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' => 'HOM05D001576', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '406', 'num_species' => '29' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'Aqoxy1G01456' => 'aox', 'Aqoxy1G02949' => 'aox', 'Aqoxy3G01274' => 'aox', 'Aqoxy3G02110' => 'aox', 'Aqoxy3G02268' => 'aox', 'Aqoxy5G02702' => 'aox', 'Aqoxy5G02988' => 'aox', 'Aqoxy5G03427' => 'aox', 'Aqoxy6G02363' => 'aox', 'Atru.chr1.3225' => 'acertr', 'Atru.chr8.1198' => 'acertr', 'Atru.chr9.790' => 'acertr', 'CANSAT01G3197' => 'cansat', 'Ciclev10003979m.g' => 'ccl', 'Ciclev10017471m.g' => 'ccl', 'Ciclev10018206m.g' => 'ccl', 'Ciclev10033751m.g' => 'ccl', 'CiPaw.01G000900' => 'cil', 'CiPaw.01G001000' => 'cil', 'CiPaw.01G033500' => 'cil', 'CiPaw.01G060300' => 'cil', 'CiPaw.01G070200' => 'cil', 'CiPaw.01G075100' => 'cil', 'CiPaw.01G084700' => 'cil', 'CiPaw.01G087900' => 'cil', 'CiPaw.01G092600' => 'cil', 'CiPaw.01G097200' => 'cil', 'CiPaw.01G098300' => 'cil', 'CiPaw.01G110200' => 'cil', 'CiPaw.01G118700' => 'cil', 'CiPaw.01G121200' => 'cil', 'CiPaw.01G132500' => 'cil', 'CiPaw.01G146900' => 'cil', 'CiPaw.01G174000' => 'cil', 'CiPaw.01G179900' => 'cil', 'CiPaw.01G183400' => 'cil', 'CiPaw.01G240000' => 'cil', 'CiPaw.01G283500' => 'cil', 'CiPaw.01G307400' => 'cil', 'CiPaw.02G030800' => 'cil', 'CiPaw.02G047200' => 'cil', 'CiPaw.02G050500' => 'cil', 'CiPaw.02G069900' => 'cil', 'CiPaw.02G091600' => 'cil', 'CiPaw.02G095000' => 'cil', 'CiPaw.02G131900' => 'cil', 'CiPaw.03G043000' => 'cil', 'CiPaw.03G069900' => 'cil', 'CiPaw.03G088100' => 'cil', 'CiPaw.03G089300' => 'cil', 'CiPaw.03G093100' => 'cil', 'CiPaw.03G129800' => 'cil', 'CiPaw.03G131200' => 'cil', 'CiPaw.03G134500' => 'cil', 'CiPaw.03G152100' => 'cil', 'CiPaw.03G162700' => 'cil', 'CiPaw.03G172800' => 'cil', 'CiPaw.03G175800' => 'cil', 'CiPaw.03G181800' => 'cil', 'CiPaw.03G191400' => 'cil', 'CiPaw.03G198300' => 'cil', 'CiPaw.03G201300' => 'cil', 'CiPaw.03G224700' => 'cil', 'CiPaw.03G225000' => 'cil', 'CiPaw.04G065100' => 'cil', 'CiPaw.04G080400' => 'cil', 'CiPaw.04G113500' => 'cil', 'CiPaw.04G121900' => 'cil', 'CiPaw.04G144100' => 'cil', 'CiPaw.04G176500' => 'cil', 'CiPaw.05G086200' => 'cil', 'CiPaw.05G100200' => 'cil', 'CiPaw.05G114200' => 'cil', 'CiPaw.05G126800' => 'cil', 'CiPaw.05G228800' => 'cil', 'CiPaw.05G230600' => 'cil', 'CiPaw.05G236500' => 'cil', 'CiPaw.05G244800' => 'cil', 'CiPaw.06G026600' => 'cil', 'CiPaw.06G027900' => 'cil', 'CiPaw.06G051800' => 'cil', 'CiPaw.06G128500' => 'cil', 'CiPaw.06G165900' => 'cil', 'CiPaw.07G045400' => 'cil', 'CiPaw.07G048000' => 'cil', 'CiPaw.07G052000' => 'cil', 'CiPaw.07G073800' => 'cil', 'CiPaw.07G099700' => 'cil', 'CiPaw.07G108700' => 'cil', 'CiPaw.07G120000' => 'cil', 'CiPaw.07G134100' => 'cil', 'CiPaw.07G147000' => 'cil', 'CiPaw.07G149700' => 'cil', 'CiPaw.07G178300' => 'cil', 'CiPaw.07G184900' => 'cil', 'CiPaw.08G044500' => 'cil', 'CiPaw.08G046900' => 'cil', 'CiPaw.08G047300' => 'cil', 'CiPaw.08G115400' => 'cil', 'CiPaw.08G134700' => 'cil', 'CiPaw.08G157400' => 'cil', 'CiPaw.09G014300' => 'cil', 'CiPaw.09G088900' => 'cil', 'CiPaw.09G130900' => 'cil', 'CiPaw.09G133100' => 'cil', 'CiPaw.09G151300' => 'cil', 'CiPaw.09G172800' => 'cil', 'CiPaw.09G174900' => 'cil', 'CiPaw.09G175000' => 'cil', 'CiPaw.10G012800' => 'cil', 'CiPaw.10G028800' => 'cil', 'CiPaw.10G044700' => 'cil', 'CiPaw.10G067400' => 'cil', 'CiPaw.10G115900' => 'cil', 'CiPaw.10G126200' => 'cil', 'CiPaw.10G139700' => 'cil', 'CiPaw.10G155100' => 'cil', 'CiPaw.11G011300' => 'cil', 'CiPaw.11G025900' => 'cil', 'CiPaw.11G104100' => 'cil', 'CiPaw.11G142700' => 'cil', 'CiPaw.11G164500' => 'cil', 'CiPaw.11G189100' => 'cil', 'CiPaw.11G197100' => 'cil', 'CiPaw.12G006100' => 'cil', 'CiPaw.12G038500' => 'cil', 'CiPaw.12G041400' => 'cil', 'CiPaw.12G041600' => 'cil', 'CiPaw.12G051300' => 'cil', 'CiPaw.12G101800' => 'cil', 'CiPaw.12G107800' => 'cil', 'CiPaw.13G033200' => 'cil', 'CiPaw.13G129900' => 'cil', 'CiPaw.13G160200' => 'cil', 'CiPaw.14G018900' => 'cil', 'CiPaw.14G029000' => 'cil', 'CiPaw.14G031000' => 'cil', 'CiPaw.14G032000' => 'cil', 'CiPaw.14G032300' => 'cil', 'CiPaw.14G040600' => 'cil', 'CiPaw.14G060500' => 'cil', 'CiPaw.14G061500' => 'cil', 'CiPaw.14G077500' => 'cil', 'CiPaw.14G088300' => 'cil', 'CiPaw.14G108500' => 'cil', 'CiPaw.14G121300' => 'cil', 'CiPaw.14G133000' => 'cil', 'CiPaw.14G134600' => 'cil', 'CiPaw.15G027200' => 'cil', 'CiPaw.15G037700' => 'cil', 'CiPaw.15G050900' => 'cil', 'CiPaw.15G067200' => 'cil', 'CiPaw.15G072000' => 'cil', 'CiPaw.15G112900' => 'cil', 'CiPaw.15G133200' => 'cil', 'CiPaw.15G139500' => 'cil', 'CiPaw.15G155400' => 'cil', 'CiPaw.16G006000' => 'cil', 'CiPaw.16G013100' => 'cil', 'CiPaw.16G047100' => 'cil', 'CiPaw.16G048900' => 'cil', 'CiPaw.16G070300' => 'cil', 'CSS0000195' => 'camsi', 'CSS0001664' => 'camsi', 'CSS0002566' => 'camsi', 'CSS0003077' => 'camsi', 'CSS0004257' => 'camsi', 'CSS0004495' => 'camsi', 'CSS0004599' => 'camsi', 'CSS0004943' => 'camsi', 'CSS0005302' => 'camsi', 'CSS0006274' => 'camsi', 'CSS0006547' => 'camsi', 'CSS0006860' => 'camsi', 'CSS0008814' => 'camsi', 'CSS0008946' => 'camsi', 'CSS0009093' => 'camsi', 'CSS0010221' => 'camsi', 'CSS0010296' => 'camsi', 'CSS0010386' => 'camsi', 'CSS0010831' => 'camsi', 'CSS0011061' => 'camsi', 'CSS0012008' => 'camsi', 'CSS0012194' => 'camsi', 'CSS0013580' => 'camsi', 'CSS0014176' => 'camsi', 'CSS0014280' => 'camsi', 'CSS0014799' => 'camsi', 'CSS0015368' => 'camsi', 'CSS0017473' => 'camsi', 'CSS0019281' => 'camsi', 'CSS0021320' => 'camsi', 'CSS0021750' => 'camsi', 'CSS0023642' => 'camsi', 'CSS0023792' => 'camsi', 'CSS0031528' => 'camsi', 'CSS0033894' => 'camsi', 'CSS0034959' => 'camsi', 'CSS0035632' => 'camsi', 'CSS0038450' => 'camsi', 'CSS0039293' => 'camsi', 'CSS0041053' => 'camsi', 'CSS0041981' => 'camsi', 'CSS0042573' => 'camsi', 'CSS0042927' => 'camsi', 'CSS0047725' => 'camsi', 'CSS0049636' => 'camsi', 'CSS0050513' => 'camsi', 'DCAR_030203' => 'dca', 'Dinv07939' => 'din', 'FAN01G0456' => 'fan', 'FAN02G3001' => 'fan', 'FAN04G2781' => 'fan', 'FAN05G1385' => 'fan', 'FAN05G3062' => 'fan', 'FAN08G2267' => 'fan', 'FAN10G0481' => 'fan', 'FAN10G1257' => 'fan', 'FAN14G0954' => 'fan', 'FAN14G2347' => 'fan', 'FAN15G0187' => 'fan', 'FAN25G2214' => 'fan', 'FvH4_1g21031' => 'fve', 'FvH4_3g16231' => 'fve', 'FvH4_3g26413' => 'fve', 'FvH4_3g29014' => 'fve', 'FvH4_3g31921' => 'fve', 'FvH4_4g19882' => 'fve', 'FvH4_5g21960' => 'fve', 'FvH4_5g29683' => 'fve', 'FvH4_7g13271' => 'fve', 'Glyma.01G062500' => 'gma', 'Glyma.07G140900' => 'gma', 'Glyma.09G140900' => 'gma', 'Glyma.12G112700' => 'gma', 'Glyma.17G168800' => 'gma', 'HanXRQChr01g0027001' => 'han', 'HanXRQChr04g0120511' => 'han', 'HanXRQChr08g0232381' => 'han', 'HanXRQChr09g0265661' => 'han', 'HanXRQChr13g0416031' => 'han', 'Haze_05835' => 'cav', 'Haze_06597' => 'cav', 'Haze_07921' => 'cav', 'Haze_08599' => 'cav', 'Haze_10686' => 'cav', 'Haze_12994' => 'cav', 'Haze_13466' => 'cav', 'Haze_16101' => 'cav', 'Haze_17766' => 'cav', 'Haze_18456' => 'cav', 'Haze_20229' => 'cav', 'Hma1.2p1_0324F.1_g125640' => 'hma', 'Hma1.2p1_0733F.1_g210230' => 'hma', 'Hma1.2p1_0921F.1_g236870' => 'hma', 'Hma1.2p1_1313F.1_g274940' => 'hma', 'Hma1.2p1_3059F.1_g332230' => 'hma', 'Hund15925' => 'sun', 'Hund19562' => 'sun', 'Hund21925' => 'sun', 'MD03G1177400' => 'mdo', 'MD07G1026100' => 'mdo', 'MD17G1218600' => 'mdo', 'Medtr0867s0010' => 'mtr', 'Medtr6g081150' => 'mtr', 'Os01g0527900' => 'osa', 'Os02g0463725' => 'osa', 'Os02g0785600' => 'osa', 'Os03g0433733' => 'osa', 'Os04g0286500' => 'osa', 'Os05g0227800' => 'osa', 'Os06g0521000' => 'osa', 'Os06g0635500' => 'osa', 'Os06g0660650' => 'osa', 'Os07g0554400' => 'osa', 'Os08g0225900' => 'osa', 'Os08g0561000' => 'osa', 'Os09g0241700' => 'osa', 'Os09g0351900' => 'osa', 'Os11g0220700' => 'osa', 'Os11g0282700' => 'osa', 'Os12g0169300' => 'osa', 'Os12g0228500' => 'osa', 'Os12g0543800' => 'osa', 'PGR044G1547' => 'pgr', 'Potri.005G239150' => 'ptr', 'Potri.010G014250' => 'ptr', 'Prupe.1G172500' => 'ppe', 'Prupe.1G196800' => 'ppe', 'Prupe.1G279700' => 'ppe', 'Prupe.2G026400' => 'ppe', 'Prupe.3G094000' => 'ppe', 'Prupe.4G287300' => 'ppe', 'QL01p022166' => 'qlo', 'QL01p051890' => 'qlo', 'QL02p009469' => 'qlo', 'QL02p046053' => 'qlo', 'QL02p057958' => 'qlo', 'QL02p093127' => 'qlo', 'QL03p006855' => 'qlo', 'QL03p071586' => 'qlo', 'QL04p000022' => 'qlo', 'QL04p000024' => 'qlo', 'QL04p003192' => 'qlo', 'QL05p011416' => 'qlo', 'QL06p039590' => 'qlo', 'QL06p052750' => 'qlo', 'QL06p053821' => 'qlo', 'QL07p025287' => 'qlo', 'QL09p033218' => 'qlo', 'QL09p040841' => 'qlo', 'QL10p020337' => 'qlo', 'QL10p027209' => 'qlo', 'QL10p027969' => 'qlo', 'QL10p048988' => 'qlo', 'QL11p001241' => 'qlo', 'QL11p028487' => 'qlo', 'RcHm_v2.0_Chr2g0105031' => 'rch', 'RcHm_v2.0_Chr2g0117811' => 'rch', 'RcHm_v2.0_Chr6g0270241' => 'rch', 'RcHm_v2.0_Chr7g0215961' => 'rch', 'RcHm_v2.0_Chr7g0231991' => 'rch', 'Rhsim01G0041500' => 'rsi', 'Rhsim01G0115000' => 'rsi', 'Rhsim01G0115400' => 'rsi', 'Rhsim01G0133600' => 'rsi', 'Rhsim01G0159900' => 'rsi', 'Rhsim02G0189400' => 'rsi', 'Rhsim03G0135600' => 'rsi', 'Rhsim03G0149900' => 'rsi', 'Rhsim04G0125600' => 'rsi', 'Rhsim05G0091700' => 'rsi', 'Rhsim05G0092900' => 'rsi', 'Rhsim06G0075000' => 'rsi', 'Rhsim07G0066400' => 'rsi', 'Rhsim07G0156400' => 'rsi', 'Rhsim07G0182200' => 'rsi', 'Rhsim07G0182300' => 'rsi', 'Rhsim08G0180400' => 'rsi', 'Rhsim09G0056800' => 'rsi', 'Rhsim10G0153300' => 'rsi', 'Rhsim11G0012700' => 'rsi', 'Rhsim12G0031800' => 'rsi', 'Rhsim12G0055400' => 'rsi', 'Rhsim12G0091400' => 'rsi', 'Rhsim13G0070800' => 'rsi', 'Rhsim13G0193300' => 'rsi', 'RhsimUnG0111600' => 'rsi', 'RhsimUnG0137500' => 'rsi', 'RhsimUnG0172900' => 'rsi', 'SGA_v2.0_scaffold11G05878' => 'sas', 'SGA_v2.0_scaffold167G38458' => 'sas', 'SGA_v2.0_scaffold19G08588' => 'sas', 'SGA_v2.0_scaffold239G43990' => 'sas', 'SGA_v2.0_scaffold260G45865' => 'sas', 'SGA_v2.0_scaffold309G48177' => 'sas', 'SGA_v2.0_scaffold76G25122' => 'sas', 'SGA_v2.0_scaffold85G26708' => 'sas', 'SHI13914' => 'shi', 'SHI30402' => 'shi', 'TWI09G0020' => 'twi', 'TWI09G0456' => 'twi', 'TWI09G1572' => 'twi', 'TWI12G0266' => 'twi', 'TWI12G1451' => 'twi', 'TWI14G0851' => 'twi', 'TWI15G0796' => 'twi', 'TWI18G0820' => 'twi', 'TWI18G1152' => 'twi', 'TWI23G0007' => 'twi', 'TWI23G0314' => 'twi', 'TWI31G0674' => 'twi', 'TWI31G0938' => 'twi', 'TWI34G0641' => 'twi', 'TWI34G1527' => 'twi', 'TWI36G0193' => 'twi', 'TWI36G0405' => 'twi', 'TWI38G0892' => 'twi', 'TWI38G0936' => 'twi', 'TWI38G2218' => 'twi', 'TWI53G0679' => 'twi', 'TWI53G0863' => 'twi', 'TWI53G1133' => 'twi', 'TWI60G0823' => 'twi', 'TWI63G0919' => 'twi', 'TWI63G1436' => 'twi', 'TWI73G0140' => 'twi', 'TWI73G0419' => 'twi', 'TWI73G0420' => 'twi', 'TWI73G1276' => 'twi', 'TWI74G0405' => 'twi', 'TWI74G0837' => 'twi', 'TWI75G0594' => 'twi', 'TWI75G1615' => 'twi', 'TWI77G0816' => 'twi', 'vmacro03831' => 'vma', 'vmacro13746' => 'vma', 'vmacro16089' => 'vma', 'vmacro22863' => 'vma', 'Zm00001eb085790' => 'zma', 'Zm00001eb114250' => 'zma', 'Zm00001eb138070' => 'zma', 'Zm00001eb167560' => 'zma', 'Zm00001eb199990' => 'zma', 'Zm00001eb368180' => 'zma', 'Zm00001eb382470' => 'zma' ), 'gf_id' => 'HOM05D001576', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001576' ), 'data_identifier' => 'HOM05D001576', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001576', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '406', 'num_species' => '29' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'Aqoxy1G01456' => 'aox', 'Aqoxy1G02949' => 'aox', 'Aqoxy3G01274' => 'aox', 'Aqoxy3G02110' => 'aox', 'Aqoxy3G02268' => 'aox', 'Aqoxy5G02702' => 'aox', 'Aqoxy5G02988' => 'aox', 'Aqoxy5G03427' => 'aox', 'Aqoxy6G02363' => 'aox', 'Atru.chr1.3225' => 'acertr', 'Atru.chr8.1198' => 'acertr', 'Atru.chr9.790' => 'acertr', 'CANSAT01G3197' => 'cansat', 'Ciclev10003979m.g' => 'ccl', 'Ciclev10017471m.g' => 'ccl', 'Ciclev10018206m.g' => 'ccl', 'Ciclev10033751m.g' => 'ccl', 'CiPaw.01G000900' => 'cil', 'CiPaw.01G001000' => 'cil', 'CiPaw.01G033500' => 'cil', 'CiPaw.01G060300' => 'cil', 'CiPaw.01G070200' => 'cil', 'CiPaw.01G075100' => 'cil', 'CiPaw.01G084700' => 'cil', 'CiPaw.01G087900' => 'cil', 'CiPaw.01G092600' => 'cil', 'CiPaw.01G097200' => 'cil', 'CiPaw.01G098300' => 'cil', 'CiPaw.01G110200' => 'cil', 'CiPaw.01G118700' => 'cil', 'CiPaw.01G121200' => 'cil', 'CiPaw.01G132500' => 'cil', 'CiPaw.01G146900' => 'cil', 'CiPaw.01G174000' => 'cil', 'CiPaw.01G179900' => 'cil', 'CiPaw.01G183400' => 'cil', 'CiPaw.01G240000' => 'cil', 'CiPaw.01G283500' => 'cil', 'CiPaw.01G307400' => 'cil', 'CiPaw.02G030800' => 'cil', 'CiPaw.02G047200' => 'cil', 'CiPaw.02G050500' => 'cil', 'CiPaw.02G069900' => 'cil', 'CiPaw.02G091600' => 'cil', 'CiPaw.02G095000' => 'cil', 'CiPaw.02G131900' => 'cil', 'CiPaw.03G043000' => 'cil', 'CiPaw.03G069900' => 'cil', 'CiPaw.03G088100' => 'cil', 'CiPaw.03G089300' => 'cil', 'CiPaw.03G093100' => 'cil', 'CiPaw.03G129800' => 'cil', 'CiPaw.03G131200' => 'cil', 'CiPaw.03G134500' => 'cil', 'CiPaw.03G152100' => 'cil', 'CiPaw.03G162700' => 'cil', 'CiPaw.03G172800' => 'cil', 'CiPaw.03G175800' => 'cil', 'CiPaw.03G181800' => 'cil', 'CiPaw.03G191400' => 'cil', 'CiPaw.03G198300' => 'cil', 'CiPaw.03G201300' => 'cil', 'CiPaw.03G224700' => 'cil', 'CiPaw.03G225000' => 'cil', 'CiPaw.04G065100' => 'cil', 'CiPaw.04G080400' => 'cil', 'CiPaw.04G113500' => 'cil', 'CiPaw.04G121900' => 'cil', 'CiPaw.04G144100' => 'cil', 'CiPaw.04G176500' => 'cil', 'CiPaw.05G086200' => 'cil', 'CiPaw.05G100200' => 'cil', 'CiPaw.05G114200' => 'cil', 'CiPaw.05G126800' => 'cil', 'CiPaw.05G228800' => 'cil', 'CiPaw.05G230600' => 'cil', 'CiPaw.05G236500' => 'cil', 'CiPaw.05G244800' => 'cil', 'CiPaw.06G026600' => 'cil', 'CiPaw.06G027900' => 'cil', 'CiPaw.06G051800' => 'cil', 'CiPaw.06G128500' => 'cil', 'CiPaw.06G165900' => 'cil', 'CiPaw.07G045400' => 'cil', 'CiPaw.07G048000' => 'cil', 'CiPaw.07G052000' => 'cil', 'CiPaw.07G073800' => 'cil', 'CiPaw.07G099700' => 'cil', 'CiPaw.07G108700' => 'cil', 'CiPaw.07G120000' => 'cil', 'CiPaw.07G134100' => 'cil', 'CiPaw.07G147000' => 'cil', 'CiPaw.07G149700' => 'cil', 'CiPaw.07G178300' => 'cil', 'CiPaw.07G184900' => 'cil', 'CiPaw.08G044500' => 'cil', 'CiPaw.08G046900' => 'cil', 'CiPaw.08G047300' => 'cil', 'CiPaw.08G115400' => 'cil', 'CiPaw.08G134700' => 'cil', 'CiPaw.08G157400' => 'cil', 'CiPaw.09G014300' => 'cil', 'CiPaw.09G088900' => 'cil', 'CiPaw.09G130900' => 'cil', 'CiPaw.09G133100' => 'cil', 'CiPaw.09G151300' => 'cil', 'CiPaw.09G172800' => 'cil', 'CiPaw.09G174900' => 'cil', 'CiPaw.09G175000' => 'cil', 'CiPaw.10G012800' => 'cil', 'CiPaw.10G028800' => 'cil', 'CiPaw.10G044700' => 'cil', 'CiPaw.10G067400' => 'cil', 'CiPaw.10G115900' => 'cil', 'CiPaw.10G126200' => 'cil', 'CiPaw.10G139700' => 'cil', 'CiPaw.10G155100' => 'cil', 'CiPaw.11G011300' => 'cil', 'CiPaw.11G025900' => 'cil', 'CiPaw.11G104100' => 'cil', 'CiPaw.11G142700' => 'cil', 'CiPaw.11G164500' => 'cil', 'CiPaw.11G189100' => 'cil', 'CiPaw.11G197100' => 'cil', 'CiPaw.12G006100' => 'cil', 'CiPaw.12G038500' => 'cil', 'CiPaw.12G041400' => 'cil', 'CiPaw.12G041600' => 'cil', 'CiPaw.12G051300' => 'cil', 'CiPaw.12G101800' => 'cil', 'CiPaw.12G107800' => 'cil', 'CiPaw.13G033200' => 'cil', 'CiPaw.13G129900' => 'cil', 'CiPaw.13G160200' => 'cil', 'CiPaw.14G018900' => 'cil', 'CiPaw.14G029000' => 'cil', 'CiPaw.14G031000' => 'cil', 'CiPaw.14G032000' => 'cil', 'CiPaw.14G032300' => 'cil', 'CiPaw.14G040600' => 'cil', 'CiPaw.14G060500' => 'cil', 'CiPaw.14G061500' => 'cil', 'CiPaw.14G077500' => 'cil', 'CiPaw.14G088300' => 'cil', 'CiPaw.14G108500' => 'cil', 'CiPaw.14G121300' => 'cil', 'CiPaw.14G133000' => 'cil', 'CiPaw.14G134600' => 'cil', 'CiPaw.15G027200' => 'cil', 'CiPaw.15G037700' => 'cil', 'CiPaw.15G050900' => 'cil', 'CiPaw.15G067200' => 'cil', 'CiPaw.15G072000' => 'cil', 'CiPaw.15G112900' => 'cil', 'CiPaw.15G133200' => 'cil', 'CiPaw.15G139500' => 'cil', 'CiPaw.15G155400' => 'cil', 'CiPaw.16G006000' => 'cil', 'CiPaw.16G013100' => 'cil', 'CiPaw.16G047100' => 'cil', 'CiPaw.16G048900' => 'cil', 'CiPaw.16G070300' => 'cil', 'CSS0000195' => 'camsi', 'CSS0001664' => 'camsi', 'CSS0002566' => 'camsi', 'CSS0003077' => 'camsi', 'CSS0004257' => 'camsi', 'CSS0004495' => 'camsi', 'CSS0004599' => 'camsi', 'CSS0004943' => 'camsi', 'CSS0005302' => 'camsi', 'CSS0006274' => 'camsi', 'CSS0006547' => 'camsi', 'CSS0006860' => 'camsi', 'CSS0008814' => 'camsi', 'CSS0008946' => 'camsi', 'CSS0009093' => 'camsi', 'CSS0010221' => 'camsi', 'CSS0010296' => 'camsi', 'CSS0010386' => 'camsi', 'CSS0010831' => 'camsi', 'CSS0011061' => 'camsi', 'CSS0012008' => 'camsi', 'CSS0012194' => 'camsi', 'CSS0013580' => 'camsi', 'CSS0014176' => 'camsi', 'CSS0014280' => 'camsi', 'CSS0014799' => 'camsi', 'CSS0015368' => 'camsi', 'CSS0017473' => 'camsi', 'CSS0019281' => 'camsi', 'CSS0021320' => 'camsi', 'CSS0021750' => 'camsi', 'CSS0023642' => 'camsi', 'CSS0023792' => 'camsi', 'CSS0031528' => 'camsi', 'CSS0033894' => 'camsi', 'CSS0034959' => 'camsi', 'CSS0035632' => 'camsi', 'CSS0038450' => 'camsi', 'CSS0039293' => 'camsi', 'CSS0041053' => 'camsi', 'CSS0041981' => 'camsi', 'CSS0042573' => 'camsi', 'CSS0042927' => 'camsi', 'CSS0047725' => 'camsi', 'CSS0049636' => 'camsi', 'CSS0050513' => 'camsi', 'DCAR_030203' => 'dca', 'Dinv07939' => 'din', 'FAN01G0456' => 'fan', 'FAN02G3001' => 'fan', 'FAN04G2781' => 'fan', 'FAN05G1385' => 'fan', 'FAN05G3062' => 'fan', 'FAN08G2267' => 'fan', 'FAN10G0481' => 'fan', 'FAN10G1257' => 'fan', 'FAN14G0954' => 'fan', 'FAN14G2347' => 'fan', 'FAN15G0187' => 'fan', 'FAN25G2214' => 'fan', 'FvH4_1g21031' => 'fve', 'FvH4_3g16231' => 'fve', 'FvH4_3g26413' => 'fve', 'FvH4_3g29014' => 'fve', 'FvH4_3g31921' => 'fve', 'FvH4_4g19882' => 'fve', 'FvH4_5g21960' => 'fve', 'FvH4_5g29683' => 'fve', 'FvH4_7g13271' => 'fve', 'Glyma.01G062500' => 'gma', 'Glyma.07G140900' => 'gma', 'Glyma.09G140900' => 'gma', 'Glyma.12G112700' => 'gma', 'Glyma.17G168800' => 'gma', 'HanXRQChr01g0027001' => 'han', 'HanXRQChr04g0120511' => 'han', 'HanXRQChr08g0232381' => 'han', 'HanXRQChr09g0265661' => 'han', 'HanXRQChr13g0416031' => 'han', 'Haze_05835' => 'cav', 'Haze_06597' => 'cav', 'Haze_07921' => 'cav', 'Haze_08599' => 'cav', 'Haze_10686' => 'cav', 'Haze_12994' => 'cav', 'Haze_13466' => 'cav', 'Haze_16101' => 'cav', 'Haze_17766' => 'cav', 'Haze_18456' => 'cav', 'Haze_20229' => 'cav', 'Hma1.2p1_0324F.1_g125640' => 'hma', 'Hma1.2p1_0733F.1_g210230' => 'hma', 'Hma1.2p1_0921F.1_g236870' => 'hma', 'Hma1.2p1_1313F.1_g274940' => 'hma', 'Hma1.2p1_3059F.1_g332230' => 'hma', 'Hund15925' => 'sun', 'Hund19562' => 'sun', 'Hund21925' => 'sun', 'MD03G1177400' => 'mdo', 'MD07G1026100' => 'mdo', 'MD17G1218600' => 'mdo', 'Medtr0867s0010' => 'mtr', 'Medtr6g081150' => 'mtr', 'Os01g0527900' => 'osa', 'Os02g0463725' => 'osa', 'Os02g0785600' => 'osa', 'Os03g0433733' => 'osa', 'Os04g0286500' => 'osa', 'Os05g0227800' => 'osa', 'Os06g0521000' => 'osa', 'Os06g0635500' => 'osa', 'Os06g0660650' => 'osa', 'Os07g0554400' => 'osa', 'Os08g0225900' => 'osa', 'Os08g0561000' => 'osa', 'Os09g0241700' => 'osa', 'Os09g0351900' => 'osa', 'Os11g0220700' => 'osa', 'Os11g0282700' => 'osa', 'Os12g0169300' => 'osa', 'Os12g0228500' => 'osa', 'Os12g0543800' => 'osa', 'PGR044G1547' => 'pgr', 'Potri.005G239150' => 'ptr', 'Potri.010G014250' => 'ptr', 'Prupe.1G172500' => 'ppe', 'Prupe.1G196800' => 'ppe', 'Prupe.1G279700' => 'ppe', 'Prupe.2G026400' => 'ppe', 'Prupe.3G094000' => 'ppe', 'Prupe.4G287300' => 'ppe', 'QL01p022166' => 'qlo', 'QL01p051890' => 'qlo', 'QL02p009469' => 'qlo', 'QL02p046053' => 'qlo', 'QL02p057958' => 'qlo', 'QL02p093127' => 'qlo', 'QL03p006855' => 'qlo', 'QL03p071586' => 'qlo', 'QL04p000022' => 'qlo', 'QL04p000024' => 'qlo', 'QL04p003192' => 'qlo', 'QL05p011416' => 'qlo', 'QL06p039590' => 'qlo', 'QL06p052750' => 'qlo', 'QL06p053821' => 'qlo', 'QL07p025287' => 'qlo', 'QL09p033218' => 'qlo', 'QL09p040841' => 'qlo', 'QL10p020337' => 'qlo', 'QL10p027209' => 'qlo', 'QL10p027969' => 'qlo', 'QL10p048988' => 'qlo', 'QL11p001241' => 'qlo', 'QL11p028487' => 'qlo', 'RcHm_v2.0_Chr2g0105031' => 'rch', 'RcHm_v2.0_Chr2g0117811' => 'rch', 'RcHm_v2.0_Chr6g0270241' => 'rch', 'RcHm_v2.0_Chr7g0215961' => 'rch', 'RcHm_v2.0_Chr7g0231991' => 'rch', 'Rhsim01G0041500' => 'rsi', 'Rhsim01G0115000' => 'rsi', 'Rhsim01G0115400' => 'rsi', 'Rhsim01G0133600' => 'rsi', 'Rhsim01G0159900' => 'rsi', 'Rhsim02G0189400' => 'rsi', 'Rhsim03G0135600' => 'rsi', 'Rhsim03G0149900' => 'rsi', 'Rhsim04G0125600' => 'rsi', 'Rhsim05G0091700' => 'rsi', 'Rhsim05G0092900' => 'rsi', 'Rhsim06G0075000' => 'rsi', 'Rhsim07G0066400' => 'rsi', 'Rhsim07G0156400' => 'rsi', 'Rhsim07G0182200' => 'rsi', 'Rhsim07G0182300' => 'rsi', 'Rhsim08G0180400' => 'rsi', 'Rhsim09G0056800' => 'rsi', 'Rhsim10G0153300' => 'rsi', 'Rhsim11G0012700' => 'rsi', 'Rhsim12G0031800' => 'rsi', 'Rhsim12G0055400' => 'rsi', 'Rhsim12G0091400' => 'rsi', 'Rhsim13G0070800' => 'rsi', 'Rhsim13G0193300' => 'rsi', 'RhsimUnG0111600' => 'rsi', 'RhsimUnG0137500' => 'rsi', 'RhsimUnG0172900' => 'rsi', 'SGA_v2.0_scaffold11G05878' => 'sas', 'SGA_v2.0_scaffold167G38458' => 'sas', 'SGA_v2.0_scaffold19G08588' => 'sas', 'SGA_v2.0_scaffold239G43990' => 'sas', 'SGA_v2.0_scaffold260G45865' => 'sas', 'SGA_v2.0_scaffold309G48177' => 'sas', 'SGA_v2.0_scaffold76G25122' => 'sas', 'SGA_v2.0_scaffold85G26708' => 'sas', 'SHI13914' => 'shi', 'SHI30402' => 'shi', 'TWI09G0020' => 'twi', 'TWI09G0456' => 'twi', 'TWI09G1572' => 'twi', 'TWI12G0266' => 'twi', 'TWI12G1451' => 'twi', 'TWI14G0851' => 'twi', 'TWI15G0796' => 'twi', 'TWI18G0820' => 'twi', 'TWI18G1152' => 'twi', 'TWI23G0007' => 'twi', 'TWI23G0314' => 'twi', 'TWI31G0674' => 'twi', 'TWI31G0938' => 'twi', 'TWI34G0641' => 'twi', 'TWI34G1527' => 'twi', 'TWI36G0193' => 'twi', 'TWI36G0405' => 'twi', 'TWI38G0892' => 'twi', 'TWI38G0936' => 'twi', 'TWI38G2218' => 'twi', 'TWI53G0679' => 'twi', 'TWI53G0863' => 'twi', 'TWI53G1133' => 'twi', 'TWI60G0823' => 'twi', 'TWI63G0919' => 'twi', 'TWI63G1436' => 'twi', 'TWI73G0140' => 'twi', 'TWI73G0419' => 'twi', 'TWI73G0420' => 'twi', 'TWI73G1276' => 'twi', 'TWI74G0405' => 'twi', 'TWI74G0837' => 'twi', 'TWI75G0594' => 'twi', 'TWI75G1615' => 'twi', 'TWI77G0816' => 'twi', 'vmacro03831' => 'vma', 'vmacro13746' => 'vma', 'vmacro16089' => 'vma', 'vmacro22863' => 'vma', 'Zm00001eb085790' => 'zma', 'Zm00001eb114250' => 'zma', 'Zm00001eb138070' => 'zma', 'Zm00001eb167560' => 'zma', 'Zm00001eb199990' => 'zma', 'Zm00001eb368180' => 'zma', 'Zm00001eb382470' => 'zma' ) $gf_id = 'HOM05D001576' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001576' ) $data_identifier = 'HOM05D001576' $data_type = 'gf_id' $species_gene_counts = array( 'aox' => (int) 9, 'acertr' => (int) 3, 'cansat' => (int) 1, 'ccl' => (int) 4, 'cil' => (int) 145, 'camsi' => (int) 46, 'dca' => (int) 1, 'din' => (int) 1, 'fan' => (int) 12, 'fve' => (int) 9, 'gma' => (int) 5, 'han' => (int) 5, 'cav' => (int) 11, 'hma' => (int) 5, 'sun' => (int) 3, 'mdo' => (int) 3, 'mtr' => (int) 2, 'osa' => (int) 19, 'pgr' => (int) 1, 'ptr' => (int) 2, 'ppe' => (int) 6, 'qlo' => (int) 24, 'rch' => (int) 5, 'rsi' => (int) 28, 'sas' => (int) 8, 'shi' => (int) 2, 'twi' => (int) 35, 'vma' => (int) 4, 'zma' => (int) 7 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb382470' $species_info = array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ) $local_species = 'acertr' $disabled = '' $selected = ''include - APP/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp, line 33 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933 View::_renderElement() - CORE/Cake/View/View.php, line 1224 View::element() - CORE/Cake/View/View.php, line 418 include - APP/View/Elements/analysis/phylogenetics_module/gf_data_settings.ctp, line 37 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933 View::_renderElement() - CORE/Cake/View/View.php, line 1224 View::element() - CORE/Cake/View/View.php, line 418 include - APP/View/Elements/analysis/phylogenetics_module/parameter_selection.ctp, line 64 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933 View::_renderElement() - CORE/Cake/View/View.php, line 1224 View::element() - CORE/Cake/View/View.php, line 418 include - APP/View/Analysis/custom_tree_creation.ctp, line 27 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933
$disabled = (!array_key_exists($local_species,$species_gene_counts))?"disabled":""; $selected = (isset($selected_species) && array_key_exists($local_species,$selected_species))?"checked='checked'":""; $num_hits = (array_key_exists($local_species,$species_gene_counts))?count($species_gene_counts[$local_species]):0;
$disabled = (!array_key_exists($local_species,$species_gene_counts))?"disabled":"";
$selected = (isset($selected_species) && array_key_exists($local_species,$selected_species))?"checked='checked'":"";
$num_hits = (array_key_exists($local_species,$species_gene_counts))?count($species_gene_counts[$local_species]):0;
$viewFile = '/www/bioinformatics01_ro/plaza/_dev_instances/feedback/app/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp' $dataForView = array( 'sidebar_info' => array( 'gf_id' => 'HOM05D001576', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '406', 'num_species' => '29' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'Aqoxy1G01456' => 'aox', 'Aqoxy1G02949' => 'aox', 'Aqoxy3G01274' => 'aox', 'Aqoxy3G02110' => 'aox', 'Aqoxy3G02268' => 'aox', 'Aqoxy5G02702' => 'aox', 'Aqoxy5G02988' => 'aox', 'Aqoxy5G03427' => 'aox', 'Aqoxy6G02363' => 'aox', 'Atru.chr1.3225' => 'acertr', 'Atru.chr8.1198' => 'acertr', 'Atru.chr9.790' => 'acertr', 'CANSAT01G3197' => 'cansat', 'Ciclev10003979m.g' => 'ccl', 'Ciclev10017471m.g' => 'ccl', 'Ciclev10018206m.g' => 'ccl', 'Ciclev10033751m.g' => 'ccl', 'CiPaw.01G000900' => 'cil', 'CiPaw.01G001000' => 'cil', 'CiPaw.01G033500' => 'cil', 'CiPaw.01G060300' => 'cil', 'CiPaw.01G070200' => 'cil', 'CiPaw.01G075100' => 'cil', 'CiPaw.01G084700' => 'cil', 'CiPaw.01G087900' => 'cil', 'CiPaw.01G092600' => 'cil', 'CiPaw.01G097200' => 'cil', 'CiPaw.01G098300' => 'cil', 'CiPaw.01G110200' => 'cil', 'CiPaw.01G118700' => 'cil', 'CiPaw.01G121200' => 'cil', 'CiPaw.01G132500' => 'cil', 'CiPaw.01G146900' => 'cil', 'CiPaw.01G174000' => 'cil', 'CiPaw.01G179900' => 'cil', 'CiPaw.01G183400' => 'cil', 'CiPaw.01G240000' => 'cil', 'CiPaw.01G283500' => 'cil', 'CiPaw.01G307400' => 'cil', 'CiPaw.02G030800' => 'cil', 'CiPaw.02G047200' => 'cil', 'CiPaw.02G050500' => 'cil', 'CiPaw.02G069900' => 'cil', 'CiPaw.02G091600' => 'cil', 'CiPaw.02G095000' => 'cil', 'CiPaw.02G131900' => 'cil', 'CiPaw.03G043000' => 'cil', 'CiPaw.03G069900' => 'cil', 'CiPaw.03G088100' => 'cil', 'CiPaw.03G089300' => 'cil', 'CiPaw.03G093100' => 'cil', 'CiPaw.03G129800' => 'cil', 'CiPaw.03G131200' => 'cil', 'CiPaw.03G134500' => 'cil', 'CiPaw.03G152100' => 'cil', 'CiPaw.03G162700' => 'cil', 'CiPaw.03G172800' => 'cil', 'CiPaw.03G175800' => 'cil', 'CiPaw.03G181800' => 'cil', 'CiPaw.03G191400' => 'cil', 'CiPaw.03G198300' => 'cil', 'CiPaw.03G201300' => 'cil', 'CiPaw.03G224700' => 'cil', 'CiPaw.03G225000' => 'cil', 'CiPaw.04G065100' => 'cil', 'CiPaw.04G080400' => 'cil', 'CiPaw.04G113500' => 'cil', 'CiPaw.04G121900' => 'cil', 'CiPaw.04G144100' => 'cil', 'CiPaw.04G176500' => 'cil', 'CiPaw.05G086200' => 'cil', 'CiPaw.05G100200' => 'cil', 'CiPaw.05G114200' => 'cil', 'CiPaw.05G126800' => 'cil', 'CiPaw.05G228800' => 'cil', 'CiPaw.05G230600' => 'cil', 'CiPaw.05G236500' => 'cil', 'CiPaw.05G244800' => 'cil', 'CiPaw.06G026600' => 'cil', 'CiPaw.06G027900' => 'cil', 'CiPaw.06G051800' => 'cil', 'CiPaw.06G128500' => 'cil', 'CiPaw.06G165900' => 'cil', 'CiPaw.07G045400' => 'cil', 'CiPaw.07G048000' => 'cil', 'CiPaw.07G052000' => 'cil', 'CiPaw.07G073800' => 'cil', 'CiPaw.07G099700' => 'cil', 'CiPaw.07G108700' => 'cil', 'CiPaw.07G120000' => 'cil', 'CiPaw.07G134100' => 'cil', 'CiPaw.07G147000' => 'cil', 'CiPaw.07G149700' => 'cil', 'CiPaw.07G178300' => 'cil', 'CiPaw.07G184900' => 'cil', 'CiPaw.08G044500' => 'cil', 'CiPaw.08G046900' => 'cil', 'CiPaw.08G047300' => 'cil', 'CiPaw.08G115400' => 'cil', 'CiPaw.08G134700' => 'cil', 'CiPaw.08G157400' => 'cil', 'CiPaw.09G014300' => 'cil', 'CiPaw.09G088900' => 'cil', 'CiPaw.09G130900' => 'cil', 'CiPaw.09G133100' => 'cil', 'CiPaw.09G151300' => 'cil', 'CiPaw.09G172800' => 'cil', 'CiPaw.09G174900' => 'cil', 'CiPaw.09G175000' => 'cil', 'CiPaw.10G012800' => 'cil', 'CiPaw.10G028800' => 'cil', 'CiPaw.10G044700' => 'cil', 'CiPaw.10G067400' => 'cil', 'CiPaw.10G115900' => 'cil', 'CiPaw.10G126200' => 'cil', 'CiPaw.10G139700' => 'cil', 'CiPaw.10G155100' => 'cil', 'CiPaw.11G011300' => 'cil', 'CiPaw.11G025900' => 'cil', 'CiPaw.11G104100' => 'cil', 'CiPaw.11G142700' => 'cil', 'CiPaw.11G164500' => 'cil', 'CiPaw.11G189100' => 'cil', 'CiPaw.11G197100' => 'cil', 'CiPaw.12G006100' => 'cil', 'CiPaw.12G038500' => 'cil', 'CiPaw.12G041400' => 'cil', 'CiPaw.12G041600' => 'cil', 'CiPaw.12G051300' => 'cil', 'CiPaw.12G101800' => 'cil', 'CiPaw.12G107800' => 'cil', 'CiPaw.13G033200' => 'cil', 'CiPaw.13G129900' => 'cil', 'CiPaw.13G160200' => 'cil', 'CiPaw.14G018900' => 'cil', 'CiPaw.14G029000' => 'cil', 'CiPaw.14G031000' => 'cil', 'CiPaw.14G032000' => 'cil', 'CiPaw.14G032300' => 'cil', 'CiPaw.14G040600' => 'cil', 'CiPaw.14G060500' => 'cil', 'CiPaw.14G061500' => 'cil', 'CiPaw.14G077500' => 'cil', 'CiPaw.14G088300' => 'cil', 'CiPaw.14G108500' => 'cil', 'CiPaw.14G121300' => 'cil', 'CiPaw.14G133000' => 'cil', 'CiPaw.14G134600' => 'cil', 'CiPaw.15G027200' => 'cil', 'CiPaw.15G037700' => 'cil', 'CiPaw.15G050900' => 'cil', 'CiPaw.15G067200' => 'cil', 'CiPaw.15G072000' => 'cil', 'CiPaw.15G112900' => 'cil', 'CiPaw.15G133200' => 'cil', 'CiPaw.15G139500' => 'cil', 'CiPaw.15G155400' => 'cil', 'CiPaw.16G006000' => 'cil', 'CiPaw.16G013100' => 'cil', 'CiPaw.16G047100' => 'cil', 'CiPaw.16G048900' => 'cil', 'CiPaw.16G070300' => 'cil', 'CSS0000195' => 'camsi', 'CSS0001664' => 'camsi', 'CSS0002566' => 'camsi', 'CSS0003077' => 'camsi', 'CSS0004257' => 'camsi', 'CSS0004495' => 'camsi', 'CSS0004599' => 'camsi', 'CSS0004943' => 'camsi', 'CSS0005302' => 'camsi', 'CSS0006274' => 'camsi', 'CSS0006547' => 'camsi', 'CSS0006860' => 'camsi', 'CSS0008814' => 'camsi', 'CSS0008946' => 'camsi', 'CSS0009093' => 'camsi', 'CSS0010221' => 'camsi', 'CSS0010296' => 'camsi', 'CSS0010386' => 'camsi', 'CSS0010831' => 'camsi', 'CSS0011061' => 'camsi', 'CSS0012008' => 'camsi', 'CSS0012194' => 'camsi', 'CSS0013580' => 'camsi', 'CSS0014176' => 'camsi', 'CSS0014280' => 'camsi', 'CSS0014799' => 'camsi', 'CSS0015368' => 'camsi', 'CSS0017473' => 'camsi', 'CSS0019281' => 'camsi', 'CSS0021320' => 'camsi', 'CSS0021750' => 'camsi', 'CSS0023642' => 'camsi', 'CSS0023792' => 'camsi', 'CSS0031528' => 'camsi', 'CSS0033894' => 'camsi', 'CSS0034959' => 'camsi', 'CSS0035632' => 'camsi', 'CSS0038450' => 'camsi', 'CSS0039293' => 'camsi', 'CSS0041053' => 'camsi', 'CSS0041981' => 'camsi', 'CSS0042573' => 'camsi', 'CSS0042927' => 'camsi', 'CSS0047725' => 'camsi', 'CSS0049636' => 'camsi', 'CSS0050513' => 'camsi', 'DCAR_030203' => 'dca', 'Dinv07939' => 'din', 'FAN01G0456' => 'fan', 'FAN02G3001' => 'fan', 'FAN04G2781' => 'fan', 'FAN05G1385' => 'fan', 'FAN05G3062' => 'fan', 'FAN08G2267' => 'fan', 'FAN10G0481' => 'fan', 'FAN10G1257' => 'fan', 'FAN14G0954' => 'fan', 'FAN14G2347' => 'fan', 'FAN15G0187' => 'fan', 'FAN25G2214' => 'fan', 'FvH4_1g21031' => 'fve', 'FvH4_3g16231' => 'fve', 'FvH4_3g26413' => 'fve', 'FvH4_3g29014' => 'fve', 'FvH4_3g31921' => 'fve', 'FvH4_4g19882' => 'fve', 'FvH4_5g21960' => 'fve', 'FvH4_5g29683' => 'fve', 'FvH4_7g13271' => 'fve', 'Glyma.01G062500' => 'gma', 'Glyma.07G140900' => 'gma', 'Glyma.09G140900' => 'gma', 'Glyma.12G112700' => 'gma', 'Glyma.17G168800' => 'gma', 'HanXRQChr01g0027001' => 'han', 'HanXRQChr04g0120511' => 'han', 'HanXRQChr08g0232381' => 'han', 'HanXRQChr09g0265661' => 'han', 'HanXRQChr13g0416031' => 'han', 'Haze_05835' => 'cav', 'Haze_06597' => 'cav', 'Haze_07921' => 'cav', 'Haze_08599' => 'cav', 'Haze_10686' => 'cav', 'Haze_12994' => 'cav', 'Haze_13466' => 'cav', 'Haze_16101' => 'cav', 'Haze_17766' => 'cav', 'Haze_18456' => 'cav', 'Haze_20229' => 'cav', 'Hma1.2p1_0324F.1_g125640' => 'hma', 'Hma1.2p1_0733F.1_g210230' => 'hma', 'Hma1.2p1_0921F.1_g236870' => 'hma', 'Hma1.2p1_1313F.1_g274940' => 'hma', 'Hma1.2p1_3059F.1_g332230' => 'hma', 'Hund15925' => 'sun', 'Hund19562' => 'sun', 'Hund21925' => 'sun', 'MD03G1177400' => 'mdo', 'MD07G1026100' => 'mdo', 'MD17G1218600' => 'mdo', 'Medtr0867s0010' => 'mtr', 'Medtr6g081150' => 'mtr', 'Os01g0527900' => 'osa', 'Os02g0463725' => 'osa', 'Os02g0785600' => 'osa', 'Os03g0433733' => 'osa', 'Os04g0286500' => 'osa', 'Os05g0227800' => 'osa', 'Os06g0521000' => 'osa', 'Os06g0635500' => 'osa', 'Os06g0660650' => 'osa', 'Os07g0554400' => 'osa', 'Os08g0225900' => 'osa', 'Os08g0561000' => 'osa', 'Os09g0241700' => 'osa', 'Os09g0351900' => 'osa', 'Os11g0220700' => 'osa', 'Os11g0282700' => 'osa', 'Os12g0169300' => 'osa', 'Os12g0228500' => 'osa', 'Os12g0543800' => 'osa', 'PGR044G1547' => 'pgr', 'Potri.005G239150' => 'ptr', 'Potri.010G014250' => 'ptr', 'Prupe.1G172500' => 'ppe', 'Prupe.1G196800' => 'ppe', 'Prupe.1G279700' => 'ppe', 'Prupe.2G026400' => 'ppe', 'Prupe.3G094000' => 'ppe', 'Prupe.4G287300' => 'ppe', 'QL01p022166' => 'qlo', 'QL01p051890' => 'qlo', 'QL02p009469' => 'qlo', 'QL02p046053' => 'qlo', 'QL02p057958' => 'qlo', 'QL02p093127' => 'qlo', 'QL03p006855' => 'qlo', 'QL03p071586' => 'qlo', 'QL04p000022' => 'qlo', 'QL04p000024' => 'qlo', 'QL04p003192' => 'qlo', 'QL05p011416' => 'qlo', 'QL06p039590' => 'qlo', 'QL06p052750' => 'qlo', 'QL06p053821' => 'qlo', 'QL07p025287' => 'qlo', 'QL09p033218' => 'qlo', 'QL09p040841' => 'qlo', 'QL10p020337' => 'qlo', 'QL10p027209' => 'qlo', 'QL10p027969' => 'qlo', 'QL10p048988' => 'qlo', 'QL11p001241' => 'qlo', 'QL11p028487' => 'qlo', 'RcHm_v2.0_Chr2g0105031' => 'rch', 'RcHm_v2.0_Chr2g0117811' => 'rch', 'RcHm_v2.0_Chr6g0270241' => 'rch', 'RcHm_v2.0_Chr7g0215961' => 'rch', 'RcHm_v2.0_Chr7g0231991' => 'rch', 'Rhsim01G0041500' => 'rsi', 'Rhsim01G0115000' => 'rsi', 'Rhsim01G0115400' => 'rsi', 'Rhsim01G0133600' => 'rsi', 'Rhsim01G0159900' => 'rsi', 'Rhsim02G0189400' => 'rsi', 'Rhsim03G0135600' => 'rsi', 'Rhsim03G0149900' => 'rsi', 'Rhsim04G0125600' => 'rsi', 'Rhsim05G0091700' => 'rsi', 'Rhsim05G0092900' => 'rsi', 'Rhsim06G0075000' => 'rsi', 'Rhsim07G0066400' => 'rsi', 'Rhsim07G0156400' => 'rsi', 'Rhsim07G0182200' => 'rsi', 'Rhsim07G0182300' => 'rsi', 'Rhsim08G0180400' => 'rsi', 'Rhsim09G0056800' => 'rsi', 'Rhsim10G0153300' => 'rsi', 'Rhsim11G0012700' => 'rsi', 'Rhsim12G0031800' => 'rsi', 'Rhsim12G0055400' => 'rsi', 'Rhsim12G0091400' => 'rsi', 'Rhsim13G0070800' => 'rsi', 'Rhsim13G0193300' => 'rsi', 'RhsimUnG0111600' => 'rsi', 'RhsimUnG0137500' => 'rsi', 'RhsimUnG0172900' => 'rsi', 'SGA_v2.0_scaffold11G05878' => 'sas', 'SGA_v2.0_scaffold167G38458' => 'sas', 'SGA_v2.0_scaffold19G08588' => 'sas', 'SGA_v2.0_scaffold239G43990' => 'sas', 'SGA_v2.0_scaffold260G45865' => 'sas', 'SGA_v2.0_scaffold309G48177' => 'sas', 'SGA_v2.0_scaffold76G25122' => 'sas', 'SGA_v2.0_scaffold85G26708' => 'sas', 'SHI13914' => 'shi', 'SHI30402' => 'shi', 'TWI09G0020' => 'twi', 'TWI09G0456' => 'twi', 'TWI09G1572' => 'twi', 'TWI12G0266' => 'twi', 'TWI12G1451' => 'twi', 'TWI14G0851' => 'twi', 'TWI15G0796' => 'twi', 'TWI18G0820' => 'twi', 'TWI18G1152' => 'twi', 'TWI23G0007' => 'twi', 'TWI23G0314' => 'twi', 'TWI31G0674' => 'twi', 'TWI31G0938' => 'twi', 'TWI34G0641' => 'twi', 'TWI34G1527' => 'twi', 'TWI36G0193' => 'twi', 'TWI36G0405' => 'twi', 'TWI38G0892' => 'twi', 'TWI38G0936' => 'twi', 'TWI38G2218' => 'twi', 'TWI53G0679' => 'twi', 'TWI53G0863' => 'twi', 'TWI53G1133' => 'twi', 'TWI60G0823' => 'twi', 'TWI63G0919' => 'twi', 'TWI63G1436' => 'twi', 'TWI73G0140' => 'twi', 'TWI73G0419' => 'twi', 'TWI73G0420' => 'twi', 'TWI73G1276' => 'twi', 'TWI74G0405' => 'twi', 'TWI74G0837' => 'twi', 'TWI75G0594' => 'twi', 'TWI75G1615' => 'twi', 'TWI77G0816' => 'twi', 'vmacro03831' => 'vma', 'vmacro13746' => 'vma', 'vmacro16089' => 'vma', 'vmacro22863' => 'vma', 'Zm00001eb085790' => 'zma', 'Zm00001eb114250' => 'zma', 'Zm00001eb138070' => 'zma', 'Zm00001eb167560' => 'zma', 'Zm00001eb199990' => 'zma', 'Zm00001eb368180' => 'zma', 'Zm00001eb382470' => 'zma' ), 'gf_id' => 'HOM05D001576', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001576' ), 'data_identifier' => 'HOM05D001576', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001576', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '406', 'num_species' => '29' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'Aqoxy1G01456' => 'aox', 'Aqoxy1G02949' => 'aox', 'Aqoxy3G01274' => 'aox', 'Aqoxy3G02110' => 'aox', 'Aqoxy3G02268' => 'aox', 'Aqoxy5G02702' => 'aox', 'Aqoxy5G02988' => 'aox', 'Aqoxy5G03427' => 'aox', 'Aqoxy6G02363' => 'aox', 'Atru.chr1.3225' => 'acertr', 'Atru.chr8.1198' => 'acertr', 'Atru.chr9.790' => 'acertr', 'CANSAT01G3197' => 'cansat', 'Ciclev10003979m.g' => 'ccl', 'Ciclev10017471m.g' => 'ccl', 'Ciclev10018206m.g' => 'ccl', 'Ciclev10033751m.g' => 'ccl', 'CiPaw.01G000900' => 'cil', 'CiPaw.01G001000' => 'cil', 'CiPaw.01G033500' => 'cil', 'CiPaw.01G060300' => 'cil', 'CiPaw.01G070200' => 'cil', 'CiPaw.01G075100' => 'cil', 'CiPaw.01G084700' => 'cil', 'CiPaw.01G087900' => 'cil', 'CiPaw.01G092600' => 'cil', 'CiPaw.01G097200' => 'cil', 'CiPaw.01G098300' => 'cil', 'CiPaw.01G110200' => 'cil', 'CiPaw.01G118700' => 'cil', 'CiPaw.01G121200' => 'cil', 'CiPaw.01G132500' => 'cil', 'CiPaw.01G146900' => 'cil', 'CiPaw.01G174000' => 'cil', 'CiPaw.01G179900' => 'cil', 'CiPaw.01G183400' => 'cil', 'CiPaw.01G240000' => 'cil', 'CiPaw.01G283500' => 'cil', 'CiPaw.01G307400' => 'cil', 'CiPaw.02G030800' => 'cil', 'CiPaw.02G047200' => 'cil', 'CiPaw.02G050500' => 'cil', 'CiPaw.02G069900' => 'cil', 'CiPaw.02G091600' => 'cil', 'CiPaw.02G095000' => 'cil', 'CiPaw.02G131900' => 'cil', 'CiPaw.03G043000' => 'cil', 'CiPaw.03G069900' => 'cil', 'CiPaw.03G088100' => 'cil', 'CiPaw.03G089300' => 'cil', 'CiPaw.03G093100' => 'cil', 'CiPaw.03G129800' => 'cil', 'CiPaw.03G131200' => 'cil', 'CiPaw.03G134500' => 'cil', 'CiPaw.03G152100' => 'cil', 'CiPaw.03G162700' => 'cil', 'CiPaw.03G172800' => 'cil', 'CiPaw.03G175800' => 'cil', 'CiPaw.03G181800' => 'cil', 'CiPaw.03G191400' => 'cil', 'CiPaw.03G198300' => 'cil', 'CiPaw.03G201300' => 'cil', 'CiPaw.03G224700' => 'cil', 'CiPaw.03G225000' => 'cil', 'CiPaw.04G065100' => 'cil', 'CiPaw.04G080400' => 'cil', 'CiPaw.04G113500' => 'cil', 'CiPaw.04G121900' => 'cil', 'CiPaw.04G144100' => 'cil', 'CiPaw.04G176500' => 'cil', 'CiPaw.05G086200' => 'cil', 'CiPaw.05G100200' => 'cil', 'CiPaw.05G114200' => 'cil', 'CiPaw.05G126800' => 'cil', 'CiPaw.05G228800' => 'cil', 'CiPaw.05G230600' => 'cil', 'CiPaw.05G236500' => 'cil', 'CiPaw.05G244800' => 'cil', 'CiPaw.06G026600' => 'cil', 'CiPaw.06G027900' => 'cil', 'CiPaw.06G051800' => 'cil', 'CiPaw.06G128500' => 'cil', 'CiPaw.06G165900' => 'cil', 'CiPaw.07G045400' => 'cil', 'CiPaw.07G048000' => 'cil', 'CiPaw.07G052000' => 'cil', 'CiPaw.07G073800' => 'cil', 'CiPaw.07G099700' => 'cil', 'CiPaw.07G108700' => 'cil', 'CiPaw.07G120000' => 'cil', 'CiPaw.07G134100' => 'cil', 'CiPaw.07G147000' => 'cil', 'CiPaw.07G149700' => 'cil', 'CiPaw.07G178300' => 'cil', 'CiPaw.07G184900' => 'cil', 'CiPaw.08G044500' => 'cil', 'CiPaw.08G046900' => 'cil', 'CiPaw.08G047300' => 'cil', 'CiPaw.08G115400' => 'cil', 'CiPaw.08G134700' => 'cil', 'CiPaw.08G157400' => 'cil', 'CiPaw.09G014300' => 'cil', 'CiPaw.09G088900' => 'cil', 'CiPaw.09G130900' => 'cil', 'CiPaw.09G133100' => 'cil', 'CiPaw.09G151300' => 'cil', 'CiPaw.09G172800' => 'cil', 'CiPaw.09G174900' => 'cil', 'CiPaw.09G175000' => 'cil', 'CiPaw.10G012800' => 'cil', 'CiPaw.10G028800' => 'cil', 'CiPaw.10G044700' => 'cil', 'CiPaw.10G067400' => 'cil', 'CiPaw.10G115900' => 'cil', 'CiPaw.10G126200' => 'cil', 'CiPaw.10G139700' => 'cil', 'CiPaw.10G155100' => 'cil', 'CiPaw.11G011300' => 'cil', 'CiPaw.11G025900' => 'cil', 'CiPaw.11G104100' => 'cil', 'CiPaw.11G142700' => 'cil', 'CiPaw.11G164500' => 'cil', 'CiPaw.11G189100' => 'cil', 'CiPaw.11G197100' => 'cil', 'CiPaw.12G006100' => 'cil', 'CiPaw.12G038500' => 'cil', 'CiPaw.12G041400' => 'cil', 'CiPaw.12G041600' => 'cil', 'CiPaw.12G051300' => 'cil', 'CiPaw.12G101800' => 'cil', 'CiPaw.12G107800' => 'cil', 'CiPaw.13G033200' => 'cil', 'CiPaw.13G129900' => 'cil', 'CiPaw.13G160200' => 'cil', 'CiPaw.14G018900' => 'cil', 'CiPaw.14G029000' => 'cil', 'CiPaw.14G031000' => 'cil', 'CiPaw.14G032000' => 'cil', 'CiPaw.14G032300' => 'cil', 'CiPaw.14G040600' => 'cil', 'CiPaw.14G060500' => 'cil', 'CiPaw.14G061500' => 'cil', 'CiPaw.14G077500' => 'cil', 'CiPaw.14G088300' => 'cil', 'CiPaw.14G108500' => 'cil', 'CiPaw.14G121300' => 'cil', 'CiPaw.14G133000' => 'cil', 'CiPaw.14G134600' => 'cil', 'CiPaw.15G027200' => 'cil', 'CiPaw.15G037700' => 'cil', 'CiPaw.15G050900' => 'cil', 'CiPaw.15G067200' => 'cil', 'CiPaw.15G072000' => 'cil', 'CiPaw.15G112900' => 'cil', 'CiPaw.15G133200' => 'cil', 'CiPaw.15G139500' => 'cil', 'CiPaw.15G155400' => 'cil', 'CiPaw.16G006000' => 'cil', 'CiPaw.16G013100' => 'cil', 'CiPaw.16G047100' => 'cil', 'CiPaw.16G048900' => 'cil', 'CiPaw.16G070300' => 'cil', 'CSS0000195' => 'camsi', 'CSS0001664' => 'camsi', 'CSS0002566' => 'camsi', 'CSS0003077' => 'camsi', 'CSS0004257' => 'camsi', 'CSS0004495' => 'camsi', 'CSS0004599' => 'camsi', 'CSS0004943' => 'camsi', 'CSS0005302' => 'camsi', 'CSS0006274' => 'camsi', 'CSS0006547' => 'camsi', 'CSS0006860' => 'camsi', 'CSS0008814' => 'camsi', 'CSS0008946' => 'camsi', 'CSS0009093' => 'camsi', 'CSS0010221' => 'camsi', 'CSS0010296' => 'camsi', 'CSS0010386' => 'camsi', 'CSS0010831' => 'camsi', 'CSS0011061' => 'camsi', 'CSS0012008' => 'camsi', 'CSS0012194' => 'camsi', 'CSS0013580' => 'camsi', 'CSS0014176' => 'camsi', 'CSS0014280' => 'camsi', 'CSS0014799' => 'camsi', 'CSS0015368' => 'camsi', 'CSS0017473' => 'camsi', 'CSS0019281' => 'camsi', 'CSS0021320' => 'camsi', 'CSS0021750' => 'camsi', 'CSS0023642' => 'camsi', 'CSS0023792' => 'camsi', 'CSS0031528' => 'camsi', 'CSS0033894' => 'camsi', 'CSS0034959' => 'camsi', 'CSS0035632' => 'camsi', 'CSS0038450' => 'camsi', 'CSS0039293' => 'camsi', 'CSS0041053' => 'camsi', 'CSS0041981' => 'camsi', 'CSS0042573' => 'camsi', 'CSS0042927' => 'camsi', 'CSS0047725' => 'camsi', 'CSS0049636' => 'camsi', 'CSS0050513' => 'camsi', 'DCAR_030203' => 'dca', 'Dinv07939' => 'din', 'FAN01G0456' => 'fan', 'FAN02G3001' => 'fan', 'FAN04G2781' => 'fan', 'FAN05G1385' => 'fan', 'FAN05G3062' => 'fan', 'FAN08G2267' => 'fan', 'FAN10G0481' => 'fan', 'FAN10G1257' => 'fan', 'FAN14G0954' => 'fan', 'FAN14G2347' => 'fan', 'FAN15G0187' => 'fan', 'FAN25G2214' => 'fan', 'FvH4_1g21031' => 'fve', 'FvH4_3g16231' => 'fve', 'FvH4_3g26413' => 'fve', 'FvH4_3g29014' => 'fve', 'FvH4_3g31921' => 'fve', 'FvH4_4g19882' => 'fve', 'FvH4_5g21960' => 'fve', 'FvH4_5g29683' => 'fve', 'FvH4_7g13271' => 'fve', 'Glyma.01G062500' => 'gma', 'Glyma.07G140900' => 'gma', 'Glyma.09G140900' => 'gma', 'Glyma.12G112700' => 'gma', 'Glyma.17G168800' => 'gma', 'HanXRQChr01g0027001' => 'han', 'HanXRQChr04g0120511' => 'han', 'HanXRQChr08g0232381' => 'han', 'HanXRQChr09g0265661' => 'han', 'HanXRQChr13g0416031' => 'han', 'Haze_05835' => 'cav', 'Haze_06597' => 'cav', 'Haze_07921' => 'cav', 'Haze_08599' => 'cav', 'Haze_10686' => 'cav', 'Haze_12994' => 'cav', 'Haze_13466' => 'cav', 'Haze_16101' => 'cav', 'Haze_17766' => 'cav', 'Haze_18456' => 'cav', 'Haze_20229' => 'cav', 'Hma1.2p1_0324F.1_g125640' => 'hma', 'Hma1.2p1_0733F.1_g210230' => 'hma', 'Hma1.2p1_0921F.1_g236870' => 'hma', 'Hma1.2p1_1313F.1_g274940' => 'hma', 'Hma1.2p1_3059F.1_g332230' => 'hma', 'Hund15925' => 'sun', 'Hund19562' => 'sun', 'Hund21925' => 'sun', 'MD03G1177400' => 'mdo', 'MD07G1026100' => 'mdo', 'MD17G1218600' => 'mdo', 'Medtr0867s0010' => 'mtr', 'Medtr6g081150' => 'mtr', 'Os01g0527900' => 'osa', 'Os02g0463725' => 'osa', 'Os02g0785600' => 'osa', 'Os03g0433733' => 'osa', 'Os04g0286500' => 'osa', 'Os05g0227800' => 'osa', 'Os06g0521000' => 'osa', 'Os06g0635500' => 'osa', 'Os06g0660650' => 'osa', 'Os07g0554400' => 'osa', 'Os08g0225900' => 'osa', 'Os08g0561000' => 'osa', 'Os09g0241700' => 'osa', 'Os09g0351900' => 'osa', 'Os11g0220700' => 'osa', 'Os11g0282700' => 'osa', 'Os12g0169300' => 'osa', 'Os12g0228500' => 'osa', 'Os12g0543800' => 'osa', 'PGR044G1547' => 'pgr', 'Potri.005G239150' => 'ptr', 'Potri.010G014250' => 'ptr', 'Prupe.1G172500' => 'ppe', 'Prupe.1G196800' => 'ppe', 'Prupe.1G279700' => 'ppe', 'Prupe.2G026400' => 'ppe', 'Prupe.3G094000' => 'ppe', 'Prupe.4G287300' => 'ppe', 'QL01p022166' => 'qlo', 'QL01p051890' => 'qlo', 'QL02p009469' => 'qlo', 'QL02p046053' => 'qlo', 'QL02p057958' => 'qlo', 'QL02p093127' => 'qlo', 'QL03p006855' => 'qlo', 'QL03p071586' => 'qlo', 'QL04p000022' => 'qlo', 'QL04p000024' => 'qlo', 'QL04p003192' => 'qlo', 'QL05p011416' => 'qlo', 'QL06p039590' => 'qlo', 'QL06p052750' => 'qlo', 'QL06p053821' => 'qlo', 'QL07p025287' => 'qlo', 'QL09p033218' => 'qlo', 'QL09p040841' => 'qlo', 'QL10p020337' => 'qlo', 'QL10p027209' => 'qlo', 'QL10p027969' => 'qlo', 'QL10p048988' => 'qlo', 'QL11p001241' => 'qlo', 'QL11p028487' => 'qlo', 'RcHm_v2.0_Chr2g0105031' => 'rch', 'RcHm_v2.0_Chr2g0117811' => 'rch', 'RcHm_v2.0_Chr6g0270241' => 'rch', 'RcHm_v2.0_Chr7g0215961' => 'rch', 'RcHm_v2.0_Chr7g0231991' => 'rch', 'Rhsim01G0041500' => 'rsi', 'Rhsim01G0115000' => 'rsi', 'Rhsim01G0115400' => 'rsi', 'Rhsim01G0133600' => 'rsi', 'Rhsim01G0159900' => 'rsi', 'Rhsim02G0189400' => 'rsi', 'Rhsim03G0135600' => 'rsi', 'Rhsim03G0149900' => 'rsi', 'Rhsim04G0125600' => 'rsi', 'Rhsim05G0091700' => 'rsi', 'Rhsim05G0092900' => 'rsi', 'Rhsim06G0075000' => 'rsi', 'Rhsim07G0066400' => 'rsi', 'Rhsim07G0156400' => 'rsi', 'Rhsim07G0182200' => 'rsi', 'Rhsim07G0182300' => 'rsi', 'Rhsim08G0180400' => 'rsi', 'Rhsim09G0056800' => 'rsi', 'Rhsim10G0153300' => 'rsi', 'Rhsim11G0012700' => 'rsi', 'Rhsim12G0031800' => 'rsi', 'Rhsim12G0055400' => 'rsi', 'Rhsim12G0091400' => 'rsi', 'Rhsim13G0070800' => 'rsi', 'Rhsim13G0193300' => 'rsi', 'RhsimUnG0111600' => 'rsi', 'RhsimUnG0137500' => 'rsi', 'RhsimUnG0172900' => 'rsi', 'SGA_v2.0_scaffold11G05878' => 'sas', 'SGA_v2.0_scaffold167G38458' => 'sas', 'SGA_v2.0_scaffold19G08588' => 'sas', 'SGA_v2.0_scaffold239G43990' => 'sas', 'SGA_v2.0_scaffold260G45865' => 'sas', 'SGA_v2.0_scaffold309G48177' => 'sas', 'SGA_v2.0_scaffold76G25122' => 'sas', 'SGA_v2.0_scaffold85G26708' => 'sas', 'SHI13914' => 'shi', 'SHI30402' => 'shi', 'TWI09G0020' => 'twi', 'TWI09G0456' => 'twi', 'TWI09G1572' => 'twi', 'TWI12G0266' => 'twi', 'TWI12G1451' => 'twi', 'TWI14G0851' => 'twi', 'TWI15G0796' => 'twi', 'TWI18G0820' => 'twi', 'TWI18G1152' => 'twi', 'TWI23G0007' => 'twi', 'TWI23G0314' => 'twi', 'TWI31G0674' => 'twi', 'TWI31G0938' => 'twi', 'TWI34G0641' => 'twi', 'TWI34G1527' => 'twi', 'TWI36G0193' => 'twi', 'TWI36G0405' => 'twi', 'TWI38G0892' => 'twi', 'TWI38G0936' => 'twi', 'TWI38G2218' => 'twi', 'TWI53G0679' => 'twi', 'TWI53G0863' => 'twi', 'TWI53G1133' => 'twi', 'TWI60G0823' => 'twi', 'TWI63G0919' => 'twi', 'TWI63G1436' => 'twi', 'TWI73G0140' => 'twi', 'TWI73G0419' => 'twi', 'TWI73G0420' => 'twi', 'TWI73G1276' => 'twi', 'TWI74G0405' => 'twi', 'TWI74G0837' => 'twi', 'TWI75G0594' => 'twi', 'TWI75G1615' => 'twi', 'TWI77G0816' => 'twi', 'vmacro03831' => 'vma', 'vmacro13746' => 'vma', 'vmacro16089' => 'vma', 'vmacro22863' => 'vma', 'Zm00001eb085790' => 'zma', 'Zm00001eb114250' => 'zma', 'Zm00001eb138070' => 'zma', 'Zm00001eb167560' => 'zma', 'Zm00001eb199990' => 'zma', 'Zm00001eb368180' => 'zma', 'Zm00001eb382470' => 'zma' ) $gf_id = 'HOM05D001576' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001576' ) $data_identifier = 'HOM05D001576' $data_type = 'gf_id' $species_gene_counts = array( 'aox' => (int) 9, 'acertr' => (int) 3, 'cansat' => (int) 1, 'ccl' => (int) 4, 'cil' => (int) 145, 'camsi' => (int) 46, 'dca' => (int) 1, 'din' => (int) 1, 'fan' => (int) 12, 'fve' => (int) 9, 'gma' => (int) 5, 'han' => (int) 5, 'cav' => (int) 11, 'hma' => (int) 5, 'sun' => (int) 3, 'mdo' => (int) 3, 'mtr' => (int) 2, 'osa' => (int) 19, 'pgr' => (int) 1, 'ptr' => (int) 2, 'ppe' => (int) 6, 'qlo' => (int) 24, 'rch' => (int) 5, 'rsi' => (int) 28, 'sas' => (int) 8, 'shi' => (int) 2, 'twi' => (int) 35, 'vma' => (int) 4, 'zma' => (int) 7 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb382470' $species_info = array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ) $local_species = 'acertr' $disabled = '' $selected = ''
include - APP/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp, line 33 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933 View::_renderElement() - CORE/Cake/View/View.php, line 1224 View::element() - CORE/Cake/View/View.php, line 418 include - APP/View/Elements/analysis/phylogenetics_module/gf_data_settings.ctp, line 37 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933 View::_renderElement() - CORE/Cake/View/View.php, line 1224 View::element() - CORE/Cake/View/View.php, line 418 include - APP/View/Elements/analysis/phylogenetics_module/parameter_selection.ctp, line 64 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933 View::_renderElement() - CORE/Cake/View/View.php, line 1224 View::element() - CORE/Cake/View/View.php, line 418 include - APP/View/Analysis/custom_tree_creation.ctp, line 27 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933
Warning (2): count(): Parameter must be an array or an object that implements Countable [APP/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp, line 33]Code Context $disabled = (!array_key_exists($local_species,$species_gene_counts))?"disabled":""; $selected = (isset($selected_species) && array_key_exists($local_species,$selected_species))?"checked='checked'":""; $num_hits = (array_key_exists($local_species,$species_gene_counts))?count($species_gene_counts[$local_species]):0; $viewFile = '/www/bioinformatics01_ro/plaza/_dev_instances/feedback/app/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp' $dataForView = array( 'sidebar_info' => array( 'gf_id' => 'HOM05D001576', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '406', 'num_species' => '29' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'Aqoxy1G01456' => 'aox', 'Aqoxy1G02949' => 'aox', 'Aqoxy3G01274' => 'aox', 'Aqoxy3G02110' => 'aox', 'Aqoxy3G02268' => 'aox', 'Aqoxy5G02702' => 'aox', 'Aqoxy5G02988' => 'aox', 'Aqoxy5G03427' => 'aox', 'Aqoxy6G02363' => 'aox', 'Atru.chr1.3225' => 'acertr', 'Atru.chr8.1198' => 'acertr', 'Atru.chr9.790' => 'acertr', 'CANSAT01G3197' => 'cansat', 'Ciclev10003979m.g' => 'ccl', 'Ciclev10017471m.g' => 'ccl', 'Ciclev10018206m.g' => 'ccl', 'Ciclev10033751m.g' => 'ccl', 'CiPaw.01G000900' => 'cil', 'CiPaw.01G001000' => 'cil', 'CiPaw.01G033500' => 'cil', 'CiPaw.01G060300' => 'cil', 'CiPaw.01G070200' => 'cil', 'CiPaw.01G075100' => 'cil', 'CiPaw.01G084700' => 'cil', 'CiPaw.01G087900' => 'cil', 'CiPaw.01G092600' => 'cil', 'CiPaw.01G097200' => 'cil', 'CiPaw.01G098300' => 'cil', 'CiPaw.01G110200' => 'cil', 'CiPaw.01G118700' => 'cil', 'CiPaw.01G121200' => 'cil', 'CiPaw.01G132500' => 'cil', 'CiPaw.01G146900' => 'cil', 'CiPaw.01G174000' => 'cil', 'CiPaw.01G179900' => 'cil', 'CiPaw.01G183400' => 'cil', 'CiPaw.01G240000' => 'cil', 'CiPaw.01G283500' => 'cil', 'CiPaw.01G307400' => 'cil', 'CiPaw.02G030800' => 'cil', 'CiPaw.02G047200' => 'cil', 'CiPaw.02G050500' => 'cil', 'CiPaw.02G069900' => 'cil', 'CiPaw.02G091600' => 'cil', 'CiPaw.02G095000' => 'cil', 'CiPaw.02G131900' => 'cil', 'CiPaw.03G043000' => 'cil', 'CiPaw.03G069900' => 'cil', 'CiPaw.03G088100' => 'cil', 'CiPaw.03G089300' => 'cil', 'CiPaw.03G093100' => 'cil', 'CiPaw.03G129800' => 'cil', 'CiPaw.03G131200' => 'cil', 'CiPaw.03G134500' => 'cil', 'CiPaw.03G152100' => 'cil', 'CiPaw.03G162700' => 'cil', 'CiPaw.03G172800' => 'cil', 'CiPaw.03G175800' => 'cil', 'CiPaw.03G181800' => 'cil', 'CiPaw.03G191400' => 'cil', 'CiPaw.03G198300' => 'cil', 'CiPaw.03G201300' => 'cil', 'CiPaw.03G224700' => 'cil', 'CiPaw.03G225000' => 'cil', 'CiPaw.04G065100' => 'cil', 'CiPaw.04G080400' => 'cil', 'CiPaw.04G113500' => 'cil', 'CiPaw.04G121900' => 'cil', 'CiPaw.04G144100' => 'cil', 'CiPaw.04G176500' => 'cil', 'CiPaw.05G086200' => 'cil', 'CiPaw.05G100200' => 'cil', 'CiPaw.05G114200' => 'cil', 'CiPaw.05G126800' => 'cil', 'CiPaw.05G228800' => 'cil', 'CiPaw.05G230600' => 'cil', 'CiPaw.05G236500' => 'cil', 'CiPaw.05G244800' => 'cil', 'CiPaw.06G026600' => 'cil', 'CiPaw.06G027900' => 'cil', 'CiPaw.06G051800' => 'cil', 'CiPaw.06G128500' => 'cil', 'CiPaw.06G165900' => 'cil', 'CiPaw.07G045400' => 'cil', 'CiPaw.07G048000' => 'cil', 'CiPaw.07G052000' => 'cil', 'CiPaw.07G073800' => 'cil', 'CiPaw.07G099700' => 'cil', 'CiPaw.07G108700' => 'cil', 'CiPaw.07G120000' => 'cil', 'CiPaw.07G134100' => 'cil', 'CiPaw.07G147000' => 'cil', 'CiPaw.07G149700' => 'cil', 'CiPaw.07G178300' => 'cil', 'CiPaw.07G184900' => 'cil', 'CiPaw.08G044500' => 'cil', 'CiPaw.08G046900' => 'cil', 'CiPaw.08G047300' => 'cil', 'CiPaw.08G115400' => 'cil', 'CiPaw.08G134700' => 'cil', 'CiPaw.08G157400' => 'cil', 'CiPaw.09G014300' => 'cil', 'CiPaw.09G088900' => 'cil', 'CiPaw.09G130900' => 'cil', 'CiPaw.09G133100' => 'cil', 'CiPaw.09G151300' => 'cil', 'CiPaw.09G172800' => 'cil', 'CiPaw.09G174900' => 'cil', 'CiPaw.09G175000' => 'cil', 'CiPaw.10G012800' => 'cil', 'CiPaw.10G028800' => 'cil', 'CiPaw.10G044700' => 'cil', 'CiPaw.10G067400' => 'cil', 'CiPaw.10G115900' => 'cil', 'CiPaw.10G126200' => 'cil', 'CiPaw.10G139700' => 'cil', 'CiPaw.10G155100' => 'cil', 'CiPaw.11G011300' => 'cil', 'CiPaw.11G025900' => 'cil', 'CiPaw.11G104100' => 'cil', 'CiPaw.11G142700' => 'cil', 'CiPaw.11G164500' => 'cil', 'CiPaw.11G189100' => 'cil', 'CiPaw.11G197100' => 'cil', 'CiPaw.12G006100' => 'cil', 'CiPaw.12G038500' => 'cil', 'CiPaw.12G041400' => 'cil', 'CiPaw.12G041600' => 'cil', 'CiPaw.12G051300' => 'cil', 'CiPaw.12G101800' => 'cil', 'CiPaw.12G107800' => 'cil', 'CiPaw.13G033200' => 'cil', 'CiPaw.13G129900' => 'cil', 'CiPaw.13G160200' => 'cil', 'CiPaw.14G018900' => 'cil', 'CiPaw.14G029000' => 'cil', 'CiPaw.14G031000' => 'cil', 'CiPaw.14G032000' => 'cil', 'CiPaw.14G032300' => 'cil', 'CiPaw.14G040600' => 'cil', 'CiPaw.14G060500' => 'cil', 'CiPaw.14G061500' => 'cil', 'CiPaw.14G077500' => 'cil', 'CiPaw.14G088300' => 'cil', 'CiPaw.14G108500' => 'cil', 'CiPaw.14G121300' => 'cil', 'CiPaw.14G133000' => 'cil', 'CiPaw.14G134600' => 'cil', 'CiPaw.15G027200' => 'cil', 'CiPaw.15G037700' => 'cil', 'CiPaw.15G050900' => 'cil', 'CiPaw.15G067200' => 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=> 'camsi', 'CSS0021320' => 'camsi', 'CSS0021750' => 'camsi', 'CSS0023642' => 'camsi', 'CSS0023792' => 'camsi', 'CSS0031528' => 'camsi', 'CSS0033894' => 'camsi', 'CSS0034959' => 'camsi', 'CSS0035632' => 'camsi', 'CSS0038450' => 'camsi', 'CSS0039293' => 'camsi', 'CSS0041053' => 'camsi', 'CSS0041981' => 'camsi', 'CSS0042573' => 'camsi', 'CSS0042927' => 'camsi', 'CSS0047725' => 'camsi', 'CSS0049636' => 'camsi', 'CSS0050513' => 'camsi', 'DCAR_030203' => 'dca', 'Dinv07939' => 'din', 'FAN01G0456' => 'fan', 'FAN02G3001' => 'fan', 'FAN04G2781' => 'fan', 'FAN05G1385' => 'fan', 'FAN05G3062' => 'fan', 'FAN08G2267' => 'fan', 'FAN10G0481' => 'fan', 'FAN10G1257' => 'fan', 'FAN14G0954' => 'fan', 'FAN14G2347' => 'fan', 'FAN15G0187' => 'fan', 'FAN25G2214' => 'fan', 'FvH4_1g21031' => 'fve', 'FvH4_3g16231' => 'fve', 'FvH4_3g26413' => 'fve', 'FvH4_3g29014' => 'fve', 'FvH4_3g31921' => 'fve', 'FvH4_4g19882' => 'fve', 'FvH4_5g21960' => 'fve', 'FvH4_5g29683' => 'fve', 'FvH4_7g13271' => 'fve', 'Glyma.01G062500' => 'gma', 'Glyma.07G140900' => 'gma', 'Glyma.09G140900' => 'gma', 'Glyma.12G112700' => 'gma', 'Glyma.17G168800' => 'gma', 'HanXRQChr01g0027001' => 'han', 'HanXRQChr04g0120511' => 'han', 'HanXRQChr08g0232381' => 'han', 'HanXRQChr09g0265661' => 'han', 'HanXRQChr13g0416031' => 'han', 'Haze_05835' => 'cav', 'Haze_06597' => 'cav', 'Haze_07921' => 'cav', 'Haze_08599' => 'cav', 'Haze_10686' => 'cav', 'Haze_12994' => 'cav', 'Haze_13466' => 'cav', 'Haze_16101' => 'cav', 'Haze_17766' => 'cav', 'Haze_18456' => 'cav', 'Haze_20229' => 'cav', 'Hma1.2p1_0324F.1_g125640' => 'hma', 'Hma1.2p1_0733F.1_g210230' => 'hma', 'Hma1.2p1_0921F.1_g236870' => 'hma', 'Hma1.2p1_1313F.1_g274940' => 'hma', 'Hma1.2p1_3059F.1_g332230' => 'hma', 'Hund15925' => 'sun', 'Hund19562' => 'sun', 'Hund21925' => 'sun', 'MD03G1177400' => 'mdo', 'MD07G1026100' => 'mdo', 'MD17G1218600' => 'mdo', 'Medtr0867s0010' => 'mtr', 'Medtr6g081150' => 'mtr', 'Os01g0527900' => 'osa', 'Os02g0463725' => 'osa', 'Os02g0785600' => 'osa', 'Os03g0433733' => 'osa', 'Os04g0286500' => 'osa', 'Os05g0227800' => 'osa', 'Os06g0521000' => 'osa', 'Os06g0635500' => 'osa', 'Os06g0660650' => 'osa', 'Os07g0554400' => 'osa', 'Os08g0225900' => 'osa', 'Os08g0561000' => 'osa', 'Os09g0241700' => 'osa', 'Os09g0351900' => 'osa', 'Os11g0220700' => 'osa', 'Os11g0282700' => 'osa', 'Os12g0169300' => 'osa', 'Os12g0228500' => 'osa', 'Os12g0543800' => 'osa', 'PGR044G1547' => 'pgr', 'Potri.005G239150' => 'ptr', 'Potri.010G014250' => 'ptr', 'Prupe.1G172500' => 'ppe', 'Prupe.1G196800' => 'ppe', 'Prupe.1G279700' => 'ppe', 'Prupe.2G026400' => 'ppe', 'Prupe.3G094000' => 'ppe', 'Prupe.4G287300' => 'ppe', 'QL01p022166' => 'qlo', 'QL01p051890' => 'qlo', 'QL02p009469' => 'qlo', 'QL02p046053' => 'qlo', 'QL02p057958' => 'qlo', 'QL02p093127' => 'qlo', 'QL03p006855' => 'qlo', 'QL03p071586' => 'qlo', 'QL04p000022' => 'qlo', 'QL04p000024' => 'qlo', 'QL04p003192' => 'qlo', 'QL05p011416' => 'qlo', 'QL06p039590' => 'qlo', 'QL06p052750' => 'qlo', 'QL06p053821' => 'qlo', 'QL07p025287' => 'qlo', 'QL09p033218' => 'qlo', 'QL09p040841' => 'qlo', 'QL10p020337' => 'qlo', 'QL10p027209' => 'qlo', 'QL10p027969' => 'qlo', 'QL10p048988' => 'qlo', 'QL11p001241' => 'qlo', 'QL11p028487' => 'qlo', 'RcHm_v2.0_Chr2g0105031' => 'rch', 'RcHm_v2.0_Chr2g0117811' => 'rch', 'RcHm_v2.0_Chr6g0270241' => 'rch', 'RcHm_v2.0_Chr7g0215961' => 'rch', 'RcHm_v2.0_Chr7g0231991' => 'rch', 'Rhsim01G0041500' => 'rsi', 'Rhsim01G0115000' => 'rsi', 'Rhsim01G0115400' => 'rsi', 'Rhsim01G0133600' => 'rsi', 'Rhsim01G0159900' => 'rsi', 'Rhsim02G0189400' => 'rsi', 'Rhsim03G0135600' => 'rsi', 'Rhsim03G0149900' => 'rsi', 'Rhsim04G0125600' => 'rsi', 'Rhsim05G0091700' => 'rsi', 'Rhsim05G0092900' => 'rsi', 'Rhsim06G0075000' => 'rsi', 'Rhsim07G0066400' => 'rsi', 'Rhsim07G0156400' => 'rsi', 'Rhsim07G0182200' => 'rsi', 'Rhsim07G0182300' => 'rsi', 'Rhsim08G0180400' => 'rsi', 'Rhsim09G0056800' => 'rsi', 'Rhsim10G0153300' => 'rsi', 'Rhsim11G0012700' => 'rsi', 'Rhsim12G0031800' => 'rsi', 'Rhsim12G0055400' => 'rsi', 'Rhsim12G0091400' => 'rsi', 'Rhsim13G0070800' => 'rsi', 'Rhsim13G0193300' => 'rsi', 'RhsimUnG0111600' => 'rsi', 'RhsimUnG0137500' => 'rsi', 'RhsimUnG0172900' => 'rsi', 'SGA_v2.0_scaffold11G05878' => 'sas', 'SGA_v2.0_scaffold167G38458' => 'sas', 'SGA_v2.0_scaffold19G08588' => 'sas', 'SGA_v2.0_scaffold239G43990' => 'sas', 'SGA_v2.0_scaffold260G45865' => 'sas', 'SGA_v2.0_scaffold309G48177' => 'sas', 'SGA_v2.0_scaffold76G25122' => 'sas', 'SGA_v2.0_scaffold85G26708' => 'sas', 'SHI13914' => 'shi', 'SHI30402' => 'shi', 'TWI09G0020' => 'twi', 'TWI09G0456' => 'twi', 'TWI09G1572' => 'twi', 'TWI12G0266' => 'twi', 'TWI12G1451' => 'twi', 'TWI14G0851' => 'twi', 'TWI15G0796' => 'twi', 'TWI18G0820' => 'twi', 'TWI18G1152' => 'twi', 'TWI23G0007' => 'twi', 'TWI23G0314' => 'twi', 'TWI31G0674' => 'twi', 'TWI31G0938' => 'twi', 'TWI34G0641' => 'twi', 'TWI34G1527' => 'twi', 'TWI36G0193' => 'twi', 'TWI36G0405' => 'twi', 'TWI38G0892' => 'twi', 'TWI38G0936' => 'twi', 'TWI38G2218' => 'twi', 'TWI53G0679' => 'twi', 'TWI53G0863' => 'twi', 'TWI53G1133' => 'twi', 'TWI60G0823' => 'twi', 'TWI63G0919' => 'twi', 'TWI63G1436' => 'twi', 'TWI73G0140' => 'twi', 'TWI73G0419' => 'twi', 'TWI73G0420' => 'twi', 'TWI73G1276' => 'twi', 'TWI74G0405' => 'twi', 'TWI74G0837' => 'twi', 'TWI75G0594' => 'twi', 'TWI75G1615' => 'twi', 'TWI77G0816' => 'twi', 'vmacro03831' => 'vma', 'vmacro13746' => 'vma', 'vmacro16089' => 'vma', 'vmacro22863' => 'vma', 'Zm00001eb085790' => 'zma', 'Zm00001eb114250' => 'zma', 'Zm00001eb138070' => 'zma', 'Zm00001eb167560' => 'zma', 'Zm00001eb199990' => 'zma', 'Zm00001eb368180' => 'zma', 'Zm00001eb382470' => 'zma' ), 'gf_id' => 'HOM05D001576', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001576' ), 'data_identifier' => 'HOM05D001576', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001576', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '406', 'num_species' => '29' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'Aqoxy1G01456' => 'aox', 'Aqoxy1G02949' => 'aox', 'Aqoxy3G01274' => 'aox', 'Aqoxy3G02110' => 'aox', 'Aqoxy3G02268' => 'aox', 'Aqoxy5G02702' => 'aox', 'Aqoxy5G02988' => 'aox', 'Aqoxy5G03427' => 'aox', 'Aqoxy6G02363' => 'aox', 'Atru.chr1.3225' => 'acertr', 'Atru.chr8.1198' => 'acertr', 'Atru.chr9.790' => 'acertr', 'CANSAT01G3197' => 'cansat', 'Ciclev10003979m.g' => 'ccl', 'Ciclev10017471m.g' => 'ccl', 'Ciclev10018206m.g' => 'ccl', 'Ciclev10033751m.g' => 'ccl', 'CiPaw.01G000900' => 'cil', 'CiPaw.01G001000' => 'cil', 'CiPaw.01G033500' => 'cil', 'CiPaw.01G060300' => 'cil', 'CiPaw.01G070200' => 'cil', 'CiPaw.01G075100' => 'cil', 'CiPaw.01G084700' => 'cil', 'CiPaw.01G087900' => 'cil', 'CiPaw.01G092600' => 'cil', 'CiPaw.01G097200' => 'cil', 'CiPaw.01G098300' => 'cil', 'CiPaw.01G110200' => 'cil', 'CiPaw.01G118700' => 'cil', 'CiPaw.01G121200' => 'cil', 'CiPaw.01G132500' => 'cil', 'CiPaw.01G146900' => 'cil', 'CiPaw.01G174000' => 'cil', 'CiPaw.01G179900' => 'cil', 'CiPaw.01G183400' => 'cil', 'CiPaw.01G240000' => 'cil', 'CiPaw.01G283500' => 'cil', 'CiPaw.01G307400' => 'cil', 'CiPaw.02G030800' => 'cil', 'CiPaw.02G047200' => 'cil', 'CiPaw.02G050500' => 'cil', 'CiPaw.02G069900' => 'cil', 'CiPaw.02G091600' => 'cil', 'CiPaw.02G095000' => 'cil', 'CiPaw.02G131900' => 'cil', 'CiPaw.03G043000' => 'cil', 'CiPaw.03G069900' => 'cil', 'CiPaw.03G088100' => 'cil', 'CiPaw.03G089300' => 'cil', 'CiPaw.03G093100' => 'cil', 'CiPaw.03G129800' => 'cil', 'CiPaw.03G131200' => 'cil', 'CiPaw.03G134500' => 'cil', 'CiPaw.03G152100' => 'cil', 'CiPaw.03G162700' => 'cil', 'CiPaw.03G172800' => 'cil', 'CiPaw.03G175800' => 'cil', 'CiPaw.03G181800' => 'cil', 'CiPaw.03G191400' => 'cil', 'CiPaw.03G198300' => 'cil', 'CiPaw.03G201300' => 'cil', 'CiPaw.03G224700' => 'cil', 'CiPaw.03G225000' => 'cil', 'CiPaw.04G065100' => 'cil', 'CiPaw.04G080400' => 'cil', 'CiPaw.04G113500' => 'cil', 'CiPaw.04G121900' => 'cil', 'CiPaw.04G144100' => 'cil', 'CiPaw.04G176500' => 'cil', 'CiPaw.05G086200' => 'cil', 'CiPaw.05G100200' => 'cil', 'CiPaw.05G114200' => 'cil', 'CiPaw.05G126800' => 'cil', 'CiPaw.05G228800' => 'cil', 'CiPaw.05G230600' => 'cil', 'CiPaw.05G236500' => 'cil', 'CiPaw.05G244800' => 'cil', 'CiPaw.06G026600' => 'cil', 'CiPaw.06G027900' => 'cil', 'CiPaw.06G051800' => 'cil', 'CiPaw.06G128500' => 'cil', 'CiPaw.06G165900' => 'cil', 'CiPaw.07G045400' => 'cil', 'CiPaw.07G048000' => 'cil', 'CiPaw.07G052000' => 'cil', 'CiPaw.07G073800' => 'cil', 'CiPaw.07G099700' => 'cil', 'CiPaw.07G108700' => 'cil', 'CiPaw.07G120000' => 'cil', 'CiPaw.07G134100' => 'cil', 'CiPaw.07G147000' => 'cil', 'CiPaw.07G149700' => 'cil', 'CiPaw.07G178300' => 'cil', 'CiPaw.07G184900' => 'cil', 'CiPaw.08G044500' => 'cil', 'CiPaw.08G046900' => 'cil', 'CiPaw.08G047300' => 'cil', 'CiPaw.08G115400' => 'cil', 'CiPaw.08G134700' => 'cil', 'CiPaw.08G157400' => 'cil', 'CiPaw.09G014300' => 'cil', 'CiPaw.09G088900' => 'cil', 'CiPaw.09G130900' => 'cil', 'CiPaw.09G133100' => 'cil', 'CiPaw.09G151300' => 'cil', 'CiPaw.09G172800' => 'cil', 'CiPaw.09G174900' => 'cil', 'CiPaw.09G175000' => 'cil', 'CiPaw.10G012800' => 'cil', 'CiPaw.10G028800' => 'cil', 'CiPaw.10G044700' => 'cil', 'CiPaw.10G067400' => 'cil', 'CiPaw.10G115900' => 'cil', 'CiPaw.10G126200' => 'cil', 'CiPaw.10G139700' => 'cil', 'CiPaw.10G155100' => 'cil', 'CiPaw.11G011300' => 'cil', 'CiPaw.11G025900' => 'cil', 'CiPaw.11G104100' => 'cil', 'CiPaw.11G142700' => 'cil', 'CiPaw.11G164500' => 'cil', 'CiPaw.11G189100' => 'cil', 'CiPaw.11G197100' => 'cil', 'CiPaw.12G006100' => 'cil', 'CiPaw.12G038500' => 'cil', 'CiPaw.12G041400' => 'cil', 'CiPaw.12G041600' => 'cil', 'CiPaw.12G051300' => 'cil', 'CiPaw.12G101800' => 'cil', 'CiPaw.12G107800' => 'cil', 'CiPaw.13G033200' => 'cil', 'CiPaw.13G129900' => 'cil', 'CiPaw.13G160200' => 'cil', 'CiPaw.14G018900' => 'cil', 'CiPaw.14G029000' => 'cil', 'CiPaw.14G031000' => 'cil', 'CiPaw.14G032000' => 'cil', 'CiPaw.14G032300' => 'cil', 'CiPaw.14G040600' => 'cil', 'CiPaw.14G060500' => 'cil', 'CiPaw.14G061500' => 'cil', 'CiPaw.14G077500' => 'cil', 'CiPaw.14G088300' => 'cil', 'CiPaw.14G108500' => 'cil', 'CiPaw.14G121300' => 'cil', 'CiPaw.14G133000' => 'cil', 'CiPaw.14G134600' => 'cil', 'CiPaw.15G027200' => 'cil', 'CiPaw.15G037700' => 'cil', 'CiPaw.15G050900' => 'cil', 'CiPaw.15G067200' => 'cil', 'CiPaw.15G072000' => 'cil', 'CiPaw.15G112900' => 'cil', 'CiPaw.15G133200' => 'cil', 'CiPaw.15G139500' => 'cil', 'CiPaw.15G155400' => 'cil', 'CiPaw.16G006000' => 'cil', 'CiPaw.16G013100' => 'cil', 'CiPaw.16G047100' => 'cil', 'CiPaw.16G048900' => 'cil', 'CiPaw.16G070300' => 'cil', 'CSS0000195' => 'camsi', 'CSS0001664' => 'camsi', 'CSS0002566' => 'camsi', 'CSS0003077' => 'camsi', 'CSS0004257' => 'camsi', 'CSS0004495' => 'camsi', 'CSS0004599' => 'camsi', 'CSS0004943' => 'camsi', 'CSS0005302' => 'camsi', 'CSS0006274' => 'camsi', 'CSS0006547' => 'camsi', 'CSS0006860' => 'camsi', 'CSS0008814' => 'camsi', 'CSS0008946' => 'camsi', 'CSS0009093' => 'camsi', 'CSS0010221' => 'camsi', 'CSS0010296' => 'camsi', 'CSS0010386' => 'camsi', 'CSS0010831' => 'camsi', 'CSS0011061' => 'camsi', 'CSS0012008' => 'camsi', 'CSS0012194' => 'camsi', 'CSS0013580' => 'camsi', 'CSS0014176' => 'camsi', 'CSS0014280' => 'camsi', 'CSS0014799' => 'camsi', 'CSS0015368' => 'camsi', 'CSS0017473' => 'camsi', 'CSS0019281' => 'camsi', 'CSS0021320' => 'camsi', 'CSS0021750' => 'camsi', 'CSS0023642' => 'camsi', 'CSS0023792' => 'camsi', 'CSS0031528' => 'camsi', 'CSS0033894' => 'camsi', 'CSS0034959' => 'camsi', 'CSS0035632' => 'camsi', 'CSS0038450' => 'camsi', 'CSS0039293' => 'camsi', 'CSS0041053' => 'camsi', 'CSS0041981' => 'camsi', 'CSS0042573' => 'camsi', 'CSS0042927' => 'camsi', 'CSS0047725' => 'camsi', 'CSS0049636' => 'camsi', 'CSS0050513' => 'camsi', 'DCAR_030203' => 'dca', 'Dinv07939' => 'din', 'FAN01G0456' => 'fan', 'FAN02G3001' => 'fan', 'FAN04G2781' => 'fan', 'FAN05G1385' => 'fan', 'FAN05G3062' => 'fan', 'FAN08G2267' => 'fan', 'FAN10G0481' => 'fan', 'FAN10G1257' => 'fan', 'FAN14G0954' => 'fan', 'FAN14G2347' => 'fan', 'FAN15G0187' => 'fan', 'FAN25G2214' => 'fan', 'FvH4_1g21031' => 'fve', 'FvH4_3g16231' => 'fve', 'FvH4_3g26413' => 'fve', 'FvH4_3g29014' => 'fve', 'FvH4_3g31921' => 'fve', 'FvH4_4g19882' => 'fve', 'FvH4_5g21960' => 'fve', 'FvH4_5g29683' => 'fve', 'FvH4_7g13271' => 'fve', 'Glyma.01G062500' => 'gma', 'Glyma.07G140900' => 'gma', 'Glyma.09G140900' => 'gma', 'Glyma.12G112700' => 'gma', 'Glyma.17G168800' => 'gma', 'HanXRQChr01g0027001' => 'han', 'HanXRQChr04g0120511' => 'han', 'HanXRQChr08g0232381' => 'han', 'HanXRQChr09g0265661' => 'han', 'HanXRQChr13g0416031' => 'han', 'Haze_05835' => 'cav', 'Haze_06597' => 'cav', 'Haze_07921' => 'cav', 'Haze_08599' => 'cav', 'Haze_10686' => 'cav', 'Haze_12994' => 'cav', 'Haze_13466' => 'cav', 'Haze_16101' => 'cav', 'Haze_17766' => 'cav', 'Haze_18456' => 'cav', 'Haze_20229' => 'cav', 'Hma1.2p1_0324F.1_g125640' => 'hma', 'Hma1.2p1_0733F.1_g210230' => 'hma', 'Hma1.2p1_0921F.1_g236870' => 'hma', 'Hma1.2p1_1313F.1_g274940' => 'hma', 'Hma1.2p1_3059F.1_g332230' => 'hma', 'Hund15925' => 'sun', 'Hund19562' => 'sun', 'Hund21925' => 'sun', 'MD03G1177400' => 'mdo', 'MD07G1026100' => 'mdo', 'MD17G1218600' => 'mdo', 'Medtr0867s0010' => 'mtr', 'Medtr6g081150' => 'mtr', 'Os01g0527900' => 'osa', 'Os02g0463725' => 'osa', 'Os02g0785600' => 'osa', 'Os03g0433733' => 'osa', 'Os04g0286500' => 'osa', 'Os05g0227800' => 'osa', 'Os06g0521000' => 'osa', 'Os06g0635500' => 'osa', 'Os06g0660650' => 'osa', 'Os07g0554400' => 'osa', 'Os08g0225900' => 'osa', 'Os08g0561000' => 'osa', 'Os09g0241700' => 'osa', 'Os09g0351900' => 'osa', 'Os11g0220700' => 'osa', 'Os11g0282700' => 'osa', 'Os12g0169300' => 'osa', 'Os12g0228500' => 'osa', 'Os12g0543800' => 'osa', 'PGR044G1547' => 'pgr', 'Potri.005G239150' => 'ptr', 'Potri.010G014250' => 'ptr', 'Prupe.1G172500' => 'ppe', 'Prupe.1G196800' => 'ppe', 'Prupe.1G279700' => 'ppe', 'Prupe.2G026400' => 'ppe', 'Prupe.3G094000' => 'ppe', 'Prupe.4G287300' => 'ppe', 'QL01p022166' => 'qlo', 'QL01p051890' => 'qlo', 'QL02p009469' => 'qlo', 'QL02p046053' => 'qlo', 'QL02p057958' => 'qlo', 'QL02p093127' => 'qlo', 'QL03p006855' => 'qlo', 'QL03p071586' => 'qlo', 'QL04p000022' => 'qlo', 'QL04p000024' => 'qlo', 'QL04p003192' => 'qlo', 'QL05p011416' => 'qlo', 'QL06p039590' => 'qlo', 'QL06p052750' => 'qlo', 'QL06p053821' => 'qlo', 'QL07p025287' => 'qlo', 'QL09p033218' => 'qlo', 'QL09p040841' => 'qlo', 'QL10p020337' => 'qlo', 'QL10p027209' => 'qlo', 'QL10p027969' => 'qlo', 'QL10p048988' => 'qlo', 'QL11p001241' => 'qlo', 'QL11p028487' => 'qlo', 'RcHm_v2.0_Chr2g0105031' => 'rch', 'RcHm_v2.0_Chr2g0117811' => 'rch', 'RcHm_v2.0_Chr6g0270241' => 'rch', 'RcHm_v2.0_Chr7g0215961' => 'rch', 'RcHm_v2.0_Chr7g0231991' => 'rch', 'Rhsim01G0041500' => 'rsi', 'Rhsim01G0115000' => 'rsi', 'Rhsim01G0115400' => 'rsi', 'Rhsim01G0133600' => 'rsi', 'Rhsim01G0159900' => 'rsi', 'Rhsim02G0189400' => 'rsi', 'Rhsim03G0135600' => 'rsi', 'Rhsim03G0149900' => 'rsi', 'Rhsim04G0125600' => 'rsi', 'Rhsim05G0091700' => 'rsi', 'Rhsim05G0092900' => 'rsi', 'Rhsim06G0075000' => 'rsi', 'Rhsim07G0066400' => 'rsi', 'Rhsim07G0156400' => 'rsi', 'Rhsim07G0182200' => 'rsi', 'Rhsim07G0182300' => 'rsi', 'Rhsim08G0180400' => 'rsi', 'Rhsim09G0056800' => 'rsi', 'Rhsim10G0153300' => 'rsi', 'Rhsim11G0012700' => 'rsi', 'Rhsim12G0031800' => 'rsi', 'Rhsim12G0055400' => 'rsi', 'Rhsim12G0091400' => 'rsi', 'Rhsim13G0070800' => 'rsi', 'Rhsim13G0193300' => 'rsi', 'RhsimUnG0111600' => 'rsi', 'RhsimUnG0137500' => 'rsi', 'RhsimUnG0172900' => 'rsi', 'SGA_v2.0_scaffold11G05878' => 'sas', 'SGA_v2.0_scaffold167G38458' => 'sas', 'SGA_v2.0_scaffold19G08588' => 'sas', 'SGA_v2.0_scaffold239G43990' => 'sas', 'SGA_v2.0_scaffold260G45865' => 'sas', 'SGA_v2.0_scaffold309G48177' => 'sas', 'SGA_v2.0_scaffold76G25122' => 'sas', 'SGA_v2.0_scaffold85G26708' => 'sas', 'SHI13914' => 'shi', 'SHI30402' => 'shi', 'TWI09G0020' => 'twi', 'TWI09G0456' => 'twi', 'TWI09G1572' => 'twi', 'TWI12G0266' => 'twi', 'TWI12G1451' => 'twi', 'TWI14G0851' => 'twi', 'TWI15G0796' => 'twi', 'TWI18G0820' => 'twi', 'TWI18G1152' => 'twi', 'TWI23G0007' => 'twi', 'TWI23G0314' => 'twi', 'TWI31G0674' => 'twi', 'TWI31G0938' => 'twi', 'TWI34G0641' => 'twi', 'TWI34G1527' => 'twi', 'TWI36G0193' => 'twi', 'TWI36G0405' => 'twi', 'TWI38G0892' => 'twi', 'TWI38G0936' => 'twi', 'TWI38G2218' => 'twi', 'TWI53G0679' => 'twi', 'TWI53G0863' => 'twi', 'TWI53G1133' => 'twi', 'TWI60G0823' => 'twi', 'TWI63G0919' => 'twi', 'TWI63G1436' => 'twi', 'TWI73G0140' => 'twi', 'TWI73G0419' => 'twi', 'TWI73G0420' => 'twi', 'TWI73G1276' => 'twi', 'TWI74G0405' => 'twi', 'TWI74G0837' => 'twi', 'TWI75G0594' => 'twi', 'TWI75G1615' => 'twi', 'TWI77G0816' => 'twi', 'vmacro03831' => 'vma', 'vmacro13746' => 'vma', 'vmacro16089' => 'vma', 'vmacro22863' => 'vma', 'Zm00001eb085790' => 'zma', 'Zm00001eb114250' => 'zma', 'Zm00001eb138070' => 'zma', 'Zm00001eb167560' => 'zma', 'Zm00001eb199990' => 'zma', 'Zm00001eb368180' => 'zma', 'Zm00001eb382470' => 'zma' ) $gf_id = 'HOM05D001576' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001576' ) $data_identifier = 'HOM05D001576' $data_type = 'gf_id' $species_gene_counts = array( 'aox' => (int) 9, 'acertr' => (int) 3, 'cansat' => (int) 1, 'ccl' => (int) 4, 'cil' => (int) 145, 'camsi' => (int) 46, 'dca' => (int) 1, 'din' => (int) 1, 'fan' => (int) 12, 'fve' => (int) 9, 'gma' => (int) 5, 'han' => (int) 5, 'cav' => (int) 11, 'hma' => (int) 5, 'sun' => (int) 3, 'mdo' => (int) 3, 'mtr' => (int) 2, 'osa' => (int) 19, 'pgr' => (int) 1, 'ptr' => (int) 2, 'ppe' => (int) 6, 'qlo' => (int) 24, 'rch' => (int) 5, 'rsi' => (int) 28, 'sas' => (int) 8, 'shi' => (int) 2, 'twi' => (int) 35, 'vma' => (int) 4, 'zma' => (int) 7 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb382470' $species_info = array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ) $local_species = 'aox' $disabled = '' $selected = '' $num_hits = (int) 0include - APP/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp, line 33 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933 View::_renderElement() - CORE/Cake/View/View.php, line 1224 View::element() - CORE/Cake/View/View.php, line 418 include - APP/View/Elements/analysis/phylogenetics_module/gf_data_settings.ctp, line 37 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933 View::_renderElement() - CORE/Cake/View/View.php, line 1224 View::element() - CORE/Cake/View/View.php, line 418 include - APP/View/Elements/analysis/phylogenetics_module/parameter_selection.ctp, line 64 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933 View::_renderElement() - CORE/Cake/View/View.php, line 1224 View::element() - CORE/Cake/View/View.php, line 418 include - APP/View/Analysis/custom_tree_creation.ctp, line 27 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933
