G1733' => 'fan', 'FAN20G0258' => 'fan', 'FAN20G1095' => 'fan', 'FAN20G1557' => 'fan', 'FAN21G0302' => 'fan', 'FAN21G0519' => 'fan', 'FAN21G0970' => 'fan', 'FAN21G1159' => 'fan', 'FAN21G1312' => 'fan', 'FAN21G1440' => 'fan', 'FAN21G1715' => 'fan', 'FAN23G1584' => 'fan', 'FAN24G0045' => 'fan', 'FAN24G0053' => 'fan', 'FAN24G1500' => 'fan', 'FAN24G1817' => 'fan', 'FAN24G2147' => 'fan', 'FAN24G2236' => 'fan', 'FAN24G2446' => 'fan', 'FAN24G2684' => 'fan', 'FAN25G0187' => 'fan', 'FAN25G0505' => 'fan', 'FAN25G0589' => 'fan', 'FAN25G3663' => 'fan', 'FAN26G1025' => 'fan', 'FAN26G2860' => 'fan', 'FAN27G1329' => 'fan', 'FAN27G3392' => 'fan', 'FvH4_1g02011' => 'fve', 'FvH4_1g06511' => 'fve', 'FvH4_2g19900' => 'fve', 'FvH4_2g19920' => 'fve', 'FvH4_2g24261' => 'fve', 'FvH4_2g24270' => 'fve', 'FvH4_2g24631' => 'fve', 'FvH4_2g30622' => 'fve', 'FvH4_3g12920' => 'fve', 'FvH4_3g30171' => 'fve', 'FvH4_3g35490' => 'fve', 'FvH4_3g43682' => 'fve', 'FvH4_3g43730' => 'fve', 'FvH4_3g43732' => 'fve', 'FvH4_3g43751' => 'fve', 'FvH4_3g43752' => 'fve', 'FvH4_3g43770' => 'fve', 'FvH4_3g44471' => 'fve', 'FvH4_3g44510' => 'fve', 'FvH4_3g44582' => 'fve', 'FvH4_4g16921' => 'fve', 'FvH4_4g17121' => 'fve', 'FvH4_4g17782' => 'fve', 'FvH4_4g17783' => 'fve', 'FvH4_4g18120' => 'fve', 'FvH4_4g31310' => 'fve', 'FvH4_4g35052' => 'fve', 'FvH4_5g30862' => 'fve', 'FvH4_6g01541' => 'fve', 'FvH4_6g02021' => 'fve', 'FvH4_6g02041' => 'fve', 'FvH4_6g02071' => 'fve', 'FvH4_6g02171' => 'fve', 'FvH4_6g03181' => 'fve', 'FvH4_6g03182' => 'fve', 'FvH4_6g03221' => 'fve', 'FvH4_6g03380' => 'fve', 'FvH4_6g05201' => 'fve', 'FvH4_6g05203' => 'fve', 'FvH4_6g20231' => 'fve', 'FvH4_6g31981' => 'fve', 'FvH4_6g32061' => 'fve', 'FvH4_6g37041' => 'fve', 'FvH4_6g37932' => 'fve', 'FvH4_6g38731' => 'fve', 'FvH4_6g39370' => 'fve', 'FvH4_6g39371' => 'fve', 'FvH4_6g40891' => 'fve', 'FvH4_6g40892' => 'fve', 'FvH4_6g43143' => 'fve', 'FvH4_6g45251' => 'fve', 'FvH4_6g45260' => 'fve', 'FvH4_6g45291' => 'fve', 'FvH4_6g45890' => 'fve', 'FvH4_6g46240' => 'fve', 'FvH4_6g46241' => 'fve', 'FvH4_6g46242' => 'fve', 'FvH4_6g46260' => 'fve', 'FvH4_6g46280' => 'fve', 'FvH4_6g46380' => 'fve', 'FvH4_7g12841' => 'fve', 'FvH4_7g31431' => 'fve', 'Glyma.09G075900' => 'gma', 'Gohir.A09G096401' => 'ghi', 'Gohir.D09G096101' => 'ghi', 'Gorai.006G112800' => 'gra', 'HanXRQChr04g0121411' => 'han', 'Hund15878' => 'sun', 'Lj2A1107G68' => 'lonja', 'Lj2A630G63' => 'lonja', 'Lj2A946T25' => 'lonja', 'Lj2C714T1' => 'lonja', 'Lj2C966T3' => 'lonja', 'Lj2C966T4' => 'lonja', 'Lj4g0002979' => 'lja', 'Lsat_1_v5_gn_5_30901' => 'lsa', 'Lsat_1_v5_gn_5_31100' => 'lsa', 'Lsat_1_v5_gn_5_38600' => 'lsa', 'Lsat_1_v5_gn_6_92061' => 'lsa', 'Manes.05G071301' => 'mes', 'MD02G1008700' => 'mdo', 'MD02G1008900' => 'mdo', 'MD03G1256400' => 'mdo', 'MD04G1180900' => 'mdo', 'MD04G1181000' => 'mdo', 'MD04G1181200' => 'mdo', 'MD05G1244200' => 'mdo', 'MD05G1324200' => 'mdo', 'MD09G1201600' => 'mdo', 'MD10G1000600' => 'mdo', 'MD14G1026900' => 'mdo', 'MD14G1187900' => 'mdo', 'MD15G1017800' => 'mdo', 'MD15G1018100' => 'mdo', 'Medtr4g124160' => 'mtr', 'Migut.L01260' => 'egut', 'Nitab4.5_0000008g0440' => 'nta', 'Nitab4.5_0000207g0170' => 'nta', 'Nitab4.5_0007671g0030' => 'nta', 'Nitab4.5_0010853g0020' => 'nta', 'Oeu057656.1' => 'oeu', 'PGSC0003DMG400005638' => 'stu', 'PGSC0003DMG400005639' => 'stu', 'Phvul.009G222800' => 'pvu', 'Potri.009G132400' => 'ptr', 'Potri.009G163001' => 'ptr', 'Potri.011G000700' => 'ptr', 'Potri.011G004800' => 'ptr', 'Prupe.1G509300' => 'ppe', 'Prupe.1G509700' => 'ppe', 'Prupe.1G510400' => 'ppe', 'Prupe.1G510700' => 'ppe', 'Prupe.1G512600' => 'ppe', 'Prupe.2G073200' => 'ppe', 'Prupe.3G059500' => 'ppe', 'Prupe.3G059600' => 'ppe', 'Prupe.3G246100' => 'ppe', 'Prupe.3G265100' => 'ppe', 'Prupe.4G034700' => 'ppe', 'Prupe.4G052100' => 'ppe', 'Prupe.4G053600' => 'ppe', 'Prupe.5G068800' => 'ppe', 'Prupe.5G070600' => 'ppe', 'Prupe.6G075400' => 'ppe', 'Prupe.6G075500' => 'ppe', 'Prupe.6G076400' => 'ppe', 'Prupe.8G110700' => 'ppe', 'Psat4g020960' => 'psa', 'PSO135G0788' => 'pso', 'PSO210G6463' => 'pso', 'PSO384G0370' => 'pso', 'PSO386G0056' => 'pso', 'QL01p006048' => 'qlo', 'QL02p054283' => 'qlo', 'QL05p008000' => 'qlo', 'QL05p008212' => 'qlo', 'QL05p008950' => 'qlo', 'QL05p009042' => 'qlo', 'QL05p009518' => 'qlo', 'QL05p012589' => 'qlo', 'QL05p012608' => 'qlo', 'QL05p012650' => 'qlo', 'QL05p012667' => 'qlo', 'QL05p014501' => 'qlo', 'QL05p052800' => 'qlo', 'QL05p065010' => 'qlo', 'QL05p074156' => 'qlo', 'QL05p074160' => 'qlo', 'QL05p074174' => 'qlo', 'QL05p074178' => 'qlo', 'QL05p074214' => 'qlo', 'QL06p001050' => 'qlo', 'QL06p001056' => 'qlo', 'QL06p006093' => 'qlo', 'QL06p006111' => 'qlo', 'QL07p019784' => 'qlo', 'QL07p019801' => 'qlo', 'QL07p036110' => 'qlo', 'QL07p036134' => 'qlo', 'QL07p036147' => 'qlo', 'QL07p036156' => 'qlo', 'QL07p036300' => 'qlo', 'QL07p036320' => 'qlo', 'QL08p014547' => 'qlo', 'QL08p014551' => 'qlo', 'QL08p043319' => 'qlo', 'QL08p043324' => 'qlo', 'QL11p009094' => 