$viewFile = '/www/bioinformatics01_ro/plaza/_dev_instances/feedback/app/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp' $dataForView = array( 'sidebar_info' => array( 'gf_id' => 'HOM05D001576', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '406', 'num_species' => '29' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'Aqoxy1G01456' => 'aox', 'Aqoxy1G02949' => 'aox', 'Aqoxy3G01274' => 'aox', 'Aqoxy3G02110' => 'aox', 'Aqoxy3G02268' => 'aox', 'Aqoxy5G02702' => 'aox', 'Aqoxy5G02988' => 'aox', 'Aqoxy5G03427' => 'aox', 'Aqoxy6G02363' => 'aox', 'Atru.chr1.3225' => 'acertr', 'Atru.chr8.1198' => 'acertr', 'Atru.chr9.790' => 'acertr', 'CANSAT01G3197' => 'cansat', 'Ciclev10003979m.g' => 'ccl', 'Ciclev10017471m.g' => 'ccl', 'Ciclev10018206m.g' => 'ccl', 'Ciclev10033751m.g' => 'ccl', 'CiPaw.01G000900' => 'cil', 'CiPaw.01G001000' => 'cil', 'CiPaw.01G033500' => 'cil', 'CiPaw.01G060300' => 'cil', 'CiPaw.01G070200' => 'cil', 'CiPaw.01G075100' => 'cil', 'CiPaw.01G084700' => 'cil', 'CiPaw.01G087900' => 'cil', 'CiPaw.01G092600' => 'cil', 'CiPaw.01G097200' => 'cil', 'CiPaw.01G098300' => 'cil', 'CiPaw.01G110200' => 'cil', 'CiPaw.01G118700' => 'cil', 'CiPaw.01G121200' => 'cil', 'CiPaw.01G132500' => 'cil', 'CiPaw.01G146900' => 'cil', 'CiPaw.01G174000' => 'cil', 'CiPaw.01G179900' => 'cil', 'CiPaw.01G183400' => 'cil', 'CiPaw.01G240000' => 'cil', 'CiPaw.01G283500' => 'cil', 'CiPaw.01G307400' => 'cil', 'CiPaw.02G030800' => 'cil', 'CiPaw.02G047200' => 'cil', 'CiPaw.02G050500' => 'cil', 'CiPaw.02G069900' => 'cil', 'CiPaw.02G091600' => 'cil', 'CiPaw.02G095000' => 'cil', 'CiPaw.02G131900' => 'cil', 'CiPaw.03G043000' => 'cil', 'CiPaw.03G069900' => 'cil', 'CiPaw.03G088100' => 'cil', 'CiPaw.03G089300' => 'cil', 'CiPaw.03G093100' => 'cil', 'CiPaw.03G129800' => 'cil', 'CiPaw.03G131200' => 'cil', 'CiPaw.03G134500' => 'cil', 'CiPaw.03G152100' => 'cil', 'CiPaw.03G162700' => 'cil', 'CiPaw.03G172800' => 'cil', 'CiPaw.03G175800' => 'cil', 'CiPaw.03G181800' => 'cil', 'CiPaw.03G191400' => 'cil', 'CiPaw.03G198300' => 'cil', 'CiPaw.03G201300' => 'cil', 'CiPaw.03G224700' => 'cil', 'CiPaw.03G225000' => 'cil', 'CiPaw.04G065100' => 'cil', 'CiPaw.04G080400' => 'cil', 'CiPaw.04G113500' => 'cil', 'CiPaw.04G121900' => 'cil', 'CiPaw.04G144100' => 'cil', 'CiPaw.04G176500' => 'cil', 'CiPaw.05G086200' => 'cil', 'CiPaw.05G100200' => 'cil', 'CiPaw.05G114200' => 'cil', 'CiPaw.05G126800' => 'cil', 'CiPaw.05G228800' => 'cil', 'CiPaw.05G230600' => 'cil', 'CiPaw.05G236500' => 'cil', 'CiPaw.05G244800' => 'cil', 'CiPaw.06G026600' => 'cil', 'CiPaw.06G027900' => 'cil', 'CiPaw.06G051800' => 'cil', 'CiPaw.06G128500' => 'cil', 'CiPaw.06G165900' => 'cil', 'CiPaw.07G045400' => 'cil', 'CiPaw.07G048000' => 'cil', 'CiPaw.07G052000' => 'cil', 'CiPaw.07G073800' => 'cil', 'CiPaw.07G099700' => 'cil', 'CiPaw.07G108700' => 'cil', 'CiPaw.07G120000' => 'cil', 'CiPaw.07G134100' => 'cil', 'CiPaw.07G147000' => 'cil', 'CiPaw.07G149700' => 'cil', 'CiPaw.07G178300' => 'cil', 'CiPaw.07G184900' => 'cil', 'CiPaw.08G044500' => 'cil', 'CiPaw.08G046900' => 'cil', 'CiPaw.08G047300' => 'cil', 'CiPaw.08G115400' => 'cil', 'CiPaw.08G134700' => 'cil', 'CiPaw.08G157400' => 'cil', 'CiPaw.09G014300' => 'cil', 'CiPaw.09G088900' => 'cil', 'CiPaw.09G130900' => 'cil', 'CiPaw.09G133100' => 'cil', 'CiPaw.09G151300' => 'cil', 'CiPaw.09G172800' => 'cil', 'CiPaw.09G174900' => 'cil', 'CiPaw.09G175000' => 'cil', 'CiPaw.10G012800' => 'cil', 'CiPaw.10G028800' => 'cil', 'CiPaw.10G044700' => 'cil', 'CiPaw.10G067400' => 'cil', 'CiPaw.10G115900' => 'cil', 'CiPaw.10G126200' => 'cil', 'CiPaw.10G139700' => 'cil', 'CiPaw.10G155100' => 'cil', 'CiPaw.11G011300' => 'cil', 'CiPaw.11G025900' => 'cil', 'CiPaw.11G104100' => 'cil', 'CiPaw.11G142700' => 'cil', 'CiPaw.11G164500' => 'cil', 'CiPaw.11G189100' => 'cil', 'CiPaw.11G197100' => 'cil', 'CiPaw.12G006100' => 'cil', 'CiPaw.12G038500' => 'cil', 'CiPaw.12G041400' => 'cil', 'CiPaw.12G041600' => 'cil', 'CiPaw.12G051300' => 'cil', 'CiPaw.12G101800' => 'cil', 'CiPaw.12G107800' => 'cil', 'CiPaw.13G033200' => 'cil', 'CiPaw.13G129900' => 'cil', 'CiPaw.13G160200' => 'cil', 'CiPaw.14G018900' => 'cil', 'CiPaw.14G029000' => 'cil', 'CiPaw.14G031000' => 'cil', 'CiPaw.14G032000' => 'cil', 'CiPaw.14G032300' => 'cil', 'CiPaw.14G040600' => 'cil', 'CiPaw.14G060500' => 'cil', 'CiPaw.14G061500' => 'cil', 'CiPaw.14G077500' => 'cil', 'CiPaw.14G088300' => 'cil', 'CiPaw.14G108500' => 'cil', 'CiPaw.14G121300' => 'cil', 'CiPaw.14G133000' => 'cil', 'CiPaw.14G134600' => 'cil', 'CiPaw.15G027200' => 'cil', 'CiPaw.15G037700' => 'cil', 'CiPaw.15G050900' => 'cil', 'CiPaw.15G067200' => 'cil', 'CiPaw.15G072000' => 'cil', 'CiPaw.15G112900' => 'cil', 'CiPaw.15G133200' => 'cil', 'CiPaw.15G139500' => 'cil', 'CiPaw.15G155400' => 'cil', 'CiPaw.16G006000' => 'cil', 'CiPaw.16G013100' => 'cil', 'CiPaw.16G047100' => 'cil', 'CiPaw.16G048900' => 'cil', 'CiPaw.16G070300' => 'cil', 'CSS0000195' => 'camsi', 'CSS0001664' => 'camsi', 'CSS0002566' => 'camsi', 'CSS0003077' => 'camsi', 'CSS0004257' => 'camsi', 'CSS0004495' => 'camsi', 'CSS0004599' => 'camsi', 'CSS0004943' => 'camsi', 'CSS0005302' => 'camsi', 'CSS0006274' => 'camsi', 'CSS0006547' => 'camsi', 'CSS0006860' => 'camsi', 'CSS0008814' => 'camsi', 'CSS0008946' => 'camsi', 'CSS0009093' => 'camsi', 'CSS0010221' => 'camsi', 'CSS0010296' => 'camsi', 'CSS0010386' => 'camsi', 'CSS0010831' => 'camsi', 'CSS0011061' => 'camsi', 'CSS0012008' => 'camsi', 'CSS0012194' => 'camsi', 'CSS0013580' => 'camsi', 'CSS0014176' => 'camsi', 'CSS0014280' => 'camsi', 'CSS0014799' => 'camsi', 'CSS0015368' => 'camsi', 'CSS0017473' => 'camsi', 'CSS0019281' => 'camsi', 'CSS0021320' => 'camsi', 'CSS0021750' => 'camsi', 'CSS0023642' => 'camsi', 'CSS0023792' => 'camsi', 'CSS0031528' => 'camsi', 'CSS0033894' => 'camsi', 'CSS0034959' => 'camsi', 'CSS0035632' => 'camsi', 'CSS0038450' => 'camsi', 'CSS0039293' => 'camsi', 'CSS0041053' => 'camsi', 'CSS0041981' => 'camsi', 'CSS0042573' => 'camsi', 'CSS0042927' => 'camsi', 'CSS0047725' => 'camsi', 'CSS0049636' => 'camsi', 'CSS0050513' => 'camsi', 'DCAR_030203' => 'dca', 'Dinv07939' => 'din', 'FAN01G0456' => 'fan', 'FAN02G3001' => 'fan', 'FAN04G2781' => 'fan', 'FAN05G1385' => 'fan', 'FAN05G3062' => 'fan', 'FAN08G2267' => 'fan', 'FAN10G0481' => 'fan', 'FAN10G1257' => 'fan', 'FAN14G0954' => 'fan', 'FAN14G2347' => 'fan', 'FAN15G0187' => 'fan', 'FAN25G2214' => 'fan', 'FvH4_1g21031' => 'fve', 'FvH4_3g16231' => 'fve', 'FvH4_3g26413' => 'fve', 'FvH4_3g29014' => 'fve', 'FvH4_3g31921' => 'fve', 'FvH4_4g19882' => 'fve', 'FvH4_5g21960' => 'fve', 'FvH4_5g29683' => 'fve', 'FvH4_7g13271' => 'fve', 'Glyma.01G062500' => 'gma', 'Glyma.07G140900' => 'gma', 'Glyma.09G140900' => 'gma', 'Glyma.12G112700' => 'gma', 'Glyma.17G168800' => 'gma', 'HanXRQChr01g0027001' => 'han', 'HanXRQChr04g0120511' => 'han', 'HanXRQChr08g0232381' => 'han', 'HanXRQChr09g0265661' => 'han', 'HanXRQChr13g0416031' => 'han', 'Haze_05835' => 'cav', 'Haze_06597' => 'cav', 'Haze_07921' => 'cav', 'Haze_08599' => 'cav', 'Haze_10686' => 'cav', 'Haze_12994' => 'cav', 'Haze_13466' => 'cav', 'Haze_16101' => 'cav', 'Haze_17766' => 'cav', 'Haze_18456' => 'cav', 'Haze_20229' => 'cav', 'Hma1.2p1_0324F.1_g125640' => 'hma', 'Hma1.2p1_0733F.1_g210230' => 'hma', 'Hma1.2p1_0921F.1_g236870' => 'hma', 'Hma1.2p1_1313F.1_g274940' => 'hma', 'Hma1.2p1_3059F.1_g332230' => 'hma', 'Hund15925' => 'sun', 'Hund19562' => 'sun', 'Hund21925' => 'sun', 'MD03G1177400' => 'mdo', 'MD07G1026100' => 'mdo', 'MD17G1218600' => 'mdo', 'Medtr0867s0010' => 'mtr', 'Medtr6g081150' => 'mtr', 'Os01g0527900' => 'osa', 'Os02g0463725' => 'osa', 'Os02g0785600' => 'osa', 'Os03g0433733' => 'osa', 'Os04g0286500' => 'osa', 'Os05g0227800' => 'osa', 'Os06g0521000' => 'osa', 'Os06g0635500' => 'osa', 'Os06g0660650' => 'osa', 'Os07g0554400' => 'osa', 'Os08g0225900' => 'osa', 'Os08g0561000' => 'osa', 'Os09g0241700' => 'osa', 'Os09g0351900' => 'osa', 'Os11g0220700' => 'osa', 'Os11g0282700' => 'osa', 'Os12g0169300' => 'osa', 'Os12g0228500' => 'osa', 'Os12g0543800' => 'osa', 'PGR044G1547' => 'pgr', 'Potri.005G239150' => 'ptr', 'Potri.010G014250' => 'ptr', 'Prupe.1G172500' => 'ppe', 'Prupe.1G196800' => 'ppe', 'Prupe.1G279700' => 'ppe', 'Prupe.2G026400' => 'ppe', 'Prupe.3G094000' => 'ppe', 'Prupe.4G287300' => 'ppe', 'QL01p022166' => 'qlo', 'QL01p051890' => 'qlo', 'QL02p009469' => 'qlo', 'QL02p046053' => 'qlo', 'QL02p057958' => 'qlo', 'QL02p093127' => 'qlo', 'QL03p006855' => 'qlo', 'QL03p071586' => 'qlo', 'QL04p000022' => 'qlo', 'QL04p000024' => 'qlo', 'QL04p003192' => 'qlo', 'QL05p011416' => 'qlo', 'QL06p039590' => 'qlo', 'QL06p052750' => 'qlo', 'QL06p053821' => 'qlo', 'QL07p025287' => 'qlo', 'QL09p033218' => 'qlo', 'QL09p040841' => 'qlo', 'QL10p020337' => 'qlo', 'QL10p027209' => 'qlo', 'QL10p027969' => 'qlo', 'QL10p048988' => 'qlo', 'QL11p001241' => 'qlo', 'QL11p028487' => 'qlo', 'RcHm_v2.0_Chr2g0105031' => 'rch', 'RcHm_v2.0_Chr2g0117811' => 'rch', 'RcHm_v2.0_Chr6g0270241' => 'rch', 'RcHm_v2.0_Chr7g0215961' => 'rch', 'RcHm_v2.0_Chr7g0231991' => 'rch', 'Rhsim01G0041500' => 'rsi', 'Rhsim01G0115000' => 'rsi', 'Rhsim01G0115400' => 'rsi', 'Rhsim01G0133600' => 'rsi', 'Rhsim01G0159900' => 'rsi', 'Rhsim02G0189400' => 'rsi', 'Rhsim03G0135600' => 'rsi', 'Rhsim03G0149900' => 'rsi', 'Rhsim04G0125600' => 'rsi', 'Rhsim05G0091700' => 'rsi', 'Rhsim05G0092900' => 'rsi', 'Rhsim06G0075000' => 'rsi', 'Rhsim07G0066400' => 'rsi', 'Rhsim07G0156400' => 'rsi', 'Rhsim07G0182200' => 'rsi', 'Rhsim07G0182300' => 'rsi', 'Rhsim08G0180400' => 'rsi', 'Rhsim09G0056800' => 'rsi', 'Rhsim10G0153300' => 'rsi', 'Rhsim11G0012700' => 'rsi', 'Rhsim12G0031800' => 'rsi', 'Rhsim12G0055400' => 'rsi', 'Rhsim12G0091400' => 'rsi', 'Rhsim13G0070800' => 'rsi', 'Rhsim13G0193300' => 'rsi', 'RhsimUnG0111600' => 'rsi', 'RhsimUnG0137500' => 'rsi', 'RhsimUnG0172900' => 'rsi', 'SGA_v2.0_scaffold11G05878' => 'sas', 'SGA_v2.0_scaffold167G38458' => 'sas', 'SGA_v2.0_scaffold19G08588' => 'sas', 'SGA_v2.0_scaffold239G43990' => 'sas', 'SGA_v2.0_scaffold260G45865' => 'sas', 'SGA_v2.0_scaffold309G48177' => 'sas', 'SGA_v2.0_scaffold76G25122' => 'sas', 'SGA_v2.0_scaffold85G26708' => 'sas', 'SHI13914' => 'shi', 'SHI30402' => 'shi', 'TWI09G0020' => 'twi', 'TWI09G0456' => 'twi', 'TWI09G1572' => 'twi', 'TWI12G0266' => 'twi', 'TWI12G1451' => 'twi', 'TWI14G0851' => 'twi', 'TWI15G0796' => 'twi', 'TWI18G0820' => 'twi', 'TWI18G1152' => 'twi', 'TWI23G0007' => 'twi', 'TWI23G0314' => 'twi', 'TWI31G0674' => 'twi', 'TWI31G0938' => 'twi', 'TWI34G0641' => 'twi', 'TWI34G1527' => 'twi', 'TWI36G0193' => 'twi', 'TWI36G0405' => 'twi', 'TWI38G0892' => 'twi', 'TWI38G0936' => 'twi', 'TWI38G2218' => 'twi', 'TWI53G0679' => 'twi', 'TWI53G0863' => 'twi', 'TWI53G1133' => 'twi', 'TWI60G0823' => 'twi', 'TWI63G0919' => 'twi', 'TWI63G1436' => 'twi', 'TWI73G0140' => 'twi', 'TWI73G0419' => 'twi', 'TWI73G0420' => 'twi', 'TWI73G1276' => 'twi', 'TWI74G0405' => 'twi', 'TWI74G0837' => 'twi', 'TWI75G0594' => 'twi', 'TWI75G1615' => 'twi', 'TWI77G0816' => 'twi', 'vmacro03831' => 'vma', 'vmacro13746' => 'vma', 'vmacro16089' => 'vma', 'vmacro22863' => 'vma', 'Zm00001eb085790' => 'zma', 'Zm00001eb114250' => 'zma', 'Zm00001eb138070' => 'zma', 'Zm00001eb167560' => 'zma', 'Zm00001eb199990' => 'zma', 'Zm00001eb368180' => 'zma', 'Zm00001eb382470' => 'zma' ), 'gf_id' => 'HOM05D001576', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001576' ), 'data_identifier' => 'HOM05D001576', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001576', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '406', 'num_species' => '29' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'Aqoxy1G01456' => 'aox', 'Aqoxy1G02949' => 'aox', 'Aqoxy3G01274' => 'aox', 'Aqoxy3G02110' => 'aox', 'Aqoxy3G02268' => 'aox', 'Aqoxy5G02702' => 'aox', 'Aqoxy5G02988' => 'aox', 'Aqoxy5G03427' => 'aox', 'Aqoxy6G02363' => 'aox', 'Atru.chr1.3225' => 'acertr', 'Atru.chr8.1198' => 'acertr', 'Atru.chr9.790' => 'acertr', 'CANSAT01G3197' => 'cansat', 'Ciclev10003979m.g' => 'ccl', 'Ciclev10017471m.g' => 'ccl', 'Ciclev10018206m.g' => 'ccl', 'Ciclev10033751m.g' => 'ccl', 'CiPaw.01G000900' => 'cil', 'CiPaw.01G001000' => 'cil', 'CiPaw.01G033500' => 'cil', 'CiPaw.01G060300' => 'cil', 'CiPaw.01G070200' => 'cil', 'CiPaw.01G075100' => 'cil', 'CiPaw.01G084700' => 'cil', 'CiPaw.01G087900' => 'cil', 'CiPaw.01G092600' => 'cil', 'CiPaw.01G097200' => 'cil', 'CiPaw.01G098300' => 'cil', 'CiPaw.01G110200' => 'cil', 'CiPaw.01G118700' => 'cil', 'CiPaw.01G121200' 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'cil', 'CiPaw.09G088900' => 'cil', 'CiPaw.09G130900' => 'cil', 'CiPaw.09G133100' => 'cil', 'CiPaw.09G151300' => 'cil', 'CiPaw.09G172800' => 'cil', 'CiPaw.09G174900' => 'cil', 'CiPaw.09G175000' => 'cil', 'CiPaw.10G012800' => 'cil', 'CiPaw.10G028800' => 'cil', 'CiPaw.10G044700' => 'cil', 'CiPaw.10G067400' => 'cil', 'CiPaw.10G115900' => 'cil', 'CiPaw.10G126200' => 'cil', 'CiPaw.10G139700' => 'cil', 'CiPaw.10G155100' => 'cil', 'CiPaw.11G011300' => 'cil', 'CiPaw.11G025900' => 'cil', 'CiPaw.11G104100' => 'cil', 'CiPaw.11G142700' => 'cil', 'CiPaw.11G164500' => 'cil', 'CiPaw.11G189100' => 'cil', 'CiPaw.11G197100' => 'cil', 'CiPaw.12G006100' => 'cil', 'CiPaw.12G038500' => 'cil', 'CiPaw.12G041400' => 'cil', 'CiPaw.12G041600' => 'cil', 'CiPaw.12G051300' => 'cil', 'CiPaw.12G101800' => 'cil', 'CiPaw.12G107800' => 'cil', 'CiPaw.13G033200' => 'cil', 'CiPaw.13G129900' => 'cil', 'CiPaw.13G160200' => 'cil', 'CiPaw.14G018900' => 'cil', 'CiPaw.14G029000' => 'cil', 'CiPaw.14G031000' => 'cil', 'CiPaw.14G032000' => 'cil', 'CiPaw.14G032300' => 'cil', 'CiPaw.14G040600' => 'cil', 'CiPaw.14G060500' => 'cil', 'CiPaw.14G061500' => 'cil', 'CiPaw.14G077500' => 'cil', 'CiPaw.14G088300' => 'cil', 'CiPaw.14G108500' => 'cil', 'CiPaw.14G121300' => 'cil', 'CiPaw.14G133000' => 'cil', 'CiPaw.14G134600' => 'cil', 'CiPaw.15G027200' => 'cil', 'CiPaw.15G037700' => 'cil', 'CiPaw.15G050900' => 'cil', 'CiPaw.15G067200' => 'cil', 'CiPaw.15G072000' => 'cil', 'CiPaw.15G112900' => 'cil', 'CiPaw.15G133200' => 'cil', 'CiPaw.15G139500' => 'cil', 'CiPaw.15G155400' => 'cil', 'CiPaw.16G006000' => 'cil', 'CiPaw.16G013100' => 'cil', 'CiPaw.16G047100' => 'cil', 'CiPaw.16G048900' => 'cil', 'CiPaw.16G070300' => 'cil', 'CSS0000195' => 'camsi', 'CSS0001664' => 'camsi', 'CSS0002566' => 'camsi', 'CSS0003077' => 'camsi', 'CSS0004257' => 'camsi', 'CSS0004495' => 'camsi', 'CSS0004599' => 'camsi', 'CSS0004943' => 'camsi', 'CSS0005302' => 'camsi', 'CSS0006274' => 'camsi', 'CSS0006547' => 'camsi', 'CSS0006860' => 'camsi', 'CSS0008814' => 'camsi', 'CSS0008946' => 'camsi', 'CSS0009093' => 'camsi', 'CSS0010221' => 'camsi', 'CSS0010296' => 'camsi', 'CSS0010386' => 'camsi', 'CSS0010831' => 'camsi', 'CSS0011061' => 'camsi', 'CSS0012008' => 'camsi', 'CSS0012194' => 'camsi', 'CSS0013580' => 'camsi', 'CSS0014176' => 'camsi', 'CSS0014280' => 'camsi', 'CSS0014799' => 'camsi', 'CSS0015368' => 'camsi', 'CSS0017473' => 'camsi', 'CSS0019281' => 'camsi', 'CSS0021320' => 'camsi', 'CSS0021750' => 'camsi', 'CSS0023642' => 'camsi', 'CSS0023792' => 'camsi', 'CSS0031528' => 'camsi', 'CSS0033894' => 'camsi', 'CSS0034959' => 'camsi', 'CSS0035632' => 'camsi', 'CSS0038450' => 'camsi', 'CSS0039293' => 'camsi', 'CSS0041053' => 'camsi', 'CSS0041981' => 'camsi', 'CSS0042573' => 'camsi', 'CSS0042927' => 'camsi', 'CSS0047725' => 'camsi', 'CSS0049636' => 'camsi', 'CSS0050513' => 'camsi', 'DCAR_030203' => 'dca', 'Dinv07939' => 'din', 'FAN01G0456' => 'fan', 'FAN02G3001' => 'fan', 'FAN04G2781' => 'fan', 'FAN05G1385' => 'fan', 'FAN05G3062' => 'fan', 'FAN08G2267' => 'fan', 'FAN10G0481' => 'fan', 'FAN10G1257' => 'fan', 'FAN14G0954' => 'fan', 'FAN14G2347' => 'fan', 'FAN15G0187' => 'fan', 'FAN25G2214' => 'fan', 'FvH4_1g21031' => 'fve', 'FvH4_3g16231' => 'fve', 'FvH4_3g26413' => 'fve', 'FvH4_3g29014' => 'fve', 'FvH4_3g31921' => 'fve', 'FvH4_4g19882' => 'fve', 'FvH4_5g21960' => 'fve', 'FvH4_5g29683' => 'fve', 'FvH4_7g13271' => 'fve', 'Glyma.01G062500' => 'gma', 'Glyma.07G140900' => 'gma', 'Glyma.09G140900' => 'gma', 'Glyma.12G112700' => 'gma', 'Glyma.17G168800' => 'gma', 'HanXRQChr01g0027001' => 'han', 'HanXRQChr04g0120511' => 'han', 'HanXRQChr08g0232381' => 'han', 'HanXRQChr09g0265661' => 'han', 'HanXRQChr13g0416031' => 'han', 'Haze_05835' => 'cav', 'Haze_06597' => 'cav', 'Haze_07921' => 'cav', 'Haze_08599' => 'cav', 'Haze_10686' => 'cav', 'Haze_12994' => 'cav', 'Haze_13466' => 'cav', 'Haze_16101' => 'cav', 'Haze_17766' => 'cav', 'Haze_18456' => 'cav', 'Haze_20229' => 'cav', 'Hma1.2p1_0324F.1_g125640' => 'hma', 'Hma1.2p1_0733F.1_g210230' => 'hma', 'Hma1.2p1_0921F.1_g236870' => 'hma', 'Hma1.2p1_1313F.1_g274940' => 'hma', 'Hma1.2p1_3059F.1_g332230' => 'hma', 'Hund15925' => 'sun', 'Hund19562' => 'sun', 'Hund21925' => 'sun', 'MD03G1177400' => 'mdo', 'MD07G1026100' => 'mdo', 'MD17G1218600' => 'mdo', 'Medtr0867s0010' => 'mtr', 'Medtr6g081150' => 'mtr', 'Os01g0527900' => 'osa', 'Os02g0463725' => 'osa', 'Os02g0785600' => 'osa', 'Os03g0433733' => 'osa', 'Os04g0286500' => 'osa', 'Os05g0227800' => 'osa', 'Os06g0521000' => 'osa', 'Os06g0635500' => 'osa', 'Os06g0660650' => 'osa', 'Os07g0554400' => 'osa', 'Os08g0225900' => 'osa', 'Os08g0561000' => 'osa', 'Os09g0241700' => 'osa', 'Os09g0351900' => 'osa', 'Os11g0220700' => 'osa', 'Os11g0282700' => 'osa', 'Os12g0169300' => 'osa', 'Os12g0228500' => 'osa', 'Os12g0543800' => 'osa', 'PGR044G1547' => 'pgr', 'Potri.005G239150' => 'ptr', 'Potri.010G014250' => 'ptr', 'Prupe.1G172500' => 'ppe', 'Prupe.1G196800' => 'ppe', 'Prupe.1G279700' => 'ppe', 'Prupe.2G026400' => 'ppe', 'Prupe.3G094000' => 'ppe', 'Prupe.4G287300' => 'ppe', 'QL01p022166' => 'qlo', 'QL01p051890' => 'qlo', 'QL02p009469' => 'qlo', 'QL02p046053' => 'qlo', 'QL02p057958' => 'qlo', 'QL02p093127' => 'qlo', 'QL03p006855' => 'qlo', 'QL03p071586' => 'qlo', 'QL04p000022' => 'qlo', 'QL04p000024' => 'qlo', 'QL04p003192' => 'qlo', 'QL05p011416' => 'qlo', 'QL06p039590' => 'qlo', 'QL06p052750' => 'qlo', 'QL06p053821' => 'qlo', 'QL07p025287' => 'qlo', 'QL09p033218' => 'qlo', 'QL09p040841' => 'qlo', 'QL10p020337' => 'qlo', 'QL10p027209' => 'qlo', 'QL10p027969' => 'qlo', 'QL10p048988' => 'qlo', 'QL11p001241' => 'qlo', 'QL11p028487' => 'qlo', 'RcHm_v2.0_Chr2g0105031' => 'rch', 'RcHm_v2.0_Chr2g0117811' => 'rch', 'RcHm_v2.0_Chr6g0270241' => 'rch', 'RcHm_v2.0_Chr7g0215961' => 'rch', 'RcHm_v2.0_Chr7g0231991' => 'rch', 'Rhsim01G0041500' => 'rsi', 'Rhsim01G0115000' => 'rsi', 'Rhsim01G0115400' => 'rsi', 'Rhsim01G0133600' => 'rsi', 'Rhsim01G0159900' => 'rsi', 'Rhsim02G0189400' => 'rsi', 'Rhsim03G0135600' => 'rsi', 'Rhsim03G0149900' => 'rsi', 'Rhsim04G0125600' => 'rsi', 'Rhsim05G0091700' => 'rsi', 'Rhsim05G0092900' => 'rsi', 'Rhsim06G0075000' => 'rsi', 'Rhsim07G0066400' => 'rsi', 'Rhsim07G0156400' => 'rsi', 'Rhsim07G0182200' => 'rsi', 'Rhsim07G0182300' => 'rsi', 'Rhsim08G0180400' => 'rsi', 'Rhsim09G0056800' => 'rsi', 'Rhsim10G0153300' => 'rsi', 'Rhsim11G0012700' => 'rsi', 'Rhsim12G0031800' => 'rsi', 'Rhsim12G0055400' => 'rsi', 'Rhsim12G0091400' => 'rsi', 'Rhsim13G0070800' => 'rsi', 'Rhsim13G0193300' => 'rsi', 'RhsimUnG0111600' => 'rsi', 'RhsimUnG0137500' => 'rsi', 'RhsimUnG0172900' => 'rsi', 'SGA_v2.0_scaffold11G05878' => 'sas', 'SGA_v2.0_scaffold167G38458' => 'sas', 'SGA_v2.0_scaffold19G08588' => 'sas', 'SGA_v2.0_scaffold239G43990' => 'sas', 'SGA_v2.0_scaffold260G45865' => 'sas', 'SGA_v2.0_scaffold309G48177' => 'sas', 'SGA_v2.0_scaffold76G25122' => 'sas', 'SGA_v2.0_scaffold85G26708' => 'sas', 'SHI13914' => 'shi', 'SHI30402' => 'shi', 'TWI09G0020' => 'twi', 'TWI09G0456' => 'twi', 'TWI09G1572' => 'twi', 'TWI12G0266' => 'twi', 'TWI12G1451' => 'twi', 'TWI14G0851' => 'twi', 'TWI15G0796' => 'twi', 'TWI18G0820' => 'twi', 'TWI18G1152' => 'twi', 'TWI23G0007' => 'twi', 'TWI23G0314' => 'twi', 'TWI31G0674' => 'twi', 'TWI31G0938' => 'twi', 'TWI34G0641' => 'twi', 'TWI34G1527' => 'twi', 'TWI36G0193' => 'twi', 'TWI36G0405' => 'twi', 'TWI38G0892' => 'twi', 'TWI38G0936' => 'twi', 'TWI38G2218' => 'twi', 'TWI53G0679' => 'twi', 'TWI53G0863' => 'twi', 'TWI53G1133' => 'twi', 'TWI60G0823' => 'twi', 'TWI63G0919' => 'twi', 'TWI63G1436' => 'twi', 'TWI73G0140' => 'twi', 'TWI73G0419' => 'twi', 'TWI73G0420' => 'twi', 'TWI73G1276' => 'twi', 'TWI74G0405' => 'twi', 'TWI74G0837' => 'twi', 'TWI75G0594' => 'twi', 'TWI75G1615' => 'twi', 'TWI77G0816' => 'twi', 'vmacro03831' => 'vma', 'vmacro13746' => 'vma', 'vmacro16089' => 'vma', 'vmacro22863' => 'vma', 'Zm00001eb085790' => 'zma', 'Zm00001eb114250' => 'zma', 'Zm00001eb138070' => 'zma', 'Zm00001eb167560' => 'zma', 'Zm00001eb199990' => 'zma', 'Zm00001eb368180' => 'zma', 'Zm00001eb382470' => 'zma' ) $gf_id = 'HOM05D001576' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001576' ) $data_identifier = 'HOM05D001576' $data_type = 'gf_id' $species_gene_counts = array( 'aox' => (int) 9, 'acertr' => (int) 3, 'cansat' => (int) 1, 'ccl' => (int) 4, 'cil' => (int) 145, 'camsi' => (int) 46, 'dca' => (int) 1, 'din' => (int) 1, 'fan' => (int) 12, 'fve' => (int) 9, 'gma' => (int) 5, 'han' => (int) 5, 'cav' => (int) 11, 'hma' => (int) 5, 'sun' => (int) 3, 'mdo' => (int) 3, 'mtr' => (int) 2, 'osa' => (int) 19, 'pgr' => (int) 1, 'ptr' => (int) 2, 'ppe' => (int) 6, 'qlo' => (int) 24, 'rch' => (int) 5, 'rsi' => (int) 28, 'sas' => (int) 8, 'shi' => (int) 2, 'twi' => (int) 35, 'vma' => (int) 4, 'zma' => (int) 7 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb382470' $species_info = array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ) $local_species = 'aox' $disabled = '' $selected = '' $num_hits = (int) 0
Warning (2): count(): Parameter must be an array or an object that implements Countable [APP/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp, line 33]Code Context $disabled = (!array_key_exists($local_species,$species_gene_counts))?"disabled":""; $selected = (isset($selected_species) && array_key_exists($local_species,$selected_species))?"checked='checked'":""; $num_hits = (array_key_exists($local_species,$species_gene_counts))?count($species_gene_counts[$local_species]):0; $viewFile = '/www/bioinformatics01_ro/plaza/_dev_instances/feedback/app/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp' $dataForView = array( 'sidebar_info' => array( 'gf_id' => 'HOM05D001576', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '406', 'num_species' => '29' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'Aqoxy1G01456' => 'aox', 'Aqoxy1G02949' => 'aox', 'Aqoxy3G01274' => 'aox', 'Aqoxy3G02110' => 'aox', 'Aqoxy3G02268' => 'aox', 'Aqoxy5G02702' => 'aox', 'Aqoxy5G02988' => 'aox', 'Aqoxy5G03427' => 'aox', 'Aqoxy6G02363' => 'aox', 'Atru.chr1.3225' => 'acertr', 'Atru.chr8.1198' => 'acertr', 'Atru.chr9.790' => 'acertr', 'CANSAT01G3197' => 'cansat', 'Ciclev10003979m.g' => 'ccl', 'Ciclev10017471m.g' => 'ccl', 'Ciclev10018206m.g' => 'ccl', 'Ciclev10033751m.g' => 'ccl', 'CiPaw.01G000900' => 'cil', 'CiPaw.01G001000' => 'cil', 'CiPaw.01G033500' => 'cil', 'CiPaw.01G060300' => 'cil', 'CiPaw.01G070200' => 'cil', 'CiPaw.01G075100' => 'cil', 'CiPaw.01G084700' => 'cil', 'CiPaw.01G087900' => 'cil', 'CiPaw.01G092600' => 'cil', 'CiPaw.01G097200' => 'cil', 'CiPaw.01G098300' => 'cil', 'CiPaw.01G110200' => 'cil', 'CiPaw.01G118700' => 'cil', 'CiPaw.01G121200' => 'cil', 'CiPaw.01G132500' => 'cil', 'CiPaw.01G146900' => 'cil', 'CiPaw.01G174000' => 'cil', 'CiPaw.01G179900' => 'cil', 'CiPaw.01G183400' => 'cil', 'CiPaw.01G240000' => 'cil', 'CiPaw.01G283500' => 'cil', 'CiPaw.01G307400' => 'cil', 'CiPaw.02G030800' => 'cil', 'CiPaw.02G047200' => 'cil', 'CiPaw.02G050500' => 'cil', 'CiPaw.02G069900' => 'cil', 'CiPaw.02G091600' => 'cil', 'CiPaw.02G095000' => 'cil', 'CiPaw.02G131900' => 'cil', 'CiPaw.03G043000' => 'cil', 'CiPaw.03G069900' => 'cil', 'CiPaw.03G088100' => 'cil', 'CiPaw.03G089300' => 'cil', 'CiPaw.03G093100' => 'cil', 'CiPaw.03G129800' => 'cil', 'CiPaw.03G131200' => 'cil', 'CiPaw.03G134500' => 'cil', 'CiPaw.03G152100' => 'cil', 'CiPaw.03G162700' => 'cil', 'CiPaw.03G172800' => 'cil', 'CiPaw.03G175800' => 'cil', 'CiPaw.03G181800' => 'cil', 'CiPaw.03G191400' => 'cil', 'CiPaw.03G198300' => 'cil', 'CiPaw.03G201300' => 'cil', 'CiPaw.03G224700' => 'cil', 'CiPaw.03G225000' => 'cil', 'CiPaw.04G065100' => 'cil', 'CiPaw.04G080400' => 'cil', 'CiPaw.04G113500' => 'cil', 'CiPaw.04G121900' => 'cil', 'CiPaw.04G144100' => 'cil', 'CiPaw.04G176500' => 'cil', 'CiPaw.05G086200' => 'cil', 'CiPaw.05G100200' => 'cil', 'CiPaw.05G114200' => 'cil', 'CiPaw.05G126800' => 'cil', 'CiPaw.05G228800' => 'cil', 'CiPaw.05G230600' => 'cil', 'CiPaw.05G236500' => 'cil', 'CiPaw.05G244800' => 'cil', 'CiPaw.06G026600' => 'cil', 'CiPaw.06G027900' => 'cil', 'CiPaw.06G051800' => 'cil', 'CiPaw.06G128500' => 'cil', 'CiPaw.06G165900' => 'cil', 'CiPaw.07G045400' => 'cil', 'CiPaw.07G048000' => 'cil', 'CiPaw.07G052000' => 'cil', 'CiPaw.07G073800' => 'cil', 'CiPaw.07G099700' => 'cil', 'CiPaw.07G108700' => 'cil', 'CiPaw.07G120000' => 'cil', 'CiPaw.07G134100' => 'cil', 'CiPaw.07G147000' => 'cil', 'CiPaw.07G149700' => 'cil', 'CiPaw.07G178300' => 'cil', 'CiPaw.07G184900' => 'cil', 'CiPaw.08G044500' => 'cil', 'CiPaw.08G046900' => 'cil', 'CiPaw.08G047300' => 'cil', 'CiPaw.08G115400' => 'cil', 'CiPaw.08G134700' => 'cil', 'CiPaw.08G157400' => 'cil', 'CiPaw.09G014300' => 'cil', 'CiPaw.09G088900' => 'cil', 'CiPaw.09G130900' => 'cil', 'CiPaw.09G133100' => 'cil', 'CiPaw.09G151300' => 'cil', 'CiPaw.09G172800' => 'cil', 'CiPaw.09G174900' => 'cil', 'CiPaw.09G175000' => 'cil', 'CiPaw.10G012800' => 'cil', 'CiPaw.10G028800' => 'cil', 'CiPaw.10G044700' => 'cil', 'CiPaw.10G067400' => 'cil', 'CiPaw.10G115900' => 'cil', 'CiPaw.10G126200' => 'cil', 'CiPaw.10G139700' => 'cil', 'CiPaw.10G155100' => 'cil', 'CiPaw.11G011300' => 'cil', 'CiPaw.11G025900' => 'cil', 'CiPaw.11G104100' => 'cil', 'CiPaw.11G142700' => 'cil', 'CiPaw.11G164500' => 'cil', 'CiPaw.11G189100' => 'cil', 'CiPaw.11G197100' => 'cil', 'CiPaw.12G006100' => 'cil', 'CiPaw.12G038500' => 'cil', 'CiPaw.12G041400' => 'cil', 'CiPaw.12G041600' => 'cil', 'CiPaw.12G051300' => 'cil', 'CiPaw.12G101800' => 'cil', 'CiPaw.12G107800' => 'cil', 'CiPaw.13G033200' => 'cil', 'CiPaw.13G129900' => 'cil', 'CiPaw.13G160200' => 'cil', 'CiPaw.14G018900' => 'cil', 'CiPaw.14G029000' => 'cil', 'CiPaw.14G031000' => 'cil', 'CiPaw.14G032000' => 'cil', 'CiPaw.14G032300' => 'cil', 'CiPaw.14G040600' => 'cil', 'CiPaw.14G060500' => 'cil', 'CiPaw.14G061500' => 'cil', 'CiPaw.14G077500' => 'cil', 'CiPaw.14G088300' => 'cil', 'CiPaw.14G108500' => 'cil', 'CiPaw.14G121300' => 'cil', 'CiPaw.14G133000' => 'cil', 'CiPaw.14G134600' => 'cil', 'CiPaw.15G027200' => 'cil', 'CiPaw.15G037700' => 'cil', 'CiPaw.15G050900' => 'cil', 'CiPaw.15G067200' => 'cil', 'CiPaw.15G072000' => 'cil', 'CiPaw.15G112900' => 'cil', 'CiPaw.15G133200' => 'cil', 'CiPaw.15G139500' => 'cil', 'CiPaw.15G155400' => 'cil', 'CiPaw.16G006000' => 'cil', 'CiPaw.16G013100' => 'cil', 'CiPaw.16G047100' => 'cil', 'CiPaw.16G048900' => 'cil', 'CiPaw.16G070300' => 'cil', 'CSS0000195' => 'camsi', 'CSS0001664' => 'camsi', 'CSS0002566' => 'camsi', 'CSS0003077' => 'camsi', 'CSS0004257' => 'camsi', 'CSS0004495' => 'camsi', 'CSS0004599' => 'camsi', 'CSS0004943' => 'camsi', 'CSS0005302' => 'camsi', 'CSS0006274' => 'camsi', 'CSS0006547' => 'camsi', 'CSS0006860' => 'camsi', 'CSS0008814' => 'camsi', 'CSS0008946' => 'camsi', 'CSS0009093' => 'camsi', 'CSS0010221' => 'camsi', 'CSS0010296' => 'camsi', 'CSS0010386' => 'camsi', 'CSS0010831' => 'camsi', 'CSS0011061' => 'camsi', 'CSS0012008' => 'camsi', 'CSS0012194' => 'camsi', 'CSS0013580' => 'camsi', 'CSS0014176' => 'camsi', 'CSS0014280' => 'camsi', 'CSS0014799' => 'camsi', 'CSS0015368' => 'camsi', 'CSS0017473' => 'camsi', 'CSS0019281' => 'camsi', 'CSS0021320' => 'camsi', 'CSS0021750' => 'camsi', 'CSS0023642' => 'camsi', 'CSS0023792' => 'camsi', 'CSS0031528' => 'camsi', 'CSS0033894' => 'camsi', 'CSS0034959' => 'camsi', 'CSS0035632' => 'camsi', 'CSS0038450' => 'camsi', 'CSS0039293' => 'camsi', 'CSS0041053' => 'camsi', 'CSS0041981' => 'camsi', 'CSS0042573' => 'camsi', 'CSS0042927' => 'camsi', 'CSS0047725' => 'camsi', 'CSS0049636' => 'camsi', 'CSS0050513' => 'camsi', 'DCAR_030203' => 'dca', 'Dinv07939' => 'din', 'FAN01G0456' => 'fan', 'FAN02G3001' => 'fan', 'FAN04G2781' => 'fan', 'FAN05G1385' => 'fan', 'FAN05G3062' => 'fan', 'FAN08G2267' => 'fan', 'FAN10G0481' => 'fan', 'FAN10G1257' => 'fan', 'FAN14G0954' => 'fan', 'FAN14G2347' => 'fan', 'FAN15G0187' => 'fan', 'FAN25G2214' => 'fan', 'FvH4_1g21031' => 'fve', 'FvH4_3g16231' => 'fve', 'FvH4_3g26413' => 'fve', 'FvH4_3g29014' => 'fve', 'FvH4_3g31921' => 'fve', 'FvH4_4g19882' => 'fve', 'FvH4_5g21960' => 'fve', 'FvH4_5g29683' => 'fve', 'FvH4_7g13271' => 'fve', 'Glyma.01G062500' => 'gma', 'Glyma.07G140900' => 'gma', 'Glyma.09G140900' => 'gma', 'Glyma.12G112700' => 'gma', 'Glyma.17G168800' => 'gma', 'HanXRQChr01g0027001' => 'han', 'HanXRQChr04g0120511' => 'han', 'HanXRQChr08g0232381' => 'han', 'HanXRQChr09g0265661' => 'han', 'HanXRQChr13g0416031' => 'han', 'Haze_05835' => 'cav', 'Haze_06597' => 'cav', 'Haze_07921' => 'cav', 'Haze_08599' => 'cav', 'Haze_10686' => 'cav', 'Haze_12994' => 'cav', 'Haze_13466' => 'cav', 'Haze_16101' => 'cav', 'Haze_17766' => 'cav', 'Haze_18456' => 'cav', 'Haze_20229' => 'cav', 'Hma1.2p1_0324F.1_g125640' => 'hma', 'Hma1.2p1_0733F.1_g210230' => 'hma', 'Hma1.2p1_0921F.1_g236870' => 'hma', 'Hma1.2p1_1313F.1_g274940' => 'hma', 'Hma1.2p1_3059F.1_g332230' => 'hma', 'Hund15925' => 'sun', 'Hund19562' => 'sun', 'Hund21925' => 'sun', 'MD03G1177400' => 'mdo', 'MD07G1026100' => 'mdo', 'MD17G1218600' => 'mdo', 'Medtr0867s0010' => 'mtr', 'Medtr6g081150' => 'mtr', 'Os01g0527900' => 'osa', 'Os02g0463725' => 'osa', 'Os02g0785600' => 'osa', 'Os03g0433733' => 'osa', 'Os04g0286500' => 'osa', 'Os05g0227800' => 'osa', 'Os06g0521000' => 'osa', 'Os06g0635500' => 'osa', 'Os06g0660650' => 'osa', 'Os07g0554400' => 'osa', 'Os08g0225900' => 'osa', 'Os08g0561000' => 'osa', 'Os09g0241700' => 'osa', 'Os09g0351900' => 'osa', 'Os11g0220700' => 'osa', 'Os11g0282700' => 'osa', 'Os12g0169300' => 'osa', 'Os12g0228500' => 'osa', 'Os12g0543800' => 'osa', 'PGR044G1547' => 'pgr', 'Potri.005G239150' => 'ptr', 'Potri.010G014250' => 'ptr', 'Prupe.1G172500' => 'ppe', 'Prupe.1G196800' => 'ppe', 'Prupe.1G279700' => 'ppe', 'Prupe.2G026400' => 'ppe', 'Prupe.3G094000' => 'ppe', 'Prupe.4G287300' => 'ppe', 'QL01p022166' => 'qlo', 'QL01p051890' => 'qlo', 'QL02p009469' => 'qlo', 'QL02p046053' => 'qlo', 'QL02p057958' => 'qlo', 'QL02p093127' => 'qlo', 'QL03p006855' => 'qlo', 'QL03p071586' => 'qlo', 'QL04p000022' => 'qlo', 'QL04p000024' => 'qlo', 'QL04p003192' => 'qlo', 'QL05p011416' => 'qlo', 'QL06p039590' => 'qlo', 'QL06p052750' => 'qlo', 'QL06p053821' => 'qlo', 'QL07p025287' => 'qlo', 'QL09p033218' => 'qlo', 'QL09p040841' => 'qlo', 'QL10p020337' => 'qlo', 'QL10p027209' => 'qlo', 'QL10p027969' => 'qlo', 'QL10p048988' => 'qlo', 'QL11p001241' => 'qlo', 'QL11p028487' => 'qlo', 'RcHm_v2.0_Chr2g0105031' => 'rch', 'RcHm_v2.0_Chr2g0117811' => 'rch', 'RcHm_v2.0_Chr6g0270241' => 'rch', 'RcHm_v2.0_Chr7g0215961' => 'rch', 'RcHm_v2.0_Chr7g0231991' => 'rch', 'Rhsim01G0041500' => 'rsi', 'Rhsim01G0115000' => 'rsi', 'Rhsim01G0115400' => 'rsi', 'Rhsim01G0133600' => 'rsi', 'Rhsim01G0159900' => 'rsi', 'Rhsim02G0189400' => 'rsi', 'Rhsim03G0135600' => 'rsi', 'Rhsim03G0149900' => 'rsi', 'Rhsim04G0125600' => 'rsi', 'Rhsim05G0091700' => 'rsi', 'Rhsim05G0092900' => 'rsi', 'Rhsim06G0075000' => 'rsi', 'Rhsim07G0066400' => 'rsi', 'Rhsim07G0156400' => 'rsi', 'Rhsim07G0182200' => 'rsi', 'Rhsim07G0182300' => 'rsi', 'Rhsim08G0180400' => 'rsi', 'Rhsim09G0056800' => 'rsi', 'Rhsim10G0153300' => 'rsi', 'Rhsim11G0012700' => 'rsi', 'Rhsim12G0031800' => 'rsi', 'Rhsim12G0055400' => 'rsi', 'Rhsim12G0091400' => 'rsi', 'Rhsim13G0070800' => 'rsi', 'Rhsim13G0193300' => 'rsi', 'RhsimUnG0111600' => 'rsi', 'RhsimUnG0137500' => 'rsi', 'RhsimUnG0172900' => 'rsi', 'SGA_v2.0_scaffold11G05878' => 'sas', 'SGA_v2.0_scaffold167G38458' => 'sas', 'SGA_v2.0_scaffold19G08588' => 'sas', 'SGA_v2.0_scaffold239G43990' => 'sas', 'SGA_v2.0_scaffold260G45865' => 'sas', 'SGA_v2.0_scaffold309G48177' => 'sas', 'SGA_v2.0_scaffold76G25122' => 'sas', 'SGA_v2.0_scaffold85G26708' => 'sas', 'SHI13914' => 'shi', 'SHI30402' => 'shi', 'TWI09G0020' => 'twi', 'TWI09G0456' => 'twi', 'TWI09G1572' => 'twi', 'TWI12G0266' => 'twi', 'TWI12G1451' => 'twi', 'TWI14G0851' => 'twi', 'TWI15G0796' => 'twi', 'TWI18G0820' => 'twi', 'TWI18G1152' => 'twi', 'TWI23G0007' => 'twi', 'TWI23G0314' => 'twi', 'TWI31G0674' => 'twi', 'TWI31G0938' => 'twi', 'TWI34G0641' => 'twi', 'TWI34G1527' => 'twi', 'TWI36G0193' => 'twi', 'TWI36G0405' => 'twi', 'TWI38G0892' => 'twi', 'TWI38G0936' => 'twi', 'TWI38G2218' => 'twi', 'TWI53G0679' => 'twi', 'TWI53G0863' => 'twi', 'TWI53G1133' => 'twi', 'TWI60G0823' => 'twi', 'TWI63G0919' => 'twi', 'TWI63G1436' => 'twi', 'TWI73G0140' => 'twi', 'TWI73G0419' => 'twi', 'TWI73G0420' => 'twi', 'TWI73G1276' => 'twi', 'TWI74G0405' => 'twi', 'TWI74G0837' => 'twi', 'TWI75G0594' => 'twi', 'TWI75G1615' => 'twi', 'TWI77G0816' => 'twi', 'vmacro03831' => 'vma', 'vmacro13746' => 'vma', 'vmacro16089' => 'vma', 'vmacro22863' => 'vma', 'Zm00001eb085790' => 'zma', 'Zm00001eb114250' => 'zma', 'Zm00001eb138070' => 'zma', 'Zm00001eb167560' => 'zma', 'Zm00001eb199990' => 'zma', 'Zm00001eb368180' => 'zma', 'Zm00001eb382470' => 'zma' ), 'gf_id' => 'HOM05D001576', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001576' ), 'data_identifier' => 'HOM05D001576', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001576', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '406', 'num_species' => '29' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'Aqoxy1G01456' => 'aox', 'Aqoxy1G02949' => 'aox', 'Aqoxy3G01274' => 'aox', 'Aqoxy3G02110' => 'aox', 'Aqoxy3G02268' => 'aox', 'Aqoxy5G02702' => 'aox', 'Aqoxy5G02988' => 'aox', 'Aqoxy5G03427' => 'aox', 'Aqoxy6G02363' => 'aox', 'Atru.chr1.3225' => 'acertr', 'Atru.chr8.1198' => 'acertr', 'Atru.chr9.790' => 'acertr', 'CANSAT01G3197' => 'cansat', 'Ciclev10003979m.g' => 'ccl', 'Ciclev10017471m.g' => 'ccl', 'Ciclev10018206m.g' => 'ccl', 'Ciclev10033751m.g' => 'ccl', 'CiPaw.01G000900' => 'cil', 'CiPaw.01G001000' => 'cil', 'CiPaw.01G033500' => 'cil', 'CiPaw.01G060300' => 'cil', 'CiPaw.01G070200' => 'cil', 'CiPaw.01G075100' => 'cil', 'CiPaw.01G084700' => 'cil', 'CiPaw.01G087900' => 'cil', 'CiPaw.01G092600' => 'cil', 'CiPaw.01G097200' => 'cil', 'CiPaw.01G098300' => 'cil', 'CiPaw.01G110200' => 'cil', 'CiPaw.01G118700' => 'cil', 'CiPaw.01G121200' => 'cil', 'CiPaw.01G132500' => 'cil', 'CiPaw.01G146900' => 'cil', 'CiPaw.01G174000' => 'cil', 'CiPaw.01G179900' => 'cil', 'CiPaw.01G183400' => 'cil', 'CiPaw.01G240000' => 'cil', 'CiPaw.01G283500' => 'cil', 'CiPaw.01G307400' => 'cil', 'CiPaw.02G030800' => 'cil', 'CiPaw.02G047200' => 'cil', 'CiPaw.02G050500' => 'cil', 'CiPaw.02G069900' => 'cil', 'CiPaw.02G091600' => 'cil', 'CiPaw.02G095000' => 'cil', 'CiPaw.02G131900' => 'cil', 'CiPaw.03G043000' => 'cil', 'CiPaw.03G069900' => 'cil', 'CiPaw.03G088100' => 'cil', 'CiPaw.03G089300' => 'cil', 'CiPaw.03G093100' => 'cil', 'CiPaw.03G129800' => 'cil', 'CiPaw.03G131200' => 'cil', 'CiPaw.03G134500' => 'cil', 'CiPaw.03G152100' => 'cil', 'CiPaw.03G162700' => 'cil', 'CiPaw.03G172800' => 'cil', 'CiPaw.03G175800' => 'cil', 'CiPaw.03G181800' => 'cil', 'CiPaw.03G191400' => 'cil', 'CiPaw.03G198300' => 'cil', 'CiPaw.03G201300' => 'cil', 'CiPaw.03G224700' => 'cil', 'CiPaw.03G225000' => 'cil', 'CiPaw.04G065100' => 'cil', 'CiPaw.04G080400' => 'cil', 'CiPaw.04G113500' => 'cil', 'CiPaw.04G121900' => 'cil', 'CiPaw.04G144100' => 'cil', 'CiPaw.04G176500' => 'cil', 'CiPaw.05G086200' => 'cil', 'CiPaw.05G100200' => 'cil', 'CiPaw.05G114200' => 'cil', 'CiPaw.05G126800' => 'cil', 'CiPaw.05G228800' => 'cil', 'CiPaw.05G230600' => 'cil', 'CiPaw.05G236500' => 'cil', 'CiPaw.05G244800' => 'cil', 'CiPaw.06G026600' => 'cil', 'CiPaw.06G027900' => 'cil', 'CiPaw.06G051800' => 'cil', 'CiPaw.06G128500' => 'cil', 'CiPaw.06G165900' => 'cil', 'CiPaw.07G045400' => 'cil', 'CiPaw.07G048000' => 'cil', 'CiPaw.07G052000' => 'cil', 'CiPaw.07G073800' => 'cil', 'CiPaw.07G099700' => 'cil', 'CiPaw.07G108700' => 'cil', 'CiPaw.07G120000' => 'cil', 'CiPaw.07G134100' => 'cil', 'CiPaw.07G147000' => 'cil', 'CiPaw.07G149700' => 'cil', 'CiPaw.07G178300' => 'cil', 'CiPaw.07G184900' => 'cil', 'CiPaw.08G044500' => 'cil', 'CiPaw.08G046900' => 'cil', 'CiPaw.08G047300' => 'cil', 'CiPaw.08G115400' => 'cil', 'CiPaw.08G134700' => 'cil', 'CiPaw.08G157400' => 'cil', 'CiPaw.09G014300' => 'cil', 'CiPaw.09G088900' => 'cil', 'CiPaw.09G130900' => 'cil', 'CiPaw.09G133100' => 'cil', 'CiPaw.09G151300' => 'cil', 'CiPaw.09G172800' => 'cil', 'CiPaw.09G174900' => 'cil', 'CiPaw.09G175000' => 'cil', 'CiPaw.10G012800' => 'cil', 'CiPaw.10G028800' => 'cil', 'CiPaw.10G044700' => 'cil', 'CiPaw.10G067400' => 'cil', 'CiPaw.10G115900' => 'cil', 'CiPaw.10G126200' => 'cil', 'CiPaw.10G139700' => 'cil', 'CiPaw.10G155100' => 'cil', 'CiPaw.11G011300' => 'cil', 'CiPaw.11G025900' => 'cil', 'CiPaw.11G104100' => 'cil', 'CiPaw.11G142700' => 'cil', 'CiPaw.11G164500' => 'cil', 'CiPaw.11G189100' => 'cil', 'CiPaw.11G197100' => 'cil', 'CiPaw.12G006100' => 'cil', 'CiPaw.12G038500' => 'cil', 'CiPaw.12G041400' => 'cil', 'CiPaw.12G041600' => 'cil', 'CiPaw.12G051300' => 'cil', 'CiPaw.12G101800' => 'cil', 'CiPaw.12G107800' => 'cil', 'CiPaw.13G033200' => 'cil', 'CiPaw.13G129900' => 'cil', 'CiPaw.13G160200' => 'cil', 'CiPaw.14G018900' => 'cil', 'CiPaw.14G029000' => 'cil', 'CiPaw.14G031000' => 'cil', 'CiPaw.14G032000' => 'cil', 'CiPaw.14G032300' => 'cil', 'CiPaw.14G040600' => 'cil', 'CiPaw.14G060500' => 'cil', 'CiPaw.14G061500' => 'cil', 'CiPaw.14G077500' => 'cil', 'CiPaw.14G088300' => 'cil', 'CiPaw.14G108500' => 'cil', 'CiPaw.14G121300' => 'cil', 'CiPaw.14G133000' => 'cil', 'CiPaw.14G134600' => 'cil', 'CiPaw.15G027200' => 'cil', 'CiPaw.15G037700' => 'cil', 'CiPaw.15G050900' => 'cil', 'CiPaw.15G067200' => 'cil', 'CiPaw.15G072000' => 'cil', 'CiPaw.15G112900' => 'cil', 'CiPaw.15G133200' => 'cil', 'CiPaw.15G139500' => 'cil', 'CiPaw.15G155400' => 'cil', 'CiPaw.16G006000' => 'cil', 'CiPaw.16G013100' => 'cil', 'CiPaw.16G047100' => 'cil', 'CiPaw.16G048900' => 'cil', 'CiPaw.16G070300' => 'cil', 'CSS0000195' => 'camsi', 'CSS0001664' => 'camsi', 'CSS0002566' => 'camsi', 'CSS0003077' => 'camsi', 'CSS0004257' => 'camsi', 'CSS0004495' => 'camsi', 'CSS0004599' => 'camsi', 'CSS0004943' => 'camsi', 'CSS0005302' => 'camsi', 'CSS0006274' => 'camsi', 'CSS0006547' => 'camsi', 'CSS0006860' => 'camsi', 'CSS0008814' => 'camsi', 'CSS0008946' => 'camsi', 'CSS0009093' => 'camsi', 'CSS0010221' => 'camsi', 'CSS0010296' => 'camsi', 'CSS0010386' => 'camsi', 'CSS0010831' => 'camsi', 'CSS0011061' => 'camsi', 'CSS0012008' => 'camsi', 'CSS0012194' => 'camsi', 'CSS0013580' => 'camsi', 'CSS0014176' => 'camsi', 'CSS0014280' => 'camsi', 'CSS0014799' => 'camsi', 'CSS0015368' => 'camsi', 'CSS0017473' => 'camsi', 'CSS0019281' => 'camsi', 'CSS0021320' => 'camsi', 'CSS0021750' => 'camsi', 'CSS0023642' => 'camsi', 'CSS0023792' => 'camsi', 'CSS0031528' => 'camsi', 'CSS0033894' => 'camsi', 'CSS0034959' => 'camsi', 'CSS0035632' => 'camsi', 'CSS0038450' => 'camsi', 'CSS0039293' => 'camsi', 'CSS0041053' => 'camsi', 'CSS0041981' => 'camsi', 'CSS0042573' => 'camsi', 'CSS0042927' => 'camsi', 'CSS0047725' => 'camsi', 'CSS0049636' => 'camsi', 'CSS0050513' => 'camsi', 'DCAR_030203' => 'dca', 'Dinv07939' => 'din', 'FAN01G0456' => 'fan', 'FAN02G3001' => 'fan', 'FAN04G2781' => 'fan', 'FAN05G1385' => 'fan', 'FAN05G3062' => 'fan', 'FAN08G2267' => 'fan', 'FAN10G0481' => 'fan', 'FAN10G1257' => 'fan', 'FAN14G0954' => 'fan', 'FAN14G2347' => 'fan', 'FAN15G0187' => 'fan', 'FAN25G2214' => 'fan', 'FvH4_1g21031' => 'fve', 'FvH4_3g16231' => 'fve', 'FvH4_3g26413' => 'fve', 'FvH4_3g29014' => 'fve', 'FvH4_3g31921' => 'fve', 'FvH4_4g19882' => 'fve', 'FvH4_5g21960' => 'fve', 'FvH4_5g29683' => 'fve', 'FvH4_7g13271' => 'fve', 'Glyma.01G062500' => 'gma', 'Glyma.07G140900' => 'gma', 'Glyma.09G140900' => 'gma', 'Glyma.12G112700' => 'gma', 'Glyma.17G168800' => 'gma', 'HanXRQChr01g0027001' => 'han', 'HanXRQChr04g0120511' => 'han', 'HanXRQChr08g0232381' => 'han', 'HanXRQChr09g0265661' => 'han', 'HanXRQChr13g0416031' => 'han', 'Haze_05835' => 'cav', 'Haze_06597' => 'cav', 'Haze_07921' => 'cav', 'Haze_08599' => 'cav', 'Haze_10686' => 'cav', 'Haze_12994' => 'cav', 'Haze_13466' => 'cav', 'Haze_16101' => 'cav', 'Haze_17766' => 'cav', 'Haze_18456' => 'cav', 'Haze_20229' => 'cav', 'Hma1.2p1_0324F.1_g125640' => 'hma', 'Hma1.2p1_0733F.1_g210230' => 'hma', 'Hma1.2p1_0921F.1_g236870' => 'hma', 'Hma1.2p1_1313F.1_g274940' => 'hma', 'Hma1.2p1_3059F.1_g332230' => 'hma', 'Hund15925' => 'sun', 'Hund19562' => 'sun', 'Hund21925' => 'sun', 'MD03G1177400' => 'mdo', 'MD07G1026100' => 'mdo', 'MD17G1218600' => 'mdo', 'Medtr0867s0010' => 'mtr', 'Medtr6g081150' => 'mtr', 'Os01g0527900' => 'osa', 'Os02g0463725' => 'osa', 'Os02g0785600' => 'osa', 'Os03g0433733' => 'osa', 'Os04g0286500' => 'osa', 'Os05g0227800' => 'osa', 'Os06g0521000' => 'osa', 'Os06g0635500' => 'osa', 'Os06g0660650' => 'osa', 'Os07g0554400' => 'osa', 'Os08g0225900' => 'osa', 'Os08g0561000' => 'osa', 'Os09g0241700' => 'osa', 'Os09g0351900' => 'osa', 'Os11g0220700' => 'osa', 'Os11g0282700' => 'osa', 'Os12g0169300' => 'osa', 'Os12g0228500' => 'osa', 'Os12g0543800' => 'osa', 'PGR044G1547' => 'pgr', 'Potri.005G239150' => 'ptr', 'Potri.010G014250' => 'ptr', 'Prupe.1G172500' => 'ppe', 'Prupe.1G196800' => 'ppe', 'Prupe.1G279700' => 'ppe', 'Prupe.2G026400' => 'ppe', 'Prupe.3G094000' => 'ppe', 'Prupe.4G287300' => 'ppe', 'QL01p022166' => 'qlo', 'QL01p051890' => 'qlo', 'QL02p009469' => 'qlo', 'QL02p046053' => 'qlo', 'QL02p057958' => 'qlo', 'QL02p093127' => 'qlo', 'QL03p006855' => 'qlo', 'QL03p071586' => 'qlo', 'QL04p000022' => 'qlo', 'QL04p000024' => 'qlo', 'QL04p003192' => 'qlo', 'QL05p011416' => 'qlo', 'QL06p039590' => 'qlo', 'QL06p052750' => 'qlo', 'QL06p053821' => 'qlo', 'QL07p025287' => 'qlo', 'QL09p033218' => 'qlo', 'QL09p040841' => 'qlo', 'QL10p020337' => 'qlo', 'QL10p027209' => 'qlo', 'QL10p027969' => 'qlo', 'QL10p048988' => 'qlo', 'QL11p001241' => 'qlo', 'QL11p028487' => 'qlo', 'RcHm_v2.0_Chr2g0105031' => 'rch', 'RcHm_v2.0_Chr2g0117811' => 'rch', 'RcHm_v2.0_Chr6g0270241' => 'rch', 'RcHm_v2.0_Chr7g0215961' => 'rch', 'RcHm_v2.0_Chr7g0231991' => 'rch', 'Rhsim01G0041500' => 'rsi', 'Rhsim01G0115000' => 'rsi', 'Rhsim01G0115400' => 'rsi', 'Rhsim01G0133600' => 'rsi', 'Rhsim01G0159900' => 'rsi', 'Rhsim02G0189400' => 'rsi', 'Rhsim03G0135600' => 'rsi', 'Rhsim03G0149900' => 'rsi', 'Rhsim04G0125600' => 'rsi', 'Rhsim05G0091700' => 'rsi', 'Rhsim05G0092900' => 'rsi', 'Rhsim06G0075000' => 'rsi', 'Rhsim07G0066400' => 'rsi', 'Rhsim07G0156400' => 'rsi', 'Rhsim07G0182200' => 'rsi', 'Rhsim07G0182300' => 'rsi', 'Rhsim08G0180400' => 'rsi', 'Rhsim09G0056800' => 'rsi', 'Rhsim10G0153300' => 'rsi', 'Rhsim11G0012700' => 'rsi', 'Rhsim12G0031800' => 'rsi', 'Rhsim12G0055400' => 'rsi', 'Rhsim12G0091400' => 'rsi', 'Rhsim13G0070800' => 'rsi', 'Rhsim13G0193300' => 'rsi', 'RhsimUnG0111600' => 'rsi', 'RhsimUnG0137500' => 'rsi', 'RhsimUnG0172900' => 'rsi', 'SGA_v2.0_scaffold11G05878' => 'sas', 'SGA_v2.0_scaffold167G38458' => 'sas', 'SGA_v2.0_scaffold19G08588' => 'sas', 'SGA_v2.0_scaffold239G43990' => 'sas', 'SGA_v2.0_scaffold260G45865' => 'sas', 'SGA_v2.0_scaffold309G48177' => 'sas', 'SGA_v2.0_scaffold76G25122' => 'sas', 'SGA_v2.0_scaffold85G26708' => 'sas', 'SHI13914' => 'shi', 'SHI30402' => 'shi', 'TWI09G0020' => 'twi', 'TWI09G0456' => 'twi', 'TWI09G1572' => 'twi', 'TWI12G0266' => 'twi', 'TWI12G1451' => 'twi', 'TWI14G0851' => 'twi', 'TWI15G0796' => 'twi', 'TWI18G0820' => 'twi', 'TWI18G1152' => 'twi', 'TWI23G0007' => 'twi', 'TWI23G0314' => 'twi', 'TWI31G0674' => 'twi', 'TWI31G0938' => 'twi', 'TWI34G0641' => 'twi', 'TWI34G1527' => 'twi', 'TWI36G0193' => 'twi', 'TWI36G0405' => 'twi', 'TWI38G0892' => 'twi', 'TWI38G0936' => 'twi', 'TWI38G2218' => 'twi', 'TWI53G0679' => 'twi', 'TWI53G0863' => 'twi', 'TWI53G1133' => 'twi', 'TWI60G0823' => 'twi', 'TWI63G0919' => 'twi', 'TWI63G1436' => 'twi', 'TWI73G0140' => 'twi', 'TWI73G0419' => 'twi', 'TWI73G0420' => 'twi', 'TWI73G1276' => 'twi', 'TWI74G0405' => 'twi', 'TWI74G0837' => 'twi', 'TWI75G0594' => 'twi', 'TWI75G1615' => 'twi', 'TWI77G0816' => 'twi', 'vmacro03831' => 'vma', 'vmacro13746' => 'vma', 'vmacro16089' => 'vma', 'vmacro22863' => 'vma', 'Zm00001eb085790' => 'zma', 'Zm00001eb114250' => 'zma', 'Zm00001eb138070' => 'zma', 'Zm00001eb167560' => 'zma', 'Zm00001eb199990' => 'zma', 'Zm00001eb368180' => 'zma', 'Zm00001eb382470' => 'zma' ) $gf_id = 'HOM05D001576' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001576' ) $data_identifier = 'HOM05D001576' $data_type = 'gf_id' $species_gene_counts = array( 'aox' => (int) 9, 'acertr' => (int) 3, 'cansat' => (int) 1, 'ccl' => (int) 4, 'cil' => (int) 145, 'camsi' => (int) 46, 'dca' => (int) 1, 'din' => (int) 1, 'fan' => (int) 12, 'fve' => (int) 9, 'gma' => (int) 5, 'han' => (int) 5, 'cav' => (int) 11, 'hma' => (int) 5, 'sun' => (int) 3, 'mdo' => (int) 3, 'mtr' => (int) 2, 'osa' => (int) 19, 'pgr' => (int) 1, 'ptr' => (int) 2, 'ppe' => (int) 6, 'qlo' => (int) 24, 'rch' => (int) 5, 'rsi' => (int) 28, 'sas' => (int) 8, 'shi' => (int) 2, 'twi' => (int) 35, 'vma' => (int) 4, 'zma' => (int) 7 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb382470' $species_info = array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ) $local_species = 'camsi' $disabled = '' $selected = '' $num_hits = (int) 0include - APP/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp, line 33 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933 View::_renderElement() - CORE/Cake/View/View.php, line 1224 View::element() - CORE/Cake/View/View.php, line 418 include - APP/View/Elements/analysis/phylogenetics_module/gf_data_settings.ctp, line 37 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933 View::_renderElement() - CORE/Cake/View/View.php, line 1224 View::element() - CORE/Cake/View/View.php, line 418 include - APP/View/Elements/analysis/phylogenetics_module/parameter_selection.ctp, line 64 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933 View::_renderElement() - CORE/Cake/View/View.php, line 1224 View::element() - CORE/Cake/View/View.php, line 418 include - APP/View/Analysis/custom_tree_creation.ctp, line 27 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933