'qlo', 'RcHm_v2.0_Chr1g0380481' => 'rch', 'RcHm_v2.0_Chr2g0089331' => 'rch', 'RcHm_v2.0_Chr2g0123691' => 'rch', 'RcHm_v2.0_Chr2g0151111' => 'rch', 'RcHm_v2.0_Chr2g0163011' => 'rch', 'RcHm_v2.0_Chr2g0163051' => 'rch', 'RcHm_v2.0_Chr2g0164671' => 'rch', 'RcHm_v2.0_Chr2g0164681' => 'rch', 'RcHm_v2.0_Chr2g0164721' => 'rch', 'RcHm_v2.0_Chr3g0449911' => 'rch', 'RcHm_v2.0_Chr3g0450211' => 'rch', 'RcHm_v2.0_Chr3g0457271' => 'rch', 'RcHm_v2.0_Chr5g0018111' => 'rch', 'RcHm_v2.0_Chr5g0021011' => 'rch', 'RcHm_v2.0_Chr5g0081171' => 'rch', 'RcHm_v2.0_Chr5g0081211' => 'rch', 'RcHm_v2.0_Chr6g0275871' => 'rch', 'RcHm_v2.0_Chr6g0276071' => 'rch', 'RcHm_v2.0_Chr6g0285591' => 'rch', 'RcHm_v2.0_Chr6g0291931' => 'rch', 'RcHm_v2.0_Chr6g0292091' => 'rch', 'RcHm_v2.0_Chr6g0292271' => 'rch', 'RcHm_v2.0_Chr7g0221261' => 'rch', 'Rhsim08G0219900' => 'rsi', 'Rhsim08G0220200' => 'rsi', 'Rhsim08G0237800' => 'rsi', 'Rhsim08G0238800' => 'rsi', 'Sabra09G0102700' => 'sbr', 'Sabra09G0127200' => 'sbr', 'Sabra11G0003700' => 'sbr', 'Sabra15G0014700' => 'sbr', 'Sc19g0000590' => 'sci', 'Sc19g0001870' => 'sci', 'SGA_v2.0_scaffold1G00346' => 'sas', 'SGA_v2.0_scaffold1G00575' => 'sas', 'SGA_v2.0_scaffold1G00761' => 'sas', 'SGA_v2.0_scaffold232G43501' => 'sas', 'TAR625G1137' => 'tar', 'Thecc.03G222100' => 'tca', 'TPR.G12691' => 'tpr', 'TWI34G0727' => 'twi', 'TWI36G0117' => 'twi', 'VMungo1309G0868' => 'vmu' ), 'gf_id' => 'HOM05D001729', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001729' ), 'data_identifier' => 'HOM05D001729', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001729', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '375', 'num_species' => '42' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'Ah.07g204710' => 'amhyb', 'AUR62006001' => 'cqu', 'AUR62006002' => 'cqu', 'AUR62006003' => 'cqu', 'AUR62015641' => 'cqu', 'AUR62027174' => 'cqu', 'AUR62035623' => 'cqu', 'AUR62035624' => 'cqu', 'AUR62035625' => 'cqu', 'AUR62035626' => 'cqu', 'CAN.G1110.53' => 'can', 'CANSAT80G0415' => 'cansat', 'Ca_21364_v3' => 'car', 'COL.COLO4_30693' => 'col', 'COL.COLO4_30694' => 'col', 'COL.COLO4_30695' => 'col', 'COL.COLO4_30696' => 'col', 'COL.COLO4_34020' => 'col', 'DCAR_004585' => 'dca', 'Dinv04029' => 'din', 'Dinv34857' => 'din', 'Duzib147G0011' => 'dzi', 'Duzib170G0599' => 'dzi', 'Duzib192G1051' => 'dzi', 'FAN01G0708' => 'fan', 'FAN01G0742' => 'fan', 'FAN02G0048' => 'fan', 'FAN02G0583' => 'fan', 'FAN02G0688' => 'fan', 'FAN02G1588' => 'fan', 'FAN02G2194' => 'fan', 