$viewFile = '/www/bioinformatics01_ro/plaza/_dev_instances/feedback/app/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp' $dataForView = array( 'sidebar_info' => array( 'gf_id' => 'HOM05D001576', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '406', 'num_species' => '29' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'Aqoxy1G01456' => 'aox', 'Aqoxy1G02949' => 'aox', 'Aqoxy3G01274' => 'aox', 'Aqoxy3G02110' => 'aox', 'Aqoxy3G02268' => 'aox', 'Aqoxy5G02702' => 'aox', 'Aqoxy5G02988' => 'aox', 'Aqoxy5G03427' => 'aox', 'Aqoxy6G02363' => 'aox', 'Atru.chr1.3225' => 'acertr', 'Atru.chr8.1198' => 'acertr', 'Atru.chr9.790' => 'acertr', 'CANSAT01G3197' => 'cansat', 'Ciclev10003979m.g' => 'ccl', 'Ciclev10017471m.g' => 'ccl', 'Ciclev10018206m.g' => 'ccl', 'Ciclev10033751m.g' => 'ccl', 'CiPaw.01G000900' => 'cil', 'CiPaw.01G001000' => 'cil', 'CiPaw.01G033500' => 'cil', 'CiPaw.01G060300' => 'cil', 'CiPaw.01G070200' => 'cil', 'CiPaw.01G075100' => 'cil', 'CiPaw.01G084700' => 'cil', 'CiPaw.01G087900' => 'cil', 'CiPaw.01G092600' => 'cil', 'CiPaw.01G097200' => 'cil', 'CiPaw.01G098300' => 'cil', 'CiPaw.01G110200' => 'cil', 'CiPaw.01G118700' => 'cil', 'CiPaw.01G121200' => 'cil', 'CiPaw.01G132500' => 'cil', 'CiPaw.01G146900' => 'cil', 'CiPaw.01G174000' => 'cil', 'CiPaw.01G179900' => 'cil', 'CiPaw.01G183400' => 'cil', 'CiPaw.01G240000' => 'cil', 'CiPaw.01G283500' => 'cil', 'CiPaw.01G307400' => 'cil', 'CiPaw.02G030800' => 'cil', 'CiPaw.02G047200' => 'cil', 'CiPaw.02G050500' => 'cil', 'CiPaw.02G069900' => 'cil', 'CiPaw.02G091600' => 'cil', 'CiPaw.02G095000' => 'cil', 'CiPaw.02G131900' => 'cil', 'CiPaw.03G043000' => 'cil', 'CiPaw.03G069900' => 'cil', 'CiPaw.03G088100' => 'cil', 'CiPaw.03G089300' => 'cil', 'CiPaw.03G093100' => 'cil', 'CiPaw.03G129800' => 'cil', 'CiPaw.03G131200' => 'cil', 'CiPaw.03G134500' => 'cil', 'CiPaw.03G152100' => 'cil', 'CiPaw.03G162700' => 'cil', 'CiPaw.03G172800' => 'cil', 'CiPaw.03G175800' => 'cil', 'CiPaw.03G181800' => 'cil', 'CiPaw.03G191400' => 'cil', 'CiPaw.03G198300' => 'cil', 'CiPaw.03G201300' => 'cil', 'CiPaw.03G224700' => 'cil', 'CiPaw.03G225000' => 'cil', 'CiPaw.04G065100' => 'cil', 'CiPaw.04G080400' => 'cil', 'CiPaw.04G113500' => 'cil', 'CiPaw.04G121900' => 'cil', 'CiPaw.04G144100' => 'cil', 'CiPaw.04G176500' => 'cil', 'CiPaw.05G086200' => 'cil', 'CiPaw.05G100200' => 'cil', 'CiPaw.05G114200' => 'cil', 'CiPaw.05G126800' => 'cil', 'CiPaw.05G228800' => 'cil', 'CiPaw.05G230600' => 'cil', 'CiPaw.05G236500' => 'cil', 'CiPaw.05G244800' => 'cil', 'CiPaw.06G026600' => 'cil', 'CiPaw.06G027900' => 'cil', 'CiPaw.06G051800' => 'cil', 'CiPaw.06G128500' => 'cil', 'CiPaw.06G165900' => 'cil', 'CiPaw.07G045400' => 'cil', 'CiPaw.07G048000' => 'cil', 'CiPaw.07G052000' => 'cil', 'CiPaw.07G073800' => 'cil', 'CiPaw.07G099700' => 'cil', 'CiPaw.07G108700' => 'cil', 'CiPaw.07G120000' => 'cil', 'CiPaw.07G134100' => 'cil', 'CiPaw.07G147000' => 'cil', 'CiPaw.07G149700' => 'cil', 'CiPaw.07G178300' => 'cil', 'CiPaw.07G184900' => 'cil', 'CiPaw.08G044500' => 'cil', 'CiPaw.08G046900' => 'cil', 'CiPaw.08G047300' => 'cil', 'CiPaw.08G115400' => 'cil', 'CiPaw.08G134700' => 'cil', 'CiPaw.08G157400' => 'cil', 'CiPaw.09G014300' => 'cil', 'CiPaw.09G088900' => 'cil', 'CiPaw.09G130900' => 'cil', 'CiPaw.09G133100' => 'cil', 'CiPaw.09G151300' => 'cil', 'CiPaw.09G172800' => 'cil', 'CiPaw.09G174900' => 'cil', 'CiPaw.09G175000' => 'cil', 'CiPaw.10G012800' => 'cil', 'CiPaw.10G028800' => 'cil', 'CiPaw.10G044700' => 'cil', 'CiPaw.10G067400' => 'cil', 'CiPaw.10G115900' => 'cil', 'CiPaw.10G126200' => 'cil', 'CiPaw.10G139700' => 'cil', 'CiPaw.10G155100' => 'cil', 'CiPaw.11G011300' => 'cil', 'CiPaw.11G025900' => 'cil', 'CiPaw.11G104100' => 'cil', 'CiPaw.11G142700' => 'cil', 'CiPaw.11G164500' => 'cil', 'CiPaw.11G189100' => 'cil', 'CiPaw.11G197100' => 'cil', 'CiPaw.12G006100' => 'cil', 'CiPaw.12G038500' => 'cil', 'CiPaw.12G041400' => 'cil', 'CiPaw.12G041600' => 'cil', 'CiPaw.12G051300' => 'cil', 'CiPaw.12G101800' => 'cil', 'CiPaw.12G107800' => 'cil', 'CiPaw.13G033200' => 'cil', 'CiPaw.13G129900' => 'cil', 'CiPaw.13G160200' => 'cil', 'CiPaw.14G018900' => 'cil', 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'FAN04G2781' => 'fan', 'FAN05G1385' => 'fan', 'FAN05G3062' => 'fan', 'FAN08G2267' => 'fan', 'FAN10G0481' => 'fan', 'FAN10G1257' => 'fan', 'FAN14G0954' => 'fan', 'FAN14G2347' => 'fan', 'FAN15G0187' => 'fan', 'FAN25G2214' => 'fan', 'FvH4_1g21031' => 'fve', 'FvH4_3g16231' => 'fve', 'FvH4_3g26413' => 'fve', 'FvH4_3g29014' => 'fve', 'FvH4_3g31921' => 'fve', 'FvH4_4g19882' => 'fve', 'FvH4_5g21960' => 'fve', 'FvH4_5g29683' => 'fve', 'FvH4_7g13271' => 'fve', 'Glyma.01G062500' => 'gma', 'Glyma.07G140900' => 'gma', 'Glyma.09G140900' => 'gma', 'Glyma.12G112700' => 'gma', 'Glyma.17G168800' => 'gma', 'HanXRQChr01g0027001' => 'han', 'HanXRQChr04g0120511' => 'han', 'HanXRQChr08g0232381' => 'han', 'HanXRQChr09g0265661' => 'han', 'HanXRQChr13g0416031' => 'han', 'Haze_05835' => 'cav', 'Haze_06597' => 'cav', 'Haze_07921' => 'cav', 'Haze_08599' => 'cav', 'Haze_10686' => 'cav', 'Haze_12994' => 'cav', 'Haze_13466' => 'cav', 'Haze_16101' => 'cav', 'Haze_17766' => 'cav', 'Haze_18456' => 'cav', 'Haze_20229' => 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'Rhsim02G0189400' => 'rsi', 'Rhsim03G0135600' => 'rsi', 'Rhsim03G0149900' => 'rsi', 'Rhsim04G0125600' => 'rsi', 'Rhsim05G0091700' => 'rsi', 'Rhsim05G0092900' => 'rsi', 'Rhsim06G0075000' => 'rsi', 'Rhsim07G0066400' => 'rsi', 'Rhsim07G0156400' => 'rsi', 'Rhsim07G0182200' => 'rsi', 'Rhsim07G0182300' => 'rsi', 'Rhsim08G0180400' => 'rsi', 'Rhsim09G0056800' => 'rsi', 'Rhsim10G0153300' => 'rsi', 'Rhsim11G0012700' => 'rsi', 'Rhsim12G0031800' => 'rsi', 'Rhsim12G0055400' => 'rsi', 'Rhsim12G0091400' => 'rsi', 'Rhsim13G0070800' => 'rsi', 'Rhsim13G0193300' => 'rsi', 'RhsimUnG0111600' => 'rsi', 'RhsimUnG0137500' => 'rsi', 'RhsimUnG0172900' => 'rsi', 'SGA_v2.0_scaffold11G05878' => 'sas', 'SGA_v2.0_scaffold167G38458' => 'sas', 'SGA_v2.0_scaffold19G08588' => 'sas', 'SGA_v2.0_scaffold239G43990' => 'sas', 'SGA_v2.0_scaffold260G45865' => 'sas', 'SGA_v2.0_scaffold309G48177' => 'sas', 'SGA_v2.0_scaffold76G25122' => 'sas', 'SGA_v2.0_scaffold85G26708' => 'sas', 'SHI13914' => 'shi', 'SHI30402' => 'shi', 'TWI09G0020' => 'twi', 'TWI09G0456' => 'twi', 'TWI09G1572' => 'twi', 'TWI12G0266' => 'twi', 'TWI12G1451' => 'twi', 'TWI14G0851' => 'twi', 'TWI15G0796' => 'twi', 'TWI18G0820' => 'twi', 'TWI18G1152' => 'twi', 'TWI23G0007' => 'twi', 'TWI23G0314' => 'twi', 'TWI31G0674' => 'twi', 'TWI31G0938' => 'twi', 'TWI34G0641' => 'twi', 'TWI34G1527' => 'twi', 'TWI36G0193' => 'twi', 'TWI36G0405' => 'twi', 'TWI38G0892' => 'twi', 'TWI38G0936' => 'twi', 'TWI38G2218' => 'twi', 'TWI53G0679' => 'twi', 'TWI53G0863' => 'twi', 'TWI53G1133' => 'twi', 'TWI60G0823' => 'twi', 'TWI63G0919' => 'twi', 'TWI63G1436' => 'twi', 'TWI73G0140' => 'twi', 'TWI73G0419' => 'twi', 'TWI73G0420' => 'twi', 'TWI73G1276' => 'twi', 'TWI74G0405' => 'twi', 'TWI74G0837' => 'twi', 'TWI75G0594' => 'twi', 'TWI75G1615' => 'twi', 'TWI77G0816' => 'twi', 'vmacro03831' => 'vma', 'vmacro13746' => 'vma', 'vmacro16089' => 'vma', 'vmacro22863' => 'vma', 'Zm00001eb085790' => 'zma', 'Zm00001eb114250' => 'zma', 'Zm00001eb138070' => 'zma', 'Zm00001eb167560' => 'zma', 'Zm00001eb199990' => 'zma', 'Zm00001eb368180' => 'zma', 'Zm00001eb382470' => 'zma' ), 'gf_id' => 'HOM05D001576', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001576' ), 'data_identifier' => 'HOM05D001576', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001576', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '406', 'num_species' => '29' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'Aqoxy1G01456' => 'aox', 'Aqoxy1G02949' => 'aox', 'Aqoxy3G01274' => 'aox', 'Aqoxy3G02110' => 'aox', 'Aqoxy3G02268' => 'aox', 'Aqoxy5G02702' => 'aox', 'Aqoxy5G02988' => 'aox', 'Aqoxy5G03427' => 'aox', 'Aqoxy6G02363' => 'aox', 'Atru.chr1.3225' => 'acertr', 'Atru.chr8.1198' => 'acertr', 'Atru.chr9.790' => 'acertr', 'CANSAT01G3197' => 'cansat', 'Ciclev10003979m.g' => 'ccl', 'Ciclev10017471m.g' => 'ccl', 'Ciclev10018206m.g' => 'ccl', 'Ciclev10033751m.g' => 'ccl', 'CiPaw.01G000900' => 'cil', 'CiPaw.01G001000' => 'cil', 'CiPaw.01G033500' => 'cil', 'CiPaw.01G060300' => 'cil', 'CiPaw.01G070200' => 'cil', 'CiPaw.01G075100' => 'cil', 'CiPaw.01G084700' => 'cil', 'CiPaw.01G087900' => 'cil', 'CiPaw.01G092600' => 'cil', 'CiPaw.01G097200' => 'cil', 'CiPaw.01G098300' => 'cil', 'CiPaw.01G110200' => 'cil', 'CiPaw.01G118700' => 'cil', 'CiPaw.01G121200' => 'cil', 'CiPaw.01G132500' => 'cil', 'CiPaw.01G146900' => 'cil', 'CiPaw.01G174000' => 'cil', 'CiPaw.01G179900' => 'cil', 'CiPaw.01G183400' => 'cil', 'CiPaw.01G240000' => 'cil', 'CiPaw.01G283500' => 'cil', 'CiPaw.01G307400' => 'cil', 'CiPaw.02G030800' => 'cil', 'CiPaw.02G047200' => 'cil', 'CiPaw.02G050500' => 'cil', 'CiPaw.02G069900' => 'cil', 'CiPaw.02G091600' => 'cil', 'CiPaw.02G095000' => 'cil', 'CiPaw.02G131900' => 'cil', 'CiPaw.03G043000' => 'cil', 'CiPaw.03G069900' => 'cil', 'CiPaw.03G088100' => 'cil', 'CiPaw.03G089300' => 'cil', 'CiPaw.03G093100' => 'cil', 'CiPaw.03G129800' => 'cil', 'CiPaw.03G131200' => 'cil', 'CiPaw.03G134500' => 'cil', 'CiPaw.03G152100' => 'cil', 'CiPaw.03G162700' => 'cil', 'CiPaw.03G172800' => 'cil', 'CiPaw.03G175800' => 'cil', 'CiPaw.03G181800' => 'cil', 'CiPaw.03G191400' => 'cil', 'CiPaw.03G198300' => 'cil', 'CiPaw.03G201300' => 'cil', 'CiPaw.03G224700' => 'cil', 'CiPaw.03G225000' => 'cil', 'CiPaw.04G065100' => 'cil', 'CiPaw.04G080400' => 'cil', 'CiPaw.04G113500' => 'cil', 'CiPaw.04G121900' => 'cil', 'CiPaw.04G144100' => 'cil', 'CiPaw.04G176500' => 'cil', 'CiPaw.05G086200' => 'cil', 'CiPaw.05G100200' => 'cil', 'CiPaw.05G114200' => 'cil', 'CiPaw.05G126800' => 'cil', 'CiPaw.05G228800' => 'cil', 'CiPaw.05G230600' => 'cil', 'CiPaw.05G236500' => 'cil', 'CiPaw.05G244800' => 'cil', 'CiPaw.06G026600' => 'cil', 'CiPaw.06G027900' => 'cil', 'CiPaw.06G051800' => 'cil', 'CiPaw.06G128500' => 'cil', 'CiPaw.06G165900' => 'cil', 'CiPaw.07G045400' => 'cil', 'CiPaw.07G048000' => 'cil', 'CiPaw.07G052000' => 'cil', 'CiPaw.07G073800' => 'cil', 'CiPaw.07G099700' => 'cil', 'CiPaw.07G108700' => 'cil', 'CiPaw.07G120000' => 'cil', 'CiPaw.07G134100' => 'cil', 'CiPaw.07G147000' => 'cil', 'CiPaw.07G149700' => 'cil', 'CiPaw.07G178300' => 'cil', 'CiPaw.07G184900' => 'cil', 'CiPaw.08G044500' => 'cil', 'CiPaw.08G046900' => 'cil', 'CiPaw.08G047300' => 'cil', 'CiPaw.08G115400' => 'cil', 'CiPaw.08G134700' => 'cil', 'CiPaw.08G157400' => 'cil', 'CiPaw.09G014300' => 'cil', 'CiPaw.09G088900' => 'cil', 'CiPaw.09G130900' => 'cil', 'CiPaw.09G133100' => 'cil', 'CiPaw.09G151300' => 'cil', 'CiPaw.09G172800' => 'cil', 'CiPaw.09G174900' => 'cil', 'CiPaw.09G175000' => 'cil', 'CiPaw.10G012800' => 'cil', 'CiPaw.10G028800' => 'cil', 'CiPaw.10G044700' => 'cil', 'CiPaw.10G067400' => 'cil', 'CiPaw.10G115900' => 'cil', 'CiPaw.10G126200' => 'cil', 'CiPaw.10G139700' => 'cil', 'CiPaw.10G155100' => 'cil', 'CiPaw.11G011300' => 'cil', 'CiPaw.11G025900' => 'cil', 'CiPaw.11G104100' => 'cil', 'CiPaw.11G142700' => 'cil', 'CiPaw.11G164500' => 'cil', 'CiPaw.11G189100' => 'cil', 'CiPaw.11G197100' => 'cil', 'CiPaw.12G006100' => 'cil', 'CiPaw.12G038500' => 'cil', 'CiPaw.12G041400' => 'cil', 'CiPaw.12G041600' => 'cil', 'CiPaw.12G051300' => 'cil', 'CiPaw.12G101800' => 'cil', 'CiPaw.12G107800' => 'cil', 'CiPaw.13G033200' => 'cil', 'CiPaw.13G129900' => 'cil', 'CiPaw.13G160200' => 'cil', 'CiPaw.14G018900' => 'cil', 'CiPaw.14G029000' => 'cil', 'CiPaw.14G031000' => 'cil', 'CiPaw.14G032000' => 'cil', 'CiPaw.14G032300' => 'cil', 'CiPaw.14G040600' => 'cil', 'CiPaw.14G060500' => 'cil', 'CiPaw.14G061500' => 'cil', 'CiPaw.14G077500' => 'cil', 'CiPaw.14G088300' => 'cil', 'CiPaw.14G108500' => 'cil', 'CiPaw.14G121300' => 'cil', 'CiPaw.14G133000' => 'cil', 'CiPaw.14G134600' => 'cil', 'CiPaw.15G027200' => 'cil', 'CiPaw.15G037700' => 'cil', 'CiPaw.15G050900' => 'cil', 'CiPaw.15G067200' => 'cil', 'CiPaw.15G072000' => 'cil', 'CiPaw.15G112900' => 'cil', 'CiPaw.15G133200' => 'cil', 'CiPaw.15G139500' => 'cil', 'CiPaw.15G155400' => 'cil', 'CiPaw.16G006000' => 'cil', 'CiPaw.16G013100' => 'cil', 'CiPaw.16G047100' => 'cil', 'CiPaw.16G048900' => 'cil', 'CiPaw.16G070300' => 'cil', 'CSS0000195' => 'camsi', 'CSS0001664' => 'camsi', 'CSS0002566' => 'camsi', 'CSS0003077' => 'camsi', 'CSS0004257' => 'camsi', 'CSS0004495' => 'camsi', 'CSS0004599' => 'camsi', 'CSS0004943' => 'camsi', 'CSS0005302' => 'camsi', 'CSS0006274' => 'camsi', 'CSS0006547' => 'camsi', 'CSS0006860' => 'camsi', 'CSS0008814' => 'camsi', 'CSS0008946' => 'camsi', 'CSS0009093' => 'camsi', 'CSS0010221' => 'camsi', 'CSS0010296' => 'camsi', 'CSS0010386' => 'camsi', 'CSS0010831' => 'camsi', 'CSS0011061' => 'camsi', 'CSS0012008' => 'camsi', 'CSS0012194' => 'camsi', 'CSS0013580' => 'camsi', 'CSS0014176' => 'camsi', 'CSS0014280' => 'camsi', 'CSS0014799' => 'camsi', 'CSS0015368' => 'camsi', 'CSS0017473' => 'camsi', 'CSS0019281' => 'camsi', 'CSS0021320' => 'camsi', 'CSS0021750' => 'camsi', 'CSS0023642' => 'camsi', 'CSS0023792' => 'camsi', 'CSS0031528' => 'camsi', 'CSS0033894' => 'camsi', 'CSS0034959' => 'camsi', 'CSS0035632' => 'camsi', 'CSS0038450' => 'camsi', 'CSS0039293' => 'camsi', 'CSS0041053' => 'camsi', 'CSS0041981' => 'camsi', 'CSS0042573' => 'camsi', 'CSS0042927' => 'camsi', 'CSS0047725' => 'camsi', 'CSS0049636' => 'camsi', 'CSS0050513' => 'camsi', 'DCAR_030203' => 'dca', 'Dinv07939' => 'din', 'FAN01G0456' => 'fan', 'FAN02G3001' => 'fan', 'FAN04G2781' => 'fan', 'FAN05G1385' => 'fan', 'FAN05G3062' => 'fan', 'FAN08G2267' => 'fan', 'FAN10G0481' => 'fan', 'FAN10G1257' => 'fan', 'FAN14G0954' => 'fan', 'FAN14G2347' => 'fan', 'FAN15G0187' => 'fan', 'FAN25G2214' => 'fan', 'FvH4_1g21031' => 'fve', 'FvH4_3g16231' => 'fve', 'FvH4_3g26413' => 'fve', 'FvH4_3g29014' => 'fve', 'FvH4_3g31921' => 'fve', 'FvH4_4g19882' => 'fve', 'FvH4_5g21960' => 'fve', 'FvH4_5g29683' => 'fve', 'FvH4_7g13271' => 'fve', 'Glyma.01G062500' => 'gma', 'Glyma.07G140900' => 'gma', 'Glyma.09G140900' => 'gma', 'Glyma.12G112700' => 'gma', 'Glyma.17G168800' => 'gma', 'HanXRQChr01g0027001' => 'han', 'HanXRQChr04g0120511' => 'han', 'HanXRQChr08g0232381' => 'han', 'HanXRQChr09g0265661' => 'han', 'HanXRQChr13g0416031' => 'han', 'Haze_05835' => 'cav', 'Haze_06597' => 'cav', 'Haze_07921' => 'cav', 'Haze_08599' => 'cav', 'Haze_10686' => 'cav', 'Haze_12994' => 'cav', 'Haze_13466' => 'cav', 'Haze_16101' => 'cav', 'Haze_17766' => 'cav', 'Haze_18456' => 'cav', 'Haze_20229' => 'cav', 'Hma1.2p1_0324F.1_g125640' => 'hma', 'Hma1.2p1_0733F.1_g210230' => 'hma', 'Hma1.2p1_0921F.1_g236870' => 'hma', 'Hma1.2p1_1313F.1_g274940' => 'hma', 'Hma1.2p1_3059F.1_g332230' => 'hma', 'Hund15925' => 'sun', 'Hund19562' => 'sun', 'Hund21925' => 'sun', 'MD03G1177400' => 'mdo', 'MD07G1026100' => 'mdo', 'MD17G1218600' => 'mdo', 'Medtr0867s0010' => 'mtr', 'Medtr6g081150' => 'mtr', 'Os01g0527900' => 'osa', 'Os02g0463725' => 'osa', 'Os02g0785600' => 'osa', 'Os03g0433733' => 'osa', 'Os04g0286500' => 'osa', 'Os05g0227800' => 'osa', 'Os06g0521000' => 'osa', 'Os06g0635500' => 'osa', 'Os06g0660650' => 'osa', 'Os07g0554400' => 'osa', 'Os08g0225900' => 'osa', 'Os08g0561000' => 'osa', 'Os09g0241700' => 'osa', 'Os09g0351900' => 'osa', 'Os11g0220700' => 'osa', 'Os11g0282700' => 'osa', 'Os12g0169300' => 'osa', 'Os12g0228500' => 'osa', 'Os12g0543800' => 'osa', 'PGR044G1547' => 'pgr', 'Potri.005G239150' => 'ptr', 'Potri.010G014250' => 'ptr', 'Prupe.1G172500' => 'ppe', 'Prupe.1G196800' => 'ppe', 'Prupe.1G279700' => 'ppe', 'Prupe.2G026400' => 'ppe', 'Prupe.3G094000' => 'ppe', 'Prupe.4G287300' => 'ppe', 'QL01p022166' => 'qlo', 'QL01p051890' => 'qlo', 'QL02p009469' => 'qlo', 'QL02p046053' => 'qlo', 'QL02p057958' => 'qlo', 'QL02p093127' => 'qlo', 'QL03p006855' => 'qlo', 'QL03p071586' => 'qlo', 'QL04p000022' => 'qlo', 'QL04p000024' => 'qlo', 'QL04p003192' => 'qlo', 'QL05p011416' => 'qlo', 'QL06p039590' => 'qlo', 'QL06p052750' => 'qlo', 'QL06p053821' => 'qlo', 'QL07p025287' => 'qlo', 'QL09p033218' => 'qlo', 'QL09p040841' => 'qlo', 'QL10p020337' => 'qlo', 'QL10p027209' => 'qlo', 'QL10p027969' => 'qlo', 'QL10p048988' => 'qlo', 'QL11p001241' => 'qlo', 'QL11p028487' => 'qlo', 'RcHm_v2.0_Chr2g0105031' => 'rch', 'RcHm_v2.0_Chr2g0117811' => 'rch', 'RcHm_v2.0_Chr6g0270241' => 'rch', 'RcHm_v2.0_Chr7g0215961' => 'rch', 'RcHm_v2.0_Chr7g0231991' => 'rch', 'Rhsim01G0041500' => 'rsi', 'Rhsim01G0115000' => 'rsi', 'Rhsim01G0115400' => 'rsi', 'Rhsim01G0133600' => 'rsi', 'Rhsim01G0159900' => 'rsi', 'Rhsim02G0189400' => 'rsi', 'Rhsim03G0135600' => 'rsi', 'Rhsim03G0149900' => 'rsi', 'Rhsim04G0125600' => 'rsi', 'Rhsim05G0091700' => 'rsi', 'Rhsim05G0092900' => 'rsi', 'Rhsim06G0075000' => 'rsi', 'Rhsim07G0066400' => 'rsi', 'Rhsim07G0156400' => 'rsi', 'Rhsim07G0182200' => 'rsi', 'Rhsim07G0182300' => 'rsi', 'Rhsim08G0180400' => 'rsi', 'Rhsim09G0056800' => 'rsi', 'Rhsim10G0153300' => 'rsi', 'Rhsim11G0012700' => 'rsi', 'Rhsim12G0031800' => 'rsi', 'Rhsim12G0055400' => 'rsi', 'Rhsim12G0091400' => 'rsi', 'Rhsim13G0070800' => 'rsi', 'Rhsim13G0193300' => 'rsi', 'RhsimUnG0111600' => 'rsi', 'RhsimUnG0137500' => 'rsi', 'RhsimUnG0172900' => 'rsi', 'SGA_v2.0_scaffold11G05878' => 'sas', 'SGA_v2.0_scaffold167G38458' => 'sas', 'SGA_v2.0_scaffold19G08588' => 'sas', 'SGA_v2.0_scaffold239G43990' => 'sas', 'SGA_v2.0_scaffold260G45865' => 'sas', 'SGA_v2.0_scaffold309G48177' => 'sas', 'SGA_v2.0_scaffold76G25122' => 'sas', 'SGA_v2.0_scaffold85G26708' => 'sas', 'SHI13914' => 'shi', 'SHI30402' => 'shi', 'TWI09G0020' => 'twi', 'TWI09G0456' => 'twi', 'TWI09G1572' => 'twi', 'TWI12G0266' => 'twi', 'TWI12G1451' => 'twi', 'TWI14G0851' => 'twi', 'TWI15G0796' => 'twi', 'TWI18G0820' => 'twi', 'TWI18G1152' => 'twi', 'TWI23G0007' => 'twi', 'TWI23G0314' => 'twi', 'TWI31G0674' => 'twi', 'TWI31G0938' => 'twi', 'TWI34G0641' => 'twi', 'TWI34G1527' => 'twi', 'TWI36G0193' => 'twi', 'TWI36G0405' => 'twi', 'TWI38G0892' => 'twi', 'TWI38G0936' => 'twi', 'TWI38G2218' => 'twi', 'TWI53G0679' => 'twi', 'TWI53G0863' => 'twi', 'TWI53G1133' => 'twi', 'TWI60G0823' => 'twi', 'TWI63G0919' => 'twi', 'TWI63G1436' => 'twi', 'TWI73G0140' => 'twi', 'TWI73G0419' => 'twi', 'TWI73G0420' => 'twi', 'TWI73G1276' => 'twi', 'TWI74G0405' => 'twi', 'TWI74G0837' => 'twi', 'TWI75G0594' => 'twi', 'TWI75G1615' => 'twi', 'TWI77G0816' => 'twi', 'vmacro03831' => 'vma', 'vmacro13746' => 'vma', 'vmacro16089' => 'vma', 'vmacro22863' => 'vma', 'Zm00001eb085790' => 'zma', 'Zm00001eb114250' => 'zma', 'Zm00001eb138070' => 'zma', 'Zm00001eb167560' => 'zma', 'Zm00001eb199990' => 'zma', 'Zm00001eb368180' => 'zma', 'Zm00001eb382470' => 'zma' ) $gf_id = 'HOM05D001576' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001576' ) $data_identifier = 'HOM05D001576' $data_type = 'gf_id' $species_gene_counts = array( 'aox' => (int) 9, 'acertr' => (int) 3, 'cansat' => (int) 1, 'ccl' => (int) 4, 'cil' => (int) 145, 'camsi' => (int) 46, 'dca' => (int) 1, 'din' => (int) 1, 'fan' => (int) 12, 'fve' => (int) 9, 'gma' => (int) 5, 'han' => (int) 5, 'cav' => (int) 11, 'hma' => (int) 5, 'sun' => (int) 3, 'mdo' => (int) 3, 'mtr' => (int) 2, 'osa' => (int) 19, 'pgr' => (int) 1, 'ptr' => (int) 2, 'ppe' => (int) 6, 'qlo' => (int) 24, 'rch' => (int) 5, 'rsi' => (int) 28, 'sas' => (int) 8, 'shi' => (int) 2, 'twi' => (int) 35, 'vma' => (int) 4, 'zma' => (int) 7 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb382470' $species_info = array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ) $local_species = 'camsi' $disabled = '' $selected = '' $num_hits = (int) 0
Warning (2): count(): Parameter must be an array or an object that implements Countable [APP/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp, line 33]Code Context $disabled = (!array_key_exists($local_species,$species_gene_counts))?"disabled":""; $selected = (isset($selected_species) && array_key_exists($local_species,$selected_species))?"checked='checked'":""; $num_hits = (array_key_exists($local_species,$species_gene_counts))?count($species_gene_counts[$local_species]):0; $viewFile = '/www/bioinformatics01_ro/plaza/_dev_instances/feedback/app/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp' $dataForView = array( 'sidebar_info' => array( 'gf_id' => 'HOM05D001576', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '406', 'num_species' => '29' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'Aqoxy1G01456' => 'aox', 'Aqoxy1G02949' => 'aox', 'Aqoxy3G01274' => 'aox', 'Aqoxy3G02110' => 'aox', 'Aqoxy3G02268' => 'aox', 'Aqoxy5G02702' => 'aox', 'Aqoxy5G02988' => 'aox', 'Aqoxy5G03427' => 'aox', 'Aqoxy6G02363' => 'aox', 'Atru.chr1.3225' => 'acertr', 'Atru.chr8.1198' => 'acertr', 'Atru.chr9.790' => 'acertr', 'CANSAT01G3197' => 'cansat', 'Ciclev10003979m.g' => 'ccl', 'Ciclev10017471m.g' => 'ccl', 'Ciclev10018206m.g' => 'ccl', 'Ciclev10033751m.g' => 'ccl', 'CiPaw.01G000900' => 'cil', 'CiPaw.01G001000' => 'cil', 'CiPaw.01G033500' => 'cil', 'CiPaw.01G060300' => 'cil', 'CiPaw.01G070200' => 'cil', 'CiPaw.01G075100' => 'cil', 'CiPaw.01G084700' => 'cil', 'CiPaw.01G087900' => 'cil', 'CiPaw.01G092600' => 'cil', 'CiPaw.01G097200' => 'cil', 'CiPaw.01G098300' => 'cil', 'CiPaw.01G110200' => 'cil', 'CiPaw.01G118700' => 'cil', 'CiPaw.01G121200' => 'cil', 'CiPaw.01G132500' => 'cil', 'CiPaw.01G146900' => 'cil', 'CiPaw.01G174000' => 'cil', 'CiPaw.01G179900' => 'cil', 'CiPaw.01G183400' => 'cil', 'CiPaw.01G240000' => 'cil', 'CiPaw.01G283500' => 'cil', 'CiPaw.01G307400' => 'cil', 'CiPaw.02G030800' => 'cil', 'CiPaw.02G047200' => 'cil', 'CiPaw.02G050500' => 'cil', 'CiPaw.02G069900' => 'cil', 'CiPaw.02G091600' => 'cil', 'CiPaw.02G095000' => 'cil', 'CiPaw.02G131900' => 'cil', 'CiPaw.03G043000' => 'cil', 'CiPaw.03G069900' => 'cil', 'CiPaw.03G088100' => 'cil', 'CiPaw.03G089300' => 'cil', 'CiPaw.03G093100' => 'cil', 'CiPaw.03G129800' => 'cil', 'CiPaw.03G131200' => 'cil', 'CiPaw.03G134500' => 'cil', 'CiPaw.03G152100' => 'cil', 'CiPaw.03G162700' => 'cil', 'CiPaw.03G172800' => 'cil', 'CiPaw.03G175800' => 'cil', 'CiPaw.03G181800' => 'cil', 'CiPaw.03G191400' => 'cil', 'CiPaw.03G198300' => 'cil', 'CiPaw.03G201300' => 'cil', 'CiPaw.03G224700' => 'cil', 'CiPaw.03G225000' => 'cil', 'CiPaw.04G065100' => 'cil', 'CiPaw.04G080400' => 'cil', 'CiPaw.04G113500' => 'cil', 'CiPaw.04G121900' => 'cil', 'CiPaw.04G144100' => 'cil', 'CiPaw.04G176500' => 'cil', 'CiPaw.05G086200' => 'cil', 'CiPaw.05G100200' => 'cil', 'CiPaw.05G114200' => 'cil', 'CiPaw.05G126800' => 'cil', 'CiPaw.05G228800' => 'cil', 'CiPaw.05G230600' => 'cil', 'CiPaw.05G236500' => 'cil', 'CiPaw.05G244800' => 'cil', 'CiPaw.06G026600' => 'cil', 'CiPaw.06G027900' => 'cil', 'CiPaw.06G051800' => 'cil', 'CiPaw.06G128500' => 'cil', 'CiPaw.06G165900' => 'cil', 'CiPaw.07G045400' => 'cil', 'CiPaw.07G048000' => 'cil', 'CiPaw.07G052000' => 'cil', 'CiPaw.07G073800' => 'cil', 'CiPaw.07G099700' => 'cil', 'CiPaw.07G108700' => 'cil', 'CiPaw.07G120000' => 'cil', 'CiPaw.07G134100' => 'cil', 'CiPaw.07G147000' => 'cil', 'CiPaw.07G149700' => 'cil', 'CiPaw.07G178300' => 'cil', 'CiPaw.07G184900' => 'cil', 'CiPaw.08G044500' => 'cil', 'CiPaw.08G046900' => 'cil', 'CiPaw.08G047300' => 'cil', 'CiPaw.08G115400' => 'cil', 'CiPaw.08G134700' => 'cil', 'CiPaw.08G157400' => 'cil', 'CiPaw.09G014300' => 'cil', 'CiPaw.09G088900' => 'cil', 'CiPaw.09G130900' => 'cil', 'CiPaw.09G133100' => 'cil', 'CiPaw.09G151300' => 'cil', 'CiPaw.09G172800' => 'cil', 'CiPaw.09G174900' => 'cil', 'CiPaw.09G175000' => 'cil', 'CiPaw.10G012800' => 'cil', 'CiPaw.10G028800' => 'cil', 'CiPaw.10G044700' => 'cil', 'CiPaw.10G067400' => 'cil', 'CiPaw.10G115900' => 'cil', 'CiPaw.10G126200' => 'cil', 'CiPaw.10G139700' => 'cil', 'CiPaw.10G155100' => 'cil', 'CiPaw.11G011300' => 'cil', 'CiPaw.11G025900' => 'cil', 'CiPaw.11G104100' => 'cil', 'CiPaw.11G142700' => 'cil', 'CiPaw.11G164500' => 'cil', 'CiPaw.11G189100' => 'cil', 'CiPaw.11G197100' => 'cil', 'CiPaw.12G006100' => 'cil', 'CiPaw.12G038500' => 'cil', 'CiPaw.12G041400' => 'cil', 'CiPaw.12G041600' => 'cil', 'CiPaw.12G051300' => 'cil', 'CiPaw.12G101800' => 'cil', 'CiPaw.12G107800' => 'cil', 'CiPaw.13G033200' => 'cil', 'CiPaw.13G129900' => 'cil', 'CiPaw.13G160200' => 'cil', 'CiPaw.14G018900' => 'cil', 'CiPaw.14G029000' => 'cil', 'CiPaw.14G031000' => 'cil', 'CiPaw.14G032000' => 'cil', 'CiPaw.14G032300' => 'cil', 'CiPaw.14G040600' => 'cil', 'CiPaw.14G060500' => 'cil', 'CiPaw.14G061500' => 'cil', 'CiPaw.14G077500' => 'cil', 'CiPaw.14G088300' => 'cil', 'CiPaw.14G108500' => 'cil', 'CiPaw.14G121300' => 'cil', 'CiPaw.14G133000' => 'cil', 'CiPaw.14G134600' => 'cil', 'CiPaw.15G027200' => 'cil', 'CiPaw.15G037700' => 'cil', 'CiPaw.15G050900' => 'cil', 'CiPaw.15G067200' => 'cil', 'CiPaw.15G072000' => 'cil', 'CiPaw.15G112900' => 'cil', 'CiPaw.15G133200' => 'cil', 'CiPaw.15G139500' => 'cil', 'CiPaw.15G155400' => 'cil', 'CiPaw.16G006000' => 'cil', 'CiPaw.16G013100' => 'cil', 'CiPaw.16G047100' => 'cil', 'CiPaw.16G048900' => 'cil', 'CiPaw.16G070300' => 'cil', 'CSS0000195' => 'camsi', 'CSS0001664' => 'camsi', 'CSS0002566' => 'camsi', 'CSS0003077' => 'camsi', 'CSS0004257' => 'camsi', 'CSS0004495' => 'camsi', 'CSS0004599' => 'camsi', 'CSS0004943' => 'camsi', 'CSS0005302' => 'camsi', 'CSS0006274' => 'camsi', 'CSS0006547' => 'camsi', 'CSS0006860' => 'camsi', 'CSS0008814' => 'camsi', 'CSS0008946' => 'camsi', 'CSS0009093' => 'camsi', 'CSS0010221' => 'camsi', 'CSS0010296' => 'camsi', 'CSS0010386' => 'camsi', 'CSS0010831' => 'camsi', 'CSS0011061' => 'camsi', 'CSS0012008' => 'camsi', 'CSS0012194' => 'camsi', 'CSS0013580' => 'camsi', 'CSS0014176' => 'camsi', 'CSS0014280' => 'camsi', 'CSS0014799' => 'camsi', 'CSS0015368' => 'camsi', 'CSS0017473' => 'camsi', 'CSS0019281' => 'camsi', 'CSS0021320' => 'camsi', 'CSS0021750' => 'camsi', 'CSS0023642' => 'camsi', 'CSS0023792' => 'camsi', 'CSS0031528' => 'camsi', 'CSS0033894' => 'camsi', 'CSS0034959' => 'camsi', 'CSS0035632' => 'camsi', 'CSS0038450' => 'camsi', 'CSS0039293' => 'camsi', 'CSS0041053' => 'camsi', 'CSS0041981' => 'camsi', 'CSS0042573' => 'camsi', 'CSS0042927' => 'camsi', 'CSS0047725' => 'camsi', 'CSS0049636' => 'camsi', 'CSS0050513' => 'camsi', 'DCAR_030203' => 'dca', 'Dinv07939' => 'din', 'FAN01G0456' => 'fan', 'FAN02G3001' => 'fan', 'FAN04G2781' => 'fan', 'FAN05G1385' => 'fan', 'FAN05G3062' => 'fan', 'FAN08G2267' => 'fan', 'FAN10G0481' => 'fan', 'FAN10G1257' => 'fan', 'FAN14G0954' => 'fan', 'FAN14G2347' => 'fan', 'FAN15G0187' => 'fan', 'FAN25G2214' => 'fan', 'FvH4_1g21031' => 'fve', 'FvH4_3g16231' => 'fve', 'FvH4_3g26413' => 'fve', 'FvH4_3g29014' => 'fve', 'FvH4_3g31921' => 'fve', 'FvH4_4g19882' => 'fve', 'FvH4_5g21960' => 'fve', 'FvH4_5g29683' => 'fve', 'FvH4_7g13271' => 'fve', 'Glyma.01G062500' => 'gma', 'Glyma.07G140900' => 'gma', 'Glyma.09G140900' => 'gma', 'Glyma.12G112700' => 'gma', 'Glyma.17G168800' => 'gma', 'HanXRQChr01g0027001' => 'han', 'HanXRQChr04g0120511' => 'han', 'HanXRQChr08g0232381' => 'han', 'HanXRQChr09g0265661' => 'han', 'HanXRQChr13g0416031' => 'han', 'Haze_05835' => 'cav', 'Haze_06597' => 'cav', 'Haze_07921' => 'cav', 'Haze_08599' => 'cav', 'Haze_10686' => 'cav', 'Haze_12994' => 'cav', 'Haze_13466' => 'cav', 'Haze_16101' => 'cav', 'Haze_17766' => 'cav', 'Haze_18456' => 'cav', 'Haze_20229' => 'cav', 'Hma1.2p1_0324F.1_g125640' => 'hma', 'Hma1.2p1_0733F.1_g210230' => 'hma', 'Hma1.2p1_0921F.1_g236870' => 'hma', 'Hma1.2p1_1313F.1_g274940' => 'hma', 'Hma1.2p1_3059F.1_g332230' => 'hma', 'Hund15925' => 'sun', 'Hund19562' => 'sun', 'Hund21925' => 'sun', 'MD03G1177400' => 'mdo', 'MD07G1026100' => 'mdo', 'MD17G1218600' => 'mdo', 'Medtr0867s0010' => 'mtr', 'Medtr6g081150' => 'mtr', 'Os01g0527900' => 'osa', 'Os02g0463725' => 'osa', 'Os02g0785600' => 'osa', 'Os03g0433733' => 'osa', 'Os04g0286500' => 'osa', 'Os05g0227800' => 'osa', 'Os06g0521000' => 'osa', 'Os06g0635500' => 'osa', 'Os06g0660650' => 'osa', 'Os07g0554400' => 'osa', 'Os08g0225900' => 'osa', 'Os08g0561000' => 'osa', 'Os09g0241700' => 'osa', 'Os09g0351900' => 'osa', 'Os11g0220700' => 'osa', 'Os11g0282700' => 'osa', 'Os12g0169300' => 'osa', 'Os12g0228500' => 'osa', 'Os12g0543800' => 'osa', 'PGR044G1547' => 'pgr', 'Potri.005G239150' => 'ptr', 'Potri.010G014250' => 'ptr', 'Prupe.1G172500' => 'ppe', 'Prupe.1G196800' => 'ppe', 'Prupe.1G279700' => 'ppe', 'Prupe.2G026400' => 'ppe', 'Prupe.3G094000' => 'ppe', 'Prupe.4G287300' => 'ppe', 'QL01p022166' => 'qlo', 'QL01p051890' => 'qlo', 'QL02p009469' => 'qlo', 'QL02p046053' => 'qlo', 'QL02p057958' => 'qlo', 'QL02p093127' => 'qlo', 'QL03p006855' => 'qlo', 'QL03p071586' => 'qlo', 'QL04p000022' => 'qlo', 'QL04p000024' => 'qlo', 'QL04p003192' => 'qlo', 'QL05p011416' => 'qlo', 'QL06p039590' => 'qlo', 'QL06p052750' => 'qlo', 'QL06p053821' => 'qlo', 'QL07p025287' => 'qlo', 'QL09p033218' => 'qlo', 'QL09p040841' => 'qlo', 'QL10p020337' => 'qlo', 'QL10p027209' => 'qlo', 'QL10p027969' => 'qlo', 'QL10p048988' => 'qlo', 'QL11p001241' => 'qlo', 'QL11p028487' => 'qlo', 'RcHm_v2.0_Chr2g0105031' => 'rch', 'RcHm_v2.0_Chr2g0117811' => 'rch', 'RcHm_v2.0_Chr6g0270241' => 'rch', 'RcHm_v2.0_Chr7g0215961' => 'rch', 'RcHm_v2.0_Chr7g0231991' => 'rch', 'Rhsim01G0041500' => 'rsi', 'Rhsim01G0115000' => 'rsi', 'Rhsim01G0115400' => 'rsi', 'Rhsim01G0133600' => 'rsi', 'Rhsim01G0159900' => 'rsi', 'Rhsim02G0189400' => 'rsi', 'Rhsim03G0135600' => 'rsi', 'Rhsim03G0149900' => 'rsi', 'Rhsim04G0125600' => 'rsi', 'Rhsim05G0091700' => 'rsi', 'Rhsim05G0092900' => 'rsi', 'Rhsim06G0075000' => 'rsi', 'Rhsim07G0066400' => 'rsi', 'Rhsim07G0156400' => 'rsi', 'Rhsim07G0182200' => 'rsi', 'Rhsim07G0182300' => 'rsi', 'Rhsim08G0180400' => 'rsi', 'Rhsim09G0056800' => 'rsi', 'Rhsim10G0153300' => 'rsi', 'Rhsim11G0012700' => 'rsi', 'Rhsim12G0031800' => 'rsi', 'Rhsim12G0055400' => 'rsi', 'Rhsim12G0091400' => 'rsi', 'Rhsim13G0070800' => 'rsi', 'Rhsim13G0193300' => 'rsi', 'RhsimUnG0111600' => 'rsi', 'RhsimUnG0137500' => 'rsi', 'RhsimUnG0172900' => 'rsi', 'SGA_v2.0_scaffold11G05878' => 'sas', 'SGA_v2.0_scaffold167G38458' => 'sas', 'SGA_v2.0_scaffold19G08588' => 'sas', 'SGA_v2.0_scaffold239G43990' => 'sas', 'SGA_v2.0_scaffold260G45865' => 'sas', 'SGA_v2.0_scaffold309G48177' => 'sas', 'SGA_v2.0_scaffold76G25122' => 'sas', 'SGA_v2.0_scaffold85G26708' => 'sas', 'SHI13914' => 'shi', 'SHI30402' => 'shi', 'TWI09G0020' => 'twi', 'TWI09G0456' => 'twi', 'TWI09G1572' => 'twi', 'TWI12G0266' => 'twi', 'TWI12G1451' => 'twi', 'TWI14G0851' => 'twi', 'TWI15G0796' => 'twi', 'TWI18G0820' => 'twi', 'TWI18G1152' => 'twi', 'TWI23G0007' => 'twi', 'TWI23G0314' => 'twi', 'TWI31G0674' => 'twi', 'TWI31G0938' => 'twi', 'TWI34G0641' => 'twi', 'TWI34G1527' => 'twi', 'TWI36G0193' => 'twi', 'TWI36G0405' => 'twi', 'TWI38G0892' => 'twi', 'TWI38G0936' => 'twi', 'TWI38G2218' => 'twi', 'TWI53G0679' => 'twi', 'TWI53G0863' => 'twi', 'TWI53G1133' => 'twi', 'TWI60G0823' => 'twi', 'TWI63G0919' => 'twi', 'TWI63G1436' => 'twi', 'TWI73G0140' => 'twi', 'TWI73G0419' => 'twi', 'TWI73G0420' => 'twi', 'TWI73G1276' => 'twi', 'TWI74G0405' => 'twi', 'TWI74G0837' => 'twi', 'TWI75G0594' => 'twi', 'TWI75G1615' => 'twi', 'TWI77G0816' => 'twi', 'vmacro03831' => 'vma', 'vmacro13746' => 'vma', 'vmacro16089' => 'vma', 'vmacro22863' => 'vma', 'Zm00001eb085790' => 'zma', 'Zm00001eb114250' => 'zma', 'Zm00001eb138070' => 'zma', 'Zm00001eb167560' => 'zma', 'Zm00001eb199990' => 'zma', 'Zm00001eb368180' => 'zma', 'Zm00001eb382470' => 'zma' ), 'gf_id' => 'HOM05D001576', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001576' ), 'data_identifier' => 'HOM05D001576', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001576', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '406', 'num_species' => '29' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'Aqoxy1G01456' => 'aox', 'Aqoxy1G02949' => 'aox', 'Aqoxy3G01274' => 'aox', 'Aqoxy3G02110' => 'aox', 'Aqoxy3G02268' => 'aox', 'Aqoxy5G02702' => 'aox', 'Aqoxy5G02988' => 'aox', 'Aqoxy5G03427' => 'aox', 'Aqoxy6G02363' => 'aox', 'Atru.chr1.3225' => 'acertr', 'Atru.chr8.1198' => 'acertr', 'Atru.chr9.790' => 'acertr', 'CANSAT01G3197' => 'cansat', 'Ciclev10003979m.g' => 'ccl', 'Ciclev10017471m.g' => 'ccl', 'Ciclev10018206m.g' => 'ccl', 'Ciclev10033751m.g' => 'ccl', 'CiPaw.01G000900' => 'cil', 'CiPaw.01G001000' => 'cil', 'CiPaw.01G033500' => 'cil', 'CiPaw.01G060300' => 'cil', 'CiPaw.01G070200' => 'cil', 'CiPaw.01G075100' => 'cil', 'CiPaw.01G084700' => 'cil', 'CiPaw.01G087900' => 'cil', 'CiPaw.01G092600' => 'cil', 'CiPaw.01G097200' => 'cil', 'CiPaw.01G098300' => 'cil', 'CiPaw.01G110200' => 'cil', 'CiPaw.01G118700' => 'cil', 'CiPaw.01G121200' => 'cil', 'CiPaw.01G132500' => 'cil', 'CiPaw.01G146900' => 'cil', 'CiPaw.01G174000' => 'cil', 'CiPaw.01G179900' => 'cil', 'CiPaw.01G183400' => 'cil', 'CiPaw.01G240000' => 'cil', 'CiPaw.01G283500' => 'cil', 'CiPaw.01G307400' => 'cil', 'CiPaw.02G030800' => 'cil', 'CiPaw.02G047200' => 'cil', 'CiPaw.02G050500' => 'cil', 'CiPaw.02G069900' => 'cil', 'CiPaw.02G091600' => 'cil', 'CiPaw.02G095000' => 'cil', 'CiPaw.02G131900' => 'cil', 'CiPaw.03G043000' => 'cil', 'CiPaw.03G069900' => 'cil', 'CiPaw.03G088100' => 'cil', 'CiPaw.03G089300' => 'cil', 'CiPaw.03G093100' => 'cil', 'CiPaw.03G129800' => 'cil', 'CiPaw.03G131200' => 'cil', 'CiPaw.03G134500' => 'cil', 'CiPaw.03G152100' => 'cil', 'CiPaw.03G162700' => 'cil', 'CiPaw.03G172800' => 'cil', 'CiPaw.03G175800' => 'cil', 'CiPaw.03G181800' => 'cil', 'CiPaw.03G191400' => 'cil', 'CiPaw.03G198300' => 'cil', 'CiPaw.03G201300' => 'cil', 'CiPaw.03G224700' => 'cil', 'CiPaw.03G225000' => 'cil', 'CiPaw.04G065100' => 'cil', 'CiPaw.04G080400' => 'cil', 'CiPaw.04G113500' => 'cil', 'CiPaw.04G121900' => 'cil', 'CiPaw.04G144100' => 'cil', 'CiPaw.04G176500' => 'cil', 'CiPaw.05G086200' => 'cil', 'CiPaw.05G100200' => 'cil', 'CiPaw.05G114200' => 'cil', 'CiPaw.05G126800' => 'cil', 'CiPaw.05G228800' => 'cil', 'CiPaw.05G230600' => 'cil', 'CiPaw.05G236500' => 'cil', 'CiPaw.05G244800' => 'cil', 'CiPaw.06G026600' => 'cil', 'CiPaw.06G027900' => 'cil', 'CiPaw.06G051800' => 'cil', 'CiPaw.06G128500' => 'cil', 'CiPaw.06G165900' => 'cil', 'CiPaw.07G045400' => 'cil', 'CiPaw.07G048000' => 'cil', 'CiPaw.07G052000' => 'cil', 'CiPaw.07G073800' => 'cil', 'CiPaw.07G099700' => 'cil', 'CiPaw.07G108700' => 'cil', 'CiPaw.07G120000' => 'cil', 'CiPaw.07G134100' => 'cil', 'CiPaw.07G147000' => 'cil', 'CiPaw.07G149700' => 'cil', 'CiPaw.07G178300' => 'cil', 'CiPaw.07G184900' => 'cil', 'CiPaw.08G044500' => 'cil', 'CiPaw.08G046900' => 'cil', 'CiPaw.08G047300' => 'cil', 'CiPaw.08G115400' => 'cil', 'CiPaw.08G134700' => 'cil', 'CiPaw.08G157400' => 'cil', 'CiPaw.09G014300' => 'cil', 'CiPaw.09G088900' => 'cil', 'CiPaw.09G130900' => 'cil', 'CiPaw.09G133100' => 'cil', 'CiPaw.09G151300' => 'cil', 'CiPaw.09G172800' => 'cil', 'CiPaw.09G174900' => 'cil', 'CiPaw.09G175000' => 'cil', 'CiPaw.10G012800' => 'cil', 'CiPaw.10G028800' => 'cil', 'CiPaw.10G044700' => 'cil', 'CiPaw.10G067400' => 'cil', 'CiPaw.10G115900' => 'cil', 'CiPaw.10G126200' => 'cil', 'CiPaw.10G139700' => 'cil', 'CiPaw.10G155100' => 'cil', 'CiPaw.11G011300' => 'cil', 'CiPaw.11G025900' => 'cil', 'CiPaw.11G104100' => 'cil', 'CiPaw.11G142700' => 'cil', 'CiPaw.11G164500' => 'cil', 'CiPaw.11G189100' => 'cil', 'CiPaw.11G197100' => 'cil', 'CiPaw.12G006100' => 'cil', 'CiPaw.12G038500' => 'cil', 'CiPaw.12G041400' => 'cil', 'CiPaw.12G041600' => 'cil', 'CiPaw.12G051300' => 'cil', 'CiPaw.12G101800' => 'cil', 'CiPaw.12G107800' => 'cil', 'CiPaw.13G033200' => 'cil', 'CiPaw.13G129900' => 'cil', 'CiPaw.13G160200' => 'cil', 'CiPaw.14G018900' => 'cil', 'CiPaw.14G029000' => 'cil', 'CiPaw.14G031000' => 'cil', 'CiPaw.14G032000' => 'cil', 'CiPaw.14G032300' => 'cil', 'CiPaw.14G040600' => 'cil', 'CiPaw.14G060500' => 'cil', 'CiPaw.14G061500' => 'cil', 'CiPaw.14G077500' => 'cil', 'CiPaw.14G088300' => 'cil', 'CiPaw.14G108500' => 'cil', 'CiPaw.14G121300' => 'cil', 'CiPaw.14G133000' => 'cil', 'CiPaw.14G134600' => 'cil', 'CiPaw.15G027200' => 'cil', 'CiPaw.15G037700' => 'cil', 'CiPaw.15G050900' => 'cil', 'CiPaw.15G067200' => 'cil', 'CiPaw.15G072000' => 'cil', 'CiPaw.15G112900' => 'cil', 'CiPaw.15G133200' => 'cil', 'CiPaw.15G139500' => 'cil', 'CiPaw.15G155400' => 'cil', 'CiPaw.16G006000' => 'cil', 'CiPaw.16G013100' => 'cil', 'CiPaw.16G047100' => 'cil', 'CiPaw.16G048900' => 'cil', 'CiPaw.16G070300' => 'cil', 'CSS0000195' => 'camsi', 'CSS0001664' => 'camsi', 'CSS0002566' => 'camsi', 'CSS0003077' => 'camsi', 'CSS0004257' => 'camsi', 'CSS0004495' => 'camsi', 'CSS0004599' => 'camsi', 'CSS0004943' => 'camsi', 'CSS0005302' => 'camsi', 'CSS0006274' => 'camsi', 'CSS0006547' => 'camsi', 'CSS0006860' => 'camsi', 'CSS0008814' => 'camsi', 'CSS0008946' => 'camsi', 'CSS0009093' => 'camsi', 'CSS0010221' => 'camsi', 'CSS0010296' => 'camsi', 'CSS0010386' => 'camsi', 'CSS0010831' => 'camsi', 'CSS0011061' => 'camsi', 'CSS0012008' => 'camsi', 'CSS0012194' => 'camsi', 'CSS0013580' => 'camsi', 'CSS0014176' => 'camsi', 'CSS0014280' => 'camsi', 'CSS0014799' => 'camsi', 'CSS0015368' => 'camsi', 'CSS0017473' => 'camsi', 'CSS0019281' => 'camsi', 'CSS0021320' => 'camsi', 'CSS0021750' => 'camsi', 'CSS0023642' => 'camsi', 'CSS0023792' => 'camsi', 'CSS0031528' => 'camsi', 'CSS0033894' => 'camsi', 'CSS0034959' => 'camsi', 'CSS0035632' => 'camsi', 'CSS0038450' => 'camsi', 'CSS0039293' => 'camsi', 'CSS0041053' => 'camsi', 'CSS0041981' => 'camsi', 'CSS0042573' => 'camsi', 'CSS0042927' => 'camsi', 'CSS0047725' => 'camsi', 'CSS0049636' => 'camsi', 'CSS0050513' => 'camsi', 'DCAR_030203' => 'dca', 'Dinv07939' => 'din', 'FAN01G0456' => 'fan', 'FAN02G3001' => 'fan', 'FAN04G2781' => 'fan', 'FAN05G1385' => 'fan', 'FAN05G3062' => 'fan', 'FAN08G2267' => 'fan', 'FAN10G0481' => 'fan', 'FAN10G1257' => 'fan', 'FAN14G0954' => 'fan', 'FAN14G2347' => 'fan', 'FAN15G0187' => 'fan', 'FAN25G2214' => 'fan', 'FvH4_1g21031' => 'fve', 'FvH4_3g16231' => 'fve', 'FvH4_3g26413' => 'fve', 'FvH4_3g29014' => 'fve', 'FvH4_3g31921' => 'fve', 'FvH4_4g19882' => 'fve', 'FvH4_5g21960' => 'fve', 'FvH4_5g29683' => 'fve', 'FvH4_7g13271' => 'fve', 'Glyma.01G062500' => 'gma', 'Glyma.07G140900' => 'gma', 'Glyma.09G140900' => 'gma', 'Glyma.12G112700' => 'gma', 'Glyma.17G168800' => 'gma', 'HanXRQChr01g0027001' => 'han', 'HanXRQChr04g0120511' => 'han', 'HanXRQChr08g0232381' => 'han', 'HanXRQChr09g0265661' => 'han', 'HanXRQChr13g0416031' => 'han', 'Haze_05835' => 'cav', 'Haze_06597' => 'cav', 'Haze_07921' => 'cav', 'Haze_08599' => 'cav', 'Haze_10686' => 'cav', 'Haze_12994' => 'cav', 'Haze_13466' => 'cav', 'Haze_16101' => 'cav', 'Haze_17766' => 'cav', 'Haze_18456' => 'cav', 'Haze_20229' => 'cav', 'Hma1.2p1_0324F.1_g125640' => 'hma', 'Hma1.2p1_0733F.1_g210230' => 'hma', 'Hma1.2p1_0921F.1_g236870' => 'hma', 'Hma1.2p1_1313F.1_g274940' => 'hma', 'Hma1.2p1_3059F.1_g332230' => 'hma', 'Hund15925' => 'sun', 'Hund19562' => 'sun', 'Hund21925' => 'sun', 'MD03G1177400' => 'mdo', 'MD07G1026100' => 'mdo', 'MD17G1218600' => 'mdo', 'Medtr0867s0010' => 'mtr', 'Medtr6g081150' => 'mtr', 'Os01g0527900' => 'osa', 'Os02g0463725' => 'osa', 'Os02g0785600' => 'osa', 'Os03g0433733' => 'osa', 'Os04g0286500' => 'osa', 'Os05g0227800' => 'osa', 'Os06g0521000' => 'osa', 'Os06g0635500' => 'osa', 'Os06g0660650' => 'osa', 'Os07g0554400' => 'osa', 'Os08g0225900' => 'osa', 'Os08g0561000' => 'osa', 'Os09g0241700' => 'osa', 'Os09g0351900' => 'osa', 'Os11g0220700' => 'osa', 'Os11g0282700' => 'osa', 'Os12g0169300' => 'osa', 'Os12g0228500' => 'osa', 'Os12g0543800' => 'osa', 'PGR044G1547' => 'pgr', 'Potri.005G239150' => 'ptr', 'Potri.010G014250' => 'ptr', 'Prupe.1G172500' => 'ppe', 'Prupe.1G196800' => 'ppe', 'Prupe.1G279700' => 'ppe', 'Prupe.2G026400' => 'ppe', 'Prupe.3G094000' => 'ppe', 'Prupe.4G287300' => 'ppe', 'QL01p022166' => 'qlo', 'QL01p051890' => 'qlo', 'QL02p009469' => 'qlo', 'QL02p046053' => 'qlo', 'QL02p057958' => 'qlo', 'QL02p093127' => 'qlo', 'QL03p006855' => 'qlo', 'QL03p071586' => 'qlo', 'QL04p000022' => 'qlo', 'QL04p000024' => 'qlo', 'QL04p003192' => 'qlo', 'QL05p011416' => 'qlo', 'QL06p039590' => 'qlo', 'QL06p052750' => 'qlo', 'QL06p053821' => 'qlo', 'QL07p025287' => 'qlo', 'QL09p033218' => 'qlo', 'QL09p040841' => 'qlo', 'QL10p020337' => 'qlo', 'QL10p027209' => 'qlo', 'QL10p027969' => 'qlo', 'QL10p048988' => 'qlo', 'QL11p001241' => 'qlo', 'QL11p028487' => 'qlo', 'RcHm_v2.0_Chr2g0105031' => 'rch', 'RcHm_v2.0_Chr2g0117811' => 'rch', 'RcHm_v2.0_Chr6g0270241' => 'rch', 'RcHm_v2.0_Chr7g0215961' => 'rch', 'RcHm_v2.0_Chr7g0231991' => 'rch', 'Rhsim01G0041500' => 'rsi', 'Rhsim01G0115000' => 'rsi', 'Rhsim01G0115400' => 'rsi', 'Rhsim01G0133600' => 'rsi', 'Rhsim01G0159900' => 'rsi', 'Rhsim02G0189400' => 'rsi', 'Rhsim03G0135600' => 'rsi', 'Rhsim03G0149900' => 'rsi', 'Rhsim04G0125600' => 'rsi', 'Rhsim05G0091700' => 'rsi', 'Rhsim05G0092900' => 'rsi', 'Rhsim06G0075000' => 'rsi', 'Rhsim07G0066400' => 'rsi', 'Rhsim07G0156400' => 'rsi', 'Rhsim07G0182200' => 'rsi', 'Rhsim07G0182300' => 'rsi', 'Rhsim08G0180400' => 'rsi', 'Rhsim09G0056800' => 'rsi', 'Rhsim10G0153300' => 'rsi', 'Rhsim11G0012700' => 'rsi', 'Rhsim12G0031800' => 'rsi', 'Rhsim12G0055400' => 'rsi', 'Rhsim12G0091400' => 'rsi', 'Rhsim13G0070800' => 'rsi', 'Rhsim13G0193300' => 'rsi', 'RhsimUnG0111600' => 'rsi', 'RhsimUnG0137500' => 'rsi', 'RhsimUnG0172900' => 'rsi', 'SGA_v2.0_scaffold11G05878' => 'sas', 'SGA_v2.0_scaffold167G38458' => 'sas', 'SGA_v2.0_scaffold19G08588' => 'sas', 'SGA_v2.0_scaffold239G43990' => 'sas', 'SGA_v2.0_scaffold260G45865' => 'sas', 'SGA_v2.0_scaffold309G48177' => 'sas', 'SGA_v2.0_scaffold76G25122' => 'sas', 'SGA_v2.0_scaffold85G26708' => 'sas', 'SHI13914' => 'shi', 'SHI30402' => 'shi', 'TWI09G0020' => 'twi', 'TWI09G0456' => 'twi', 'TWI09G1572' => 'twi', 'TWI12G0266' => 'twi', 'TWI12G1451' => 'twi', 'TWI14G0851' => 'twi', 'TWI15G0796' => 'twi', 'TWI18G0820' => 'twi', 'TWI18G1152' => 'twi', 'TWI23G0007' => 'twi', 'TWI23G0314' => 'twi', 'TWI31G0674' => 'twi', 'TWI31G0938' => 'twi', 'TWI34G0641' => 'twi', 'TWI34G1527' => 'twi', 'TWI36G0193' => 'twi', 'TWI36G0405' => 'twi', 'TWI38G0892' => 'twi', 'TWI38G0936' => 'twi', 'TWI38G2218' => 'twi', 'TWI53G0679' => 'twi', 'TWI53G0863' => 'twi', 'TWI53G1133' => 'twi', 'TWI60G0823' => 'twi', 'TWI63G0919' => 'twi', 'TWI63G1436' => 'twi', 'TWI73G0140' => 'twi', 'TWI73G0419' => 'twi', 'TWI73G0420' => 'twi', 'TWI73G1276' => 'twi', 'TWI74G0405' => 'twi', 'TWI74G0837' => 'twi', 'TWI75G0594' => 'twi', 'TWI75G1615' => 'twi', 'TWI77G0816' => 'twi', 'vmacro03831' => 'vma', 'vmacro13746' => 'vma', 'vmacro16089' => 'vma', 'vmacro22863' => 'vma', 'Zm00001eb085790' => 'zma', 'Zm00001eb114250' => 'zma', 'Zm00001eb138070' => 'zma', 'Zm00001eb167560' => 'zma', 'Zm00001eb199990' => 'zma', 'Zm00001eb368180' => 'zma', 'Zm00001eb382470' => 'zma' ) $gf_id = 'HOM05D001576' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001576' ) $data_identifier = 'HOM05D001576' $data_type = 'gf_id' $species_gene_counts = array( 'aox' => (int) 9, 'acertr' => (int) 3, 'cansat' => (int) 1, 'ccl' => (int) 4, 'cil' => (int) 145, 'camsi' => (int) 46, 'dca' => (int) 1, 'din' => (int) 1, 'fan' => (int) 12, 'fve' => (int) 9, 'gma' => (int) 5, 'han' => (int) 5, 'cav' => (int) 11, 'hma' => (int) 5, 'sun' => (int) 3, 'mdo' => (int) 3, 'mtr' => (int) 2, 'osa' => (int) 19, 'pgr' => (int) 1, 'ptr' => (int) 2, 'ppe' => (int) 6, 'qlo' => (int) 24, 'rch' => (int) 5, 'rsi' => (int) 28, 'sas' => (int) 8, 'shi' => (int) 2, 'twi' => (int) 35, 'vma' => (int) 4, 'zma' => (int) 7 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb382470' $species_info = array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ) $local_species = 'cansat' $disabled = '' $selected = '' $num_hits = (int) 1include - APP/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp, line 33 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933 View::_renderElement() - CORE/Cake/View/View.php, line 1224 View::element() - CORE/Cake/View/View.php, line 418 include - APP/View/Elements/analysis/phylogenetics_module/gf_data_settings.ctp, line 37 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933 View::_renderElement() - CORE/Cake/View/View.php, line 1224 View::element() - CORE/Cake/View/View.php, line 418 include - APP/View/Elements/analysis/phylogenetics_module/parameter_selection.ctp, line 64 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933 View::_renderElement() - CORE/Cake/View/View.php, line 1224 View::element() - CORE/Cake/View/View.php, line 418 include - APP/View/Analysis/custom_tree_creation.ctp, line 27 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933
$viewFile = '/www/bioinformatics01_ro/plaza/_dev_instances/feedback/app/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp' $dataForView = array( 'sidebar_info' => array( 'gf_id' => 'HOM05D001576', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '406', 'num_species' => '29' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'Aqoxy1G01456' => 'aox', 'Aqoxy1G02949' => 'aox', 'Aqoxy3G01274' => 'aox', 'Aqoxy3G02110' => 'aox', 'Aqoxy3G02268' => 'aox', 'Aqoxy5G02702' => 'aox', 'Aqoxy5G02988' => 'aox', 'Aqoxy5G03427' => 'aox', 'Aqoxy6G02363' => 'aox', 'Atru.chr1.3225' => 'acertr', 'Atru.chr8.1198' => 'acertr', 'Atru.chr9.790' => 'acertr', 'CANSAT01G3197' => 'cansat', 'Ciclev10003979m.g' => 'ccl', 'Ciclev10017471m.g' => 'ccl', 'Ciclev10018206m.g' => 'ccl', 'Ciclev10033751m.g' => 'ccl', 'CiPaw.01G000900' => 'cil', 'CiPaw.01G001000' => 'cil', 'CiPaw.01G033500' => 'cil', 'CiPaw.01G060300' => 'cil', 'CiPaw.01G070200' => 'cil', 'CiPaw.01G075100' => 'cil', 'CiPaw.01G084700' => 'cil', 'CiPaw.01G087900' => 'cil', 'CiPaw.01G092600' => 'cil', 'CiPaw.01G097200' => 'cil', 'CiPaw.01G098300' => 'cil', 'CiPaw.01G110200' => 'cil', 'CiPaw.01G118700' => 'cil', 'CiPaw.01G121200' => 'cil', 'CiPaw.01G132500' => 'cil', 'CiPaw.01G146900' => 'cil', 'CiPaw.01G174000' => 'cil', 'CiPaw.01G179900' => 'cil', 'CiPaw.01G183400' => 'cil', 'CiPaw.01G240000' => 'cil', 'CiPaw.01G283500' => 'cil', 'CiPaw.01G307400' => 'cil', 'CiPaw.02G030800' => 'cil', 'CiPaw.02G047200' => 'cil', 'CiPaw.02G050500' => 'cil', 'CiPaw.02G069900' => 'cil', 'CiPaw.02G091600' => 'cil', 'CiPaw.02G095000' => 'cil', 'CiPaw.02G131900' => 'cil', 'CiPaw.03G043000' => 'cil', 'CiPaw.03G069900' => 'cil', 'CiPaw.03G088100' => 'cil', 'CiPaw.03G089300' => 'cil', 'CiPaw.03G093100' => 'cil', 'CiPaw.03G129800' => 'cil', 'CiPaw.03G131200' => 'cil', 'CiPaw.03G134500' => 'cil', 'CiPaw.03G152100' => 'cil', 'CiPaw.03G162700' => 'cil', 'CiPaw.03G172800' => 'cil', 'CiPaw.03G175800' => 'cil', 'CiPaw.03G181800' => 'cil', 'CiPaw.03G191400' => 'cil', 'CiPaw.03G198300' => 'cil', 'CiPaw.03G201300' => 'cil', 'CiPaw.03G224700' => 'cil', 'CiPaw.03G225000' => 'cil', 'CiPaw.04G065100' => 'cil', 'CiPaw.04G080400' => 'cil', 'CiPaw.04G113500' => 'cil', 'CiPaw.04G121900' => 'cil', 'CiPaw.04G144100' => 'cil', 'CiPaw.04G176500' => 'cil', 'CiPaw.05G086200' => 'cil', 'CiPaw.05G100200' => 'cil', 'CiPaw.05G114200' => 'cil', 'CiPaw.05G126800' => 'cil', 'CiPaw.05G228800' => 'cil', 'CiPaw.05G230600' => 'cil', 'CiPaw.05G236500' => 'cil', 'CiPaw.05G244800' => 'cil', 'CiPaw.06G026600' => 'cil', 'CiPaw.06G027900' => 'cil', 'CiPaw.06G051800' => 'cil', 'CiPaw.06G128500' => 'cil', 'CiPaw.06G165900' => 'cil', 'CiPaw.07G045400' => 'cil', 'CiPaw.07G048000' => 'cil', 'CiPaw.07G052000' => 'cil', 'CiPaw.07G073800' => 'cil', 'CiPaw.07G099700' => 'cil', 'CiPaw.07G108700' => 'cil', 'CiPaw.07G120000' => 'cil', 'CiPaw.07G134100' => 'cil', 'CiPaw.07G147000' => 'cil', 'CiPaw.07G149700' => 'cil', 'CiPaw.07G178300' => 'cil', 'CiPaw.07G184900' => 'cil', 'CiPaw.08G044500' => 'cil', 'CiPaw.08G046900' => 'cil', 'CiPaw.08G047300' => 'cil', 'CiPaw.08G115400' => 'cil', 'CiPaw.08G134700' => 'cil', 'CiPaw.08G157400' => 'cil', 'CiPaw.09G014300' => 'cil', 'CiPaw.09G088900' => 'cil', 'CiPaw.09G130900' => 'cil', 'CiPaw.09G133100' => 'cil', 'CiPaw.09G151300' => 'cil', 'CiPaw.09G172800' => 'cil', 'CiPaw.09G174900' => 'cil', 'CiPaw.09G175000' => 'cil', 'CiPaw.10G012800' => 'cil', 'CiPaw.10G028800' => 'cil', 'CiPaw.10G044700' => 'cil', 'CiPaw.10G067400' => 'cil', 'CiPaw.10G115900' => 'cil', 'CiPaw.10G126200' => 'cil', 'CiPaw.10G139700' => 'cil', 'CiPaw.10G155100' => 'cil', 'CiPaw.11G011300' => 'cil', 'CiPaw.11G025900' => 'cil', 'CiPaw.11G104100' => 'cil', 'CiPaw.11G142700' => 'cil', 'CiPaw.11G164500' => 'cil', 'CiPaw.11G189100' => 'cil', 'CiPaw.11G197100' => 'cil', 'CiPaw.12G006100' => 'cil', 'CiPaw.12G038500' => 'cil', 'CiPaw.12G041400' => 'cil', 'CiPaw.12G041600' => 'cil', 'CiPaw.12G051300' => 'cil', 'CiPaw.12G101800' => 'cil', 'CiPaw.12G107800' => 'cil', 'CiPaw.13G033200' => 'cil', 'CiPaw.13G129900' => 'cil', 'CiPaw.13G160200' => 'cil', 'CiPaw.14G018900' => 'cil', 'CiPaw.14G029000' => 'cil', 'CiPaw.14G031000' => 'cil', 'CiPaw.14G032000' => 'cil', 'CiPaw.14G032300' => 'cil', 'CiPaw.14G040600' => 'cil', 'CiPaw.14G060500' => 'cil', 'CiPaw.14G061500' => 'cil', 'CiPaw.14G077500' => 'cil', 'CiPaw.14G088300' => 'cil', 'CiPaw.14G108500' => 'cil', 'CiPaw.14G121300' => 'cil', 'CiPaw.14G133000' => 'cil', 'CiPaw.14G134600' => 'cil', 'CiPaw.15G027200' => 'cil', 'CiPaw.15G037700' => 'cil', 'CiPaw.15G050900' => 'cil', 'CiPaw.15G067200' => 'cil', 'CiPaw.15G072000' => 'cil', 'CiPaw.15G112900' => 'cil', 'CiPaw.15G133200' => 'cil', 'CiPaw.15G139500' => 'cil', 'CiPaw.15G155400' => 'cil', 'CiPaw.16G006000' => 'cil', 'CiPaw.16G013100' => 'cil', 'CiPaw.16G047100' => 'cil', 'CiPaw.16G048900' => 'cil', 'CiPaw.16G070300' => 'cil', 'CSS0000195' => 'camsi', 'CSS0001664' => 'camsi', 'CSS0002566' => 'camsi', 'CSS0003077' => 'camsi', 'CSS0004257' => 'camsi', 'CSS0004495' => 'camsi', 'CSS0004599' => 'camsi', 'CSS0004943' => 'camsi', 'CSS0005302' => 'camsi', 'CSS0006274' => 'camsi', 'CSS0006547' => 'camsi', 'CSS0006860' => 'camsi', 'CSS0008814' => 'camsi', 'CSS0008946' => 'camsi', 'CSS0009093' => 'camsi', 'CSS0010221' => 'camsi', 'CSS0010296' => 'camsi', 'CSS0010386' => 'camsi', 'CSS0010831' => 'camsi', 'CSS0011061' => 'camsi', 'CSS0012008' => 'camsi', 'CSS0012194' => 'camsi', 'CSS0013580' => 'camsi', 'CSS0014176' => 'camsi', 'CSS0014280' => 'camsi', 'CSS0014799' => 'camsi', 'CSS0015368' => 'camsi', 'CSS0017473' => 'camsi', 'CSS0019281' => 'camsi', 'CSS0021320' => 'camsi', 'CSS0021750' => 'camsi', 'CSS0023642' => 'camsi', 'CSS0023792' => 'camsi', 'CSS0031528' => 'camsi', 'CSS0033894' => 'camsi', 'CSS0034959' => 'camsi', 'CSS0035632' => 'camsi', 'CSS0038450' => 'camsi', 'CSS0039293' => 'camsi', 'CSS0041053' => 'camsi', 'CSS0041981' => 'camsi', 'CSS0042573' => 'camsi', 'CSS0042927' => 'camsi', 'CSS0047725' => 'camsi', 'CSS0049636' => 'camsi', 'CSS0050513' => 'camsi', 'DCAR_030203' => 'dca', 'Dinv07939' => 'din', 'FAN01G0456' => 'fan', 'FAN02G3001' => 'fan', 'FAN04G2781' => 'fan', 'FAN05G1385' => 'fan', 'FAN05G3062' => 'fan', 'FAN08G2267' => 'fan', 'FAN10G0481' => 'fan', 'FAN10G1257' => 'fan', 'FAN14G0954' => 'fan', 'FAN14G2347' => 'fan', 'FAN15G0187' => 'fan', 'FAN25G2214' => 'fan', 'FvH4_1g21031' => 'fve', 'FvH4_3g16231' => 'fve', 'FvH4_3g26413' => 'fve', 'FvH4_3g29014' => 'fve', 'FvH4_3g31921' => 'fve', 'FvH4_4g19882' => 'fve', 'FvH4_5g21960' => 'fve', 'FvH4_5g29683' => 'fve', 'FvH4_7g13271' => 'fve', 'Glyma.01G062500' => 'gma', 'Glyma.07G140900' => 'gma', 'Glyma.09G140900' => 'gma', 'Glyma.12G112700' => 'gma', 'Glyma.17G168800' => 'gma', 'HanXRQChr01g0027001' => 'han', 'HanXRQChr04g0120511' => 'han', 'HanXRQChr08g0232381' => 'han', 'HanXRQChr09g0265661' => 'han', 'HanXRQChr13g0416031' => 'han', 'Haze_05835' => 'cav', 'Haze_06597' => 'cav', 'Haze_07921' => 'cav', 'Haze_08599' => 'cav', 'Haze_10686' => 'cav', 'Haze_12994' => 'cav', 'Haze_13466' => 'cav', 'Haze_16101' => 'cav', 'Haze_17766' => 'cav', 'Haze_18456' => 'cav', 'Haze_20229' => 'cav', 'Hma1.2p1_0324F.1_g125640' => 'hma', 'Hma1.2p1_0733F.1_g210230' => 'hma', 'Hma1.2p1_0921F.1_g236870' => 'hma', 'Hma1.2p1_1313F.1_g274940' => 'hma', 'Hma1.2p1_3059F.1_g332230' => 'hma', 'Hund15925' => 'sun', 'Hund19562' => 'sun', 'Hund21925' => 'sun', 'MD03G1177400' => 'mdo', 'MD07G1026100' => 'mdo', 'MD17G1218600' => 'mdo', 'Medtr0867s0010' => 'mtr', 'Medtr6g081150' => 'mtr', 'Os01g0527900' => 'osa', 'Os02g0463725' => 'osa', 'Os02g0785600' => 'osa', 'Os03g0433733' => 'osa', 'Os04g0286500' => 'osa', 'Os05g0227800' => 'osa', 'Os06g0521000' => 'osa', 'Os06g0635500' => 'osa', 'Os06g0660650' => 'osa', 'Os07g0554400' => 'osa', 'Os08g0225900' => 'osa', 'Os08g0561000' => 'osa', 'Os09g0241700' => 'osa', 'Os09g0351900' => 'osa', 'Os11g0220700' => 'osa', 'Os11g0282700' => 'osa', 'Os12g0169300' => 'osa', 'Os12g0228500' => 'osa', 'Os12g0543800' => 'osa', 'PGR044G1547' => 'pgr', 'Potri.005G239150' => 'ptr', 'Potri.010G014250' => 'ptr', 'Prupe.1G172500' => 'ppe', 'Prupe.1G196800' => 'ppe', 'Prupe.1G279700' => 'ppe', 'Prupe.2G026400' => 'ppe', 'Prupe.3G094000' => 'ppe', 'Prupe.4G287300' => 'ppe', 'QL01p022166' => 'qlo', 'QL01p051890' => 'qlo', 'QL02p009469' => 'qlo', 'QL02p046053' => 'qlo', 'QL02p057958' => 'qlo', 'QL02p093127' => 'qlo', 'QL03p006855' => 'qlo', 'QL03p071586' => 'qlo', 'QL04p000022' => 'qlo', 'QL04p000024' => 'qlo', 'QL04p003192' => 'qlo', 'QL05p011416' => 'qlo', 'QL06p039590' => 'qlo', 'QL06p052750' => 'qlo', 'QL06p053821' => 'qlo', 'QL07p025287' => 'qlo', 'QL09p033218' => 'qlo', 'QL09p040841' => 'qlo', 'QL10p020337' => 'qlo', 'QL10p027209' => 'qlo', 'QL10p027969' => 'qlo', 'QL10p048988' => 'qlo', 'QL11p001241' => 'qlo', 'QL11p028487' => 'qlo', 'RcHm_v2.0_Chr2g0105031' => 'rch', 'RcHm_v2.0_Chr2g0117811' => 'rch', 'RcHm_v2.0_Chr6g0270241' => 'rch', 'RcHm_v2.0_Chr7g0215961' => 'rch', 'RcHm_v2.0_Chr7g0231991' => 'rch', 'Rhsim01G0041500' => 'rsi', 'Rhsim01G0115000' => 'rsi', 'Rhsim01G0115400' => 'rsi', 'Rhsim01G0133600' => 'rsi', 'Rhsim01G0159900' => 'rsi', 'Rhsim02G0189400' => 'rsi', 'Rhsim03G0135600' => 'rsi', 'Rhsim03G0149900' => 'rsi', 'Rhsim04G0125600' => 'rsi', 'Rhsim05G0091700' => 'rsi', 'Rhsim05G0092900' => 'rsi', 'Rhsim06G0075000' => 'rsi', 'Rhsim07G0066400' => 'rsi', 'Rhsim07G0156400' => 'rsi', 'Rhsim07G0182200' => 'rsi', 'Rhsim07G0182300' => 'rsi', 'Rhsim08G0180400' => 'rsi', 'Rhsim09G0056800' => 'rsi', 'Rhsim10G0153300' => 'rsi', 'Rhsim11G0012700' => 'rsi', 'Rhsim12G0031800' => 'rsi', 'Rhsim12G0055400' => 'rsi', 'Rhsim12G0091400' => 'rsi', 'Rhsim13G0070800' => 'rsi', 'Rhsim13G0193300' => 'rsi', 'RhsimUnG0111600' => 'rsi', 'RhsimUnG0137500' => 'rsi', 'RhsimUnG0172900' => 'rsi', 'SGA_v2.0_scaffold11G05878' => 'sas', 'SGA_v2.0_scaffold167G38458' => 'sas', 'SGA_v2.0_scaffold19G08588' => 'sas', 'SGA_v2.0_scaffold239G43990' => 'sas', 'SGA_v2.0_scaffold260G45865' => 'sas', 'SGA_v2.0_scaffold309G48177' => 'sas', 'SGA_v2.0_scaffold76G25122' => 'sas', 'SGA_v2.0_scaffold85G26708' => 'sas', 'SHI13914' => 'shi', 'SHI30402' => 'shi', 'TWI09G0020' => 'twi', 'TWI09G0456' => 'twi', 'TWI09G1572' => 'twi', 'TWI12G0266' => 'twi', 'TWI12G1451' => 'twi', 'TWI14G0851' => 'twi', 'TWI15G0796' => 'twi', 'TWI18G0820' => 'twi', 'TWI18G1152' => 'twi', 'TWI23G0007' => 'twi', 'TWI23G0314' => 'twi', 'TWI31G0674' => 'twi', 'TWI31G0938' => 'twi', 'TWI34G0641' => 'twi', 'TWI34G1527' => 'twi', 'TWI36G0193' => 'twi', 'TWI36G0405' => 'twi', 'TWI38G0892' => 'twi', 'TWI38G0936' => 'twi', 'TWI38G2218' => 'twi', 'TWI53G0679' => 'twi', 'TWI53G0863' => 'twi', 'TWI53G1133' => 'twi', 'TWI60G0823' => 'twi', 'TWI63G0919' => 'twi', 'TWI63G1436' => 'twi', 'TWI73G0140' => 'twi', 'TWI73G0419' => 'twi', 'TWI73G0420' => 'twi', 'TWI73G1276' => 'twi', 'TWI74G0405' => 'twi', 'TWI74G0837' => 'twi', 'TWI75G0594' => 'twi', 'TWI75G1615' => 'twi', 'TWI77G0816' => 'twi', 'vmacro03831' => 'vma', 'vmacro13746' => 'vma', 'vmacro16089' => 'vma', 'vmacro22863' => 'vma', 'Zm00001eb085790' => 'zma', 'Zm00001eb114250' => 'zma', 'Zm00001eb138070' => 'zma', 'Zm00001eb167560' => 'zma', 'Zm00001eb199990' => 'zma', 'Zm00001eb368180' => 'zma', 'Zm00001eb382470' => 'zma' ), 'gf_id' => 'HOM05D001576', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001576' ), 'data_identifier' => 'HOM05D001576', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001576', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '406', 'num_species' => '29' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'Aqoxy1G01456' => 'aox', 'Aqoxy1G02949' => 'aox', 'Aqoxy3G01274' => 'aox', 'Aqoxy3G02110' => 'aox', 'Aqoxy3G02268' => 'aox', 'Aqoxy5G02702' => 'aox', 'Aqoxy5G02988' => 'aox', 'Aqoxy5G03427' => 'aox', 'Aqoxy6G02363' => 'aox', 'Atru.chr1.3225' => 'acertr', 'Atru.chr8.1198' => 'acertr', 'Atru.chr9.790' => 'acertr', 'CANSAT01G3197' => 'cansat', 'Ciclev10003979m.g' => 'ccl', 'Ciclev10017471m.g' => 'ccl', 'Ciclev10018206m.g' => 'ccl', 'Ciclev10033751m.g' => 'ccl', 'CiPaw.01G000900' => 'cil', 'CiPaw.01G001000' => 'cil', 'CiPaw.01G033500' => 'cil', 'CiPaw.01G060300' => 'cil', 'CiPaw.01G070200' => 'cil', 'CiPaw.01G075100' => 'cil', 'CiPaw.01G084700' => 'cil', 'CiPaw.01G087900' => 'cil', 'CiPaw.01G092600' => 'cil', 'CiPaw.01G097200' => 'cil', 'CiPaw.01G098300' => 'cil', 'CiPaw.01G110200' => 'cil', 'CiPaw.01G118700' => 'cil', 'CiPaw.01G121200' => 'cil', 'CiPaw.01G132500' => 'cil', 'CiPaw.01G146900' => 'cil', 'CiPaw.01G174000' => 'cil', 'CiPaw.01G179900' => 'cil', 'CiPaw.01G183400' => 'cil', 'CiPaw.01G240000' => 'cil', 'CiPaw.01G283500' => 'cil', 'CiPaw.01G307400' => 'cil', 'CiPaw.02G030800' => 'cil', 'CiPaw.02G047200' => 'cil', 'CiPaw.02G050500' => 'cil', 'CiPaw.02G069900' => 'cil', 'CiPaw.02G091600' => 'cil', 'CiPaw.02G095000' => 'cil', 'CiPaw.02G131900' => 'cil', 'CiPaw.03G043000' => 'cil', 'CiPaw.03G069900' => 'cil', 'CiPaw.03G088100' => 'cil', 'CiPaw.03G089300' => 'cil', 'CiPaw.03G093100' => 'cil', 'CiPaw.03G129800' => 'cil', 'CiPaw.03G131200' => 'cil', 'CiPaw.03G134500' => 'cil', 'CiPaw.03G152100' => 'cil', 'CiPaw.03G162700' => 'cil', 'CiPaw.03G172800' => 'cil', 'CiPaw.03G175800' => 'cil', 'CiPaw.03G181800' => 'cil', 'CiPaw.03G191400' => 'cil', 'CiPaw.03G198300' => 'cil', 'CiPaw.03G201300' => 'cil', 'CiPaw.03G224700' => 'cil', 'CiPaw.03G225000' => 'cil', 'CiPaw.04G065100' => 'cil', 'CiPaw.04G080400' => 'cil', 'CiPaw.04G113500' => 'cil', 'CiPaw.04G121900' => 'cil', 'CiPaw.04G144100' => 'cil', 'CiPaw.04G176500' => 'cil', 'CiPaw.05G086200' => 'cil', 'CiPaw.05G100200' => 'cil', 'CiPaw.05G114200' => 'cil', 'CiPaw.05G126800' => 'cil', 'CiPaw.05G228800' => 'cil', 'CiPaw.05G230600' => 'cil', 'CiPaw.05G236500' => 'cil', 'CiPaw.05G244800' => 'cil', 'CiPaw.06G026600' => 'cil', 'CiPaw.06G027900' => 'cil', 'CiPaw.06G051800' => 'cil', 'CiPaw.06G128500' => 'cil', 'CiPaw.06G165900' => 'cil', 'CiPaw.07G045400' => 'cil', 'CiPaw.07G048000' => 'cil', 'CiPaw.07G052000' => 'cil', 'CiPaw.07G073800' => 'cil', 'CiPaw.07G099700' => 'cil', 'CiPaw.07G108700' => 'cil', 'CiPaw.07G120000' => 'cil', 'CiPaw.07G134100' => 'cil', 'CiPaw.07G147000' => 'cil', 'CiPaw.07G149700' => 'cil', 'CiPaw.07G178300' => 'cil', 'CiPaw.07G184900' => 'cil', 'CiPaw.08G044500' => 'cil', 'CiPaw.08G046900' => 'cil', 'CiPaw.08G047300' => 'cil', 'CiPaw.08G115400' => 'cil', 'CiPaw.08G134700' => 'cil', 'CiPaw.08G157400' => 'cil', 'CiPaw.09G014300' => 'cil', 'CiPaw.09G088900' => 'cil', 'CiPaw.09G130900' => 'cil', 'CiPaw.09G133100' => 'cil', 'CiPaw.09G151300' => 'cil', 'CiPaw.09G172800' => 'cil', 'CiPaw.09G174900' => 'cil', 'CiPaw.09G175000' => 'cil', 'CiPaw.10G012800' => 'cil', 'CiPaw.10G028800' => 'cil', 'CiPaw.10G044700' => 'cil', 'CiPaw.10G067400' => 'cil', 'CiPaw.10G115900' => 'cil', 'CiPaw.10G126200' => 'cil', 'CiPaw.10G139700' => 'cil', 'CiPaw.10G155100' => 'cil', 'CiPaw.11G011300' => 'cil', 'CiPaw.11G025900' => 'cil', 'CiPaw.11G104100' => 'cil', 'CiPaw.11G142700' => 'cil', 'CiPaw.11G164500' => 'cil', 'CiPaw.11G189100' => 'cil', 'CiPaw.11G197100' => 'cil', 'CiPaw.12G006100' => 'cil', 'CiPaw.12G038500' => 'cil', 'CiPaw.12G041400' => 'cil', 'CiPaw.12G041600' => 'cil', 'CiPaw.12G051300' => 'cil', 'CiPaw.12G101800' => 'cil', 'CiPaw.12G107800' => 'cil', 'CiPaw.13G033200' => 'cil', 'CiPaw.13G129900' => 'cil', 'CiPaw.13G160200' => 'cil', 'CiPaw.14G018900' => 'cil', 'CiPaw.14G029000' => 'cil', 'CiPaw.14G031000' => 'cil', 'CiPaw.14G032000' => 'cil', 'CiPaw.14G032300' => 'cil', 'CiPaw.14G040600' => 'cil', 'CiPaw.14G060500' => 'cil', 'CiPaw.14G061500' => 'cil', 'CiPaw.14G077500' => 'cil', 'CiPaw.14G088300' => 'cil', 'CiPaw.14G108500' => 'cil', 'CiPaw.14G121300' => 'cil', 'CiPaw.14G133000' => 'cil', 'CiPaw.14G134600' => 'cil', 'CiPaw.15G027200' => 'cil', 'CiPaw.15G037700' => 'cil', 'CiPaw.15G050900' => 'cil', 'CiPaw.15G067200' => 'cil', 'CiPaw.15G072000' => 'cil', 'CiPaw.15G112900' => 'cil', 'CiPaw.15G133200' => 'cil', 'CiPaw.15G139500' => 'cil', 'CiPaw.15G155400' => 'cil', 'CiPaw.16G006000' => 'cil', 'CiPaw.16G013100' => 'cil', 'CiPaw.16G047100' => 'cil', 'CiPaw.16G048900' => 'cil', 'CiPaw.16G070300' => 'cil', 'CSS0000195' => 'camsi', 'CSS0001664' => 'camsi', 'CSS0002566' => 'camsi', 'CSS0003077' => 'camsi', 'CSS0004257' => 'camsi', 'CSS0004495' => 'camsi', 'CSS0004599' => 'camsi', 'CSS0004943' => 'camsi', 'CSS0005302' => 'camsi', 'CSS0006274' => 'camsi', 'CSS0006547' => 'camsi', 'CSS0006860' => 'camsi', 'CSS0008814' => 'camsi', 'CSS0008946' => 'camsi', 'CSS0009093' => 'camsi', 'CSS0010221' => 'camsi', 'CSS0010296' => 'camsi', 'CSS0010386' => 'camsi', 'CSS0010831' => 'camsi', 'CSS0011061' => 'camsi', 'CSS0012008' => 'camsi', 'CSS0012194' => 'camsi', 'CSS0013580' => 'camsi', 'CSS0014176' => 'camsi', 'CSS0014280' => 'camsi', 'CSS0014799' => 'camsi', 'CSS0015368' => 'camsi', 'CSS0017473' => 'camsi', 'CSS0019281' => 'camsi', 'CSS0021320' => 'camsi', 'CSS0021750' => 'camsi', 'CSS0023642' => 'camsi', 'CSS0023792' => 'camsi', 'CSS0031528' => 'camsi', 'CSS0033894' => 'camsi', 'CSS0034959' => 'camsi', 'CSS0035632' => 'camsi', 'CSS0038450' => 'camsi', 'CSS0039293' => 'camsi', 'CSS0041053' => 'camsi', 'CSS0041981' => 'camsi', 'CSS0042573' => 'camsi', 'CSS0042927' => 'camsi', 'CSS0047725' => 'camsi', 'CSS0049636' => 'camsi', 'CSS0050513' => 'camsi', 'DCAR_030203' => 'dca', 'Dinv07939' => 'din', 'FAN01G0456' => 'fan', 'FAN02G3001' => 'fan', 'FAN04G2781' => 'fan', 'FAN05G1385' => 'fan', 'FAN05G3062' => 'fan', 'FAN08G2267' => 'fan', 'FAN10G0481' => 'fan', 'FAN10G1257' => 'fan', 'FAN14G0954' => 'fan', 'FAN14G2347' => 'fan', 'FAN15G0187' => 'fan', 'FAN25G2214' => 'fan', 'FvH4_1g21031' => 'fve', 'FvH4_3g16231' => 'fve', 'FvH4_3g26413' => 'fve', 'FvH4_3g29014' => 'fve', 'FvH4_3g31921' => 'fve', 'FvH4_4g19882' => 'fve', 'FvH4_5g21960' => 'fve', 'FvH4_5g29683' => 'fve', 'FvH4_7g13271' => 'fve', 'Glyma.01G062500' => 'gma', 'Glyma.07G140900' => 'gma', 'Glyma.09G140900' => 'gma', 'Glyma.12G112700' => 'gma', 'Glyma.17G168800' => 'gma', 'HanXRQChr01g0027001' => 'han', 'HanXRQChr04g0120511' => 'han', 'HanXRQChr08g0232381' => 'han', 'HanXRQChr09g0265661' => 'han', 'HanXRQChr13g0416031' => 'han', 'Haze_05835' => 'cav', 'Haze_06597' => 'cav', 'Haze_07921' => 'cav', 'Haze_08599' => 'cav', 'Haze_10686' => 'cav', 'Haze_12994' => 'cav', 'Haze_13466' => 'cav', 'Haze_16101' => 'cav', 'Haze_17766' => 'cav', 'Haze_18456' => 'cav', 'Haze_20229' => 'cav', 'Hma1.2p1_0324F.1_g125640' => 'hma', 'Hma1.2p1_0733F.1_g210230' => 'hma', 'Hma1.2p1_0921F.1_g236870' => 'hma', 'Hma1.2p1_1313F.1_g274940' => 'hma', 'Hma1.2p1_3059F.1_g332230' => 'hma', 'Hund15925' => 'sun', 'Hund19562' => 'sun', 'Hund21925' => 'sun', 'MD03G1177400' => 'mdo', 'MD07G1026100' => 'mdo', 'MD17G1218600' => 'mdo', 'Medtr0867s0010' => 'mtr', 'Medtr6g081150' => 'mtr', 'Os01g0527900' => 'osa', 'Os02g0463725' => 'osa', 'Os02g0785600' => 'osa', 'Os03g0433733' => 'osa', 'Os04g0286500' => 'osa', 'Os05g0227800' => 'osa', 'Os06g0521000' => 'osa', 'Os06g0635500' => 'osa', 'Os06g0660650' => 'osa', 'Os07g0554400' => 'osa', 'Os08g0225900' => 'osa', 'Os08g0561000' => 'osa', 'Os09g0241700' => 'osa', 'Os09g0351900' => 'osa', 'Os11g0220700' => 'osa', 'Os11g0282700' => 'osa', 'Os12g0169300' => 'osa', 'Os12g0228500' => 'osa', 'Os12g0543800' => 'osa', 'PGR044G1547' => 'pgr', 'Potri.005G239150' => 'ptr', 'Potri.010G014250' => 'ptr', 'Prupe.1G172500' => 'ppe', 'Prupe.1G196800' => 'ppe', 'Prupe.1G279700' => 'ppe', 'Prupe.2G026400' => 'ppe', 'Prupe.3G094000' => 'ppe', 'Prupe.4G287300' => 'ppe', 'QL01p022166' => 'qlo', 'QL01p051890' => 'qlo', 'QL02p009469' => 'qlo', 'QL02p046053' => 'qlo', 'QL02p057958' => 'qlo', 'QL02p093127' => 'qlo', 'QL03p006855' => 'qlo', 'QL03p071586' => 'qlo', 'QL04p000022' => 'qlo', 'QL04p000024' => 'qlo', 'QL04p003192' => 'qlo', 'QL05p011416' => 'qlo', 'QL06p039590' => 'qlo', 'QL06p052750' => 'qlo', 'QL06p053821' => 'qlo', 'QL07p025287' => 'qlo', 'QL09p033218' => 'qlo', 'QL09p040841' => 'qlo', 'QL10p020337' => 'qlo', 'QL10p027209' => 'qlo', 'QL10p027969' => 'qlo', 'QL10p048988' => 'qlo', 'QL11p001241' => 'qlo', 'QL11p028487' => 'qlo', 'RcHm_v2.0_Chr2g0105031' => 'rch', 'RcHm_v2.0_Chr2g0117811' => 'rch', 'RcHm_v2.0_Chr6g0270241' => 'rch', 'RcHm_v2.0_Chr7g0215961' => 'rch', 'RcHm_v2.0_Chr7g0231991' => 'rch', 'Rhsim01G0041500' => 'rsi', 'Rhsim01G0115000' => 'rsi', 'Rhsim01G0115400' => 'rsi', 'Rhsim01G0133600' => 'rsi', 'Rhsim01G0159900' => 'rsi', 'Rhsim02G0189400' => 'rsi', 'Rhsim03G0135600' => 'rsi', 'Rhsim03G0149900' => 'rsi', 'Rhsim04G0125600' => 'rsi', 'Rhsim05G0091700' => 'rsi', 'Rhsim05G0092900' => 'rsi', 'Rhsim06G0075000' => 'rsi', 'Rhsim07G0066400' => 'rsi', 'Rhsim07G0156400' => 'rsi', 'Rhsim07G0182200' => 'rsi', 'Rhsim07G0182300' => 'rsi', 'Rhsim08G0180400' => 'rsi', 'Rhsim09G0056800' => 'rsi', 'Rhsim10G0153300' => 'rsi', 'Rhsim11G0012700' => 'rsi', 'Rhsim12G0031800' => 'rsi', 'Rhsim12G0055400' => 'rsi', 'Rhsim12G0091400' => 'rsi', 'Rhsim13G0070800' => 'rsi', 'Rhsim13G0193300' => 'rsi', 'RhsimUnG0111600' => 'rsi', 'RhsimUnG0137500' => 'rsi', 'RhsimUnG0172900' => 'rsi', 'SGA_v2.0_scaffold11G05878' => 'sas', 'SGA_v2.0_scaffold167G38458' => 'sas', 'SGA_v2.0_scaffold19G08588' => 'sas', 'SGA_v2.0_scaffold239G43990' => 'sas', 'SGA_v2.0_scaffold260G45865' => 'sas', 'SGA_v2.0_scaffold309G48177' => 'sas', 'SGA_v2.0_scaffold76G25122' => 'sas', 'SGA_v2.0_scaffold85G26708' => 'sas', 'SHI13914' => 'shi', 'SHI30402' => 'shi', 'TWI09G0020' => 'twi', 'TWI09G0456' => 'twi', 'TWI09G1572' => 'twi', 'TWI12G0266' => 'twi', 'TWI12G1451' => 'twi', 'TWI14G0851' => 'twi', 'TWI15G0796' => 'twi', 'TWI18G0820' => 'twi', 'TWI18G1152' => 'twi', 'TWI23G0007' => 'twi', 'TWI23G0314' => 'twi', 'TWI31G0674' => 'twi', 'TWI31G0938' => 'twi', 'TWI34G0641' => 'twi', 'TWI34G1527' => 'twi', 'TWI36G0193' => 'twi', 'TWI36G0405' => 'twi', 'TWI38G0892' => 'twi', 'TWI38G0936' => 'twi', 'TWI38G2218' => 'twi', 'TWI53G0679' => 'twi', 'TWI53G0863' => 'twi', 'TWI53G1133' => 'twi', 'TWI60G0823' => 'twi', 'TWI63G0919' => 'twi', 'TWI63G1436' => 'twi', 'TWI73G0140' => 'twi', 'TWI73G0419' => 'twi', 'TWI73G0420' => 'twi', 'TWI73G1276' => 'twi', 'TWI74G0405' => 'twi', 'TWI74G0837' => 'twi', 'TWI75G0594' => 'twi', 'TWI75G1615' => 'twi', 'TWI77G0816' => 'twi', 'vmacro03831' => 'vma', 'vmacro13746' => 'vma', 'vmacro16089' => 'vma', 'vmacro22863' => 'vma', 'Zm00001eb085790' => 'zma', 'Zm00001eb114250' => 'zma', 'Zm00001eb138070' => 'zma', 'Zm00001eb167560' => 'zma', 'Zm00001eb199990' => 'zma', 'Zm00001eb368180' => 'zma', 'Zm00001eb382470' => 'zma' ) $gf_id = 'HOM05D001576' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001576' ) $data_identifier = 'HOM05D001576' $data_type = 'gf_id' $species_gene_counts = array( 'aox' => (int) 9, 'acertr' => (int) 3, 'cansat' => (int) 1, 'ccl' => (int) 4, 'cil' => (int) 145, 'camsi' => (int) 46, 'dca' => (int) 1, 'din' => (int) 1, 'fan' => (int) 12, 'fve' => (int) 9, 'gma' => (int) 5, 'han' => (int) 5, 'cav' => (int) 11, 'hma' => (int) 5, 'sun' => (int) 3, 'mdo' => (int) 3, 'mtr' => (int) 2, 'osa' => (int) 19, 'pgr' => (int) 1, 'ptr' => (int) 2, 'ppe' => (int) 6, 'qlo' => (int) 24, 'rch' => (int) 5, 'rsi' => (int) 28, 'sas' => (int) 8, 'shi' => (int) 2, 'twi' => (int) 35, 'vma' => (int) 4, 'zma' => (int) 7 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb382470' $species_info = array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ) $local_species = 'cansat' $disabled = '' $selected = '' $num_hits = (int) 1