'FAN02G2750' => 'fan', 'FAN02G3094' => 'fan', 'FAN02G3887' => 'fan', 'FAN02G3911' => 'fan', 'FAN02G3994' => 'fan', 'FAN02G4432' => 'fan', 'FAN02G4556' => 'fan', 'FAN03G1977' => 'fan', 'FAN03G2781' => 'fan', 'FAN03G2850' => 'fan', 'FAN03G3155' => 'fan', 'FAN04G2487' => 'fan', 'FAN05G0208' => 'fan', 'FAN05G0656' => 'fan', 'FAN05G0696' => 'fan', 'FAN05G0810' => 'fan', 'FAN05G1447' => 'fan', 'FAN05G2640' => 'fan', 'FAN05G2911' => 'fan', 'FAN05G3901' => 'fan', 'FAN05G4859' => 'fan', 'FAN05G4861' => 'fan', 'FAN05G4988' => 'fan', 'FAN05G5187' => 'fan', 'FAN05G5452' => 'fan', 'FAN05G5500' => 'fan', 'FAN05G5688' => 'fan', 'FAN06G0177' => 'fan', 'FAN06G0675' => 'fan', 'FAN06G1290' => 'fan', 'FAN06G2191' => 'fan', 'FAN06G2405' => 'fan', 'FAN06G3231' => 'fan', 'FAN06G3932' => 'fan', 'FAN07G0163' => 'fan', 'FAN07G0471' => 'fan', 'FAN07G1354' => 'fan', 'FAN08G0338' => 'fan', 'FAN08G1373' => 'fan', 'FAN08G2539' => 'fan', 'FAN08G2728' => 'fan', 'FAN09G0608' => 'fan', 'FAN09G1136' => 'fan', 'FAN09G1958' => 'fan', 'FAN09G2508' => 'fan', 'FAN09G2597' => 'fan', 'FAN09G2658' => 'fan', 'FAN09G2757' => 'fan', 'FAN09G2983' => 'fan', 'FAN09G3130' => 'fan', 'FAN09G3565' => 'fan', 'FAN09G3613' => 'fan', 'FAN09G4011' => 'fan', 'FAN09G4239' => 'fan', 'FAN09G4277' => 'fan', 'FAN09G4720' => 'fan', 'FAN11G0139' => 'fan', 'FAN11G1727' => 'fan', 'FAN11G2672' => 'fan', 'FAN11G2795' => 'fan', 'FAN11G3238' => 'fan', 'FAN11G3734' => 'fan', 'FAN12G0631' => 'fan', 'FAN12G2239' => 'fan', 'FAN12G2308' => 'fan', 'FAN12G2569' => 'fan', 'FAN12G2623' => 'fan', 'FAN13G3182' => 'fan', 'FAN14G0053' => 'fan', 'FAN14G0370' => 'fan', 'FAN14G0382' => 'fan', 'FAN14G0421' => 'fan', 'FAN14G0866' => 'fan', 'FAN14G1187' => 'fan', 'FAN14G1727' => 'fan', 'FAN14G1791' => 'fan', 'FAN14G2361' => 'fan', 'FAN14G2668' => 'fan', 'FAN14G2770' => 'fan', 'FAN14G2874' => 'fan', 'FAN14G3193' => 'fan', 'FAN14G3624' => 'fan', 'FAN14G3676' => 'fan', 'FAN14G3807' => 'fan', 'FAN14G4082' => 'fan', 'FAN14G4342' => 'fan', 'FAN14G4985' => 'fan', 'FAN14G5126' => 'fan', 'FAN14G5781' => 'fan', 'FAN14G5808' => 'fan', 'FAN14G5949' => 'fan', 'FAN15G0828' => 'fan', 'FAN15G1054' => 'fan', 'FAN15G2023' => 'fan', 'FAN15G2506' => 'fan', 'FAN16G0128' => 'fan', 'FAN16G0249' => 'fan', 'FAN16G0429' => 'fan', 'FAN16G1493' => 'fan', 'FAN16G2210' => 'fan', 'FAN16G2506' => 'fan', 'FAN18G1542' => 'fan', 'FAN18G4057' => 'fan', 'FAN19G0745' => 'fan', 'FAN19G1216' => 'fan', 'FAN19G1733' => 'fan', 'FAN20G0258' => 'fan', 'FAN20G1095' => 'fan', 'FAN20G1557' => 'fan', 'FAN21G0302' => 'fan', 'FAN21G0519' => 'fan', 'FAN21G0970' => 'fan', 'FAN21G1159' => 'fan', 'FAN21G1312' => 'fan', 'FAN21G1440' => 'fan', 'FAN21G1715' => 'fan', 'FAN23G1584' => 'fan', 'FAN24G0045' => 'fan', 'FAN24G0053' => 'fan', 'FAN24G1500' => 'fan', 'FAN24G1817' => 'fan', 'FAN24G2147' => 'fan', 'FAN24G2236' => 'fan', 'FAN24G2446' => 'fan', 'FAN24G2684' => 'fan', 'FAN25G0187' => 'fan', 'FAN25G0505' => 'fan', 'FAN25G0589' => 'fan', 'FAN25G3663' => 'fan', 'FAN26G1025' => 'fan', 'FAN26G2860' => 'fan', 'FAN27G1329' => 'fan', 'FAN27G3392' => 'fan', 'FvH4_1g02011' => 'fve', 'FvH4_1g06511' => 'fve', 'FvH4_2g19900' => 'fve', 'FvH4_2g19920' => 'fve', 'FvH4_2g24261' => 'fve', 'FvH4_2g24270' => 'fve', 'FvH4_2g24631' => 'fve', 'FvH4_2g30622' => 'fve', 'FvH4_3g12920' => 'fve', 'FvH4_3g30171' => 'fve', 'FvH4_3g35490' => 'fve', 'FvH4_3g43682' => 'fve', 'FvH4_3g43730' => 'fve', 'FvH4_3g43732' => 'fve', 'FvH4_3g43751' => 'fve', 'FvH4_3g43752' => 'fve', 'FvH4_3g43770' => 'fve', 'FvH4_3g44471' => 'fve', 'FvH4_3g44510' => 'fve', 'FvH4_3g44582' => 'fve', 'FvH4_4g16921' => 'fve', 'FvH4_4g17121' => 'fve', 'FvH4_4g17782' => 'fve', 'FvH4_4g17783' => 'fve', 'FvH4_4g18120' => 'fve', 'FvH4_4g31310' => 'fve', 'FvH4_4g35052' => 'fve', 'FvH4_5g30862' => 'fve', 'FvH4_6g01541' => 'fve', 'FvH4_6g02021' => 'fve', 'FvH4_6g02041' => 'fve', 'FvH4_6g02071' => 'fve', 'FvH4_6g02171' => 'fve', 'FvH4_6g03181' => 'fve', 'FvH4_6g03182' => 'fve', 'FvH4_6g03221' => 'fve', 'FvH4_6g03380' => 'fve', 'FvH4_6g05201' => 'fve', 'FvH4_6g05203' => 'fve', 'FvH4_6g20231' => 'fve', 'FvH4_6g31981' => 'fve', 'FvH4_6g32061' => 'fve', 'FvH4_6g37041' => 'fve', 'FvH4_6g37932' => 'fve', 'FvH4_6g38731' => 'fve', 'FvH4_6g39370' => 'fve', 'FvH4_6g39371' => 'fve', 'FvH4_6g40891' => 'fve', 'FvH4_6g40892' => 'fve', 'FvH4_6g43143' => 'fve', 'FvH4_6g45251' => 'fve', 'FvH4_6g45260' => 'fve', 'FvH4_6g45291' => 'fve', 'FvH4_6g45890' => 'fve', 'FvH4_6g46240' => 'fve', 'FvH4_6g46241' => 'fve', 'FvH4_6g46242' => 'fve', 'FvH4_6g46260' => 'fve', 'FvH4_6g46280' => 'fve', 'FvH4_6g46380' => 'fve', 'FvH4_7g12841' => 'fve', 'FvH4_7g31431' => 'fve', 'Glyma.09G075900' => 'gma', 'Gohir.A09G096401' => 'ghi', 'Gohir.D09G096101' => 'ghi', 'Gorai.006G112800' => 'gra', 'HanXRQChr04g0121411' => 'han', 'Hund15878' => 'sun', 'Lj2A1107G68' => 'lonja', 'Lj2A630G63' => 'lonja', 'Lj2A946T25' => 'lonja', 'Lj2C714T1' => 'lonja', 'Lj2C966T3' => 'lonja', 'Lj2C966T4' => 'lonja', 'Lj4g0002979' => 'lja', 