Warning (2): count(): Parameter must be an array or an object that implements Countable [APP/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp, line 33]Code Context $disabled = (!array_key_exists($local_species,$species_gene_counts))?"disabled":""; $selected = (isset($selected_species) && array_key_exists($local_species,$selected_species))?"checked='checked'":""; $num_hits = (array_key_exists($local_species,$species_gene_counts))?count($species_gene_counts[$local_species]):0; $viewFile = '/www/bioinformatics01_ro/plaza/_dev_instances/feedback/app/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp' $dataForView = array( 'sidebar_info' => array( 'gf_id' => 'HOM05D001576', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '406', 'num_species' => '29' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'Aqoxy1G01456' => 'aox', 'Aqoxy1G02949' => 'aox', 'Aqoxy3G01274' => 'aox', 'Aqoxy3G02110' => 'aox', 'Aqoxy3G02268' => 'aox', 'Aqoxy5G02702' => 'aox', 'Aqoxy5G02988' => 'aox', 'Aqoxy5G03427' => 'aox', 'Aqoxy6G02363' => 'aox', 'Atru.chr1.3225' => 'acertr', 'Atru.chr8.1198' => 'acertr', 'Atru.chr9.790' => 'acertr', 'CANSAT01G3197' => 'cansat', 'Ciclev10003979m.g' => 'ccl', 'Ciclev10017471m.g' => 'ccl', 'Ciclev10018206m.g' => 'ccl', 'Ciclev10033751m.g' => 'ccl', 'CiPaw.01G000900' => 'cil', 'CiPaw.01G001000' => 'cil', 'CiPaw.01G033500' => 'cil', 'CiPaw.01G060300' => 'cil', 'CiPaw.01G070200' => 'cil', 'CiPaw.01G075100' => 'cil', 'CiPaw.01G084700' => 'cil', 'CiPaw.01G087900' => 'cil', 'CiPaw.01G092600' => 'cil', 'CiPaw.01G097200' => 'cil', 'CiPaw.01G098300' => 'cil', 'CiPaw.01G110200' => 'cil', 'CiPaw.01G118700' => 'cil', 'CiPaw.01G121200' => 'cil', 'CiPaw.01G132500' => 'cil', 'CiPaw.01G146900' => 'cil', 'CiPaw.01G174000' => 'cil', 'CiPaw.01G179900' => 'cil', 'CiPaw.01G183400' => 'cil', 'CiPaw.01G240000' => 'cil', 'CiPaw.01G283500' => 'cil', 'CiPaw.01G307400' => 'cil', 'CiPaw.02G030800' => 'cil', 'CiPaw.02G047200' => 'cil', 'CiPaw.02G050500' => 'cil', 'CiPaw.02G069900' => 'cil', 'CiPaw.02G091600' => 'cil', 'CiPaw.02G095000' => 'cil', 'CiPaw.02G131900' => 'cil', 'CiPaw.03G043000' => 'cil', 'CiPaw.03G069900' => 'cil', 'CiPaw.03G088100' => 'cil', 'CiPaw.03G089300' => 'cil', 'CiPaw.03G093100' => 'cil', 'CiPaw.03G129800' => 'cil', 'CiPaw.03G131200' => 'cil', 'CiPaw.03G134500' => 'cil', 'CiPaw.03G152100' => 'cil', 'CiPaw.03G162700' => 'cil', 'CiPaw.03G172800' => 'cil', 'CiPaw.03G175800' => 'cil', 'CiPaw.03G181800' => 'cil', 'CiPaw.03G191400' => 'cil', 'CiPaw.03G198300' => 'cil', 'CiPaw.03G201300' => 'cil', 'CiPaw.03G224700' => 'cil', 'CiPaw.03G225000' => 'cil', 'CiPaw.04G065100' => 'cil', 'CiPaw.04G080400' => 'cil', 'CiPaw.04G113500' => 'cil', 'CiPaw.04G121900' => 'cil', 'CiPaw.04G144100' => 'cil', 'CiPaw.04G176500' => 'cil', 'CiPaw.05G086200' => 'cil', 'CiPaw.05G100200' => 'cil', 'CiPaw.05G114200' => 'cil', 'CiPaw.05G126800' => 'cil', 'CiPaw.05G228800' => 'cil', 'CiPaw.05G230600' => 'cil', 'CiPaw.05G236500' => 'cil', 'CiPaw.05G244800' => 'cil', 'CiPaw.06G026600' => 'cil', 'CiPaw.06G027900' => 'cil', 'CiPaw.06G051800' => 'cil', 'CiPaw.06G128500' => 'cil', 'CiPaw.06G165900' => 'cil', 'CiPaw.07G045400' => 'cil', 'CiPaw.07G048000' => 'cil', 'CiPaw.07G052000' => 'cil', 'CiPaw.07G073800' => 'cil', 'CiPaw.07G099700' => 'cil', 'CiPaw.07G108700' => 'cil', 'CiPaw.07G120000' => 'cil', 'CiPaw.07G134100' => 'cil', 'CiPaw.07G147000' => 'cil', 'CiPaw.07G149700' => 'cil', 'CiPaw.07G178300' => 'cil', 'CiPaw.07G184900' => 'cil', 'CiPaw.08G044500' => 'cil', 'CiPaw.08G046900' => 'cil', 'CiPaw.08G047300' => 'cil', 'CiPaw.08G115400' => 'cil', 'CiPaw.08G134700' => 'cil', 'CiPaw.08G157400' => 'cil', 'CiPaw.09G014300' => 'cil', 'CiPaw.09G088900' => 'cil', 'CiPaw.09G130900' => 'cil', 'CiPaw.09G133100' => 'cil', 'CiPaw.09G151300' => 'cil', 'CiPaw.09G172800' => 'cil', 'CiPaw.09G174900' => 'cil', 'CiPaw.09G175000' => 'cil', 'CiPaw.10G012800' => 'cil', 'CiPaw.10G028800' => 'cil', 'CiPaw.10G044700' => 'cil', 'CiPaw.10G067400' => 'cil', 'CiPaw.10G115900' => 'cil', 'CiPaw.10G126200' => 'cil', 'CiPaw.10G139700' => 'cil', 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=> 'qlo', 'QL07p025287' => 'qlo', 'QL09p033218' => 'qlo', 'QL09p040841' => 'qlo', 'QL10p020337' => 'qlo', 'QL10p027209' => 'qlo', 'QL10p027969' => 'qlo', 'QL10p048988' => 'qlo', 'QL11p001241' => 'qlo', 'QL11p028487' => 'qlo', 'RcHm_v2.0_Chr2g0105031' => 'rch', 'RcHm_v2.0_Chr2g0117811' => 'rch', 'RcHm_v2.0_Chr6g0270241' => 'rch', 'RcHm_v2.0_Chr7g0215961' => 'rch', 'RcHm_v2.0_Chr7g0231991' => 'rch', 'Rhsim01G0041500' => 'rsi', 'Rhsim01G0115000' => 'rsi', 'Rhsim01G0115400' => 'rsi', 'Rhsim01G0133600' => 'rsi', 'Rhsim01G0159900' => 'rsi', 'Rhsim02G0189400' => 'rsi', 'Rhsim03G0135600' => 'rsi', 'Rhsim03G0149900' => 'rsi', 'Rhsim04G0125600' => 'rsi', 'Rhsim05G0091700' => 'rsi', 'Rhsim05G0092900' => 'rsi', 'Rhsim06G0075000' => 'rsi', 'Rhsim07G0066400' => 'rsi', 'Rhsim07G0156400' => 'rsi', 'Rhsim07G0182200' => 'rsi', 'Rhsim07G0182300' => 'rsi', 'Rhsim08G0180400' => 'rsi', 'Rhsim09G0056800' => 'rsi', 'Rhsim10G0153300' => 'rsi', 'Rhsim11G0012700' => 'rsi', 'Rhsim12G0031800' => 'rsi', 'Rhsim12G0055400' => 'rsi', 'Rhsim12G0091400' => 'rsi', 'Rhsim13G0070800' => 'rsi', 'Rhsim13G0193300' => 'rsi', 'RhsimUnG0111600' => 'rsi', 'RhsimUnG0137500' => 'rsi', 'RhsimUnG0172900' => 'rsi', 'SGA_v2.0_scaffold11G05878' => 'sas', 'SGA_v2.0_scaffold167G38458' => 'sas', 'SGA_v2.0_scaffold19G08588' => 'sas', 'SGA_v2.0_scaffold239G43990' => 'sas', 'SGA_v2.0_scaffold260G45865' => 'sas', 'SGA_v2.0_scaffold309G48177' => 'sas', 'SGA_v2.0_scaffold76G25122' => 'sas', 'SGA_v2.0_scaffold85G26708' => 'sas', 'SHI13914' => 'shi', 'SHI30402' => 'shi', 'TWI09G0020' => 'twi', 'TWI09G0456' => 'twi', 'TWI09G1572' => 'twi', 'TWI12G0266' => 'twi', 'TWI12G1451' => 'twi', 'TWI14G0851' => 'twi', 'TWI15G0796' => 'twi', 'TWI18G0820' => 'twi', 'TWI18G1152' => 'twi', 'TWI23G0007' => 'twi', 'TWI23G0314' => 'twi', 'TWI31G0674' => 'twi', 'TWI31G0938' => 'twi', 'TWI34G0641' => 'twi', 'TWI34G1527' => 'twi', 'TWI36G0193' => 'twi', 'TWI36G0405' => 'twi', 'TWI38G0892' => 'twi', 'TWI38G0936' => 'twi', 'TWI38G2218' => 'twi', 'TWI53G0679' => 'twi', 'TWI53G0863' => 'twi', 'TWI53G1133' => 'twi', 'TWI60G0823' => 'twi', 'TWI63G0919' => 'twi', 'TWI63G1436' => 'twi', 'TWI73G0140' => 'twi', 'TWI73G0419' => 'twi', 'TWI73G0420' => 'twi', 'TWI73G1276' => 'twi', 'TWI74G0405' => 'twi', 'TWI74G0837' => 'twi', 'TWI75G0594' => 'twi', 'TWI75G1615' => 'twi', 'TWI77G0816' => 'twi', 'vmacro03831' => 'vma', 'vmacro13746' => 'vma', 'vmacro16089' => 'vma', 'vmacro22863' => 'vma', 'Zm00001eb085790' => 'zma', 'Zm00001eb114250' => 'zma', 'Zm00001eb138070' => 'zma', 'Zm00001eb167560' => 'zma', 'Zm00001eb199990' => 'zma', 'Zm00001eb368180' => 'zma', 'Zm00001eb382470' => 'zma' ), 'gf_id' => 'HOM05D001576', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001576' ), 'data_identifier' => 'HOM05D001576', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001576', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '406', 'num_species' => '29' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'Aqoxy1G01456' => 'aox', 'Aqoxy1G02949' => 'aox', 'Aqoxy3G01274' => 'aox', 'Aqoxy3G02110' => 'aox', 'Aqoxy3G02268' => 'aox', 'Aqoxy5G02702' => 'aox', 'Aqoxy5G02988' => 'aox', 'Aqoxy5G03427' => 'aox', 'Aqoxy6G02363' => 'aox', 'Atru.chr1.3225' => 'acertr', 'Atru.chr8.1198' => 'acertr', 'Atru.chr9.790' => 'acertr', 'CANSAT01G3197' => 'cansat', 'Ciclev10003979m.g' => 'ccl', 'Ciclev10017471m.g' => 'ccl', 'Ciclev10018206m.g' => 'ccl', 'Ciclev10033751m.g' => 'ccl', 'CiPaw.01G000900' => 'cil', 'CiPaw.01G001000' => 'cil', 'CiPaw.01G033500' => 'cil', 'CiPaw.01G060300' => 'cil', 'CiPaw.01G070200' => 'cil', 'CiPaw.01G075100' => 'cil', 'CiPaw.01G084700' => 'cil', 'CiPaw.01G087900' => 'cil', 'CiPaw.01G092600' => 'cil', 'CiPaw.01G097200' => 'cil', 'CiPaw.01G098300' => 'cil', 'CiPaw.01G110200' => 'cil', 'CiPaw.01G118700' => 'cil', 'CiPaw.01G121200' => 'cil', 'CiPaw.01G132500' => 'cil', 'CiPaw.01G146900' => 'cil', 'CiPaw.01G174000' => 'cil', 'CiPaw.01G179900' => 'cil', 'CiPaw.01G183400' => 'cil', 'CiPaw.01G240000' => 'cil', 'CiPaw.01G283500' => 'cil', 'CiPaw.01G307400' => 'cil', 'CiPaw.02G030800' => 'cil', 'CiPaw.02G047200' => 'cil', 'CiPaw.02G050500' => 'cil', 'CiPaw.02G069900' => 'cil', 'CiPaw.02G091600' => 'cil', 'CiPaw.02G095000' => 'cil', 'CiPaw.02G131900' => 'cil', 'CiPaw.03G043000' => 'cil', 'CiPaw.03G069900' => 'cil', 'CiPaw.03G088100' => 'cil', 'CiPaw.03G089300' => 'cil', 'CiPaw.03G093100' => 'cil', 'CiPaw.03G129800' => 'cil', 'CiPaw.03G131200' => 'cil', 'CiPaw.03G134500' => 'cil', 'CiPaw.03G152100' => 'cil', 'CiPaw.03G162700' => 'cil', 'CiPaw.03G172800' => 'cil', 'CiPaw.03G175800' => 'cil', 'CiPaw.03G181800' => 'cil', 'CiPaw.03G191400' => 'cil', 'CiPaw.03G198300' => 'cil', 'CiPaw.03G201300' => 'cil', 'CiPaw.03G224700' => 'cil', 'CiPaw.03G225000' => 'cil', 'CiPaw.04G065100' => 'cil', 'CiPaw.04G080400' => 'cil', 'CiPaw.04G113500' => 'cil', 'CiPaw.04G121900' => 'cil', 'CiPaw.04G144100' => 'cil', 'CiPaw.04G176500' => 'cil', 'CiPaw.05G086200' => 'cil', 'CiPaw.05G100200' => 'cil', 'CiPaw.05G114200' => 'cil', 'CiPaw.05G126800' => 'cil', 'CiPaw.05G228800' => 'cil', 'CiPaw.05G230600' => 'cil', 'CiPaw.05G236500' => 'cil', 'CiPaw.05G244800' => 'cil', 'CiPaw.06G026600' => 'cil', 'CiPaw.06G027900' => 'cil', 'CiPaw.06G051800' => 'cil', 'CiPaw.06G128500' => 'cil', 'CiPaw.06G165900' => 'cil', 'CiPaw.07G045400' => 'cil', 'CiPaw.07G048000' => 'cil', 'CiPaw.07G052000' => 'cil', 'CiPaw.07G073800' => 'cil', 'CiPaw.07G099700' => 'cil', 'CiPaw.07G108700' => 'cil', 'CiPaw.07G120000' => 'cil', 'CiPaw.07G134100' => 'cil', 'CiPaw.07G147000' => 'cil', 'CiPaw.07G149700' => 'cil', 'CiPaw.07G178300' => 'cil', 'CiPaw.07G184900' => 'cil', 'CiPaw.08G044500' => 'cil', 'CiPaw.08G046900' => 'cil', 'CiPaw.08G047300' => 'cil', 'CiPaw.08G115400' => 'cil', 'CiPaw.08G134700' => 'cil', 'CiPaw.08G157400' => 'cil', 'CiPaw.09G014300' => 'cil', 'CiPaw.09G088900' => 'cil', 'CiPaw.09G130900' => 'cil', 'CiPaw.09G133100' => 'cil', 'CiPaw.09G151300' => 'cil', 'CiPaw.09G172800' => 'cil', 'CiPaw.09G174900' => 'cil', 'CiPaw.09G175000' => 'cil', 'CiPaw.10G012800' => 'cil', 'CiPaw.10G028800' => 'cil', 'CiPaw.10G044700' => 'cil', 'CiPaw.10G067400' => 'cil', 'CiPaw.10G115900' => 'cil', 'CiPaw.10G126200' => 'cil', 'CiPaw.10G139700' => 'cil', 'CiPaw.10G155100' => 'cil', 'CiPaw.11G011300' => 'cil', 'CiPaw.11G025900' => 'cil', 'CiPaw.11G104100' => 'cil', 'CiPaw.11G142700' => 'cil', 'CiPaw.11G164500' => 'cil', 'CiPaw.11G189100' => 'cil', 'CiPaw.11G197100' => 'cil', 'CiPaw.12G006100' => 'cil', 'CiPaw.12G038500' => 'cil', 'CiPaw.12G041400' => 'cil', 'CiPaw.12G041600' => 'cil', 'CiPaw.12G051300' => 'cil', 'CiPaw.12G101800' => 'cil', 'CiPaw.12G107800' => 'cil', 'CiPaw.13G033200' => 'cil', 'CiPaw.13G129900' => 'cil', 'CiPaw.13G160200' => 'cil', 'CiPaw.14G018900' => 'cil', 'CiPaw.14G029000' => 'cil', 'CiPaw.14G031000' => 'cil', 'CiPaw.14G032000' => 'cil', 'CiPaw.14G032300' => 'cil', 'CiPaw.14G040600' => 'cil', 'CiPaw.14G060500' => 'cil', 'CiPaw.14G061500' => 'cil', 'CiPaw.14G077500' => 'cil', 'CiPaw.14G088300' => 'cil', 'CiPaw.14G108500' => 'cil', 'CiPaw.14G121300' => 'cil', 'CiPaw.14G133000' => 'cil', 'CiPaw.14G134600' => 'cil', 'CiPaw.15G027200' => 'cil', 'CiPaw.15G037700' => 'cil', 'CiPaw.15G050900' => 'cil', 'CiPaw.15G067200' => 'cil', 'CiPaw.15G072000' => 'cil', 'CiPaw.15G112900' => 'cil', 'CiPaw.15G133200' => 'cil', 'CiPaw.15G139500' => 'cil', 'CiPaw.15G155400' => 'cil', 'CiPaw.16G006000' => 'cil', 'CiPaw.16G013100' => 'cil', 'CiPaw.16G047100' => 'cil', 'CiPaw.16G048900' => 'cil', 'CiPaw.16G070300' => 'cil', 'CSS0000195' => 'camsi', 'CSS0001664' => 'camsi', 'CSS0002566' => 'camsi', 'CSS0003077' => 'camsi', 'CSS0004257' => 'camsi', 'CSS0004495' => 'camsi', 'CSS0004599' => 'camsi', 'CSS0004943' => 'camsi', 'CSS0005302' => 'camsi', 'CSS0006274' => 'camsi', 'CSS0006547' => 'camsi', 'CSS0006860' => 'camsi', 'CSS0008814' => 'camsi', 'CSS0008946' => 'camsi', 'CSS0009093' => 'camsi', 'CSS0010221' => 'camsi', 'CSS0010296' => 'camsi', 'CSS0010386' => 'camsi', 'CSS0010831' => 'camsi', 'CSS0011061' => 'camsi', 'CSS0012008' => 'camsi', 'CSS0012194' => 'camsi', 'CSS0013580' => 'camsi', 'CSS0014176' => 'camsi', 'CSS0014280' => 'camsi', 'CSS0014799' => 'camsi', 'CSS0015368' => 'camsi', 'CSS0017473' => 'camsi', 'CSS0019281' => 'camsi', 'CSS0021320' => 'camsi', 'CSS0021750' => 'camsi', 'CSS0023642' => 'camsi', 'CSS0023792' => 'camsi', 'CSS0031528' => 'camsi', 'CSS0033894' => 'camsi', 'CSS0034959' => 'camsi', 'CSS0035632' => 'camsi', 'CSS0038450' => 'camsi', 'CSS0039293' => 'camsi', 'CSS0041053' => 'camsi', 'CSS0041981' => 'camsi', 'CSS0042573' => 'camsi', 'CSS0042927' => 'camsi', 'CSS0047725' => 'camsi', 'CSS0049636' => 'camsi', 'CSS0050513' => 'camsi', 'DCAR_030203' => 'dca', 'Dinv07939' => 'din', 'FAN01G0456' => 'fan', 'FAN02G3001' => 'fan', 'FAN04G2781' => 'fan', 'FAN05G1385' => 'fan', 'FAN05G3062' => 'fan', 'FAN08G2267' => 'fan', 'FAN10G0481' => 'fan', 'FAN10G1257' => 'fan', 'FAN14G0954' => 'fan', 'FAN14G2347' => 'fan', 'FAN15G0187' => 'fan', 'FAN25G2214' => 'fan', 'FvH4_1g21031' => 'fve', 'FvH4_3g16231' => 'fve', 'FvH4_3g26413' => 'fve', 'FvH4_3g29014' => 'fve', 'FvH4_3g31921' => 'fve', 'FvH4_4g19882' => 'fve', 'FvH4_5g21960' => 'fve', 'FvH4_5g29683' => 'fve', 'FvH4_7g13271' => 'fve', 'Glyma.01G062500' => 'gma', 'Glyma.07G140900' => 'gma', 'Glyma.09G140900' => 'gma', 'Glyma.12G112700' => 'gma', 'Glyma.17G168800' => 'gma', 'HanXRQChr01g0027001' => 'han', 'HanXRQChr04g0120511' => 'han', 'HanXRQChr08g0232381' => 'han', 'HanXRQChr09g0265661' => 'han', 'HanXRQChr13g0416031' => 'han', 'Haze_05835' => 'cav', 'Haze_06597' => 'cav', 'Haze_07921' => 'cav', 'Haze_08599' => 'cav', 'Haze_10686' => 'cav', 'Haze_12994' => 'cav', 'Haze_13466' => 'cav', 'Haze_16101' => 'cav', 'Haze_17766' => 'cav', 'Haze_18456' => 'cav', 'Haze_20229' => 'cav', 'Hma1.2p1_0324F.1_g125640' => 'hma', 'Hma1.2p1_0733F.1_g210230' => 'hma', 'Hma1.2p1_0921F.1_g236870' => 'hma', 'Hma1.2p1_1313F.1_g274940' => 'hma', 'Hma1.2p1_3059F.1_g332230' => 'hma', 'Hund15925' => 'sun', 'Hund19562' => 'sun', 'Hund21925' => 'sun', 'MD03G1177400' => 'mdo', 'MD07G1026100' => 'mdo', 'MD17G1218600' => 'mdo', 'Medtr0867s0010' => 'mtr', 'Medtr6g081150' => 'mtr', 'Os01g0527900' => 'osa', 'Os02g0463725' => 'osa', 'Os02g0785600' => 'osa', 'Os03g0433733' => 'osa', 'Os04g0286500' => 'osa', 'Os05g0227800' => 'osa', 'Os06g0521000' => 'osa', 'Os06g0635500' => 'osa', 'Os06g0660650' => 'osa', 'Os07g0554400' => 'osa', 'Os08g0225900' => 'osa', 'Os08g0561000' => 'osa', 'Os09g0241700' => 'osa', 'Os09g0351900' => 'osa', 'Os11g0220700' => 'osa', 'Os11g0282700' => 'osa', 'Os12g0169300' => 'osa', 'Os12g0228500' => 'osa', 'Os12g0543800' => 'osa', 'PGR044G1547' => 'pgr', 'Potri.005G239150' => 'ptr', 'Potri.010G014250' => 'ptr', 'Prupe.1G172500' => 'ppe', 'Prupe.1G196800' => 'ppe', 'Prupe.1G279700' => 'ppe', 'Prupe.2G026400' => 'ppe', 'Prupe.3G094000' => 'ppe', 'Prupe.4G287300' => 'ppe', 'QL01p022166' => 'qlo', 'QL01p051890' => 'qlo', 'QL02p009469' => 'qlo', 'QL02p046053' => 'qlo', 'QL02p057958' => 'qlo', 'QL02p093127' => 'qlo', 'QL03p006855' => 'qlo', 'QL03p071586' => 'qlo', 'QL04p000022' => 'qlo', 'QL04p000024' => 'qlo', 'QL04p003192' => 'qlo', 'QL05p011416' => 'qlo', 'QL06p039590' => 'qlo', 'QL06p052750' => 'qlo', 'QL06p053821' => 'qlo', 'QL07p025287' => 'qlo', 'QL09p033218' => 'qlo', 'QL09p040841' => 'qlo', 'QL10p020337' => 'qlo', 'QL10p027209' => 'qlo', 'QL10p027969' => 'qlo', 'QL10p048988' => 'qlo', 'QL11p001241' => 'qlo', 'QL11p028487' => 'qlo', 'RcHm_v2.0_Chr2g0105031' => 'rch', 'RcHm_v2.0_Chr2g0117811' => 'rch', 'RcHm_v2.0_Chr6g0270241' => 'rch', 'RcHm_v2.0_Chr7g0215961' => 'rch', 'RcHm_v2.0_Chr7g0231991' => 'rch', 'Rhsim01G0041500' => 'rsi', 'Rhsim01G0115000' => 'rsi', 'Rhsim01G0115400' => 'rsi', 'Rhsim01G0133600' => 'rsi', 'Rhsim01G0159900' => 'rsi', 'Rhsim02G0189400' => 'rsi', 'Rhsim03G0135600' => 'rsi', 'Rhsim03G0149900' => 'rsi', 'Rhsim04G0125600' => 'rsi', 'Rhsim05G0091700' => 'rsi', 'Rhsim05G0092900' => 'rsi', 'Rhsim06G0075000' => 'rsi', 'Rhsim07G0066400' => 'rsi', 'Rhsim07G0156400' => 'rsi', 'Rhsim07G0182200' => 'rsi', 'Rhsim07G0182300' => 'rsi', 'Rhsim08G0180400' => 'rsi', 'Rhsim09G0056800' => 'rsi', 'Rhsim10G0153300' => 'rsi', 'Rhsim11G0012700' => 'rsi', 'Rhsim12G0031800' => 'rsi', 'Rhsim12G0055400' => 'rsi', 'Rhsim12G0091400' => 'rsi', 'Rhsim13G0070800' => 'rsi', 'Rhsim13G0193300' => 'rsi', 'RhsimUnG0111600' => 'rsi', 'RhsimUnG0137500' => 'rsi', 'RhsimUnG0172900' => 'rsi', 'SGA_v2.0_scaffold11G05878' => 'sas', 'SGA_v2.0_scaffold167G38458' => 'sas', 'SGA_v2.0_scaffold19G08588' => 'sas', 'SGA_v2.0_scaffold239G43990' => 'sas', 'SGA_v2.0_scaffold260G45865' => 'sas', 'SGA_v2.0_scaffold309G48177' => 'sas', 'SGA_v2.0_scaffold76G25122' => 'sas', 'SGA_v2.0_scaffold85G26708' => 'sas', 'SHI13914' => 'shi', 'SHI30402' => 'shi', 'TWI09G0020' => 'twi', 'TWI09G0456' => 'twi', 'TWI09G1572' => 'twi', 'TWI12G0266' => 'twi', 'TWI12G1451' => 'twi', 'TWI14G0851' => 'twi', 'TWI15G0796' => 'twi', 'TWI18G0820' => 'twi', 'TWI18G1152' => 'twi', 'TWI23G0007' => 'twi', 'TWI23G0314' => 'twi', 'TWI31G0674' => 'twi', 'TWI31G0938' => 'twi', 'TWI34G0641' => 'twi', 'TWI34G1527' => 'twi', 'TWI36G0193' => 'twi', 'TWI36G0405' => 'twi', 'TWI38G0892' => 'twi', 'TWI38G0936' => 'twi', 'TWI38G2218' => 'twi', 'TWI53G0679' => 'twi', 'TWI53G0863' => 'twi', 'TWI53G1133' => 'twi', 'TWI60G0823' => 'twi', 'TWI63G0919' => 'twi', 'TWI63G1436' => 'twi', 'TWI73G0140' => 'twi', 'TWI73G0419' => 'twi', 'TWI73G0420' => 'twi', 'TWI73G1276' => 'twi', 'TWI74G0405' => 'twi', 'TWI74G0837' => 'twi', 'TWI75G0594' => 'twi', 'TWI75G1615' => 'twi', 'TWI77G0816' => 'twi', 'vmacro03831' => 'vma', 'vmacro13746' => 'vma', 'vmacro16089' => 'vma', 'vmacro22863' => 'vma', 'Zm00001eb085790' => 'zma', 'Zm00001eb114250' => 'zma', 'Zm00001eb138070' => 'zma', 'Zm00001eb167560' => 'zma', 'Zm00001eb199990' => 'zma', 'Zm00001eb368180' => 'zma', 'Zm00001eb382470' => 'zma' ) $gf_id = 'HOM05D001576' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001576' ) $data_identifier = 'HOM05D001576' $data_type = 'gf_id' $species_gene_counts = array( 'aox' => (int) 9, 'acertr' => (int) 3, 'cansat' => (int) 1, 'ccl' => (int) 4, 'cil' => (int) 145, 'camsi' => (int) 46, 'dca' => (int) 1, 'din' => (int) 1, 'fan' => (int) 12, 'fve' => (int) 9, 'gma' => (int) 5, 'han' => (int) 5, 'cav' => (int) 11, 'hma' => (int) 5, 'sun' => (int) 3, 'mdo' => (int) 3, 'mtr' => (int) 2, 'osa' => (int) 19, 'pgr' => (int) 1, 'ptr' => (int) 2, 'ppe' => (int) 6, 'qlo' => (int) 24, 'rch' => (int) 5, 'rsi' => (int) 28, 'sas' => (int) 8, 'shi' => (int) 2, 'twi' => (int) 35, 'vma' => (int) 4, 'zma' => (int) 7 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb382470' $species_info = array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ) $local_species = 'cil' $disabled = '' $selected = '' $num_hits = (int) 0include - APP/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp, line 33 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933 View::_renderElement() - CORE/Cake/View/View.php, line 1224 View::element() - CORE/Cake/View/View.php, line 418 include - APP/View/Elements/analysis/phylogenetics_module/gf_data_settings.ctp, line 37 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933 View::_renderElement() - CORE/Cake/View/View.php, line 1224 View::element() - CORE/Cake/View/View.php, line 418 include - APP/View/Elements/analysis/phylogenetics_module/parameter_selection.ctp, line 64 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933 View::_renderElement() - CORE/Cake/View/View.php, line 1224 View::element() - CORE/Cake/View/View.php, line 418 include - APP/View/Analysis/custom_tree_creation.ctp, line 27 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933
$viewFile = '/www/bioinformatics01_ro/plaza/_dev_instances/feedback/app/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp' $dataForView = array( 'sidebar_info' => array( 'gf_id' => 'HOM05D001576', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '406', 'num_species' => '29' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'Aqoxy1G01456' => 'aox', 'Aqoxy1G02949' => 'aox', 'Aqoxy3G01274' => 'aox', 'Aqoxy3G02110' => 'aox', 'Aqoxy3G02268' => 'aox', 'Aqoxy5G02702' => 'aox', 'Aqoxy5G02988' => 'aox', 'Aqoxy5G03427' => 'aox', 'Aqoxy6G02363' => 'aox', 'Atru.chr1.3225' => 'acertr', 'Atru.chr8.1198' => 'acertr', 'Atru.chr9.790' => 'acertr', 'CANSAT01G3197' => 'cansat', 'Ciclev10003979m.g' => 'ccl', 'Ciclev10017471m.g' => 'ccl', 'Ciclev10018206m.g' => 'ccl', 'Ciclev10033751m.g' => 'ccl', 'CiPaw.01G000900' => 'cil', 'CiPaw.01G001000' => 'cil', 'CiPaw.01G033500' => 'cil', 'CiPaw.01G060300' => 'cil', 'CiPaw.01G070200' => 'cil', 'CiPaw.01G075100' => 'cil', 'CiPaw.01G084700' => 'cil', 'CiPaw.01G087900' => 'cil', 'CiPaw.01G092600' => 'cil', 'CiPaw.01G097200' => 'cil', 'CiPaw.01G098300' => 'cil', 'CiPaw.01G110200' => 'cil', 'CiPaw.01G118700' => 'cil', 'CiPaw.01G121200' => 'cil', 'CiPaw.01G132500' => 'cil', 'CiPaw.01G146900' => 'cil', 'CiPaw.01G174000' => 'cil', 'CiPaw.01G179900' => 'cil', 'CiPaw.01G183400' => 'cil', 'CiPaw.01G240000' => 'cil', 'CiPaw.01G283500' => 'cil', 'CiPaw.01G307400' => 'cil', 'CiPaw.02G030800' => 'cil', 'CiPaw.02G047200' => 'cil', 'CiPaw.02G050500' => 'cil', 'CiPaw.02G069900' => 'cil', 'CiPaw.02G091600' => 'cil', 'CiPaw.02G095000' => 'cil', 'CiPaw.02G131900' => 'cil', 'CiPaw.03G043000' => 'cil', 'CiPaw.03G069900' => 'cil', 'CiPaw.03G088100' => 'cil', 'CiPaw.03G089300' => 'cil', 'CiPaw.03G093100' => 'cil', 'CiPaw.03G129800' => 'cil', 'CiPaw.03G131200' => 'cil', 'CiPaw.03G134500' => 'cil', 'CiPaw.03G152100' => 'cil', 'CiPaw.03G162700' => 'cil', 'CiPaw.03G172800' => 'cil', 'CiPaw.03G175800' => 'cil', 'CiPaw.03G181800' => 'cil', 'CiPaw.03G191400' => 'cil', 'CiPaw.03G198300' => 'cil', 'CiPaw.03G201300' => 'cil', 'CiPaw.03G224700' => 'cil', 'CiPaw.03G225000' => 'cil', 'CiPaw.04G065100' => 'cil', 'CiPaw.04G080400' => 'cil', 'CiPaw.04G113500' => 'cil', 'CiPaw.04G121900' => 'cil', 'CiPaw.04G144100' => 'cil', 'CiPaw.04G176500' => 'cil', 'CiPaw.05G086200' => 'cil', 'CiPaw.05G100200' => 'cil', 'CiPaw.05G114200' => 'cil', 'CiPaw.05G126800' => 'cil', 'CiPaw.05G228800' => 'cil', 'CiPaw.05G230600' => 'cil', 'CiPaw.05G236500' => 'cil', 'CiPaw.05G244800' => 'cil', 'CiPaw.06G026600' => 'cil', 'CiPaw.06G027900' => 'cil', 'CiPaw.06G051800' => 'cil', 'CiPaw.06G128500' => 'cil', 'CiPaw.06G165900' => 'cil', 'CiPaw.07G045400' => 'cil', 'CiPaw.07G048000' => 'cil', 'CiPaw.07G052000' => 'cil', 'CiPaw.07G073800' => 'cil', 'CiPaw.07G099700' => 'cil', 'CiPaw.07G108700' => 'cil', 'CiPaw.07G120000' => 'cil', 'CiPaw.07G134100' => 'cil', 'CiPaw.07G147000' => 'cil', 'CiPaw.07G149700' => 'cil', 'CiPaw.07G178300' => 'cil', 'CiPaw.07G184900' => 'cil', 'CiPaw.08G044500' => 'cil', 'CiPaw.08G046900' => 'cil', 'CiPaw.08G047300' => 'cil', 'CiPaw.08G115400' => 'cil', 'CiPaw.08G134700' => 'cil', 'CiPaw.08G157400' => 'cil', 'CiPaw.09G014300' => 'cil', 'CiPaw.09G088900' => 'cil', 'CiPaw.09G130900' => 'cil', 'CiPaw.09G133100' => 'cil', 'CiPaw.09G151300' => 'cil', 'CiPaw.09G172800' => 'cil', 'CiPaw.09G174900' => 'cil', 'CiPaw.09G175000' => 'cil', 'CiPaw.10G012800' => 'cil', 'CiPaw.10G028800' => 'cil', 'CiPaw.10G044700' => 'cil', 'CiPaw.10G067400' => 'cil', 'CiPaw.10G115900' => 'cil', 'CiPaw.10G126200' => 'cil', 'CiPaw.10G139700' => 'cil', 'CiPaw.10G155100' => 'cil', 'CiPaw.11G011300' => 'cil', 'CiPaw.11G025900' => 'cil', 'CiPaw.11G104100' => 'cil', 'CiPaw.11G142700' => 'cil', 'CiPaw.11G164500' => 'cil', 'CiPaw.11G189100' => 'cil', 'CiPaw.11G197100' => 'cil', 'CiPaw.12G006100' => 'cil', 'CiPaw.12G038500' => 'cil', 'CiPaw.12G041400' => 'cil', 'CiPaw.12G041600' => 'cil', 'CiPaw.12G051300' => 'cil', 'CiPaw.12G101800' => 'cil', 'CiPaw.12G107800' => 'cil', 'CiPaw.13G033200' => 'cil', 'CiPaw.13G129900' => 'cil', 'CiPaw.13G160200' => 'cil', 'CiPaw.14G018900' => 'cil', 'CiPaw.14G029000' => 'cil', 'CiPaw.14G031000' => 'cil', 'CiPaw.14G032000' => 'cil', 'CiPaw.14G032300' => 'cil', 'CiPaw.14G040600' => 'cil', 'CiPaw.14G060500' => 'cil', 'CiPaw.14G061500' => 'cil', 'CiPaw.14G077500' => 'cil', 'CiPaw.14G088300' => 'cil', 'CiPaw.14G108500' => 'cil', 'CiPaw.14G121300' => 'cil', 'CiPaw.14G133000' => 'cil', 'CiPaw.14G134600' => 'cil', 'CiPaw.15G027200' => 'cil', 'CiPaw.15G037700' => 'cil', 'CiPaw.15G050900' => 'cil', 'CiPaw.15G067200' => 'cil', 'CiPaw.15G072000' => 'cil', 'CiPaw.15G112900' => 'cil', 'CiPaw.15G133200' => 'cil', 'CiPaw.15G139500' => 'cil', 'CiPaw.15G155400' => 'cil', 'CiPaw.16G006000' => 'cil', 'CiPaw.16G013100' => 'cil', 'CiPaw.16G047100' => 'cil', 'CiPaw.16G048900' => 'cil', 'CiPaw.16G070300' => 'cil', 'CSS0000195' => 'camsi', 'CSS0001664' => 'camsi', 'CSS0002566' => 'camsi', 'CSS0003077' => 'camsi', 'CSS0004257' => 'camsi', 'CSS0004495' => 'camsi', 'CSS0004599' => 'camsi', 'CSS0004943' => 'camsi', 'CSS0005302' => 'camsi', 'CSS0006274' => 'camsi', 'CSS0006547' => 'camsi', 'CSS0006860' => 'camsi', 'CSS0008814' => 'camsi', 'CSS0008946' => 'camsi', 'CSS0009093' => 'camsi', 'CSS0010221' => 'camsi', 'CSS0010296' => 'camsi', 'CSS0010386' => 'camsi', 'CSS0010831' => 'camsi', 'CSS0011061' => 'camsi', 'CSS0012008' => 'camsi', 'CSS0012194' => 'camsi', 'CSS0013580' => 'camsi', 'CSS0014176' => 'camsi', 'CSS0014280' => 'camsi', 'CSS0014799' => 'camsi', 'CSS0015368' => 'camsi', 'CSS0017473' => 'camsi', 'CSS0019281' => 'camsi', 'CSS0021320' => 'camsi', 'CSS0021750' => 'camsi', 'CSS0023642' => 'camsi', 'CSS0023792' => 'camsi', 'CSS0031528' => 'camsi', 'CSS0033894' => 'camsi', 'CSS0034959' => 'camsi', 'CSS0035632' => 'camsi', 'CSS0038450' => 'camsi', 'CSS0039293' => 'camsi', 'CSS0041053' => 'camsi', 'CSS0041981' => 'camsi', 'CSS0042573' => 'camsi', 'CSS0042927' => 'camsi', 'CSS0047725' => 'camsi', 'CSS0049636' => 'camsi', 'CSS0050513' => 'camsi', 'DCAR_030203' => 'dca', 'Dinv07939' => 'din', 'FAN01G0456' => 'fan', 'FAN02G3001' => 'fan', 'FAN04G2781' => 'fan', 'FAN05G1385' => 'fan', 'FAN05G3062' => 'fan', 'FAN08G2267' => 'fan', 'FAN10G0481' => 'fan', 'FAN10G1257' => 'fan', 'FAN14G0954' => 'fan', 'FAN14G2347' => 'fan', 'FAN15G0187' => 'fan', 'FAN25G2214' => 'fan', 'FvH4_1g21031' => 'fve', 'FvH4_3g16231' => 'fve', 'FvH4_3g26413' => 'fve', 'FvH4_3g29014' => 'fve', 'FvH4_3g31921' => 'fve', 'FvH4_4g19882' => 'fve', 'FvH4_5g21960' => 'fve', 'FvH4_5g29683' => 'fve', 'FvH4_7g13271' => 'fve', 'Glyma.01G062500' => 'gma', 'Glyma.07G140900' => 'gma', 'Glyma.09G140900' => 'gma', 'Glyma.12G112700' => 'gma', 'Glyma.17G168800' => 'gma', 'HanXRQChr01g0027001' => 'han', 'HanXRQChr04g0120511' => 'han', 'HanXRQChr08g0232381' => 'han', 'HanXRQChr09g0265661' => 'han', 'HanXRQChr13g0416031' => 'han', 'Haze_05835' => 'cav', 'Haze_06597' => 'cav', 'Haze_07921' => 'cav', 'Haze_08599' => 'cav', 'Haze_10686' => 'cav', 'Haze_12994' => 'cav', 'Haze_13466' => 'cav', 'Haze_16101' => 'cav', 'Haze_17766' => 'cav', 'Haze_18456' => 'cav', 'Haze_20229' => 'cav', 'Hma1.2p1_0324F.1_g125640' => 'hma', 'Hma1.2p1_0733F.1_g210230' => 'hma', 'Hma1.2p1_0921F.1_g236870' => 'hma', 'Hma1.2p1_1313F.1_g274940' => 'hma', 'Hma1.2p1_3059F.1_g332230' => 'hma', 'Hund15925' => 'sun', 'Hund19562' => 'sun', 'Hund21925' => 'sun', 'MD03G1177400' => 'mdo', 'MD07G1026100' => 'mdo', 'MD17G1218600' => 'mdo', 'Medtr0867s0010' => 'mtr', 'Medtr6g081150' => 'mtr', 'Os01g0527900' => 'osa', 'Os02g0463725' => 'osa', 'Os02g0785600' => 'osa', 'Os03g0433733' => 'osa', 'Os04g0286500' => 'osa', 'Os05g0227800' => 'osa', 'Os06g0521000' => 'osa', 'Os06g0635500' => 'osa', 'Os06g0660650' => 'osa', 'Os07g0554400' => 'osa', 'Os08g0225900' => 'osa', 'Os08g0561000' => 'osa', 'Os09g0241700' => 'osa', 'Os09g0351900' => 'osa', 'Os11g0220700' => 'osa', 'Os11g0282700' => 'osa', 'Os12g0169300' => 'osa', 'Os12g0228500' => 'osa', 'Os12g0543800' => 'osa', 'PGR044G1547' => 'pgr', 'Potri.005G239150' => 'ptr', 'Potri.010G014250' => 'ptr', 'Prupe.1G172500' => 'ppe', 'Prupe.1G196800' => 'ppe', 'Prupe.1G279700' => 'ppe', 'Prupe.2G026400' => 'ppe', 'Prupe.3G094000' => 'ppe', 'Prupe.4G287300' => 'ppe', 'QL01p022166' => 'qlo', 'QL01p051890' => 'qlo', 'QL02p009469' => 'qlo', 'QL02p046053' => 'qlo', 'QL02p057958' => 'qlo', 'QL02p093127' => 'qlo', 'QL03p006855' => 'qlo', 'QL03p071586' => 'qlo', 'QL04p000022' => 'qlo', 'QL04p000024' => 'qlo', 'QL04p003192' => 'qlo', 'QL05p011416' => 'qlo', 'QL06p039590' => 'qlo', 'QL06p052750' => 'qlo', 'QL06p053821' => 'qlo', 'QL07p025287' => 'qlo', 'QL09p033218' => 'qlo', 'QL09p040841' => 'qlo', 'QL10p020337' => 'qlo', 'QL10p027209' => 'qlo', 'QL10p027969' => 'qlo', 'QL10p048988' => 'qlo', 'QL11p001241' => 'qlo', 'QL11p028487' => 'qlo', 'RcHm_v2.0_Chr2g0105031' => 'rch', 'RcHm_v2.0_Chr2g0117811' => 'rch', 'RcHm_v2.0_Chr6g0270241' => 'rch', 'RcHm_v2.0_Chr7g0215961' => 'rch', 'RcHm_v2.0_Chr7g0231991' => 'rch', 'Rhsim01G0041500' => 'rsi', 'Rhsim01G0115000' => 'rsi', 'Rhsim01G0115400' => 'rsi', 'Rhsim01G0133600' => 'rsi', 'Rhsim01G0159900' => 'rsi', 'Rhsim02G0189400' => 'rsi', 'Rhsim03G0135600' => 'rsi', 'Rhsim03G0149900' => 'rsi', 'Rhsim04G0125600' => 'rsi', 'Rhsim05G0091700' => 'rsi', 'Rhsim05G0092900' => 'rsi', 'Rhsim06G0075000' => 'rsi', 'Rhsim07G0066400' => 'rsi', 'Rhsim07G0156400' => 'rsi', 'Rhsim07G0182200' => 'rsi', 'Rhsim07G0182300' => 'rsi', 'Rhsim08G0180400' => 'rsi', 'Rhsim09G0056800' => 'rsi', 'Rhsim10G0153300' => 'rsi', 'Rhsim11G0012700' => 'rsi', 'Rhsim12G0031800' => 'rsi', 'Rhsim12G0055400' => 'rsi', 'Rhsim12G0091400' => 'rsi', 'Rhsim13G0070800' => 'rsi', 'Rhsim13G0193300' => 'rsi', 'RhsimUnG0111600' => 'rsi', 'RhsimUnG0137500' => 'rsi', 'RhsimUnG0172900' => 'rsi', 'SGA_v2.0_scaffold11G05878' => 'sas', 'SGA_v2.0_scaffold167G38458' => 'sas', 'SGA_v2.0_scaffold19G08588' => 'sas', 'SGA_v2.0_scaffold239G43990' => 'sas', 'SGA_v2.0_scaffold260G45865' => 'sas', 'SGA_v2.0_scaffold309G48177' => 'sas', 'SGA_v2.0_scaffold76G25122' => 'sas', 'SGA_v2.0_scaffold85G26708' => 'sas', 'SHI13914' => 'shi', 'SHI30402' => 'shi', 'TWI09G0020' => 'twi', 'TWI09G0456' => 'twi', 'TWI09G1572' => 'twi', 'TWI12G0266' => 'twi', 'TWI12G1451' => 'twi', 'TWI14G0851' => 'twi', 'TWI15G0796' => 'twi', 'TWI18G0820' => 'twi', 'TWI18G1152' => 'twi', 'TWI23G0007' => 'twi', 'TWI23G0314' => 'twi', 'TWI31G0674' => 'twi', 'TWI31G0938' => 'twi', 'TWI34G0641' => 'twi', 'TWI34G1527' => 'twi', 'TWI36G0193' => 'twi', 'TWI36G0405' => 'twi', 'TWI38G0892' => 'twi', 'TWI38G0936' => 'twi', 'TWI38G2218' => 'twi', 'TWI53G0679' => 'twi', 'TWI53G0863' => 'twi', 'TWI53G1133' => 'twi', 'TWI60G0823' => 'twi', 'TWI63G0919' => 'twi', 'TWI63G1436' => 'twi', 'TWI73G0140' => 'twi', 'TWI73G0419' => 'twi', 'TWI73G0420' => 'twi', 'TWI73G1276' => 'twi', 'TWI74G0405' => 'twi', 'TWI74G0837' => 'twi', 'TWI75G0594' => 'twi', 'TWI75G1615' => 'twi', 'TWI77G0816' => 'twi', 'vmacro03831' => 'vma', 'vmacro13746' => 'vma', 'vmacro16089' => 'vma', 'vmacro22863' => 'vma', 'Zm00001eb085790' => 'zma', 'Zm00001eb114250' => 'zma', 'Zm00001eb138070' => 'zma', 'Zm00001eb167560' => 'zma', 'Zm00001eb199990' => 'zma', 'Zm00001eb368180' => 'zma', 'Zm00001eb382470' => 'zma' ), 'gf_id' => 'HOM05D001576', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001576' ), 'data_identifier' => 'HOM05D001576', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001576', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '406', 'num_species' => '29' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'Aqoxy1G01456' => 'aox', 'Aqoxy1G02949' => 'aox', 'Aqoxy3G01274' => 'aox', 'Aqoxy3G02110' => 'aox', 'Aqoxy3G02268' => 'aox', 'Aqoxy5G02702' => 'aox', 'Aqoxy5G02988' => 'aox', 'Aqoxy5G03427' => 'aox', 'Aqoxy6G02363' => 'aox', 'Atru.chr1.3225' => 'acertr', 'Atru.chr8.1198' => 'acertr', 'Atru.chr9.790' => 'acertr', 'CANSAT01G3197' => 'cansat', 'Ciclev10003979m.g' => 'ccl', 'Ciclev10017471m.g' => 'ccl', 'Ciclev10018206m.g' => 'ccl', 'Ciclev10033751m.g' => 'ccl', 'CiPaw.01G000900' => 'cil', 'CiPaw.01G001000' => 'cil', 'CiPaw.01G033500' => 'cil', 'CiPaw.01G060300' => 'cil', 'CiPaw.01G070200' => 'cil', 'CiPaw.01G075100' => 'cil', 'CiPaw.01G084700' => 'cil', 'CiPaw.01G087900' => 'cil', 'CiPaw.01G092600' => 'cil', 'CiPaw.01G097200' => 'cil', 'CiPaw.01G098300' => 'cil', 'CiPaw.01G110200' => 'cil', 'CiPaw.01G118700' => 'cil', 'CiPaw.01G121200' => 'cil', 'CiPaw.01G132500' => 'cil', 'CiPaw.01G146900' => 'cil', 'CiPaw.01G174000' => 'cil', 'CiPaw.01G179900' => 'cil', 'CiPaw.01G183400' => 'cil', 'CiPaw.01G240000' => 'cil', 'CiPaw.01G283500' => 'cil', 'CiPaw.01G307400' => 'cil', 'CiPaw.02G030800' => 'cil', 'CiPaw.02G047200' => 'cil', 'CiPaw.02G050500' => 'cil', 'CiPaw.02G069900' => 'cil', 'CiPaw.02G091600' => 'cil', 'CiPaw.02G095000' => 'cil', 'CiPaw.02G131900' => 'cil', 'CiPaw.03G043000' => 'cil', 'CiPaw.03G069900' => 'cil', 'CiPaw.03G088100' => 'cil', 'CiPaw.03G089300' => 'cil', 'CiPaw.03G093100' => 'cil', 'CiPaw.03G129800' => 'cil', 'CiPaw.03G131200' => 'cil', 'CiPaw.03G134500' => 'cil', 'CiPaw.03G152100' => 'cil', 'CiPaw.03G162700' => 'cil', 'CiPaw.03G172800' => 'cil', 'CiPaw.03G175800' => 'cil', 'CiPaw.03G181800' => 'cil', 'CiPaw.03G191400' => 'cil', 'CiPaw.03G198300' => 'cil', 'CiPaw.03G201300' => 'cil', 'CiPaw.03G224700' => 'cil', 'CiPaw.03G225000' => 'cil', 'CiPaw.04G065100' => 'cil', 'CiPaw.04G080400' => 'cil', 'CiPaw.04G113500' => 'cil', 'CiPaw.04G121900' => 'cil', 'CiPaw.04G144100' => 'cil', 'CiPaw.04G176500' => 'cil', 'CiPaw.05G086200' => 'cil', 'CiPaw.05G100200' => 'cil', 'CiPaw.05G114200' => 'cil', 'CiPaw.05G126800' => 'cil', 'CiPaw.05G228800' => 'cil', 'CiPaw.05G230600' => 'cil', 'CiPaw.05G236500' => 'cil', 'CiPaw.05G244800' => 'cil', 'CiPaw.06G026600' => 'cil', 'CiPaw.06G027900' => 'cil', 'CiPaw.06G051800' => 'cil', 'CiPaw.06G128500' => 'cil', 'CiPaw.06G165900' => 'cil', 'CiPaw.07G045400' => 'cil', 'CiPaw.07G048000' => 'cil', 'CiPaw.07G052000' => 'cil', 'CiPaw.07G073800' => 'cil', 'CiPaw.07G099700' => 'cil', 'CiPaw.07G108700' => 'cil', 'CiPaw.07G120000' => 'cil', 'CiPaw.07G134100' => 'cil', 'CiPaw.07G147000' => 'cil', 'CiPaw.07G149700' => 'cil', 'CiPaw.07G178300' => 'cil', 'CiPaw.07G184900' => 'cil', 'CiPaw.08G044500' => 'cil', 'CiPaw.08G046900' => 'cil', 'CiPaw.08G047300' => 'cil', 'CiPaw.08G115400' => 'cil', 'CiPaw.08G134700' => 'cil', 'CiPaw.08G157400' => 'cil', 'CiPaw.09G014300' => 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'CiPaw.14G032000' => 'cil', 'CiPaw.14G032300' => 'cil', 'CiPaw.14G040600' => 'cil', 'CiPaw.14G060500' => 'cil', 'CiPaw.14G061500' => 'cil', 'CiPaw.14G077500' => 'cil', 'CiPaw.14G088300' => 'cil', 'CiPaw.14G108500' => 'cil', 'CiPaw.14G121300' => 'cil', 'CiPaw.14G133000' => 'cil', 'CiPaw.14G134600' => 'cil', 'CiPaw.15G027200' => 'cil', 'CiPaw.15G037700' => 'cil', 'CiPaw.15G050900' => 'cil', 'CiPaw.15G067200' => 'cil', 'CiPaw.15G072000' => 'cil', 'CiPaw.15G112900' => 'cil', 'CiPaw.15G133200' => 'cil', 'CiPaw.15G139500' => 'cil', 'CiPaw.15G155400' => 'cil', 'CiPaw.16G006000' => 'cil', 'CiPaw.16G013100' => 'cil', 'CiPaw.16G047100' => 'cil', 'CiPaw.16G048900' => 'cil', 'CiPaw.16G070300' => 'cil', 'CSS0000195' => 'camsi', 'CSS0001664' => 'camsi', 'CSS0002566' => 'camsi', 'CSS0003077' => 'camsi', 'CSS0004257' => 'camsi', 'CSS0004495' => 'camsi', 'CSS0004599' => 'camsi', 'CSS0004943' => 'camsi', 'CSS0005302' => 'camsi', 'CSS0006274' => 'camsi', 'CSS0006547' => 'camsi', 'CSS0006860' => 'camsi', 'CSS0008814' => 'camsi', 'CSS0008946' => 'camsi', 'CSS0009093' => 'camsi', 'CSS0010221' => 'camsi', 'CSS0010296' => 'camsi', 'CSS0010386' => 'camsi', 'CSS0010831' => 'camsi', 'CSS0011061' => 'camsi', 'CSS0012008' => 'camsi', 'CSS0012194' => 'camsi', 'CSS0013580' => 'camsi', 'CSS0014176' => 'camsi', 'CSS0014280' => 'camsi', 'CSS0014799' => 'camsi', 'CSS0015368' => 'camsi', 'CSS0017473' => 'camsi', 'CSS0019281' => 'camsi', 'CSS0021320' => 'camsi', 'CSS0021750' => 'camsi', 'CSS0023642' => 'camsi', 'CSS0023792' => 'camsi', 'CSS0031528' => 'camsi', 'CSS0033894' => 'camsi', 'CSS0034959' => 'camsi', 'CSS0035632' => 'camsi', 'CSS0038450' => 'camsi', 'CSS0039293' => 'camsi', 'CSS0041053' => 'camsi', 'CSS0041981' => 'camsi', 'CSS0042573' => 'camsi', 'CSS0042927' => 'camsi', 'CSS0047725' => 'camsi', 'CSS0049636' => 'camsi', 'CSS0050513' => 'camsi', 'DCAR_030203' => 'dca', 'Dinv07939' => 'din', 'FAN01G0456' => 'fan', 'FAN02G3001' => 'fan', 'FAN04G2781' => 'fan', 'FAN05G1385' => 'fan', 'FAN05G3062' => 'fan', 'FAN08G2267' => 'fan', 'FAN10G0481' => 'fan', 'FAN10G1257' => 'fan', 'FAN14G0954' => 'fan', 'FAN14G2347' => 'fan', 'FAN15G0187' => 'fan', 'FAN25G2214' => 'fan', 'FvH4_1g21031' => 'fve', 'FvH4_3g16231' => 'fve', 'FvH4_3g26413' => 'fve', 'FvH4_3g29014' => 'fve', 'FvH4_3g31921' => 'fve', 'FvH4_4g19882' => 'fve', 'FvH4_5g21960' => 'fve', 'FvH4_5g29683' => 'fve', 'FvH4_7g13271' => 'fve', 'Glyma.01G062500' => 'gma', 'Glyma.07G140900' => 'gma', 'Glyma.09G140900' => 'gma', 'Glyma.12G112700' => 'gma', 'Glyma.17G168800' => 'gma', 'HanXRQChr01g0027001' => 'han', 'HanXRQChr04g0120511' => 'han', 'HanXRQChr08g0232381' => 'han', 'HanXRQChr09g0265661' => 'han', 'HanXRQChr13g0416031' => 'han', 'Haze_05835' => 'cav', 'Haze_06597' => 'cav', 'Haze_07921' => 'cav', 'Haze_08599' => 'cav', 'Haze_10686' => 'cav', 'Haze_12994' => 'cav', 'Haze_13466' => 'cav', 'Haze_16101' => 'cav', 'Haze_17766' => 'cav', 'Haze_18456' => 'cav', 'Haze_20229' => 'cav', 'Hma1.2p1_0324F.1_g125640' => 'hma', 'Hma1.2p1_0733F.1_g210230' => 'hma', 'Hma1.2p1_0921F.1_g236870' => 'hma', 'Hma1.2p1_1313F.1_g274940' => 'hma', 'Hma1.2p1_3059F.1_g332230' => 'hma', 'Hund15925' => 'sun', 'Hund19562' => 'sun', 'Hund21925' => 'sun', 'MD03G1177400' => 'mdo', 'MD07G1026100' => 'mdo', 'MD17G1218600' => 'mdo', 'Medtr0867s0010' => 'mtr', 'Medtr6g081150' => 'mtr', 'Os01g0527900' => 'osa', 'Os02g0463725' => 'osa', 'Os02g0785600' => 'osa', 'Os03g0433733' => 'osa', 'Os04g0286500' => 'osa', 'Os05g0227800' => 'osa', 'Os06g0521000' => 'osa', 'Os06g0635500' => 'osa', 'Os06g0660650' => 'osa', 'Os07g0554400' => 'osa', 'Os08g0225900' => 'osa', 'Os08g0561000' => 'osa', 'Os09g0241700' => 'osa', 'Os09g0351900' => 'osa', 'Os11g0220700' => 'osa', 'Os11g0282700' => 'osa', 'Os12g0169300' => 'osa', 'Os12g0228500' => 'osa', 'Os12g0543800' => 'osa', 'PGR044G1547' => 'pgr', 'Potri.005G239150' => 'ptr', 'Potri.010G014250' => 'ptr', 'Prupe.1G172500' => 'ppe', 'Prupe.1G196800' => 'ppe', 'Prupe.1G279700' => 'ppe', 'Prupe.2G026400' => 'ppe', 'Prupe.3G094000' => 'ppe', 'Prupe.4G287300' => 'ppe', 'QL01p022166' => 'qlo', 'QL01p051890' => 'qlo', 'QL02p009469' => 'qlo', 'QL02p046053' => 'qlo', 'QL02p057958' => 'qlo', 'QL02p093127' => 'qlo', 'QL03p006855' => 'qlo', 'QL03p071586' => 'qlo', 'QL04p000022' => 'qlo', 'QL04p000024' => 'qlo', 'QL04p003192' => 'qlo', 'QL05p011416' => 'qlo', 'QL06p039590' => 'qlo', 'QL06p052750' => 'qlo', 'QL06p053821' => 'qlo', 'QL07p025287' => 'qlo', 'QL09p033218' => 'qlo', 'QL09p040841' => 'qlo', 'QL10p020337' => 'qlo', 'QL10p027209' => 'qlo', 'QL10p027969' => 'qlo', 'QL10p048988' => 'qlo', 'QL11p001241' => 'qlo', 'QL11p028487' => 'qlo', 'RcHm_v2.0_Chr2g0105031' => 'rch', 'RcHm_v2.0_Chr2g0117811' => 'rch', 'RcHm_v2.0_Chr6g0270241' => 'rch', 'RcHm_v2.0_Chr7g0215961' => 'rch', 'RcHm_v2.0_Chr7g0231991' => 'rch', 'Rhsim01G0041500' => 'rsi', 'Rhsim01G0115000' => 'rsi', 'Rhsim01G0115400' => 'rsi', 'Rhsim01G0133600' => 'rsi', 'Rhsim01G0159900' => 'rsi', 'Rhsim02G0189400' => 'rsi', 'Rhsim03G0135600' => 'rsi', 'Rhsim03G0149900' => 'rsi', 'Rhsim04G0125600' => 'rsi', 'Rhsim05G0091700' => 'rsi', 'Rhsim05G0092900' => 'rsi', 'Rhsim06G0075000' => 'rsi', 'Rhsim07G0066400' => 'rsi', 'Rhsim07G0156400' => 'rsi', 'Rhsim07G0182200' => 'rsi', 'Rhsim07G0182300' => 'rsi', 'Rhsim08G0180400' => 'rsi', 'Rhsim09G0056800' => 'rsi', 'Rhsim10G0153300' => 'rsi', 'Rhsim11G0012700' => 'rsi', 'Rhsim12G0031800' => 'rsi', 'Rhsim12G0055400' => 'rsi', 'Rhsim12G0091400' => 'rsi', 'Rhsim13G0070800' => 'rsi', 'Rhsim13G0193300' => 'rsi', 'RhsimUnG0111600' => 'rsi', 'RhsimUnG0137500' => 'rsi', 'RhsimUnG0172900' => 'rsi', 'SGA_v2.0_scaffold11G05878' => 'sas', 'SGA_v2.0_scaffold167G38458' => 'sas', 'SGA_v2.0_scaffold19G08588' => 'sas', 'SGA_v2.0_scaffold239G43990' => 'sas', 'SGA_v2.0_scaffold260G45865' => 'sas', 'SGA_v2.0_scaffold309G48177' => 'sas', 'SGA_v2.0_scaffold76G25122' => 'sas', 'SGA_v2.0_scaffold85G26708' => 'sas', 'SHI13914' => 'shi', 'SHI30402' => 'shi', 'TWI09G0020' => 'twi', 'TWI09G0456' => 'twi', 'TWI09G1572' => 'twi', 'TWI12G0266' => 'twi', 'TWI12G1451' => 'twi', 'TWI14G0851' => 'twi', 'TWI15G0796' => 'twi', 'TWI18G0820' => 'twi', 'TWI18G1152' => 'twi', 'TWI23G0007' => 'twi', 'TWI23G0314' => 'twi', 'TWI31G0674' => 'twi', 'TWI31G0938' => 'twi', 'TWI34G0641' => 'twi', 'TWI34G1527' => 'twi', 'TWI36G0193' => 'twi', 'TWI36G0405' => 'twi', 'TWI38G0892' => 'twi', 'TWI38G0936' => 'twi', 'TWI38G2218' => 'twi', 'TWI53G0679' => 'twi', 'TWI53G0863' => 'twi', 'TWI53G1133' => 'twi', 'TWI60G0823' => 'twi', 'TWI63G0919' => 'twi', 'TWI63G1436' => 'twi', 'TWI73G0140' => 'twi', 'TWI73G0419' => 'twi', 'TWI73G0420' => 'twi', 'TWI73G1276' => 'twi', 'TWI74G0405' => 'twi', 'TWI74G0837' => 'twi', 'TWI75G0594' => 'twi', 'TWI75G1615' => 'twi', 'TWI77G0816' => 'twi', 'vmacro03831' => 'vma', 'vmacro13746' => 'vma', 'vmacro16089' => 'vma', 'vmacro22863' => 'vma', 'Zm00001eb085790' => 'zma', 'Zm00001eb114250' => 'zma', 'Zm00001eb138070' => 'zma', 'Zm00001eb167560' => 'zma', 'Zm00001eb199990' => 'zma', 'Zm00001eb368180' => 'zma', 'Zm00001eb382470' => 'zma' ) $gf_id = 'HOM05D001576' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001576' ) $data_identifier = 'HOM05D001576' $data_type = 'gf_id' $species_gene_counts = array( 'aox' => (int) 9, 'acertr' => (int) 3, 'cansat' => (int) 1, 'ccl' => (int) 4, 'cil' => (int) 145, 'camsi' => (int) 46, 'dca' => (int) 1, 'din' => (int) 1, 'fan' => (int) 12, 'fve' => (int) 9, 'gma' => (int) 5, 'han' => (int) 5, 'cav' => (int) 11, 'hma' => (int) 5, 'sun' => (int) 3, 'mdo' => (int) 3, 'mtr' => (int) 2, 'osa' => (int) 19, 'pgr' => (int) 1, 'ptr' => (int) 2, 'ppe' => (int) 6, 'qlo' => (int) 24, 'rch' => (int) 5, 'rsi' => (int) 28, 'sas' => (int) 8, 'shi' => (int) 2, 'twi' => (int) 35, 'vma' => (int) 4, 'zma' => (int) 7 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb382470' $species_info = array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ) $local_species = 'cil' $disabled = '' $selected = '' $num_hits = (int) 0
Warning (2): count(): Parameter must be an array or an object that implements Countable [APP/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp, line 33]Code Context $disabled = (!array_key_exists($local_species,$species_gene_counts))?"disabled":""; $selected = (isset($selected_species) && array_key_exists($local_species,$selected_species))?"checked='checked'":""; $num_hits = (array_key_exists($local_species,$species_gene_counts))?count($species_gene_counts[$local_species]):0; $viewFile = '/www/bioinformatics01_ro/plaza/_dev_instances/feedback/app/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp' $dataForView = array( 'sidebar_info' => array( 'gf_id' => 'HOM05D001576', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '406', 'num_species' => '29' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'Aqoxy1G01456' => 'aox', 'Aqoxy1G02949' => 'aox', 'Aqoxy3G01274' => 'aox', 'Aqoxy3G02110' => 'aox', 'Aqoxy3G02268' => 'aox', 'Aqoxy5G02702' => 'aox', 'Aqoxy5G02988' => 'aox', 'Aqoxy5G03427' => 'aox', 'Aqoxy6G02363' => 'aox', 'Atru.chr1.3225' => 'acertr', 'Atru.chr8.1198' => 'acertr', 'Atru.chr9.790' => 'acertr', 'CANSAT01G3197' => 'cansat', 'Ciclev10003979m.g' => 'ccl', 'Ciclev10017471m.g' => 'ccl', 'Ciclev10018206m.g' => 'ccl', 'Ciclev10033751m.g' => 'ccl', 'CiPaw.01G000900' => 'cil', 'CiPaw.01G001000' => 'cil', 'CiPaw.01G033500' => 'cil', 'CiPaw.01G060300' => 'cil', 'CiPaw.01G070200' => 'cil', 'CiPaw.01G075100' => 'cil', 'CiPaw.01G084700' => 'cil', 'CiPaw.01G087900' => 'cil', 'CiPaw.01G092600' => 'cil', 'CiPaw.01G097200' => 'cil', 'CiPaw.01G098300' => 'cil', 'CiPaw.01G110200' => 'cil', 'CiPaw.01G118700' => 'cil', 'CiPaw.01G121200' => 'cil', 'CiPaw.01G132500' => 'cil', 'CiPaw.01G146900' => 'cil', 'CiPaw.01G174000' => 'cil', 'CiPaw.01G179900' => 'cil', 'CiPaw.01G183400' => 'cil', 'CiPaw.01G240000' => 'cil', 'CiPaw.01G283500' => 'cil', 'CiPaw.01G307400' => 'cil', 'CiPaw.02G030800' => 'cil', 'CiPaw.02G047200' => 'cil', 'CiPaw.02G050500' => 'cil', 'CiPaw.02G069900' => 'cil', 'CiPaw.02G091600' => 'cil', 'CiPaw.02G095000' => 'cil', 'CiPaw.02G131900' => 'cil', 'CiPaw.03G043000' => 'cil', 'CiPaw.03G069900' => 'cil', 'CiPaw.03G088100' => 'cil', 'CiPaw.03G089300' => 'cil', 'CiPaw.03G093100' => 'cil', 'CiPaw.03G129800' => 'cil', 'CiPaw.03G131200' => 'cil', 'CiPaw.03G134500' => 'cil', 'CiPaw.03G152100' => 'cil', 'CiPaw.03G162700' => 'cil', 'CiPaw.03G172800' => 'cil', 'CiPaw.03G175800' => 'cil', 'CiPaw.03G181800' => 'cil', 'CiPaw.03G191400' => 'cil', 'CiPaw.03G198300' => 'cil', 'CiPaw.03G201300' => 'cil', 'CiPaw.03G224700' => 'cil', 'CiPaw.03G225000' => 'cil', 'CiPaw.04G065100' => 'cil', 'CiPaw.04G080400' => 'cil', 'CiPaw.04G113500' => 'cil', 'CiPaw.04G121900' => 'cil', 'CiPaw.04G144100' => 'cil', 'CiPaw.04G176500' => 'cil', 'CiPaw.05G086200' => 'cil', 'CiPaw.05G100200' => 'cil', 'CiPaw.05G114200' => 'cil', 'CiPaw.05G126800' => 'cil', 'CiPaw.05G228800' => 'cil', 'CiPaw.05G230600' => 'cil', 'CiPaw.05G236500' => 'cil', 'CiPaw.05G244800' => 'cil', 'CiPaw.06G026600' => 'cil', 'CiPaw.06G027900' => 'cil', 'CiPaw.06G051800' => 'cil', 'CiPaw.06G128500' => 'cil', 'CiPaw.06G165900' => 'cil', 'CiPaw.07G045400' => 'cil', 'CiPaw.07G048000' => 'cil', 'CiPaw.07G052000' => 'cil', 'CiPaw.07G073800' => 'cil', 'CiPaw.07G099700' => 'cil', 'CiPaw.07G108700' => 'cil', 'CiPaw.07G120000' => 'cil', 'CiPaw.07G134100' => 'cil', 'CiPaw.07G147000' => 'cil', 'CiPaw.07G149700' => 'cil', 'CiPaw.07G178300' => 'cil', 'CiPaw.07G184900' => 'cil', 'CiPaw.08G044500' => 'cil', 'CiPaw.08G046900' => 'cil', 'CiPaw.08G047300' => 'cil', 'CiPaw.08G115400' => 'cil', 'CiPaw.08G134700' => 'cil', 'CiPaw.08G157400' => 'cil', 'CiPaw.09G014300' => 'cil', 'CiPaw.09G088900' => 'cil', 'CiPaw.09G130900' => 'cil', 'CiPaw.09G133100' => 'cil', 'CiPaw.09G151300' => 'cil', 'CiPaw.09G172800' => 'cil', 'CiPaw.09G174900' => 'cil', 'CiPaw.09G175000' => 'cil', 'CiPaw.10G012800' => 'cil', 'CiPaw.10G028800' => 'cil', 'CiPaw.10G044700' => 'cil', 'CiPaw.10G067400' => 'cil', 'CiPaw.10G115900' => 'cil', 'CiPaw.10G126200' => 'cil', 'CiPaw.10G139700' => 'cil', 'CiPaw.10G155100' => 'cil', 'CiPaw.11G011300' => 'cil', 'CiPaw.11G025900' => 'cil', 'CiPaw.11G104100' => 'cil', 'CiPaw.11G142700' => 'cil', 'CiPaw.11G164500' => 'cil', 'CiPaw.11G189100' => 'cil', 'CiPaw.11G197100' => 'cil', 'CiPaw.12G006100' => 'cil', 'CiPaw.12G038500' => 'cil', 'CiPaw.12G041400' => 'cil', 'CiPaw.12G041600' => 'cil', 'CiPaw.12G051300' => 'cil', 'CiPaw.12G101800' => 'cil', 'CiPaw.12G107800' => 'cil', 'CiPaw.13G033200' => 'cil', 'CiPaw.13G129900' => 'cil', 'CiPaw.13G160200' => 'cil', 'CiPaw.14G018900' => 'cil', 'CiPaw.14G029000' => 'cil', 'CiPaw.14G031000' => 'cil', 'CiPaw.14G032000' => 'cil', 'CiPaw.14G032300' => 'cil', 'CiPaw.14G040600' => 'cil', 'CiPaw.14G060500' => 'cil', 'CiPaw.14G061500' => 'cil', 'CiPaw.14G077500' => 'cil', 'CiPaw.14G088300' => 'cil', 'CiPaw.14G108500' => 'cil', 'CiPaw.14G121300' => 'cil', 'CiPaw.14G133000' => 'cil', 'CiPaw.14G134600' => 'cil', 'CiPaw.15G027200' => 'cil', 'CiPaw.15G037700' => 'cil', 'CiPaw.15G050900' => 'cil', 'CiPaw.15G067200' => 'cil', 'CiPaw.15G072000' => 'cil', 'CiPaw.15G112900' => 'cil', 'CiPaw.15G133200' => 'cil', 'CiPaw.15G139500' => 'cil', 'CiPaw.15G155400' => 'cil', 'CiPaw.16G006000' => 'cil', 'CiPaw.16G013100' => 'cil', 'CiPaw.16G047100' => 'cil', 'CiPaw.16G048900' => 'cil', 'CiPaw.16G070300' => 'cil', 'CSS0000195' => 'camsi', 'CSS0001664' => 'camsi', 'CSS0002566' => 'camsi', 'CSS0003077' => 'camsi', 'CSS0004257' => 'camsi', 'CSS0004495' => 'camsi', 'CSS0004599' => 'camsi', 'CSS0004943' => 'camsi', 'CSS0005302' => 'camsi', 'CSS0006274' => 'camsi', 'CSS0006547' => 'camsi', 'CSS0006860' => 'camsi', 'CSS0008814' => 'camsi', 'CSS0008946' => 'camsi', 'CSS0009093' => 'camsi', 'CSS0010221' => 'camsi', 'CSS0010296' => 'camsi', 'CSS0010386' => 'camsi', 'CSS0010831' => 'camsi', 'CSS0011061' => 'camsi', 'CSS0012008' => 'camsi', 'CSS0012194' => 'camsi', 'CSS0013580' => 'camsi', 'CSS0014176' => 'camsi', 'CSS0014280' => 'camsi', 'CSS0014799' => 'camsi', 'CSS0015368' => 'camsi', 'CSS0017473' => 'camsi', 'CSS0019281' => 'camsi', 'CSS0021320' => 'camsi', 'CSS0021750' => 'camsi', 'CSS0023642' => 'camsi', 'CSS0023792' => 'camsi', 'CSS0031528' => 'camsi', 'CSS0033894' => 'camsi', 'CSS0034959' => 'camsi', 'CSS0035632' => 'camsi', 'CSS0038450' => 'camsi', 'CSS0039293' => 'camsi', 'CSS0041053' => 'camsi', 'CSS0041981' => 'camsi', 'CSS0042573' => 'camsi', 'CSS0042927' => 'camsi', 'CSS0047725' => 'camsi', 'CSS0049636' => 'camsi', 'CSS0050513' => 'camsi', 'DCAR_030203' => 'dca', 'Dinv07939' => 'din', 'FAN01G0456' => 'fan', 'FAN02G3001' => 'fan', 'FAN04G2781' => 'fan', 'FAN05G1385' => 'fan', 'FAN05G3062' => 'fan', 'FAN08G2267' => 'fan', 'FAN10G0481' => 'fan', 'FAN10G1257' => 'fan', 'FAN14G0954' => 'fan', 'FAN14G2347' => 'fan', 'FAN15G0187' => 'fan', 'FAN25G2214' => 'fan', 'FvH4_1g21031' => 'fve', 'FvH4_3g16231' => 'fve', 'FvH4_3g26413' => 'fve', 'FvH4_3g29014' => 'fve', 'FvH4_3g31921' => 'fve', 'FvH4_4g19882' => 'fve', 'FvH4_5g21960' => 'fve', 'FvH4_5g29683' => 'fve', 'FvH4_7g13271' => 'fve', 'Glyma.01G062500' => 'gma', 'Glyma.07G140900' => 'gma', 'Glyma.09G140900' => 'gma', 'Glyma.12G112700' => 'gma', 'Glyma.17G168800' => 'gma', 'HanXRQChr01g0027001' => 'han', 'HanXRQChr04g0120511' => 'han', 'HanXRQChr08g0232381' => 'han', 'HanXRQChr09g0265661' => 'han', 'HanXRQChr13g0416031' => 'han', 'Haze_05835' => 'cav', 'Haze_06597' => 'cav', 'Haze_07921' => 'cav', 'Haze_08599' => 'cav', 'Haze_10686' => 'cav', 'Haze_12994' => 'cav', 'Haze_13466' => 'cav', 'Haze_16101' => 'cav', 'Haze_17766' => 'cav', 'Haze_18456' => 'cav', 'Haze_20229' => 'cav', 'Hma1.2p1_0324F.1_g125640' => 'hma', 'Hma1.2p1_0733F.1_g210230' => 'hma', 'Hma1.2p1_0921F.1_g236870' => 'hma', 'Hma1.2p1_1313F.1_g274940' => 'hma', 'Hma1.2p1_3059F.1_g332230' => 'hma', 'Hund15925' => 'sun', 'Hund19562' => 'sun', 'Hund21925' => 'sun', 'MD03G1177400' => 'mdo', 'MD07G1026100' => 'mdo', 'MD17G1218600' => 'mdo', 'Medtr0867s0010' => 'mtr', 'Medtr6g081150' => 'mtr', 'Os01g0527900' => 'osa', 'Os02g0463725' => 'osa', 'Os02g0785600' => 'osa', 'Os03g0433733' => 'osa', 'Os04g0286500' => 'osa', 'Os05g0227800' => 'osa', 'Os06g0521000' => 'osa', 'Os06g0635500' => 'osa', 'Os06g0660650' => 'osa', 'Os07g0554400' => 'osa', 'Os08g0225900' => 'osa', 'Os08g0561000' => 'osa', 'Os09g0241700' => 'osa', 'Os09g0351900' => 'osa', 'Os11g0220700' => 'osa', 'Os11g0282700' => 'osa', 'Os12g0169300' => 'osa', 'Os12g0228500' => 'osa', 'Os12g0543800' => 'osa', 'PGR044G1547' => 'pgr', 'Potri.005G239150' => 'ptr', 'Potri.010G014250' => 'ptr', 'Prupe.1G172500' => 'ppe', 'Prupe.1G196800' => 'ppe', 'Prupe.1G279700' => 'ppe', 'Prupe.2G026400' => 'ppe', 'Prupe.3G094000' => 'ppe', 'Prupe.4G287300' => 'ppe', 'QL01p022166' => 'qlo', 'QL01p051890' => 'qlo', 'QL02p009469' => 'qlo', 'QL02p046053' => 'qlo', 'QL02p057958' => 'qlo', 'QL02p093127' => 'qlo', 'QL03p006855' => 'qlo', 'QL03p071586' => 'qlo', 'QL04p000022' => 'qlo', 'QL04p000024' => 'qlo', 'QL04p003192' => 'qlo', 'QL05p011416' => 'qlo', 'QL06p039590' => 'qlo', 'QL06p052750' => 'qlo', 'QL06p053821' => 'qlo', 'QL07p025287' => 'qlo', 'QL09p033218' => 'qlo', 'QL09p040841' => 'qlo', 'QL10p020337' => 'qlo', 'QL10p027209' => 'qlo', 'QL10p027969' => 'qlo', 'QL10p048988' => 'qlo', 'QL11p001241' => 'qlo', 'QL11p028487' => 'qlo', 'RcHm_v2.0_Chr2g0105031' => 'rch', 'RcHm_v2.0_Chr2g0117811' => 'rch', 'RcHm_v2.0_Chr6g0270241' => 'rch', 'RcHm_v2.0_Chr7g0215961' => 'rch', 'RcHm_v2.0_Chr7g0231991' => 'rch', 'Rhsim01G0041500' => 'rsi', 'Rhsim01G0115000' => 'rsi', 'Rhsim01G0115400' => 'rsi', 'Rhsim01G0133600' => 'rsi', 'Rhsim01G0159900' => 'rsi', 'Rhsim02G0189400' => 'rsi', 'Rhsim03G0135600' => 'rsi', 'Rhsim03G0149900' => 'rsi', 'Rhsim04G0125600' => 'rsi', 'Rhsim05G0091700' => 'rsi', 'Rhsim05G0092900' => 'rsi', 'Rhsim06G0075000' => 'rsi', 'Rhsim07G0066400' => 'rsi', 'Rhsim07G0156400' => 'rsi', 'Rhsim07G0182200' => 'rsi', 'Rhsim07G0182300' => 'rsi', 'Rhsim08G0180400' => 'rsi', 'Rhsim09G0056800' => 'rsi', 'Rhsim10G0153300' => 'rsi', 'Rhsim11G0012700' => 'rsi', 'Rhsim12G0031800' => 'rsi', 'Rhsim12G0055400' => 'rsi', 'Rhsim12G0091400' => 'rsi', 'Rhsim13G0070800' => 'rsi', 'Rhsim13G0193300' => 'rsi', 'RhsimUnG0111600' => 'rsi', 'RhsimUnG0137500' => 'rsi', 'RhsimUnG0172900' => 'rsi', 'SGA_v2.0_scaffold11G05878' => 'sas', 'SGA_v2.0_scaffold167G38458' => 'sas', 'SGA_v2.0_scaffold19G08588' => 'sas', 'SGA_v2.0_scaffold239G43990' => 'sas', 'SGA_v2.0_scaffold260G45865' => 'sas', 'SGA_v2.0_scaffold309G48177' => 'sas', 'SGA_v2.0_scaffold76G25122' => 'sas', 'SGA_v2.0_scaffold85G26708' => 'sas', 'SHI13914' => 'shi', 'SHI30402' => 'shi', 'TWI09G0020' => 'twi', 'TWI09G0456' => 'twi', 'TWI09G1572' => 'twi', 'TWI12G0266' => 'twi', 'TWI12G1451' => 'twi', 'TWI14G0851' => 'twi', 'TWI15G0796' => 'twi', 'TWI18G0820' => 'twi', 'TWI18G1152' => 'twi', 'TWI23G0007' => 'twi', 'TWI23G0314' => 'twi', 'TWI31G0674' => 'twi', 'TWI31G0938' => 'twi', 'TWI34G0641' => 'twi', 'TWI34G1527' => 'twi', 'TWI36G0193' => 'twi', 'TWI36G0405' => 'twi', 'TWI38G0892' => 'twi', 'TWI38G0936' => 'twi', 'TWI38G2218' => 'twi', 'TWI53G0679' => 'twi', 'TWI53G0863' => 'twi', 'TWI53G1133' => 'twi', 'TWI60G0823' => 'twi', 'TWI63G0919' => 'twi', 'TWI63G1436' => 'twi', 'TWI73G0140' => 'twi', 'TWI73G0419' => 'twi', 'TWI73G0420' => 'twi', 'TWI73G1276' => 'twi', 'TWI74G0405' => 'twi', 'TWI74G0837' => 'twi', 'TWI75G0594' => 'twi', 'TWI75G1615' => 'twi', 'TWI77G0816' => 'twi', 'vmacro03831' => 'vma', 'vmacro13746' => 'vma', 'vmacro16089' => 'vma', 'vmacro22863' => 'vma', 'Zm00001eb085790' => 'zma', 'Zm00001eb114250' => 'zma', 'Zm00001eb138070' => 'zma', 'Zm00001eb167560' => 'zma', 'Zm00001eb199990' => 'zma', 'Zm00001eb368180' => 'zma', 'Zm00001eb382470' => 'zma' ), 'gf_id' => 'HOM05D001576', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001576' ), 'data_identifier' => 'HOM05D001576', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001576', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '406', 'num_species' => '29' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'Aqoxy1G01456' => 'aox', 'Aqoxy1G02949' => 'aox', 'Aqoxy3G01274' => 'aox', 'Aqoxy3G02110' => 'aox', 'Aqoxy3G02268' => 'aox', 'Aqoxy5G02702' => 'aox', 'Aqoxy5G02988' => 'aox', 'Aqoxy5G03427' => 'aox', 'Aqoxy6G02363' => 'aox', 'Atru.chr1.3225' => 'acertr', 'Atru.chr8.1198' => 'acertr', 'Atru.chr9.790' => 'acertr', 'CANSAT01G3197' => 'cansat', 'Ciclev10003979m.g' => 'ccl', 'Ciclev10017471m.g' => 'ccl', 'Ciclev10018206m.g' => 'ccl', 'Ciclev10033751m.g' => 'ccl', 'CiPaw.01G000900' => 'cil', 'CiPaw.01G001000' => 'cil', 'CiPaw.01G033500' => 'cil', 'CiPaw.01G060300' => 'cil', 'CiPaw.01G070200' => 'cil', 'CiPaw.01G075100' => 'cil', 'CiPaw.01G084700' => 'cil', 'CiPaw.01G087900' => 'cil', 'CiPaw.01G092600' => 'cil', 'CiPaw.01G097200' => 'cil', 'CiPaw.01G098300' => 'cil', 'CiPaw.01G110200' => 'cil', 'CiPaw.01G118700' => 'cil', 'CiPaw.01G121200' => 'cil', 'CiPaw.01G132500' => 'cil', 'CiPaw.01G146900' => 'cil', 'CiPaw.01G174000' => 'cil', 'CiPaw.01G179900' => 'cil', 'CiPaw.01G183400' => 'cil', 'CiPaw.01G240000' => 'cil', 'CiPaw.01G283500' => 'cil', 'CiPaw.01G307400' => 'cil', 'CiPaw.02G030800' => 'cil', 'CiPaw.02G047200' => 'cil', 'CiPaw.02G050500' => 'cil', 'CiPaw.02G069900' => 'cil', 'CiPaw.02G091600' => 'cil', 'CiPaw.02G095000' => 'cil', 'CiPaw.02G131900' => 'cil', 'CiPaw.03G043000' => 'cil', 'CiPaw.03G069900' => 'cil', 'CiPaw.03G088100' => 'cil', 'CiPaw.03G089300' => 'cil', 'CiPaw.03G093100' => 'cil', 'CiPaw.03G129800' => 'cil', 'CiPaw.03G131200' => 'cil', 'CiPaw.03G134500' => 'cil', 'CiPaw.03G152100' => 'cil', 'CiPaw.03G162700' => 'cil', 'CiPaw.03G172800' => 'cil', 'CiPaw.03G175800' => 'cil', 'CiPaw.03G181800' => 'cil', 'CiPaw.03G191400' => 'cil', 'CiPaw.03G198300' => 'cil', 'CiPaw.03G201300' => 'cil', 'CiPaw.03G224700' => 'cil', 'CiPaw.03G225000' => 'cil', 'CiPaw.04G065100' => 'cil', 'CiPaw.04G080400' => 'cil', 'CiPaw.04G113500' => 'cil', 'CiPaw.04G121900' => 'cil', 'CiPaw.04G144100' => 'cil', 'CiPaw.04G176500' => 'cil', 'CiPaw.05G086200' => 'cil', 'CiPaw.05G100200' => 'cil', 'CiPaw.05G114200' => 'cil', 'CiPaw.05G126800' => 'cil', 'CiPaw.05G228800' => 'cil', 'CiPaw.05G230600' => 'cil', 'CiPaw.05G236500' => 'cil', 'CiPaw.05G244800' => 'cil', 'CiPaw.06G026600' => 'cil', 'CiPaw.06G027900' => 'cil', 'CiPaw.06G051800' => 'cil', 'CiPaw.06G128500' => 'cil', 'CiPaw.06G165900' => 'cil', 'CiPaw.07G045400' => 'cil', 'CiPaw.07G048000' => 'cil', 'CiPaw.07G052000' => 'cil', 'CiPaw.07G073800' => 'cil', 'CiPaw.07G099700' => 'cil', 'CiPaw.07G108700' => 'cil', 'CiPaw.07G120000' => 'cil', 'CiPaw.07G134100' => 'cil', 'CiPaw.07G147000' => 'cil', 'CiPaw.07G149700' => 'cil', 'CiPaw.07G178300' => 'cil', 'CiPaw.07G184900' => 'cil', 'CiPaw.08G044500' => 'cil', 'CiPaw.08G046900' => 'cil', 'CiPaw.08G047300' => 'cil', 'CiPaw.08G115400' => 'cil', 'CiPaw.08G134700' => 'cil', 'CiPaw.08G157400' => 'cil', 'CiPaw.09G014300' => 'cil', 'CiPaw.09G088900' => 'cil', 'CiPaw.09G130900' => 'cil', 'CiPaw.09G133100' => 'cil', 'CiPaw.09G151300' => 'cil', 'CiPaw.09G172800' => 'cil', 'CiPaw.09G174900' => 'cil', 'CiPaw.09G175000' => 'cil', 'CiPaw.10G012800' => 'cil', 'CiPaw.10G028800' => 'cil', 'CiPaw.10G044700' => 'cil', 'CiPaw.10G067400' => 'cil', 'CiPaw.10G115900' => 'cil', 'CiPaw.10G126200' => 'cil', 'CiPaw.10G139700' => 'cil', 'CiPaw.10G155100' => 'cil', 'CiPaw.11G011300' => 'cil', 'CiPaw.11G025900' => 'cil', 'CiPaw.11G104100' => 'cil', 'CiPaw.11G142700' => 'cil', 'CiPaw.11G164500' => 'cil', 'CiPaw.11G189100' => 'cil', 'CiPaw.11G197100' => 'cil', 'CiPaw.12G006100' => 'cil', 'CiPaw.12G038500' => 'cil', 'CiPaw.12G041400' => 'cil', 'CiPaw.12G041600' => 'cil', 'CiPaw.12G051300' => 'cil', 'CiPaw.12G101800' => 'cil', 'CiPaw.12G107800' => 'cil', 'CiPaw.13G033200' => 'cil', 'CiPaw.13G129900' => 'cil', 'CiPaw.13G160200' => 'cil', 'CiPaw.14G018900' => 'cil', 'CiPaw.14G029000' => 'cil', 'CiPaw.14G031000' => 'cil', 'CiPaw.14G032000' => 'cil', 'CiPaw.14G032300' => 'cil', 'CiPaw.14G040600' => 'cil', 'CiPaw.14G060500' => 'cil', 'CiPaw.14G061500' => 'cil', 'CiPaw.14G077500' => 'cil', 'CiPaw.14G088300' => 'cil', 'CiPaw.14G108500' => 'cil', 'CiPaw.14G121300' => 'cil', 'CiPaw.14G133000' => 'cil', 'CiPaw.14G134600' => 'cil', 'CiPaw.15G027200' => 'cil', 'CiPaw.15G037700' => 'cil', 'CiPaw.15G050900' => 'cil', 'CiPaw.15G067200' => 'cil', 'CiPaw.15G072000' => 'cil', 'CiPaw.15G112900' => 'cil', 'CiPaw.15G133200' => 'cil', 'CiPaw.15G139500' => 'cil', 'CiPaw.15G155400' => 'cil', 'CiPaw.16G006000' => 'cil', 'CiPaw.16G013100' => 'cil', 'CiPaw.16G047100' => 'cil', 'CiPaw.16G048900' => 'cil', 'CiPaw.16G070300' => 'cil', 'CSS0000195' => 'camsi', 'CSS0001664' => 'camsi', 'CSS0002566' => 'camsi', 'CSS0003077' => 'camsi', 'CSS0004257' => 'camsi', 'CSS0004495' => 'camsi', 'CSS0004599' => 'camsi', 'CSS0004943' => 'camsi', 'CSS0005302' => 'camsi', 'CSS0006274' => 'camsi', 'CSS0006547' => 'camsi', 'CSS0006860' => 'camsi', 'CSS0008814' => 'camsi', 'CSS0008946' => 'camsi', 'CSS0009093' => 'camsi', 'CSS0010221' => 'camsi', 'CSS0010296' => 'camsi', 'CSS0010386' => 'camsi', 'CSS0010831' => 'camsi', 'CSS0011061' => 'camsi', 'CSS0012008' => 'camsi', 'CSS0012194' => 'camsi', 'CSS0013580' => 'camsi', 'CSS0014176' => 'camsi', 'CSS0014280' => 'camsi', 'CSS0014799' => 'camsi', 'CSS0015368' => 'camsi', 'CSS0017473' => 'camsi', 'CSS0019281' => 'camsi', 'CSS0021320' => 'camsi', 'CSS0021750' => 'camsi', 'CSS0023642' => 'camsi', 'CSS0023792' => 'camsi', 'CSS0031528' => 'camsi', 'CSS0033894' => 'camsi', 'CSS0034959' => 'camsi', 'CSS0035632' => 'camsi', 'CSS0038450' => 'camsi', 'CSS0039293' => 'camsi', 'CSS0041053' => 'camsi', 'CSS0041981' => 'camsi', 'CSS0042573' => 'camsi', 'CSS0042927' => 'camsi', 'CSS0047725' => 'camsi', 'CSS0049636' => 'camsi', 'CSS0050513' => 'camsi', 'DCAR_030203' => 'dca', 'Dinv07939' => 'din', 'FAN01G0456' => 'fan', 'FAN02G3001' => 'fan', 'FAN04G2781' => 'fan', 'FAN05G1385' => 'fan', 'FAN05G3062' => 'fan', 'FAN08G2267' => 'fan', 'FAN10G0481' => 'fan', 'FAN10G1257' => 'fan', 'FAN14G0954' => 'fan', 'FAN14G2347' => 'fan', 'FAN15G0187' => 'fan', 'FAN25G2214' => 'fan', 'FvH4_1g21031' => 'fve', 'FvH4_3g16231' => 'fve', 'FvH4_3g26413' => 'fve', 'FvH4_3g29014' => 'fve', 'FvH4_3g31921' => 'fve', 'FvH4_4g19882' => 'fve', 'FvH4_5g21960' => 'fve', 'FvH4_5g29683' => 'fve', 'FvH4_7g13271' => 'fve', 'Glyma.01G062500' => 'gma', 'Glyma.07G140900' => 'gma', 'Glyma.09G140900' => 'gma', 'Glyma.12G112700' => 'gma', 'Glyma.17G168800' => 'gma', 'HanXRQChr01g0027001' => 'han', 'HanXRQChr04g0120511' => 'han', 'HanXRQChr08g0232381' => 'han', 'HanXRQChr09g0265661' => 'han', 'HanXRQChr13g0416031' => 'han', 'Haze_05835' => 'cav', 'Haze_06597' => 'cav', 'Haze_07921' => 'cav', 'Haze_08599' => 'cav', 'Haze_10686' => 'cav', 'Haze_12994' => 'cav', 'Haze_13466' => 'cav', 'Haze_16101' => 'cav', 'Haze_17766' => 'cav', 'Haze_18456' => 'cav', 'Haze_20229' => 'cav', 'Hma1.2p1_0324F.1_g125640' => 'hma', 'Hma1.2p1_0733F.1_g210230' => 'hma', 'Hma1.2p1_0921F.1_g236870' => 'hma', 'Hma1.2p1_1313F.1_g274940' => 'hma', 'Hma1.2p1_3059F.1_g332230' => 'hma', 'Hund15925' => 'sun', 'Hund19562' => 'sun', 'Hund21925' => 'sun', 'MD03G1177400' => 'mdo', 'MD07G1026100' => 'mdo', 'MD17G1218600' => 'mdo', 'Medtr0867s0010' => 'mtr', 'Medtr6g081150' => 'mtr', 'Os01g0527900' => 'osa', 'Os02g0463725' => 'osa', 'Os02g0785600' => 'osa', 'Os03g0433733' => 'osa', 'Os04g0286500' => 'osa', 'Os05g0227800' => 'osa', 'Os06g0521000' => 'osa', 'Os06g0635500' => 'osa', 'Os06g0660650' => 'osa', 'Os07g0554400' => 'osa', 'Os08g0225900' => 'osa', 'Os08g0561000' => 'osa', 'Os09g0241700' => 'osa', 'Os09g0351900' => 'osa', 'Os11g0220700' => 'osa', 'Os11g0282700' => 'osa', 'Os12g0169300' => 'osa', 'Os12g0228500' => 'osa', 'Os12g0543800' => 'osa', 'PGR044G1547' => 'pgr', 'Potri.005G239150' => 'ptr', 'Potri.010G014250' => 'ptr', 'Prupe.1G172500' => 'ppe', 'Prupe.1G196800' => 'ppe', 'Prupe.1G279700' => 'ppe', 'Prupe.2G026400' => 'ppe', 'Prupe.3G094000' => 'ppe', 'Prupe.4G287300' => 'ppe', 'QL01p022166' => 'qlo', 'QL01p051890' => 'qlo', 'QL02p009469' => 'qlo', 'QL02p046053' => 'qlo', 'QL02p057958' => 'qlo', 'QL02p093127' => 'qlo', 'QL03p006855' => 'qlo', 'QL03p071586' => 'qlo', 'QL04p000022' => 'qlo', 'QL04p000024' => 'qlo', 'QL04p003192' => 'qlo', 'QL05p011416' => 'qlo', 'QL06p039590' => 'qlo', 'QL06p052750' => 'qlo', 'QL06p053821' => 'qlo', 'QL07p025287' => 'qlo', 'QL09p033218' => 'qlo', 'QL09p040841' => 'qlo', 'QL10p020337' => 'qlo', 'QL10p027209' => 'qlo', 'QL10p027969' => 'qlo', 'QL10p048988' => 'qlo', 'QL11p001241' => 'qlo', 'QL11p028487' => 'qlo', 'RcHm_v2.0_Chr2g0105031' => 'rch', 'RcHm_v2.0_Chr2g0117811' => 'rch', 'RcHm_v2.0_Chr6g0270241' => 'rch', 'RcHm_v2.0_Chr7g0215961' => 'rch', 'RcHm_v2.0_Chr7g0231991' => 'rch', 'Rhsim01G0041500' => 'rsi', 'Rhsim01G0115000' => 'rsi', 'Rhsim01G0115400' => 'rsi', 'Rhsim01G0133600' => 'rsi', 'Rhsim01G0159900' => 'rsi', 'Rhsim02G0189400' => 'rsi', 'Rhsim03G0135600' => 'rsi', 'Rhsim03G0149900' => 'rsi', 'Rhsim04G0125600' => 'rsi', 'Rhsim05G0091700' => 'rsi', 'Rhsim05G0092900' => 'rsi', 'Rhsim06G0075000' => 'rsi', 'Rhsim07G0066400' => 'rsi', 'Rhsim07G0156400' => 'rsi', 'Rhsim07G0182200' => 'rsi', 'Rhsim07G0182300' => 'rsi', 'Rhsim08G0180400' => 'rsi', 'Rhsim09G0056800' => 'rsi', 'Rhsim10G0153300' => 'rsi', 'Rhsim11G0012700' => 'rsi', 'Rhsim12G0031800' => 'rsi', 'Rhsim12G0055400' => 'rsi', 'Rhsim12G0091400' => 'rsi', 'Rhsim13G0070800' => 'rsi', 'Rhsim13G0193300' => 'rsi', 'RhsimUnG0111600' => 'rsi', 'RhsimUnG0137500' => 'rsi', 'RhsimUnG0172900' => 'rsi', 'SGA_v2.0_scaffold11G05878' => 'sas', 'SGA_v2.0_scaffold167G38458' => 'sas', 'SGA_v2.0_scaffold19G08588' => 'sas', 'SGA_v2.0_scaffold239G43990' => 'sas', 'SGA_v2.0_scaffold260G45865' => 'sas', 'SGA_v2.0_scaffold309G48177' => 'sas', 'SGA_v2.0_scaffold76G25122' => 'sas', 'SGA_v2.0_scaffold85G26708' => 'sas', 'SHI13914' => 'shi', 'SHI30402' => 'shi', 'TWI09G0020' => 'twi', 'TWI09G0456' => 'twi', 'TWI09G1572' => 'twi', 'TWI12G0266' => 'twi', 'TWI12G1451' => 'twi', 'TWI14G0851' => 'twi', 'TWI15G0796' => 'twi', 'TWI18G0820' => 'twi', 'TWI18G1152' => 'twi', 'TWI23G0007' => 'twi', 'TWI23G0314' => 'twi', 'TWI31G0674' => 'twi', 'TWI31G0938' => 'twi', 'TWI34G0641' => 'twi', 'TWI34G1527' => 'twi', 'TWI36G0193' => 'twi', 'TWI36G0405' => 'twi', 'TWI38G0892' => 'twi', 'TWI38G0936' => 'twi', 'TWI38G2218' => 'twi', 'TWI53G0679' => 'twi', 'TWI53G0863' => 'twi', 'TWI53G1133' => 'twi', 'TWI60G0823' => 'twi', 'TWI63G0919' => 'twi', 'TWI63G1436' => 'twi', 'TWI73G0140' => 'twi', 'TWI73G0419' => 'twi', 'TWI73G0420' => 'twi', 'TWI73G1276' => 'twi', 'TWI74G0405' => 'twi', 'TWI74G0837' => 'twi', 'TWI75G0594' => 'twi', 'TWI75G1615' => 'twi', 'TWI77G0816' => 'twi', 'vmacro03831' => 'vma', 'vmacro13746' => 'vma', 'vmacro16089' => 'vma', 'vmacro22863' => 'vma', 'Zm00001eb085790' => 'zma', 'Zm00001eb114250' => 'zma', 'Zm00001eb138070' => 'zma', 'Zm00001eb167560' => 'zma', 'Zm00001eb199990' => 'zma', 'Zm00001eb368180' => 'zma', 'Zm00001eb382470' => 'zma' ) $gf_id = 'HOM05D001576' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001576' ) $data_identifier = 'HOM05D001576' $data_type = 'gf_id' $species_gene_counts = array( 'aox' => (int) 9, 'acertr' => (int) 3, 'cansat' => (int) 1, 'ccl' => (int) 4, 'cil' => (int) 145, 'camsi' => (int) 46, 'dca' => (int) 1, 'din' => (int) 1, 'fan' => (int) 12, 'fve' => (int) 9, 'gma' => (int) 5, 'han' => (int) 5, 'cav' => (int) 11, 'hma' => (int) 5, 'sun' => (int) 3, 'mdo' => (int) 3, 'mtr' => (int) 2, 'osa' => (int) 19, 'pgr' => (int) 1, 'ptr' => (int) 2, 'ppe' => (int) 6, 'qlo' => (int) 24, 'rch' => (int) 5, 'rsi' => (int) 28, 'sas' => (int) 8, 'shi' => (int) 2, 'twi' => (int) 35, 'vma' => (int) 4, 'zma' => (int) 7 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb382470' $species_info = array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ) $local_species = 'ccl' $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' => 'HOM05D001576', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '406', 'num_species' => '29' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'Aqoxy1G01456' => 'aox', 'Aqoxy1G02949' => 'aox', 'Aqoxy3G01274' => 'aox', 'Aqoxy3G02110' => 'aox', 'Aqoxy3G02268' => 'aox', 'Aqoxy5G02702' => 'aox', 'Aqoxy5G02988' => 'aox', 'Aqoxy5G03427' => 'aox', 'Aqoxy6G02363' => 'aox', 'Atru.chr1.3225' => 'acertr', 'Atru.chr8.1198' => 'acertr', 'Atru.chr9.790' => 'acertr', 'CANSAT01G3197' => 'cansat', 'Ciclev10003979m.g' => 'ccl', 'Ciclev10017471m.g' => 'ccl', 'Ciclev10018206m.g' => 'ccl', 'Ciclev10033751m.g' => 'ccl', 'CiPaw.01G000900' => 'cil', 'CiPaw.01G001000' => 'cil', 'CiPaw.01G033500' => 'cil', 'CiPaw.01G060300' => 'cil', 'CiPaw.01G070200' => 'cil', 'CiPaw.01G075100' => 'cil', 'CiPaw.01G084700' => 'cil', 'CiPaw.01G087900' => 'cil', 'CiPaw.01G092600' => 'cil', 'CiPaw.01G097200' => 'cil', 'CiPaw.01G098300' => 'cil', 'CiPaw.01G110200' => 'cil', 'CiPaw.01G118700' => 'cil', 'CiPaw.01G121200' => 'cil', 'CiPaw.01G132500' => 'cil', 'CiPaw.01G146900' => 'cil', 'CiPaw.01G174000' => 'cil', 'CiPaw.01G179900' => 'cil', 'CiPaw.01G183400' => 'cil', 'CiPaw.01G240000' => 'cil', 'CiPaw.01G283500' => 'cil', 'CiPaw.01G307400' => 'cil', 'CiPaw.02G030800' => 'cil', 'CiPaw.02G047200' => 'cil', 'CiPaw.02G050500' => 'cil', 'CiPaw.02G069900' => 'cil', 'CiPaw.02G091600' => 'cil', 'CiPaw.02G095000' => 'cil', 'CiPaw.02G131900' => 'cil', 'CiPaw.03G043000' => 'cil', 'CiPaw.03G069900' => 'cil', 'CiPaw.03G088100' => 'cil', 'CiPaw.03G089300' => 'cil', 'CiPaw.03G093100' => 'cil', 'CiPaw.03G129800' => 'cil', 'CiPaw.03G131200' => 'cil', 'CiPaw.03G134500' => 'cil', 'CiPaw.03G152100' => 'cil', 'CiPaw.03G162700' => 'cil', 'CiPaw.03G172800' => 'cil', 'CiPaw.03G175800' => 'cil', 'CiPaw.03G181800' => 'cil', 'CiPaw.03G191400' => 'cil', 'CiPaw.03G198300' => 'cil', 'CiPaw.03G201300' => 'cil', 'CiPaw.03G224700' => 'cil', 'CiPaw.03G225000' => 'cil', 'CiPaw.04G065100' => 'cil', 'CiPaw.04G080400' => 'cil', 'CiPaw.04G113500' => 'cil', 'CiPaw.04G121900' => 'cil', 'CiPaw.04G144100' => 'cil', 'CiPaw.04G176500' => 'cil', 'CiPaw.05G086200' => 