'Lsat_1_v5_gn_5_30901' => 'lsa', 'Lsat_1_v5_gn_5_31100' => 'lsa', 'Lsat_1_v5_gn_5_38600' => 'lsa', 'Lsat_1_v5_gn_6_92061' => 'lsa', 'Manes.05G071301' => 'mes', 'MD02G1008700' => 'mdo', 'MD02G1008900' => 'mdo', 'MD03G1256400' => 'mdo', 'MD04G1180900' => 'mdo', 'MD04G1181000' => 'mdo', 'MD04G1181200' => 'mdo', 'MD05G1244200' => 'mdo', 'MD05G1324200' => 'mdo', 'MD09G1201600' => 'mdo', 'MD10G1000600' => 'mdo', 'MD14G1026900' => 'mdo', 'MD14G1187900' => 'mdo', 'MD15G1017800' => 'mdo', 'MD15G1018100' => 'mdo', 'Medtr4g124160' => 'mtr', 'Migut.L01260' => 'egut', 'Nitab4.5_0000008g0440' => 'nta', 'Nitab4.5_0000207g0170' => 'nta', 'Nitab4.5_0007671g0030' => 'nta', 'Nitab4.5_0010853g0020' => 'nta', 'Oeu057656.1' => 'oeu', 'PGSC0003DMG400005638' => 'stu', 'PGSC0003DMG400005639' => 'stu', 'Phvul.009G222800' => 'pvu', 'Potri.009G132400' => 'ptr', 'Potri.009G163001' => 'ptr', 'Potri.011G000700' => 'ptr', 'Potri.011G004800' => 'ptr', 'Prupe.1G509300' => 'ppe', 'Prupe.1G509700' => 'ppe', 'Prupe.1G510400' => 'ppe', 'Prupe.1G510700' => 'ppe', 'Prupe.1G512600' => 'ppe', 'Prupe.2G073200' => 'ppe', 'Prupe.3G059500' => 'ppe', 'Prupe.3G059600' => 'ppe', 'Prupe.3G246100' => 'ppe', 'Prupe.3G265100' => 'ppe', 'Prupe.4G034700' => 'ppe', 'Prupe.4G052100' => 'ppe', 'Prupe.4G053600' => 'ppe', 'Prupe.5G068800' => 'ppe', 'Prupe.5G070600' => 'ppe', 'Prupe.6G075400' => 'ppe', 'Prupe.6G075500' => 'ppe', 'Prupe.6G076400' => 'ppe', 'Prupe.8G110700' => 'ppe', 'Psat4g020960' => 'psa', 'PSO135G0788' => 'pso', 'PSO210G6463' => 'pso', 'PSO384G0370' => 'pso', 'PSO386G0056' => 'pso', 'QL01p006048' => 'qlo', 'QL02p054283' => 'qlo', 'QL05p008000' => 'qlo', 'QL05p008212' => 'qlo', 'QL05p008950' => 'qlo', 'QL05p009042' => 'qlo', 'QL05p009518' => 'qlo', 'QL05p012589' => 'qlo', 'QL05p012608' => 'qlo', 'QL05p012650' => 'qlo', 'QL05p012667' => 'qlo', 'QL05p014501' => 'qlo', 'QL05p052800' => 'qlo', 'QL05p065010' => 'qlo', 'QL05p074156' => 'qlo', 'QL05p074160' => 'qlo', 'QL05p074174' => 'qlo', 'QL05p074178' => 'qlo', 'QL05p074214' => 'qlo', 'QL06p001050' => 'qlo', 'QL06p001056' => 'qlo', 'QL06p006093' => 'qlo', 'QL06p006111' => 'qlo', 'QL07p019784' => 'qlo', 'QL07p019801' => 'qlo', 'QL07p036110' => 'qlo', 'QL07p036134' => 'qlo', 'QL07p036147' => 'qlo', 'QL07p036156' => 'qlo', 'QL07p036300' => 'qlo', 'QL07p036320' => 'qlo', 'QL08p014547' => 'qlo', 'QL08p014551' => 'qlo', 'QL08p043319' => 'qlo', 'QL08p043324' => 'qlo', 'QL11p009094' => 'qlo', 'RcHm_v2.0_Chr1g0380481' => 'rch', 'RcHm_v2.0_Chr2g0089331' => 