'cil', 'CiPaw.05G100200' => 'cil', 'CiPaw.05G114200' => 'cil', 'CiPaw.05G126800' => 'cil', 'CiPaw.05G228800' => 'cil', 'CiPaw.05G230600' => 'cil', 'CiPaw.05G236500' => 'cil', 'CiPaw.05G244800' => 'cil', 'CiPaw.06G026600' => 'cil', 'CiPaw.06G027900' => 'cil', 'CiPaw.06G051800' => 'cil', 'CiPaw.06G128500' => 'cil', 'CiPaw.06G165900' => 'cil', 'CiPaw.07G045400' => 'cil', 'CiPaw.07G048000' => 'cil', 'CiPaw.07G052000' => 'cil', 'CiPaw.07G073800' => 'cil', 'CiPaw.07G099700' => 'cil', 'CiPaw.07G108700' => 'cil', 'CiPaw.07G120000' => 'cil', 'CiPaw.07G134100' => 'cil', 'CiPaw.07G147000' => 'cil', 'CiPaw.07G149700' => 'cil', 'CiPaw.07G178300' => 'cil', 'CiPaw.07G184900' => 'cil', 'CiPaw.08G044500' => 'cil', 'CiPaw.08G046900' => 'cil', 'CiPaw.08G047300' => 'cil', 'CiPaw.08G115400' => 'cil', 'CiPaw.08G134700' => 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'TWI09G0020' => 'twi', 'TWI09G0456' => 'twi', 'TWI09G1572' => 'twi', 'TWI12G0266' => 'twi', 'TWI12G1451' => 'twi', 'TWI14G0851' => 'twi', 'TWI15G0796' => 'twi', 'TWI18G0820' => 'twi', 'TWI18G1152' => 'twi', 'TWI23G0007' => 'twi', 'TWI23G0314' => 'twi', 'TWI31G0674' => 'twi', 'TWI31G0938' => 'twi', 'TWI34G0641' => 'twi', 'TWI34G1527' => 'twi', 'TWI36G0193' => 'twi', 'TWI36G0405' => 'twi', 'TWI38G0892' => 'twi', 'TWI38G0936' => 'twi', 'TWI38G2218' => 'twi', 'TWI53G0679' => 'twi', 'TWI53G0863' => 'twi', 'TWI53G1133' => 'twi', 'TWI60G0823' => 'twi', 'TWI63G0919' => 'twi', 'TWI63G1436' => 'twi', 'TWI73G0140' => 'twi', 'TWI73G0419' => 'twi', 'TWI73G0420' => 'twi', 'TWI73G1276' => 'twi', 'TWI74G0405' => 'twi', 'TWI74G0837' => 'twi', 'TWI75G0594' => 'twi', 'TWI75G1615' => 'twi', 'TWI77G0816' => 'twi', 'vmacro03831' => 'vma', 'vmacro13746' => 'vma', 'vmacro16089' => 'vma', 'vmacro22863' => 'vma', 'Zm00001eb085790' => 'zma', 'Zm00001eb114250' => 'zma', 'Zm00001eb138070' => 'zma', 'Zm00001eb167560' => 'zma', 'Zm00001eb199990' => 'zma', 'Zm00001eb368180' => 'zma', 'Zm00001eb382470' => 'zma' ), 'gf_id' => 'HOM05D001576', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001576' ), 'data_identifier' => 'HOM05D001576', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001576', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '406', 'num_species' => '29' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'Aqoxy1G01456' => 'aox', 'Aqoxy1G02949' => 'aox', 'Aqoxy3G01274' => 'aox', 'Aqoxy3G02110' => 'aox', 'Aqoxy3G02268' => 'aox', 'Aqoxy5G02702' => 'aox', 'Aqoxy5G02988' => 'aox', 'Aqoxy5G03427' => 'aox', 'Aqoxy6G02363' => 'aox', 'Atru.chr1.3225' => 'acertr', 'Atru.chr8.1198' => 'acertr', 'Atru.chr9.790' => 'acertr', 'CANSAT01G3197' => 'cansat', 'Ciclev10003979m.g' => 'ccl', 'Ciclev10017471m.g' => 'ccl', 'Ciclev10018206m.g' => 'ccl', 'Ciclev10033751m.g' => 'ccl', 'CiPaw.01G000900' => 'cil', 'CiPaw.01G001000' => 'cil', 'CiPaw.01G033500' => 'cil', 'CiPaw.01G060300' => 'cil', 'CiPaw.01G070200' => 'cil', 'CiPaw.01G075100' => 'cil', 'CiPaw.01G084700' => 'cil', 'CiPaw.01G087900' => 'cil', 'CiPaw.01G092600' => 'cil', 'CiPaw.01G097200' => 'cil', 'CiPaw.01G098300' => 'cil', 'CiPaw.01G110200' => 'cil', 'CiPaw.01G118700' => 'cil', 'CiPaw.01G121200' => 'cil', 'CiPaw.01G132500' => 'cil', 'CiPaw.01G146900' => 'cil', 'CiPaw.01G174000' => 'cil', 'CiPaw.01G179900' => 'cil', 'CiPaw.01G183400' => 'cil', 'CiPaw.01G240000' => 'cil', 'CiPaw.01G283500' => 'cil', 'CiPaw.01G307400' => 'cil', 'CiPaw.02G030800' => 'cil', 'CiPaw.02G047200' => 'cil', 'CiPaw.02G050500' => 'cil', 'CiPaw.02G069900' => 'cil', 'CiPaw.02G091600' => 'cil', 'CiPaw.02G095000' => 'cil', 'CiPaw.02G131900' => 'cil', 'CiPaw.03G043000' => 'cil', 'CiPaw.03G069900' => 'cil', 'CiPaw.03G088100' => 'cil', 'CiPaw.03G089300' => 'cil', 'CiPaw.03G093100' => 'cil', 'CiPaw.03G129800' => 'cil', 'CiPaw.03G131200' => 'cil', 'CiPaw.03G134500' => 'cil', 'CiPaw.03G152100' => 'cil', 'CiPaw.03G162700' => 'cil', 'CiPaw.03G172800' => 'cil', 'CiPaw.03G175800' => 'cil', 'CiPaw.03G181800' => 'cil', 'CiPaw.03G191400' => 'cil', 'CiPaw.03G198300' => 'cil', 'CiPaw.03G201300' => 'cil', 'CiPaw.03G224700' => 'cil', 'CiPaw.03G225000' => 'cil', 'CiPaw.04G065100' => 'cil', 'CiPaw.04G080400' => 'cil', 'CiPaw.04G113500' => 'cil', 'CiPaw.04G121900' => 'cil', 'CiPaw.04G144100' => 'cil', 'CiPaw.04G176500' => 'cil', 'CiPaw.05G086200' => 'cil', 'CiPaw.05G100200' => 'cil', 'CiPaw.05G114200' => 'cil', 'CiPaw.05G126800' => 'cil', 'CiPaw.05G228800' => 'cil', 'CiPaw.05G230600' => 'cil', 'CiPaw.05G236500' => 'cil', 'CiPaw.05G244800' => 'cil', 'CiPaw.06G026600' => 'cil', 'CiPaw.06G027900' => 'cil', 'CiPaw.06G051800' => 'cil', 'CiPaw.06G128500' => 'cil', 'CiPaw.06G165900' => 'cil', 'CiPaw.07G045400' => 'cil', 'CiPaw.07G048000' => 'cil', 'CiPaw.07G052000' => 'cil', 'CiPaw.07G073800' => 'cil', 'CiPaw.07G099700' => 'cil', 'CiPaw.07G108700' => 'cil', 'CiPaw.07G120000' => 'cil', 'CiPaw.07G134100' => 'cil', 'CiPaw.07G147000' => 'cil', 'CiPaw.07G149700' => 'cil', 'CiPaw.07G178300' => 'cil', 'CiPaw.07G184900' => 'cil', 'CiPaw.08G044500' => 'cil', 'CiPaw.08G046900' => 'cil', 'CiPaw.08G047300' => 'cil', 'CiPaw.08G115400' => 'cil', 'CiPaw.08G134700' => 'cil', 'CiPaw.08G157400' => 'cil', 'CiPaw.09G014300' => 'cil', 'CiPaw.09G088900' => 'cil', 'CiPaw.09G130900' => 'cil', 'CiPaw.09G133100' => 'cil', 'CiPaw.09G151300' => 'cil', 'CiPaw.09G172800' => 'cil', 'CiPaw.09G174900' => 'cil', 'CiPaw.09G175000' => 'cil', 'CiPaw.10G012800' => 'cil', 'CiPaw.10G028800' => 'cil', 'CiPaw.10G044700' => 'cil', 'CiPaw.10G067400' => 'cil', 'CiPaw.10G115900' => 'cil', 'CiPaw.10G126200' => 'cil', 'CiPaw.10G139700' => 'cil', 'CiPaw.10G155100' => 'cil', 'CiPaw.11G011300' => 'cil', 'CiPaw.11G025900' => 'cil', 'CiPaw.11G104100' => 'cil', 'CiPaw.11G142700' => 'cil', 'CiPaw.11G164500' => 'cil', 'CiPaw.11G189100' => 'cil', 'CiPaw.11G197100' => 'cil', 'CiPaw.12G006100' => 'cil', 'CiPaw.12G038500' => 'cil', 'CiPaw.12G041400' => 'cil', 'CiPaw.12G041600' => 'cil', 'CiPaw.12G051300' => 'cil', 'CiPaw.12G101800' => 'cil', 'CiPaw.12G107800' => 'cil', 'CiPaw.13G033200' => 'cil', 'CiPaw.13G129900' => 'cil', 'CiPaw.13G160200' => 'cil', 'CiPaw.14G018900' => 'cil', 'CiPaw.14G029000' => 'cil', 'CiPaw.14G031000' => 'cil', 'CiPaw.14G032000' => 'cil', 'CiPaw.14G032300' => 'cil', 'CiPaw.14G040600' => 'cil', 'CiPaw.14G060500' => 'cil', 'CiPaw.14G061500' => 'cil', 'CiPaw.14G077500' => 'cil', 'CiPaw.14G088300' => 'cil', 'CiPaw.14G108500' => 'cil', 'CiPaw.14G121300' => 'cil', 'CiPaw.14G133000' => 'cil', 'CiPaw.14G134600' => 'cil', 'CiPaw.15G027200' => 'cil', 'CiPaw.15G037700' => 'cil', 'CiPaw.15G050900' => 'cil', 'CiPaw.15G067200' => 'cil', 'CiPaw.15G072000' => 'cil', 'CiPaw.15G112900' => 'cil', 'CiPaw.15G133200' => 'cil', 'CiPaw.15G139500' => 'cil', 'CiPaw.15G155400' => 'cil', 'CiPaw.16G006000' => 'cil', 'CiPaw.16G013100' => 'cil', 'CiPaw.16G047100' => 'cil', 'CiPaw.16G048900' => 'cil', 'CiPaw.16G070300' => 'cil', 'CSS0000195' => 'camsi', 'CSS0001664' => 'camsi', 'CSS0002566' => 'camsi', 'CSS0003077' => 'camsi', 'CSS0004257' => 'camsi', 'CSS0004495' => 'camsi', 'CSS0004599' => 'camsi', 'CSS0004943' => 'camsi', 'CSS0005302' => 'camsi', 'CSS0006274' => 'camsi', 'CSS0006547' => 'camsi', 'CSS0006860' => 'camsi', 'CSS0008814' => 'camsi', 'CSS0008946' => 'camsi', 'CSS0009093' => 'camsi', 'CSS0010221' => 'camsi', 'CSS0010296' => 'camsi', 'CSS0010386' => 'camsi', 'CSS0010831' => 'camsi', 'CSS0011061' => 'camsi', 'CSS0012008' => 'camsi', 'CSS0012194' => 'camsi', 'CSS0013580' => 'camsi', 'CSS0014176' => 'camsi', 'CSS0014280' => 'camsi', 'CSS0014799' => 'camsi', 'CSS0015368' => 'camsi', 'CSS0017473' => 'camsi', 'CSS0019281' => 'camsi', 'CSS0021320' => 'camsi', 'CSS0021750' => 'camsi', 'CSS0023642' => 'camsi', 'CSS0023792' => 'camsi', 'CSS0031528' => 'camsi', 'CSS0033894' => 'camsi', 'CSS0034959' => 'camsi', 'CSS0035632' => 'camsi', 'CSS0038450' => 'camsi', 'CSS0039293' => 'camsi', 'CSS0041053' => 'camsi', 'CSS0041981' => 'camsi', 'CSS0042573' => 'camsi', 'CSS0042927' => 'camsi', 'CSS0047725' => 'camsi', 'CSS0049636' => 'camsi', 'CSS0050513' => 'camsi', 'DCAR_030203' => 'dca', 'Dinv07939' => 'din', 'FAN01G0456' => 'fan', 'FAN02G3001' => 'fan', 'FAN04G2781' => 'fan', 'FAN05G1385' => 'fan', 'FAN05G3062' => 'fan', 'FAN08G2267' => 'fan', 'FAN10G0481' => 'fan', 'FAN10G1257' => 'fan', 'FAN14G0954' => 'fan', 'FAN14G2347' => 'fan', 'FAN15G0187' => 'fan', 'FAN25G2214' => 'fan', 'FvH4_1g21031' => 'fve', 'FvH4_3g16231' => 'fve', 'FvH4_3g26413' => 'fve', 'FvH4_3g29014' => 'fve', 'FvH4_3g31921' => 'fve', 'FvH4_4g19882' => 'fve', 'FvH4_5g21960' => 'fve', 'FvH4_5g29683' => 'fve', 'FvH4_7g13271' => 'fve', 'Glyma.01G062500' => 'gma', 'Glyma.07G140900' => 'gma', 'Glyma.09G140900' => 'gma', 'Glyma.12G112700' => 'gma', 'Glyma.17G168800' => 'gma', 'HanXRQChr01g0027001' => 'han', 'HanXRQChr04g0120511' => 'han', 'HanXRQChr08g0232381' => 'han', 'HanXRQChr09g0265661' => 'han', 'HanXRQChr13g0416031' => 'han', 'Haze_05835' => 'cav', 'Haze_06597' => 'cav', 'Haze_07921' => 'cav', 'Haze_08599' => 'cav', 'Haze_10686' => 'cav', 'Haze_12994' => 'cav', 'Haze_13466' => 'cav', 'Haze_16101' => 'cav', 'Haze_17766' => 'cav', 'Haze_18456' => 'cav', 'Haze_20229' => 'cav', 'Hma1.2p1_0324F.1_g125640' => 'hma', 'Hma1.2p1_0733F.1_g210230' => 'hma', 'Hma1.2p1_0921F.1_g236870' => 'hma', 'Hma1.2p1_1313F.1_g274940' => 'hma', 'Hma1.2p1_3059F.1_g332230' => 'hma', 'Hund15925' => 'sun', 'Hund19562' => 'sun', 'Hund21925' => 'sun', 'MD03G1177400' => 'mdo', 'MD07G1026100' => 'mdo', 'MD17G1218600' => 'mdo', 'Medtr0867s0010' => 'mtr', 'Medtr6g081150' => 'mtr', 'Os01g0527900' => 'osa', 'Os02g0463725' => 'osa', 'Os02g0785600' => 'osa', 'Os03g0433733' => 'osa', 'Os04g0286500' => 'osa', 'Os05g0227800' => 'osa', 'Os06g0521000' => 'osa', 'Os06g0635500' => 'osa', 'Os06g0660650' => 'osa', 'Os07g0554400' => 'osa', 'Os08g0225900' => 'osa', 'Os08g0561000' => 'osa', 'Os09g0241700' => 'osa', 'Os09g0351900' => 'osa', 'Os11g0220700' => 'osa', 'Os11g0282700' => 'osa', 'Os12g0169300' => 'osa', 'Os12g0228500' => 'osa', 'Os12g0543800' => 'osa', 'PGR044G1547' => 'pgr', 'Potri.005G239150' => 'ptr', 'Potri.010G014250' => 'ptr', 'Prupe.1G172500' => 'ppe', 'Prupe.1G196800' => 'ppe', 'Prupe.1G279700' => 'ppe', 'Prupe.2G026400' => 'ppe', 'Prupe.3G094000' => 'ppe', 'Prupe.4G287300' => 'ppe', 'QL01p022166' => 'qlo', 'QL01p051890' => 'qlo', 'QL02p009469' => 'qlo', 'QL02p046053' => 'qlo', 'QL02p057958' => 'qlo', 'QL02p093127' => 'qlo', 'QL03p006855' => 'qlo', 'QL03p071586' => 'qlo', 'QL04p000022' => 'qlo', 'QL04p000024' => 'qlo', 'QL04p003192' => 'qlo', 'QL05p011416' => 'qlo', 'QL06p039590' => 'qlo', 'QL06p052750' => 'qlo', 'QL06p053821' => 'qlo', 'QL07p025287' => 'qlo', 'QL09p033218' => 'qlo', 'QL09p040841' => 'qlo', 'QL10p020337' => 'qlo', 'QL10p027209' => 'qlo', 'QL10p027969' => 'qlo', 'QL10p048988' => 'qlo', 'QL11p001241' => 'qlo', 'QL11p028487' => 'qlo', 'RcHm_v2.0_Chr2g0105031' => 'rch', 'RcHm_v2.0_Chr2g0117811' => 'rch', 'RcHm_v2.0_Chr6g0270241' => 'rch', 'RcHm_v2.0_Chr7g0215961' => 'rch', 'RcHm_v2.0_Chr7g0231991' => 'rch', 'Rhsim01G0041500' => 'rsi', 'Rhsim01G0115000' => 'rsi', 'Rhsim01G0115400' => 'rsi', 'Rhsim01G0133600' => 'rsi', 'Rhsim01G0159900' => 'rsi', 'Rhsim02G0189400' => 'rsi', 'Rhsim03G0135600' => 'rsi', 'Rhsim03G0149900' => 'rsi', 'Rhsim04G0125600' => 'rsi', 'Rhsim05G0091700' => 'rsi', 'Rhsim05G0092900' => 'rsi', 'Rhsim06G0075000' => 'rsi', 'Rhsim07G0066400' => 'rsi', 'Rhsim07G0156400' => 'rsi', 'Rhsim07G0182200' => 'rsi', 'Rhsim07G0182300' => 'rsi', 'Rhsim08G0180400' => 'rsi', 'Rhsim09G0056800' => 'rsi', 'Rhsim10G0153300' => 'rsi', 'Rhsim11G0012700' => 'rsi', 'Rhsim12G0031800' => 'rsi', 'Rhsim12G0055400' => 'rsi', 'Rhsim12G0091400' => 'rsi', 'Rhsim13G0070800' => 'rsi', 'Rhsim13G0193300' => 'rsi', 'RhsimUnG0111600' => 'rsi', 'RhsimUnG0137500' => 'rsi', 'RhsimUnG0172900' => 'rsi', 'SGA_v2.0_scaffold11G05878' => 'sas', 'SGA_v2.0_scaffold167G38458' => 'sas', 'SGA_v2.0_scaffold19G08588' => 'sas', 'SGA_v2.0_scaffold239G43990' => 'sas', 'SGA_v2.0_scaffold260G45865' => 'sas', 'SGA_v2.0_scaffold309G48177' => 'sas', 'SGA_v2.0_scaffold76G25122' => 'sas', 'SGA_v2.0_scaffold85G26708' => 'sas', 'SHI13914' => 'shi', 'SHI30402' => 'shi', 'TWI09G0020' => 'twi', 'TWI09G0456' => 'twi', 'TWI09G1572' => 'twi', 'TWI12G0266' => 'twi', 'TWI12G1451' => 'twi', 'TWI14G0851' => 'twi', 'TWI15G0796' => 'twi', 'TWI18G0820' => 'twi', 'TWI18G1152' => 'twi', 'TWI23G0007' => 'twi', 'TWI23G0314' => 'twi', 'TWI31G0674' => 'twi', 'TWI31G0938' => 'twi', 'TWI34G0641' => 'twi', 'TWI34G1527' => 'twi', 'TWI36G0193' => 'twi', 'TWI36G0405' => 'twi', 'TWI38G0892' => 'twi', 'TWI38G0936' => 'twi', 'TWI38G2218' => 'twi', 'TWI53G0679' => 'twi', 'TWI53G0863' => 'twi', 'TWI53G1133' => 'twi', 'TWI60G0823' => 'twi', 'TWI63G0919' => 'twi', 'TWI63G1436' => 'twi', 'TWI73G0140' => 'twi', 'TWI73G0419' => 'twi', 'TWI73G0420' => 'twi', 'TWI73G1276' => 'twi', 'TWI74G0405' => 'twi', 'TWI74G0837' => 'twi', 'TWI75G0594' => 'twi', 'TWI75G1615' => 'twi', 'TWI77G0816' => 'twi', 'vmacro03831' => 'vma', 'vmacro13746' => 'vma', 'vmacro16089' => 'vma', 'vmacro22863' => 'vma', 'Zm00001eb085790' => 'zma', 'Zm00001eb114250' => 'zma', 'Zm00001eb138070' => 'zma', 'Zm00001eb167560' => 'zma', 'Zm00001eb199990' => 'zma', 'Zm00001eb368180' => 'zma', 'Zm00001eb382470' => 'zma' ) $gf_id = 'HOM05D001576' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001576' ) $data_identifier = 'HOM05D001576' $data_type = 'gf_id' $species_gene_counts = array( 'aox' => (int) 9, 'acertr' => (int) 3, 'cansat' => (int) 1, 'ccl' => (int) 4, 'cil' => (int) 145, 'camsi' => (int) 46, 'dca' => (int) 1, 'din' => (int) 1, 'fan' => (int) 12, 'fve' => (int) 9, 'gma' => (int) 5, 'han' => (int) 5, 'cav' => (int) 11, 'hma' => (int) 5, 'sun' => (int) 3, 'mdo' => (int) 3, 'mtr' => (int) 2, 'osa' => (int) 19, 'pgr' => (int) 1, 'ptr' => (int) 2, 'ppe' => (int) 6, 'qlo' => (int) 24, 'rch' => (int) 5, 'rsi' => (int) 28, 'sas' => (int) 8, 'shi' => (int) 2, 'twi' => (int) 35, 'vma' => (int) 4, 'zma' => (int) 7 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb382470' $species_info = array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ) $local_species = 'ccl' $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' => 'HOM05D001576', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '406', 'num_species' => '29' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'Aqoxy1G01456' => 'aox', 'Aqoxy1G02949' => 'aox', 'Aqoxy3G01274' => 'aox', 'Aqoxy3G02110' => 'aox', 'Aqoxy3G02268' => 'aox', 'Aqoxy5G02702' => 'aox', 'Aqoxy5G02988' => 'aox', 'Aqoxy5G03427' => 'aox', 'Aqoxy6G02363' => 'aox', 'Atru.chr1.3225' => 'acertr', 'Atru.chr8.1198' => 'acertr', 'Atru.chr9.790' => 'acertr', 'CANSAT01G3197' => 'cansat', 'Ciclev10003979m.g' => 'ccl', 'Ciclev10017471m.g' => 'ccl', 'Ciclev10018206m.g' => 'ccl', 'Ciclev10033751m.g' => 'ccl', 'CiPaw.01G000900' => 'cil', 'CiPaw.01G001000' => 'cil', 'CiPaw.01G033500' => 'cil', 'CiPaw.01G060300' => 'cil', 'CiPaw.01G070200' => 'cil', 'CiPaw.01G075100' => 'cil', 'CiPaw.01G084700' => 'cil', 'CiPaw.01G087900' => 'cil', 'CiPaw.01G092600' => 'cil', 'CiPaw.01G097200' => 'cil', 'CiPaw.01G098300' => 'cil', 'CiPaw.01G110200' => 'cil', 'CiPaw.01G118700' => 'cil', 'CiPaw.01G121200' => 'cil', 'CiPaw.01G132500' => 'cil', 'CiPaw.01G146900' => 'cil', 'CiPaw.01G174000' => 'cil', 'CiPaw.01G179900' => 'cil', 'CiPaw.01G183400' => 'cil', 'CiPaw.01G240000' => 'cil', 'CiPaw.01G283500' => 'cil', 'CiPaw.01G307400' => 'cil', 'CiPaw.02G030800' => 'cil', 'CiPaw.02G047200' => 'cil', 'CiPaw.02G050500' => 'cil', 'CiPaw.02G069900' => 'cil', 'CiPaw.02G091600' => 'cil', 'CiPaw.02G095000' => 'cil', 'CiPaw.02G131900' => 'cil', 'CiPaw.03G043000' => 'cil', 'CiPaw.03G069900' => 'cil', 'CiPaw.03G088100' => 'cil', 'CiPaw.03G089300' => 'cil', 'CiPaw.03G093100' => 'cil', 'CiPaw.03G129800' => 'cil', 'CiPaw.03G131200' => 'cil', 'CiPaw.03G134500' => 'cil', 'CiPaw.03G152100' => 'cil', 'CiPaw.03G162700' => 'cil', 'CiPaw.03G172800' => 'cil', 'CiPaw.03G175800' => 'cil', 'CiPaw.03G181800' => 'cil', 'CiPaw.03G191400' => 'cil', 'CiPaw.03G198300' => 'cil', 'CiPaw.03G201300' => 'cil', 'CiPaw.03G224700' => 'cil', 'CiPaw.03G225000' => 'cil', 'CiPaw.04G065100' => 'cil', 'CiPaw.04G080400' => 'cil', 'CiPaw.04G113500' => 'cil', 'CiPaw.04G121900' => 'cil', 'CiPaw.04G144100' => 'cil', 'CiPaw.04G176500' => 'cil', 'CiPaw.05G086200' => 'cil', 'CiPaw.05G100200' => 'cil', 'CiPaw.05G114200' => 'cil', 'CiPaw.05G126800' => 'cil', 'CiPaw.05G228800' => 'cil', 'CiPaw.05G230600' => 'cil', 'CiPaw.05G236500' => 'cil', 'CiPaw.05G244800' => 'cil', 'CiPaw.06G026600' => 'cil', 'CiPaw.06G027900' => 'cil', 'CiPaw.06G051800' => 'cil', 'CiPaw.06G128500' => 'cil', 'CiPaw.06G165900' => 'cil', 'CiPaw.07G045400' => 'cil', 'CiPaw.07G048000' => 'cil', 'CiPaw.07G052000' => 'cil', 'CiPaw.07G073800' => 'cil', 'CiPaw.07G099700' => 'cil', 'CiPaw.07G108700' => 'cil', 'CiPaw.07G120000' => 'cil', 'CiPaw.07G134100' => 'cil', 'CiPaw.07G147000' => 'cil', 'CiPaw.07G149700' => 'cil', 'CiPaw.07G178300' => 'cil', 'CiPaw.07G184900' => 'cil', 'CiPaw.08G044500' => 'cil', 'CiPaw.08G046900' => 'cil', 'CiPaw.08G047300' => 'cil', 'CiPaw.08G115400' => 'cil', 'CiPaw.08G134700' => 'cil', 'CiPaw.08G157400' => 'cil', 'CiPaw.09G014300' => 'cil', 'CiPaw.09G088900' => 'cil', 'CiPaw.09G130900' => 'cil', 'CiPaw.09G133100' => 'cil', 'CiPaw.09G151300' => 'cil', 'CiPaw.09G172800' => 'cil', 'CiPaw.09G174900' => 'cil', 'CiPaw.09G175000' => 'cil', 'CiPaw.10G012800' => 'cil', 'CiPaw.10G028800' => 'cil', 'CiPaw.10G044700' => 'cil', 'CiPaw.10G067400' => 'cil', 'CiPaw.10G115900' => 'cil', 'CiPaw.10G126200' => 'cil', 'CiPaw.10G139700' => 'cil', 'CiPaw.10G155100' => 'cil', 'CiPaw.11G011300' => 'cil', 'CiPaw.11G025900' => 'cil', 'CiPaw.11G104100' => 'cil', 'CiPaw.11G142700' => 'cil', 'CiPaw.11G164500' => 'cil', 'CiPaw.11G189100' => 'cil', 'CiPaw.11G197100' => 'cil', 'CiPaw.12G006100' => 'cil', 'CiPaw.12G038500' => 'cil', 'CiPaw.12G041400' => 'cil', 'CiPaw.12G041600' => 'cil', 'CiPaw.12G051300' => 'cil', 'CiPaw.12G101800' => 'cil', 'CiPaw.12G107800' => 'cil', 'CiPaw.13G033200' => 'cil', 'CiPaw.13G129900' => 'cil', 'CiPaw.13G160200' => 'cil', 'CiPaw.14G018900' => 'cil', 'CiPaw.14G029000' => 'cil', 'CiPaw.14G031000' => 'cil', 'CiPaw.14G032000' => 'cil', 'CiPaw.14G032300' => 'cil', 'CiPaw.14G040600' => 'cil', 'CiPaw.14G060500' => 'cil', 'CiPaw.14G061500' => 'cil', 'CiPaw.14G077500' => 'cil', 'CiPaw.14G088300' => 'cil', 'CiPaw.14G108500' => 'cil', 'CiPaw.14G121300' => 'cil', 'CiPaw.14G133000' => 'cil', 'CiPaw.14G134600' => 'cil', 'CiPaw.15G027200' => 'cil', 'CiPaw.15G037700' => 'cil', 'CiPaw.15G050900' => 'cil', 'CiPaw.15G067200' => 'cil', 'CiPaw.15G072000' => 'cil', 'CiPaw.15G112900' => 'cil', 'CiPaw.15G133200' => 'cil', 'CiPaw.15G139500' => 'cil', 'CiPaw.15G155400' => 'cil', 'CiPaw.16G006000' => 'cil', 'CiPaw.16G013100' => 'cil', 'CiPaw.16G047100' => 'cil', 'CiPaw.16G048900' => 'cil', 'CiPaw.16G070300' => 'cil', 'CSS0000195' => 'camsi', 'CSS0001664' => 'camsi', 'CSS0002566' => 'camsi', 'CSS0003077' => 'camsi', 'CSS0004257' => 'camsi', 'CSS0004495' => 'camsi', 'CSS0004599' => 'camsi', 'CSS0004943' => 'camsi', 'CSS0005302' => 'camsi', 'CSS0006274' => 'camsi', 'CSS0006547' => 'camsi', 'CSS0006860' => 'camsi', 'CSS0008814' => 'camsi', 'CSS0008946' => 'camsi', 'CSS0009093' => 'camsi', 'CSS0010221' => 'camsi', 'CSS0010296' => 'camsi', 'CSS0010386' => 'camsi', 'CSS0010831' => 'camsi', 'CSS0011061' => 'camsi', 'CSS0012008' => 'camsi', 'CSS0012194' => 'camsi', 'CSS0013580' => 'camsi', 'CSS0014176' => 'camsi', 'CSS0014280' => 'camsi', 'CSS0014799' => 'camsi', 'CSS0015368' => 'camsi', 'CSS0017473' => 'camsi', 'CSS0019281' => 'camsi', 'CSS0021320' => 'camsi', 'CSS0021750' => 'camsi', 'CSS0023642' => 'camsi', 'CSS0023792' => 'camsi', 'CSS0031528' => 'camsi', 'CSS0033894' => 'camsi', 'CSS0034959' => 'camsi', 'CSS0035632' => 'camsi', 'CSS0038450' => 'camsi', 'CSS0039293' => 'camsi', 'CSS0041053' => 'camsi', 'CSS0041981' => 'camsi', 'CSS0042573' => 'camsi', 'CSS0042927' => 'camsi', 'CSS0047725' => 'camsi', 'CSS0049636' => 'camsi', 'CSS0050513' => 'camsi', 'DCAR_030203' => 'dca', 'Dinv07939' => 'din', 'FAN01G0456' => 'fan', 'FAN02G3001' => 'fan', 'FAN04G2781' => 'fan', 'FAN05G1385' => 'fan', 'FAN05G3062' => 'fan', 'FAN08G2267' => 'fan', 'FAN10G0481' => 'fan', 'FAN10G1257' => 'fan', 'FAN14G0954' => 'fan', 'FAN14G2347' => 'fan', 'FAN15G0187' => 'fan', 'FAN25G2214' => 'fan', 'FvH4_1g21031' => 'fve', 'FvH4_3g16231' => 'fve', 'FvH4_3g26413' => 'fve', 'FvH4_3g29014' => 'fve', 'FvH4_3g31921' => 'fve', 'FvH4_4g19882' => 'fve', 'FvH4_5g21960' => 'fve', 'FvH4_5g29683' => 'fve', 'FvH4_7g13271' => 'fve', 'Glyma.01G062500' => 'gma', 'Glyma.07G140900' => 'gma', 'Glyma.09G140900' => 'gma', 'Glyma.12G112700' => 'gma', 'Glyma.17G168800' => 'gma', 'HanXRQChr01g0027001' => 'han', 'HanXRQChr04g0120511' => 'han', 'HanXRQChr08g0232381' => 'han', 'HanXRQChr09g0265661' => 'han', 'HanXRQChr13g0416031' => 'han', 'Haze_05835' => 'cav', 'Haze_06597' => 'cav', 'Haze_07921' => 'cav', 'Haze_08599' => 'cav', 'Haze_10686' => 'cav', 'Haze_12994' => 'cav', 'Haze_13466' => 'cav', 'Haze_16101' => 'cav', 'Haze_17766' => 'cav', 'Haze_18456' => 'cav', 'Haze_20229' => 'cav', 'Hma1.2p1_0324F.1_g125640' => 'hma', 'Hma1.2p1_0733F.1_g210230' => 'hma', 'Hma1.2p1_0921F.1_g236870' => 'hma', 'Hma1.2p1_1313F.1_g274940' => 'hma', 'Hma1.2p1_3059F.1_g332230' => 'hma', 'Hund15925' => 'sun', 'Hund19562' => 'sun', 'Hund21925' => 'sun', 'MD03G1177400' => 'mdo', 'MD07G1026100' => 'mdo', 'MD17G1218600' => 'mdo', 'Medtr0867s0010' => 'mtr', 'Medtr6g081150' => 'mtr', 'Os01g0527900' => 'osa', 'Os02g0463725' => 'osa', 'Os02g0785600' => 'osa', 'Os03g0433733' => 'osa', 'Os04g0286500' => 'osa', 'Os05g0227800' => 'osa', 'Os06g0521000' => 'osa', 'Os06g0635500' => 'osa', 'Os06g0660650' => 'osa', 'Os07g0554400' => 'osa', 'Os08g0225900' => 'osa', 'Os08g0561000' => 'osa', 'Os09g0241700' => 'osa', 'Os09g0351900' => 'osa', 'Os11g0220700' => 'osa', 'Os11g0282700' => 'osa', 'Os12g0169300' => 'osa', 'Os12g0228500' => 'osa', 'Os12g0543800' => 'osa', 'PGR044G1547' => 'pgr', 'Potri.005G239150' => 'ptr', 'Potri.010G014250' => 'ptr', 'Prupe.1G172500' => 'ppe', 'Prupe.1G196800' => 'ppe', 'Prupe.1G279700' => 'ppe', 'Prupe.2G026400' => 'ppe', 'Prupe.3G094000' => 'ppe', 'Prupe.4G287300' => 'ppe', 'QL01p022166' => 'qlo', 'QL01p051890' => 'qlo', 'QL02p009469' => 'qlo', 'QL02p046053' => 'qlo', 'QL02p057958' => 'qlo', 'QL02p093127' => 'qlo', 'QL03p006855' => 'qlo', 'QL03p071586' => 'qlo', 'QL04p000022' => 'qlo', 'QL04p000024' => 'qlo', 'QL04p003192' => 'qlo', 'QL05p011416' => 'qlo', 'QL06p039590' => 'qlo', 'QL06p052750' => 'qlo', 'QL06p053821' => 'qlo', 'QL07p025287' => 'qlo', 'QL09p033218' => 'qlo', 'QL09p040841' => 'qlo', 'QL10p020337' => 'qlo', 'QL10p027209' => 'qlo', 'QL10p027969' => 'qlo', 'QL10p048988' => 'qlo', 'QL11p001241' => 'qlo', 'QL11p028487' => 'qlo', 'RcHm_v2.0_Chr2g0105031' => 'rch', 'RcHm_v2.0_Chr2g0117811' => 'rch', 'RcHm_v2.0_Chr6g0270241' => 'rch', 'RcHm_v2.0_Chr7g0215961' => 'rch', 'RcHm_v2.0_Chr7g0231991' => 'rch', 'Rhsim01G0041500' => 'rsi', 'Rhsim01G0115000' => 'rsi', 'Rhsim01G0115400' => 'rsi', 'Rhsim01G0133600' => 'rsi', 'Rhsim01G0159900' => 'rsi', 'Rhsim02G0189400' => 'rsi', 'Rhsim03G0135600' => 'rsi', 'Rhsim03G0149900' => 'rsi', 'Rhsim04G0125600' => 'rsi', 'Rhsim05G0091700' => 'rsi', 'Rhsim05G0092900' => 'rsi', 'Rhsim06G0075000' => 'rsi', 'Rhsim07G0066400' => 'rsi', 'Rhsim07G0156400' => 'rsi', 'Rhsim07G0182200' => 'rsi', 'Rhsim07G0182300' => 'rsi', 'Rhsim08G0180400' => 'rsi', 'Rhsim09G0056800' => 'rsi', 'Rhsim10G0153300' => 'rsi', 'Rhsim11G0012700' => 'rsi', 'Rhsim12G0031800' => 'rsi', 'Rhsim12G0055400' => 'rsi', 'Rhsim12G0091400' => 'rsi', 'Rhsim13G0070800' => 'rsi', 'Rhsim13G0193300' => 'rsi', 'RhsimUnG0111600' => 'rsi', 'RhsimUnG0137500' => 'rsi', 'RhsimUnG0172900' => 'rsi', 'SGA_v2.0_scaffold11G05878' => 'sas', 'SGA_v2.0_scaffold167G38458' => 'sas', 'SGA_v2.0_scaffold19G08588' => 'sas', 'SGA_v2.0_scaffold239G43990' => 'sas', 'SGA_v2.0_scaffold260G45865' => 'sas', 'SGA_v2.0_scaffold309G48177' => 'sas', 'SGA_v2.0_scaffold76G25122' => 'sas', 'SGA_v2.0_scaffold85G26708' => 'sas', 'SHI13914' => 'shi', 'SHI30402' => 'shi', 'TWI09G0020' => 'twi', 'TWI09G0456' => 'twi', 'TWI09G1572' => 'twi', 'TWI12G0266' => 'twi', 'TWI12G1451' => 'twi', 'TWI14G0851' => 'twi', 'TWI15G0796' => 'twi', 'TWI18G0820' => 'twi', 'TWI18G1152' => 'twi', 'TWI23G0007' => 'twi', 'TWI23G0314' => 'twi', 'TWI31G0674' => 'twi', 'TWI31G0938' => 'twi', 'TWI34G0641' => 'twi', 'TWI34G1527' => 'twi', 'TWI36G0193' => 'twi', 'TWI36G0405' => 'twi', 'TWI38G0892' => 'twi', 'TWI38G0936' => 'twi', 'TWI38G2218' => 'twi', 'TWI53G0679' => 'twi', 'TWI53G0863' => 'twi', 'TWI53G1133' => 'twi', 'TWI60G0823' => 'twi', 'TWI63G0919' => 'twi', 'TWI63G1436' => 'twi', 'TWI73G0140' => 'twi', 'TWI73G0419' => 'twi', 'TWI73G0420' => 'twi', 'TWI73G1276' => 'twi', 'TWI74G0405' => 'twi', 'TWI74G0837' => 'twi', 'TWI75G0594' => 'twi', 'TWI75G1615' => 'twi', 'TWI77G0816' => 'twi', 'vmacro03831' => 'vma', 'vmacro13746' => 'vma', 'vmacro16089' => 'vma', 'vmacro22863' => 'vma', 'Zm00001eb085790' => 'zma', 'Zm00001eb114250' => 'zma', 'Zm00001eb138070' => 'zma', 'Zm00001eb167560' => 'zma', 'Zm00001eb199990' => 'zma', 'Zm00001eb368180' => 'zma', 'Zm00001eb382470' => 'zma' ), 'gf_id' => 'HOM05D001576', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001576' ), 'data_identifier' => 'HOM05D001576', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001576', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '406', 'num_species' => '29' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'Aqoxy1G01456' => 'aox', 'Aqoxy1G02949' => 'aox', 'Aqoxy3G01274' => 'aox', 'Aqoxy3G02110' => 'aox', 'Aqoxy3G02268' => 'aox', 'Aqoxy5G02702' => 'aox', 'Aqoxy5G02988' => 'aox', 'Aqoxy5G03427' => 'aox', 'Aqoxy6G02363' => 'aox', 'Atru.chr1.3225' => 'acertr', 'Atru.chr8.1198' => 'acertr', 'Atru.chr9.790' => 'acertr', 'CANSAT01G3197' => 'cansat', 'Ciclev10003979m.g' => 'ccl', 'Ciclev10017471m.g' => 'ccl', 'Ciclev10018206m.g' => 'ccl', 'Ciclev10033751m.g' => 'ccl', 'CiPaw.01G000900' => 'cil', 'CiPaw.01G001000' => 'cil', 'CiPaw.01G033500' => 'cil', 'CiPaw.01G060300' => 'cil', 'CiPaw.01G070200' => 'cil', 'CiPaw.01G075100' => 'cil', 'CiPaw.01G084700' => 'cil', 'CiPaw.01G087900' => 'cil', 'CiPaw.01G092600' => 'cil', 'CiPaw.01G097200' => 'cil', 'CiPaw.01G098300' => 'cil', 'CiPaw.01G110200' => 'cil', 'CiPaw.01G118700' => 'cil', 'CiPaw.01G121200' => 'cil', 'CiPaw.01G132500' => 'cil', 'CiPaw.01G146900' => 'cil', 'CiPaw.01G174000' => 'cil', 'CiPaw.01G179900' => 'cil', 'CiPaw.01G183400' => 'cil', 'CiPaw.01G240000' => 'cil', 'CiPaw.01G283500' => 'cil', 'CiPaw.01G307400' => 'cil', 'CiPaw.02G030800' => 'cil', 'CiPaw.02G047200' => 'cil', 'CiPaw.02G050500' => 'cil', 'CiPaw.02G069900' => 'cil', 'CiPaw.02G091600' => 'cil', 'CiPaw.02G095000' => 'cil', 'CiPaw.02G131900' => 'cil', 'CiPaw.03G043000' => 'cil', 'CiPaw.03G069900' => 'cil', 'CiPaw.03G088100' => 'cil', 'CiPaw.03G089300' => 'cil', 'CiPaw.03G093100' => 'cil', 'CiPaw.03G129800' => 'cil', 'CiPaw.03G131200' => 'cil', 'CiPaw.03G134500' => 'cil', 'CiPaw.03G152100' => 'cil', 'CiPaw.03G162700' => 'cil', 'CiPaw.03G172800' => 'cil', 'CiPaw.03G175800' => 'cil', 'CiPaw.03G181800' => 'cil', 'CiPaw.03G191400' => 'cil', 'CiPaw.03G198300' => 'cil', 'CiPaw.03G201300' => 'cil', 'CiPaw.03G224700' => 'cil', 'CiPaw.03G225000' => 'cil', 'CiPaw.04G065100' => 'cil', 'CiPaw.04G080400' => 'cil', 'CiPaw.04G113500' => 'cil', 'CiPaw.04G121900' => 'cil', 'CiPaw.04G144100' => 'cil', 'CiPaw.04G176500' => 'cil', 'CiPaw.05G086200' => 'cil', 'CiPaw.05G100200' => 'cil', 'CiPaw.05G114200' => 'cil', 'CiPaw.05G126800' => 'cil', 'CiPaw.05G228800' => 'cil', 'CiPaw.05G230600' => 'cil', 'CiPaw.05G236500' => 'cil', 'CiPaw.05G244800' => 'cil', 'CiPaw.06G026600' => 'cil', 'CiPaw.06G027900' => 'cil', 'CiPaw.06G051800' => 'cil', 'CiPaw.06G128500' => 'cil', 'CiPaw.06G165900' => 'cil', 'CiPaw.07G045400' => 'cil', 'CiPaw.07G048000' => 'cil', 'CiPaw.07G052000' => 'cil', 'CiPaw.07G073800' => 'cil', 'CiPaw.07G099700' => 'cil', 'CiPaw.07G108700' => 'cil', 'CiPaw.07G120000' => 'cil', 'CiPaw.07G134100' => 'cil', 'CiPaw.07G147000' => 'cil', 'CiPaw.07G149700' => 'cil', 'CiPaw.07G178300' => 'cil', 'CiPaw.07G184900' => 'cil', 'CiPaw.08G044500' => 'cil', 'CiPaw.08G046900' => 'cil', 'CiPaw.08G047300' => 'cil', 'CiPaw.08G115400' => 'cil', 'CiPaw.08G134700' => 'cil', 'CiPaw.08G157400' => 'cil', 'CiPaw.09G014300' => 'cil', 'CiPaw.09G088900' => 'cil', 'CiPaw.09G130900' => 'cil', 'CiPaw.09G133100' => 'cil', 'CiPaw.09G151300' => 'cil', 'CiPaw.09G172800' => 'cil', 'CiPaw.09G174900' => 'cil', 'CiPaw.09G175000' => 'cil', 'CiPaw.10G012800' => 'cil', 'CiPaw.10G028800' => 'cil', 'CiPaw.10G044700' => 'cil', 'CiPaw.10G067400' => 'cil', 'CiPaw.10G115900' => 'cil', 'CiPaw.10G126200' => 'cil', 'CiPaw.10G139700' => 'cil', 'CiPaw.10G155100' => 'cil', 'CiPaw.11G011300' => 'cil', 'CiPaw.11G025900' => 'cil', 'CiPaw.11G104100' => 'cil', 'CiPaw.11G142700' => 'cil', 'CiPaw.11G164500' => 'cil', 'CiPaw.11G189100' => 'cil', 'CiPaw.11G197100' => 'cil', 'CiPaw.12G006100' => 'cil', 'CiPaw.12G038500' => 'cil', 'CiPaw.12G041400' => 'cil', 'CiPaw.12G041600' => 'cil', 'CiPaw.12G051300' => 'cil', 'CiPaw.12G101800' => 'cil', 'CiPaw.12G107800' => 'cil', 'CiPaw.13G033200' => 'cil', 'CiPaw.13G129900' => 'cil', 'CiPaw.13G160200' => 'cil', 'CiPaw.14G018900' => 'cil', 'CiPaw.14G029000' => 'cil', 'CiPaw.14G031000' => 'cil', 'CiPaw.14G032000' => 'cil', 'CiPaw.14G032300' => 'cil', 'CiPaw.14G040600' => 'cil', 'CiPaw.14G060500' => 'cil', 'CiPaw.14G061500' => 'cil', 'CiPaw.14G077500' => 'cil', 'CiPaw.14G088300' => 'cil', 'CiPaw.14G108500' => 'cil', 'CiPaw.14G121300' => 'cil', 'CiPaw.14G133000' => 'cil', 'CiPaw.14G134600' => 'cil', 'CiPaw.15G027200' => 'cil', 'CiPaw.15G037700' => 'cil', 'CiPaw.15G050900' => 'cil', 'CiPaw.15G067200' => 'cil', 'CiPaw.15G072000' => 'cil', 'CiPaw.15G112900' => 'cil', 'CiPaw.15G133200' => 'cil', 'CiPaw.15G139500' => 'cil', 'CiPaw.15G155400' => 'cil', 'CiPaw.16G006000' => 'cil', 'CiPaw.16G013100' => 'cil', 'CiPaw.16G047100' => 'cil', 'CiPaw.16G048900' => 'cil', 'CiPaw.16G070300' => 'cil', 'CSS0000195' => 'camsi', 'CSS0001664' => 'camsi', 'CSS0002566' => 'camsi', 'CSS0003077' => 'camsi', 'CSS0004257' => 'camsi', 'CSS0004495' => 'camsi', 'CSS0004599' => 'camsi', 'CSS0004943' => 'camsi', 'CSS0005302' => 'camsi', 'CSS0006274' => 'camsi', 'CSS0006547' => 'camsi', 'CSS0006860' => 'camsi', 'CSS0008814' => 'camsi', 'CSS0008946' => 'camsi', 'CSS0009093' => 'camsi', 'CSS0010221' => 'camsi', 'CSS0010296' => 'camsi', 'CSS0010386' => 'camsi', 'CSS0010831' => 'camsi', 'CSS0011061' => 'camsi', 'CSS0012008' => 'camsi', 'CSS0012194' => 'camsi', 'CSS0013580' => 'camsi', 'CSS0014176' => 'camsi', 'CSS0014280' => 'camsi', 'CSS0014799' => 'camsi', 'CSS0015368' => 'camsi', 'CSS0017473' => 'camsi', 'CSS0019281' => 'camsi', 'CSS0021320' => 'camsi', 'CSS0021750' => 'camsi', 'CSS0023642' => 'camsi', 'CSS0023792' => 'camsi', 'CSS0031528' => 'camsi', 'CSS0033894' => 'camsi', 'CSS0034959' => 'camsi', 'CSS0035632' => 'camsi', 'CSS0038450' => 'camsi', 'CSS0039293' => 'camsi', 'CSS0041053' => 'camsi', 'CSS0041981' => 'camsi', 'CSS0042573' => 'camsi', 'CSS0042927' => 'camsi', 'CSS0047725' => 'camsi', 'CSS0049636' => 'camsi', 'CSS0050513' => 'camsi', 'DCAR_030203' => 'dca', 'Dinv07939' => 'din', 'FAN01G0456' => 'fan', 'FAN02G3001' => 'fan', 'FAN04G2781' => 'fan', 'FAN05G1385' => 'fan', 'FAN05G3062' => 'fan', 'FAN08G2267' => 'fan', 'FAN10G0481' => 'fan', 'FAN10G1257' => 'fan', 'FAN14G0954' => 'fan', 'FAN14G2347' => 'fan', 'FAN15G0187' => 'fan', 'FAN25G2214' => 'fan', 'FvH4_1g21031' => 'fve', 'FvH4_3g16231' => 'fve', 'FvH4_3g26413' => 'fve', 'FvH4_3g29014' => 'fve', 'FvH4_3g31921' => 'fve', 'FvH4_4g19882' => 'fve', 'FvH4_5g21960' => 'fve', 'FvH4_5g29683' => 'fve', 'FvH4_7g13271' => 'fve', 'Glyma.01G062500' => 'gma', 'Glyma.07G140900' => 'gma', 'Glyma.09G140900' => 'gma', 'Glyma.12G112700' => 'gma', 'Glyma.17G168800' => 'gma', 'HanXRQChr01g0027001' => 'han', 'HanXRQChr04g0120511' => 'han', 'HanXRQChr08g0232381' => 'han', 'HanXRQChr09g0265661' => 'han', 'HanXRQChr13g0416031' => 'han', 'Haze_05835' => 'cav', 'Haze_06597' => 'cav', 'Haze_07921' => 'cav', 'Haze_08599' => 'cav', 'Haze_10686' => 'cav', 'Haze_12994' => 'cav', 'Haze_13466' => 'cav', 'Haze_16101' => 'cav', 'Haze_17766' => 'cav', 'Haze_18456' => 'cav', 'Haze_20229' => 'cav', 'Hma1.2p1_0324F.1_g125640' => 'hma', 'Hma1.2p1_0733F.1_g210230' => 'hma', 'Hma1.2p1_0921F.1_g236870' => 'hma', 'Hma1.2p1_1313F.1_g274940' => 'hma', 'Hma1.2p1_3059F.1_g332230' => 'hma', 'Hund15925' => 'sun', 'Hund19562' => 'sun', 'Hund21925' => 'sun', 'MD03G1177400' => 'mdo', 'MD07G1026100' => 'mdo', 'MD17G1218600' => 'mdo', 'Medtr0867s0010' => 'mtr', 'Medtr6g081150' => 'mtr', 'Os01g0527900' => 'osa', 'Os02g0463725' => 'osa', 'Os02g0785600' => 'osa', 'Os03g0433733' => 'osa', 'Os04g0286500' => 'osa', 'Os05g0227800' => 'osa', 'Os06g0521000' => 'osa', 'Os06g0635500' => 'osa', 'Os06g0660650' => 'osa', 'Os07g0554400' => 'osa', 'Os08g0225900' => 'osa', 'Os08g0561000' => 'osa', 'Os09g0241700' => 'osa', 'Os09g0351900' => 'osa', 'Os11g0220700' => 'osa', 'Os11g0282700' => 'osa', 'Os12g0169300' => 'osa', 'Os12g0228500' => 'osa', 'Os12g0543800' => 'osa', 'PGR044G1547' => 'pgr', 'Potri.005G239150' => 'ptr', 'Potri.010G014250' => 'ptr', 'Prupe.1G172500' => 'ppe', 'Prupe.1G196800' => 'ppe', 'Prupe.1G279700' => 'ppe', 'Prupe.2G026400' => 'ppe', 'Prupe.3G094000' => 'ppe', 'Prupe.4G287300' => 'ppe', 'QL01p022166' => 'qlo', 'QL01p051890' => 'qlo', 'QL02p009469' => 'qlo', 'QL02p046053' => 'qlo', 'QL02p057958' => 'qlo', 'QL02p093127' => 'qlo', 'QL03p006855' => 'qlo', 'QL03p071586' => 'qlo', 'QL04p000022' => 'qlo', 'QL04p000024' => 'qlo', 'QL04p003192' => 'qlo', 'QL05p011416' => 'qlo', 'QL06p039590' => 'qlo', 'QL06p052750' => 'qlo', 'QL06p053821' => 'qlo', 'QL07p025287' => 'qlo', 'QL09p033218' => 'qlo', 'QL09p040841' => 'qlo', 'QL10p020337' => 'qlo', 'QL10p027209' => 'qlo', 'QL10p027969' => 'qlo', 'QL10p048988' => 'qlo', 'QL11p001241' => 'qlo', 'QL11p028487' => 'qlo', 'RcHm_v2.0_Chr2g0105031' => 'rch', 'RcHm_v2.0_Chr2g0117811' => 'rch', 'RcHm_v2.0_Chr6g0270241' => 'rch', 'RcHm_v2.0_Chr7g0215961' => 'rch', 'RcHm_v2.0_Chr7g0231991' => 'rch', 'Rhsim01G0041500' => 'rsi', 'Rhsim01G0115000' => 'rsi', 'Rhsim01G0115400' => 'rsi', 'Rhsim01G0133600' => 'rsi', 'Rhsim01G0159900' => 'rsi', 'Rhsim02G0189400' => 'rsi', 'Rhsim03G0135600' => 'rsi', 'Rhsim03G0149900' => 'rsi', 'Rhsim04G0125600' => 'rsi', 'Rhsim05G0091700' => 'rsi', 'Rhsim05G0092900' => 'rsi', 'Rhsim06G0075000' => 'rsi', 'Rhsim07G0066400' => 'rsi', 'Rhsim07G0156400' => 'rsi', 'Rhsim07G0182200' => 'rsi', 'Rhsim07G0182300' => 'rsi', 'Rhsim08G0180400' => 'rsi', 'Rhsim09G0056800' => 'rsi', 'Rhsim10G0153300' => 'rsi', 'Rhsim11G0012700' => 'rsi', 'Rhsim12G0031800' => 'rsi', 'Rhsim12G0055400' => 'rsi', 'Rhsim12G0091400' => 'rsi', 'Rhsim13G0070800' => 'rsi', 'Rhsim13G0193300' => 'rsi', 'RhsimUnG0111600' => 'rsi', 'RhsimUnG0137500' => 'rsi', 'RhsimUnG0172900' => 'rsi', 'SGA_v2.0_scaffold11G05878' => 'sas', 'SGA_v2.0_scaffold167G38458' => 'sas', 'SGA_v2.0_scaffold19G08588' => 'sas', 'SGA_v2.0_scaffold239G43990' => 'sas', 'SGA_v2.0_scaffold260G45865' => 'sas', 'SGA_v2.0_scaffold309G48177' => 'sas', 'SGA_v2.0_scaffold76G25122' => 'sas', 'SGA_v2.0_scaffold85G26708' => 'sas', 'SHI13914' => 'shi', 'SHI30402' => 'shi', 'TWI09G0020' => 'twi', 'TWI09G0456' => 'twi', 'TWI09G1572' => 'twi', 'TWI12G0266' => 'twi', 'TWI12G1451' => 'twi', 'TWI14G0851' => 'twi', 'TWI15G0796' => 'twi', 'TWI18G0820' => 'twi', 'TWI18G1152' => 'twi', 'TWI23G0007' => 'twi', 'TWI23G0314' => 'twi', 'TWI31G0674' => 'twi', 'TWI31G0938' => 'twi', 'TWI34G0641' => 'twi', 'TWI34G1527' => 'twi', 'TWI36G0193' => 'twi', 'TWI36G0405' => 'twi', 'TWI38G0892' => 'twi', 'TWI38G0936' => 'twi', 'TWI38G2218' => 'twi', 'TWI53G0679' => 'twi', 'TWI53G0863' => 'twi', 'TWI53G1133' => 'twi', 'TWI60G0823' => 'twi', 'TWI63G0919' => 'twi', 'TWI63G1436' => 'twi', 'TWI73G0140' => 'twi', 'TWI73G0419' => 'twi', 'TWI73G0420' => 'twi', 'TWI73G1276' => 'twi', 'TWI74G0405' => 'twi', 'TWI74G0837' => 'twi', 'TWI75G0594' => 'twi', 'TWI75G1615' => 'twi', 'TWI77G0816' => 'twi', 'vmacro03831' => 'vma', 'vmacro13746' => 'vma', 'vmacro16089' => 'vma', 'vmacro22863' => 'vma', 'Zm00001eb085790' => 'zma', 'Zm00001eb114250' => 'zma', 'Zm00001eb138070' => 'zma', 'Zm00001eb167560' => 'zma', 'Zm00001eb199990' => 'zma', 'Zm00001eb368180' => 'zma', 'Zm00001eb382470' => 'zma' ) $gf_id = 'HOM05D001576' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001576' ) $data_identifier = 'HOM05D001576' $data_type = 'gf_id' $species_gene_counts = array( 'aox' => (int) 9, 'acertr' => (int) 3, 'cansat' => (int) 1, 'ccl' => (int) 4, 'cil' => (int) 145, 'camsi' => (int) 46, 'dca' => (int) 1, 'din' => (int) 1, 'fan' => (int) 12, 'fve' => (int) 9, 'gma' => (int) 5, 'han' => (int) 5, 'cav' => (int) 11, 'hma' => (int) 5, 'sun' => (int) 3, 'mdo' => (int) 3, 'mtr' => (int) 2, 'osa' => (int) 19, 'pgr' => (int) 1, 'ptr' => (int) 2, 'ppe' => (int) 6, 'qlo' => (int) 24, 'rch' => (int) 5, 'rsi' => (int) 28, 'sas' => (int) 8, 'shi' => (int) 2, 'twi' => (int) 35, 'vma' => (int) 4, 'zma' => (int) 7 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb382470' $species_info = array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ) $local_species = 'cav' $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' => 'HOM05D001576', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '406', 'num_species' => '29' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'Aqoxy1G01456' => 'aox', 'Aqoxy1G02949' => 'aox', 'Aqoxy3G01274' => 'aox', 'Aqoxy3G02110' => 'aox', 'Aqoxy3G02268' => 'aox', 'Aqoxy5G02702' => 'aox', 'Aqoxy5G02988' => 'aox', 'Aqoxy5G03427' => 'aox', 'Aqoxy6G02363' => 'aox', 'Atru.chr1.3225' => 'acertr', 'Atru.chr8.1198' => 'acertr', 'Atru.chr9.790' => 'acertr', 'CANSAT01G3197' => 'cansat', 'Ciclev10003979m.g' => 'ccl', 'Ciclev10017471m.g' => 'ccl', 'Ciclev10018206m.g' => 'ccl', 'Ciclev10033751m.g' => 'ccl', 'CiPaw.01G000900' => 'cil', 'CiPaw.01G001000' => 'cil', 'CiPaw.01G033500' => 'cil', 'CiPaw.01G060300' => 'cil', 'CiPaw.01G070200' => 'cil', 'CiPaw.01G075100' => 'cil', 'CiPaw.01G084700' => 'cil', 'CiPaw.01G087900' => 'cil', 'CiPaw.01G092600' => 'cil', 'CiPaw.01G097200' => 'cil', 'CiPaw.01G098300' => 'cil', 'CiPaw.01G110200' => 'cil', 'CiPaw.01G118700' => 'cil', 'CiPaw.01G121200' => 'cil', 'CiPaw.01G132500' => 'cil', 'CiPaw.01G146900' => 'cil', 'CiPaw.01G174000' => 'cil', 'CiPaw.01G179900' => 'cil', 'CiPaw.01G183400' => 'cil', 'CiPaw.01G240000' => 'cil', 'CiPaw.01G283500' => 'cil', 'CiPaw.01G307400' => 'cil', 'CiPaw.02G030800' => 'cil', 'CiPaw.02G047200' => 'cil', 'CiPaw.02G050500' => 'cil', 'CiPaw.02G069900' => 'cil', 'CiPaw.02G091600' => 'cil', 'CiPaw.02G095000' => 'cil', 'CiPaw.02G131900' => 'cil', 'CiPaw.03G043000' => 'cil', 'CiPaw.03G069900' => 'cil', 'CiPaw.03G088100' => 'cil', 'CiPaw.03G089300' => 'cil', 'CiPaw.03G093100' => 'cil', 'CiPaw.03G129800' => 'cil', 'CiPaw.03G131200' => 'cil', 'CiPaw.03G134500' => 'cil', 'CiPaw.03G152100' => 'cil', 'CiPaw.03G162700' => 'cil', 'CiPaw.03G172800' => 'cil', 'CiPaw.03G175800' => 'cil', 'CiPaw.03G181800' => 'cil', 'CiPaw.03G191400' => 'cil', 'CiPaw.03G198300' => 'cil', 'CiPaw.03G201300' => 'cil', 'CiPaw.03G224700' => 'cil', 'CiPaw.03G225000' => 'cil', 'CiPaw.04G065100' => 'cil', 'CiPaw.04G080400' => 'cil', 'CiPaw.04G113500' => 'cil', 'CiPaw.04G121900' => 'cil', 'CiPaw.04G144100' => 'cil', 'CiPaw.04G176500' => 'cil', 'CiPaw.05G086200' => 'cil', 'CiPaw.05G100200' => 'cil', 'CiPaw.05G114200' => 'cil', 'CiPaw.05G126800' => 'cil', 'CiPaw.05G228800' => 'cil', 'CiPaw.05G230600' => 'cil', 'CiPaw.05G236500' => 'cil', 'CiPaw.05G244800' => 'cil', 'CiPaw.06G026600' => 'cil', 'CiPaw.06G027900' => 'cil', 'CiPaw.06G051800' => 'cil', 'CiPaw.06G128500' => 'cil', 'CiPaw.06G165900' => 'cil', 'CiPaw.07G045400' => 'cil', 'CiPaw.07G048000' => 'cil', 'CiPaw.07G052000' => 'cil', 'CiPaw.07G073800' => 'cil', 'CiPaw.07G099700' => 'cil', 'CiPaw.07G108700' => 'cil', 'CiPaw.07G120000' => 'cil', 'CiPaw.07G134100' => 'cil', 'CiPaw.07G147000' => 'cil', 'CiPaw.07G149700' => 'cil', 'CiPaw.07G178300' => 'cil', 'CiPaw.07G184900' => 'cil', 'CiPaw.08G044500' => 'cil', 'CiPaw.08G046900' => 'cil', 'CiPaw.08G047300' => 'cil', 'CiPaw.08G115400' => 'cil', 'CiPaw.08G134700' => 'cil', 'CiPaw.08G157400' => 'cil', 'CiPaw.09G014300' => 'cil', 'CiPaw.09G088900' => 'cil', 'CiPaw.09G130900' => 'cil', 'CiPaw.09G133100' => 'cil', 'CiPaw.09G151300' => 'cil', 'CiPaw.09G172800' => 'cil', 'CiPaw.09G174900' => 'cil', 'CiPaw.09G175000' => 'cil', 'CiPaw.10G012800' => 'cil', 'CiPaw.10G028800' => 'cil', 'CiPaw.10G044700' => 'cil', 'CiPaw.10G067400' => 'cil', 'CiPaw.10G115900' => 'cil', 'CiPaw.10G126200' => 'cil', 'CiPaw.10G139700' => 'cil', 'CiPaw.10G155100' => 'cil', 'CiPaw.11G011300' => 'cil', 'CiPaw.11G025900' => 'cil', 'CiPaw.11G104100' => 'cil', 'CiPaw.11G142700' => 'cil', 'CiPaw.11G164500' => 'cil', 'CiPaw.11G189100' => 'cil', 'CiPaw.11G197100' => 'cil', 'CiPaw.12G006100' => 'cil', 'CiPaw.12G038500' => 'cil', 'CiPaw.12G041400' => 'cil', 'CiPaw.12G041600' => 'cil', 'CiPaw.12G051300' => 'cil', 'CiPaw.12G101800' => 'cil', 'CiPaw.12G107800' => 'cil', 'CiPaw.13G033200' => 'cil', 'CiPaw.13G129900' => 'cil', 'CiPaw.13G160200' => 'cil', 'CiPaw.14G018900' => 'cil', 'CiPaw.14G029000' => 'cil', 'CiPaw.14G031000' => 'cil', 'CiPaw.14G032000' => 'cil', 'CiPaw.14G032300' => 'cil', 'CiPaw.14G040600' => 'cil', 'CiPaw.14G060500' => 'cil', 'CiPaw.14G061500' => 'cil', 'CiPaw.14G077500' => 'cil', 'CiPaw.14G088300' => 'cil', 'CiPaw.14G108500' => 'cil', 'CiPaw.14G121300' => 'cil', 'CiPaw.14G133000' => 'cil', 'CiPaw.14G134600' => 'cil', 'CiPaw.15G027200' => 'cil', 'CiPaw.15G037700' => 'cil', 'CiPaw.15G050900' => 'cil', 'CiPaw.15G067200' => 'cil', 'CiPaw.15G072000' => 'cil', 'CiPaw.15G112900' => 'cil', 'CiPaw.15G133200' => 'cil', 'CiPaw.15G139500' => 'cil', 'CiPaw.15G155400' => 'cil', 'CiPaw.16G006000' => 'cil', 'CiPaw.16G013100' => 'cil', 'CiPaw.16G047100' => 'cil', 'CiPaw.16G048900' => 'cil', 'CiPaw.16G070300' => 'cil', 'CSS0000195' => 'camsi', 'CSS0001664' => 'camsi', 'CSS0002566' => 'camsi', 'CSS0003077' => 'camsi', 'CSS0004257' => 'camsi', 'CSS0004495' => 'camsi', 'CSS0004599' => 'camsi', 'CSS0004943' => 'camsi', 'CSS0005302' => 'camsi', 'CSS0006274' => 'camsi', 'CSS0006547' => 'camsi', 'CSS0006860' => 'camsi', 'CSS0008814' => 'camsi', 'CSS0008946' => 'camsi', 'CSS0009093' => 'camsi', 'CSS0010221' => 'camsi', 'CSS0010296' => 'camsi', 'CSS0010386' => 'camsi', 'CSS0010831' => 'camsi', 'CSS0011061' => 'camsi', 'CSS0012008' => 'camsi', 'CSS0012194' => 'camsi', 'CSS0013580' => 'camsi', 'CSS0014176' => 'camsi', 'CSS0014280' => 'camsi', 'CSS0014799' => 'camsi', 'CSS0015368' => 'camsi', 'CSS0017473' => 'camsi', 'CSS0019281' => 'camsi', 'CSS0021320' => 'camsi', 'CSS0021750' => 'camsi', 'CSS0023642' => 'camsi', 'CSS0023792' => 'camsi', 'CSS0031528' => 'camsi', 'CSS0033894' => 'camsi', 'CSS0034959' => 'camsi', 'CSS0035632' => 'camsi', 'CSS0038450' => 'camsi', 'CSS0039293' => 'camsi', 'CSS0041053' => 'camsi', 'CSS0041981' => 'camsi', 'CSS0042573' => 'camsi', 'CSS0042927' => 'camsi', 'CSS0047725' => 'camsi', 'CSS0049636' => 'camsi', 'CSS0050513' => 'camsi', 'DCAR_030203' => 'dca', 'Dinv07939' => 'din', 'FAN01G0456' => 'fan', 'FAN02G3001' => 'fan', 'FAN04G2781' => 'fan', 'FAN05G1385' => 'fan', 'FAN05G3062' => 'fan', 'FAN08G2267' => 'fan', 'FAN10G0481' => 'fan', 'FAN10G1257' => 'fan', 'FAN14G0954' => 'fan', 'FAN14G2347' => 'fan', 'FAN15G0187' => 'fan', 'FAN25G2214' => 'fan', 'FvH4_1g21031' => 'fve', 'FvH4_3g16231' => 'fve', 'FvH4_3g26413' => 'fve', 'FvH4_3g29014' => 'fve', 'FvH4_3g31921' => 'fve', 'FvH4_4g19882' => 'fve', 'FvH4_5g21960' => 'fve', 'FvH4_5g29683' => 'fve', 'FvH4_7g13271' => 'fve', 'Glyma.01G062500' => 'gma', 'Glyma.07G140900' => 'gma', 'Glyma.09G140900' => 'gma', 'Glyma.12G112700' => 'gma', 'Glyma.17G168800' => 'gma', 'HanXRQChr01g0027001' => 'han', 'HanXRQChr04g0120511' => 'han', 'HanXRQChr08g0232381' => 'han', 'HanXRQChr09g0265661' => 'han', 'HanXRQChr13g0416031' => 'han', 'Haze_05835' => 'cav', 'Haze_06597' => 'cav', 'Haze_07921' => 'cav', 'Haze_08599' => 'cav', 'Haze_10686' => 'cav', 'Haze_12994' => 'cav', 'Haze_13466' => 'cav', 'Haze_16101' => 'cav', 'Haze_17766' => 'cav', 'Haze_18456' => 'cav', 'Haze_20229' => 'cav', 'Hma1.2p1_0324F.1_g125640' => 'hma', 'Hma1.2p1_0733F.1_g210230' => 'hma', 'Hma1.2p1_0921F.1_g236870' => 'hma', 'Hma1.2p1_1313F.1_g274940' => 'hma', 'Hma1.2p1_3059F.1_g332230' => 'hma', 'Hund15925' => 'sun', 'Hund19562' => 'sun', 'Hund21925' => 'sun', 'MD03G1177400' => 'mdo', 'MD07G1026100' => 'mdo', 'MD17G1218600' => 'mdo', 'Medtr0867s0010' => 'mtr', 'Medtr6g081150' => 'mtr', 'Os01g0527900' => 'osa', 'Os02g0463725' => 'osa', 'Os02g0785600' => 'osa', 'Os03g0433733' => 'osa', 'Os04g0286500' => 'osa', 'Os05g0227800' => 'osa', 'Os06g0521000' => 'osa', 'Os06g0635500' => 'osa', 'Os06g0660650' => 'osa', 'Os07g0554400' => 'osa', 'Os08g0225900' => 'osa', 'Os08g0561000' => 'osa', 'Os09g0241700' => 'osa', 'Os09g0351900' => 'osa', 'Os11g0220700' => 'osa', 'Os11g0282700' => 'osa', 'Os12g0169300' => 'osa', 'Os12g0228500' => 'osa', 'Os12g0543800' => 'osa', 'PGR044G1547' => 'pgr', 'Potri.005G239150' => 'ptr', 'Potri.010G014250' => 'ptr', 'Prupe.1G172500' => 'ppe', 'Prupe.1G196800' => 'ppe', 'Prupe.1G279700' => 'ppe', 'Prupe.2G026400' => 'ppe', 'Prupe.3G094000' => 'ppe', 'Prupe.4G287300' => 'ppe', 'QL01p022166' => 'qlo', 'QL01p051890' => 'qlo', 'QL02p009469' => 'qlo', 'QL02p046053' => 'qlo', 'QL02p057958' => 'qlo', 'QL02p093127' => 'qlo', 'QL03p006855' => 'qlo', 'QL03p071586' => 'qlo', 'QL04p000022' => 'qlo', 'QL04p000024' => 'qlo', 'QL04p003192' => 'qlo', 'QL05p011416' => 'qlo', 'QL06p039590' => 'qlo', 'QL06p052750' => 'qlo', 'QL06p053821' => 'qlo', 'QL07p025287' => 'qlo', 'QL09p033218' => 'qlo', 'QL09p040841' => 'qlo', 'QL10p020337' => 'qlo', 'QL10p027209' => 'qlo', 'QL10p027969' => 'qlo', 'QL10p048988' => 'qlo', 'QL11p001241' => 'qlo', 'QL11p028487' => 'qlo', 'RcHm_v2.0_Chr2g0105031' => 'rch', 'RcHm_v2.0_Chr2g0117811' => 'rch', 'RcHm_v2.0_Chr6g0270241' => 'rch', 'RcHm_v2.0_Chr7g0215961' => 'rch', 'RcHm_v2.0_Chr7g0231991' => 'rch', 'Rhsim01G0041500' => 'rsi', 'Rhsim01G0115000' => 'rsi', 'Rhsim01G0115400' => 'rsi', 'Rhsim01G0133600' => 'rsi', 'Rhsim01G0159900' => 'rsi', 'Rhsim02G0189400' => 'rsi', 'Rhsim03G0135600' => 'rsi', 'Rhsim03G0149900' => 'rsi', 'Rhsim04G0125600' => 'rsi', 'Rhsim05G0091700' => 'rsi', 'Rhsim05G0092900' => 'rsi', 'Rhsim06G0075000' => 'rsi', 'Rhsim07G0066400' => 'rsi', 'Rhsim07G0156400' => 'rsi', 'Rhsim07G0182200' => 'rsi', 'Rhsim07G0182300' => 'rsi', 'Rhsim08G0180400' => 'rsi', 'Rhsim09G0056800' => 'rsi', 'Rhsim10G0153300' => 'rsi', 'Rhsim11G0012700' => 'rsi', 'Rhsim12G0031800' => 'rsi', 'Rhsim12G0055400' => 'rsi', 'Rhsim12G0091400' => 'rsi', 'Rhsim13G0070800' => 'rsi', 'Rhsim13G0193300' => 'rsi', 'RhsimUnG0111600' => 'rsi', 'RhsimUnG0137500' => 'rsi', 'RhsimUnG0172900' => 'rsi', 'SGA_v2.0_scaffold11G05878' => 'sas', 'SGA_v2.0_scaffold167G38458' => 'sas', 'SGA_v2.0_scaffold19G08588' => 'sas', 'SGA_v2.0_scaffold239G43990' => 'sas', 'SGA_v2.0_scaffold260G45865' => 'sas', 'SGA_v2.0_scaffold309G48177' => 'sas', 'SGA_v2.0_scaffold76G25122' => 'sas', 'SGA_v2.0_scaffold85G26708' => 'sas', 'SHI13914' => 'shi', 'SHI30402' => 'shi', 'TWI09G0020' => 'twi', 'TWI09G0456' => 'twi', 'TWI09G1572' => 'twi', 'TWI12G0266' => 'twi', 'TWI12G1451' => 'twi', 'TWI14G0851' => 'twi', 'TWI15G0796' => 'twi', 'TWI18G0820' => 'twi', 'TWI18G1152' => 'twi', 'TWI23G0007' => 'twi', 'TWI23G0314' => 'twi', 'TWI31G0674' => 'twi', 'TWI31G0938' => 'twi', 'TWI34G0641' => 'twi', 'TWI34G1527' => 'twi', 'TWI36G0193' => 'twi', 'TWI36G0405' => 'twi', 'TWI38G0892' => 'twi', 'TWI38G0936' => 'twi', 'TWI38G2218' => 'twi', 'TWI53G0679' => 'twi', 'TWI53G0863' => 'twi', 'TWI53G1133' => 'twi', 'TWI60G0823' => 'twi', 'TWI63G0919' => 'twi', 'TWI63G1436' => 'twi', 'TWI73G0140' => 'twi', 'TWI73G0419' => 'twi', 'TWI73G0420' => 'twi', 'TWI73G1276' => 'twi', 'TWI74G0405' => 'twi', 'TWI74G0837' => 'twi', 'TWI75G0594' => 'twi', 'TWI75G1615' => 'twi', 'TWI77G0816' => 'twi', 'vmacro03831' => 'vma', 'vmacro13746' => 'vma', 'vmacro16089' => 'vma', 'vmacro22863' => 'vma', 'Zm00001eb085790' => 'zma', 'Zm00001eb114250' => 'zma', 'Zm00001eb138070' => 'zma', 'Zm00001eb167560' => 'zma', 'Zm00001eb199990' => 'zma', 'Zm00001eb368180' => 'zma', 'Zm00001eb382470' => 'zma' ), 'gf_id' => 'HOM05D001576', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001576' ), 'data_identifier' => 'HOM05D001576', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001576', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '406', 'num_species' => '29' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'Aqoxy1G01456' => 'aox', 'Aqoxy1G02949' => 'aox', 'Aqoxy3G01274' => 'aox', 'Aqoxy3G02110' => 'aox', 'Aqoxy3G02268' => 'aox', 'Aqoxy5G02702' => 'aox', 'Aqoxy5G02988' => 'aox', 'Aqoxy5G03427' => 'aox', 'Aqoxy6G02363' => 'aox', 'Atru.chr1.3225' => 'acertr', 'Atru.chr8.1198' => 'acertr', 'Atru.chr9.790' => 'acertr', 'CANSAT01G3197' => 'cansat', 'Ciclev10003979m.g' => 'ccl', 'Ciclev10017471m.g' => 'ccl', 'Ciclev10018206m.g' => 'ccl', 'Ciclev10033751m.g' => 'ccl', 'CiPaw.01G000900' => 'cil', 'CiPaw.01G001000' => 'cil', 'CiPaw.01G033500' => 'cil', 'CiPaw.01G060300' => 'cil', 'CiPaw.01G070200' => 'cil', 'CiPaw.01G075100' => 'cil', 'CiPaw.01G084700' => 'cil', 'CiPaw.01G087900' => 'cil', 'CiPaw.01G092600' => 'cil', 'CiPaw.01G097200' => 'cil', 'CiPaw.01G098300' => 'cil', 'CiPaw.01G110200' => 'cil', 'CiPaw.01G118700' => 'cil', 'CiPaw.01G121200' => 'cil', 'CiPaw.01G132500' => 'cil', 'CiPaw.01G146900' => 'cil', 'CiPaw.01G174000' => 'cil', 'CiPaw.01G179900' => 'cil', 'CiPaw.01G183400' => 'cil', 'CiPaw.01G240000' => 'cil', 'CiPaw.01G283500' => 'cil', 'CiPaw.01G307400' => 'cil', 'CiPaw.02G030800' => 'cil', 'CiPaw.02G047200' => 'cil', 'CiPaw.02G050500' => 'cil', 'CiPaw.02G069900' => 'cil', 'CiPaw.02G091600' => 'cil', 'CiPaw.02G095000' => 'cil', 'CiPaw.02G131900' => 'cil', 'CiPaw.03G043000' => 'cil', 'CiPaw.03G069900' => 'cil', 'CiPaw.03G088100' => 'cil', 'CiPaw.03G089300' => 'cil', 'CiPaw.03G093100' => 'cil', 'CiPaw.03G129800' => 'cil', 'CiPaw.03G131200' => 'cil', 'CiPaw.03G134500' => 'cil', 'CiPaw.03G152100' => 'cil', 'CiPaw.03G162700' => 'cil', 'CiPaw.03G172800' => 'cil', 'CiPaw.03G175800' => 'cil', 'CiPaw.03G181800' => 'cil', 'CiPaw.03G191400' => 'cil', 'CiPaw.03G198300' => 'cil', 'CiPaw.03G201300' => 'cil', 'CiPaw.03G224700' => 'cil', 'CiPaw.03G225000' => 'cil', 'CiPaw.04G065100' => 'cil', 'CiPaw.04G080400' => 'cil', 'CiPaw.04G113500' => 'cil', 'CiPaw.04G121900' => 'cil', 'CiPaw.04G144100' => 'cil', 'CiPaw.04G176500' => 'cil', 'CiPaw.05G086200' => 'cil', 'CiPaw.05G100200' => 'cil', 'CiPaw.05G114200' => 'cil', 'CiPaw.05G126800' => 'cil', 'CiPaw.05G228800' => 'cil', 'CiPaw.05G230600' => 'cil', 'CiPaw.05G236500' => 'cil', 'CiPaw.05G244800' => 'cil', 'CiPaw.06G026600' => 'cil', 'CiPaw.06G027900' => 'cil', 'CiPaw.06G051800' => 'cil', 'CiPaw.06G128500' => 'cil', 'CiPaw.06G165900' => 'cil', 'CiPaw.07G045400' => 'cil', 'CiPaw.07G048000' => 'cil', 'CiPaw.07G052000' => 'cil', 'CiPaw.07G073800' => 'cil', 'CiPaw.07G099700' => 'cil', 'CiPaw.07G108700' => 'cil', 'CiPaw.07G120000' => 'cil', 'CiPaw.07G134100' => 'cil', 'CiPaw.07G147000' => 'cil', 'CiPaw.07G149700' => 'cil', 'CiPaw.07G178300' => 'cil', 'CiPaw.07G184900' => 'cil', 'CiPaw.08G044500' => 'cil', 'CiPaw.08G046900' => 'cil', 'CiPaw.08G047300' => 'cil', 'CiPaw.08G115400' => 'cil', 'CiPaw.08G134700' => 'cil', 'CiPaw.08G157400' => 'cil', 'CiPaw.09G014300' => 'cil', 'CiPaw.09G088900' => 'cil', 'CiPaw.09G130900' => 'cil', 'CiPaw.09G133100' => 'cil', 'CiPaw.09G151300' => 'cil', 'CiPaw.09G172800' => 'cil', 'CiPaw.09G174900' => 'cil', 'CiPaw.09G175000' => 'cil', 'CiPaw.10G012800' => 'cil', 'CiPaw.10G028800' => 'cil', 'CiPaw.10G044700' => 'cil', 'CiPaw.10G067400' => 'cil', 'CiPaw.10G115900' => 'cil', 'CiPaw.10G126200' => 'cil', 'CiPaw.10G139700' => 'cil', 'CiPaw.10G155100' => 'cil', 'CiPaw.11G011300' => 'cil', 'CiPaw.11G025900' => 'cil', 'CiPaw.11G104100' => 'cil', 'CiPaw.11G142700' => 'cil', 'CiPaw.11G164500' => 'cil', 'CiPaw.11G189100' => 'cil', 'CiPaw.11G197100' => 'cil', 'CiPaw.12G006100' => 'cil', 'CiPaw.12G038500' => 'cil', 'CiPaw.12G041400' => 'cil', 'CiPaw.12G041600' => 'cil', 'CiPaw.12G051300' => 'cil', 'CiPaw.12G101800' => 'cil', 'CiPaw.12G107800' => 'cil', 'CiPaw.13G033200' => 'cil', 'CiPaw.13G129900' => 'cil', 'CiPaw.13G160200' => 'cil', 'CiPaw.14G018900' => 'cil', 'CiPaw.14G029000' => 'cil', 'CiPaw.14G031000' => 'cil', 'CiPaw.14G032000' => 'cil', 'CiPaw.14G032300' => 'cil', 'CiPaw.14G040600' => 'cil', 'CiPaw.14G060500' => 'cil', 'CiPaw.14G061500' => 'cil', 'CiPaw.14G077500' => 'cil', 'CiPaw.14G088300' => 'cil', 'CiPaw.14G108500' => 'cil', 'CiPaw.14G121300' => 'cil', 'CiPaw.14G133000' => 'cil', 'CiPaw.14G134600' => 'cil', 'CiPaw.15G027200' => 'cil', 'CiPaw.15G037700' => 'cil', 'CiPaw.15G050900' => 'cil', 'CiPaw.15G067200' => 'cil', 'CiPaw.15G072000' => 'cil', 'CiPaw.15G112900' => 'cil', 'CiPaw.15G133200' => 'cil', 'CiPaw.15G139500' => 'cil', 'CiPaw.15G155400' => 'cil', 'CiPaw.16G006000' => 'cil', 'CiPaw.16G013100' => 'cil', 'CiPaw.16G047100' => 'cil', 'CiPaw.16G048900' => 'cil', 'CiPaw.16G070300' => 'cil', 'CSS0000195' => 'camsi', 'CSS0001664' => 'camsi', 'CSS0002566' => 'camsi', 'CSS0003077' => 'camsi', 'CSS0004257' => 'camsi', 'CSS0004495' => 'camsi', 'CSS0004599' => 'camsi', 'CSS0004943' => 'camsi', 'CSS0005302' => 'camsi', 'CSS0006274' => 'camsi', 'CSS0006547' => 'camsi', 'CSS0006860' => 'camsi', 'CSS0008814' => 'camsi', 'CSS0008946' => 'camsi', 'CSS0009093' => 'camsi', 'CSS0010221' => 'camsi', 'CSS0010296' => 'camsi', 'CSS0010386' => 'camsi', 'CSS0010831' => 'camsi', 'CSS0011061' => 'camsi', 'CSS0012008' => 'camsi', 'CSS0012194' => 'camsi', 'CSS0013580' => 'camsi', 'CSS0014176' => 'camsi', 'CSS0014280' => 'camsi', 'CSS0014799' => 'camsi', 'CSS0015368' => 'camsi', 'CSS0017473' => 'camsi', 'CSS0019281' => 'camsi', 'CSS0021320' => 'camsi', 'CSS0021750' => 'camsi', 'CSS0023642' => 'camsi', 'CSS0023792' => 'camsi', 'CSS0031528' => 'camsi', 'CSS0033894' => 'camsi', 'CSS0034959' => 'camsi', 'CSS0035632' => 'camsi', 'CSS0038450' => 'camsi', 'CSS0039293' => 'camsi', 'CSS0041053' => 'camsi', 'CSS0041981' => 'camsi', 'CSS0042573' => 'camsi', 'CSS0042927' => 'camsi', 'CSS0047725' => 'camsi', 'CSS0049636' => 'camsi', 'CSS0050513' => 'camsi', 'DCAR_030203' => 'dca', 'Dinv07939' => 'din', 'FAN01G0456' => 'fan', 'FAN02G3001' => 'fan', 'FAN04G2781' => 'fan', 'FAN05G1385' => 'fan', 'FAN05G3062' => 'fan', 'FAN08G2267' => 'fan', 'FAN10G0481' => 'fan', 'FAN10G1257' => 'fan', 'FAN14G0954' => 'fan', 'FAN14G2347' => 'fan', 'FAN15G0187' => 'fan', 'FAN25G2214' => 'fan', 'FvH4_1g21031' => 'fve', 'FvH4_3g16231' => 'fve', 'FvH4_3g26413' => 'fve', 'FvH4_3g29014' => 'fve', 'FvH4_3g31921' => 'fve', 'FvH4_4g19882' => 'fve', 'FvH4_5g21960' => 'fve', 'FvH4_5g29683' => 'fve', 'FvH4_7g13271' => 'fve', 'Glyma.01G062500' => 'gma', 'Glyma.07G140900' => 'gma', 'Glyma.09G140900' => 'gma', 'Glyma.12G112700' => 'gma', 'Glyma.17G168800' => 'gma', 'HanXRQChr01g0027001' => 'han', 'HanXRQChr04g0120511' => 'han', 'HanXRQChr08g0232381' => 'han', 'HanXRQChr09g0265661' => 'han', 'HanXRQChr13g0416031' => 'han', 'Haze_05835' => 'cav', 'Haze_06597' => 'cav', 'Haze_07921' => 'cav', 'Haze_08599' => 'cav', 'Haze_10686' => 'cav', 'Haze_12994' => 'cav', 'Haze_13466' => 'cav', 'Haze_16101' => 'cav', 'Haze_17766' => 'cav', 'Haze_18456' => 'cav', 'Haze_20229' => 'cav', 'Hma1.2p1_0324F.1_g125640' => 'hma', 'Hma1.2p1_0733F.1_g210230' => 'hma', 'Hma1.2p1_0921F.1_g236870' => 'hma', 'Hma1.2p1_1313F.1_g274940' => 'hma', 'Hma1.2p1_3059F.1_g332230' => 'hma', 'Hund15925' => 'sun', 'Hund19562' => 'sun', 'Hund21925' => 'sun', 'MD03G1177400' => 'mdo', 'MD07G1026100' => 'mdo', 'MD17G1218600' => 'mdo', 'Medtr0867s0010' => 'mtr', 'Medtr6g081150' => 'mtr', 'Os01g0527900' => 'osa', 'Os02g0463725' => 'osa', 'Os02g0785600' => 'osa', 'Os03g0433733' => 'osa', 'Os04g0286500' => 'osa', 'Os05g0227800' => 'osa', 'Os06g0521000' => 'osa', 'Os06g0635500' => 'osa', 'Os06g0660650' => 'osa', 'Os07g0554400' => 'osa', 'Os08g0225900' => 'osa', 'Os08g0561000' => 'osa', 'Os09g0241700' => 'osa', 'Os09g0351900' => 'osa', 'Os11g0220700' => 'osa', 'Os11g0282700' => 'osa', 'Os12g0169300' => 'osa', 'Os12g0228500' => 'osa', 'Os12g0543800' => 'osa', 'PGR044G1547' => 'pgr', 'Potri.005G239150' => 'ptr', 'Potri.010G014250' => 'ptr', 'Prupe.1G172500' => 'ppe', 'Prupe.1G196800' => 'ppe', 'Prupe.1G279700' => 'ppe', 'Prupe.2G026400' => 'ppe', 'Prupe.3G094000' => 'ppe', 'Prupe.4G287300' => 'ppe', 'QL01p022166' => 'qlo', 'QL01p051890' => 'qlo', 'QL02p009469' => 'qlo', 'QL02p046053' => 'qlo', 'QL02p057958' => 'qlo', 'QL02p093127' => 'qlo', 'QL03p006855' => 'qlo', 'QL03p071586' => 'qlo', 'QL04p000022' => 'qlo', 'QL04p000024' => 'qlo', 'QL04p003192' => 'qlo', 'QL05p011416' => 'qlo', 'QL06p039590' => 'qlo', 'QL06p052750' => 'qlo', 'QL06p053821' => 'qlo', 'QL07p025287' => 'qlo', 'QL09p033218' => 'qlo', 'QL09p040841' => 'qlo', 'QL10p020337' => 'qlo', 'QL10p027209' => 'qlo', 'QL10p027969' => 'qlo', 'QL10p048988' => 'qlo', 'QL11p001241' => 'qlo', 'QL11p028487' => 'qlo', 'RcHm_v2.0_Chr2g0105031' => 'rch', 'RcHm_v2.0_Chr2g0117811' => 'rch', 'RcHm_v2.0_Chr6g0270241' => 'rch', 'RcHm_v2.0_Chr7g0215961' => 'rch', 'RcHm_v2.0_Chr7g0231991' => 'rch', 'Rhsim01G0041500' => 'rsi', 'Rhsim01G0115000' => 'rsi', 'Rhsim01G0115400' => 'rsi', 'Rhsim01G0133600' => 'rsi', 'Rhsim01G0159900' => 'rsi', 'Rhsim02G0189400' => 'rsi', 'Rhsim03G0135600' => 'rsi', 'Rhsim03G0149900' => 'rsi', 'Rhsim04G0125600' => 'rsi', 'Rhsim05G0091700' => 'rsi', 'Rhsim05G0092900' => 'rsi', 'Rhsim06G0075000' => 'rsi', 'Rhsim07G0066400' => 'rsi', 'Rhsim07G0156400' => 'rsi', 'Rhsim07G0182200' => 'rsi', 'Rhsim07G0182300' => 'rsi', 'Rhsim08G0180400' => 'rsi', 'Rhsim09G0056800' => 'rsi', 'Rhsim10G0153300' => 'rsi', 'Rhsim11G0012700' => 'rsi', 'Rhsim12G0031800' => 'rsi', 'Rhsim12G0055400' => 'rsi', 'Rhsim12G0091400' => 'rsi', 'Rhsim13G0070800' => 'rsi', 'Rhsim13G0193300' => 'rsi', 'RhsimUnG0111600' => 'rsi', 'RhsimUnG0137500' => 'rsi', 'RhsimUnG0172900' => 'rsi', 'SGA_v2.0_scaffold11G05878' => 'sas', 'SGA_v2.0_scaffold167G38458' => 'sas', 'SGA_v2.0_scaffold19G08588' => 'sas', 'SGA_v2.0_scaffold239G43990' => 'sas', 'SGA_v2.0_scaffold260G45865' => 'sas', 'SGA_v2.0_scaffold309G48177' => 'sas', 'SGA_v2.0_scaffold76G25122' => 'sas', 'SGA_v2.0_scaffold85G26708' => 'sas', 'SHI13914' => 'shi', 'SHI30402' => 'shi', 'TWI09G0020' => 'twi', 'TWI09G0456' => 'twi', 'TWI09G1572' => 'twi', 'TWI12G0266' => 'twi', 'TWI12G1451' => 'twi', 'TWI14G0851' => 'twi', 'TWI15G0796' => 'twi', 'TWI18G0820' => 'twi', 'TWI18G1152' => 'twi', 'TWI23G0007' => 'twi', 'TWI23G0314' => 'twi', 'TWI31G0674' => 'twi', 'TWI31G0938' => 'twi', 'TWI34G0641' => 'twi', 'TWI34G1527' => 'twi', 'TWI36G0193' => 'twi', 'TWI36G0405' => 'twi', 'TWI38G0892' => 'twi', 'TWI38G0936' => 'twi', 'TWI38G2218' => 'twi', 'TWI53G0679' => 'twi', 'TWI53G0863' => 'twi', 'TWI53G1133' => 'twi', 'TWI60G0823' => 'twi', 'TWI63G0919' => 'twi', 'TWI63G1436' => 'twi', 'TWI73G0140' => 'twi', 'TWI73G0419' => 'twi', 'TWI73G0420' => 'twi', 'TWI73G1276' => 'twi', 'TWI74G0405' => 'twi', 'TWI74G0837' => 'twi', 'TWI75G0594' => 'twi', 'TWI75G1615' => 'twi', 'TWI77G0816' => 'twi', 'vmacro03831' => 'vma', 'vmacro13746' => 'vma', 'vmacro16089' => 'vma', 'vmacro22863' => 'vma', 'Zm00001eb085790' => 'zma', 'Zm00001eb114250' => 'zma', 'Zm00001eb138070' => 'zma', 'Zm00001eb167560' => 'zma', 'Zm00001eb199990' => 'zma', 'Zm00001eb368180' => 'zma', 'Zm00001eb382470' => 'zma' ) $gf_id = 'HOM05D001576' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001576' ) $data_identifier = 'HOM05D001576' $data_type = 'gf_id' $species_gene_counts = array( 'aox' => (int) 9, 'acertr' => (int) 3, 'cansat' => (int) 1, 'ccl' => (int) 4, 'cil' => (int) 145, 'camsi' => (int) 46, 'dca' => (int) 1, 'din' => (int) 1, 'fan' => (int) 12, 'fve' => (int) 9, 'gma' => (int) 5, 'han' => (int) 5, 'cav' => (int) 11, 'hma' => (int) 5, 'sun' => (int) 3, 'mdo' => (int) 3, 'mtr' => (int) 2, 'osa' => (int) 19, 'pgr' => (int) 1, 'ptr' => (int) 2, 'ppe' => (int) 6, 'qlo' => (int) 24, 'rch' => (int) 5, 'rsi' => (int) 28, 'sas' => (int) 8, 'shi' => (int) 2, 'twi' => (int) 35, 'vma' => (int) 4, 'zma' => (int) 7 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb382470' $species_info = array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ) $local_species = 'cav' $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' => 'HOM05D001576', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '406', 'num_species' => '29' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'Aqoxy1G01456' => 'aox', 'Aqoxy1G02949' => 'aox', 'Aqoxy3G01274' => 'aox', 'Aqoxy3G02110' => 'aox', 'Aqoxy3G02268' => 'aox', 'Aqoxy5G02702' => 'aox', 'Aqoxy5G02988' => 'aox', 'Aqoxy5G03427' => 'aox', 'Aqoxy6G02363' => 'aox', 'Atru.chr1.3225' => 'acertr', 'Atru.chr8.1198' => 'acertr', 'Atru.chr9.790' => 'acertr', 'CANSAT01G3197' => 'cansat', 'Ciclev10003979m.g' => 'ccl', 'Ciclev10017471m.g' => 'ccl', 'Ciclev10018206m.g' => 'ccl', 'Ciclev10033751m.g' => 'ccl', 'CiPaw.01G000900' => 'cil', 'CiPaw.01G001000' => 'cil', 'CiPaw.01G033500' => 'cil', 'CiPaw.01G060300' => 'cil', 'CiPaw.01G070200' => 'cil', 'CiPaw.01G075100' => 'cil', 'CiPaw.01G084700' => 'cil', 'CiPaw.01G087900' => 'cil', 'CiPaw.01G092600' => 'cil', 'CiPaw.01G097200' => 'cil', 'CiPaw.01G098300' => 'cil', 'CiPaw.01G110200' => 'cil', 'CiPaw.01G118700' => 'cil', 'CiPaw.01G121200' => 'cil', 'CiPaw.01G132500' => 'cil', 'CiPaw.01G146900' => 'cil', 'CiPaw.01G174000' => 'cil', 'CiPaw.01G179900' => 'cil', 'CiPaw.01G183400' => 'cil', 'CiPaw.01G240000' => 'cil', 'CiPaw.01G283500' => 'cil', 'CiPaw.01G307400' => 'cil', 'CiPaw.02G030800' => 'cil', 'CiPaw.02G047200' => 'cil', 'CiPaw.02G050500' => 'cil', 'CiPaw.02G069900' => 'cil', 'CiPaw.02G091600' => 'cil', 'CiPaw.02G095000' => 'cil', 'CiPaw.02G131900' => 'cil', 'CiPaw.03G043000' => 'cil', 'CiPaw.03G069900' => 'cil', 'CiPaw.03G088100' => 'cil', 'CiPaw.03G089300' => 'cil', 'CiPaw.03G093100' => 'cil', 'CiPaw.03G129800' => 'cil', 'CiPaw.03G131200' => 'cil', 'CiPaw.03G134500' => 'cil', 'CiPaw.03G152100' => 'cil', 'CiPaw.03G162700' => 'cil', 'CiPaw.03G172800' => 'cil', 'CiPaw.03G175800' => 'cil', 'CiPaw.03G181800' => 'cil', 'CiPaw.03G191400' => 'cil', 'CiPaw.03G198300' => 'cil', 'CiPaw.03G201300' => 'cil', 'CiPaw.03G224700' => 'cil', 'CiPaw.03G225000' => 'cil', 'CiPaw.04G065100' => 'cil', 'CiPaw.04G080400' => 'cil', 'CiPaw.04G113500' => 'cil', 'CiPaw.04G121900' => 'cil', 'CiPaw.04G144100' => 'cil', 'CiPaw.04G176500' => 'cil', 'CiPaw.05G086200' => 'cil', 'CiPaw.05G100200' => 'cil', 'CiPaw.05G114200' => 'cil', 'CiPaw.05G126800' => 'cil', 'CiPaw.05G228800' => 'cil', 'CiPaw.05G230600' => 'cil', 'CiPaw.05G236500' => 'cil', 'CiPaw.05G244800' => 'cil', 'CiPaw.06G026600' => 'cil', 'CiPaw.06G027900' => 'cil', 'CiPaw.06G051800' => 'cil', 'CiPaw.06G128500' => 'cil', 'CiPaw.06G165900' => 'cil', 'CiPaw.07G045400' => 'cil', 'CiPaw.07G048000' => 'cil', 'CiPaw.07G052000' => 'cil', 'CiPaw.07G073800' => 'cil', 'CiPaw.07G099700' => 'cil', 'CiPaw.07G108700' => 'cil', 'CiPaw.07G120000' => 'cil', 'CiPaw.07G134100' => 'cil', 'CiPaw.07G147000' => 'cil', 'CiPaw.07G149700' => 'cil', 'CiPaw.07G178300' => 'cil', 'CiPaw.07G184900' => 'cil', 'CiPaw.08G044500' => 'cil', 'CiPaw.08G046900' => 'cil', 'CiPaw.08G047300' => 'cil', 'CiPaw.08G115400' => 'cil', 'CiPaw.08G134700' => 'cil', 'CiPaw.08G157400' => 'cil', 'CiPaw.09G014300' => 'cil', 'CiPaw.09G088900' => 'cil', 'CiPaw.09G130900' => 'cil', 'CiPaw.09G133100' => 'cil', 'CiPaw.09G151300' => 'cil', 'CiPaw.09G172800' => 'cil', 'CiPaw.09G174900' => 'cil', 'CiPaw.09G175000' => 'cil', 'CiPaw.10G012800' => 'cil', 'CiPaw.10G028800' => 'cil', 'CiPaw.10G044700' => 'cil', 'CiPaw.10G067400' => 'cil', 'CiPaw.10G115900' => 'cil', 'CiPaw.10G126200' => 'cil', 'CiPaw.10G139700' => 'cil', 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=> 'qlo', 'QL07p025287' => 'qlo', 'QL09p033218' => 'qlo', 'QL09p040841' => 'qlo', 'QL10p020337' => 'qlo', 'QL10p027209' => 'qlo', 'QL10p027969' => 'qlo', 'QL10p048988' => 'qlo', 'QL11p001241' => 'qlo', 'QL11p028487' => 'qlo', 'RcHm_v2.0_Chr2g0105031' => 'rch', 'RcHm_v2.0_Chr2g0117811' => 'rch', 'RcHm_v2.0_Chr6g0270241' => 'rch', 'RcHm_v2.0_Chr7g0215961' => 'rch', 'RcHm_v2.0_Chr7g0231991' => 'rch', 'Rhsim01G0041500' => 'rsi', 'Rhsim01G0115000' => 'rsi', 'Rhsim01G0115400' => 'rsi', 'Rhsim01G0133600' => 'rsi', 'Rhsim01G0159900' => 'rsi', 'Rhsim02G0189400' => 'rsi', 'Rhsim03G0135600' => 'rsi', 'Rhsim03G0149900' => 'rsi', 'Rhsim04G0125600' => 'rsi', 'Rhsim05G0091700' => 'rsi', 'Rhsim05G0092900' => 'rsi', 'Rhsim06G0075000' => 'rsi', 'Rhsim07G0066400' => 'rsi', 'Rhsim07G0156400' => 'rsi', 'Rhsim07G0182200' => 'rsi', 'Rhsim07G0182300' => 'rsi', 'Rhsim08G0180400' => 'rsi', 'Rhsim09G0056800' => 'rsi', 'Rhsim10G0153300' => 'rsi', 'Rhsim11G0012700' => 'rsi', 'Rhsim12G0031800' => 'rsi', 'Rhsim12G0055400' => 'rsi', 'Rhsim12G0091400' => 'rsi', 'Rhsim13G0070800' => 'rsi', 'Rhsim13G0193300' => 'rsi', 'RhsimUnG0111600' => 'rsi', 'RhsimUnG0137500' => 'rsi', 'RhsimUnG0172900' => 'rsi', 'SGA_v2.0_scaffold11G05878' => 'sas', 'SGA_v2.0_scaffold167G38458' => 'sas', 'SGA_v2.0_scaffold19G08588' => 'sas', 'SGA_v2.0_scaffold239G43990' => 'sas', 'SGA_v2.0_scaffold260G45865' => 'sas', 'SGA_v2.0_scaffold309G48177' => 'sas', 'SGA_v2.0_scaffold76G25122' => 'sas', 'SGA_v2.0_scaffold85G26708' => 'sas', 'SHI13914' => 'shi', 'SHI30402' => 'shi', 'TWI09G0020' => 'twi', 'TWI09G0456' => 'twi', 'TWI09G1572' => 'twi', 'TWI12G0266' => 'twi', 'TWI12G1451' => 'twi', 'TWI14G0851' => 'twi', 'TWI15G0796' => 'twi', 'TWI18G0820' => 'twi', 'TWI18G1152' => 'twi', 'TWI23G0007' => 'twi', 'TWI23G0314' => 'twi', 'TWI31G0674' => 'twi', 'TWI31G0938' => 'twi', 'TWI34G0641' => 'twi', 'TWI34G1527' => 'twi', 'TWI36G0193' => 'twi', 'TWI36G0405' => 'twi', 'TWI38G0892' => 'twi', 'TWI38G0936' => 'twi', 'TWI38G2218' => 'twi', 'TWI53G0679' => 'twi', 'TWI53G0863' => 'twi', 'TWI53G1133' => 'twi', 'TWI60G0823' => 'twi', 'TWI63G0919' => 'twi', 'TWI63G1436' => 'twi', 'TWI73G0140' => 'twi', 'TWI73G0419' => 'twi', 'TWI73G0420' => 'twi', 'TWI73G1276' => 'twi', 'TWI74G0405' => 'twi', 'TWI74G0837' => 'twi', 'TWI75G0594' => 'twi', 'TWI75G1615' => 'twi', 'TWI77G0816' => 'twi', 'vmacro03831' => 'vma', 'vmacro13746' => 'vma', 'vmacro16089' => 'vma', 'vmacro22863' => 'vma', 'Zm00001eb085790' => 'zma', 'Zm00001eb114250' => 'zma', 'Zm00001eb138070' => 'zma', 'Zm00001eb167560' => 'zma', 'Zm00001eb199990' => 'zma', 'Zm00001eb368180' => 'zma', 'Zm00001eb382470' => 'zma' ), 'gf_id' => 'HOM05D001576', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001576' ), 'data_identifier' => 'HOM05D001576', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001576', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '406', 'num_species' => '29' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'Aqoxy1G01456' => 'aox', 'Aqoxy1G02949' => 'aox', 'Aqoxy3G01274' => 'aox', 'Aqoxy3G02110' => 'aox', 'Aqoxy3G02268' => 'aox', 'Aqoxy5G02702' => 'aox', 'Aqoxy5G02988' => 'aox', 'Aqoxy5G03427' => 'aox', 'Aqoxy6G02363' => 'aox', 'Atru.chr1.3225' => 'acertr', 'Atru.chr8.1198' => 'acertr', 'Atru.chr9.790' => 'acertr', 'CANSAT01G3197' => 'cansat', 'Ciclev10003979m.g' => 'ccl', 'Ciclev10017471m.g' => 'ccl', 'Ciclev10018206m.g' => 'ccl', 'Ciclev10033751m.g' => 'ccl', 'CiPaw.01G000900' => 'cil', 'CiPaw.01G001000' => 'cil', 'CiPaw.01G033500' => 'cil', 'CiPaw.01G060300' => 'cil', 'CiPaw.01G070200' => 'cil', 'CiPaw.01G075100' => 'cil', 'CiPaw.01G084700' => 'cil', 'CiPaw.01G087900' => 'cil', 'CiPaw.01G092600' => 'cil', 'CiPaw.01G097200' => 'cil', 'CiPaw.01G098300' => 'cil', 'CiPaw.01G110200' => 'cil', 'CiPaw.01G118700' => 'cil', 'CiPaw.01G121200' => 'cil', 'CiPaw.01G132500' => 'cil', 'CiPaw.01G146900' => 'cil', 'CiPaw.01G174000' => 'cil', 'CiPaw.01G179900' => 'cil', 'CiPaw.01G183400' => 'cil', 'CiPaw.01G240000' => 'cil', 'CiPaw.01G283500' => 'cil', 'CiPaw.01G307400' => 'cil', 'CiPaw.02G030800' => 'cil', 'CiPaw.02G047200' => 'cil', 'CiPaw.02G050500' => 'cil', 'CiPaw.02G069900' => 'cil', 'CiPaw.02G091600' => 'cil', 'CiPaw.02G095000' => 'cil', 'CiPaw.02G131900' => 'cil', 'CiPaw.03G043000' => 'cil', 'CiPaw.03G069900' => 'cil', 'CiPaw.03G088100' => 'cil', 'CiPaw.03G089300' => 'cil', 'CiPaw.03G093100' => 'cil', 'CiPaw.03G129800' => 'cil', 'CiPaw.03G131200' => 'cil', 'CiPaw.03G134500' => 'cil', 'CiPaw.03G152100' => 'cil', 'CiPaw.03G162700' => 'cil', 'CiPaw.03G172800' => 'cil', 'CiPaw.03G175800' => 'cil', 'CiPaw.03G181800' => 'cil', 'CiPaw.03G191400' => 'cil', 'CiPaw.03G198300' => 'cil', 'CiPaw.03G201300' => 'cil', 'CiPaw.03G224700' => 'cil', 'CiPaw.03G225000' => 'cil', 'CiPaw.04G065100' => 'cil', 'CiPaw.04G080400' => 'cil', 'CiPaw.04G113500' => 'cil', 'CiPaw.04G121900' => 'cil', 'CiPaw.04G144100' => 'cil', 'CiPaw.04G176500' => 'cil', 'CiPaw.05G086200' => 'cil', 'CiPaw.05G100200' => 'cil', 'CiPaw.05G114200' => 'cil', 'CiPaw.05G126800' => 'cil', 'CiPaw.05G228800' => 'cil', 'CiPaw.05G230600' => 'cil', 'CiPaw.05G236500' => 'cil', 'CiPaw.05G244800' => 'cil', 'CiPaw.06G026600' => 'cil', 'CiPaw.06G027900' => 'cil', 'CiPaw.06G051800' => 'cil', 'CiPaw.06G128500' => 'cil', 'CiPaw.06G165900' => 'cil', 'CiPaw.07G045400' => 'cil', 'CiPaw.07G048000' => 'cil', 'CiPaw.07G052000' => 'cil', 'CiPaw.07G073800' => 'cil', 'CiPaw.07G099700' => 'cil', 'CiPaw.07G108700' => 'cil', 'CiPaw.07G120000' => 'cil', 'CiPaw.07G134100' => 'cil', 'CiPaw.07G147000' => 'cil', 'CiPaw.07G149700' => 'cil', 'CiPaw.07G178300' => 'cil', 'CiPaw.07G184900' => 'cil', 'CiPaw.08G044500' => 'cil', 'CiPaw.08G046900' => 'cil', 'CiPaw.08G047300' => 'cil', 'CiPaw.08G115400' => 'cil', 'CiPaw.08G134700' => 'cil', 'CiPaw.08G157400' => 'cil', 'CiPaw.09G014300' => 'cil', 'CiPaw.09G088900' => 'cil', 'CiPaw.09G130900' => 'cil', 'CiPaw.09G133100' => 'cil', 'CiPaw.09G151300' => 'cil', 'CiPaw.09G172800' => 'cil', 'CiPaw.09G174900' => 'cil', 'CiPaw.09G175000' => 'cil', 'CiPaw.10G012800' => 'cil', 'CiPaw.10G028800' => 'cil', 'CiPaw.10G044700' => 'cil', 'CiPaw.10G067400' => 'cil', 'CiPaw.10G115900' => 'cil', 'CiPaw.10G126200' => 'cil', 'CiPaw.10G139700' => 'cil', 'CiPaw.10G155100' => 'cil', 'CiPaw.11G011300' => 'cil', 'CiPaw.11G025900' => 'cil', 'CiPaw.11G104100' => 'cil', 'CiPaw.11G142700' => 'cil', 'CiPaw.11G164500' => 'cil', 'CiPaw.11G189100' => 'cil', 'CiPaw.11G197100' => 'cil', 'CiPaw.12G006100' => 'cil', 'CiPaw.12G038500' => 'cil', 'CiPaw.12G041400' => 'cil', 'CiPaw.12G041600' => 'cil', 'CiPaw.12G051300' => 'cil', 'CiPaw.12G101800' => 'cil', 'CiPaw.12G107800' => 'cil', 'CiPaw.13G033200' => 'cil', 'CiPaw.13G129900' => 'cil', 'CiPaw.13G160200' => 'cil', 'CiPaw.14G018900' => 'cil', 'CiPaw.14G029000' => 'cil', 'CiPaw.14G031000' => 'cil', 'CiPaw.14G032000' => 'cil', 'CiPaw.14G032300' => 'cil', 'CiPaw.14G040600' => 'cil', 'CiPaw.14G060500' => 'cil', 'CiPaw.14G061500' => 'cil', 'CiPaw.14G077500' => 'cil', 'CiPaw.14G088300' => 'cil', 'CiPaw.14G108500' => 'cil', 'CiPaw.14G121300' => 'cil', 'CiPaw.14G133000' => 'cil', 'CiPaw.14G134600' => 'cil', 'CiPaw.15G027200' => 'cil', 'CiPaw.15G037700' => 'cil', 'CiPaw.15G050900' => 'cil', 'CiPaw.15G067200' => 'cil', 'CiPaw.15G072000' => 'cil', 'CiPaw.15G112900' => 'cil', 'CiPaw.15G133200' => 'cil', 'CiPaw.15G139500' => 'cil', 'CiPaw.15G155400' => 'cil', 'CiPaw.16G006000' => 'cil', 'CiPaw.16G013100' => 'cil', 'CiPaw.16G047100' => 'cil', 'CiPaw.16G048900' => 'cil', 'CiPaw.16G070300' => 'cil', 'CSS0000195' => 'camsi', 'CSS0001664' => 'camsi', 'CSS0002566' => 'camsi', 'CSS0003077' => 'camsi', 'CSS0004257' => 'camsi', 'CSS0004495' => 'camsi', 'CSS0004599' => 'camsi', 'CSS0004943' => 'camsi', 'CSS0005302' => 'camsi', 'CSS0006274' => 'camsi', 'CSS0006547' => 'camsi', 'CSS0006860' => 'camsi', 'CSS0008814' => 'camsi', 'CSS0008946' => 'camsi', 'CSS0009093' => 'camsi', 'CSS0010221' => 'camsi', 'CSS0010296' => 'camsi', 'CSS0010386' => 'camsi', 'CSS0010831' => 'camsi', 'CSS0011061' => 'camsi', 'CSS0012008' => 'camsi', 'CSS0012194' => 'camsi', 'CSS0013580' => 'camsi', 'CSS0014176' => 'camsi', 'CSS0014280' => 'camsi', 'CSS0014799' => 'camsi', 'CSS0015368' => 'camsi', 'CSS0017473' => 'camsi', 'CSS0019281' => 'camsi', 'CSS0021320' => 'camsi', 'CSS0021750' => 'camsi', 'CSS0023642' => 'camsi', 'CSS0023792' => 'camsi', 'CSS0031528' => 'camsi', 'CSS0033894' => 'camsi', 'CSS0034959' => 'camsi', 'CSS0035632' => 'camsi', 'CSS0038450' => 'camsi', 'CSS0039293' => 'camsi', 'CSS0041053' => 'camsi', 'CSS0041981' => 'camsi', 'CSS0042573' => 'camsi', 'CSS0042927' => 'camsi', 'CSS0047725' => 'camsi', 'CSS0049636' => 'camsi', 'CSS0050513' => 'camsi', 'DCAR_030203' => 'dca', 'Dinv07939' => 'din', 'FAN01G0456' => 'fan', 'FAN02G3001' => 'fan', 'FAN04G2781' => 'fan', 'FAN05G1385' => 'fan', 'FAN05G3062' => 'fan', 'FAN08G2267' => 'fan', 'FAN10G0481' => 'fan', 'FAN10G1257' => 'fan', 'FAN14G0954' => 'fan', 'FAN14G2347' => 'fan', 'FAN15G0187' => 'fan', 'FAN25G2214' => 'fan', 'FvH4_1g21031' => 'fve', 'FvH4_3g16231' => 'fve', 'FvH4_3g26413' => 'fve', 'FvH4_3g29014' => 'fve', 'FvH4_3g31921' => 'fve', 'FvH4_4g19882' => 'fve', 'FvH4_5g21960' => 'fve', 'FvH4_5g29683' => 'fve', 'FvH4_7g13271' => 'fve', 'Glyma.01G062500' => 'gma', 'Glyma.07G140900' => 'gma', 'Glyma.09G140900' => 'gma', 'Glyma.12G112700' => 'gma', 'Glyma.17G168800' => 'gma', 'HanXRQChr01g0027001' => 'han', 'HanXRQChr04g0120511' => 'han', 'HanXRQChr08g0232381' => 'han', 'HanXRQChr09g0265661' => 'han', 'HanXRQChr13g0416031' => 'han', 'Haze_05835' => 'cav', 'Haze_06597' => 'cav', 'Haze_07921' => 'cav', 'Haze_08599' => 'cav', 'Haze_10686' => 'cav', 'Haze_12994' => 'cav', 'Haze_13466' => 'cav', 'Haze_16101' => 'cav', 'Haze_17766' => 'cav', 'Haze_18456' => 'cav', 'Haze_20229' => 'cav', 'Hma1.2p1_0324F.1_g125640' => 'hma', 'Hma1.2p1_0733F.1_g210230' => 'hma', 'Hma1.2p1_0921F.1_g236870' => 'hma', 'Hma1.2p1_1313F.1_g274940' => 'hma', 'Hma1.2p1_3059F.1_g332230' => 'hma', 'Hund15925' => 'sun', 'Hund19562' => 'sun', 'Hund21925' => 'sun', 'MD03G1177400' => 'mdo', 'MD07G1026100' => 'mdo', 'MD17G1218600' => 'mdo', 'Medtr0867s0010' => 'mtr', 'Medtr6g081150' => 'mtr', 'Os01g0527900' => 'osa', 'Os02g0463725' => 'osa', 'Os02g0785600' => 'osa', 'Os03g0433733' => 'osa', 'Os04g0286500' => 'osa', 'Os05g0227800' => 'osa', 'Os06g0521000' => 'osa', 'Os06g0635500' => 'osa', 'Os06g0660650' => 'osa', 'Os07g0554400' => 'osa', 'Os08g0225900' => 'osa', 'Os08g0561000' => 'osa', 'Os09g0241700' => 'osa', 'Os09g0351900' => 'osa', 'Os11g0220700' => 'osa', 'Os11g0282700' => 'osa', 'Os12g0169300' => 'osa', 'Os12g0228500' => 'osa', 'Os12g0543800' => 'osa', 'PGR044G1547' => 'pgr', 'Potri.005G239150' => 'ptr', 'Potri.010G014250' => 'ptr', 'Prupe.1G172500' => 'ppe', 'Prupe.1G196800' => 'ppe', 'Prupe.1G279700' => 'ppe', 'Prupe.2G026400' => 'ppe', 'Prupe.3G094000' => 'ppe', 'Prupe.4G287300' => 'ppe', 'QL01p022166' => 'qlo', 'QL01p051890' => 'qlo', 'QL02p009469' => 'qlo', 'QL02p046053' => 'qlo', 'QL02p057958' => 'qlo', 'QL02p093127' => 'qlo', 'QL03p006855' => 'qlo', 'QL03p071586' => 'qlo', 'QL04p000022' => 'qlo', 'QL04p000024' => 'qlo', 'QL04p003192' => 'qlo', 'QL05p011416' => 'qlo', 'QL06p039590' => 'qlo', 'QL06p052750' => 'qlo', 'QL06p053821' => 'qlo', 'QL07p025287' => 'qlo', 'QL09p033218' => 'qlo', 'QL09p040841' => 'qlo', 'QL10p020337' => 'qlo', 'QL10p027209' => 'qlo', 'QL10p027969' => 'qlo', 'QL10p048988' => 'qlo', 'QL11p001241' => 'qlo', 'QL11p028487' => 'qlo', 'RcHm_v2.0_Chr2g0105031' => 'rch', 'RcHm_v2.0_Chr2g0117811' => 'rch', 'RcHm_v2.0_Chr6g0270241' => 'rch', 'RcHm_v2.0_Chr7g0215961' => 'rch', 'RcHm_v2.0_Chr7g0231991' => 'rch', 'Rhsim01G0041500' => 'rsi', 'Rhsim01G0115000' => 'rsi', 'Rhsim01G0115400' => 'rsi', 'Rhsim01G0133600' => 'rsi', 'Rhsim01G0159900' => 'rsi', 'Rhsim02G0189400' => 'rsi', 'Rhsim03G0135600' => 'rsi', 'Rhsim03G0149900' => 'rsi', 'Rhsim04G0125600' => 'rsi', 'Rhsim05G0091700' => 'rsi', 'Rhsim05G0092900' => 'rsi', 'Rhsim06G0075000' => 'rsi', 'Rhsim07G0066400' => 'rsi', 'Rhsim07G0156400' => 'rsi', 'Rhsim07G0182200' => 'rsi', 'Rhsim07G0182300' => 'rsi', 'Rhsim08G0180400' => 'rsi', 'Rhsim09G0056800' => 'rsi', 'Rhsim10G0153300' => 'rsi', 'Rhsim11G0012700' => 'rsi', 'Rhsim12G0031800' => 'rsi', 'Rhsim12G0055400' => 'rsi', 'Rhsim12G0091400' => 'rsi', 'Rhsim13G0070800' => 'rsi', 'Rhsim13G0193300' => 'rsi', 'RhsimUnG0111600' => 'rsi', 'RhsimUnG0137500' => 'rsi', 'RhsimUnG0172900' => 'rsi', 'SGA_v2.0_scaffold11G05878' => 'sas', 'SGA_v2.0_scaffold167G38458' => 'sas', 'SGA_v2.0_scaffold19G08588' => 'sas', 'SGA_v2.0_scaffold239G43990' => 'sas', 'SGA_v2.0_scaffold260G45865' => 'sas', 'SGA_v2.0_scaffold309G48177' => 'sas', 'SGA_v2.0_scaffold76G25122' => 'sas', 'SGA_v2.0_scaffold85G26708' => 'sas', 'SHI13914' => 'shi', 'SHI30402' => 'shi', 'TWI09G0020' => 'twi', 'TWI09G0456' => 'twi', 'TWI09G1572' => 'twi', 'TWI12G0266' => 'twi', 'TWI12G1451' => 'twi', 'TWI14G0851' => 'twi', 'TWI15G0796' => 'twi', 'TWI18G0820' => 'twi', 'TWI18G1152' => 'twi', 'TWI23G0007' => 'twi', 'TWI23G0314' => 'twi', 'TWI31G0674' => 'twi', 'TWI31G0938' => 'twi', 'TWI34G0641' => 'twi', 'TWI34G1527' => 'twi', 'TWI36G0193' => 'twi', 'TWI36G0405' => 'twi', 'TWI38G0892' => 'twi', 'TWI38G0936' => 'twi', 'TWI38G2218' => 'twi', 'TWI53G0679' => 'twi', 'TWI53G0863' => 'twi', 'TWI53G1133' => 'twi', 'TWI60G0823' => 'twi', 'TWI63G0919' => 'twi', 'TWI63G1436' => 'twi', 'TWI73G0140' => 'twi', 'TWI73G0419' => 'twi', 'TWI73G0420' => 'twi', 'TWI73G1276' => 'twi', 'TWI74G0405' => 'twi', 'TWI74G0837' => 'twi', 'TWI75G0594' => 'twi', 'TWI75G1615' => 'twi', 'TWI77G0816' => 'twi', 'vmacro03831' => 'vma', 'vmacro13746' => 'vma', 'vmacro16089' => 'vma', 'vmacro22863' => 'vma', 'Zm00001eb085790' => 'zma', 'Zm00001eb114250' => 'zma', 'Zm00001eb138070' => 'zma', 'Zm00001eb167560' => 'zma', 'Zm00001eb199990' => 'zma', 'Zm00001eb368180' => 'zma', 'Zm00001eb382470' => 'zma' ) $gf_id = 'HOM05D001576' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001576' ) $data_identifier = 'HOM05D001576' $data_type = 'gf_id' $species_gene_counts = array( 'aox' => (int) 9, 'acertr' => (int) 3, 'cansat' => (int) 1, 'ccl' => (int) 4, 'cil' => (int) 145, 'camsi' => (int) 46, 'dca' => (int) 1, 'din' => (int) 1, 'fan' => (int) 12, 'fve' => (int) 9, 'gma' => (int) 5, 'han' => (int) 5, 'cav' => (int) 11, 'hma' => (int) 5, 'sun' => (int) 3, 'mdo' => (int) 3, 'mtr' => (int) 2, 'osa' => (int) 19, 'pgr' => (int) 1, 'ptr' => (int) 2, 'ppe' => (int) 6, 'qlo' => (int) 24, 'rch' => (int) 5, 'rsi' => (int) 28, 'sas' => (int) 8, 'shi' => (int) 2, 'twi' => (int) 35, 'vma' => (int) 4, 'zma' => (int) 7 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb382470' $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' => 'HOM05D001576', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '406', 'num_species' => '29' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'Aqoxy1G01456' => 'aox', 'Aqoxy1G02949' => 'aox', 'Aqoxy3G01274' => 'aox', 'Aqoxy3G02110' => 'aox', 'Aqoxy3G02268' => 'aox', 'Aqoxy5G02702' => 'aox', 'Aqoxy5G02988' => 'aox', 'Aqoxy5G03427' => 'aox', 'Aqoxy6G02363' => 'aox', 'Atru.chr1.3225' => 'acertr', 'Atru.chr8.1198' => 'acertr', 'Atru.chr9.790' => 'acertr', 'CANSAT01G3197' => 'cansat', 'Ciclev10003979m.g' => 'ccl', 'Ciclev10017471m.g' => 'ccl', 'Ciclev10018206m.g' => 'ccl', 'Ciclev10033751m.g' => 'ccl', 'CiPaw.01G000900' => 'cil', 'CiPaw.01G001000' => 'cil', 'CiPaw.01G033500' => 'cil', 'CiPaw.01G060300' => 'cil', 'CiPaw.01G070200' => 'cil', 'CiPaw.01G075100' => 'cil', 'CiPaw.01G084700' => 'cil', 'CiPaw.01G087900' => 'cil', 'CiPaw.01G092600' => 'cil', 'CiPaw.01G097200' => 'cil', 'CiPaw.01G098300' => 'cil', 'CiPaw.01G110200' => 'cil', 'CiPaw.01G118700' => 'cil', 'CiPaw.01G121200' => 'cil', 'CiPaw.01G132500' => 'cil', 'CiPaw.01G146900' => 'cil', 'CiPaw.01G174000' => 'cil', 'CiPaw.01G179900' => 'cil', 'CiPaw.01G183400' => 'cil', 'CiPaw.01G240000' => 'cil', 'CiPaw.01G283500' => 'cil', 'CiPaw.01G307400' => 'cil', 'CiPaw.02G030800' => 'cil', 'CiPaw.02G047200' => 'cil', 'CiPaw.02G050500' => 'cil', 'CiPaw.02G069900' => 'cil', 'CiPaw.02G091600' => 'cil', 'CiPaw.02G095000' => 'cil', 'CiPaw.02G131900' => 'cil', 'CiPaw.03G043000' => 'cil', 'CiPaw.03G069900' => 'cil', 'CiPaw.03G088100' => 'cil', 'CiPaw.03G089300' => 'cil', 'CiPaw.03G093100' => 'cil', 'CiPaw.03G129800' => 'cil', 'CiPaw.03G131200' => 'cil', 'CiPaw.03G134500' => 'cil', 'CiPaw.03G152100' => 'cil', 'CiPaw.03G162700' => 'cil', 'CiPaw.03G172800' => 'cil', 'CiPaw.03G175800' => 'cil', 'CiPaw.03G181800' => 'cil', 'CiPaw.03G191400' => 'cil', 'CiPaw.03G198300' => 'cil', 'CiPaw.03G201300' => 'cil', 'CiPaw.03G224700' => 'cil', 'CiPaw.03G225000' => 'cil', 'CiPaw.04G065100' => 'cil', 'CiPaw.04G080400' => 'cil', 'CiPaw.04G113500' => 'cil', 'CiPaw.04G121900' => 'cil', 'CiPaw.04G144100' => 'cil', 'CiPaw.04G176500' => 'cil', 'CiPaw.05G086200' => 'cil', 'CiPaw.05G100200' => 'cil', 'CiPaw.05G114200' => 'cil', 'CiPaw.05G126800' => 'cil', 'CiPaw.05G228800' => 'cil', 'CiPaw.05G230600' => 'cil', 'CiPaw.05G236500' => 'cil', 'CiPaw.05G244800' => 'cil', 'CiPaw.06G026600' => 'cil', 'CiPaw.06G027900' => 'cil', 'CiPaw.06G051800' => 'cil', 'CiPaw.06G128500' => 'cil', 'CiPaw.06G165900' => 'cil', 'CiPaw.07G045400' => 'cil', 'CiPaw.07G048000' => 'cil', 'CiPaw.07G052000' => 'cil', 'CiPaw.07G073800' => 'cil', 'CiPaw.07G099700' => 'cil', 'CiPaw.07G108700' => 'cil', 'CiPaw.07G120000' => 'cil', 'CiPaw.07G134100' => 'cil', 'CiPaw.07G147000' => 'cil', 'CiPaw.07G149700' => 'cil', 'CiPaw.07G178300' => 'cil', 'CiPaw.07G184900' => 'cil', 'CiPaw.08G044500' => 'cil', 'CiPaw.08G046900' => 'cil', 'CiPaw.08G047300' => 'cil', 'CiPaw.08G115400' => 'cil', 'CiPaw.08G134700' => 'cil', 'CiPaw.08G157400' => 'cil', 'CiPaw.09G014300' => 'cil', 'CiPaw.09G088900' => 'cil', 'CiPaw.09G130900' => 'cil', 'CiPaw.09G133100' => 'cil', 'CiPaw.09G151300' => 'cil', 'CiPaw.09G172800' => 'cil', 'CiPaw.09G174900' => 'cil', 'CiPaw.09G175000' => 'cil', 'CiPaw.10G012800' => 'cil', 'CiPaw.10G028800' => 'cil', 'CiPaw.10G044700' => 'cil', 'CiPaw.10G067400' => 'cil', 'CiPaw.10G115900' => 'cil', 'CiPaw.10G126200' => 'cil', 'CiPaw.10G139700' => 'cil', 'CiPaw.10G155100' => 'cil', 'CiPaw.11G011300' => 'cil', 'CiPaw.11G025900' => 'cil', 'CiPaw.11G104100' => 'cil', 'CiPaw.11G142700' => 'cil', 'CiPaw.11G164500' => 'cil', 'CiPaw.11G189100' => 'cil', 'CiPaw.11G197100' => 'cil', 'CiPaw.12G006100' => 'cil', 'CiPaw.12G038500' => 'cil', 'CiPaw.12G041400' => 'cil', 'CiPaw.12G041600' => 'cil', 'CiPaw.12G051300' => 'cil', 'CiPaw.12G101800' => 'cil', 'CiPaw.12G107800' => 'cil', 'CiPaw.13G033200' => 'cil', 'CiPaw.13G129900' => 'cil', 'CiPaw.13G160200' => 'cil', 'CiPaw.14G018900' => 'cil', 'CiPaw.14G029000' => 'cil', 'CiPaw.14G031000' => 'cil', 'CiPaw.14G032000' => 'cil', 'CiPaw.14G032300' => 'cil', 'CiPaw.14G040600' => 'cil', 'CiPaw.14G060500' => 'cil', 'CiPaw.14G061500' => 'cil', 'CiPaw.14G077500' => 'cil', 'CiPaw.14G088300' => 'cil', 'CiPaw.14G108500' => 'cil', 'CiPaw.14G121300' => 'cil', 'CiPaw.14G133000' => 'cil', 'CiPaw.14G134600' => 'cil', 'CiPaw.15G027200' => 'cil', 'CiPaw.15G037700' => 'cil', 'CiPaw.15G050900' => 'cil', 'CiPaw.15G067200' => 'cil', 'CiPaw.15G072000' => 'cil', 'CiPaw.15G112900' => 'cil', 'CiPaw.15G133200' => 'cil', 'CiPaw.15G139500' => 'cil', 'CiPaw.15G155400' => 'cil', 'CiPaw.16G006000' => 'cil', 'CiPaw.16G013100' => 'cil', 'CiPaw.16G047100' => 'cil', 'CiPaw.16G048900' => 'cil', 'CiPaw.16G070300' => 'cil', 'CSS0000195' => 'camsi', 'CSS0001664' => 'camsi', 'CSS0002566' => 'camsi', 'CSS0003077' => 'camsi', 'CSS0004257' => 'camsi', 'CSS0004495' => 'camsi', 'CSS0004599' => 'camsi', 'CSS0004943' => 'camsi', 'CSS0005302' => 'camsi', 'CSS0006274' => 'camsi', 'CSS0006547' => 'camsi', 'CSS0006860' => 'camsi', 'CSS0008814' => 'camsi', 'CSS0008946' => 'camsi', 'CSS0009093' => 'camsi', 'CSS0010221' => 'camsi', 'CSS0010296' => 'camsi', 'CSS0010386' => 'camsi', 'CSS0010831' => 'camsi', 'CSS0011061' => 'camsi', 'CSS0012008' => 'camsi', 'CSS0012194' => 'camsi', 'CSS0013580' => 'camsi', 'CSS0014176' => 'camsi', 'CSS0014280' => 'camsi', 'CSS0014799' => 'camsi', 'CSS0015368' => 'camsi', 'CSS0017473' => 'camsi', 'CSS0019281' => 'camsi', 'CSS0021320' => 'camsi', 'CSS0021750' => 'camsi', 'CSS0023642' => 'camsi', 'CSS0023792' => 'camsi', 'CSS0031528' => 'camsi', 'CSS0033894' => 'camsi', 'CSS0034959' => 'camsi', 'CSS0035632' => 'camsi', 'CSS0038450' => 'camsi', 'CSS0039293' => 'camsi', 'CSS0041053' => 'camsi', 'CSS0041981' => 'camsi', 'CSS0042573' => 'camsi', 'CSS0042927' => 'camsi', 'CSS0047725' => 'camsi', 'CSS0049636' => 'camsi', 'CSS0050513' => 'camsi', 'DCAR_030203' => 'dca', 'Dinv07939' => 'din', 'FAN01G0456' => 'fan', 'FAN02G3001' => 'fan', 'FAN04G2781' => 'fan', 'FAN05G1385' => 'fan', 'FAN05G3062' => 'fan', 'FAN08G2267' => 'fan', 'FAN10G0481' => 'fan', 'FAN10G1257' => 'fan', 'FAN14G0954' => 'fan', 'FAN14G2347' => 'fan', 'FAN15G0187' => 'fan', 'FAN25G2214' => 'fan', 'FvH4_1g21031' => 'fve', 'FvH4_3g16231' => 'fve', 'FvH4_3g26413' => 'fve', 'FvH4_3g29014' => 'fve', 'FvH4_3g31921' => 'fve', 'FvH4_4g19882' => 'fve', 'FvH4_5g21960' => 'fve', 'FvH4_5g29683' => 'fve', 'FvH4_7g13271' => 'fve', 'Glyma.01G062500' => 'gma', 'Glyma.07G140900' => 'gma', 'Glyma.09G140900' => 'gma', 'Glyma.12G112700' => 'gma', 'Glyma.17G168800' => 'gma', 'HanXRQChr01g0027001' => 'han', 'HanXRQChr04g0120511' => 'han', 'HanXRQChr08g0232381' => 'han', 'HanXRQChr09g0265661' => 'han', 'HanXRQChr13g0416031' => 'han', 'Haze_05835' => 'cav', 'Haze_06597' => 'cav', 'Haze_07921' => 'cav', 'Haze_08599' => 'cav', 'Haze_10686' => 'cav', 'Haze_12994' => 'cav', 'Haze_13466' => 'cav', 'Haze_16101' => 'cav', 'Haze_17766' => 'cav', 'Haze_18456' => 'cav', 'Haze_20229' => 'cav', 'Hma1.2p1_0324F.1_g125640' => 'hma', 'Hma1.2p1_0733F.1_g210230' => 'hma', 'Hma1.2p1_0921F.1_g236870' => 'hma', 'Hma1.2p1_1313F.1_g274940' => 'hma', 'Hma1.2p1_3059F.1_g332230' => 'hma', 'Hund15925' => 'sun', 'Hund19562' => 'sun', 'Hund21925' => 'sun', 'MD03G1177400' => 'mdo', 'MD07G1026100' => 'mdo', 'MD17G1218600' => 'mdo', 'Medtr0867s0010' => 'mtr', 'Medtr6g081150' => 'mtr', 'Os01g0527900' => 'osa', 'Os02g0463725' => 'osa', 'Os02g0785600' => 'osa', 'Os03g0433733' => 'osa', 'Os04g0286500' => 'osa', 'Os05g0227800' => 'osa', 'Os06g0521000' => 'osa', 'Os06g0635500' => 'osa', 'Os06g0660650' => 'osa', 'Os07g0554400' => 'osa', 'Os08g0225900' => 'osa', 'Os08g0561000' => 'osa', 'Os09g0241700' => 'osa', 'Os09g0351900' => 'osa', 'Os11g0220700' => 'osa', 'Os11g0282700' => 'osa', 'Os12g0169300' => 'osa', 'Os12g0228500' => 'osa', 'Os12g0543800' => 'osa', 'PGR044G1547' => 'pgr', 'Potri.005G239150' => 'ptr', 'Potri.010G014250' => 'ptr', 'Prupe.1G172500' => 'ppe', 'Prupe.1G196800' => 'ppe', 'Prupe.1G279700' => 'ppe', 'Prupe.2G026400' => 'ppe', 'Prupe.3G094000' => 'ppe', 'Prupe.4G287300' => 'ppe', 'QL01p022166' => 'qlo', 'QL01p051890' => 'qlo', 'QL02p009469' => 'qlo', 'QL02p046053' => 'qlo', 'QL02p057958' => 'qlo', 'QL02p093127' => 'qlo', 'QL03p006855' => 'qlo', 'QL03p071586' => 'qlo', 'QL04p000022' => 'qlo', 'QL04p000024' => 'qlo', 'QL04p003192' => 'qlo', 'QL05p011416' => 'qlo', 'QL06p039590' => 'qlo', 'QL06p052750' => 'qlo', 'QL06p053821' => 'qlo', 'QL07p025287' => 'qlo', 'QL09p033218' => 'qlo', 'QL09p040841' => 'qlo', 'QL10p020337' => 'qlo', 'QL10p027209' => 'qlo', 'QL10p027969' => 'qlo', 'QL10p048988' => 'qlo', 'QL11p001241' => 'qlo', 'QL11p028487' => 'qlo', 'RcHm_v2.0_Chr2g0105031' => 'rch', 'RcHm_v2.0_Chr2g0117811' => 'rch', 'RcHm_v2.0_Chr6g0270241' => 'rch', 'RcHm_v2.0_Chr7g0215961' => 'rch', 'RcHm_v2.0_Chr7g0231991' => 'rch', 'Rhsim01G0041500' => 'rsi', 'Rhsim01G0115000' => 'rsi', 'Rhsim01G0115400' => 'rsi', 'Rhsim01G0133600' => 'rsi', 'Rhsim01G0159900' => 'rsi', 'Rhsim02G0189400' => 'rsi', 'Rhsim03G0135600' => 'rsi', 'Rhsim03G0149900' => 'rsi', 'Rhsim04G0125600' => 'rsi', 'Rhsim05G0091700' => 'rsi', 'Rhsim05G0092900' => 'rsi', 'Rhsim06G0075000' => 'rsi', 'Rhsim07G0066400' => 'rsi', 'Rhsim07G0156400' => 'rsi', 'Rhsim07G0182200' => 'rsi', 'Rhsim07G0182300' => 'rsi', 'Rhsim08G0180400' => 'rsi', 'Rhsim09G0056800' => 'rsi', 'Rhsim10G0153300' => 'rsi', 'Rhsim11G0012700' => 'rsi', 'Rhsim12G0031800' => 'rsi', 'Rhsim12G0055400' => 'rsi', 'Rhsim12G0091400' => 'rsi', 'Rhsim13G0070800' => 'rsi', 'Rhsim13G0193300' => 'rsi', 'RhsimUnG0111600' => 'rsi', 'RhsimUnG0137500' => 'rsi', 'RhsimUnG0172900' => 'rsi', 'SGA_v2.0_scaffold11G05878' => 'sas', 'SGA_v2.0_scaffold167G38458' => 'sas', 'SGA_v2.0_scaffold19G08588' => 'sas', 'SGA_v2.0_scaffold239G43990' => 'sas', 'SGA_v2.0_scaffold260G45865' => 'sas', 'SGA_v2.0_scaffold309G48177' => 'sas', 'SGA_v2.0_scaffold76G25122' => 'sas', 'SGA_v2.0_scaffold85G26708' => 'sas', 'SHI13914' => 'shi', 'SHI30402' => 'shi', 'TWI09G0020' => 'twi', 'TWI09G0456' => 'twi', 'TWI09G1572' => 'twi', 'TWI12G0266' => 'twi', 'TWI12G1451' => 'twi', 'TWI14G0851' => 'twi', 'TWI15G0796' => 'twi', 'TWI18G0820' => 'twi', 'TWI18G1152' => 'twi', 'TWI23G0007' => 'twi', 'TWI23G0314' => 'twi', 'TWI31G0674' => 'twi', 'TWI31G0938' => 'twi', 'TWI34G0641' => 'twi', 'TWI34G1527' => 'twi', 'TWI36G0193' => 'twi', 'TWI36G0405' => 'twi', 'TWI38G0892' => 'twi', 'TWI38G0936' => 'twi', 'TWI38G2218' => 'twi', 'TWI53G0679' => 'twi', 'TWI53G0863' => 'twi', 'TWI53G1133' => 'twi', 'TWI60G0823' => 'twi', 'TWI63G0919' => 'twi', 'TWI63G1436' => 'twi', 'TWI73G0140' => 'twi', 'TWI73G0419' => 'twi', 'TWI73G0420' => 'twi', 'TWI73G1276' => 'twi', 'TWI74G0405' => 'twi', 'TWI74G0837' => 'twi', 'TWI75G0594' => 'twi', 'TWI75G1615' => 'twi', 'TWI77G0816' => 'twi', 'vmacro03831' => 'vma', 'vmacro13746' => 'vma', 'vmacro16089' => 'vma', 'vmacro22863' => 'vma', 'Zm00001eb085790' => 'zma', 'Zm00001eb114250' => 'zma', 'Zm00001eb138070' => 'zma', 'Zm00001eb167560' => 'zma', 'Zm00001eb199990' => 'zma', 'Zm00001eb368180' => 'zma', 'Zm00001eb382470' => 'zma' ), 'gf_id' => 'HOM05D001576', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001576' ), 'data_identifier' => 'HOM05D001576', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001576', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '406', 'num_species' => '29' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'Aqoxy1G01456' => 'aox', 'Aqoxy1G02949' => 'aox', 'Aqoxy3G01274' => 'aox', 'Aqoxy3G02110' => 'aox', 'Aqoxy3G02268' => 'aox', 'Aqoxy5G02702' => 'aox', 'Aqoxy5G02988' => 'aox', 'Aqoxy5G03427' => 'aox', 'Aqoxy6G02363' => 'aox', 'Atru.chr1.3225' => 'acertr', 'Atru.chr8.1198' => 'acertr', 'Atru.chr9.790' => 'acertr', 'CANSAT01G3197' => 'cansat', 'Ciclev10003979m.g' => 'ccl', 'Ciclev10017471m.g' => 'ccl', 'Ciclev10018206m.g' => 'ccl', 'Ciclev10033751m.g' => 'ccl', 'CiPaw.01G000900' => 'cil', 'CiPaw.01G001000' => 'cil', 'CiPaw.01G033500' => 'cil', 'CiPaw.01G060300' => 'cil', 'CiPaw.01G070200' => 'cil', 'CiPaw.01G075100' => 'cil', 'CiPaw.01G084700' => 'cil', 'CiPaw.01G087900' => 'cil', 'CiPaw.01G092600' => 'cil', 'CiPaw.01G097200' => 'cil', 'CiPaw.01G098300' => 'cil', 'CiPaw.01G110200' => 'cil', 'CiPaw.01G118700' => 'cil', 'CiPaw.01G121200' => 'cil', 'CiPaw.01G132500' => 'cil', 'CiPaw.01G146900' => 'cil', 'CiPaw.01G174000' => 'cil', 'CiPaw.01G179900' => 'cil', 'CiPaw.01G183400' => 'cil', 'CiPaw.01G240000' => 'cil', 'CiPaw.01G283500' => 'cil', 'CiPaw.01G307400' => 'cil', 'CiPaw.02G030800' => 'cil', 'CiPaw.02G047200' => 'cil', 'CiPaw.02G050500' => 'cil', 'CiPaw.02G069900' => 'cil', 'CiPaw.02G091600' => 'cil', 'CiPaw.02G095000' => 'cil', 'CiPaw.02G131900' => 'cil', 'CiPaw.03G043000' => 'cil', 'CiPaw.03G069900' => 'cil', 'CiPaw.03G088100' => 'cil', 'CiPaw.03G089300' => 'cil', 'CiPaw.03G093100' => 'cil', 'CiPaw.03G129800' => 'cil', 'CiPaw.03G131200' => 'cil', 'CiPaw.03G134500' => 'cil', 'CiPaw.03G152100' => 'cil', 'CiPaw.03G162700' => 'cil', 'CiPaw.03G172800' => 'cil', 'CiPaw.03G175800' => 'cil', 'CiPaw.03G181800' => 'cil', 'CiPaw.03G191400' => 'cil', 'CiPaw.03G198300' => 'cil', 'CiPaw.03G201300' => 'cil', 'CiPaw.03G224700' => 'cil', 'CiPaw.03G225000' => 'cil', 'CiPaw.04G065100' => 'cil', 'CiPaw.04G080400' => 'cil', 'CiPaw.04G113500' => 'cil', 'CiPaw.04G121900' => 'cil', 'CiPaw.04G144100' => 'cil', 'CiPaw.04G176500' => 'cil', 'CiPaw.05G086200' => 'cil', 'CiPaw.05G100200' => 'cil', 'CiPaw.05G114200' => 'cil', 'CiPaw.05G126800' => 'cil', 'CiPaw.05G228800' => 'cil', 'CiPaw.05G230600' => 'cil', 'CiPaw.05G236500' => 'cil', 'CiPaw.05G244800' => 'cil', 'CiPaw.06G026600' => 'cil', 'CiPaw.06G027900' => 'cil', 'CiPaw.06G051800' => 'cil', 'CiPaw.06G128500' => 'cil', 'CiPaw.06G165900' => 'cil', 'CiPaw.07G045400' => 'cil', 'CiPaw.07G048000' => 'cil', 'CiPaw.07G052000' => 'cil', 'CiPaw.07G073800' => 'cil', 'CiPaw.07G099700' => 'cil', 'CiPaw.07G108700' => 'cil', 'CiPaw.07G120000' => 'cil', 'CiPaw.07G134100' => 'cil', 'CiPaw.07G147000' => 'cil', 'CiPaw.07G149700' => 'cil', 'CiPaw.07G178300' => 'cil', 'CiPaw.07G184900' => 'cil', 'CiPaw.08G044500' => 'cil', 'CiPaw.08G046900' => 'cil', 'CiPaw.08G047300' => 'cil', 'CiPaw.08G115400' => 'cil', 'CiPaw.08G134700' => 'cil', 'CiPaw.08G157400' => 'cil', 'CiPaw.09G014300' => 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'CiPaw.14G032000' => 'cil', 'CiPaw.14G032300' => 'cil', 'CiPaw.14G040600' => 'cil', 'CiPaw.14G060500' => 'cil', 'CiPaw.14G061500' => 'cil', 'CiPaw.14G077500' => 'cil', 'CiPaw.14G088300' => 'cil', 'CiPaw.14G108500' => 'cil', 'CiPaw.14G121300' => 'cil', 'CiPaw.14G133000' => 'cil', 'CiPaw.14G134600' => 'cil', 'CiPaw.15G027200' => 'cil', 'CiPaw.15G037700' => 'cil', 'CiPaw.15G050900' => 'cil', 'CiPaw.15G067200' => 'cil', 'CiPaw.15G072000' => 'cil', 'CiPaw.15G112900' => 'cil', 'CiPaw.15G133200' => 'cil', 'CiPaw.15G139500' => 'cil', 'CiPaw.15G155400' => 'cil', 'CiPaw.16G006000' => 'cil', 'CiPaw.16G013100' => 'cil', 'CiPaw.16G047100' => 'cil', 'CiPaw.16G048900' => 'cil', 'CiPaw.16G070300' => 'cil', 'CSS0000195' => 'camsi', 'CSS0001664' => 'camsi', 'CSS0002566' => 'camsi', 'CSS0003077' => 'camsi', 'CSS0004257' => 'camsi', 'CSS0004495' => 'camsi', 'CSS0004599' => 'camsi', 'CSS0004943' => 'camsi', 'CSS0005302' => 'camsi', 'CSS0006274' => 'camsi', 'CSS0006547' => 'camsi', 'CSS0006860' => 'camsi', 'CSS0008814' => 'camsi', 'CSS0008946' => 'camsi', 'CSS0009093' => 'camsi', 'CSS0010221' => 'camsi', 'CSS0010296' => 'camsi', 'CSS0010386' => 'camsi', 'CSS0010831' => 'camsi', 'CSS0011061' => 'camsi', 'CSS0012008' => 'camsi', 'CSS0012194' => 'camsi', 'CSS0013580' => 'camsi', 'CSS0014176' => 'camsi', 'CSS0014280' => 'camsi', 'CSS0014799' => 'camsi', 'CSS0015368' => 'camsi', 'CSS0017473' => 'camsi', 'CSS0019281' => 'camsi', 'CSS0021320' => 'camsi', 'CSS0021750' => 'camsi', 'CSS0023642' => 'camsi', 'CSS0023792' => 'camsi', 'CSS0031528' => 'camsi', 'CSS0033894' => 'camsi', 'CSS0034959' => 'camsi', 'CSS0035632' => 'camsi', 'CSS0038450' => 'camsi', 'CSS0039293' => 'camsi', 'CSS0041053' => 'camsi', 'CSS0041981' => 'camsi', 'CSS0042573' => 'camsi', 'CSS0042927' => 'camsi', 'CSS0047725' => 'camsi', 'CSS0049636' => 'camsi', 'CSS0050513' => 'camsi', 'DCAR_030203' => 'dca', 'Dinv07939' => 'din', 'FAN01G0456' => 'fan', 'FAN02G3001' => 'fan', 'FAN04G2781' => 'fan', 'FAN05G1385' => 'fan', 'FAN05G3062' => 'fan', 'FAN08G2267' => 'fan', 'FAN10G0481' => 'fan', 'FAN10G1257' => 'fan', 'FAN14G0954' => 'fan', 'FAN14G2347' => 'fan', 'FAN15G0187' => 'fan', 'FAN25G2214' => 'fan', 'FvH4_1g21031' => 'fve', 'FvH4_3g16231' => 'fve', 'FvH4_3g26413' => 'fve', 'FvH4_3g29014' => 'fve', 'FvH4_3g31921' => 'fve', 'FvH4_4g19882' => 'fve', 'FvH4_5g21960' => 'fve', 'FvH4_5g29683' => 'fve', 'FvH4_7g13271' => 'fve', 'Glyma.01G062500' => 'gma', 'Glyma.07G140900' => 'gma', 'Glyma.09G140900' => 'gma', 'Glyma.12G112700' => 'gma', 'Glyma.17G168800' => 'gma', 'HanXRQChr01g0027001' => 'han', 'HanXRQChr04g0120511' => 'han', 'HanXRQChr08g0232381' => 'han', 'HanXRQChr09g0265661' => 'han', 'HanXRQChr13g0416031' => 'han', 'Haze_05835' => 'cav', 'Haze_06597' => 'cav', 'Haze_07921' => 'cav', 'Haze_08599' => 'cav', 'Haze_10686' => 'cav', 'Haze_12994' => 'cav', 'Haze_13466' => 'cav', 'Haze_16101' => 'cav', 'Haze_17766' => 'cav', 'Haze_18456' => 'cav', 'Haze_20229' => 'cav', 'Hma1.2p1_0324F.1_g125640' => 'hma', 'Hma1.2p1_0733F.1_g210230' => 'hma', 'Hma1.2p1_0921F.1_g236870' => 'hma', 'Hma1.2p1_1313F.1_g274940' => 'hma', 'Hma1.2p1_3059F.1_g332230' => 'hma', 'Hund15925' => 'sun', 'Hund19562' => 'sun', 'Hund21925' => 'sun', 'MD03G1177400' => 'mdo', 'MD07G1026100' => 'mdo', 'MD17G1218600' => 'mdo', 'Medtr0867s0010' => 'mtr', 'Medtr6g081150' => 'mtr', 'Os01g0527900' => 'osa', 'Os02g0463725' => 'osa', 'Os02g0785600' => 'osa', 'Os03g0433733' => 'osa', 'Os04g0286500' => 'osa', 'Os05g0227800' => 'osa', 'Os06g0521000' => 'osa', 'Os06g0635500' => 'osa', 'Os06g0660650' => 'osa', 'Os07g0554400' => 'osa', 'Os08g0225900' => 'osa', 'Os08g0561000' => 'osa', 'Os09g0241700' => 'osa', 'Os09g0351900' => 'osa', 'Os11g0220700' => 'osa', 'Os11g0282700' => 'osa', 'Os12g0169300' => 'osa', 'Os12g0228500' => 'osa', 'Os12g0543800' => 'osa', 'PGR044G1547' => 'pgr', 'Potri.005G239150' => 'ptr', 'Potri.010G014250' => 'ptr', 'Prupe.1G172500' => 'ppe', 'Prupe.1G196800' => 'ppe', 'Prupe.1G279700' => 'ppe', 'Prupe.2G026400' => 'ppe', 'Prupe.3G094000' => 'ppe', 'Prupe.4G287300' => 'ppe', 'QL01p022166' => 'qlo', 'QL01p051890' => 'qlo', 'QL02p009469' => 'qlo', 'QL02p046053' => 'qlo', 'QL02p057958' => 'qlo', 'QL02p093127' => 'qlo', 'QL03p006855' => 'qlo', 'QL03p071586' => 'qlo', 'QL04p000022' => 'qlo', 'QL04p000024' => 'qlo', 'QL04p003192' => 'qlo', 'QL05p011416' => 'qlo', 'QL06p039590' => 'qlo', 'QL06p052750' => 'qlo', 'QL06p053821' => 'qlo', 'QL07p025287' => 'qlo', 'QL09p033218' => 'qlo', 'QL09p040841' => 'qlo', 'QL10p020337' => 'qlo', 'QL10p027209' => 'qlo', 'QL10p027969' => 'qlo', 'QL10p048988' => 'qlo', 'QL11p001241' => 'qlo', 'QL11p028487' => 'qlo', 'RcHm_v2.0_Chr2g0105031' => 'rch', 'RcHm_v2.0_Chr2g0117811' => 'rch', 'RcHm_v2.0_Chr6g0270241' => 'rch', 'RcHm_v2.0_Chr7g0215961' => 'rch', 'RcHm_v2.0_Chr7g0231991' => 'rch', 'Rhsim01G0041500' => 'rsi', 'Rhsim01G0115000' => 'rsi', 'Rhsim01G0115400' => 'rsi', 'Rhsim01G0133600' => 'rsi', 'Rhsim01G0159900' => 'rsi', 'Rhsim02G0189400' => 'rsi', 'Rhsim03G0135600' => 'rsi', 'Rhsim03G0149900' => 'rsi', 'Rhsim04G0125600' => 'rsi', 'Rhsim05G0091700' => 'rsi', 'Rhsim05G0092900' => 'rsi', 'Rhsim06G0075000' => 'rsi', 'Rhsim07G0066400' => 'rsi', 'Rhsim07G0156400' => 'rsi', 'Rhsim07G0182200' => 'rsi', 'Rhsim07G0182300' => 'rsi', 'Rhsim08G0180400' => 'rsi', 'Rhsim09G0056800' => 'rsi', 'Rhsim10G0153300' => 'rsi', 'Rhsim11G0012700' => 'rsi', 'Rhsim12G0031800' => 'rsi', 'Rhsim12G0055400' => 'rsi', 'Rhsim12G0091400' => 'rsi', 'Rhsim13G0070800' => 'rsi', 'Rhsim13G0193300' => 'rsi', 'RhsimUnG0111600' => 'rsi', 'RhsimUnG0137500' => 'rsi', 'RhsimUnG0172900' => 'rsi', 'SGA_v2.0_scaffold11G05878' => 'sas', 'SGA_v2.0_scaffold167G38458' => 'sas', 'SGA_v2.0_scaffold19G08588' => 'sas', 'SGA_v2.0_scaffold239G43990' => 'sas', 'SGA_v2.0_scaffold260G45865' => 'sas', 'SGA_v2.0_scaffold309G48177' => 'sas', 'SGA_v2.0_scaffold76G25122' => 'sas', 'SGA_v2.0_scaffold85G26708' => 'sas', 'SHI13914' => 'shi', 'SHI30402' => 'shi', 'TWI09G0020' => 'twi', 'TWI09G0456' => 'twi', 'TWI09G1572' => 'twi', 'TWI12G0266' => 'twi', 'TWI12G1451' => 'twi', 'TWI14G0851' => 'twi', 'TWI15G0796' => 'twi', 'TWI18G0820' => 'twi', 'TWI18G1152' => 'twi', 'TWI23G0007' => 'twi', 'TWI23G0314' => 'twi', 'TWI31G0674' => 'twi', 'TWI31G0938' => 'twi', 'TWI34G0641' => 'twi', 'TWI34G1527' => 'twi', 'TWI36G0193' => 'twi', 'TWI36G0405' => 'twi', 'TWI38G0892' => 'twi', 'TWI38G0936' => 'twi', 'TWI38G2218' => 'twi', 'TWI53G0679' => 'twi', 'TWI53G0863' => 'twi', 'TWI53G1133' => 'twi', 'TWI60G0823' => 'twi', 'TWI63G0919' => 'twi', 'TWI63G1436' => 'twi', 'TWI73G0140' => 'twi', 'TWI73G0419' => 'twi', 'TWI73G0420' => 'twi', 'TWI73G1276' => 'twi', 'TWI74G0405' => 'twi', 'TWI74G0837' => 'twi', 'TWI75G0594' => 'twi', 'TWI75G1615' => 'twi', 'TWI77G0816' => 'twi', 'vmacro03831' => 'vma', 'vmacro13746' => 'vma', 'vmacro16089' => 'vma', 'vmacro22863' => 'vma', 'Zm00001eb085790' => 'zma', 'Zm00001eb114250' => 'zma', 'Zm00001eb138070' => 'zma', 'Zm00001eb167560' => 'zma', 'Zm00001eb199990' => 'zma', 'Zm00001eb368180' => 'zma', 'Zm00001eb382470' => 'zma' ) $gf_id = 'HOM05D001576' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001576' ) $data_identifier = 'HOM05D001576' $data_type = 'gf_id' $species_gene_counts = array( 'aox' => (int) 9, 'acertr' => (int) 3, 'cansat' => (int) 1, 'ccl' => (int) 4, 'cil' => (int) 145, 'camsi' => (int) 46, 'dca' => (int) 1, 'din' => (int) 1, 'fan' => (int) 12, 'fve' => (int) 9, 'gma' => (int) 5, 'han' => (int) 5, 'cav' => (int) 11, 'hma' => (int) 5, 'sun' => (int) 3, 'mdo' => (int) 3, 'mtr' => (int) 2, 'osa' => (int) 19, 'pgr' => (int) 1, 'ptr' => (int) 2, 'ppe' => (int) 6, 'qlo' => (int) 24, 'rch' => (int) 5, 'rsi' => (int) 28, 'sas' => (int) 8, 'shi' => (int) 2, 'twi' => (int) 35, 'vma' => (int) 4, 'zma' => (int) 7 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb382470' $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' => 'HOM05D001576', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '406', 'num_species' => '29' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'Aqoxy1G01456' => 'aox', 'Aqoxy1G02949' => 'aox', 'Aqoxy3G01274' => 'aox', 'Aqoxy3G02110' => 'aox', 'Aqoxy3G02268' => 'aox', 'Aqoxy5G02702' => 'aox', 'Aqoxy5G02988' => 'aox', 'Aqoxy5G03427' => 'aox', 'Aqoxy6G02363' => 'aox', 'Atru.chr1.3225' => 'acertr', 'Atru.chr8.1198' => 'acertr', 'Atru.chr9.790' => 'acertr', 'CANSAT01G3197' => 'cansat', 'Ciclev10003979m.g' => 'ccl', 'Ciclev10017471m.g' => 'ccl', 'Ciclev10018206m.g' => 'ccl', 'Ciclev10033751m.g' => 'ccl', 'CiPaw.01G000900' => 'cil', 'CiPaw.01G001000' => 'cil', 'CiPaw.01G033500' => 'cil', 'CiPaw.01G060300' => 'cil', 'CiPaw.01G070200' => 'cil', 'CiPaw.01G075100' => 'cil', 'CiPaw.01G084700' => 'cil', 'CiPaw.01G087900' => 'cil', 'CiPaw.01G092600' => 'cil', 'CiPaw.01G097200' => 'cil', 'CiPaw.01G098300' => 'cil', 'CiPaw.01G110200' => 'cil', 'CiPaw.01G118700' => 'cil', 'CiPaw.01G121200' => 'cil', 'CiPaw.01G132500' => 'cil', 'CiPaw.01G146900' => 'cil', 'CiPaw.01G174000' => 'cil', 'CiPaw.01G179900' => 'cil', 'CiPaw.01G183400' => 'cil', 'CiPaw.01G240000' => 'cil', 'CiPaw.01G283500' => 'cil', 'CiPaw.01G307400' => 'cil', 'CiPaw.02G030800' => 'cil', 'CiPaw.02G047200' => 'cil', 'CiPaw.02G050500' => 'cil', 'CiPaw.02G069900' => 'cil', 'CiPaw.02G091600' => 'cil', 'CiPaw.02G095000' => 'cil', 'CiPaw.02G131900' => 'cil', 'CiPaw.03G043000' => 'cil', 'CiPaw.03G069900' => 'cil', 'CiPaw.03G088100' => 'cil', 'CiPaw.03G089300' => 'cil', 'CiPaw.03G093100' => 'cil', 'CiPaw.03G129800' => 'cil', 'CiPaw.03G131200' => 'cil', 'CiPaw.03G134500' => 'cil', 'CiPaw.03G152100' => 'cil', 'CiPaw.03G162700' => 'cil', 'CiPaw.03G172800' => 'cil', 'CiPaw.03G175800' => 'cil', 'CiPaw.03G181800' => 'cil', 'CiPaw.03G191400' => 'cil', 'CiPaw.03G198300' => 'cil', 'CiPaw.03G201300' => 'cil', 'CiPaw.03G224700' => 'cil', 'CiPaw.03G225000' => 'cil', 'CiPaw.04G065100' => 'cil', 'CiPaw.04G080400' => 'cil', 'CiPaw.04G113500' => 'cil', 'CiPaw.04G121900' => 'cil', 'CiPaw.04G144100' => 'cil', 'CiPaw.04G176500' => 'cil', 'CiPaw.05G086200' => 'cil', 'CiPaw.05G100200' => 'cil', 'CiPaw.05G114200' => 'cil', 'CiPaw.05G126800' => 'cil', 'CiPaw.05G228800' => 'cil', 'CiPaw.05G230600' => 'cil', 'CiPaw.05G236500' => 'cil', 'CiPaw.05G244800' => 'cil', 'CiPaw.06G026600' => 'cil', 'CiPaw.06G027900' => 'cil', 'CiPaw.06G051800' => 'cil', 'CiPaw.06G128500' => 'cil', 'CiPaw.06G165900' => 'cil', 'CiPaw.07G045400' => 'cil', 'CiPaw.07G048000' => 'cil', 'CiPaw.07G052000' => 'cil', 'CiPaw.07G073800' => 'cil', 'CiPaw.07G099700' => 'cil', 'CiPaw.07G108700' => 'cil', 'CiPaw.07G120000' => 'cil', 'CiPaw.07G134100' => 'cil', 'CiPaw.07G147000' => 'cil', 'CiPaw.07G149700' => 'cil', 'CiPaw.07G178300' => 'cil', 'CiPaw.07G184900' => 'cil', 'CiPaw.08G044500' => 'cil', 'CiPaw.08G046900' => 'cil', 'CiPaw.08G047300' => 'cil', 'CiPaw.08G115400' => 'cil', 'CiPaw.08G134700' => 'cil', 'CiPaw.08G157400' => 'cil', 'CiPaw.09G014300' => 'cil', 'CiPaw.09G088900' => 'cil', 'CiPaw.09G130900' => 'cil', 'CiPaw.09G133100' => 'cil', 'CiPaw.09G151300' => 'cil', 'CiPaw.09G172800' => 'cil', 'CiPaw.09G174900' => 'cil', 'CiPaw.09G175000' => 'cil', 'CiPaw.10G012800' => 'cil', 'CiPaw.10G028800' => 'cil', 'CiPaw.10G044700' => 'cil', 'CiPaw.10G067400' => 'cil', 'CiPaw.10G115900' => 'cil', 'CiPaw.10G126200' => 'cil', 'CiPaw.10G139700' => 'cil', 'CiPaw.10G155100' => 'cil', 'CiPaw.11G011300' => 'cil', 'CiPaw.11G025900' => 'cil', 'CiPaw.11G104100' => 'cil', 'CiPaw.11G142700' => 'cil', 'CiPaw.11G164500' => 'cil', 'CiPaw.11G189100' => 'cil', 'CiPaw.11G197100' => 'cil', 'CiPaw.12G006100' => 'cil', 'CiPaw.12G038500' => 'cil', 'CiPaw.12G041400' => 'cil', 'CiPaw.12G041600' => 'cil', 'CiPaw.12G051300' => 'cil', 'CiPaw.12G101800' => 'cil', 'CiPaw.12G107800' => 'cil', 'CiPaw.13G033200' => 'cil', 'CiPaw.13G129900' => 'cil', 'CiPaw.13G160200' => 'cil', 'CiPaw.14G018900' => 'cil', 'CiPaw.14G029000' => 'cil', 'CiPaw.14G031000' => 'cil', 'CiPaw.14G032000' => 'cil', 'CiPaw.14G032300' => 'cil', 'CiPaw.14G040600' => 'cil', 'CiPaw.14G060500' => 'cil', 'CiPaw.14G061500' => 'cil', 'CiPaw.14G077500' => 'cil', 'CiPaw.14G088300' => 'cil', 'CiPaw.14G108500' => 'cil', 'CiPaw.14G121300' => 'cil', 'CiPaw.14G133000' => 'cil', 'CiPaw.14G134600' => 'cil', 'CiPaw.15G027200' => 'cil', 'CiPaw.15G037700' => 'cil', 'CiPaw.15G050900' => 'cil', 'CiPaw.15G067200' => 'cil', 'CiPaw.15G072000' => 'cil', 'CiPaw.15G112900' => 'cil', 'CiPaw.15G133200' => 'cil', 'CiPaw.15G139500' => 'cil', 'CiPaw.15G155400' => 'cil', 'CiPaw.16G006000' => 'cil', 'CiPaw.16G013100' => 'cil', 'CiPaw.16G047100' => 'cil', 'CiPaw.16G048900' => 'cil', 'CiPaw.16G070300' => 'cil', 'CSS0000195' => 'camsi', 'CSS0001664' => 'camsi', 'CSS0002566' => 'camsi', 'CSS0003077' => 'camsi', 'CSS0004257' => 'camsi', 'CSS0004495' => 'camsi', 'CSS0004599' => 'camsi', 'CSS0004943' => 'camsi', 'CSS0005302' => 'camsi', 'CSS0006274' => 'camsi', 'CSS0006547' => 'camsi', 'CSS0006860' => 'camsi', 'CSS0008814' => 'camsi', 'CSS0008946' => 'camsi', 'CSS0009093' => 'camsi', 'CSS0010221' => 'camsi', 'CSS0010296' => 'camsi', 'CSS0010386' => 'camsi', 'CSS0010831' => 'camsi', 'CSS0011061' => 'camsi', 'CSS0012008' => 'camsi', 'CSS0012194' => 'camsi', 'CSS0013580' => 'camsi', 'CSS0014176' => 'camsi', 'CSS0014280' => 'camsi', 'CSS0014799' => 'camsi', 'CSS0015368' => 'camsi', 'CSS0017473' => 'camsi', 'CSS0019281' => 'camsi', 'CSS0021320' => 'camsi', 'CSS0021750' => 'camsi', 'CSS0023642' => 'camsi', 'CSS0023792' => 'camsi', 'CSS0031528' => 'camsi', 'CSS0033894' => 'camsi', 'CSS0034959' => 'camsi', 'CSS0035632' => 'camsi', 'CSS0038450' => 'camsi', 'CSS0039293' => 'camsi', 'CSS0041053' => 'camsi', 'CSS0041981' => 'camsi', 'CSS0042573' => 'camsi', 'CSS0042927' => 'camsi', 'CSS0047725' => 'camsi', 'CSS0049636' => 'camsi', 'CSS0050513' => 'camsi', 'DCAR_030203' => 'dca', 'Dinv07939' => 'din', 'FAN01G0456' => 'fan', 'FAN02G3001' => 'fan', 'FAN04G2781' => 'fan', 'FAN05G1385' => 'fan', 'FAN05G3062' => 'fan', 'FAN08G2267' => 'fan', 'FAN10G0481' => 'fan', 'FAN10G1257' => 'fan', 'FAN14G0954' => 'fan', 'FAN14G2347' => 'fan', 'FAN15G0187' => 'fan', 'FAN25G2214' => 'fan', 'FvH4_1g21031' => 'fve', 'FvH4_3g16231' => 'fve', 'FvH4_3g26413' => 'fve', 'FvH4_3g29014' => 'fve', 'FvH4_3g31921' => 'fve', 'FvH4_4g19882' => 'fve', 'FvH4_5g21960' => 'fve', 'FvH4_5g29683' => 'fve', 'FvH4_7g13271' => 'fve', 'Glyma.01G062500' => 'gma', 'Glyma.07G140900' => 'gma', 'Glyma.09G140900' => 'gma', 'Glyma.12G112700' => 'gma', 'Glyma.17G168800' => 'gma', 'HanXRQChr01g0027001' => 'han', 'HanXRQChr04g0120511' => 'han', 'HanXRQChr08g0232381' => 'han', 'HanXRQChr09g0265661' => 'han', 'HanXRQChr13g0416031' => 'han', 'Haze_05835' => 'cav', 'Haze_06597' => 'cav', 'Haze_07921' => 'cav', 'Haze_08599' => 'cav', 'Haze_10686' => 'cav', 'Haze_12994' => 'cav', 'Haze_13466' => 'cav', 'Haze_16101' => 'cav', 'Haze_17766' => 'cav', 'Haze_18456' => 'cav', 'Haze_20229' => 'cav', 'Hma1.2p1_0324F.1_g125640' => 'hma', 'Hma1.2p1_0733F.1_g210230' => 'hma', 'Hma1.2p1_0921F.1_g236870' => 'hma', 'Hma1.2p1_1313F.1_g274940' => 'hma', 'Hma1.2p1_3059F.1_g332230' => 'hma', 'Hund15925' => 'sun', 'Hund19562' => 'sun', 'Hund21925' => 'sun', 'MD03G1177400' => 'mdo', 'MD07G1026100' => 'mdo', 'MD17G1218600' => 'mdo', 'Medtr0867s0010' => 'mtr', 'Medtr6g081150' => 'mtr', 'Os01g0527900' => 'osa', 'Os02g0463725' => 'osa', 'Os02g0785600' => 'osa', 'Os03g0433733' => 'osa', 'Os04g0286500' => 'osa', 'Os05g0227800' => 'osa', 'Os06g0521000' => 'osa', 'Os06g0635500' => 'osa', 'Os06g0660650' => 'osa', 'Os07g0554400' => 'osa', 'Os08g0225900' => 'osa', 'Os08g0561000' => 'osa', 'Os09g0241700' => 'osa', 'Os09g0351900' => 'osa', 'Os11g0220700' => 'osa', 'Os11g0282700' => 'osa', 'Os12g0169300' => 'osa', 'Os12g0228500' => 'osa', 'Os12g0543800' => 'osa', 'PGR044G1547' => 'pgr', 'Potri.005G239150' => 'ptr', 'Potri.010G014250' => 'ptr', 'Prupe.1G172500' => 'ppe', 'Prupe.1G196800' => 'ppe', 'Prupe.1G279700' => 'ppe', 'Prupe.2G026400' => 'ppe', 'Prupe.3G094000' => 'ppe', 'Prupe.4G287300' => 'ppe', 'QL01p022166' => 'qlo', 'QL01p051890' => 'qlo', 'QL02p009469' => 'qlo', 'QL02p046053' => 'qlo', 'QL02p057958' => 'qlo', 'QL02p093127' => 'qlo', 'QL03p006855' => 'qlo', 'QL03p071586' => 'qlo', 'QL04p000022' => 'qlo', 'QL04p000024' => 'qlo', 'QL04p003192' => 'qlo', 'QL05p011416' => 'qlo', 'QL06p039590' => 'qlo', 'QL06p052750' => 'qlo', 'QL06p053821' => 'qlo', 'QL07p025287' => 'qlo', 'QL09p033218' => 'qlo', 'QL09p040841' => 'qlo', 'QL10p020337' => 'qlo', 'QL10p027209' => 'qlo', 'QL10p027969' => 'qlo', 'QL10p048988' => 'qlo', 'QL11p001241' => 'qlo', 'QL11p028487' => 'qlo', 'RcHm_v2.0_Chr2g0105031' => 'rch', 'RcHm_v2.0_Chr2g0117811' => 'rch', 'RcHm_v2.0_Chr6g0270241' => 'rch', 'RcHm_v2.0_Chr7g0215961' => 'rch', 'RcHm_v2.0_Chr7g0231991' => 'rch', 'Rhsim01G0041500' => 'rsi', 'Rhsim01G0115000' => 'rsi', 'Rhsim01G0115400' => 'rsi', 'Rhsim01G0133600' => 'rsi', 'Rhsim01G0159900' => 'rsi', 'Rhsim02G0189400' => 'rsi', 'Rhsim03G0135600' => 'rsi', 'Rhsim03G0149900' => 'rsi', 'Rhsim04G0125600' => 'rsi', 'Rhsim05G0091700' => 'rsi', 'Rhsim05G0092900' => 'rsi', 'Rhsim06G0075000' => 'rsi', 'Rhsim07G0066400' => 'rsi', 'Rhsim07G0156400' => 'rsi', 'Rhsim07G0182200' => 'rsi', 'Rhsim07G0182300' => 'rsi', 'Rhsim08G0180400' => 'rsi', 'Rhsim09G0056800' => 'rsi', 'Rhsim10G0153300' => 'rsi', 'Rhsim11G0012700' => 'rsi', 'Rhsim12G0031800' => 'rsi', 'Rhsim12G0055400' => 'rsi', 'Rhsim12G0091400' => 'rsi', 'Rhsim13G0070800' => 'rsi', 'Rhsim13G0193300' => 'rsi', 'RhsimUnG0111600' => 'rsi', 'RhsimUnG0137500' => 'rsi', 'RhsimUnG0172900' => 'rsi', 'SGA_v2.0_scaffold11G05878' => 'sas', 'SGA_v2.0_scaffold167G38458' => 'sas', 'SGA_v2.0_scaffold19G08588' => 'sas', 'SGA_v2.0_scaffold239G43990' => 'sas', 'SGA_v2.0_scaffold260G45865' => 'sas', 'SGA_v2.0_scaffold309G48177' => 'sas', 'SGA_v2.0_scaffold76G25122' => 'sas', 'SGA_v2.0_scaffold85G26708' => 'sas', 'SHI13914' => 'shi', 'SHI30402' => 'shi', 'TWI09G0020' => 'twi', 'TWI09G0456' => 'twi', 'TWI09G1572' => 'twi', 'TWI12G0266' => 'twi', 'TWI12G1451' => 'twi', 'TWI14G0851' => 'twi', 'TWI15G0796' => 'twi', 'TWI18G0820' => 'twi', 'TWI18G1152' => 'twi', 'TWI23G0007' => 'twi', 'TWI23G0314' => 'twi', 'TWI31G0674' => 'twi', 'TWI31G0938' => 'twi', 'TWI34G0641' => 'twi', 'TWI34G1527' => 'twi', 'TWI36G0193' => 'twi', 'TWI36G0405' => 'twi', 'TWI38G0892' => 'twi', 'TWI38G0936' => 'twi', 'TWI38G2218' => 'twi', 'TWI53G0679' => 'twi', 'TWI53G0863' => 'twi', 'TWI53G1133' => 'twi', 'TWI60G0823' => 'twi', 'TWI63G0919' => 'twi', 'TWI63G1436' => 'twi', 'TWI73G0140' => 'twi', 'TWI73G0419' => 'twi', 'TWI73G0420' => 'twi', 'TWI73G1276' => 'twi', 'TWI74G0405' => 'twi', 'TWI74G0837' => 'twi', 'TWI75G0594' => 'twi', 'TWI75G1615' => 'twi', 'TWI77G0816' => 'twi', 'vmacro03831' => 'vma', 'vmacro13746' => 'vma', 'vmacro16089' => 'vma', 'vmacro22863' => 'vma', 'Zm00001eb085790' => 'zma', 'Zm00001eb114250' => 'zma', 'Zm00001eb138070' => 'zma', 'Zm00001eb167560' => 'zma', 'Zm00001eb199990' => 'zma', 'Zm00001eb368180' => 'zma', 'Zm00001eb382470' => 'zma' ), 'gf_id' => 'HOM05D001576', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001576' ), 'data_identifier' => 'HOM05D001576', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001576', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '406', 'num_species' => '29' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'Aqoxy1G01456' => 'aox', 'Aqoxy1G02949' => 'aox', 'Aqoxy3G01274' => 'aox', 'Aqoxy3G02110' => 'aox', 'Aqoxy3G02268' => 'aox', 'Aqoxy5G02702' => 'aox', 'Aqoxy5G02988' => 'aox', 'Aqoxy5G03427' => 'aox', 'Aqoxy6G02363' => 'aox', 'Atru.chr1.3225' => 'acertr', 'Atru.chr8.1198' => 'acertr', 'Atru.chr9.790' => 'acertr', 'CANSAT01G3197' => 'cansat', 'Ciclev10003979m.g' => 'ccl', 'Ciclev10017471m.g' => 'ccl', 'Ciclev10018206m.g' => 'ccl', 'Ciclev10033751m.g' => 'ccl', 'CiPaw.01G000900' => 'cil', 'CiPaw.01G001000' => 'cil', 'CiPaw.01G033500' => 'cil', 'CiPaw.01G060300' => 'cil', 'CiPaw.01G070200' => 'cil', 'CiPaw.01G075100' => 'cil', 'CiPaw.01G084700' => 'cil', 'CiPaw.01G087900' => 'cil', 'CiPaw.01G092600' => 'cil', 'CiPaw.01G097200' => 'cil', 'CiPaw.01G098300' => 'cil', 'CiPaw.01G110200' => 'cil', 'CiPaw.01G118700' => 'cil', 'CiPaw.01G121200' => 'cil', 'CiPaw.01G132500' => 'cil', 'CiPaw.01G146900' => 'cil', 'CiPaw.01G174000' => 'cil', 'CiPaw.01G179900' => 'cil', 'CiPaw.01G183400' => 'cil', 'CiPaw.01G240000' => 'cil', 'CiPaw.01G283500' => 'cil', 'CiPaw.01G307400' => 'cil', 'CiPaw.02G030800' => 'cil', 'CiPaw.02G047200' => 'cil', 'CiPaw.02G050500' => 'cil', 'CiPaw.02G069900' => 'cil', 'CiPaw.02G091600' => 'cil', 'CiPaw.02G095000' => 'cil', 'CiPaw.02G131900' => 'cil', 'CiPaw.03G043000' => 'cil', 'CiPaw.03G069900' => 'cil', 'CiPaw.03G088100' => 'cil', 'CiPaw.03G089300' => 'cil', 'CiPaw.03G093100' => 'cil', 'CiPaw.03G129800' => 'cil', 'CiPaw.03G131200' => 'cil', 'CiPaw.03G134500' => 'cil', 'CiPaw.03G152100' => 'cil', 'CiPaw.03G162700' => 'cil', 'CiPaw.03G172800' => 'cil', 'CiPaw.03G175800' => 'cil', 'CiPaw.03G181800' => 'cil', 'CiPaw.03G191400' => 'cil', 'CiPaw.03G198300' => 'cil', 'CiPaw.03G201300' => 'cil', 'CiPaw.03G224700' => 'cil', 'CiPaw.03G225000' => 'cil', 'CiPaw.04G065100' => 'cil', 'CiPaw.04G080400' => 'cil', 'CiPaw.04G113500' => 'cil', 'CiPaw.04G121900' => 'cil', 'CiPaw.04G144100' => 'cil', 'CiPaw.04G176500' => 'cil', 'CiPaw.05G086200' => 'cil', 'CiPaw.05G100200' => 'cil', 'CiPaw.05G114200' => 'cil', 'CiPaw.05G126800' => 'cil', 'CiPaw.05G228800' => 'cil', 'CiPaw.05G230600' => 'cil', 'CiPaw.05G236500' => 'cil', 'CiPaw.05G244800' => 'cil', 'CiPaw.06G026600' => 'cil', 'CiPaw.06G027900' => 'cil', 'CiPaw.06G051800' => 'cil', 'CiPaw.06G128500' => 'cil', 'CiPaw.06G165900' => 'cil', 'CiPaw.07G045400' => 'cil', 'CiPaw.07G048000' => 'cil', 'CiPaw.07G052000' => 'cil', 'CiPaw.07G073800' => 'cil', 'CiPaw.07G099700' => 'cil', 'CiPaw.07G108700' => 'cil', 'CiPaw.07G120000' => 'cil', 'CiPaw.07G134100' => 'cil', 'CiPaw.07G147000' => 'cil', 'CiPaw.07G149700' => 'cil', 'CiPaw.07G178300' => 'cil', 'CiPaw.07G184900' => 'cil', 'CiPaw.08G044500' => 'cil', 'CiPaw.08G046900' => 'cil', 'CiPaw.08G047300' => 'cil', 'CiPaw.08G115400' => 'cil', 'CiPaw.08G134700' => 'cil', 'CiPaw.08G157400' => 'cil', 'CiPaw.09G014300' => 'cil', 'CiPaw.09G088900' => 'cil', 'CiPaw.09G130900' => 'cil', 'CiPaw.09G133100' => 'cil', 'CiPaw.09G151300' => 'cil', 'CiPaw.09G172800' => 'cil', 'CiPaw.09G174900' => 'cil', 'CiPaw.09G175000' => 'cil', 'CiPaw.10G012800' => 'cil', 'CiPaw.10G028800' => 'cil', 'CiPaw.10G044700' => 'cil', 'CiPaw.10G067400' => 'cil', 'CiPaw.10G115900' => 'cil', 'CiPaw.10G126200' => 'cil', 'CiPaw.10G139700' => 'cil', 'CiPaw.10G155100' => 'cil', 'CiPaw.11G011300' => 'cil', 'CiPaw.11G025900' => 'cil', 'CiPaw.11G104100' => 'cil', 'CiPaw.11G142700' => 'cil', 'CiPaw.11G164500' => 'cil', 'CiPaw.11G189100' => 'cil', 'CiPaw.11G197100' => 'cil', 'CiPaw.12G006100' => 'cil', 'CiPaw.12G038500' => 'cil', 'CiPaw.12G041400' => 'cil', 'CiPaw.12G041600' => 'cil', 'CiPaw.12G051300' => 'cil', 'CiPaw.12G101800' => 'cil', 'CiPaw.12G107800' => 'cil', 'CiPaw.13G033200' => 'cil', 'CiPaw.13G129900' => 'cil', 'CiPaw.13G160200' => 'cil', 'CiPaw.14G018900' => 'cil', 'CiPaw.14G029000' => 'cil', 'CiPaw.14G031000' => 'cil', 'CiPaw.14G032000' => 'cil', 'CiPaw.14G032300' => 'cil', 'CiPaw.14G040600' => 'cil', 'CiPaw.14G060500' => 'cil', 'CiPaw.14G061500' => 'cil', 'CiPaw.14G077500' => 'cil', 'CiPaw.14G088300' => 'cil', 'CiPaw.14G108500' => 'cil', 'CiPaw.14G121300' => 'cil', 'CiPaw.14G133000' => 'cil', 'CiPaw.14G134600' => 'cil', 'CiPaw.15G027200' => 'cil', 'CiPaw.15G037700' => 'cil', 'CiPaw.15G050900' => 'cil', 'CiPaw.15G067200' => 'cil', 'CiPaw.15G072000' => 'cil', 'CiPaw.15G112900' => 'cil', 'CiPaw.15G133200' => 'cil', 'CiPaw.15G139500' => 'cil', 'CiPaw.15G155400' => 'cil', 'CiPaw.16G006000' => 'cil', 'CiPaw.16G013100' => 'cil', 'CiPaw.16G047100' => 'cil', 'CiPaw.16G048900' => 'cil', 'CiPaw.16G070300' => 'cil', 'CSS0000195' => 'camsi', 'CSS0001664' => 'camsi', 'CSS0002566' => 'camsi', 'CSS0003077' => 'camsi', 'CSS0004257' => 'camsi', 'CSS0004495' => 'camsi', 'CSS0004599' => 'camsi', 'CSS0004943' => 'camsi', 'CSS0005302' => 'camsi', 'CSS0006274' => 'camsi', 'CSS0006547' => 'camsi', 'CSS0006860' => 'camsi', 'CSS0008814' => 'camsi', 'CSS0008946' => 'camsi', 'CSS0009093' => 'camsi', 'CSS0010221' => 'camsi', 'CSS0010296' => 'camsi', 'CSS0010386' => 'camsi', 'CSS0010831' => 'camsi', 'CSS0011061' => 'camsi', 'CSS0012008' => 'camsi', 'CSS0012194' => 'camsi', 'CSS0013580' => 'camsi', 'CSS0014176' => 'camsi', 'CSS0014280' => 'camsi', 'CSS0014799' => 'camsi', 'CSS0015368' => 'camsi', 'CSS0017473' => 'camsi', 'CSS0019281' => 'camsi', 'CSS0021320' => 'camsi', 'CSS0021750' => 'camsi', 'CSS0023642' => 'camsi', 'CSS0023792' => 'camsi', 'CSS0031528' => 'camsi', 'CSS0033894' => 'camsi', 'CSS0034959' => 'camsi', 'CSS0035632' => 'camsi', 'CSS0038450' => 'camsi', 'CSS0039293' => 'camsi', 'CSS0041053' => 'camsi', 'CSS0041981' => 'camsi', 'CSS0042573' => 'camsi', 'CSS0042927' => 'camsi', 'CSS0047725' => 'camsi', 'CSS0049636' => 'camsi', 'CSS0050513' => 'camsi', 'DCAR_030203' => 'dca', 'Dinv07939' => 'din', 'FAN01G0456' => 'fan', 'FAN02G3001' => 'fan', 'FAN04G2781' => 'fan', 'FAN05G1385' => 'fan', 'FAN05G3062' => 'fan', 'FAN08G2267' => 'fan', 'FAN10G0481' => 'fan', 'FAN10G1257' => 'fan', 'FAN14G0954' => 'fan', 'FAN14G2347' => 'fan', 'FAN15G0187' => 'fan', 'FAN25G2214' => 'fan', 'FvH4_1g21031' => 'fve', 'FvH4_3g16231' => 'fve', 'FvH4_3g26413' => 'fve', 'FvH4_3g29014' => 'fve', 'FvH4_3g31921' => 'fve', 'FvH4_4g19882' => 'fve', 'FvH4_5g21960' => 'fve', 'FvH4_5g29683' => 'fve', 'FvH4_7g13271' => 'fve', 'Glyma.01G062500' => 'gma', 'Glyma.07G140900' => 'gma', 'Glyma.09G140900' => 'gma', 'Glyma.12G112700' => 'gma', 'Glyma.17G168800' => 'gma', 'HanXRQChr01g0027001' => 'han', 'HanXRQChr04g0120511' => 'han', 'HanXRQChr08g0232381' => 'han', 'HanXRQChr09g0265661' => 'han', 'HanXRQChr13g0416031' => 'han', 'Haze_05835' => 'cav', 'Haze_06597' => 'cav', 'Haze_07921' => 'cav', 'Haze_08599' => 'cav', 'Haze_10686' => 'cav', 'Haze_12994' => 'cav', 'Haze_13466' => 'cav', 'Haze_16101' => 'cav', 'Haze_17766' => 'cav', 'Haze_18456' => 'cav', 'Haze_20229' => 'cav', 'Hma1.2p1_0324F.1_g125640' => 'hma', 'Hma1.2p1_0733F.1_g210230' => 'hma', 'Hma1.2p1_0921F.1_g236870' => 'hma', 'Hma1.2p1_1313F.1_g274940' => 'hma', 'Hma1.2p1_3059F.1_g332230' => 'hma', 'Hund15925' => 'sun', 'Hund19562' => 'sun', 'Hund21925' => 'sun', 'MD03G1177400' => 'mdo', 'MD07G1026100' => 'mdo', 'MD17G1218600' => 'mdo', 'Medtr0867s0010' => 'mtr', 'Medtr6g081150' => 'mtr', 'Os01g0527900' => 'osa', 'Os02g0463725' => 'osa', 'Os02g0785600' => 'osa', 'Os03g0433733' => 'osa', 'Os04g0286500' => 'osa', 'Os05g0227800' => 'osa', 'Os06g0521000' => 'osa', 'Os06g0635500' => 'osa', 'Os06g0660650' => 'osa', 'Os07g0554400' => 'osa', 'Os08g0225900' => 'osa', 'Os08g0561000' => 'osa', 'Os09g0241700' => 'osa', 'Os09g0351900' => 'osa', 'Os11g0220700' => 'osa', 'Os11g0282700' => 'osa', 'Os12g0169300' => 'osa', 'Os12g0228500' => 'osa', 'Os12g0543800' => 'osa', 'PGR044G1547' => 'pgr', 'Potri.005G239150' => 'ptr', 'Potri.010G014250' => 'ptr', 'Prupe.1G172500' => 'ppe', 'Prupe.1G196800' => 'ppe', 'Prupe.1G279700' => 'ppe', 'Prupe.2G026400' => 'ppe', 'Prupe.3G094000' => 'ppe', 'Prupe.4G287300' => 'ppe', 'QL01p022166' => 'qlo', 'QL01p051890' => 'qlo', 'QL02p009469' => 'qlo', 'QL02p046053' => 'qlo', 'QL02p057958' => 'qlo', 'QL02p093127' => 'qlo', 'QL03p006855' => 'qlo', 'QL03p071586' => 'qlo', 'QL04p000022' => 'qlo', 'QL04p000024' => 'qlo', 'QL04p003192' => 'qlo', 'QL05p011416' => 'qlo', 'QL06p039590' => 'qlo', 'QL06p052750' => 'qlo', 'QL06p053821' => 'qlo', 'QL07p025287' => 'qlo', 'QL09p033218' => 'qlo', 'QL09p040841' => 'qlo', 'QL10p020337' => 'qlo', 'QL10p027209' => 'qlo', 'QL10p027969' => 'qlo', 'QL10p048988' => 'qlo', 'QL11p001241' => 'qlo', 'QL11p028487' => 'qlo', 'RcHm_v2.0_Chr2g0105031' => 'rch', 'RcHm_v2.0_Chr2g0117811' => 'rch', 'RcHm_v2.0_Chr6g0270241' => 'rch', 'RcHm_v2.0_Chr7g0215961' => 'rch', 'RcHm_v2.0_Chr7g0231991' => 'rch', 'Rhsim01G0041500' => 'rsi', 'Rhsim01G0115000' => 'rsi', 'Rhsim01G0115400' => 'rsi', 'Rhsim01G0133600' => 'rsi', 'Rhsim01G0159900' => 'rsi', 'Rhsim02G0189400' => 'rsi', 'Rhsim03G0135600' => 'rsi', 'Rhsim03G0149900' => 'rsi', 'Rhsim04G0125600' => 'rsi', 'Rhsim05G0091700' => 'rsi', 'Rhsim05G0092900' => 'rsi', 'Rhsim06G0075000' => 'rsi', 'Rhsim07G0066400' => 'rsi', 'Rhsim07G0156400' => 'rsi', 'Rhsim07G0182200' => 'rsi', 'Rhsim07G0182300' => 'rsi', 'Rhsim08G0180400' => 'rsi', 'Rhsim09G0056800' => 'rsi', 'Rhsim10G0153300' => 'rsi', 'Rhsim11G0012700' => 'rsi', 'Rhsim12G0031800' => 'rsi', 'Rhsim12G0055400' => 'rsi', 'Rhsim12G0091400' => 'rsi', 'Rhsim13G0070800' => 'rsi', 'Rhsim13G0193300' => 'rsi', 'RhsimUnG0111600' => 'rsi', 'RhsimUnG0137500' => 'rsi', 'RhsimUnG0172900' => 'rsi', 'SGA_v2.0_scaffold11G05878' => 'sas', 'SGA_v2.0_scaffold167G38458' => 'sas', 'SGA_v2.0_scaffold19G08588' => 'sas', 'SGA_v2.0_scaffold239G43990' => 'sas', 'SGA_v2.0_scaffold260G45865' => 'sas', 'SGA_v2.0_scaffold309G48177' => 'sas', 'SGA_v2.0_scaffold76G25122' => 'sas', 'SGA_v2.0_scaffold85G26708' => 'sas', 'SHI13914' => 'shi', 'SHI30402' => 'shi', 'TWI09G0020' => 'twi', 'TWI09G0456' => 'twi', 'TWI09G1572' => 'twi', 'TWI12G0266' => 'twi', 'TWI12G1451' => 'twi', 'TWI14G0851' => 'twi', 'TWI15G0796' => 'twi', 'TWI18G0820' => 'twi', 'TWI18G1152' => 'twi', 'TWI23G0007' => 'twi', 'TWI23G0314' => 'twi', 'TWI31G0674' => 'twi', 'TWI31G0938' => 'twi', 'TWI34G0641' => 'twi', 'TWI34G1527' => 'twi', 'TWI36G0193' => 'twi', 'TWI36G0405' => 'twi', 'TWI38G0892' => 'twi', 'TWI38G0936' => 'twi', 'TWI38G2218' => 'twi', 'TWI53G0679' => 'twi', 'TWI53G0863' => 'twi', 'TWI53G1133' => 'twi', 'TWI60G0823' => 'twi', 'TWI63G0919' => 'twi', 'TWI63G1436' => 'twi', 'TWI73G0140' => 'twi', 'TWI73G0419' => 'twi', 'TWI73G0420' => 'twi', 'TWI73G1276' => 'twi', 'TWI74G0405' => 'twi', 'TWI74G0837' => 'twi', 'TWI75G0594' => 'twi', 'TWI75G1615' => 'twi', 'TWI77G0816' => 'twi', 'vmacro03831' => 'vma', 'vmacro13746' => 'vma', 'vmacro16089' => 'vma', 'vmacro22863' => 'vma', 'Zm00001eb085790' => 'zma', 'Zm00001eb114250' => 'zma', 'Zm00001eb138070' => 'zma', 'Zm00001eb167560' => 'zma', 'Zm00001eb199990' => 'zma', 'Zm00001eb368180' => 'zma', 'Zm00001eb382470' => 'zma' ) $gf_id = 'HOM05D001576' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001576' ) $data_identifier = 'HOM05D001576' $data_type = 'gf_id' $species_gene_counts = array( 'aox' => (int) 9, 'acertr' => (int) 3, 'cansat' => (int) 1, 'ccl' => (int) 4, 'cil' => (int) 145, 'camsi' => (int) 46, 'dca' => (int) 1, 'din' => (int) 1, 'fan' => (int) 12, 'fve' => (int) 9, 'gma' => (int) 5, 'han' => (int) 5, 'cav' => (int) 11, 'hma' => (int) 5, 'sun' => (int) 3, 'mdo' => (int) 3, 'mtr' => (int) 2, 'osa' => (int) 19, 'pgr' => (int) 1, 'ptr' => (int) 2, 'ppe' => (int) 6, 'qlo' => (int) 24, 'rch' => (int) 5, 'rsi' => (int) 28, 'sas' => (int) 8, 'shi' => (int) 2, 'twi' => (int) 35, 'vma' => (int) 4, 'zma' => (int) 7 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb382470' $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' => 'HOM05D001576', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '406', 'num_species' => '29' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'Aqoxy1G01456' => 'aox', 'Aqoxy1G02949' => 'aox', 'Aqoxy3G01274' => 'aox', 'Aqoxy3G02110' => 'aox', 'Aqoxy3G02268' => 'aox', 'Aqoxy5G02702' => 'aox', 'Aqoxy5G02988' => 'aox', 'Aqoxy5G03427' => 'aox', 'Aqoxy6G02363' => 'aox', 'Atru.chr1.3225' => 'acertr', 'Atru.chr8.1198' => 'acertr', 'Atru.chr9.790' => 'acertr', 'CANSAT01G3197' => 'cansat', 'Ciclev10003979m.g' => 'ccl', 'Ciclev10017471m.g' => 'ccl', 'Ciclev10018206m.g' => 'ccl', 'Ciclev10033751m.g' => 'ccl', 'CiPaw.01G000900' => 'cil', 'CiPaw.01G001000' => 'cil', 'CiPaw.01G033500' => 'cil', 'CiPaw.01G060300' => 'cil', 'CiPaw.01G070200' => 'cil', 'CiPaw.01G075100' => 'cil', 'CiPaw.01G084700' => 'cil', 'CiPaw.01G087900' => 'cil', 'CiPaw.01G092600' => 'cil', 'CiPaw.01G097200' => 'cil', 'CiPaw.01G098300' => 'cil', 'CiPaw.01G110200' => 'cil', 'CiPaw.01G118700' => 'cil', 'CiPaw.01G121200' => 'cil', 'CiPaw.01G132500' => 'cil', 'CiPaw.01G146900' => 'cil', 'CiPaw.01G174000' => 'cil', 'CiPaw.01G179900' => 'cil', 'CiPaw.01G183400' => 'cil', 'CiPaw.01G240000' => 'cil', 'CiPaw.01G283500' => 'cil', 'CiPaw.01G307400' => 'cil', 'CiPaw.02G030800' => 'cil', 'CiPaw.02G047200' => 'cil', 'CiPaw.02G050500' => 'cil', 'CiPaw.02G069900' => 'cil', 'CiPaw.02G091600' => 'cil', 'CiPaw.02G095000' => 'cil', 'CiPaw.02G131900' => 'cil', 'CiPaw.03G043000' => 'cil', 'CiPaw.03G069900' => 'cil', 'CiPaw.03G088100' => 'cil', 'CiPaw.03G089300' => 'cil', 'CiPaw.03G093100' => 'cil', 'CiPaw.03G129800' => 'cil', 'CiPaw.03G131200' => 'cil', 'CiPaw.03G134500' => 'cil', 'CiPaw.03G152100' => 'cil', 'CiPaw.03G162700' => 'cil', 'CiPaw.03G172800' => 'cil', 'CiPaw.03G175800' => 'cil', 'CiPaw.03G181800' => 'cil', 'CiPaw.03G191400' => 'cil', 'CiPaw.03G198300' => 'cil', 'CiPaw.03G201300' => 'cil', 'CiPaw.03G224700' => 'cil', 'CiPaw.03G225000' => 'cil', 'CiPaw.04G065100' => 'cil', 'CiPaw.04G080400' => 'cil', 'CiPaw.04G113500' => 'cil', 'CiPaw.04G121900' => 'cil', 'CiPaw.04G144100' => 'cil', 'CiPaw.04G176500' => 'cil', 'CiPaw.05G086200' => 'cil', 'CiPaw.05G100200' => 'cil', 'CiPaw.05G114200' => 'cil', 'CiPaw.05G126800' => 'cil', 'CiPaw.05G228800' => 'cil', 'CiPaw.05G230600' => 'cil', 'CiPaw.05G236500' => 'cil', 'CiPaw.05G244800' => 'cil', 'CiPaw.06G026600' => 'cil', 'CiPaw.06G027900' => 'cil', 'CiPaw.06G051800' => 'cil', 'CiPaw.06G128500' => 'cil', 'CiPaw.06G165900' => 'cil', 'CiPaw.07G045400' => 'cil', 'CiPaw.07G048000' => 'cil', 'CiPaw.07G052000' => 'cil', 'CiPaw.07G073800' => 'cil', 'CiPaw.07G099700' => 'cil', 'CiPaw.07G108700' => 'cil', 'CiPaw.07G120000' => 'cil', 'CiPaw.07G134100' => 'cil', 'CiPaw.07G147000' => 'cil', 'CiPaw.07G149700' => 'cil', 'CiPaw.07G178300' => 'cil', 'CiPaw.07G184900' => 'cil', 'CiPaw.08G044500' => 'cil', 'CiPaw.08G046900' => 'cil', 'CiPaw.08G047300' => 'cil', 'CiPaw.08G115400' => 'cil', 'CiPaw.08G134700' => 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'TWI09G0020' => 'twi', 'TWI09G0456' => 'twi', 'TWI09G1572' => 'twi', 'TWI12G0266' => 'twi', 'TWI12G1451' => 'twi', 'TWI14G0851' => 'twi', 'TWI15G0796' => 'twi', 'TWI18G0820' => 'twi', 'TWI18G1152' => 'twi', 'TWI23G0007' => 'twi', 'TWI23G0314' => 'twi', 'TWI31G0674' => 'twi', 'TWI31G0938' => 'twi', 'TWI34G0641' => 'twi', 'TWI34G1527' => 'twi', 'TWI36G0193' => 'twi', 'TWI36G0405' => 'twi', 'TWI38G0892' => 'twi', 'TWI38G0936' => 'twi', 'TWI38G2218' => 'twi', 'TWI53G0679' => 'twi', 