'rch', 'RcHm_v2.0_Chr2g0123691' => 'rch', 'RcHm_v2.0_Chr2g0151111' => 'rch', 'RcHm_v2.0_Chr2g0163011' => 'rch', 'RcHm_v2.0_Chr2g0163051' => 'rch', 'RcHm_v2.0_Chr2g0164671' => 'rch', 'RcHm_v2.0_Chr2g0164681' => 'rch', 'RcHm_v2.0_Chr2g0164721' => 'rch', 'RcHm_v2.0_Chr3g0449911' => 'rch', 'RcHm_v2.0_Chr3g0450211' => 'rch', 'RcHm_v2.0_Chr3g0457271' => 'rch', 'RcHm_v2.0_Chr5g0018111' => 'rch', 'RcHm_v2.0_Chr5g0021011' => 'rch', 'RcHm_v2.0_Chr5g0081171' => 'rch', 'RcHm_v2.0_Chr5g0081211' => 'rch', 'RcHm_v2.0_Chr6g0275871' => 'rch', 'RcHm_v2.0_Chr6g0276071' => 'rch', 'RcHm_v2.0_Chr6g0285591' => 'rch', 'RcHm_v2.0_Chr6g0291931' => 'rch', 'RcHm_v2.0_Chr6g0292091' => 'rch', 'RcHm_v2.0_Chr6g0292271' => 'rch', 'RcHm_v2.0_Chr7g0221261' => 'rch', 'Rhsim08G0219900' => 'rsi', 'Rhsim08G0220200' => 'rsi', 'Rhsim08G0237800' => 'rsi', 'Rhsim08G0238800' => 'rsi', 'Sabra09G0102700' => 'sbr', 'Sabra09G0127200' => 'sbr', 'Sabra11G0003700' => 'sbr', 'Sabra15G0014700' => 'sbr', 'Sc19g0000590' => 'sci', 'Sc19g0001870' => 'sci', 'SGA_v2.0_scaffold1G00346' => 'sas', 'SGA_v2.0_scaffold1G00575' => 'sas', 'SGA_v2.0_scaffold1G00761' => 'sas', 'SGA_v2.0_scaffold232G43501' => 'sas', 'TAR625G1137' => 'tar', 'Thecc.03G222100' => 'tca', 'TPR.G12691' => 'tpr', 'TWI34G0727' => 'twi', 'TWI36G0117' => 'twi', 'VMungo1309G0868' => 'vmu' ) $gf_id = 'HOM05D001729' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001729' ) $data_identifier = 'HOM05D001729' $data_type = 'gf_id' $species_gene_counts = array( 'amhyb' => (int) 1, 'cqu' => (int) 9, 'can' => (int) 1, 'cansat' => (int) 1, 'car' => (int) 1, 'col' => (int) 5, 'dca' => (int) 1, 'din' => (int) 2, 'dzi' => (int) 3, 'fan' => (int) 140, 'fve' => (int) 62, 'gma' => (int) 1, 'ghi' => (int) 2, 'gra' => (int) 1, 'han' => (int) 1, 'sun' => (int) 1, 'lonja' => (int) 6, 'lja' => (int) 1, 'lsa' => (int) 4, 'mes' => (int) 1, 'mdo' => (int) 14, 'mtr' => (int) 1, 'egut' => (int) 1, 'nta' => (int) 4, 'oeu' => (int) 1, 'stu' => (int) 2, 'pvu' => (int) 1, 'ptr' => (int) 4, 'ppe' => (int) 19, 'psa' => (int) 1, 'pso' => (int) 4, 'qlo' => (int) 36, 'rch' => (int) 23, 'rsi' => (int) 4, 'sbr' => (int) 4, 'sci' => (int) 2, 'sas' => (int) 4, 'tar' => (int) 1, 'tca' => (int) 1, 'tpr' => (int) 1, 'twi' => (int) 2, 'vmu' => (int) 1 ) $gf_gene_species = 'vmu' $gf_gene_id = 'VMungo1309G0868' $species_info = array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ) $local_species = 'vmu' $disabled = '' $selected = '' $num_hits = (int) 0