'TWI53G0863' => 'twi', 'TWI53G1133' => 'twi', 'TWI60G0823' => 'twi', 'TWI63G0919' => 'twi', 'TWI63G1436' => 'twi', 'TWI73G0140' => 'twi', 'TWI73G0419' => 'twi', 'TWI73G0420' => 'twi', 'TWI73G1276' => 'twi', 'TWI74G0405' => 'twi', 'TWI74G0837' => 'twi', 'TWI75G0594' => 'twi', 'TWI75G1615' => 'twi', 'TWI77G0816' => 'twi', 'vmacro03831' => 'vma', 'vmacro13746' => 'vma', 'vmacro16089' => 'vma', 'vmacro22863' => 'vma', 'Zm00001eb085790' => 'zma', 'Zm00001eb114250' => 'zma', 'Zm00001eb138070' => 'zma', 'Zm00001eb167560' => 'zma', 'Zm00001eb199990' => 'zma', 'Zm00001eb368180' => 'zma', 'Zm00001eb382470' => 'zma' ), 'gf_id' => 'HOM05D001576', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001576' ), 'data_identifier' => 'HOM05D001576', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001576', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '406', 'num_species' => '29' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'Aqoxy1G01456' => 'aox', 'Aqoxy1G02949' => 'aox', 'Aqoxy3G01274' => 'aox', 'Aqoxy3G02110' => 'aox', 'Aqoxy3G02268' => 'aox', 'Aqoxy5G02702' => 'aox', 'Aqoxy5G02988' => 'aox', 'Aqoxy5G03427' => 'aox', 'Aqoxy6G02363' => 'aox', 'Atru.chr1.3225' => 'acertr', 'Atru.chr8.1198' => 'acertr', 'Atru.chr9.790' => 'acertr', 'CANSAT01G3197' => 'cansat', 'Ciclev10003979m.g' => 'ccl', 'Ciclev10017471m.g' => 'ccl', 'Ciclev10018206m.g' => 'ccl', 'Ciclev10033751m.g' => 'ccl', 'CiPaw.01G000900' => 'cil', 'CiPaw.01G001000' => 'cil', 'CiPaw.01G033500' => 'cil', 'CiPaw.01G060300' => 'cil', 'CiPaw.01G070200' => 'cil', 'CiPaw.01G075100' => 'cil', 'CiPaw.01G084700' => 'cil', 'CiPaw.01G087900' => 'cil', 'CiPaw.01G092600' => 'cil', 'CiPaw.01G097200' => 'cil', 'CiPaw.01G098300' => 'cil', 'CiPaw.01G110200' => 'cil', 'CiPaw.01G118700' => 'cil', 'CiPaw.01G121200' => 'cil', 'CiPaw.01G132500' => 'cil', 'CiPaw.01G146900' => 'cil', 'CiPaw.01G174000' => 'cil', 'CiPaw.01G179900' => 'cil', 'CiPaw.01G183400' => 'cil', 'CiPaw.01G240000' => 'cil', 'CiPaw.01G283500' => 'cil', 'CiPaw.01G307400' => 'cil', 'CiPaw.02G030800' => 'cil', 'CiPaw.02G047200' => 'cil', 'CiPaw.02G050500' => 'cil', 'CiPaw.02G069900' => 'cil', 'CiPaw.02G091600' => 'cil', 'CiPaw.02G095000' => 'cil', 'CiPaw.02G131900' => 'cil', 'CiPaw.03G043000' => 'cil', 'CiPaw.03G069900' => 'cil', 'CiPaw.03G088100' => 'cil', 'CiPaw.03G089300' => 'cil', 'CiPaw.03G093100' => 'cil', 'CiPaw.03G129800' => 'cil', 'CiPaw.03G131200' => 'cil', 'CiPaw.03G134500' => 'cil', 'CiPaw.03G152100' => 'cil', 'CiPaw.03G162700' => 'cil', 'CiPaw.03G172800' => 'cil', 'CiPaw.03G175800' => 'cil', 'CiPaw.03G181800' => 'cil', 'CiPaw.03G191400' => 'cil', 'CiPaw.03G198300' => 'cil', 'CiPaw.03G201300' => 'cil', 'CiPaw.03G224700' => 'cil', 'CiPaw.03G225000' => 'cil', 'CiPaw.04G065100' => 'cil', 'CiPaw.04G080400' => 'cil', 'CiPaw.04G113500' => 'cil', 'CiPaw.04G121900' => 'cil', 'CiPaw.04G144100' => 'cil', 'CiPaw.04G176500' => 'cil', 'CiPaw.05G086200' => 'cil', 'CiPaw.05G100200' => 'cil', 'CiPaw.05G114200' => 'cil', 'CiPaw.05G126800' => 'cil', 'CiPaw.05G228800' => 'cil', 'CiPaw.05G230600' => 'cil', 'CiPaw.05G236500' => 'cil', 'CiPaw.05G244800' => 'cil', 'CiPaw.06G026600' => 'cil', 'CiPaw.06G027900' => 'cil', 'CiPaw.06G051800' => 'cil', 'CiPaw.06G128500' => 'cil', 'CiPaw.06G165900' => 'cil', 'CiPaw.07G045400' => 'cil', 'CiPaw.07G048000' => 'cil', 'CiPaw.07G052000' => 'cil', 'CiPaw.07G073800' => 'cil', 'CiPaw.07G099700' => 'cil', 'CiPaw.07G108700' => 'cil', 'CiPaw.07G120000' => 'cil', 'CiPaw.07G134100' => 'cil', 'CiPaw.07G147000' => 'cil', 'CiPaw.07G149700' => 'cil', 'CiPaw.07G178300' => 'cil', 'CiPaw.07G184900' => 'cil', 'CiPaw.08G044500' => 'cil', 'CiPaw.08G046900' => 'cil', 'CiPaw.08G047300' => 'cil', 'CiPaw.08G115400' => 'cil', 'CiPaw.08G134700' => 'cil', 'CiPaw.08G157400' => 'cil', 'CiPaw.09G014300' => 'cil', 'CiPaw.09G088900' => 'cil', 'CiPaw.09G130900' => 'cil', 'CiPaw.09G133100' => 'cil', 'CiPaw.09G151300' => 'cil', 'CiPaw.09G172800' => 'cil', 'CiPaw.09G174900' => 'cil', 'CiPaw.09G175000' => 'cil', 'CiPaw.10G012800' => 'cil', 'CiPaw.10G028800' => 'cil', 'CiPaw.10G044700' => 'cil', 'CiPaw.10G067400' => 'cil', 'CiPaw.10G115900' => 'cil', 'CiPaw.10G126200' => 'cil', 'CiPaw.10G139700' => 'cil', 'CiPaw.10G155100' => 'cil', 'CiPaw.11G011300' => 'cil', 'CiPaw.11G025900' => 'cil', 'CiPaw.11G104100' => 'cil', 'CiPaw.11G142700' => 'cil', 'CiPaw.11G164500' => 'cil', 'CiPaw.11G189100' => 'cil', 'CiPaw.11G197100' => 'cil', 'CiPaw.12G006100' => 'cil', 'CiPaw.12G038500' => 'cil', 'CiPaw.12G041400' => 'cil', 'CiPaw.12G041600' => 'cil', 'CiPaw.12G051300' => 'cil', 'CiPaw.12G101800' => 'cil', 'CiPaw.12G107800' => 'cil', 'CiPaw.13G033200' => 'cil', 'CiPaw.13G129900' => 'cil', 'CiPaw.13G160200' => 'cil', 'CiPaw.14G018900' => 'cil', 'CiPaw.14G029000' => 'cil', 'CiPaw.14G031000' => 'cil', 'CiPaw.14G032000' => 'cil', 'CiPaw.14G032300' => 'cil', 'CiPaw.14G040600' => 'cil', 'CiPaw.14G060500' => 'cil', 'CiPaw.14G061500' => 'cil', 'CiPaw.14G077500' => 'cil', 'CiPaw.14G088300' => 'cil', 'CiPaw.14G108500' => 'cil', 'CiPaw.14G121300' => 'cil', 'CiPaw.14G133000' => 'cil', 'CiPaw.14G134600' => 'cil', 'CiPaw.15G027200' => 'cil', 'CiPaw.15G037700' => 'cil', 'CiPaw.15G050900' => 'cil', 'CiPaw.15G067200' => 'cil', 'CiPaw.15G072000' => 'cil', 'CiPaw.15G112900' => 'cil', 'CiPaw.15G133200' => 'cil', 'CiPaw.15G139500' => 'cil', 'CiPaw.15G155400' => 'cil', 'CiPaw.16G006000' => 'cil', 'CiPaw.16G013100' => 'cil', 'CiPaw.16G047100' => 'cil', 'CiPaw.16G048900' => 'cil', 'CiPaw.16G070300' => 'cil', 'CSS0000195' => 'camsi', 'CSS0001664' => 'camsi', 'CSS0002566' => 'camsi', 'CSS0003077' => 'camsi', 'CSS0004257' => 'camsi', 'CSS0004495' => 'camsi', 'CSS0004599' => 'camsi', 'CSS0004943' => 'camsi', 'CSS0005302' => 'camsi', 'CSS0006274' => 'camsi', 'CSS0006547' => 'camsi', 'CSS0006860' => 'camsi', 'CSS0008814' => 'camsi', 'CSS0008946' => 'camsi', 'CSS0009093' => 'camsi', 'CSS0010221' => 'camsi', 'CSS0010296' => 'camsi', 'CSS0010386' => 'camsi', 'CSS0010831' => 'camsi', 'CSS0011061' => 'camsi', 'CSS0012008' => 'camsi', 'CSS0012194' => 'camsi', 'CSS0013580' => 'camsi', 'CSS0014176' => 'camsi', 'CSS0014280' => 'camsi', 'CSS0014799' => 'camsi', 'CSS0015368' => 'camsi', 'CSS0017473' => 'camsi', 'CSS0019281' => 'camsi', 'CSS0021320' => 'camsi', 'CSS0021750' => 'camsi', 'CSS0023642' => 'camsi', 'CSS0023792' => 'camsi', 'CSS0031528' => 'camsi', 'CSS0033894' => 'camsi', 'CSS0034959' => 'camsi', 'CSS0035632' => 'camsi', 'CSS0038450' => 'camsi', 'CSS0039293' => 'camsi', 'CSS0041053' => 'camsi', 'CSS0041981' => 'camsi', 'CSS0042573' => 'camsi', 'CSS0042927' => 'camsi', 'CSS0047725' => 'camsi', 'CSS0049636' => 'camsi', 'CSS0050513' => 'camsi', 'DCAR_030203' => 'dca', 'Dinv07939' => 'din', 'FAN01G0456' => 'fan', 'FAN02G3001' => 'fan', 'FAN04G2781' => 'fan', 'FAN05G1385' => 'fan', 'FAN05G3062' => 'fan', 'FAN08G2267' => 'fan', 'FAN10G0481' => 'fan', 'FAN10G1257' => 'fan', 'FAN14G0954' => 'fan', 'FAN14G2347' => 'fan', 'FAN15G0187' => 'fan', 'FAN25G2214' => 'fan', 'FvH4_1g21031' => 'fve', 'FvH4_3g16231' => 'fve', 'FvH4_3g26413' => 'fve', 'FvH4_3g29014' => 'fve', 'FvH4_3g31921' => 'fve', 'FvH4_4g19882' => 'fve', 'FvH4_5g21960' => 'fve', 'FvH4_5g29683' => 'fve', 'FvH4_7g13271' => 'fve', 'Glyma.01G062500' => 'gma', 'Glyma.07G140900' => 'gma', 'Glyma.09G140900' => 'gma', 'Glyma.12G112700' => 'gma', 'Glyma.17G168800' => 'gma', 'HanXRQChr01g0027001' => 'han', 'HanXRQChr04g0120511' => 'han', 'HanXRQChr08g0232381' => 'han', 'HanXRQChr09g0265661' => 'han', 'HanXRQChr13g0416031' => 'han', 'Haze_05835' => 'cav', 'Haze_06597' => 'cav', 'Haze_07921' => 'cav', 'Haze_08599' => 'cav', 'Haze_10686' => 'cav', 'Haze_12994' => 'cav', 'Haze_13466' => 'cav', 'Haze_16101' => 'cav', 'Haze_17766' => 'cav', 'Haze_18456' => 'cav', 'Haze_20229' => 'cav', 'Hma1.2p1_0324F.1_g125640' => 'hma', 'Hma1.2p1_0733F.1_g210230' => 'hma', 'Hma1.2p1_0921F.1_g236870' => 'hma', 'Hma1.2p1_1313F.1_g274940' => 'hma', 'Hma1.2p1_3059F.1_g332230' => 'hma', 'Hund15925' => 'sun', 'Hund19562' => 'sun', 'Hund21925' => 'sun', 'MD03G1177400' => 'mdo', 'MD07G1026100' => 'mdo', 'MD17G1218600' => 'mdo', 'Medtr0867s0010' => 'mtr', 'Medtr6g081150' => 'mtr', 'Os01g0527900' => 'osa', 'Os02g0463725' => 'osa', 'Os02g0785600' => 'osa', 'Os03g0433733' => 'osa', 'Os04g0286500' => 'osa', 'Os05g0227800' => 'osa', 'Os06g0521000' => 'osa', 'Os06g0635500' => 'osa', 'Os06g0660650' => 'osa', 'Os07g0554400' => 'osa', 'Os08g0225900' => 'osa', 'Os08g0561000' => 'osa', 'Os09g0241700' => 'osa', 'Os09g0351900' => 'osa', 'Os11g0220700' => 'osa', 'Os11g0282700' => 'osa', 'Os12g0169300' => 'osa', 'Os12g0228500' => 'osa', 'Os12g0543800' => 'osa', 'PGR044G1547' => 'pgr', 'Potri.005G239150' => 'ptr', 'Potri.010G014250' => 'ptr', 'Prupe.1G172500' => 'ppe', 'Prupe.1G196800' => 'ppe', 'Prupe.1G279700' => 'ppe', 'Prupe.2G026400' => 'ppe', 'Prupe.3G094000' => 'ppe', 'Prupe.4G287300' => 'ppe', 'QL01p022166' => 'qlo', 'QL01p051890' => 'qlo', 'QL02p009469' => 'qlo', 'QL02p046053' => 'qlo', 'QL02p057958' => 'qlo', 'QL02p093127' => 'qlo', 'QL03p006855' => 'qlo', 'QL03p071586' => 'qlo', 'QL04p000022' => 'qlo', 'QL04p000024' => 'qlo', 'QL04p003192' => 'qlo', 'QL05p011416' => 'qlo', 'QL06p039590' => 'qlo', 'QL06p052750' => 'qlo', 'QL06p053821' => 'qlo', 'QL07p025287' => 'qlo', 'QL09p033218' => 'qlo', 'QL09p040841' => 'qlo', 'QL10p020337' => 'qlo', 'QL10p027209' => 'qlo', 'QL10p027969' => 'qlo', 'QL10p048988' => 'qlo', 'QL11p001241' => 'qlo', 'QL11p028487' => 'qlo', 'RcHm_v2.0_Chr2g0105031' => 'rch', 'RcHm_v2.0_Chr2g0117811' => 'rch', 'RcHm_v2.0_Chr6g0270241' => 'rch', 'RcHm_v2.0_Chr7g0215961' => 'rch', 'RcHm_v2.0_Chr7g0231991' => 'rch', 'Rhsim01G0041500' => 'rsi', 'Rhsim01G0115000' => 'rsi', 'Rhsim01G0115400' => 'rsi', 'Rhsim01G0133600' => 'rsi', 'Rhsim01G0159900' => 'rsi', 'Rhsim02G0189400' => 'rsi', 'Rhsim03G0135600' => 'rsi', 'Rhsim03G0149900' => 'rsi', 'Rhsim04G0125600' => 'rsi', 'Rhsim05G0091700' => 'rsi', 'Rhsim05G0092900' => 'rsi', 'Rhsim06G0075000' => 'rsi', 'Rhsim07G0066400' => 'rsi', 'Rhsim07G0156400' => 'rsi', 'Rhsim07G0182200' => 'rsi', 'Rhsim07G0182300' => 'rsi', 'Rhsim08G0180400' => 'rsi', 'Rhsim09G0056800' => 'rsi', 'Rhsim10G0153300' => 'rsi', 'Rhsim11G0012700' => 'rsi', 'Rhsim12G0031800' => 'rsi', 'Rhsim12G0055400' => 'rsi', 'Rhsim12G0091400' => 'rsi', 'Rhsim13G0070800' => 'rsi', 'Rhsim13G0193300' => 'rsi', 'RhsimUnG0111600' => 'rsi', 'RhsimUnG0137500' => 'rsi', 'RhsimUnG0172900' => 'rsi', 'SGA_v2.0_scaffold11G05878' => 'sas', 'SGA_v2.0_scaffold167G38458' => 'sas', 'SGA_v2.0_scaffold19G08588' => 'sas', 'SGA_v2.0_scaffold239G43990' => 'sas', 'SGA_v2.0_scaffold260G45865' => 'sas', 'SGA_v2.0_scaffold309G48177' => 'sas', 'SGA_v2.0_scaffold76G25122' => 'sas', 'SGA_v2.0_scaffold85G26708' => 'sas', 'SHI13914' => 'shi', 'SHI30402' => 'shi', 'TWI09G0020' => 'twi', 'TWI09G0456' => 'twi', 'TWI09G1572' => 'twi', 'TWI12G0266' => 'twi', 'TWI12G1451' => 'twi', 'TWI14G0851' => 'twi', 'TWI15G0796' => 'twi', 'TWI18G0820' => 'twi', 'TWI18G1152' => 'twi', 'TWI23G0007' => 'twi', 'TWI23G0314' => 'twi', 'TWI31G0674' => 'twi', 'TWI31G0938' => 'twi', 'TWI34G0641' => 'twi', 'TWI34G1527' => 'twi', 'TWI36G0193' => 'twi', 'TWI36G0405' => 'twi', 'TWI38G0892' => 'twi', 'TWI38G0936' => 'twi', 'TWI38G2218' => 'twi', 'TWI53G0679' => 'twi', 'TWI53G0863' => 'twi', 'TWI53G1133' => 'twi', 'TWI60G0823' => 'twi', 'TWI63G0919' => 'twi', 'TWI63G1436' => 'twi', 'TWI73G0140' => 'twi', 'TWI73G0419' => 'twi', 'TWI73G0420' => 'twi', 'TWI73G1276' => 'twi', 'TWI74G0405' => 'twi', 'TWI74G0837' => 'twi', 'TWI75G0594' => 'twi', 'TWI75G1615' => 'twi', 'TWI77G0816' => 'twi', 'vmacro03831' => 'vma', 'vmacro13746' => 'vma', 'vmacro16089' => 'vma', 'vmacro22863' => 'vma', 'Zm00001eb085790' => 'zma', 'Zm00001eb114250' => 'zma', 'Zm00001eb138070' => 'zma', 'Zm00001eb167560' => 'zma', 'Zm00001eb199990' => 'zma', 'Zm00001eb368180' => 'zma', 'Zm00001eb382470' => 'zma' ) $gf_id = 'HOM05D001576' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001576' ) $data_identifier = 'HOM05D001576' $data_type = 'gf_id' $species_gene_counts = array( 'aox' => (int) 9, 'acertr' => (int) 3, 'cansat' => (int) 1, 'ccl' => (int) 4, 'cil' => (int) 145, 'camsi' => (int) 46, 'dca' => (int) 1, 'din' => (int) 1, 'fan' => (int) 12, 'fve' => (int) 9, 'gma' => (int) 5, 'han' => (int) 5, 'cav' => (int) 11, 'hma' => (int) 5, 'sun' => (int) 3, 'mdo' => (int) 3, 'mtr' => (int) 2, 'osa' => (int) 19, 'pgr' => (int) 1, 'ptr' => (int) 2, 'ppe' => (int) 6, 'qlo' => (int) 24, 'rch' => (int) 5, 'rsi' => (int) 28, 'sas' => (int) 8, 'shi' => (int) 2, 'twi' => (int) 35, 'vma' => (int) 4, 'zma' => (int) 7 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb382470' $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' => 'HOM05D001576', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '406', 'num_species' => '29' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'Aqoxy1G01456' => 'aox', 'Aqoxy1G02949' => 'aox', 'Aqoxy3G01274' => 'aox', 'Aqoxy3G02110' => 'aox', 'Aqoxy3G02268' => 'aox', 'Aqoxy5G02702' => 'aox', 'Aqoxy5G02988' => 'aox', 'Aqoxy5G03427' => 'aox', 'Aqoxy6G02363' => 'aox', 'Atru.chr1.3225' => 'acertr', 'Atru.chr8.1198' => 'acertr', 'Atru.chr9.790' => 'acertr', 'CANSAT01G3197' => 'cansat', 'Ciclev10003979m.g' => 'ccl', 'Ciclev10017471m.g' => 'ccl', 'Ciclev10018206m.g' => 'ccl', 'Ciclev10033751m.g' => 'ccl', 'CiPaw.01G000900' => 'cil', 'CiPaw.01G001000' => 'cil', 'CiPaw.01G033500' => 'cil', 'CiPaw.01G060300' => 'cil', 'CiPaw.01G070200' => 'cil', 'CiPaw.01G075100' => 'cil', 'CiPaw.01G084700' => 'cil', 'CiPaw.01G087900' => 'cil', 'CiPaw.01G092600' => 'cil', 'CiPaw.01G097200' => 'cil', 'CiPaw.01G098300' => 'cil', 'CiPaw.01G110200' => 'cil', 'CiPaw.01G118700' => 'cil', 'CiPaw.01G121200' => 'cil', 'CiPaw.01G132500' => 'cil', 'CiPaw.01G146900' => 'cil', 'CiPaw.01G174000' => 'cil', 'CiPaw.01G179900' => 'cil', 'CiPaw.01G183400' => 'cil', 'CiPaw.01G240000' => 'cil', 'CiPaw.01G283500' => 'cil', 'CiPaw.01G307400' => 'cil', 'CiPaw.02G030800' => 'cil', 'CiPaw.02G047200' => 'cil', 'CiPaw.02G050500' => 'cil', 'CiPaw.02G069900' => 'cil', 'CiPaw.02G091600' => 'cil', 'CiPaw.02G095000' => 'cil', 'CiPaw.02G131900' => 'cil', 'CiPaw.03G043000' => 'cil', 'CiPaw.03G069900' => 'cil', 'CiPaw.03G088100' => 'cil', 'CiPaw.03G089300' => 'cil', 'CiPaw.03G093100' => 'cil', 'CiPaw.03G129800' => 'cil', 'CiPaw.03G131200' => 'cil', 'CiPaw.03G134500' => 'cil', 'CiPaw.03G152100' => 'cil', 'CiPaw.03G162700' => 'cil', 'CiPaw.03G172800' => 'cil', 'CiPaw.03G175800' => 'cil', 'CiPaw.03G181800' => 'cil', 'CiPaw.03G191400' => 'cil', 'CiPaw.03G198300' => 'cil', 'CiPaw.03G201300' => 'cil', 'CiPaw.03G224700' => 'cil', 'CiPaw.03G225000' => 'cil', 'CiPaw.04G065100' => 'cil', 'CiPaw.04G080400' => 'cil', 'CiPaw.04G113500' => 'cil', 'CiPaw.04G121900' => 'cil', 'CiPaw.04G144100' => 'cil', 'CiPaw.04G176500' => 'cil', 'CiPaw.05G086200' => 'cil', 'CiPaw.05G100200' => 'cil', 'CiPaw.05G114200' => 'cil', 'CiPaw.05G126800' => 'cil', 'CiPaw.05G228800' => 'cil', 'CiPaw.05G230600' => 'cil', 'CiPaw.05G236500' => 'cil', 'CiPaw.05G244800' => 'cil', 'CiPaw.06G026600' => 'cil', 'CiPaw.06G027900' => 'cil', 'CiPaw.06G051800' => 'cil', 'CiPaw.06G128500' => 'cil', 'CiPaw.06G165900' => 'cil', 'CiPaw.07G045400' => 'cil', 'CiPaw.07G048000' => 'cil', 'CiPaw.07G052000' => 'cil', 'CiPaw.07G073800' => 'cil', 'CiPaw.07G099700' => 'cil', 'CiPaw.07G108700' => 'cil', 'CiPaw.07G120000' => 'cil', 'CiPaw.07G134100' => 'cil', 'CiPaw.07G147000' => 'cil', 'CiPaw.07G149700' => 'cil', 'CiPaw.07G178300' => 'cil', 'CiPaw.07G184900' => 'cil', 'CiPaw.08G044500' => 'cil', 'CiPaw.08G046900' => 'cil', 'CiPaw.08G047300' => 'cil', 'CiPaw.08G115400' => 'cil', 'CiPaw.08G134700' => 'cil', 'CiPaw.08G157400' => 'cil', 'CiPaw.09G014300' => 'cil', 'CiPaw.09G088900' => 'cil', 'CiPaw.09G130900' => 'cil', 'CiPaw.09G133100' => 'cil', 'CiPaw.09G151300' => 'cil', 'CiPaw.09G172800' => 'cil', 'CiPaw.09G174900' => 'cil', 'CiPaw.09G175000' => 'cil', 'CiPaw.10G012800' => 'cil', 'CiPaw.10G028800' => 'cil', 'CiPaw.10G044700' => 'cil', 'CiPaw.10G067400' => 'cil', 'CiPaw.10G115900' => 'cil', 'CiPaw.10G126200' => 'cil', 'CiPaw.10G139700' => 'cil', 'CiPaw.10G155100' => 'cil', 'CiPaw.11G011300' => 'cil', 'CiPaw.11G025900' => 'cil', 'CiPaw.11G104100' => 'cil', 'CiPaw.11G142700' => 'cil', 'CiPaw.11G164500' => 'cil', 'CiPaw.11G189100' => 'cil', 'CiPaw.11G197100' => 'cil', 'CiPaw.12G006100' => 'cil', 'CiPaw.12G038500' => 'cil', 'CiPaw.12G041400' => 'cil', 'CiPaw.12G041600' => 'cil', 'CiPaw.12G051300' => 'cil', 'CiPaw.12G101800' => 'cil', 'CiPaw.12G107800' => 'cil', 'CiPaw.13G033200' => 'cil', 'CiPaw.13G129900' => 'cil', 'CiPaw.13G160200' => 'cil', 'CiPaw.14G018900' => 'cil', 'CiPaw.14G029000' => 'cil', 'CiPaw.14G031000' => 'cil', 'CiPaw.14G032000' => 'cil', 'CiPaw.14G032300' => 'cil', 'CiPaw.14G040600' => 'cil', 'CiPaw.14G060500' => 'cil', 'CiPaw.14G061500' => 'cil', 'CiPaw.14G077500' => 'cil', 'CiPaw.14G088300' => 'cil', 'CiPaw.14G108500' => 'cil', 'CiPaw.14G121300' => 'cil', 'CiPaw.14G133000' => 'cil', 'CiPaw.14G134600' => 'cil', 'CiPaw.15G027200' => 'cil', 'CiPaw.15G037700' => 'cil', 'CiPaw.15G050900' => 'cil', 'CiPaw.15G067200' => 'cil', 'CiPaw.15G072000' => 'cil', 'CiPaw.15G112900' => 'cil', 'CiPaw.15G133200' => 'cil', 'CiPaw.15G139500' => 'cil', 'CiPaw.15G155400' => 'cil', 'CiPaw.16G006000' => 'cil', 'CiPaw.16G013100' => 'cil', 'CiPaw.16G047100' => 'cil', 'CiPaw.16G048900' => 'cil', 'CiPaw.16G070300' => 'cil', 'CSS0000195' => 'camsi', 'CSS0001664' => 'camsi', 'CSS0002566' => 'camsi', 'CSS0003077' => 'camsi', 'CSS0004257' => 'camsi', 'CSS0004495' => 'camsi', 'CSS0004599' => 'camsi', 'CSS0004943' => 'camsi', 'CSS0005302' => 'camsi', 'CSS0006274' => 'camsi', 'CSS0006547' => 'camsi', 'CSS0006860' => 'camsi', 'CSS0008814' => 'camsi', 'CSS0008946' => 'camsi', 'CSS0009093' => 'camsi', 'CSS0010221' => 'camsi', 'CSS0010296' => 'camsi', 'CSS0010386' => 'camsi', 'CSS0010831' => 'camsi', 'CSS0011061' => 'camsi', 'CSS0012008' => 'camsi', 'CSS0012194' => 'camsi', 'CSS0013580' => 'camsi', 'CSS0014176' => 'camsi', 'CSS0014280' => 'camsi', 'CSS0014799' => 'camsi', 'CSS0015368' => 'camsi', 'CSS0017473' => 'camsi', 'CSS0019281' => 'camsi', 'CSS0021320' => 'camsi', 'CSS0021750' => 'camsi', 'CSS0023642' => 'camsi', 'CSS0023792' => 'camsi', 'CSS0031528' => 'camsi', 'CSS0033894' => 'camsi', 'CSS0034959' => 'camsi', 'CSS0035632' => 'camsi', 'CSS0038450' => 'camsi', 'CSS0039293' => 'camsi', 'CSS0041053' => 'camsi', 'CSS0041981' => 'camsi', 'CSS0042573' => 'camsi', 'CSS0042927' => 'camsi', 'CSS0047725' => 'camsi', 'CSS0049636' => 'camsi', 'CSS0050513' => 'camsi', 'DCAR_030203' => 'dca', 'Dinv07939' => 'din', 'FAN01G0456' => 'fan', 'FAN02G3001' => 'fan', 'FAN04G2781' => 'fan', 'FAN05G1385' => 'fan', 'FAN05G3062' => 'fan', 'FAN08G2267' => 'fan', 'FAN10G0481' => 'fan', 'FAN10G1257' => 'fan', 'FAN14G0954' => 'fan', 'FAN14G2347' => 'fan', 'FAN15G0187' => 'fan', 'FAN25G2214' => 'fan', 'FvH4_1g21031' => 'fve', 'FvH4_3g16231' => 'fve', 'FvH4_3g26413' => 'fve', 'FvH4_3g29014' => 'fve', 'FvH4_3g31921' => 'fve', 'FvH4_4g19882' => 'fve', 'FvH4_5g21960' => 'fve', 'FvH4_5g29683' => 'fve', 'FvH4_7g13271' => 'fve', 'Glyma.01G062500' => 'gma', 'Glyma.07G140900' => 'gma', 'Glyma.09G140900' => 'gma', 'Glyma.12G112700' => 'gma', 'Glyma.17G168800' => 'gma', 'HanXRQChr01g0027001' => 'han', 'HanXRQChr04g0120511' => 'han', 'HanXRQChr08g0232381' => 'han', 'HanXRQChr09g0265661' => 'han', 'HanXRQChr13g0416031' => 'han', 'Haze_05835' => 'cav', 'Haze_06597' => 'cav', 'Haze_07921' => 'cav', 'Haze_08599' => 'cav', 'Haze_10686' => 'cav', 'Haze_12994' => 'cav', 'Haze_13466' => 'cav', 'Haze_16101' => 'cav', 'Haze_17766' => 'cav', 'Haze_18456' => 'cav', 'Haze_20229' => 'cav', 'Hma1.2p1_0324F.1_g125640' => 'hma', 'Hma1.2p1_0733F.1_g210230' => 'hma', 'Hma1.2p1_0921F.1_g236870' => 'hma', 'Hma1.2p1_1313F.1_g274940' => 'hma', 'Hma1.2p1_3059F.1_g332230' => 'hma', 'Hund15925' => 'sun', 'Hund19562' => 'sun', 'Hund21925' => 'sun', 'MD03G1177400' => 'mdo', 'MD07G1026100' => 'mdo', 'MD17G1218600' => 'mdo', 'Medtr0867s0010' => 'mtr', 'Medtr6g081150' => 'mtr', 'Os01g0527900' => 'osa', 'Os02g0463725' => 'osa', 'Os02g0785600' => 'osa', 'Os03g0433733' => 'osa', 'Os04g0286500' => 'osa', 'Os05g0227800' => 'osa', 'Os06g0521000' => 'osa', 'Os06g0635500' => 'osa', 'Os06g0660650' => 'osa', 'Os07g0554400' => 'osa', 'Os08g0225900' => 'osa', 'Os08g0561000' => 'osa', 'Os09g0241700' => 'osa', 'Os09g0351900' => 'osa', 'Os11g0220700' => 'osa', 'Os11g0282700' => 'osa', 'Os12g0169300' => 'osa', 'Os12g0228500' => 'osa', 'Os12g0543800' => 'osa', 'PGR044G1547' => 'pgr', 'Potri.005G239150' => 'ptr', 'Potri.010G014250' => 'ptr', 'Prupe.1G172500' => 'ppe', 'Prupe.1G196800' => 'ppe', 'Prupe.1G279700' => 'ppe', 'Prupe.2G026400' => 'ppe', 'Prupe.3G094000' => 'ppe', 'Prupe.4G287300' => 'ppe', 'QL01p022166' => 'qlo', 'QL01p051890' => 'qlo', 'QL02p009469' => 'qlo', 'QL02p046053' => 'qlo', 'QL02p057958' => 'qlo', 'QL02p093127' => 'qlo', 'QL03p006855' => 'qlo', 'QL03p071586' => 'qlo', 'QL04p000022' => 'qlo', 'QL04p000024' => 'qlo', 'QL04p003192' => 'qlo', 'QL05p011416' => 'qlo', 'QL06p039590' => 'qlo', 'QL06p052750' => 'qlo', 'QL06p053821' => 'qlo', 'QL07p025287' => 'qlo', 'QL09p033218' => 'qlo', 'QL09p040841' => 'qlo', 'QL10p020337' => 'qlo', 'QL10p027209' => 'qlo', 'QL10p027969' => 'qlo', 'QL10p048988' => 'qlo', 'QL11p001241' => 'qlo', 'QL11p028487' => 'qlo', 'RcHm_v2.0_Chr2g0105031' => 'rch', 'RcHm_v2.0_Chr2g0117811' => 'rch', 'RcHm_v2.0_Chr6g0270241' => 'rch', 'RcHm_v2.0_Chr7g0215961' => 'rch', 'RcHm_v2.0_Chr7g0231991' => 'rch', 'Rhsim01G0041500' => 'rsi', 'Rhsim01G0115000' => 'rsi', 'Rhsim01G0115400' => 'rsi', 'Rhsim01G0133600' => 'rsi', 'Rhsim01G0159900' => 'rsi', 'Rhsim02G0189400' => 'rsi', 'Rhsim03G0135600' => 'rsi', 'Rhsim03G0149900' => 'rsi', 'Rhsim04G0125600' => 'rsi', 'Rhsim05G0091700' => 'rsi', 'Rhsim05G0092900' => 'rsi', 'Rhsim06G0075000' => 'rsi', 'Rhsim07G0066400' => 'rsi', 'Rhsim07G0156400' => 'rsi', 'Rhsim07G0182200' => 'rsi', 'Rhsim07G0182300' => 'rsi', 'Rhsim08G0180400' => 'rsi', 'Rhsim09G0056800' => 'rsi', 'Rhsim10G0153300' => 'rsi', 'Rhsim11G0012700' => 'rsi', 'Rhsim12G0031800' => 'rsi', 'Rhsim12G0055400' => 'rsi', 'Rhsim12G0091400' => 'rsi', 'Rhsim13G0070800' => 'rsi', 'Rhsim13G0193300' => 'rsi', 'RhsimUnG0111600' => 'rsi', 'RhsimUnG0137500' => 'rsi', 'RhsimUnG0172900' => 'rsi', 'SGA_v2.0_scaffold11G05878' => 'sas', 'SGA_v2.0_scaffold167G38458' => 'sas', 'SGA_v2.0_scaffold19G08588' => 'sas', 'SGA_v2.0_scaffold239G43990' => 'sas', 'SGA_v2.0_scaffold260G45865' => 'sas', 'SGA_v2.0_scaffold309G48177' => 'sas', 'SGA_v2.0_scaffold76G25122' => 'sas', 'SGA_v2.0_scaffold85G26708' => 'sas', 'SHI13914' => 'shi', 'SHI30402' => 'shi', 'TWI09G0020' => 'twi', 'TWI09G0456' => 'twi', 'TWI09G1572' => 'twi', 'TWI12G0266' => 'twi', 'TWI12G1451' => 'twi', 'TWI14G0851' => 'twi', 'TWI15G0796' => 'twi', 'TWI18G0820' => 'twi', 'TWI18G1152' => 'twi', 'TWI23G0007' => 'twi', 'TWI23G0314' => 'twi', 'TWI31G0674' => 'twi', 'TWI31G0938' => 'twi', 'TWI34G0641' => 'twi', 'TWI34G1527' => 'twi', 'TWI36G0193' => 'twi', 'TWI36G0405' => 'twi', 'TWI38G0892' => 'twi', 'TWI38G0936' => 'twi', 'TWI38G2218' => 'twi', 'TWI53G0679' => 'twi', 'TWI53G0863' => 'twi', 'TWI53G1133' => 'twi', 'TWI60G0823' => 'twi', 'TWI63G0919' => 'twi', 'TWI63G1436' => 'twi', 'TWI73G0140' => 'twi', 'TWI73G0419' => 'twi', 'TWI73G0420' => 'twi', 'TWI73G1276' => 'twi', 'TWI74G0405' => 'twi', 'TWI74G0837' => 'twi', 'TWI75G0594' => 'twi', 'TWI75G1615' => 'twi', 'TWI77G0816' => 'twi', 'vmacro03831' => 'vma', 'vmacro13746' => 'vma', 'vmacro16089' => 'vma', 'vmacro22863' => 'vma', 'Zm00001eb085790' => 'zma', 'Zm00001eb114250' => 'zma', 'Zm00001eb138070' => 'zma', 'Zm00001eb167560' => 'zma', 'Zm00001eb199990' => 'zma', 'Zm00001eb368180' => 'zma', 'Zm00001eb382470' => 'zma' ), 'gf_id' => 'HOM05D001576', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001576' ), 'data_identifier' => 'HOM05D001576', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001576', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '406', 'num_species' => '29' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'Aqoxy1G01456' => 'aox', 'Aqoxy1G02949' => 'aox', 'Aqoxy3G01274' => 'aox', 'Aqoxy3G02110' => 'aox', 'Aqoxy3G02268' => 'aox', 'Aqoxy5G02702' => 'aox', 'Aqoxy5G02988' => 'aox', 'Aqoxy5G03427' => 'aox', 'Aqoxy6G02363' => 'aox', 'Atru.chr1.3225' => 'acertr', 'Atru.chr8.1198' => 'acertr', 'Atru.chr9.790' => 'acertr', 'CANSAT01G3197' => 'cansat', 'Ciclev10003979m.g' => 'ccl', 'Ciclev10017471m.g' => 'ccl', 'Ciclev10018206m.g' => 'ccl', 'Ciclev10033751m.g' => 'ccl', 'CiPaw.01G000900' => 'cil', 'CiPaw.01G001000' => 'cil', 'CiPaw.01G033500' => 'cil', 'CiPaw.01G060300' => 'cil', 'CiPaw.01G070200' => 'cil', 'CiPaw.01G075100' => 'cil', 'CiPaw.01G084700' => 'cil', 'CiPaw.01G087900' => 'cil', 'CiPaw.01G092600' => 'cil', 'CiPaw.01G097200' => 'cil', 'CiPaw.01G098300' => 'cil', 'CiPaw.01G110200' => 'cil', 'CiPaw.01G118700' => 'cil', 'CiPaw.01G121200' => 'cil', 'CiPaw.01G132500' => 'cil', 'CiPaw.01G146900' => 'cil', 'CiPaw.01G174000' => 'cil', 'CiPaw.01G179900' => 'cil', 'CiPaw.01G183400' => 'cil', 'CiPaw.01G240000' => 'cil', 'CiPaw.01G283500' => 'cil', 'CiPaw.01G307400' => 'cil', 'CiPaw.02G030800' => 'cil', 'CiPaw.02G047200' => 'cil', 'CiPaw.02G050500' => 'cil', 'CiPaw.02G069900' => 'cil', 'CiPaw.02G091600' => 'cil', 'CiPaw.02G095000' => 'cil', 'CiPaw.02G131900' => 'cil', 'CiPaw.03G043000' => 'cil', 'CiPaw.03G069900' => 'cil', 'CiPaw.03G088100' => 'cil', 'CiPaw.03G089300' => 'cil', 'CiPaw.03G093100' => 'cil', 'CiPaw.03G129800' => 'cil', 'CiPaw.03G131200' => 'cil', 'CiPaw.03G134500' => 'cil', 'CiPaw.03G152100' => 'cil', 'CiPaw.03G162700' => 'cil', 'CiPaw.03G172800' => 'cil', 'CiPaw.03G175800' => 'cil', 'CiPaw.03G181800' => 'cil', 'CiPaw.03G191400' => 'cil', 'CiPaw.03G198300' => 'cil', 'CiPaw.03G201300' => 'cil', 'CiPaw.03G224700' => 'cil', 'CiPaw.03G225000' => 'cil', 'CiPaw.04G065100' => 'cil', 'CiPaw.04G080400' => 'cil', 'CiPaw.04G113500' => 'cil', 'CiPaw.04G121900' => 'cil', 'CiPaw.04G144100' => 'cil', 'CiPaw.04G176500' => 'cil', 'CiPaw.05G086200' => 'cil', 'CiPaw.05G100200' => 'cil', 'CiPaw.05G114200' => 'cil', 'CiPaw.05G126800' => 'cil', 'CiPaw.05G228800' => 'cil', 'CiPaw.05G230600' => 'cil', 'CiPaw.05G236500' => 'cil', 'CiPaw.05G244800' => 'cil', 'CiPaw.06G026600' => 'cil', 'CiPaw.06G027900' => 'cil', 'CiPaw.06G051800' => 'cil', 'CiPaw.06G128500' => 'cil', 'CiPaw.06G165900' => 'cil', 'CiPaw.07G045400' => 'cil', 'CiPaw.07G048000' => 'cil', 'CiPaw.07G052000' => 'cil', 'CiPaw.07G073800' => 'cil', 'CiPaw.07G099700' => 'cil', 'CiPaw.07G108700' => 'cil', 'CiPaw.07G120000' => 'cil', 'CiPaw.07G134100' => 'cil', 'CiPaw.07G147000' => 'cil', 'CiPaw.07G149700' => 'cil', 'CiPaw.07G178300' => 'cil', 'CiPaw.07G184900' => 'cil', 'CiPaw.08G044500' => 'cil', 'CiPaw.08G046900' => 'cil', 'CiPaw.08G047300' => 'cil', 'CiPaw.08G115400' => 'cil', 'CiPaw.08G134700' => 'cil', 'CiPaw.08G157400' => 'cil', 'CiPaw.09G014300' => 'cil', 'CiPaw.09G088900' => 'cil', 'CiPaw.09G130900' => 'cil', 'CiPaw.09G133100' => 'cil', 'CiPaw.09G151300' => 'cil', 'CiPaw.09G172800' => 'cil', 'CiPaw.09G174900' => 'cil', 'CiPaw.09G175000' => 'cil', 'CiPaw.10G012800' => 'cil', 'CiPaw.10G028800' => 'cil', 'CiPaw.10G044700' => 'cil', 'CiPaw.10G067400' => 'cil', 'CiPaw.10G115900' => 'cil', 'CiPaw.10G126200' => 'cil', 'CiPaw.10G139700' => 'cil', 'CiPaw.10G155100' => 'cil', 'CiPaw.11G011300' => 'cil', 'CiPaw.11G025900' => 'cil', 'CiPaw.11G104100' => 'cil', 'CiPaw.11G142700' => 'cil', 'CiPaw.11G164500' => 'cil', 'CiPaw.11G189100' => 'cil', 'CiPaw.11G197100' => 'cil', 'CiPaw.12G006100' => 'cil', 'CiPaw.12G038500' => 'cil', 'CiPaw.12G041400' => 'cil', 'CiPaw.12G041600' => 'cil', 'CiPaw.12G051300' => 'cil', 'CiPaw.12G101800' => 'cil', 'CiPaw.12G107800' => 'cil', 'CiPaw.13G033200' => 'cil', 'CiPaw.13G129900' => 'cil', 'CiPaw.13G160200' => 'cil', 'CiPaw.14G018900' => 'cil', 'CiPaw.14G029000' => 'cil', 'CiPaw.14G031000' => 'cil', 'CiPaw.14G032000' => 'cil', 'CiPaw.14G032300' => 'cil', 'CiPaw.14G040600' => 'cil', 'CiPaw.14G060500' => 'cil', 'CiPaw.14G061500' => 'cil', 'CiPaw.14G077500' => 'cil', 'CiPaw.14G088300' => 'cil', 'CiPaw.14G108500' => 'cil', 'CiPaw.14G121300' => 'cil', 'CiPaw.14G133000' => 'cil', 'CiPaw.14G134600' => 'cil', 'CiPaw.15G027200' => 'cil', 'CiPaw.15G037700' => 'cil', 'CiPaw.15G050900' => 'cil', 'CiPaw.15G067200' => 'cil', 'CiPaw.15G072000' => 'cil', 'CiPaw.15G112900' => 'cil', 'CiPaw.15G133200' => 'cil', 'CiPaw.15G139500' => 'cil', 'CiPaw.15G155400' => 'cil', 'CiPaw.16G006000' => 'cil', 'CiPaw.16G013100' => 'cil', 'CiPaw.16G047100' => 'cil', 'CiPaw.16G048900' => 'cil', 'CiPaw.16G070300' => 'cil', 'CSS0000195' => 'camsi', 'CSS0001664' => 'camsi', 'CSS0002566' => 'camsi', 'CSS0003077' => 'camsi', 'CSS0004257' => 'camsi', 'CSS0004495' => 'camsi', 'CSS0004599' => 'camsi', 'CSS0004943' => 'camsi', 'CSS0005302' => 'camsi', 'CSS0006274' => 'camsi', 'CSS0006547' => 'camsi', 'CSS0006860' => 'camsi', 'CSS0008814' => 'camsi', 'CSS0008946' => 'camsi', 'CSS0009093' => 'camsi', 'CSS0010221' => 'camsi', 'CSS0010296' => 'camsi', 'CSS0010386' => 'camsi', 'CSS0010831' => 'camsi', 'CSS0011061' => 'camsi', 'CSS0012008' => 'camsi', 'CSS0012194' => 'camsi', 'CSS0013580' => 'camsi', 'CSS0014176' => 'camsi', 'CSS0014280' => 'camsi', 'CSS0014799' => 'camsi', 'CSS0015368' => 'camsi', 'CSS0017473' => 'camsi', 'CSS0019281' => 'camsi', 'CSS0021320' => 'camsi', 'CSS0021750' => 'camsi', 'CSS0023642' => 'camsi', 'CSS0023792' => 'camsi', 'CSS0031528' => 'camsi', 'CSS0033894' => 'camsi', 'CSS0034959' => 'camsi', 'CSS0035632' => 'camsi', 'CSS0038450' => 'camsi', 'CSS0039293' => 'camsi', 'CSS0041053' => 'camsi', 'CSS0041981' => 'camsi', 'CSS0042573' => 'camsi', 'CSS0042927' => 'camsi', 'CSS0047725' => 'camsi', 'CSS0049636' => 'camsi', 'CSS0050513' => 'camsi', 'DCAR_030203' => 'dca', 'Dinv07939' => 'din', 'FAN01G0456' => 'fan', 'FAN02G3001' => 'fan', 'FAN04G2781' => 'fan', 'FAN05G1385' => 'fan', 'FAN05G3062' => 'fan', 'FAN08G2267' => 'fan', 'FAN10G0481' => 'fan', 'FAN10G1257' => 'fan', 'FAN14G0954' => 'fan', 'FAN14G2347' => 'fan', 'FAN15G0187' => 'fan', 'FAN25G2214' => 'fan', 'FvH4_1g21031' => 'fve', 'FvH4_3g16231' => 'fve', 'FvH4_3g26413' => 'fve', 'FvH4_3g29014' => 'fve', 'FvH4_3g31921' => 'fve', 'FvH4_4g19882' => 'fve', 'FvH4_5g21960' => 'fve', 'FvH4_5g29683' => 'fve', 'FvH4_7g13271' => 'fve', 'Glyma.01G062500' => 'gma', 'Glyma.07G140900' => 'gma', 'Glyma.09G140900' => 'gma', 'Glyma.12G112700' => 'gma', 'Glyma.17G168800' => 'gma', 'HanXRQChr01g0027001' => 'han', 'HanXRQChr04g0120511' => 'han', 'HanXRQChr08g0232381' => 'han', 'HanXRQChr09g0265661' => 'han', 'HanXRQChr13g0416031' => 'han', 'Haze_05835' => 'cav', 'Haze_06597' => 'cav', 'Haze_07921' => 'cav', 'Haze_08599' => 'cav', 'Haze_10686' => 'cav', 'Haze_12994' => 'cav', 'Haze_13466' => 'cav', 'Haze_16101' => 'cav', 'Haze_17766' => 'cav', 'Haze_18456' => 'cav', 'Haze_20229' => 'cav', 'Hma1.2p1_0324F.1_g125640' => 'hma', 'Hma1.2p1_0733F.1_g210230' => 'hma', 'Hma1.2p1_0921F.1_g236870' => 'hma', 'Hma1.2p1_1313F.1_g274940' => 'hma', 'Hma1.2p1_3059F.1_g332230' => 'hma', 'Hund15925' => 'sun', 'Hund19562' => 'sun', 'Hund21925' => 'sun', 'MD03G1177400' => 'mdo', 'MD07G1026100' => 'mdo', 'MD17G1218600' => 'mdo', 'Medtr0867s0010' => 'mtr', 'Medtr6g081150' => 'mtr', 'Os01g0527900' => 'osa', 'Os02g0463725' => 'osa', 'Os02g0785600' => 'osa', 'Os03g0433733' => 'osa', 'Os04g0286500' => 'osa', 'Os05g0227800' => 'osa', 'Os06g0521000' => 'osa', 'Os06g0635500' => 'osa', 'Os06g0660650' => 'osa', 'Os07g0554400' => 'osa', 'Os08g0225900' => 'osa', 'Os08g0561000' => 'osa', 'Os09g0241700' => 'osa', 'Os09g0351900' => 'osa', 'Os11g0220700' => 'osa', 'Os11g0282700' => 'osa', 'Os12g0169300' => 'osa', 'Os12g0228500' => 'osa', 'Os12g0543800' => 'osa', 'PGR044G1547' => 'pgr', 'Potri.005G239150' => 'ptr', 'Potri.010G014250' => 'ptr', 'Prupe.1G172500' => 'ppe', 'Prupe.1G196800' => 'ppe', 'Prupe.1G279700' => 'ppe', 'Prupe.2G026400' => 'ppe', 'Prupe.3G094000' => 'ppe', 'Prupe.4G287300' => 'ppe', 'QL01p022166' => 'qlo', 'QL01p051890' => 'qlo', 'QL02p009469' => 'qlo', 'QL02p046053' => 'qlo', 'QL02p057958' => 'qlo', 'QL02p093127' => 'qlo', 'QL03p006855' => 'qlo', 'QL03p071586' => 'qlo', 'QL04p000022' => 'qlo', 'QL04p000024' => 'qlo', 'QL04p003192' => 'qlo', 'QL05p011416' => 'qlo', 'QL06p039590' => 'qlo', 'QL06p052750' => 'qlo', 'QL06p053821' => 'qlo', 'QL07p025287' => 'qlo', 'QL09p033218' => 'qlo', 'QL09p040841' => 'qlo', 'QL10p020337' => 'qlo', 'QL10p027209' => 'qlo', 'QL10p027969' => 'qlo', 'QL10p048988' => 'qlo', 'QL11p001241' => 'qlo', 'QL11p028487' => 'qlo', 'RcHm_v2.0_Chr2g0105031' => 'rch', 'RcHm_v2.0_Chr2g0117811' => 'rch', 'RcHm_v2.0_Chr6g0270241' => 'rch', 'RcHm_v2.0_Chr7g0215961' => 'rch', 'RcHm_v2.0_Chr7g0231991' => 'rch', 'Rhsim01G0041500' => 'rsi', 'Rhsim01G0115000' => 'rsi', 'Rhsim01G0115400' => 'rsi', 'Rhsim01G0133600' => 'rsi', 'Rhsim01G0159900' => 'rsi', 'Rhsim02G0189400' => 'rsi', 'Rhsim03G0135600' => 'rsi', 'Rhsim03G0149900' => 'rsi', 'Rhsim04G0125600' => 'rsi', 'Rhsim05G0091700' => 'rsi', 'Rhsim05G0092900' => 'rsi', 'Rhsim06G0075000' => 'rsi', 'Rhsim07G0066400' => 'rsi', 'Rhsim07G0156400' => 'rsi', 'Rhsim07G0182200' => 'rsi', 'Rhsim07G0182300' => 'rsi', 'Rhsim08G0180400' => 'rsi', 'Rhsim09G0056800' => 'rsi', 'Rhsim10G0153300' => 'rsi', 'Rhsim11G0012700' => 'rsi', 'Rhsim12G0031800' => 'rsi', 'Rhsim12G0055400' => 'rsi', 'Rhsim12G0091400' => 'rsi', 'Rhsim13G0070800' => 'rsi', 'Rhsim13G0193300' => 'rsi', 'RhsimUnG0111600' => 'rsi', 'RhsimUnG0137500' => 'rsi', 'RhsimUnG0172900' => 'rsi', 'SGA_v2.0_scaffold11G05878' => 'sas', 'SGA_v2.0_scaffold167G38458' => 'sas', 'SGA_v2.0_scaffold19G08588' => 'sas', 'SGA_v2.0_scaffold239G43990' => 'sas', 'SGA_v2.0_scaffold260G45865' => 'sas', 'SGA_v2.0_scaffold309G48177' => 'sas', 'SGA_v2.0_scaffold76G25122' => 'sas', 'SGA_v2.0_scaffold85G26708' => 'sas', 'SHI13914' => 'shi', 'SHI30402' => 'shi', 'TWI09G0020' => 'twi', 'TWI09G0456' => 'twi', 'TWI09G1572' => 'twi', 'TWI12G0266' => 'twi', 'TWI12G1451' => 'twi', 'TWI14G0851' => 'twi', 'TWI15G0796' => 'twi', 'TWI18G0820' => 'twi', 'TWI18G1152' => 'twi', 'TWI23G0007' => 'twi', 'TWI23G0314' => 'twi', 'TWI31G0674' => 'twi', 'TWI31G0938' => 'twi', 'TWI34G0641' => 'twi', 'TWI34G1527' => 'twi', 'TWI36G0193' => 'twi', 'TWI36G0405' => 'twi', 'TWI38G0892' => 'twi', 'TWI38G0936' => 'twi', 'TWI38G2218' => 'twi', 'TWI53G0679' => 'twi', 'TWI53G0863' => 'twi', 'TWI53G1133' => 'twi', 'TWI60G0823' => 'twi', 'TWI63G0919' => 'twi', 'TWI63G1436' => 'twi', 'TWI73G0140' => 'twi', 'TWI73G0419' => 'twi', 'TWI73G0420' => 'twi', 'TWI73G1276' => 'twi', 'TWI74G0405' => 'twi', 'TWI74G0837' => 'twi', 'TWI75G0594' => 'twi', 'TWI75G1615' => 'twi', 'TWI77G0816' => 'twi', 'vmacro03831' => 'vma', 'vmacro13746' => 'vma', 'vmacro16089' => 'vma', 'vmacro22863' => 'vma', 'Zm00001eb085790' => 'zma', 'Zm00001eb114250' => 'zma', 'Zm00001eb138070' => 'zma', 'Zm00001eb167560' => 'zma', 'Zm00001eb199990' => 'zma', 'Zm00001eb368180' => 'zma', 'Zm00001eb382470' => 'zma' ) $gf_id = 'HOM05D001576' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001576' ) $data_identifier = 'HOM05D001576' $data_type = 'gf_id' $species_gene_counts = array( 'aox' => (int) 9, 'acertr' => (int) 3, 'cansat' => (int) 1, 'ccl' => (int) 4, 'cil' => (int) 145, 'camsi' => (int) 46, 'dca' => (int) 1, 'din' => (int) 1, 'fan' => (int) 12, 'fve' => (int) 9, 'gma' => (int) 5, 'han' => (int) 5, 'cav' => (int) 11, 'hma' => (int) 5, 'sun' => (int) 3, 'mdo' => (int) 3, 'mtr' => (int) 2, 'osa' => (int) 19, 'pgr' => (int) 1, 'ptr' => (int) 2, 'ppe' => (int) 6, 'qlo' => (int) 24, 'rch' => (int) 5, 'rsi' => (int) 28, 'sas' => (int) 8, 'shi' => (int) 2, 'twi' => (int) 35, 'vma' => (int) 4, 'zma' => (int) 7 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb382470' $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' => 'HOM05D001576', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '406', 'num_species' => '29' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'Aqoxy1G01456' => 'aox', 'Aqoxy1G02949' => 'aox', 'Aqoxy3G01274' => 'aox', 'Aqoxy3G02110' => 'aox', 'Aqoxy3G02268' => 'aox', 'Aqoxy5G02702' => 'aox', 'Aqoxy5G02988' => 'aox', 'Aqoxy5G03427' => 'aox', 'Aqoxy6G02363' => 'aox', 'Atru.chr1.3225' => 'acertr', 'Atru.chr8.1198' => 'acertr', 'Atru.chr9.790' => 'acertr', 'CANSAT01G3197' => 'cansat', 'Ciclev10003979m.g' => 'ccl', 'Ciclev10017471m.g' => 'ccl', 'Ciclev10018206m.g' => 'ccl', 'Ciclev10033751m.g' => 'ccl', 'CiPaw.01G000900' => 'cil', 'CiPaw.01G001000' => 'cil', 'CiPaw.01G033500' => 'cil', 'CiPaw.01G060300' => 'cil', 'CiPaw.01G070200' => 'cil', 'CiPaw.01G075100' => 'cil', 'CiPaw.01G084700' => 'cil', 'CiPaw.01G087900' => 'cil', 'CiPaw.01G092600' => 'cil', 'CiPaw.01G097200' => 'cil', 'CiPaw.01G098300' => 'cil', 'CiPaw.01G110200' => 'cil', 'CiPaw.01G118700' => 'cil', 'CiPaw.01G121200' => 'cil', 'CiPaw.01G132500' => 'cil', 'CiPaw.01G146900' => 'cil', 'CiPaw.01G174000' => 'cil', 'CiPaw.01G179900' => 'cil', 'CiPaw.01G183400' => 'cil', 'CiPaw.01G240000' => 'cil', 'CiPaw.01G283500' => 'cil', 'CiPaw.01G307400' => 'cil', 'CiPaw.02G030800' => 'cil', 'CiPaw.02G047200' => 'cil', 'CiPaw.02G050500' => 'cil', 'CiPaw.02G069900' => 'cil', 'CiPaw.02G091600' => 'cil', 'CiPaw.02G095000' => 'cil', 'CiPaw.02G131900' => 'cil', 'CiPaw.03G043000' => 'cil', 'CiPaw.03G069900' => 'cil', 'CiPaw.03G088100' => 'cil', 'CiPaw.03G089300' => 'cil', 'CiPaw.03G093100' => 'cil', 'CiPaw.03G129800' => 'cil', 'CiPaw.03G131200' => 'cil', 'CiPaw.03G134500' => 'cil', 'CiPaw.03G152100' => 'cil', 'CiPaw.03G162700' => 'cil', 'CiPaw.03G172800' => 'cil', 'CiPaw.03G175800' => 'cil', 'CiPaw.03G181800' => 'cil', 'CiPaw.03G191400' => 'cil', 'CiPaw.03G198300' => 'cil', 'CiPaw.03G201300' => 'cil', 'CiPaw.03G224700' => 'cil', 'CiPaw.03G225000' => 'cil', 'CiPaw.04G065100' => 'cil', 'CiPaw.04G080400' => 'cil', 'CiPaw.04G113500' => 'cil', 'CiPaw.04G121900' => 'cil', 'CiPaw.04G144100' => 'cil', 'CiPaw.04G176500' => 'cil', 'CiPaw.05G086200' => 'cil', 'CiPaw.05G100200' => 'cil', 'CiPaw.05G114200' => 'cil', 'CiPaw.05G126800' => 'cil', 'CiPaw.05G228800' => 'cil', 'CiPaw.05G230600' => 'cil', 'CiPaw.05G236500' => 'cil', 'CiPaw.05G244800' => 'cil', 'CiPaw.06G026600' => 'cil', 'CiPaw.06G027900' => 'cil', 'CiPaw.06G051800' => 'cil', 'CiPaw.06G128500' => 'cil', 'CiPaw.06G165900' => 'cil', 'CiPaw.07G045400' => 'cil', 'CiPaw.07G048000' => 'cil', 'CiPaw.07G052000' => 'cil', 'CiPaw.07G073800' => 'cil', 'CiPaw.07G099700' => 'cil', 'CiPaw.07G108700' => 'cil', 'CiPaw.07G120000' => 'cil', 'CiPaw.07G134100' => 'cil', 'CiPaw.07G147000' => 'cil', 'CiPaw.07G149700' => 'cil', 'CiPaw.07G178300' => 'cil', 'CiPaw.07G184900' => 'cil', 'CiPaw.08G044500' => 'cil', 'CiPaw.08G046900' => 'cil', 'CiPaw.08G047300' => 'cil', 'CiPaw.08G115400' => 'cil', 'CiPaw.08G134700' => 'cil', 'CiPaw.08G157400' => 'cil', 'CiPaw.09G014300' => 'cil', 'CiPaw.09G088900' => 'cil', 'CiPaw.09G130900' => 'cil', 'CiPaw.09G133100' => 'cil', 'CiPaw.09G151300' => 'cil', 'CiPaw.09G172800' => 'cil', 'CiPaw.09G174900' => 'cil', 'CiPaw.09G175000' => 'cil', 'CiPaw.10G012800' => 'cil', 'CiPaw.10G028800' => 'cil', 'CiPaw.10G044700' => 'cil', 'CiPaw.10G067400' => 'cil', 'CiPaw.10G115900' => 'cil', 'CiPaw.10G126200' => 'cil', 'CiPaw.10G139700' => 'cil', 'CiPaw.10G155100' => 'cil', 'CiPaw.11G011300' => 'cil', 'CiPaw.11G025900' => 'cil', 'CiPaw.11G104100' => 'cil', 'CiPaw.11G142700' => 'cil', 'CiPaw.11G164500' => 'cil', 'CiPaw.11G189100' => 'cil', 'CiPaw.11G197100' => 'cil', 'CiPaw.12G006100' => 'cil', 'CiPaw.12G038500' => 'cil', 'CiPaw.12G041400' => 'cil', 'CiPaw.12G041600' => 'cil', 'CiPaw.12G051300' => 'cil', 'CiPaw.12G101800' => 'cil', 'CiPaw.12G107800' => 'cil', 'CiPaw.13G033200' => 'cil', 'CiPaw.13G129900' => 'cil', 'CiPaw.13G160200' => 'cil', 'CiPaw.14G018900' => 'cil', 'CiPaw.14G029000' => 'cil', 'CiPaw.14G031000' => 'cil', 'CiPaw.14G032000' => 'cil', 'CiPaw.14G032300' => 'cil', 'CiPaw.14G040600' => 'cil', 'CiPaw.14G060500' => 'cil', 'CiPaw.14G061500' => 'cil', 'CiPaw.14G077500' => 'cil', 'CiPaw.14G088300' => 'cil', 'CiPaw.14G108500' => 'cil', 'CiPaw.14G121300' => 'cil', 'CiPaw.14G133000' => 'cil', 'CiPaw.14G134600' => 'cil', 'CiPaw.15G027200' => 'cil', 'CiPaw.15G037700' => 'cil', 'CiPaw.15G050900' => 'cil', 'CiPaw.15G067200' => 'cil', 'CiPaw.15G072000' => 'cil', 'CiPaw.15G112900' => 'cil', 'CiPaw.15G133200' => 'cil', 'CiPaw.15G139500' => 'cil', 'CiPaw.15G155400' => 'cil', 'CiPaw.16G006000' => 'cil', 'CiPaw.16G013100' => 'cil', 'CiPaw.16G047100' => 'cil', 'CiPaw.16G048900' => 'cil', 'CiPaw.16G070300' => 'cil', 'CSS0000195' => 'camsi', 'CSS0001664' => 'camsi', 'CSS0002566' => 'camsi', 'CSS0003077' => 'camsi', 'CSS0004257' => 'camsi', 'CSS0004495' => 'camsi', 'CSS0004599' => 'camsi', 'CSS0004943' => 'camsi', 'CSS0005302' => 'camsi', 'CSS0006274' => 'camsi', 'CSS0006547' => 'camsi', 'CSS0006860' => 'camsi', 'CSS0008814' => 'camsi', 'CSS0008946' => 'camsi', 'CSS0009093' => 'camsi', 'CSS0010221' => 'camsi', 'CSS0010296' => 'camsi', 'CSS0010386' => 'camsi', 'CSS0010831' => 'camsi', 'CSS0011061' => 'camsi', 'CSS0012008' => 'camsi', 'CSS0012194' => 'camsi', 'CSS0013580' => 'camsi', 'CSS0014176' => 'camsi', 'CSS0014280' => 'camsi', 'CSS0014799' => 'camsi', 'CSS0015368' => 'camsi', 'CSS0017473' => 'camsi', 'CSS0019281' => 'camsi', 'CSS0021320' => 'camsi', 'CSS0021750' => 'camsi', 'CSS0023642' => 'camsi', 'CSS0023792' => 'camsi', 'CSS0031528' => 'camsi', 'CSS0033894' => 'camsi', 'CSS0034959' => 'camsi', 'CSS0035632' => 'camsi', 'CSS0038450' => 'camsi', 'CSS0039293' => 'camsi', 'CSS0041053' => 'camsi', 'CSS0041981' => 'camsi', 'CSS0042573' => 'camsi', 'CSS0042927' => 'camsi', 'CSS0047725' => 'camsi', 'CSS0049636' => 'camsi', 'CSS0050513' => 'camsi', 'DCAR_030203' => 'dca', 'Dinv07939' => 'din', 'FAN01G0456' => 'fan', 'FAN02G3001' => 'fan', 'FAN04G2781' => 'fan', 'FAN05G1385' => 'fan', 'FAN05G3062' => 'fan', 'FAN08G2267' => 'fan', 'FAN10G0481' => 'fan', 'FAN10G1257' => 'fan', 'FAN14G0954' => 'fan', 'FAN14G2347' => 'fan', 'FAN15G0187' => 'fan', 'FAN25G2214' => 'fan', 'FvH4_1g21031' => 'fve', 'FvH4_3g16231' => 'fve', 'FvH4_3g26413' => 'fve', 'FvH4_3g29014' => 'fve', 'FvH4_3g31921' => 'fve', 'FvH4_4g19882' => 'fve', 'FvH4_5g21960' => 'fve', 'FvH4_5g29683' => 'fve', 'FvH4_7g13271' => 'fve', 'Glyma.01G062500' => 'gma', 'Glyma.07G140900' => 'gma', 'Glyma.09G140900' => 'gma', 'Glyma.12G112700' => 'gma', 'Glyma.17G168800' => 'gma', 'HanXRQChr01g0027001' => 'han', 'HanXRQChr04g0120511' => 'han', 'HanXRQChr08g0232381' => 'han', 'HanXRQChr09g0265661' => 'han', 'HanXRQChr13g0416031' => 'han', 'Haze_05835' => 'cav', 'Haze_06597' => 'cav', 'Haze_07921' => 'cav', 'Haze_08599' => 'cav', 'Haze_10686' => 'cav', 'Haze_12994' => 'cav', 'Haze_13466' => 'cav', 'Haze_16101' => 'cav', 'Haze_17766' => 'cav', 'Haze_18456' => 'cav', 'Haze_20229' => 'cav', 'Hma1.2p1_0324F.1_g125640' => 'hma', 'Hma1.2p1_0733F.1_g210230' => 'hma', 'Hma1.2p1_0921F.1_g236870' => 'hma', 'Hma1.2p1_1313F.1_g274940' => 'hma', 'Hma1.2p1_3059F.1_g332230' => 'hma', 'Hund15925' => 'sun', 'Hund19562' => 'sun', 'Hund21925' => 'sun', 'MD03G1177400' => 'mdo', 'MD07G1026100' => 'mdo', 'MD17G1218600' => 'mdo', 'Medtr0867s0010' => 'mtr', 'Medtr6g081150' => 'mtr', 'Os01g0527900' => 'osa', 'Os02g0463725' => 'osa', 'Os02g0785600' => 'osa', 'Os03g0433733' => 'osa', 'Os04g0286500' => 'osa', 'Os05g0227800' => 'osa', 'Os06g0521000' => 'osa', 'Os06g0635500' => 'osa', 'Os06g0660650' => 'osa', 'Os07g0554400' => 'osa', 'Os08g0225900' => 'osa', 'Os08g0561000' => 'osa', 'Os09g0241700' => 'osa', 'Os09g0351900' => 'osa', 'Os11g0220700' => 'osa', 'Os11g0282700' => 'osa', 'Os12g0169300' => 'osa', 'Os12g0228500' => 'osa', 'Os12g0543800' => 'osa', 'PGR044G1547' => 'pgr', 'Potri.005G239150' => 'ptr', 'Potri.010G014250' => 'ptr', 'Prupe.1G172500' => 'ppe', 'Prupe.1G196800' => 'ppe', 'Prupe.1G279700' => 'ppe', 'Prupe.2G026400' => 'ppe', 'Prupe.3G094000' => 'ppe', 'Prupe.4G287300' => 'ppe', 'QL01p022166' => 'qlo', 'QL01p051890' => 'qlo', 'QL02p009469' => 'qlo', 'QL02p046053' => 'qlo', 'QL02p057958' => 'qlo', 'QL02p093127' => 'qlo', 'QL03p006855' => 'qlo', 'QL03p071586' => 'qlo', 'QL04p000022' => 'qlo', 'QL04p000024' => 'qlo', 'QL04p003192' => 'qlo', 'QL05p011416' => 'qlo', 'QL06p039590' => 'qlo', 'QL06p052750' => 'qlo', 'QL06p053821' => 'qlo', 'QL07p025287' => 'qlo', 'QL09p033218' => 'qlo', 'QL09p040841' => 'qlo', 'QL10p020337' => 'qlo', 'QL10p027209' => 'qlo', 'QL10p027969' => 'qlo', 'QL10p048988' => 'qlo', 'QL11p001241' => 'qlo', 'QL11p028487' => 'qlo', 'RcHm_v2.0_Chr2g0105031' => 'rch', 'RcHm_v2.0_Chr2g0117811' => 'rch', 'RcHm_v2.0_Chr6g0270241' => 'rch', 'RcHm_v2.0_Chr7g0215961' => 'rch', 'RcHm_v2.0_Chr7g0231991' => 'rch', 'Rhsim01G0041500' => 'rsi', 'Rhsim01G0115000' => 'rsi', 'Rhsim01G0115400' => 'rsi', 'Rhsim01G0133600' => 'rsi', 'Rhsim01G0159900' => 'rsi', 'Rhsim02G0189400' => 'rsi', 'Rhsim03G0135600' => 'rsi', 'Rhsim03G0149900' => 'rsi', 'Rhsim04G0125600' => 'rsi', 'Rhsim05G0091700' => 'rsi', 'Rhsim05G0092900' => 'rsi', 'Rhsim06G0075000' => 'rsi', 'Rhsim07G0066400' => 'rsi', 'Rhsim07G0156400' => 'rsi', 'Rhsim07G0182200' => 'rsi', 'Rhsim07G0182300' => 'rsi', 'Rhsim08G0180400' => 'rsi', 'Rhsim09G0056800' => 'rsi', 'Rhsim10G0153300' => 'rsi', 'Rhsim11G0012700' => 'rsi', 'Rhsim12G0031800' => 'rsi', 'Rhsim12G0055400' => 'rsi', 'Rhsim12G0091400' => 'rsi', 'Rhsim13G0070800' => 'rsi', 'Rhsim13G0193300' => 'rsi', 'RhsimUnG0111600' => 'rsi', 'RhsimUnG0137500' => 'rsi', 'RhsimUnG0172900' => 'rsi', 'SGA_v2.0_scaffold11G05878' => 'sas', 'SGA_v2.0_scaffold167G38458' => 'sas', 'SGA_v2.0_scaffold19G08588' => 'sas', 'SGA_v2.0_scaffold239G43990' => 'sas', 'SGA_v2.0_scaffold260G45865' => 'sas', 'SGA_v2.0_scaffold309G48177' => 'sas', 'SGA_v2.0_scaffold76G25122' => 'sas', 'SGA_v2.0_scaffold85G26708' => 'sas', 'SHI13914' => 'shi', 'SHI30402' => 'shi', 'TWI09G0020' => 'twi', 'TWI09G0456' => 'twi', 'TWI09G1572' => 'twi', 'TWI12G0266' => 'twi', 'TWI12G1451' => 'twi', 'TWI14G0851' => 'twi', 'TWI15G0796' => 'twi', 'TWI18G0820' => 'twi', 'TWI18G1152' => 'twi', 'TWI23G0007' => 'twi', 'TWI23G0314' => 'twi', 'TWI31G0674' => 'twi', 'TWI31G0938' => 'twi', 'TWI34G0641' => 'twi', 'TWI34G1527' => 'twi', 'TWI36G0193' => 'twi', 'TWI36G0405' => 'twi', 'TWI38G0892' => 'twi', 'TWI38G0936' => 'twi', 'TWI38G2218' => 'twi', 'TWI53G0679' => 'twi', 'TWI53G0863' => 'twi', 'TWI53G1133' => 'twi', 'TWI60G0823' => 'twi', 'TWI63G0919' => 'twi', 'TWI63G1436' => 'twi', 'TWI73G0140' => 'twi', 'TWI73G0419' => 'twi', 'TWI73G0420' => 'twi', 'TWI73G1276' => 'twi', 'TWI74G0405' => 'twi', 'TWI74G0837' => 'twi', 'TWI75G0594' => 'twi', 'TWI75G1615' => 'twi', 'TWI77G0816' => 'twi', 'vmacro03831' => 'vma', 'vmacro13746' => 'vma', 'vmacro16089' => 'vma', 'vmacro22863' => 'vma', 'Zm00001eb085790' => 'zma', 'Zm00001eb114250' => 'zma', 'Zm00001eb138070' => 'zma', 'Zm00001eb167560' => 'zma', 'Zm00001eb199990' => 'zma', 'Zm00001eb368180' => 'zma', 'Zm00001eb382470' => 'zma' ), 'gf_id' => 'HOM05D001576', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001576' ), 'data_identifier' => 'HOM05D001576', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001576', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '406', 'num_species' => '29' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'Aqoxy1G01456' => 'aox', 'Aqoxy1G02949' => 'aox', 'Aqoxy3G01274' => 'aox', 'Aqoxy3G02110' => 'aox', 'Aqoxy3G02268' => 'aox', 'Aqoxy5G02702' => 'aox', 'Aqoxy5G02988' => 'aox', 'Aqoxy5G03427' => 'aox', 'Aqoxy6G02363' => 'aox', 'Atru.chr1.3225' => 'acertr', 'Atru.chr8.1198' => 'acertr', 'Atru.chr9.790' => 'acertr', 'CANSAT01G3197' => 'cansat', 'Ciclev10003979m.g' => 'ccl', 'Ciclev10017471m.g' => 'ccl', 'Ciclev10018206m.g' => 'ccl', 'Ciclev10033751m.g' => 'ccl', 'CiPaw.01G000900' => 'cil', 'CiPaw.01G001000' => 'cil', 'CiPaw.01G033500' => 'cil', 'CiPaw.01G060300' => 'cil', 'CiPaw.01G070200' => 'cil', 'CiPaw.01G075100' => 'cil', 'CiPaw.01G084700' => 'cil', 'CiPaw.01G087900' => 'cil', 'CiPaw.01G092600' => 'cil', 'CiPaw.01G097200' => 'cil', 'CiPaw.01G098300' => 'cil', 'CiPaw.01G110200' => 'cil', 'CiPaw.01G118700' => 'cil', 'CiPaw.01G121200' => 'cil', 'CiPaw.01G132500' => 'cil', 'CiPaw.01G146900' => 'cil', 'CiPaw.01G174000' => 'cil', 'CiPaw.01G179900' => 'cil', 'CiPaw.01G183400' => 'cil', 'CiPaw.01G240000' => 'cil', 'CiPaw.01G283500' => 'cil', 'CiPaw.01G307400' => 'cil', 'CiPaw.02G030800' => 'cil', 'CiPaw.02G047200' => 'cil', 'CiPaw.02G050500' => 'cil', 'CiPaw.02G069900' => 'cil', 'CiPaw.02G091600' => 'cil', 'CiPaw.02G095000' => 'cil', 'CiPaw.02G131900' => 'cil', 'CiPaw.03G043000' => 'cil', 'CiPaw.03G069900' => 'cil', 'CiPaw.03G088100' => 'cil', 'CiPaw.03G089300' => 'cil', 'CiPaw.03G093100' => 'cil', 'CiPaw.03G129800' => 'cil', 'CiPaw.03G131200' => 'cil', 'CiPaw.03G134500' => 'cil', 'CiPaw.03G152100' => 'cil', 'CiPaw.03G162700' => 'cil', 'CiPaw.03G172800' => 'cil', 'CiPaw.03G175800' => 'cil', 'CiPaw.03G181800' => 'cil', 'CiPaw.03G191400' => 'cil', 'CiPaw.03G198300' => 'cil', 'CiPaw.03G201300' => 'cil', 'CiPaw.03G224700' => 'cil', 'CiPaw.03G225000' => 'cil', 'CiPaw.04G065100' => 'cil', 'CiPaw.04G080400' => 'cil', 'CiPaw.04G113500' => 'cil', 'CiPaw.04G121900' => 'cil', 'CiPaw.04G144100' => 'cil', 'CiPaw.04G176500' => 'cil', 'CiPaw.05G086200' => 'cil', 'CiPaw.05G100200' => 'cil', 'CiPaw.05G114200' => 'cil', 'CiPaw.05G126800' => 'cil', 'CiPaw.05G228800' => 'cil', 'CiPaw.05G230600' => 'cil', 'CiPaw.05G236500' => 'cil', 'CiPaw.05G244800' => 'cil', 'CiPaw.06G026600' => 'cil', 'CiPaw.06G027900' => 'cil', 'CiPaw.06G051800' => 'cil', 'CiPaw.06G128500' => 'cil', 'CiPaw.06G165900' => 'cil', 'CiPaw.07G045400' => 'cil', 'CiPaw.07G048000' => 'cil', 'CiPaw.07G052000' => 'cil', 'CiPaw.07G073800' => 'cil', 'CiPaw.07G099700' => 'cil', 'CiPaw.07G108700' => 'cil', 'CiPaw.07G120000' => 'cil', 'CiPaw.07G134100' => 'cil', 'CiPaw.07G147000' => 'cil', 'CiPaw.07G149700' => 'cil', 'CiPaw.07G178300' => 'cil', 'CiPaw.07G184900' => 'cil', 'CiPaw.08G044500' => 'cil', 'CiPaw.08G046900' => 'cil', 'CiPaw.08G047300' => 'cil', 'CiPaw.08G115400' => 'cil', 'CiPaw.08G134700' => 'cil', 'CiPaw.08G157400' => 'cil', 'CiPaw.09G014300' => 'cil', 'CiPaw.09G088900' => 'cil', 'CiPaw.09G130900' => 'cil', 'CiPaw.09G133100' => 'cil', 'CiPaw.09G151300' => 'cil', 'CiPaw.09G172800' => 'cil', 'CiPaw.09G174900' => 'cil', 'CiPaw.09G175000' => 'cil', 'CiPaw.10G012800' => 'cil', 'CiPaw.10G028800' => 'cil', 'CiPaw.10G044700' => 'cil', 'CiPaw.10G067400' => 'cil', 'CiPaw.10G115900' => 'cil', 'CiPaw.10G126200' => 'cil', 'CiPaw.10G139700' => 'cil', 'CiPaw.10G155100' => 'cil', 'CiPaw.11G011300' => 'cil', 'CiPaw.11G025900' => 'cil', 'CiPaw.11G104100' => 'cil', 'CiPaw.11G142700' => 'cil', 'CiPaw.11G164500' => 'cil', 'CiPaw.11G189100' => 'cil', 'CiPaw.11G197100' => 'cil', 'CiPaw.12G006100' => 'cil', 'CiPaw.12G038500' => 'cil', 'CiPaw.12G041400' => 'cil', 'CiPaw.12G041600' => 'cil', 'CiPaw.12G051300' => 'cil', 'CiPaw.12G101800' => 'cil', 'CiPaw.12G107800' => 'cil', 'CiPaw.13G033200' => 'cil', 'CiPaw.13G129900' => 'cil', 'CiPaw.13G160200' => 'cil', 'CiPaw.14G018900' => 'cil', 'CiPaw.14G029000' => 'cil', 'CiPaw.14G031000' => 'cil', 'CiPaw.14G032000' => 'cil', 'CiPaw.14G032300' => 'cil', 'CiPaw.14G040600' => 'cil', 'CiPaw.14G060500' => 'cil', 'CiPaw.14G061500' => 'cil', 'CiPaw.14G077500' => 'cil', 'CiPaw.14G088300' => 'cil', 'CiPaw.14G108500' => 'cil', 'CiPaw.14G121300' => 'cil', 'CiPaw.14G133000' => 'cil', 'CiPaw.14G134600' => 'cil', 'CiPaw.15G027200' => 'cil', 'CiPaw.15G037700' => 'cil', 'CiPaw.15G050900' => 'cil', 'CiPaw.15G067200' => 'cil', 'CiPaw.15G072000' => 'cil', 'CiPaw.15G112900' => 'cil', 'CiPaw.15G133200' => 'cil', 'CiPaw.15G139500' => 'cil', 'CiPaw.15G155400' => 'cil', 'CiPaw.16G006000' => 'cil', 'CiPaw.16G013100' => 'cil', 'CiPaw.16G047100' => 'cil', 'CiPaw.16G048900' => 'cil', 'CiPaw.16G070300' => 'cil', 'CSS0000195' => 'camsi', 'CSS0001664' => 'camsi', 'CSS0002566' => 'camsi', 'CSS0003077' => 'camsi', 'CSS0004257' => 'camsi', 'CSS0004495' => 'camsi', 'CSS0004599' => 'camsi', 'CSS0004943' => 'camsi', 'CSS0005302' => 'camsi', 'CSS0006274' => 'camsi', 'CSS0006547' => 'camsi', 'CSS0006860' => 'camsi', 'CSS0008814' => 'camsi', 'CSS0008946' => 'camsi', 'CSS0009093' => 'camsi', 'CSS0010221' => 'camsi', 'CSS0010296' => 'camsi', 'CSS0010386' => 'camsi', 'CSS0010831' => 'camsi', 'CSS0011061' => 'camsi', 'CSS0012008' => 'camsi', 'CSS0012194' => 'camsi', 'CSS0013580' => 'camsi', 'CSS0014176' => 'camsi', 'CSS0014280' => 'camsi', 'CSS0014799' => 'camsi', 'CSS0015368' => 'camsi', 'CSS0017473' => 'camsi', 'CSS0019281' => 'camsi', 'CSS0021320' => 'camsi', 'CSS0021750' => 'camsi', 'CSS0023642' => 'camsi', 'CSS0023792' => 'camsi', 'CSS0031528' => 'camsi', 'CSS0033894' => 'camsi', 'CSS0034959' => 'camsi', 'CSS0035632' => 'camsi', 'CSS0038450' => 'camsi', 'CSS0039293' => 'camsi', 'CSS0041053' => 'camsi', 'CSS0041981' => 'camsi', 'CSS0042573' => 'camsi', 'CSS0042927' => 'camsi', 'CSS0047725' => 'camsi', 'CSS0049636' => 'camsi', 'CSS0050513' => 'camsi', 'DCAR_030203' => 'dca', 'Dinv07939' => 'din', 'FAN01G0456' => 'fan', 'FAN02G3001' => 'fan', 'FAN04G2781' => 'fan', 'FAN05G1385' => 'fan', 'FAN05G3062' => 'fan', 'FAN08G2267' => 'fan', 'FAN10G0481' => 'fan', 'FAN10G1257' => 'fan', 'FAN14G0954' => 'fan', 'FAN14G2347' => 'fan', 'FAN15G0187' => 'fan', 'FAN25G2214' => 'fan', 'FvH4_1g21031' => 'fve', 'FvH4_3g16231' => 'fve', 'FvH4_3g26413' => 'fve', 'FvH4_3g29014' => 'fve', 'FvH4_3g31921' => 'fve', 'FvH4_4g19882' => 'fve', 'FvH4_5g21960' => 'fve', 'FvH4_5g29683' => 'fve', 'FvH4_7g13271' => 'fve', 'Glyma.01G062500' => 'gma', 'Glyma.07G140900' => 'gma', 'Glyma.09G140900' => 'gma', 'Glyma.12G112700' => 'gma', 'Glyma.17G168800' => 'gma', 'HanXRQChr01g0027001' => 'han', 'HanXRQChr04g0120511' => 'han', 'HanXRQChr08g0232381' => 'han', 'HanXRQChr09g0265661' => 'han', 'HanXRQChr13g0416031' => 'han', 'Haze_05835' => 'cav', 'Haze_06597' => 'cav', 'Haze_07921' => 'cav', 'Haze_08599' => 'cav', 'Haze_10686' => 'cav', 'Haze_12994' => 'cav', 'Haze_13466' => 'cav', 'Haze_16101' => 'cav', 'Haze_17766' => 'cav', 'Haze_18456' => 'cav', 'Haze_20229' => 'cav', 'Hma1.2p1_0324F.1_g125640' => 'hma', 'Hma1.2p1_0733F.1_g210230' => 'hma', 'Hma1.2p1_0921F.1_g236870' => 'hma', 'Hma1.2p1_1313F.1_g274940' => 'hma', 'Hma1.2p1_3059F.1_g332230' => 'hma', 'Hund15925' => 'sun', 'Hund19562' => 'sun', 'Hund21925' => 'sun', 'MD03G1177400' => 'mdo', 'MD07G1026100' => 'mdo', 'MD17G1218600' => 'mdo', 'Medtr0867s0010' => 'mtr', 'Medtr6g081150' => 'mtr', 'Os01g0527900' => 'osa', 'Os02g0463725' => 'osa', 'Os02g0785600' => 'osa', 'Os03g0433733' => 'osa', 'Os04g0286500' => 'osa', 'Os05g0227800' => 'osa', 'Os06g0521000' => 'osa', 'Os06g0635500' => 'osa', 'Os06g0660650' => 'osa', 'Os07g0554400' => 'osa', 'Os08g0225900' => 'osa', 'Os08g0561000' => 'osa', 'Os09g0241700' => 'osa', 'Os09g0351900' => 'osa', 'Os11g0220700' => 'osa', 'Os11g0282700' => 'osa', 'Os12g0169300' => 'osa', 'Os12g0228500' => 'osa', 'Os12g0543800' => 'osa', 'PGR044G1547' => 'pgr', 'Potri.005G239150' => 'ptr', 'Potri.010G014250' => 'ptr', 'Prupe.1G172500' => 'ppe', 'Prupe.1G196800' => 'ppe', 'Prupe.1G279700' => 'ppe', 'Prupe.2G026400' => 'ppe', 'Prupe.3G094000' => 'ppe', 'Prupe.4G287300' => 'ppe', 'QL01p022166' => 'qlo', 'QL01p051890' => 'qlo', 'QL02p009469' => 'qlo', 'QL02p046053' => 'qlo', 'QL02p057958' => 'qlo', 'QL02p093127' => 'qlo', 'QL03p006855' => 'qlo', 'QL03p071586' => 'qlo', 'QL04p000022' => 'qlo', 'QL04p000024' => 'qlo', 'QL04p003192' => 'qlo', 'QL05p011416' => 'qlo', 'QL06p039590' => 'qlo', 'QL06p052750' => 'qlo', 'QL06p053821' => 'qlo', 'QL07p025287' => 'qlo', 'QL09p033218' => 'qlo', 'QL09p040841' => 'qlo', 'QL10p020337' => 'qlo', 'QL10p027209' => 'qlo', 'QL10p027969' => 'qlo', 'QL10p048988' => 'qlo', 'QL11p001241' => 'qlo', 'QL11p028487' => 'qlo', 'RcHm_v2.0_Chr2g0105031' => 'rch', 'RcHm_v2.0_Chr2g0117811' => 'rch', 'RcHm_v2.0_Chr6g0270241' => 'rch', 'RcHm_v2.0_Chr7g0215961' => 'rch', 'RcHm_v2.0_Chr7g0231991' => 'rch', 'Rhsim01G0041500' => 'rsi', 'Rhsim01G0115000' => 'rsi', 'Rhsim01G0115400' => 'rsi', 'Rhsim01G0133600' => 'rsi', 'Rhsim01G0159900' => 'rsi', 'Rhsim02G0189400' => 'rsi', 'Rhsim03G0135600' => 'rsi', 'Rhsim03G0149900' => 'rsi', 'Rhsim04G0125600' => 'rsi', 'Rhsim05G0091700' => 'rsi', 'Rhsim05G0092900' => 'rsi', 'Rhsim06G0075000' => 'rsi', 'Rhsim07G0066400' => 'rsi', 'Rhsim07G0156400' => 'rsi', 'Rhsim07G0182200' => 'rsi', 'Rhsim07G0182300' => 'rsi', 'Rhsim08G0180400' => 'rsi', 'Rhsim09G0056800' => 'rsi', 'Rhsim10G0153300' => 'rsi', 'Rhsim11G0012700' => 'rsi', 'Rhsim12G0031800' => 'rsi', 'Rhsim12G0055400' => 'rsi', 'Rhsim12G0091400' => 'rsi', 'Rhsim13G0070800' => 'rsi', 'Rhsim13G0193300' => 'rsi', 'RhsimUnG0111600' => 'rsi', 'RhsimUnG0137500' => 'rsi', 'RhsimUnG0172900' => 'rsi', 'SGA_v2.0_scaffold11G05878' => 'sas', 'SGA_v2.0_scaffold167G38458' => 'sas', 'SGA_v2.0_scaffold19G08588' => 'sas', 'SGA_v2.0_scaffold239G43990' => 'sas', 'SGA_v2.0_scaffold260G45865' => 'sas', 'SGA_v2.0_scaffold309G48177' => 'sas', 'SGA_v2.0_scaffold76G25122' => 'sas', 'SGA_v2.0_scaffold85G26708' => 'sas', 'SHI13914' => 'shi', 'SHI30402' => 'shi', 'TWI09G0020' => 'twi', 'TWI09G0456' => 'twi', 'TWI09G1572' => 'twi', 'TWI12G0266' => 'twi', 'TWI12G1451' => 'twi', 'TWI14G0851' => 'twi', 'TWI15G0796' => 'twi', 'TWI18G0820' => 'twi', 'TWI18G1152' => 'twi', 'TWI23G0007' => 'twi', 'TWI23G0314' => 'twi', 'TWI31G0674' => 'twi', 'TWI31G0938' => 'twi', 'TWI34G0641' => 'twi', 'TWI34G1527' => 'twi', 'TWI36G0193' => 'twi', 'TWI36G0405' => 'twi', 'TWI38G0892' => 'twi', 'TWI38G0936' => 'twi', 'TWI38G2218' => 'twi', 'TWI53G0679' => 'twi', 'TWI53G0863' => 'twi', 'TWI53G1133' => 'twi', 'TWI60G0823' => 'twi', 'TWI63G0919' => 'twi', 'TWI63G1436' => 'twi', 'TWI73G0140' => 'twi', 'TWI73G0419' => 'twi', 'TWI73G0420' => 'twi', 'TWI73G1276' => 'twi', 'TWI74G0405' => 'twi', 'TWI74G0837' => 'twi', 'TWI75G0594' => 'twi', 'TWI75G1615' => 'twi', 'TWI77G0816' => 'twi', 'vmacro03831' => 'vma', 'vmacro13746' => 'vma', 'vmacro16089' => 'vma', 'vmacro22863' => 'vma', 'Zm00001eb085790' => 'zma', 'Zm00001eb114250' => 'zma', 'Zm00001eb138070' => 'zma', 'Zm00001eb167560' => 'zma', 'Zm00001eb199990' => 'zma', 'Zm00001eb368180' => 'zma', 'Zm00001eb382470' => 'zma' ) $gf_id = 'HOM05D001576' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001576' ) $data_identifier = 'HOM05D001576' $data_type = 'gf_id' $species_gene_counts = array( 'aox' => (int) 9, 'acertr' => (int) 3, 'cansat' => (int) 1, 'ccl' => (int) 4, 'cil' => (int) 145, 'camsi' => (int) 46, 'dca' => (int) 1, 'din' => (int) 1, 'fan' => (int) 12, 'fve' => (int) 9, 'gma' => (int) 5, 'han' => (int) 5, 'cav' => (int) 11, 'hma' => (int) 5, 'sun' => (int) 3, 'mdo' => (int) 3, 'mtr' => (int) 2, 'osa' => (int) 19, 'pgr' => (int) 1, 'ptr' => (int) 2, 'ppe' => (int) 6, 'qlo' => (int) 24, 'rch' => (int) 5, 'rsi' => (int) 28, 'sas' => (int) 8, 'shi' => (int) 2, 'twi' => (int) 35, 'vma' => (int) 4, 'zma' => (int) 7 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb382470' $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' => 'HOM05D001576', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '406', 'num_species' => '29' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'Aqoxy1G01456' => 'aox', 'Aqoxy1G02949' => 'aox', 'Aqoxy3G01274' => 'aox', 'Aqoxy3G02110' => 'aox', 'Aqoxy3G02268' => 'aox', 'Aqoxy5G02702' => 'aox', 'Aqoxy5G02988' => 'aox', 'Aqoxy5G03427' => 'aox', 'Aqoxy6G02363' => 'aox', 'Atru.chr1.3225' => 'acertr', 'Atru.chr8.1198' => 'acertr', 'Atru.chr9.790' => 'acertr', 'CANSAT01G3197' => 'cansat', 'Ciclev10003979m.g' => 'ccl', 'Ciclev10017471m.g' => 'ccl', 'Ciclev10018206m.g' => 'ccl', 'Ciclev10033751m.g' => 'ccl', 'CiPaw.01G000900' => 'cil', 'CiPaw.01G001000' => 'cil', 'CiPaw.01G033500' => 'cil', 'CiPaw.01G060300' => 'cil', 'CiPaw.01G070200' => 'cil', 'CiPaw.01G075100' => 'cil', 'CiPaw.01G084700' => 'cil', 'CiPaw.01G087900' => 'cil', 'CiPaw.01G092600' => 'cil', 'CiPaw.01G097200' => 'cil', 'CiPaw.01G098300' => 'cil', 'CiPaw.01G110200' => 'cil', 'CiPaw.01G118700' => 'cil', 'CiPaw.01G121200' => 'cil', 'CiPaw.01G132500' => 'cil', 'CiPaw.01G146900' => 'cil', 'CiPaw.01G174000' => 'cil', 'CiPaw.01G179900' => 'cil', 'CiPaw.01G183400' => 'cil', 'CiPaw.01G240000' => 'cil', 'CiPaw.01G283500' => 'cil', 'CiPaw.01G307400' => 'cil', 'CiPaw.02G030800' => 'cil', 'CiPaw.02G047200' => 'cil', 'CiPaw.02G050500' => 'cil', 'CiPaw.02G069900' => 'cil', 'CiPaw.02G091600' => 'cil', 'CiPaw.02G095000' => 'cil', 'CiPaw.02G131900' => 'cil', 'CiPaw.03G043000' => 'cil', 'CiPaw.03G069900' => 'cil', 'CiPaw.03G088100' => 'cil', 'CiPaw.03G089300' => 'cil', 'CiPaw.03G093100' => 'cil', 'CiPaw.03G129800' => 'cil', 'CiPaw.03G131200' => 'cil', 'CiPaw.03G134500' => 'cil', 'CiPaw.03G152100' => 'cil', 'CiPaw.03G162700' => 'cil', 'CiPaw.03G172800' => 'cil', 'CiPaw.03G175800' => 'cil', 'CiPaw.03G181800' => 'cil', 'CiPaw.03G191400' => 'cil', 'CiPaw.03G198300' => 'cil', 'CiPaw.03G201300' => 'cil', 'CiPaw.03G224700' => 'cil', 'CiPaw.03G225000' => 'cil', 'CiPaw.04G065100' => 'cil', 'CiPaw.04G080400' => 'cil', 'CiPaw.04G113500' => 'cil', 'CiPaw.04G121900' => 'cil', 'CiPaw.04G144100' => 'cil', 'CiPaw.04G176500' => 'cil', 'CiPaw.05G086200' => 'cil', 'CiPaw.05G100200' => 'cil', 'CiPaw.05G114200' => 'cil', 'CiPaw.05G126800' => 'cil', 'CiPaw.05G228800' => 'cil', 'CiPaw.05G230600' => 'cil', 'CiPaw.05G236500' => 'cil', 'CiPaw.05G244800' => 'cil', 'CiPaw.06G026600' => 'cil', 'CiPaw.06G027900' => 'cil', 'CiPaw.06G051800' => 'cil', 'CiPaw.06G128500' => 'cil', 'CiPaw.06G165900' => 'cil', 'CiPaw.07G045400' => 'cil', 'CiPaw.07G048000' => 'cil', 'CiPaw.07G052000' => 'cil', 'CiPaw.07G073800' => 'cil', 'CiPaw.07G099700' => 'cil', 'CiPaw.07G108700' => 'cil', 'CiPaw.07G120000' => 'cil', 'CiPaw.07G134100' => 'cil', 'CiPaw.07G147000' => 'cil', 'CiPaw.07G149700' => 'cil', 'CiPaw.07G178300' => 'cil', 'CiPaw.07G184900' => 'cil', 'CiPaw.08G044500' => 'cil', 'CiPaw.08G046900' => 'cil', 'CiPaw.08G047300' => 'cil', 'CiPaw.08G115400' => 'cil', 'CiPaw.08G134700' => 'cil', 'CiPaw.08G157400' => 'cil', 'CiPaw.09G014300' => 'cil', 'CiPaw.09G088900' => 'cil', 'CiPaw.09G130900' => 'cil', 'CiPaw.09G133100' => 'cil', 'CiPaw.09G151300' => 'cil', 'CiPaw.09G172800' => 'cil', 'CiPaw.09G174900' => 'cil', 'CiPaw.09G175000' => 'cil', 'CiPaw.10G012800' => 'cil', 'CiPaw.10G028800' => 'cil', 'CiPaw.10G044700' => 'cil', 'CiPaw.10G067400' => 'cil', 'CiPaw.10G115900' => 'cil', 'CiPaw.10G126200' => 'cil', 'CiPaw.10G139700' => 'cil', 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=> 'qlo', 'QL07p025287' => 'qlo', 'QL09p033218' => 'qlo', 'QL09p040841' => 'qlo', 'QL10p020337' => 'qlo', 'QL10p027209' => 'qlo', 'QL10p027969' => 'qlo', 'QL10p048988' => 'qlo', 'QL11p001241' => 'qlo', 'QL11p028487' => 'qlo', 'RcHm_v2.0_Chr2g0105031' => 'rch', 'RcHm_v2.0_Chr2g0117811' => 'rch', 'RcHm_v2.0_Chr6g0270241' => 'rch', 'RcHm_v2.0_Chr7g0215961' => 'rch', 'RcHm_v2.0_Chr7g0231991' => 'rch', 'Rhsim01G0041500' => 'rsi', 'Rhsim01G0115000' => 'rsi', 'Rhsim01G0115400' => 'rsi', 'Rhsim01G0133600' => 'rsi', 'Rhsim01G0159900' => 'rsi', 'Rhsim02G0189400' => 'rsi', 'Rhsim03G0135600' => 'rsi', 'Rhsim03G0149900' => 'rsi', 'Rhsim04G0125600' => 'rsi', 'Rhsim05G0091700' => 'rsi', 'Rhsim05G0092900' => 'rsi', 'Rhsim06G0075000' => 'rsi', 'Rhsim07G0066400' => 'rsi', 'Rhsim07G0156400' => 'rsi', 'Rhsim07G0182200' => 'rsi', 'Rhsim07G0182300' => 'rsi', 'Rhsim08G0180400' => 'rsi', 'Rhsim09G0056800' => 'rsi', 'Rhsim10G0153300' => 'rsi', 'Rhsim11G0012700' => 'rsi', 'Rhsim12G0031800' => 'rsi', 'Rhsim12G0055400' => 'rsi', 'Rhsim12G0091400' => 'rsi', 'Rhsim13G0070800' => 'rsi', 'Rhsim13G0193300' => 'rsi', 'RhsimUnG0111600' => 'rsi', 'RhsimUnG0137500' => 'rsi', 'RhsimUnG0172900' => 'rsi', 'SGA_v2.0_scaffold11G05878' => 'sas', 'SGA_v2.0_scaffold167G38458' => 'sas', 'SGA_v2.0_scaffold19G08588' => 'sas', 'SGA_v2.0_scaffold239G43990' => 'sas', 'SGA_v2.0_scaffold260G45865' => 'sas', 'SGA_v2.0_scaffold309G48177' => 'sas', 'SGA_v2.0_scaffold76G25122' => 'sas', 'SGA_v2.0_scaffold85G26708' => 'sas', 'SHI13914' => 'shi', 'SHI30402' => 'shi', 'TWI09G0020' => 'twi', 'TWI09G0456' => 'twi', 'TWI09G1572' => 'twi', 'TWI12G0266' => 'twi', 'TWI12G1451' => 'twi', 'TWI14G0851' => 'twi', 'TWI15G0796' => 'twi', 'TWI18G0820' => 'twi', 'TWI18G1152' => 'twi', 'TWI23G0007' => 'twi', 'TWI23G0314' => 'twi', 'TWI31G0674' => 'twi', 'TWI31G0938' => 'twi', 'TWI34G0641' => 'twi', 'TWI34G1527' => 'twi', 'TWI36G0193' => 'twi', 'TWI36G0405' => 'twi', 'TWI38G0892' => 'twi', 'TWI38G0936' => 'twi', 'TWI38G2218' => 'twi', 'TWI53G0679' => 'twi', 'TWI53G0863' => 'twi', 'TWI53G1133' => 'twi', 'TWI60G0823' => 'twi', 'TWI63G0919' => 'twi', 'TWI63G1436' => 'twi', 'TWI73G0140' => 'twi', 'TWI73G0419' => 'twi', 'TWI73G0420' => 'twi', 'TWI73G1276' => 'twi', 'TWI74G0405' => 'twi', 'TWI74G0837' => 'twi', 'TWI75G0594' => 'twi', 'TWI75G1615' => 'twi', 'TWI77G0816' => 'twi', 'vmacro03831' => 'vma', 'vmacro13746' => 'vma', 'vmacro16089' => 'vma', 'vmacro22863' => 'vma', 'Zm00001eb085790' => 'zma', 'Zm00001eb114250' => 'zma', 'Zm00001eb138070' => 'zma', 'Zm00001eb167560' => 'zma', 'Zm00001eb199990' => 'zma', 'Zm00001eb368180' => 'zma', 'Zm00001eb382470' => 'zma' ), 'gf_id' => 'HOM05D001576', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001576' ), 'data_identifier' => 'HOM05D001576', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001576', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '406', 'num_species' => '29' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'Aqoxy1G01456' => 'aox', 'Aqoxy1G02949' => 'aox', 'Aqoxy3G01274' => 'aox', 'Aqoxy3G02110' => 'aox', 'Aqoxy3G02268' => 'aox', 'Aqoxy5G02702' => 'aox', 'Aqoxy5G02988' => 'aox', 'Aqoxy5G03427' => 'aox', 'Aqoxy6G02363' => 'aox', 'Atru.chr1.3225' => 'acertr', 'Atru.chr8.1198' => 'acertr', 'Atru.chr9.790' => 'acertr', 'CANSAT01G3197' => 'cansat', 'Ciclev10003979m.g' => 'ccl', 'Ciclev10017471m.g' => 'ccl', 'Ciclev10018206m.g' => 'ccl', 'Ciclev10033751m.g' => 'ccl', 'CiPaw.01G000900' => 'cil', 'CiPaw.01G001000' => 'cil', 'CiPaw.01G033500' => 'cil', 'CiPaw.01G060300' => 'cil', 'CiPaw.01G070200' => 'cil', 'CiPaw.01G075100' => 'cil', 'CiPaw.01G084700' => 'cil', 'CiPaw.01G087900' => 'cil', 'CiPaw.01G092600' => 'cil', 'CiPaw.01G097200' => 'cil', 'CiPaw.01G098300' => 'cil', 'CiPaw.01G110200' => 'cil', 'CiPaw.01G118700' => 'cil', 'CiPaw.01G121200' => 'cil', 'CiPaw.01G132500' => 'cil', 'CiPaw.01G146900' => 'cil', 'CiPaw.01G174000' => 'cil', 'CiPaw.01G179900' => 'cil', 'CiPaw.01G183400' => 'cil', 'CiPaw.01G240000' => 'cil', 'CiPaw.01G283500' => 'cil', 'CiPaw.01G307400' => 'cil', 'CiPaw.02G030800' => 'cil', 'CiPaw.02G047200' => 'cil', 'CiPaw.02G050500' => 'cil', 'CiPaw.02G069900' => 'cil', 'CiPaw.02G091600' => 'cil', 'CiPaw.02G095000' => 'cil', 'CiPaw.02G131900' => 'cil', 'CiPaw.03G043000' => 'cil', 'CiPaw.03G069900' => 'cil', 'CiPaw.03G088100' => 'cil', 'CiPaw.03G089300' => 'cil', 'CiPaw.03G093100' => 'cil', 'CiPaw.03G129800' => 'cil', 'CiPaw.03G131200' => 'cil', 'CiPaw.03G134500' => 'cil', 'CiPaw.03G152100' => 'cil', 'CiPaw.03G162700' => 'cil', 'CiPaw.03G172800' => 'cil', 'CiPaw.03G175800' => 'cil', 'CiPaw.03G181800' => 'cil', 'CiPaw.03G191400' => 'cil', 'CiPaw.03G198300' => 'cil', 'CiPaw.03G201300' => 'cil', 'CiPaw.03G224700' => 'cil', 'CiPaw.03G225000' => 'cil', 'CiPaw.04G065100' => 'cil', 'CiPaw.04G080400' => 'cil', 'CiPaw.04G113500' => 'cil', 'CiPaw.04G121900' => 'cil', 'CiPaw.04G144100' => 'cil', 'CiPaw.04G176500' => 'cil', 'CiPaw.05G086200' => 'cil', 'CiPaw.05G100200' => 'cil', 'CiPaw.05G114200' => 'cil', 'CiPaw.05G126800' => 'cil', 'CiPaw.05G228800' => 'cil', 'CiPaw.05G230600' => 'cil', 'CiPaw.05G236500' => 'cil', 'CiPaw.05G244800' => 'cil', 'CiPaw.06G026600' => 'cil', 'CiPaw.06G027900' => 'cil', 'CiPaw.06G051800' => 'cil', 'CiPaw.06G128500' => 'cil', 'CiPaw.06G165900' => 'cil', 'CiPaw.07G045400' => 'cil', 'CiPaw.07G048000' => 'cil', 'CiPaw.07G052000' => 'cil', 'CiPaw.07G073800' => 'cil', 'CiPaw.07G099700' => 'cil', 'CiPaw.07G108700' => 'cil', 'CiPaw.07G120000' => 'cil', 'CiPaw.07G134100' => 'cil', 'CiPaw.07G147000' => 'cil', 'CiPaw.07G149700' => 'cil', 'CiPaw.07G178300' => 'cil', 'CiPaw.07G184900' => 'cil', 'CiPaw.08G044500' => 'cil', 'CiPaw.08G046900' => 'cil', 'CiPaw.08G047300' => 'cil', 'CiPaw.08G115400' => 'cil', 'CiPaw.08G134700' => 'cil', 'CiPaw.08G157400' => 'cil', 'CiPaw.09G014300' => 'cil', 'CiPaw.09G088900' => 'cil', 'CiPaw.09G130900' => 'cil', 'CiPaw.09G133100' => 'cil', 'CiPaw.09G151300' => 'cil', 'CiPaw.09G172800' => 'cil', 'CiPaw.09G174900' => 'cil', 'CiPaw.09G175000' => 'cil', 'CiPaw.10G012800' => 'cil', 'CiPaw.10G028800' => 'cil', 'CiPaw.10G044700' => 'cil', 'CiPaw.10G067400' => 'cil', 'CiPaw.10G115900' => 'cil', 'CiPaw.10G126200' => 'cil', 'CiPaw.10G139700' => 'cil', 'CiPaw.10G155100' => 'cil', 'CiPaw.11G011300' => 'cil', 'CiPaw.11G025900' => 'cil', 'CiPaw.11G104100' => 'cil', 'CiPaw.11G142700' => 'cil', 'CiPaw.11G164500' => 'cil', 'CiPaw.11G189100' => 'cil', 'CiPaw.11G197100' => 'cil', 'CiPaw.12G006100' => 'cil', 'CiPaw.12G038500' => 'cil', 'CiPaw.12G041400' => 'cil', 'CiPaw.12G041600' => 'cil', 'CiPaw.12G051300' => 'cil', 'CiPaw.12G101800' => 'cil', 'CiPaw.12G107800' => 'cil', 'CiPaw.13G033200' => 'cil', 'CiPaw.13G129900' => 'cil', 'CiPaw.13G160200' => 'cil', 'CiPaw.14G018900' => 'cil', 'CiPaw.14G029000' => 'cil', 'CiPaw.14G031000' => 'cil', 'CiPaw.14G032000' => 'cil', 'CiPaw.14G032300' => 'cil', 'CiPaw.14G040600' => 'cil', 'CiPaw.14G060500' => 'cil', 'CiPaw.14G061500' => 'cil', 'CiPaw.14G077500' => 'cil', 'CiPaw.14G088300' => 'cil', 'CiPaw.14G108500' => 'cil', 'CiPaw.14G121300' => 'cil', 'CiPaw.14G133000' => 'cil', 'CiPaw.14G134600' => 'cil', 'CiPaw.15G027200' => 'cil', 'CiPaw.15G037700' => 'cil', 'CiPaw.15G050900' => 'cil', 'CiPaw.15G067200' => 'cil', 'CiPaw.15G072000' => 'cil', 'CiPaw.15G112900' => 'cil', 'CiPaw.15G133200' => 'cil', 'CiPaw.15G139500' => 'cil', 'CiPaw.15G155400' => 'cil', 'CiPaw.16G006000' => 'cil', 'CiPaw.16G013100' => 'cil', 'CiPaw.16G047100' => 'cil', 'CiPaw.16G048900' => 'cil', 'CiPaw.16G070300' => 'cil', 'CSS0000195' => 'camsi', 'CSS0001664' => 'camsi', 'CSS0002566' => 'camsi', 'CSS0003077' => 'camsi', 'CSS0004257' => 'camsi', 'CSS0004495' => 'camsi', 'CSS0004599' => 'camsi', 'CSS0004943' => 'camsi', 'CSS0005302' => 'camsi', 'CSS0006274' => 'camsi', 'CSS0006547' => 'camsi', 'CSS0006860' => 'camsi', 'CSS0008814' => 'camsi', 'CSS0008946' => 'camsi', 'CSS0009093' => 'camsi', 'CSS0010221' => 'camsi', 'CSS0010296' => 'camsi', 'CSS0010386' => 'camsi', 'CSS0010831' => 'camsi', 'CSS0011061' => 'camsi', 'CSS0012008' => 'camsi', 'CSS0012194' => 'camsi', 'CSS0013580' => 'camsi', 'CSS0014176' => 'camsi', 'CSS0014280' => 'camsi', 'CSS0014799' => 'camsi', 'CSS0015368' => 'camsi', 'CSS0017473' => 'camsi', 'CSS0019281' => 'camsi', 'CSS0021320' => 'camsi', 'CSS0021750' => 'camsi', 'CSS0023642' => 'camsi', 'CSS0023792' => 'camsi', 'CSS0031528' => 'camsi', 'CSS0033894' => 'camsi', 'CSS0034959' => 'camsi', 'CSS0035632' => 'camsi', 'CSS0038450' => 'camsi', 'CSS0039293' => 'camsi', 'CSS0041053' => 'camsi', 'CSS0041981' => 'camsi', 'CSS0042573' => 'camsi', 'CSS0042927' => 'camsi', 'CSS0047725' => 'camsi', 'CSS0049636' => 'camsi', 'CSS0050513' => 'camsi', 'DCAR_030203' => 'dca', 'Dinv07939' => 'din', 'FAN01G0456' => 'fan', 'FAN02G3001' => 'fan', 'FAN04G2781' => 'fan', 'FAN05G1385' => 'fan', 'FAN05G3062' => 'fan', 'FAN08G2267' => 'fan', 'FAN10G0481' => 'fan', 'FAN10G1257' => 'fan', 'FAN14G0954' => 'fan', 'FAN14G2347' => 'fan', 'FAN15G0187' => 'fan', 'FAN25G2214' => 'fan', 'FvH4_1g21031' => 'fve', 'FvH4_3g16231' => 'fve', 'FvH4_3g26413' => 'fve', 'FvH4_3g29014' => 'fve', 'FvH4_3g31921' => 'fve', 'FvH4_4g19882' => 'fve', 'FvH4_5g21960' => 'fve', 'FvH4_5g29683' => 'fve', 'FvH4_7g13271' => 'fve', 'Glyma.01G062500' => 'gma', 'Glyma.07G140900' => 'gma', 'Glyma.09G140900' => 'gma', 'Glyma.12G112700' => 'gma', 'Glyma.17G168800' => 'gma', 'HanXRQChr01g0027001' => 'han', 'HanXRQChr04g0120511' => 'han', 'HanXRQChr08g0232381' => 'han', 'HanXRQChr09g0265661' => 'han', 'HanXRQChr13g0416031' => 'han', 'Haze_05835' => 'cav', 'Haze_06597' => 'cav', 'Haze_07921' => 'cav', 'Haze_08599' => 'cav', 'Haze_10686' => 'cav', 'Haze_12994' => 'cav', 'Haze_13466' => 'cav', 'Haze_16101' => 'cav', 'Haze_17766' => 'cav', 'Haze_18456' => 'cav', 'Haze_20229' => 'cav', 'Hma1.2p1_0324F.1_g125640' => 'hma', 'Hma1.2p1_0733F.1_g210230' => 'hma', 'Hma1.2p1_0921F.1_g236870' => 'hma', 'Hma1.2p1_1313F.1_g274940' => 'hma', 'Hma1.2p1_3059F.1_g332230' => 'hma', 'Hund15925' => 'sun', 'Hund19562' => 'sun', 'Hund21925' => 'sun', 'MD03G1177400' => 'mdo', 'MD07G1026100' => 'mdo', 'MD17G1218600' => 'mdo', 'Medtr0867s0010' => 'mtr', 'Medtr6g081150' => 'mtr', 'Os01g0527900' => 'osa', 'Os02g0463725' => 'osa', 'Os02g0785600' => 'osa', 'Os03g0433733' => 'osa', 'Os04g0286500' => 'osa', 'Os05g0227800' => 'osa', 'Os06g0521000' => 'osa', 'Os06g0635500' => 'osa', 'Os06g0660650' => 'osa', 'Os07g0554400' => 'osa', 'Os08g0225900' => 'osa', 'Os08g0561000' => 'osa', 'Os09g0241700' => 'osa', 'Os09g0351900' => 'osa', 'Os11g0220700' => 'osa', 'Os11g0282700' => 'osa', 'Os12g0169300' => 'osa', 'Os12g0228500' => 'osa', 'Os12g0543800' => 'osa', 'PGR044G1547' => 'pgr', 'Potri.005G239150' => 'ptr', 'Potri.010G014250' => 'ptr', 'Prupe.1G172500' => 'ppe', 'Prupe.1G196800' => 'ppe', 'Prupe.1G279700' => 'ppe', 'Prupe.2G026400' => 'ppe', 'Prupe.3G094000' => 'ppe', 'Prupe.4G287300' => 'ppe', 'QL01p022166' => 'qlo', 'QL01p051890' => 'qlo', 'QL02p009469' => 'qlo', 'QL02p046053' => 'qlo', 'QL02p057958' => 'qlo', 'QL02p093127' => 'qlo', 'QL03p006855' => 'qlo', 'QL03p071586' => 'qlo', 'QL04p000022' => 'qlo', 'QL04p000024' => 'qlo', 'QL04p003192' => 'qlo', 'QL05p011416' => 'qlo', 'QL06p039590' => 'qlo', 'QL06p052750' => 'qlo', 'QL06p053821' => 'qlo', 'QL07p025287' => 'qlo', 'QL09p033218' => 'qlo', 'QL09p040841' => 'qlo', 'QL10p020337' => 'qlo', 'QL10p027209' => 'qlo', 'QL10p027969' => 'qlo', 'QL10p048988' => 'qlo', 'QL11p001241' => 'qlo', 'QL11p028487' => 'qlo', 'RcHm_v2.0_Chr2g0105031' => 'rch', 'RcHm_v2.0_Chr2g0117811' => 'rch', 'RcHm_v2.0_Chr6g0270241' => 'rch', 'RcHm_v2.0_Chr7g0215961' => 'rch', 'RcHm_v2.0_Chr7g0231991' => 'rch', 'Rhsim01G0041500' => 'rsi', 'Rhsim01G0115000' => 'rsi', 'Rhsim01G0115400' => 'rsi', 'Rhsim01G0133600' => 'rsi', 'Rhsim01G0159900' => 'rsi', 'Rhsim02G0189400' => 'rsi', 'Rhsim03G0135600' => 'rsi', 'Rhsim03G0149900' => 'rsi', 'Rhsim04G0125600' => 'rsi', 'Rhsim05G0091700' => 'rsi', 'Rhsim05G0092900' => 'rsi', 'Rhsim06G0075000' => 'rsi', 'Rhsim07G0066400' => 'rsi', 'Rhsim07G0156400' => 'rsi', 'Rhsim07G0182200' => 'rsi', 'Rhsim07G0182300' => 'rsi', 'Rhsim08G0180400' => 'rsi', 'Rhsim09G0056800' => 'rsi', 'Rhsim10G0153300' => 'rsi', 'Rhsim11G0012700' => 'rsi', 'Rhsim12G0031800' => 'rsi', 'Rhsim12G0055400' => 'rsi', 'Rhsim12G0091400' => 'rsi', 'Rhsim13G0070800' => 'rsi', 'Rhsim13G0193300' => 'rsi', 'RhsimUnG0111600' => 'rsi', 'RhsimUnG0137500' => 'rsi', 'RhsimUnG0172900' => 'rsi', 'SGA_v2.0_scaffold11G05878' => 'sas', 'SGA_v2.0_scaffold167G38458' => 'sas', 'SGA_v2.0_scaffold19G08588' => 'sas', 'SGA_v2.0_scaffold239G43990' => 'sas', 'SGA_v2.0_scaffold260G45865' => 'sas', 'SGA_v2.0_scaffold309G48177' => 'sas', 'SGA_v2.0_scaffold76G25122' => 'sas', 'SGA_v2.0_scaffold85G26708' => 'sas', 'SHI13914' => 'shi', 'SHI30402' => 'shi', 'TWI09G0020' => 'twi', 'TWI09G0456' => 'twi', 'TWI09G1572' => 'twi', 'TWI12G0266' => 'twi', 'TWI12G1451' => 'twi', 'TWI14G0851' => 'twi', 'TWI15G0796' => 'twi', 'TWI18G0820' => 'twi', 'TWI18G1152' => 'twi', 'TWI23G0007' => 'twi', 'TWI23G0314' => 'twi', 'TWI31G0674' => 'twi', 'TWI31G0938' => 'twi', 'TWI34G0641' => 'twi', 'TWI34G1527' => 'twi', 'TWI36G0193' => 'twi', 'TWI36G0405' => 'twi', 'TWI38G0892' => 'twi', 'TWI38G0936' => 'twi', 'TWI38G2218' => 'twi', 'TWI53G0679' => 'twi', 'TWI53G0863' => 'twi', 'TWI53G1133' => 'twi', 'TWI60G0823' => 'twi', 'TWI63G0919' => 'twi', 'TWI63G1436' => 'twi', 'TWI73G0140' => 'twi', 'TWI73G0419' => 'twi', 'TWI73G0420' => 'twi', 'TWI73G1276' => 'twi', 'TWI74G0405' => 'twi', 'TWI74G0837' => 'twi', 'TWI75G0594' => 'twi', 'TWI75G1615' => 'twi', 'TWI77G0816' => 'twi', 'vmacro03831' => 'vma', 'vmacro13746' => 'vma', 'vmacro16089' => 'vma', 'vmacro22863' => 'vma', 'Zm00001eb085790' => 'zma', 'Zm00001eb114250' => 'zma', 'Zm00001eb138070' => 'zma', 'Zm00001eb167560' => 'zma', 'Zm00001eb199990' => 'zma', 'Zm00001eb368180' => 'zma', 'Zm00001eb382470' => 'zma' ) $gf_id = 'HOM05D001576' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001576' ) $data_identifier = 'HOM05D001576' $data_type = 'gf_id' $species_gene_counts = array( 'aox' => (int) 9, 'acertr' => (int) 3, 'cansat' => (int) 1, 'ccl' => (int) 4, 'cil' => (int) 145, 'camsi' => (int) 46, 'dca' => (int) 1, 'din' => (int) 1, 'fan' => (int) 12, 'fve' => (int) 9, 'gma' => (int) 5, 'han' => (int) 5, 'cav' => (int) 11, 'hma' => (int) 5, 'sun' => (int) 3, 'mdo' => (int) 3, 'mtr' => (int) 2, 'osa' => (int) 19, 'pgr' => (int) 1, 'ptr' => (int) 2, 'ppe' => (int) 6, 'qlo' => (int) 24, 'rch' => (int) 5, 'rsi' => (int) 28, 'sas' => (int) 8, 'shi' => (int) 2, 'twi' => (int) 35, 'vma' => (int) 4, 'zma' => (int) 7 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb382470' $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' => 'HOM05D001576', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '406', 'num_species' => '29' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'Aqoxy1G01456' => 'aox', 'Aqoxy1G02949' => 'aox', 'Aqoxy3G01274' => 'aox', 'Aqoxy3G02110' => 'aox', 'Aqoxy3G02268' => 'aox', 'Aqoxy5G02702' => 'aox', 'Aqoxy5G02988' => 'aox', 'Aqoxy5G03427' => 'aox', 'Aqoxy6G02363' => 'aox', 'Atru.chr1.3225' => 'acertr', 'Atru.chr8.1198' => 'acertr', 'Atru.chr9.790' => 'acertr', 'CANSAT01G3197' => 'cansat', 'Ciclev10003979m.g' => 'ccl', 'Ciclev10017471m.g' => 'ccl', 'Ciclev10018206m.g' => 'ccl', 'Ciclev10033751m.g' => 'ccl', 'CiPaw.01G000900' => 'cil', 'CiPaw.01G001000' => 'cil', 'CiPaw.01G033500' => 'cil', 'CiPaw.01G060300' => 'cil', 'CiPaw.01G070200' => 'cil', 'CiPaw.01G075100' => 'cil', 'CiPaw.01G084700' => 'cil', 'CiPaw.01G087900' => 'cil', 'CiPaw.01G092600' => 'cil', 'CiPaw.01G097200' => 'cil', 'CiPaw.01G098300' => 'cil', 'CiPaw.01G110200' => 'cil', 'CiPaw.01G118700' => 'cil', 'CiPaw.01G121200' => 'cil', 'CiPaw.01G132500' => 'cil', 'CiPaw.01G146900' => 'cil', 'CiPaw.01G174000' => 'cil', 'CiPaw.01G179900' => 'cil', 'CiPaw.01G183400' => 'cil', 'CiPaw.01G240000' => 'cil', 'CiPaw.01G283500' => 'cil', 'CiPaw.01G307400' => 'cil', 'CiPaw.02G030800' => 'cil', 'CiPaw.02G047200' => 'cil', 'CiPaw.02G050500' => 'cil', 'CiPaw.02G069900' => 'cil', 'CiPaw.02G091600' => 'cil', 'CiPaw.02G095000' => 'cil', 'CiPaw.02G131900' => 'cil', 'CiPaw.03G043000' => 'cil', 'CiPaw.03G069900' => 'cil', 'CiPaw.03G088100' => 'cil', 'CiPaw.03G089300' => 'cil', 'CiPaw.03G093100' => 'cil', 'CiPaw.03G129800' => 'cil', 'CiPaw.03G131200' => 'cil', 'CiPaw.03G134500' => 'cil', 'CiPaw.03G152100' => 'cil', 'CiPaw.03G162700' => 'cil', 'CiPaw.03G172800' => 'cil', 'CiPaw.03G175800' => 'cil', 'CiPaw.03G181800' => 'cil', 'CiPaw.03G191400' => 'cil', 'CiPaw.03G198300' => 'cil', 'CiPaw.03G201300' => 'cil', 'CiPaw.03G224700' => 'cil', 'CiPaw.03G225000' => 'cil', 'CiPaw.04G065100' => 'cil', 'CiPaw.04G080400' => 'cil', 'CiPaw.04G113500' => 'cil', 'CiPaw.04G121900' => 'cil', 'CiPaw.04G144100' => 'cil', 'CiPaw.04G176500' => 'cil', 'CiPaw.05G086200' => 'cil', 'CiPaw.05G100200' => 'cil', 'CiPaw.05G114200' => 'cil', 'CiPaw.05G126800' => 'cil', 'CiPaw.05G228800' => 'cil', 'CiPaw.05G230600' => 'cil', 'CiPaw.05G236500' => 'cil', 'CiPaw.05G244800' => 'cil', 'CiPaw.06G026600' => 'cil', 'CiPaw.06G027900' => 'cil', 'CiPaw.06G051800' => 'cil', 'CiPaw.06G128500' => 'cil', 'CiPaw.06G165900' => 'cil', 'CiPaw.07G045400' => 'cil', 'CiPaw.07G048000' => 'cil', 'CiPaw.07G052000' => 'cil', 'CiPaw.07G073800' => 'cil', 'CiPaw.07G099700' => 'cil', 'CiPaw.07G108700' => 'cil', 'CiPaw.07G120000' => 'cil', 'CiPaw.07G134100' => 'cil', 'CiPaw.07G147000' => 'cil', 'CiPaw.07G149700' => 'cil', 'CiPaw.07G178300' => 'cil', 'CiPaw.07G184900' => 'cil', 'CiPaw.08G044500' => 'cil', 'CiPaw.08G046900' => 'cil', 'CiPaw.08G047300' => 'cil', 'CiPaw.08G115400' => 'cil', 'CiPaw.08G134700' => 'cil', 'CiPaw.08G157400' => 'cil', 'CiPaw.09G014300' => 'cil', 'CiPaw.09G088900' => 'cil', 'CiPaw.09G130900' => 'cil', 'CiPaw.09G133100' => 'cil', 'CiPaw.09G151300' => 'cil', 'CiPaw.09G172800' => 'cil', 'CiPaw.09G174900' => 'cil', 'CiPaw.09G175000' => 'cil', 'CiPaw.10G012800' => 'cil', 'CiPaw.10G028800' => 'cil', 'CiPaw.10G044700' => 'cil', 'CiPaw.10G067400' => 'cil', 'CiPaw.10G115900' => 'cil', 'CiPaw.10G126200' => 'cil', 'CiPaw.10G139700' => 'cil', 'CiPaw.10G155100' => 'cil', 'CiPaw.11G011300' => 'cil', 'CiPaw.11G025900' => 'cil', 'CiPaw.11G104100' => 'cil', 'CiPaw.11G142700' => 'cil', 'CiPaw.11G164500' => 'cil', 'CiPaw.11G189100' => 'cil', 'CiPaw.11G197100' => 'cil', 'CiPaw.12G006100' => 'cil', 'CiPaw.12G038500' => 'cil', 'CiPaw.12G041400' => 'cil', 'CiPaw.12G041600' => 'cil', 'CiPaw.12G051300' => 'cil', 'CiPaw.12G101800' => 'cil', 'CiPaw.12G107800' => 'cil', 'CiPaw.13G033200' => 'cil', 'CiPaw.13G129900' => 'cil', 'CiPaw.13G160200' => 'cil', 'CiPaw.14G018900' => 'cil', 'CiPaw.14G029000' => 'cil', 'CiPaw.14G031000' => 'cil', 'CiPaw.14G032000' => 'cil', 'CiPaw.14G032300' => 'cil', 'CiPaw.14G040600' => 'cil', 'CiPaw.14G060500' => 'cil', 'CiPaw.14G061500' => 'cil', 'CiPaw.14G077500' => 'cil', 'CiPaw.14G088300' => 'cil', 'CiPaw.14G108500' => 'cil', 'CiPaw.14G121300' => 'cil', 'CiPaw.14G133000' => 'cil', 'CiPaw.14G134600' => 'cil', 'CiPaw.15G027200' => 'cil', 'CiPaw.15G037700' => 'cil', 'CiPaw.15G050900' => 'cil', 'CiPaw.15G067200' => 'cil', 'CiPaw.15G072000' => 'cil', 'CiPaw.15G112900' => 'cil', 'CiPaw.15G133200' => 'cil', 'CiPaw.15G139500' => 'cil', 'CiPaw.15G155400' => 'cil', 'CiPaw.16G006000' => 'cil', 'CiPaw.16G013100' => 'cil', 'CiPaw.16G047100' => 'cil', 'CiPaw.16G048900' => 'cil', 'CiPaw.16G070300' => 'cil', 'CSS0000195' => 'camsi', 'CSS0001664' => 'camsi', 'CSS0002566' => 'camsi', 'CSS0003077' => 'camsi', 'CSS0004257' => 'camsi', 'CSS0004495' => 'camsi', 'CSS0004599' => 'camsi', 'CSS0004943' => 'camsi', 'CSS0005302' => 'camsi', 'CSS0006274' => 'camsi', 'CSS0006547' => 'camsi', 'CSS0006860' => 'camsi', 'CSS0008814' => 'camsi', 'CSS0008946' => 'camsi', 'CSS0009093' => 'camsi', 'CSS0010221' => 'camsi', 'CSS0010296' => 'camsi', 'CSS0010386' => 'camsi', 'CSS0010831' => 'camsi', 'CSS0011061' => 'camsi', 'CSS0012008' => 'camsi', 'CSS0012194' => 'camsi', 'CSS0013580' => 'camsi', 'CSS0014176' => 'camsi', 'CSS0014280' => 'camsi', 'CSS0014799' => 'camsi', 'CSS0015368' => 'camsi', 'CSS0017473' => 'camsi', 'CSS0019281' => 'camsi', 'CSS0021320' => 'camsi', 'CSS0021750' => 'camsi', 'CSS0023642' => 'camsi', 'CSS0023792' => 'camsi', 'CSS0031528' => 'camsi', 'CSS0033894' => 'camsi', 'CSS0034959' => 'camsi', 'CSS0035632' => 'camsi', 'CSS0038450' => 'camsi', 'CSS0039293' => 'camsi', 'CSS0041053' => 'camsi', 'CSS0041981' => 'camsi', 'CSS0042573' => 'camsi', 'CSS0042927' => 'camsi', 'CSS0047725' => 'camsi', 'CSS0049636' => 'camsi', 'CSS0050513' => 'camsi', 'DCAR_030203' => 'dca', 'Dinv07939' => 'din', 'FAN01G0456' => 'fan', 'FAN02G3001' => 'fan', 'FAN04G2781' => 'fan', 'FAN05G1385' => 'fan', 'FAN05G3062' => 'fan', 'FAN08G2267' => 'fan', 'FAN10G0481' => 'fan', 'FAN10G1257' => 'fan', 'FAN14G0954' => 'fan', 'FAN14G2347' => 'fan', 'FAN15G0187' => 'fan', 'FAN25G2214' => 'fan', 'FvH4_1g21031' => 'fve', 'FvH4_3g16231' => 'fve', 'FvH4_3g26413' => 'fve', 'FvH4_3g29014' => 'fve', 'FvH4_3g31921' => 'fve', 'FvH4_4g19882' => 'fve', 'FvH4_5g21960' => 'fve', 'FvH4_5g29683' => 'fve', 'FvH4_7g13271' => 'fve', 'Glyma.01G062500' => 'gma', 'Glyma.07G140900' => 'gma', 'Glyma.09G140900' => 'gma', 'Glyma.12G112700' => 'gma', 'Glyma.17G168800' => 'gma', 'HanXRQChr01g0027001' => 'han', 'HanXRQChr04g0120511' => 'han', 'HanXRQChr08g0232381' => 'han', 'HanXRQChr09g0265661' => 'han', 'HanXRQChr13g0416031' => 'han', 'Haze_05835' => 'cav', 'Haze_06597' => 'cav', 'Haze_07921' => 'cav', 'Haze_08599' => 'cav', 'Haze_10686' => 'cav', 'Haze_12994' => 'cav', 'Haze_13466' => 'cav', 'Haze_16101' => 'cav', 'Haze_17766' => 'cav', 'Haze_18456' => 'cav', 'Haze_20229' => 'cav', 'Hma1.2p1_0324F.1_g125640' => 'hma', 'Hma1.2p1_0733F.1_g210230' => 'hma', 'Hma1.2p1_0921F.1_g236870' => 'hma', 'Hma1.2p1_1313F.1_g274940' => 'hma', 'Hma1.2p1_3059F.1_g332230' => 'hma', 'Hund15925' => 'sun', 'Hund19562' => 'sun', 'Hund21925' => 'sun', 'MD03G1177400' => 'mdo', 'MD07G1026100' => 'mdo', 'MD17G1218600' => 'mdo', 'Medtr0867s0010' => 'mtr', 'Medtr6g081150' => 'mtr', 'Os01g0527900' => 'osa', 'Os02g0463725' => 'osa', 'Os02g0785600' => 'osa', 'Os03g0433733' => 'osa', 'Os04g0286500' => 'osa', 'Os05g0227800' => 'osa', 'Os06g0521000' => 'osa', 'Os06g0635500' => 'osa', 'Os06g0660650' => 'osa', 'Os07g0554400' => 'osa', 'Os08g0225900' => 'osa', 'Os08g0561000' => 'osa', 'Os09g0241700' => 'osa', 'Os09g0351900' => 'osa', 'Os11g0220700' => 'osa', 'Os11g0282700' => 'osa', 'Os12g0169300' => 'osa', 'Os12g0228500' => 'osa', 'Os12g0543800' => 'osa', 'PGR044G1547' => 'pgr', 'Potri.005G239150' => 'ptr', 'Potri.010G014250' => 'ptr', 'Prupe.1G172500' => 'ppe', 'Prupe.1G196800' => 'ppe', 'Prupe.1G279700' => 'ppe', 'Prupe.2G026400' => 'ppe', 'Prupe.3G094000' => 'ppe', 'Prupe.4G287300' => 'ppe', 'QL01p022166' => 'qlo', 'QL01p051890' => 'qlo', 'QL02p009469' => 'qlo', 'QL02p046053' => 'qlo', 'QL02p057958' => 'qlo', 'QL02p093127' => 'qlo', 'QL03p006855' => 'qlo', 'QL03p071586' => 'qlo', 'QL04p000022' => 'qlo', 'QL04p000024' => 'qlo', 'QL04p003192' => 'qlo', 'QL05p011416' => 'qlo', 'QL06p039590' => 'qlo', 'QL06p052750' => 'qlo', 'QL06p053821' => 'qlo', 'QL07p025287' => 'qlo', 'QL09p033218' => 'qlo', 'QL09p040841' => 'qlo', 'QL10p020337' => 'qlo', 'QL10p027209' => 'qlo', 'QL10p027969' => 'qlo', 'QL10p048988' => 'qlo', 'QL11p001241' => 'qlo', 'QL11p028487' => 'qlo', 'RcHm_v2.0_Chr2g0105031' => 'rch', 'RcHm_v2.0_Chr2g0117811' => 'rch', 'RcHm_v2.0_Chr6g0270241' => 'rch', 'RcHm_v2.0_Chr7g0215961' => 'rch', 'RcHm_v2.0_Chr7g0231991' => 'rch', 'Rhsim01G0041500' => 'rsi', 'Rhsim01G0115000' => 'rsi', 'Rhsim01G0115400' => 'rsi', 'Rhsim01G0133600' => 'rsi', 'Rhsim01G0159900' => 'rsi', 'Rhsim02G0189400' => 'rsi', 'Rhsim03G0135600' => 'rsi', 'Rhsim03G0149900' => 'rsi', 'Rhsim04G0125600' => 'rsi', 'Rhsim05G0091700' => 'rsi', 'Rhsim05G0092900' => 'rsi', 'Rhsim06G0075000' => 'rsi', 'Rhsim07G0066400' => 'rsi', 'Rhsim07G0156400' => 'rsi', 'Rhsim07G0182200' => 'rsi', 'Rhsim07G0182300' => 'rsi', 'Rhsim08G0180400' => 'rsi', 'Rhsim09G0056800' => 'rsi', 'Rhsim10G0153300' => 'rsi', 'Rhsim11G0012700' => 'rsi', 'Rhsim12G0031800' => 'rsi', 'Rhsim12G0055400' => 'rsi', 'Rhsim12G0091400' => 'rsi', 'Rhsim13G0070800' => 'rsi', 'Rhsim13G0193300' => 'rsi', 'RhsimUnG0111600' => 'rsi', 'RhsimUnG0137500' => 'rsi', 'RhsimUnG0172900' => 'rsi', 'SGA_v2.0_scaffold11G05878' => 'sas', 'SGA_v2.0_scaffold167G38458' => 'sas', 'SGA_v2.0_scaffold19G08588' => 'sas', 'SGA_v2.0_scaffold239G43990' => 'sas', 'SGA_v2.0_scaffold260G45865' => 'sas', 'SGA_v2.0_scaffold309G48177' => 'sas', 'SGA_v2.0_scaffold76G25122' => 'sas', 'SGA_v2.0_scaffold85G26708' => 'sas', 'SHI13914' => 'shi', 'SHI30402' => 'shi', 'TWI09G0020' => 'twi', 'TWI09G0456' => 'twi', 'TWI09G1572' => 'twi', 'TWI12G0266' => 'twi', 'TWI12G1451' => 'twi', 'TWI14G0851' => 'twi', 'TWI15G0796' => 'twi', 'TWI18G0820' => 'twi', 'TWI18G1152' => 'twi', 'TWI23G0007' => 'twi', 'TWI23G0314' => 'twi', 'TWI31G0674' => 'twi', 'TWI31G0938' => 'twi', 'TWI34G0641' => 'twi', 'TWI34G1527' => 'twi', 'TWI36G0193' => 'twi', 'TWI36G0405' => 'twi', 'TWI38G0892' => 'twi', 'TWI38G0936' => 'twi', 'TWI38G2218' => 'twi', 'TWI53G0679' => 'twi', 'TWI53G0863' => 'twi', 'TWI53G1133' => 'twi', 'TWI60G0823' => 'twi', 'TWI63G0919' => 'twi', 'TWI63G1436' => 'twi', 'TWI73G0140' => 'twi', 'TWI73G0419' => 'twi', 'TWI73G0420' => 'twi', 'TWI73G1276' => 'twi', 'TWI74G0405' => 'twi', 'TWI74G0837' => 'twi', 'TWI75G0594' => 'twi', 'TWI75G1615' => 'twi', 'TWI77G0816' => 'twi', 'vmacro03831' => 'vma', 'vmacro13746' => 'vma', 'vmacro16089' => 'vma', 'vmacro22863' => 'vma', 'Zm00001eb085790' => 'zma', 'Zm00001eb114250' => 'zma', 'Zm00001eb138070' => 'zma', 'Zm00001eb167560' => 'zma', 'Zm00001eb199990' => 'zma', 'Zm00001eb368180' => 'zma', 'Zm00001eb382470' => 'zma' ), 'gf_id' => 'HOM05D001576', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001576' ), 'data_identifier' => 'HOM05D001576', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001576', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '406', 'num_species' => '29' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'Aqoxy1G01456' => 'aox', 'Aqoxy1G02949' => 'aox', 'Aqoxy3G01274' => 'aox', 'Aqoxy3G02110' => 'aox', 'Aqoxy3G02268' => 'aox', 'Aqoxy5G02702' => 'aox', 'Aqoxy5G02988' => 'aox', 'Aqoxy5G03427' => 'aox', 'Aqoxy6G02363' => 'aox', 'Atru.chr1.3225' => 'acertr', 'Atru.chr8.1198' => 'acertr', 'Atru.chr9.790' => 'acertr', 'CANSAT01G3197' => 'cansat', 'Ciclev10003979m.g' => 'ccl', 'Ciclev10017471m.g' => 'ccl', 'Ciclev10018206m.g' => 'ccl', 'Ciclev10033751m.g' => 'ccl', 'CiPaw.01G000900' => 'cil', 'CiPaw.01G001000' => 'cil', 'CiPaw.01G033500' => 'cil', 'CiPaw.01G060300' => 'cil', 'CiPaw.01G070200' => 'cil', 'CiPaw.01G075100' => 'cil', 'CiPaw.01G084700' => 'cil', 'CiPaw.01G087900' => 'cil', 'CiPaw.01G092600' => 'cil', 'CiPaw.01G097200' => 'cil', 'CiPaw.01G098300' => 'cil', 'CiPaw.01G110200' => 'cil', 'CiPaw.01G118700' => 'cil', 'CiPaw.01G121200' => 'cil', 'CiPaw.01G132500' => 'cil', 'CiPaw.01G146900' => 'cil', 'CiPaw.01G174000' => 'cil', 'CiPaw.01G179900' => 'cil', 'CiPaw.01G183400' => 'cil', 'CiPaw.01G240000' => 'cil', 'CiPaw.01G283500' => 'cil', 'CiPaw.01G307400' => 'cil', 'CiPaw.02G030800' => 'cil', 'CiPaw.02G047200' => 'cil', 'CiPaw.02G050500' => 'cil', 'CiPaw.02G069900' => 'cil', 'CiPaw.02G091600' => 'cil', 'CiPaw.02G095000' => 'cil', 'CiPaw.02G131900' => 'cil', 'CiPaw.03G043000' => 'cil', 'CiPaw.03G069900' => 'cil', 'CiPaw.03G088100' => 'cil', 'CiPaw.03G089300' => 'cil', 'CiPaw.03G093100' => 'cil', 'CiPaw.03G129800' => 'cil', 'CiPaw.03G131200' => 'cil', 'CiPaw.03G134500' => 'cil', 'CiPaw.03G152100' => 'cil', 'CiPaw.03G162700' => 'cil', 'CiPaw.03G172800' => 'cil', 'CiPaw.03G175800' => 'cil', 'CiPaw.03G181800' => 'cil', 'CiPaw.03G191400' => 'cil', 'CiPaw.03G198300' => 'cil', 'CiPaw.03G201300' => 'cil', 'CiPaw.03G224700' => 'cil', 'CiPaw.03G225000' => 'cil', 'CiPaw.04G065100' => 'cil', 'CiPaw.04G080400' => 'cil', 'CiPaw.04G113500' => 'cil', 'CiPaw.04G121900' => 'cil', 'CiPaw.04G144100' => 'cil', 'CiPaw.04G176500' => 'cil', 'CiPaw.05G086200' => 'cil', 'CiPaw.05G100200' => 'cil', 'CiPaw.05G114200' => 'cil', 'CiPaw.05G126800' => 'cil', 'CiPaw.05G228800' => 'cil', 'CiPaw.05G230600' => 'cil', 'CiPaw.05G236500' => 'cil', 'CiPaw.05G244800' => 'cil', 'CiPaw.06G026600' => 'cil', 'CiPaw.06G027900' => 'cil', 'CiPaw.06G051800' => 'cil', 'CiPaw.06G128500' => 'cil', 'CiPaw.06G165900' => 'cil', 'CiPaw.07G045400' => 'cil', 'CiPaw.07G048000' => 'cil', 'CiPaw.07G052000' => 'cil', 'CiPaw.07G073800' => 'cil', 'CiPaw.07G099700' => 'cil', 'CiPaw.07G108700' => 'cil', 'CiPaw.07G120000' => 'cil', 'CiPaw.07G134100' => 'cil', 'CiPaw.07G147000' => 'cil', 'CiPaw.07G149700' => 'cil', 'CiPaw.07G178300' => 'cil', 'CiPaw.07G184900' => 'cil', 'CiPaw.08G044500' => 'cil', 'CiPaw.08G046900' => 'cil', 'CiPaw.08G047300' => 'cil', 'CiPaw.08G115400' => 'cil', 'CiPaw.08G134700' => 'cil', 'CiPaw.08G157400' => 'cil', 'CiPaw.09G014300' => 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'CiPaw.14G032000' => 'cil', 'CiPaw.14G032300' => 'cil', 'CiPaw.14G040600' => 'cil', 'CiPaw.14G060500' => 'cil', 'CiPaw.14G061500' => 'cil', 'CiPaw.14G077500' => 'cil', 'CiPaw.14G088300' => 'cil', 'CiPaw.14G108500' => 'cil', 'CiPaw.14G121300' => 'cil', 'CiPaw.14G133000' => 'cil', 'CiPaw.14G134600' => 'cil', 'CiPaw.15G027200' => 'cil', 'CiPaw.15G037700' => 'cil', 'CiPaw.15G050900' => 'cil', 'CiPaw.15G067200' => 'cil', 'CiPaw.15G072000' => 'cil', 'CiPaw.15G112900' => 'cil', 'CiPaw.15G133200' => 'cil', 'CiPaw.15G139500' => 'cil', 'CiPaw.15G155400' => 'cil', 'CiPaw.16G006000' => 'cil', 'CiPaw.16G013100' => 'cil', 'CiPaw.16G047100' => 'cil', 'CiPaw.16G048900' => 'cil', 'CiPaw.16G070300' => 'cil', 'CSS0000195' => 'camsi', 'CSS0001664' => 'camsi', 'CSS0002566' => 'camsi', 'CSS0003077' => 'camsi', 'CSS0004257' => 'camsi', 'CSS0004495' => 'camsi', 'CSS0004599' => 'camsi', 'CSS0004943' => 'camsi', 'CSS0005302' => 'camsi', 'CSS0006274' => 'camsi', 'CSS0006547' => 'camsi', 'CSS0006860' => 'camsi', 'CSS0008814' => 'camsi', 'CSS0008946' => 'camsi', 'CSS0009093' => 'camsi', 'CSS0010221' => 'camsi', 'CSS0010296' => 'camsi', 'CSS0010386' => 'camsi', 'CSS0010831' => 'camsi', 'CSS0011061' => 'camsi', 'CSS0012008' => 'camsi', 'CSS0012194' => 'camsi', 'CSS0013580' => 'camsi', 'CSS0014176' => 'camsi', 'CSS0014280' => 'camsi', 'CSS0014799' => 'camsi', 'CSS0015368' => 'camsi', 'CSS0017473' => 'camsi', 'CSS0019281' => 'camsi', 'CSS0021320' => 'camsi', 'CSS0021750' => 'camsi', 'CSS0023642' => 'camsi', 'CSS0023792' => 'camsi', 'CSS0031528' => 'camsi', 'CSS0033894' => 'camsi', 'CSS0034959' => 'camsi', 'CSS0035632' => 'camsi', 'CSS0038450' => 'camsi', 'CSS0039293' => 'camsi', 'CSS0041053' => 'camsi', 'CSS0041981' => 'camsi', 'CSS0042573' => 'camsi', 'CSS0042927' => 'camsi', 'CSS0047725' => 'camsi', 'CSS0049636' => 'camsi', 'CSS0050513' => 'camsi', 'DCAR_030203' => 'dca', 'Dinv07939' => 'din', 'FAN01G0456' => 'fan', 'FAN02G3001' => 'fan', 'FAN04G2781' => 'fan', 'FAN05G1385' => 'fan', 'FAN05G3062' => 'fan', 'FAN08G2267' => 'fan', 'FAN10G0481' => 'fan', 'FAN10G1257' => 'fan', 'FAN14G0954' => 'fan', 'FAN14G2347' => 'fan', 'FAN15G0187' => 'fan', 'FAN25G2214' => 'fan', 'FvH4_1g21031' => 'fve', 'FvH4_3g16231' => 'fve', 'FvH4_3g26413' => 'fve', 'FvH4_3g29014' => 'fve', 'FvH4_3g31921' => 'fve', 'FvH4_4g19882' => 'fve', 'FvH4_5g21960' => 'fve', 'FvH4_5g29683' => 'fve', 'FvH4_7g13271' => 'fve', 'Glyma.01G062500' => 'gma', 'Glyma.07G140900' => 'gma', 'Glyma.09G140900' => 'gma', 'Glyma.12G112700' => 'gma', 'Glyma.17G168800' => 'gma', 'HanXRQChr01g0027001' => 'han', 'HanXRQChr04g0120511' => 'han', 'HanXRQChr08g0232381' => 'han', 'HanXRQChr09g0265661' => 'han', 'HanXRQChr13g0416031' => 'han', 'Haze_05835' => 'cav', 'Haze_06597' => 'cav', 'Haze_07921' => 'cav', 'Haze_08599' => 'cav', 'Haze_10686' => 'cav', 'Haze_12994' => 'cav', 'Haze_13466' => 'cav', 'Haze_16101' => 'cav', 'Haze_17766' => 'cav', 'Haze_18456' => 'cav', 'Haze_20229' => 'cav', 'Hma1.2p1_0324F.1_g125640' => 'hma', 'Hma1.2p1_0733F.1_g210230' => 'hma', 'Hma1.2p1_0921F.1_g236870' => 'hma', 'Hma1.2p1_1313F.1_g274940' => 'hma', 'Hma1.2p1_3059F.1_g332230' => 'hma', 'Hund15925' => 'sun', 'Hund19562' => 'sun', 'Hund21925' => 'sun', 'MD03G1177400' => 'mdo', 'MD07G1026100' => 'mdo', 'MD17G1218600' => 'mdo', 'Medtr0867s0010' => 'mtr', 'Medtr6g081150' => 'mtr', 'Os01g0527900' => 'osa', 'Os02g0463725' => 'osa', 'Os02g0785600' => 'osa', 'Os03g0433733' => 'osa', 'Os04g0286500' => 'osa', 'Os05g0227800' => 'osa', 'Os06g0521000' => 'osa', 'Os06g0635500' => 'osa', 'Os06g0660650' => 'osa', 'Os07g0554400' => 'osa', 'Os08g0225900' => 'osa', 'Os08g0561000' => 'osa', 'Os09g0241700' => 'osa', 'Os09g0351900' => 'osa', 'Os11g0220700' => 'osa', 'Os11g0282700' => 'osa', 'Os12g0169300' => 'osa', 'Os12g0228500' => 'osa', 'Os12g0543800' => 'osa', 'PGR044G1547' => 'pgr', 'Potri.005G239150' => 'ptr', 'Potri.010G014250' => 'ptr', 'Prupe.1G172500' => 'ppe', 'Prupe.1G196800' => 'ppe', 'Prupe.1G279700' => 'ppe', 'Prupe.2G026400' => 'ppe', 'Prupe.3G094000' => 'ppe', 'Prupe.4G287300' => 'ppe', 'QL01p022166' => 'qlo', 'QL01p051890' => 'qlo', 'QL02p009469' => 'qlo', 'QL02p046053' => 'qlo', 'QL02p057958' => 'qlo', 'QL02p093127' => 'qlo', 'QL03p006855' => 'qlo', 'QL03p071586' => 'qlo', 'QL04p000022' => 'qlo', 'QL04p000024' => 'qlo', 'QL04p003192' => 'qlo', 'QL05p011416' => 'qlo', 'QL06p039590' => 'qlo', 'QL06p052750' => 'qlo', 'QL06p053821' => 'qlo', 'QL07p025287' => 'qlo', 'QL09p033218' => 'qlo', 'QL09p040841' => 'qlo', 'QL10p020337' => 'qlo', 'QL10p027209' => 'qlo', 'QL10p027969' => 'qlo', 'QL10p048988' => 'qlo', 'QL11p001241' => 'qlo', 'QL11p028487' => 'qlo', 'RcHm_v2.0_Chr2g0105031' => 'rch', 'RcHm_v2.0_Chr2g0117811' => 'rch', 'RcHm_v2.0_Chr6g0270241' => 'rch', 'RcHm_v2.0_Chr7g0215961' => 'rch', 'RcHm_v2.0_Chr7g0231991' => 'rch', 'Rhsim01G0041500' => 'rsi', 'Rhsim01G0115000' => 'rsi', 'Rhsim01G0115400' => 'rsi', 'Rhsim01G0133600' => 'rsi', 'Rhsim01G0159900' => 'rsi', 'Rhsim02G0189400' => 'rsi', 'Rhsim03G0135600' => 'rsi', 'Rhsim03G0149900' => 'rsi', 'Rhsim04G0125600' => 'rsi', 'Rhsim05G0091700' => 'rsi', 'Rhsim05G0092900' => 'rsi', 'Rhsim06G0075000' => 'rsi', 'Rhsim07G0066400' => 'rsi', 'Rhsim07G0156400' => 'rsi', 'Rhsim07G0182200' => 'rsi', 'Rhsim07G0182300' => 'rsi', 'Rhsim08G0180400' => 'rsi', 'Rhsim09G0056800' => 'rsi', 'Rhsim10G0153300' => 'rsi', 'Rhsim11G0012700' => 'rsi', 'Rhsim12G0031800' => 'rsi', 'Rhsim12G0055400' => 'rsi', 'Rhsim12G0091400' => 'rsi', 'Rhsim13G0070800' => 'rsi', 'Rhsim13G0193300' => 'rsi', 'RhsimUnG0111600' => 'rsi', 'RhsimUnG0137500' => 'rsi', 'RhsimUnG0172900' => 'rsi', 'SGA_v2.0_scaffold11G05878' => 'sas', 'SGA_v2.0_scaffold167G38458' => 'sas', 'SGA_v2.0_scaffold19G08588' => 'sas', 'SGA_v2.0_scaffold239G43990' => 'sas', 'SGA_v2.0_scaffold260G45865' => 'sas', 'SGA_v2.0_scaffold309G48177' => 'sas', 'SGA_v2.0_scaffold76G25122' => 'sas', 'SGA_v2.0_scaffold85G26708' => 'sas', 'SHI13914' => 'shi', 'SHI30402' => 'shi', 'TWI09G0020' => 'twi', 'TWI09G0456' => 'twi', 'TWI09G1572' => 'twi', 'TWI12G0266' => 'twi', 'TWI12G1451' => 'twi', 'TWI14G0851' => 'twi', 'TWI15G0796' => 'twi', 'TWI18G0820' => 'twi', 'TWI18G1152' => 'twi', 'TWI23G0007' => 'twi', 'TWI23G0314' => 'twi', 'TWI31G0674' => 'twi', 'TWI31G0938' => 'twi', 'TWI34G0641' => 'twi', 'TWI34G1527' => 'twi', 'TWI36G0193' => 'twi', 'TWI36G0405' => 'twi', 'TWI38G0892' => 'twi', 'TWI38G0936' => 'twi', 'TWI38G2218' => 'twi', 'TWI53G0679' => 'twi', 'TWI53G0863' => 'twi', 'TWI53G1133' => 'twi', 'TWI60G0823' => 'twi', 'TWI63G0919' => 'twi', 'TWI63G1436' => 'twi', 'TWI73G0140' => 'twi', 'TWI73G0419' => 'twi', 'TWI73G0420' => 'twi', 'TWI73G1276' => 'twi', 'TWI74G0405' => 'twi', 'TWI74G0837' => 'twi', 'TWI75G0594' => 'twi', 'TWI75G1615' => 'twi', 'TWI77G0816' => 'twi', 'vmacro03831' => 'vma', 'vmacro13746' => 'vma', 'vmacro16089' => 'vma', 'vmacro22863' => 'vma', 'Zm00001eb085790' => 'zma', 'Zm00001eb114250' => 'zma', 'Zm00001eb138070' => 'zma', 'Zm00001eb167560' => 'zma', 'Zm00001eb199990' => 'zma', 'Zm00001eb368180' => 'zma', 'Zm00001eb382470' => 'zma' ) $gf_id = 'HOM05D001576' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001576' ) $data_identifier = 'HOM05D001576' $data_type = 'gf_id' $species_gene_counts = array( 'aox' => (int) 9, 'acertr' => (int) 3, 'cansat' => (int) 1, 'ccl' => (int) 4, 'cil' => (int) 145, 'camsi' => (int) 46, 'dca' => (int) 1, 'din' => (int) 1, 'fan' => (int) 12, 'fve' => (int) 9, 'gma' => (int) 5, 'han' => (int) 5, 'cav' => (int) 11, 'hma' => (int) 5, 'sun' => (int) 3, 'mdo' => (int) 3, 'mtr' => (int) 2, 'osa' => (int) 19, 'pgr' => (int) 1, 'ptr' => (int) 2, 'ppe' => (int) 6, 'qlo' => (int) 24, 'rch' => (int) 5, 'rsi' => (int) 28, 'sas' => (int) 8, 'shi' => (int) 2, 'twi' => (int) 35, 'vma' => (int) 4, 'zma' => (int) 7 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb382470' $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' => 'HOM05D001576', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '406', 'num_species' => '29' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'Aqoxy1G01456' => 'aox', 'Aqoxy1G02949' => 'aox', 'Aqoxy3G01274' => 'aox', 'Aqoxy3G02110' => 'aox', 'Aqoxy3G02268' => 'aox', 'Aqoxy5G02702' => 'aox', 'Aqoxy5G02988' => 'aox', 'Aqoxy5G03427' => 'aox', 'Aqoxy6G02363' => 'aox', 'Atru.chr1.3225' => 'acertr', 'Atru.chr8.1198' => 'acertr', 'Atru.chr9.790' => 'acertr', 'CANSAT01G3197' => 'cansat', 'Ciclev10003979m.g' => 'ccl', 'Ciclev10017471m.g' => 'ccl', 'Ciclev10018206m.g' => 'ccl', 'Ciclev10033751m.g' => 'ccl', 'CiPaw.01G000900' => 'cil', 'CiPaw.01G001000' => 'cil', 'CiPaw.01G033500' => 'cil', 'CiPaw.01G060300' => 'cil', 'CiPaw.01G070200' => 'cil', 'CiPaw.01G075100' => 'cil', 'CiPaw.01G084700' => 'cil', 'CiPaw.01G087900' => 'cil', 'CiPaw.01G092600' => 'cil', 'CiPaw.01G097200' => 'cil', 'CiPaw.01G098300' => 'cil', 'CiPaw.01G110200' => 'cil', 'CiPaw.01G118700' => 'cil', 'CiPaw.01G121200' => 'cil', 'CiPaw.01G132500' => 'cil', 'CiPaw.01G146900' => 'cil', 'CiPaw.01G174000' => 'cil', 'CiPaw.01G179900' => 'cil', 'CiPaw.01G183400' => 'cil', 'CiPaw.01G240000' => 'cil', 'CiPaw.01G283500' => 'cil', 'CiPaw.01G307400' => 'cil', 'CiPaw.02G030800' => 'cil', 'CiPaw.02G047200' => 'cil', 'CiPaw.02G050500' => 'cil', 'CiPaw.02G069900' => 'cil', 'CiPaw.02G091600' => 'cil', 'CiPaw.02G095000' => 'cil', 'CiPaw.02G131900' => 'cil', 'CiPaw.03G043000' => 'cil', 'CiPaw.03G069900' => 'cil', 'CiPaw.03G088100' => 'cil', 'CiPaw.03G089300' => 'cil', 'CiPaw.03G093100' => 'cil', 'CiPaw.03G129800' => 'cil', 'CiPaw.03G131200' => 'cil', 'CiPaw.03G134500' => 'cil', 'CiPaw.03G152100' => 'cil', 'CiPaw.03G162700' => 'cil', 'CiPaw.03G172800' => 'cil', 'CiPaw.03G175800' => 'cil', 'CiPaw.03G181800' => 'cil', 'CiPaw.03G191400' => 'cil', 'CiPaw.03G198300' => 'cil', 'CiPaw.03G201300' => 'cil', 'CiPaw.03G224700' => 'cil', 'CiPaw.03G225000' => 'cil', 'CiPaw.04G065100' => 'cil', 'CiPaw.04G080400' => 'cil', 'CiPaw.04G113500' => 'cil', 'CiPaw.04G121900' => 'cil', 'CiPaw.04G144100' => 'cil', 'CiPaw.04G176500' => 'cil', 'CiPaw.05G086200' => 'cil', 'CiPaw.05G100200' => 'cil', 'CiPaw.05G114200' => 'cil', 'CiPaw.05G126800' => 'cil', 'CiPaw.05G228800' => 'cil', 'CiPaw.05G230600' => 'cil', 'CiPaw.05G236500' => 'cil', 'CiPaw.05G244800' => 'cil', 'CiPaw.06G026600' => 'cil', 'CiPaw.06G027900' => 'cil', 'CiPaw.06G051800' => 'cil', 'CiPaw.06G128500' => 'cil', 'CiPaw.06G165900' => 'cil', 'CiPaw.07G045400' => 'cil', 'CiPaw.07G048000' => 'cil', 'CiPaw.07G052000' => 'cil', 'CiPaw.07G073800' => 'cil', 'CiPaw.07G099700' => 'cil', 'CiPaw.07G108700' => 'cil', 'CiPaw.07G120000' => 'cil', 'CiPaw.07G134100' => 'cil', 'CiPaw.07G147000' => 'cil', 'CiPaw.07G149700' => 'cil', 'CiPaw.07G178300' => 'cil', 'CiPaw.07G184900' => 'cil', 'CiPaw.08G044500' => 'cil', 'CiPaw.08G046900' => 'cil', 'CiPaw.08G047300' => 'cil', 'CiPaw.08G115400' => 'cil', 'CiPaw.08G134700' => 'cil', 'CiPaw.08G157400' => 'cil', 'CiPaw.09G014300' => 'cil', 'CiPaw.09G088900' => 'cil', 'CiPaw.09G130900' => 'cil', 'CiPaw.09G133100' => 'cil', 'CiPaw.09G151300' => 'cil', 'CiPaw.09G172800' => 'cil', 'CiPaw.09G174900' => 'cil', 'CiPaw.09G175000' => 'cil', 'CiPaw.10G012800' => 'cil', 'CiPaw.10G028800' => 'cil', 'CiPaw.10G044700' => 'cil', 'CiPaw.10G067400' => 'cil', 'CiPaw.10G115900' => 'cil', 'CiPaw.10G126200' => 'cil', 'CiPaw.10G139700' => 'cil', 'CiPaw.10G155100' => 'cil', 'CiPaw.11G011300' => 'cil', 'CiPaw.11G025900' => 'cil', 'CiPaw.11G104100' => 'cil', 'CiPaw.11G142700' => 'cil', 'CiPaw.11G164500' => 'cil', 'CiPaw.11G189100' => 'cil', 'CiPaw.11G197100' => 'cil', 'CiPaw.12G006100' => 'cil', 'CiPaw.12G038500' => 'cil', 'CiPaw.12G041400' => 'cil', 'CiPaw.12G041600' => 'cil', 'CiPaw.12G051300' => 'cil', 'CiPaw.12G101800' => 'cil', 'CiPaw.12G107800' => 'cil', 'CiPaw.13G033200' => 'cil', 'CiPaw.13G129900' => 'cil', 'CiPaw.13G160200' => 'cil', 'CiPaw.14G018900' => 'cil', 'CiPaw.14G029000' => 'cil', 'CiPaw.14G031000' => 'cil', 'CiPaw.14G032000' => 'cil', 'CiPaw.14G032300' => 'cil', 'CiPaw.14G040600' => 'cil', 'CiPaw.14G060500' => 'cil', 'CiPaw.14G061500' => 'cil', 'CiPaw.14G077500' => 'cil', 'CiPaw.14G088300' => 'cil', 'CiPaw.14G108500' => 'cil', 'CiPaw.14G121300' => 'cil', 'CiPaw.14G133000' => 'cil', 'CiPaw.14G134600' => 'cil', 'CiPaw.15G027200' => 'cil', 'CiPaw.15G037700' => 'cil', 'CiPaw.15G050900' => 'cil', 'CiPaw.15G067200' => 'cil', 'CiPaw.15G072000' => 'cil', 'CiPaw.15G112900' => 'cil', 'CiPaw.15G133200' => 'cil', 'CiPaw.15G139500' => 'cil', 'CiPaw.15G155400' => 'cil', 'CiPaw.16G006000' => 'cil', 'CiPaw.16G013100' => 'cil', 'CiPaw.16G047100' => 'cil', 'CiPaw.16G048900' => 'cil', 'CiPaw.16G070300' => 'cil', 'CSS0000195' => 'camsi', 'CSS0001664' => 'camsi', 'CSS0002566' => 'camsi', 'CSS0003077' => 'camsi', 'CSS0004257' => 'camsi', 'CSS0004495' => 'camsi', 'CSS0004599' => 'camsi', 'CSS0004943' => 'camsi', 'CSS0005302' => 'camsi', 'CSS0006274' => 'camsi', 'CSS0006547' => 'camsi', 'CSS0006860' => 'camsi', 'CSS0008814' => 'camsi', 'CSS0008946' => 'camsi', 'CSS0009093' => 'camsi', 'CSS0010221' => 'camsi', 'CSS0010296' => 'camsi', 'CSS0010386' => 'camsi', 'CSS0010831' => 'camsi', 'CSS0011061' => 'camsi', 'CSS0012008' => 'camsi', 'CSS0012194' => 'camsi', 'CSS0013580' => 'camsi', 'CSS0014176' => 'camsi', 'CSS0014280' => 'camsi', 'CSS0014799' => 'camsi', 'CSS0015368' => 'camsi', 'CSS0017473' => 'camsi', 'CSS0019281' => 'camsi', 'CSS0021320' => 'camsi', 'CSS0021750' => 'camsi', 'CSS0023642' => 'camsi', 'CSS0023792' => 'camsi', 'CSS0031528' => 'camsi', 'CSS0033894' => 'camsi', 'CSS0034959' => 'camsi', 'CSS0035632' => 'camsi', 'CSS0038450' => 'camsi', 'CSS0039293' => 'camsi', 'CSS0041053' => 'camsi', 'CSS0041981' => 'camsi', 'CSS0042573' => 'camsi', 'CSS0042927' => 'camsi', 'CSS0047725' => 'camsi', 'CSS0049636' => 'camsi', 'CSS0050513' => 'camsi', 'DCAR_030203' => 'dca', 'Dinv07939' => 'din', 'FAN01G0456' => 'fan', 'FAN02G3001' => 'fan', 'FAN04G2781' => 'fan', 'FAN05G1385' => 'fan', 'FAN05G3062' => 'fan', 'FAN08G2267' => 'fan', 'FAN10G0481' => 'fan', 'FAN10G1257' => 'fan', 'FAN14G0954' => 'fan', 'FAN14G2347' => 'fan', 'FAN15G0187' => 'fan', 'FAN25G2214' => 'fan', 'FvH4_1g21031' => 'fve', 'FvH4_3g16231' => 'fve', 'FvH4_3g26413' => 'fve', 'FvH4_3g29014' => 'fve', 'FvH4_3g31921' => 'fve', 'FvH4_4g19882' => 'fve', 'FvH4_5g21960' => 'fve', 'FvH4_5g29683' => 'fve', 'FvH4_7g13271' => 'fve', 'Glyma.01G062500' => 'gma', 'Glyma.07G140900' => 'gma', 'Glyma.09G140900' => 'gma', 'Glyma.12G112700' => 'gma', 'Glyma.17G168800' => 'gma', 'HanXRQChr01g0027001' => 'han', 'HanXRQChr04g0120511' => 'han', 'HanXRQChr08g0232381' => 'han', 'HanXRQChr09g0265661' => 'han', 'HanXRQChr13g0416031' => 'han', 'Haze_05835' => 'cav', 'Haze_06597' => 'cav', 'Haze_07921' => 'cav', 'Haze_08599' => 'cav', 'Haze_10686' => 'cav', 'Haze_12994' => 'cav', 'Haze_13466' => 'cav', 'Haze_16101' => 'cav', 'Haze_17766' => 'cav', 'Haze_18456' => 'cav', 'Haze_20229' => 'cav', 'Hma1.2p1_0324F.1_g125640' => 'hma', 'Hma1.2p1_0733F.1_g210230' => 'hma', 'Hma1.2p1_0921F.1_g236870' => 'hma', 'Hma1.2p1_1313F.1_g274940' => 'hma', 'Hma1.2p1_3059F.1_g332230' => 'hma', 'Hund15925' => 'sun', 'Hund19562' => 'sun', 'Hund21925' => 'sun', 'MD03G1177400' => 'mdo', 'MD07G1026100' => 'mdo', 'MD17G1218600' => 'mdo', 'Medtr0867s0010' => 'mtr', 'Medtr6g081150' => 'mtr', 'Os01g0527900' => 'osa', 'Os02g0463725' => 'osa', 'Os02g0785600' => 'osa', 'Os03g0433733' => 'osa', 'Os04g0286500' => 'osa', 'Os05g0227800' => 'osa', 'Os06g0521000' => 'osa', 'Os06g0635500' => 'osa', 'Os06g0660650' => 'osa', 'Os07g0554400' => 'osa', 'Os08g0225900' => 'osa', 'Os08g0561000' => 'osa', 'Os09g0241700' => 'osa', 'Os09g0351900' => 'osa', 'Os11g0220700' => 'osa', 'Os11g0282700' => 'osa', 'Os12g0169300' => 'osa', 'Os12g0228500' => 'osa', 'Os12g0543800' => 'osa', 'PGR044G1547' => 'pgr', 'Potri.005G239150' => 'ptr', 'Potri.010G014250' => 'ptr', 'Prupe.1G172500' => 'ppe', 'Prupe.1G196800' => 'ppe', 'Prupe.1G279700' => 'ppe', 'Prupe.2G026400' => 'ppe', 'Prupe.3G094000' => 'ppe', 'Prupe.4G287300' => 'ppe', 'QL01p022166' => 'qlo', 'QL01p051890' => 'qlo', 'QL02p009469' => 'qlo', 'QL02p046053' => 'qlo', 'QL02p057958' => 'qlo', 'QL02p093127' => 'qlo', 'QL03p006855' => 'qlo', 'QL03p071586' => 'qlo', 'QL04p000022' => 'qlo', 'QL04p000024' => 'qlo', 'QL04p003192' => 'qlo', 'QL05p011416' => 'qlo', 'QL06p039590' => 'qlo', 'QL06p052750' => 'qlo', 'QL06p053821' => 'qlo', 'QL07p025287' => 'qlo', 'QL09p033218' => 'qlo', 'QL09p040841' => 'qlo', 'QL10p020337' => 'qlo', 'QL10p027209' => 'qlo', 'QL10p027969' => 'qlo', 'QL10p048988' => 'qlo', 'QL11p001241' => 'qlo', 'QL11p028487' => 'qlo', 'RcHm_v2.0_Chr2g0105031' => 'rch', 'RcHm_v2.0_Chr2g0117811' => 'rch', 'RcHm_v2.0_Chr6g0270241' => 'rch', 'RcHm_v2.0_Chr7g0215961' => 'rch', 'RcHm_v2.0_Chr7g0231991' => 'rch', 'Rhsim01G0041500' => 'rsi', 'Rhsim01G0115000' => 'rsi', 'Rhsim01G0115400' => 'rsi', 'Rhsim01G0133600' => 'rsi', 'Rhsim01G0159900' => 'rsi', 'Rhsim02G0189400' => 'rsi', 'Rhsim03G0135600' => 'rsi', 'Rhsim03G0149900' => 'rsi', 'Rhsim04G0125600' => 'rsi', 'Rhsim05G0091700' => 'rsi', 'Rhsim05G0092900' => 'rsi', 'Rhsim06G0075000' => 'rsi', 'Rhsim07G0066400' => 'rsi', 'Rhsim07G0156400' => 'rsi', 'Rhsim07G0182200' => 'rsi', 'Rhsim07G0182300' => 'rsi', 'Rhsim08G0180400' => 'rsi', 'Rhsim09G0056800' => 'rsi', 'Rhsim10G0153300' => 'rsi', 'Rhsim11G0012700' => 'rsi', 'Rhsim12G0031800' => 'rsi', 'Rhsim12G0055400' => 'rsi', 'Rhsim12G0091400' => 'rsi', 'Rhsim13G0070800' => 'rsi', 'Rhsim13G0193300' => 'rsi', 'RhsimUnG0111600' => 'rsi', 'RhsimUnG0137500' => 'rsi', 'RhsimUnG0172900' => 'rsi', 'SGA_v2.0_scaffold11G05878' => 'sas', 'SGA_v2.0_scaffold167G38458' => 'sas', 'SGA_v2.0_scaffold19G08588' => 'sas', 'SGA_v2.0_scaffold239G43990' => 'sas', 'SGA_v2.0_scaffold260G45865' => 'sas', 'SGA_v2.0_scaffold309G48177' => 'sas', 'SGA_v2.0_scaffold76G25122' => 'sas', 'SGA_v2.0_scaffold85G26708' => 'sas', 'SHI13914' => 'shi', 'SHI30402' => 'shi', 'TWI09G0020' => 'twi', 'TWI09G0456' => 'twi', 'TWI09G1572' => 'twi', 'TWI12G0266' => 'twi', 'TWI12G1451' => 'twi', 'TWI14G0851' => 'twi', 'TWI15G0796' => 'twi', 'TWI18G0820' => 'twi', 'TWI18G1152' => 'twi', 'TWI23G0007' => 'twi', 'TWI23G0314' => 'twi', 'TWI31G0674' => 'twi', 'TWI31G0938' => 'twi', 'TWI34G0641' => 'twi', 'TWI34G1527' => 'twi', 'TWI36G0193' => 'twi', 'TWI36G0405' => 'twi', 'TWI38G0892' => 'twi', 'TWI38G0936' => 'twi', 'TWI38G2218' => 'twi', 'TWI53G0679' => 'twi', 'TWI53G0863' => 'twi', 'TWI53G1133' => 'twi', 'TWI60G0823' => 'twi', 'TWI63G0919' => 'twi', 'TWI63G1436' => 'twi', 'TWI73G0140' => 'twi', 'TWI73G0419' => 'twi', 'TWI73G0420' => 'twi', 'TWI73G1276' => 'twi', 'TWI74G0405' => 'twi', 'TWI74G0837' => 'twi', 'TWI75G0594' => 'twi', 'TWI75G1615' => 'twi', 'TWI77G0816' => 'twi', 'vmacro03831' => 'vma', 'vmacro13746' => 'vma', 'vmacro16089' => 'vma', 'vmacro22863' => 'vma', 'Zm00001eb085790' => 'zma', 'Zm00001eb114250' => 'zma', 'Zm00001eb138070' => 'zma', 'Zm00001eb167560' => 'zma', 'Zm00001eb199990' => 'zma', 'Zm00001eb368180' => 'zma', 'Zm00001eb382470' => 'zma' ), 'gf_id' => 'HOM05D001576', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001576' ), 'data_identifier' => 'HOM05D001576', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001576', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '406', 'num_species' => '29' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'Aqoxy1G01456' => 'aox', 'Aqoxy1G02949' => 'aox', 'Aqoxy3G01274' => 'aox', 'Aqoxy3G02110' => 'aox', 'Aqoxy3G02268' => 'aox', 'Aqoxy5G02702' => 'aox', 'Aqoxy5G02988' => 'aox', 'Aqoxy5G03427' => 'aox', 'Aqoxy6G02363' => 'aox', 'Atru.chr1.3225' => 'acertr', 'Atru.chr8.1198' => 'acertr', 'Atru.chr9.790' => 'acertr', 'CANSAT01G3197' => 'cansat', 'Ciclev10003979m.g' => 'ccl', 'Ciclev10017471m.g' => 'ccl', 'Ciclev10018206m.g' => 'ccl', 'Ciclev10033751m.g' => 'ccl', 'CiPaw.01G000900' => 'cil', 'CiPaw.01G001000' => 'cil', 'CiPaw.01G033500' => 'cil', 'CiPaw.01G060300' => 'cil', 'CiPaw.01G070200' => 'cil', 'CiPaw.01G075100' => 'cil', 'CiPaw.01G084700' => 'cil', 'CiPaw.01G087900' => 'cil', 'CiPaw.01G092600' => 'cil', 'CiPaw.01G097200' => 'cil', 'CiPaw.01G098300' => 'cil', 'CiPaw.01G110200' => 'cil', 'CiPaw.01G118700' => 'cil', 'CiPaw.01G121200' => 'cil', 'CiPaw.01G132500' => 'cil', 'CiPaw.01G146900' => 'cil', 'CiPaw.01G174000' => 'cil', 'CiPaw.01G179900' => 'cil', 'CiPaw.01G183400' => 'cil', 'CiPaw.01G240000' => 'cil', 'CiPaw.01G283500' => 'cil', 'CiPaw.01G307400' => 'cil', 'CiPaw.02G030800' => 'cil', 'CiPaw.02G047200' => 'cil', 'CiPaw.02G050500' => 'cil', 'CiPaw.02G069900' => 'cil', 'CiPaw.02G091600' => 'cil', 'CiPaw.02G095000' => 'cil', 'CiPaw.02G131900' => 'cil', 'CiPaw.03G043000' => 'cil', 'CiPaw.03G069900' => 'cil', 'CiPaw.03G088100' => 'cil', 'CiPaw.03G089300' => 'cil', 'CiPaw.03G093100' => 'cil', 'CiPaw.03G129800' => 'cil', 'CiPaw.03G131200' => 'cil', 'CiPaw.03G134500' => 'cil', 'CiPaw.03G152100' => 'cil', 'CiPaw.03G162700' => 'cil', 'CiPaw.03G172800' => 'cil', 'CiPaw.03G175800' => 'cil', 'CiPaw.03G181800' => 'cil', 'CiPaw.03G191400' => 'cil', 'CiPaw.03G198300' => 'cil', 'CiPaw.03G201300' => 'cil', 'CiPaw.03G224700' => 'cil', 'CiPaw.03G225000' => 'cil', 'CiPaw.04G065100' => 'cil', 'CiPaw.04G080400' => 'cil', 'CiPaw.04G113500' => 'cil', 'CiPaw.04G121900' => 'cil', 'CiPaw.04G144100' => 'cil', 'CiPaw.04G176500' => 'cil', 'CiPaw.05G086200' => 'cil', 'CiPaw.05G100200' => 'cil', 'CiPaw.05G114200' => 'cil', 'CiPaw.05G126800' => 'cil', 'CiPaw.05G228800' => 'cil', 'CiPaw.05G230600' => 'cil', 'CiPaw.05G236500' => 'cil', 'CiPaw.05G244800' => 'cil', 'CiPaw.06G026600' => 'cil', 'CiPaw.06G027900' => 'cil', 'CiPaw.06G051800' => 'cil', 'CiPaw.06G128500' => 'cil', 'CiPaw.06G165900' => 'cil', 'CiPaw.07G045400' => 'cil', 'CiPaw.07G048000' => 'cil', 'CiPaw.07G052000' => 'cil', 'CiPaw.07G073800' => 'cil', 'CiPaw.07G099700' => 'cil', 'CiPaw.07G108700' => 'cil', 'CiPaw.07G120000' => 'cil', 'CiPaw.07G134100' => 'cil', 'CiPaw.07G147000' => 'cil', 'CiPaw.07G149700' => 'cil', 'CiPaw.07G178300' => 'cil', 'CiPaw.07G184900' => 'cil', 'CiPaw.08G044500' => 'cil', 'CiPaw.08G046900' => 'cil', 'CiPaw.08G047300' => 'cil', 'CiPaw.08G115400' => 'cil', 'CiPaw.08G134700' => 'cil', 'CiPaw.08G157400' => 'cil', 'CiPaw.09G014300' => 'cil', 'CiPaw.09G088900' => 'cil', 'CiPaw.09G130900' => 'cil', 'CiPaw.09G133100' => 'cil', 'CiPaw.09G151300' => 'cil', 'CiPaw.09G172800' => 'cil', 'CiPaw.09G174900' => 'cil', 'CiPaw.09G175000' => 'cil', 'CiPaw.10G012800' => 'cil', 'CiPaw.10G028800' => 'cil', 'CiPaw.10G044700' => 'cil', 'CiPaw.10G067400' => 'cil', 'CiPaw.10G115900' => 'cil', 'CiPaw.10G126200' => 'cil', 'CiPaw.10G139700' => 'cil', 'CiPaw.10G155100' => 'cil', 'CiPaw.11G011300' => 'cil', 'CiPaw.11G025900' => 'cil', 'CiPaw.11G104100' => 'cil', 'CiPaw.11G142700' => 'cil', 'CiPaw.11G164500' => 'cil', 'CiPaw.11G189100' => 'cil', 'CiPaw.11G197100' => 'cil', 'CiPaw.12G006100' => 'cil', 'CiPaw.12G038500' => 'cil', 'CiPaw.12G041400' => 'cil', 'CiPaw.12G041600' => 'cil', 'CiPaw.12G051300' => 'cil', 'CiPaw.12G101800' => 'cil', 'CiPaw.12G107800' => 'cil', 'CiPaw.13G033200' => 'cil', 'CiPaw.13G129900' => 'cil', 'CiPaw.13G160200' => 'cil', 'CiPaw.14G018900' => 'cil', 'CiPaw.14G029000' => 'cil', 'CiPaw.14G031000' => 'cil', 'CiPaw.14G032000' => 'cil', 'CiPaw.14G032300' => 'cil', 'CiPaw.14G040600' => 'cil', 'CiPaw.14G060500' => 'cil', 'CiPaw.14G061500' => 'cil', 'CiPaw.14G077500' => 'cil', 'CiPaw.14G088300' => 'cil', 'CiPaw.14G108500' => 'cil', 'CiPaw.14G121300' => 'cil', 'CiPaw.14G133000' => 'cil', 'CiPaw.14G134600' => 'cil', 'CiPaw.15G027200' => 'cil', 'CiPaw.15G037700' => 'cil', 'CiPaw.15G050900' => 'cil', 'CiPaw.15G067200' => 'cil', 'CiPaw.15G072000' => 'cil', 'CiPaw.15G112900' => 'cil', 'CiPaw.15G133200' => 'cil', 'CiPaw.15G139500' => 'cil', 'CiPaw.15G155400' => 'cil', 'CiPaw.16G006000' => 'cil', 'CiPaw.16G013100' => 'cil', 'CiPaw.16G047100' => 'cil', 'CiPaw.16G048900' => 'cil', 'CiPaw.16G070300' => 'cil', 'CSS0000195' => 'camsi', 'CSS0001664' => 'camsi', 'CSS0002566' => 'camsi', 'CSS0003077' => 'camsi', 'CSS0004257' => 'camsi', 'CSS0004495' => 'camsi', 'CSS0004599' => 'camsi', 'CSS0004943' => 'camsi', 'CSS0005302' => 'camsi', 'CSS0006274' => 'camsi', 'CSS0006547' => 'camsi', 'CSS0006860' => 'camsi', 'CSS0008814' => 'camsi', 'CSS0008946' => 'camsi', 'CSS0009093' => 'camsi', 'CSS0010221' => 'camsi', 'CSS0010296' => 'camsi', 'CSS0010386' => 'camsi', 'CSS0010831' => 'camsi', 'CSS0011061' => 'camsi', 'CSS0012008' => 'camsi', 'CSS0012194' => 'camsi', 'CSS0013580' => 'camsi', 'CSS0014176' => 'camsi', 'CSS0014280' => 'camsi', 'CSS0014799' => 'camsi', 'CSS0015368' => 'camsi', 'CSS0017473' => 'camsi', 'CSS0019281' => 'camsi', 'CSS0021320' => 'camsi', 'CSS0021750' => 'camsi', 'CSS0023642' => 'camsi', 'CSS0023792' => 'camsi', 'CSS0031528' => 'camsi', 'CSS0033894' => 'camsi', 'CSS0034959' => 'camsi', 'CSS0035632' => 'camsi', 'CSS0038450' => 'camsi', 'CSS0039293' => 'camsi', 'CSS0041053' => 'camsi', 'CSS0041981' => 'camsi', 'CSS0042573' => 'camsi', 'CSS0042927' => 'camsi', 'CSS0047725' => 'camsi', 'CSS0049636' => 'camsi', 'CSS0050513' => 'camsi', 'DCAR_030203' => 'dca', 'Dinv07939' => 'din', 'FAN01G0456' => 'fan', 'FAN02G3001' => 'fan', 'FAN04G2781' => 'fan', 'FAN05G1385' => 'fan', 'FAN05G3062' => 'fan', 'FAN08G2267' => 'fan', 'FAN10G0481' => 'fan', 'FAN10G1257' => 'fan', 'FAN14G0954' => 'fan', 'FAN14G2347' => 'fan', 'FAN15G0187' => 'fan', 'FAN25G2214' => 'fan', 'FvH4_1g21031' => 'fve', 'FvH4_3g16231' => 'fve', 'FvH4_3g26413' => 'fve', 'FvH4_3g29014' => 'fve', 'FvH4_3g31921' => 'fve', 'FvH4_4g19882' => 'fve', 'FvH4_5g21960' => 'fve', 'FvH4_5g29683' => 'fve', 'FvH4_7g13271' => 'fve', 'Glyma.01G062500' => 'gma', 'Glyma.07G140900' => 'gma', 'Glyma.09G140900' => 'gma', 'Glyma.12G112700' => 'gma', 'Glyma.17G168800' => 'gma', 'HanXRQChr01g0027001' => 'han', 'HanXRQChr04g0120511' => 'han', 'HanXRQChr08g0232381' => 'han', 'HanXRQChr09g0265661' => 'han', 'HanXRQChr13g0416031' => 'han', 'Haze_05835' => 'cav', 'Haze_06597' => 'cav', 'Haze_07921' => 'cav', 'Haze_08599' => 'cav', 'Haze_10686' => 'cav', 'Haze_12994' => 'cav', 'Haze_13466' => 'cav', 'Haze_16101' => 'cav', 'Haze_17766' => 'cav', 'Haze_18456' => 'cav', 'Haze_20229' => 'cav', 'Hma1.2p1_0324F.1_g125640' => 'hma', 'Hma1.2p1_0733F.1_g210230' => 'hma', 'Hma1.2p1_0921F.1_g236870' => 'hma', 'Hma1.2p1_1313F.1_g274940' => 'hma', 'Hma1.2p1_3059F.1_g332230' => 'hma', 'Hund15925' => 'sun', 'Hund19562' => 'sun', 'Hund21925' => 'sun', 'MD03G1177400' => 'mdo', 'MD07G1026100' => 'mdo', 'MD17G1218600' => 'mdo', 'Medtr0867s0010' => 'mtr', 'Medtr6g081150' => 'mtr', 'Os01g0527900' => 'osa', 'Os02g0463725' => 'osa', 'Os02g0785600' => 'osa', 'Os03g0433733' => 'osa', 'Os04g0286500' => 'osa', 'Os05g0227800' => 'osa', 'Os06g0521000' => 'osa', 'Os06g0635500' => 'osa', 'Os06g0660650' => 'osa', 'Os07g0554400' => 'osa', 'Os08g0225900' => 'osa', 'Os08g0561000' => 'osa', 'Os09g0241700' => 'osa', 'Os09g0351900' => 'osa', 'Os11g0220700' => 'osa', 'Os11g0282700' => 'osa', 'Os12g0169300' => 'osa', 'Os12g0228500' => 'osa', 'Os12g0543800' => 'osa', 'PGR044G1547' => 'pgr', 'Potri.005G239150' => 'ptr', 'Potri.010G014250' => 'ptr', 'Prupe.1G172500' => 'ppe', 'Prupe.1G196800' => 'ppe', 'Prupe.1G279700' => 'ppe', 'Prupe.2G026400' => 'ppe', 'Prupe.3G094000' => 'ppe', 'Prupe.4G287300' => 'ppe', 'QL01p022166' => 'qlo', 'QL01p051890' => 'qlo', 'QL02p009469' => 'qlo', 'QL02p046053' => 'qlo', 'QL02p057958' => 'qlo', 'QL02p093127' => 'qlo', 'QL03p006855' => 'qlo', 'QL03p071586' => 'qlo', 'QL04p000022' => 'qlo', 'QL04p000024' => 'qlo', 'QL04p003192' => 'qlo', 'QL05p011416' => 'qlo', 'QL06p039590' => 'qlo', 'QL06p052750' => 'qlo', 'QL06p053821' => 'qlo', 'QL07p025287' => 'qlo', 'QL09p033218' => 'qlo', 'QL09p040841' => 'qlo', 'QL10p020337' => 'qlo', 'QL10p027209' => 'qlo', 'QL10p027969' => 'qlo', 'QL10p048988' => 'qlo', 'QL11p001241' => 'qlo', 'QL11p028487' => 'qlo', 'RcHm_v2.0_Chr2g0105031' => 'rch', 'RcHm_v2.0_Chr2g0117811' => 'rch', 'RcHm_v2.0_Chr6g0270241' => 'rch', 'RcHm_v2.0_Chr7g0215961' => 'rch', 'RcHm_v2.0_Chr7g0231991' => 'rch', 'Rhsim01G0041500' => 'rsi', 'Rhsim01G0115000' => 'rsi', 'Rhsim01G0115400' => 'rsi', 'Rhsim01G0133600' => 'rsi', 'Rhsim01G0159900' => 'rsi', 'Rhsim02G0189400' => 'rsi', 'Rhsim03G0135600' => 'rsi', 'Rhsim03G0149900' => 'rsi', 'Rhsim04G0125600' => 'rsi', 'Rhsim05G0091700' => 'rsi', 'Rhsim05G0092900' => 'rsi', 'Rhsim06G0075000' => 'rsi', 'Rhsim07G0066400' => 'rsi', 'Rhsim07G0156400' => 'rsi', 'Rhsim07G0182200' => 'rsi', 'Rhsim07G0182300' => 'rsi', 'Rhsim08G0180400' => 'rsi', 'Rhsim09G0056800' => 'rsi', 'Rhsim10G0153300' => 'rsi', 'Rhsim11G0012700' => 'rsi', 'Rhsim12G0031800' => 'rsi', 'Rhsim12G0055400' => 'rsi', 'Rhsim12G0091400' => 'rsi', 'Rhsim13G0070800' => 'rsi', 'Rhsim13G0193300' => 'rsi', 'RhsimUnG0111600' => 'rsi', 'RhsimUnG0137500' => 'rsi', 'RhsimUnG0172900' => 'rsi', 'SGA_v2.0_scaffold11G05878' => 'sas', 'SGA_v2.0_scaffold167G38458' => 'sas', 'SGA_v2.0_scaffold19G08588' => 'sas', 'SGA_v2.0_scaffold239G43990' => 'sas', 'SGA_v2.0_scaffold260G45865' => 'sas', 'SGA_v2.0_scaffold309G48177' => 'sas', 'SGA_v2.0_scaffold76G25122' => 'sas', 'SGA_v2.0_scaffold85G26708' => 'sas', 'SHI13914' => 'shi', 'SHI30402' => 'shi', 'TWI09G0020' => 'twi', 'TWI09G0456' => 'twi', 'TWI09G1572' => 'twi', 'TWI12G0266' => 'twi', 'TWI12G1451' => 'twi', 'TWI14G0851' => 'twi', 'TWI15G0796' => 'twi', 'TWI18G0820' => 'twi', 'TWI18G1152' => 'twi', 'TWI23G0007' => 'twi', 'TWI23G0314' => 'twi', 'TWI31G0674' => 'twi', 'TWI31G0938' => 'twi', 'TWI34G0641' => 'twi', 'TWI34G1527' => 'twi', 'TWI36G0193' => 'twi', 'TWI36G0405' => 'twi', 'TWI38G0892' => 'twi', 'TWI38G0936' => 'twi', 'TWI38G2218' => 'twi', 'TWI53G0679' => 'twi', 'TWI53G0863' => 'twi', 'TWI53G1133' => 'twi', 'TWI60G0823' => 'twi', 'TWI63G0919' => 'twi', 'TWI63G1436' => 'twi', 'TWI73G0140' => 'twi', 'TWI73G0419' => 'twi', 'TWI73G0420' => 'twi', 'TWI73G1276' => 'twi', 'TWI74G0405' => 'twi', 'TWI74G0837' => 'twi', 'TWI75G0594' => 'twi', 'TWI75G1615' => 'twi', 'TWI77G0816' => 'twi', 'vmacro03831' => 'vma', 'vmacro13746' => 'vma', 'vmacro16089' => 'vma', 'vmacro22863' => 'vma', 'Zm00001eb085790' => 'zma', 'Zm00001eb114250' => 'zma', 'Zm00001eb138070' => 'zma', 'Zm00001eb167560' => 'zma', 'Zm00001eb199990' => 'zma', 'Zm00001eb368180' => 'zma', 'Zm00001eb382470' => 'zma' ) $gf_id = 'HOM05D001576' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001576' ) $data_identifier = 'HOM05D001576' $data_type = 'gf_id' $species_gene_counts = array( 'aox' => (int) 9, 'acertr' => (int) 3, 'cansat' => (int) 1, 'ccl' => (int) 4, 'cil' => (int) 145, 'camsi' => (int) 46, 'dca' => (int) 1, 'din' => (int) 1, 'fan' => (int) 12, 'fve' => (int) 9, 'gma' => (int) 5, 'han' => (int) 5, 'cav' => (int) 11, 'hma' => (int) 5, 'sun' => (int) 3, 'mdo' => (int) 3, 'mtr' => (int) 2, 'osa' => (int) 19, 'pgr' => (int) 1, 'ptr' => (int) 2, 'ppe' => (int) 6, 'qlo' => (int) 24, 'rch' => (int) 5, 'rsi' => (int) 28, 'sas' => (int) 8, 'shi' => (int) 2, 'twi' => (int) 35, 'vma' => (int) 4, 'zma' => (int) 7 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb382470' $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' => 'HOM05D001576', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '406', 'num_species' => '29' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'Aqoxy1G01456' => 'aox', 'Aqoxy1G02949' => 'aox', 'Aqoxy3G01274' => 'aox', 'Aqoxy3G02110' => 'aox', 'Aqoxy3G02268' => 'aox', 'Aqoxy5G02702' => 'aox', 'Aqoxy5G02988' => 'aox', 'Aqoxy5G03427' => 'aox', 'Aqoxy6G02363' => 'aox', 'Atru.chr1.3225' => 'acertr', 'Atru.chr8.1198' => 'acertr', 'Atru.chr9.790' => 'acertr', 'CANSAT01G3197' => 'cansat', 'Ciclev10003979m.g' => 'ccl', 'Ciclev10017471m.g' => 'ccl', 'Ciclev10018206m.g' => 'ccl', 'Ciclev10033751m.g' => 'ccl', 'CiPaw.01G000900' => 'cil', 'CiPaw.01G001000' => 'cil', 'CiPaw.01G033500' => 'cil', 'CiPaw.01G060300' => 'cil', 'CiPaw.01G070200' => 'cil', 'CiPaw.01G075100' => 'cil', 'CiPaw.01G084700' => 'cil', 'CiPaw.01G087900' => 'cil', 'CiPaw.01G092600' => 'cil', 'CiPaw.01G097200' => 'cil', 'CiPaw.01G098300' => 'cil', 'CiPaw.01G110200' => 'cil', 'CiPaw.01G118700' => 'cil', 'CiPaw.01G121200' => 'cil', 'CiPaw.01G132500' => 'cil', 'CiPaw.01G146900' => 'cil', 'CiPaw.01G174000' => 'cil', 'CiPaw.01G179900' => 'cil', 'CiPaw.01G183400' => 'cil', 'CiPaw.01G240000' => 'cil', 'CiPaw.01G283500' => 'cil', 'CiPaw.01G307400' => 'cil', 'CiPaw.02G030800' => 'cil', 'CiPaw.02G047200' => 'cil', 'CiPaw.02G050500' => 'cil', 'CiPaw.02G069900' => 'cil', 'CiPaw.02G091600' => 'cil', 'CiPaw.02G095000' => 'cil', 'CiPaw.02G131900' => 'cil', 'CiPaw.03G043000' => 'cil', 'CiPaw.03G069900' => 'cil', 'CiPaw.03G088100' => 'cil', 'CiPaw.03G089300' => 'cil', 'CiPaw.03G093100' => 'cil', 'CiPaw.03G129800' => 'cil', 'CiPaw.03G131200' => 'cil', 'CiPaw.03G134500' => 'cil', 'CiPaw.03G152100' => 'cil', 'CiPaw.03G162700' => 'cil', 'CiPaw.03G172800' => 'cil', 'CiPaw.03G175800' => 'cil', 'CiPaw.03G181800' => 'cil', 'CiPaw.03G191400' => 'cil', 'CiPaw.03G198300' => 'cil', 'CiPaw.03G201300' => 'cil', 'CiPaw.03G224700' => 'cil', 'CiPaw.03G225000' => 'cil', 'CiPaw.04G065100' => 'cil', 'CiPaw.04G080400' => 'cil', 'CiPaw.04G113500' => 'cil', 'CiPaw.04G121900' => 'cil', 'CiPaw.04G144100' => 'cil', 'CiPaw.04G176500' => 'cil', 'CiPaw.05G086200' => 'cil', 'CiPaw.05G100200' => 'cil', 'CiPaw.05G114200' => 'cil', 'CiPaw.05G126800' => 'cil', 'CiPaw.05G228800' => 'cil', 'CiPaw.05G230600' => 'cil', 'CiPaw.05G236500' => 'cil', 'CiPaw.05G244800' => 'cil', 'CiPaw.06G026600' => 'cil', 'CiPaw.06G027900' => 'cil', 'CiPaw.06G051800' => 'cil', 'CiPaw.06G128500' => 'cil', 'CiPaw.06G165900' => 'cil', 'CiPaw.07G045400' => 'cil', 'CiPaw.07G048000' => 'cil', 'CiPaw.07G052000' => 'cil', 'CiPaw.07G073800' => 'cil', 'CiPaw.07G099700' => 'cil', 'CiPaw.07G108700' => 'cil', 'CiPaw.07G120000' => 'cil', 'CiPaw.07G134100' => 'cil', 'CiPaw.07G147000' => 'cil', 'CiPaw.07G149700' => 'cil', 'CiPaw.07G178300' => 'cil', 'CiPaw.07G184900' => 'cil', 'CiPaw.08G044500' => 'cil', 'CiPaw.08G046900' => 'cil', 'CiPaw.08G047300' => 'cil', 'CiPaw.08G115400' => 'cil', 'CiPaw.08G134700' => 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'TWI09G0020' => 'twi', 'TWI09G0456' => 'twi', 'TWI09G1572' => 'twi', 'TWI12G0266' => 'twi', 'TWI12G1451' => 'twi', 'TWI14G0851' => 'twi', 'TWI15G0796' => 'twi', 'TWI18G0820' => 'twi', 'TWI18G1152' => 'twi', 'TWI23G0007' => 'twi', 'TWI23G0314' => 'twi', 'TWI31G0674' => 'twi', 'TWI31G0938' => 'twi', 'TWI34G0641' => 'twi', 'TWI34G1527' => 'twi', 'TWI36G0193' => 'twi', 'TWI36G0405' => 'twi', 'TWI38G0892' => 'twi', 'TWI38G0936' => 'twi', 'TWI38G2218' => 'twi', 'TWI53G0679' => 'twi', 'TWI53G0863' => 'twi', 'TWI53G1133' => 'twi', 'TWI60G0823' => 'twi', 'TWI63G0919' => 'twi', 'TWI63G1436' => 'twi', 'TWI73G0140' => 'twi', 'TWI73G0419' => 'twi', 'TWI73G0420' => 'twi', 'TWI73G1276' => 'twi', 'TWI74G0405' => 'twi', 'TWI74G0837' => 'twi', 'TWI75G0594' => 'twi', 'TWI75G1615' => 'twi', 'TWI77G0816' => 'twi', 'vmacro03831' => 'vma', 'vmacro13746' => 'vma', 'vmacro16089' => 'vma', 'vmacro22863' => 'vma', 'Zm00001eb085790' => 'zma', 'Zm00001eb114250' => 'zma', 'Zm00001eb138070' => 'zma', 'Zm00001eb167560' => 'zma', 'Zm00001eb199990' => 'zma', 'Zm00001eb368180' => 'zma', 'Zm00001eb382470' => 'zma' ), 'gf_id' => 'HOM05D001576', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001576' ), 'data_identifier' => 'HOM05D001576', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001576', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '406', 'num_species' => '29' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'Aqoxy1G01456' => 'aox', 'Aqoxy1G02949' => 'aox', 'Aqoxy3G01274' => 'aox', 'Aqoxy3G02110' => 'aox', 'Aqoxy3G02268' => 'aox', 'Aqoxy5G02702' => 'aox', 'Aqoxy5G02988' => 'aox', 'Aqoxy5G03427' => 'aox', 'Aqoxy6G02363' => 'aox', 'Atru.chr1.3225' => 'acertr', 'Atru.chr8.1198' => 'acertr', 'Atru.chr9.790' => 'acertr', 'CANSAT01G3197' => 'cansat', 'Ciclev10003979m.g' => 'ccl', 'Ciclev10017471m.g' => 'ccl', 'Ciclev10018206m.g' => 'ccl', 'Ciclev10033751m.g' => 'ccl', 'CiPaw.01G000900' => 'cil', 'CiPaw.01G001000' => 'cil', 'CiPaw.01G033500' => 'cil', 'CiPaw.01G060300' => 'cil', 'CiPaw.01G070200' => 'cil', 'CiPaw.01G075100' => 'cil', 'CiPaw.01G084700' => 'cil', 'CiPaw.01G087900' => 'cil', 'CiPaw.01G092600' => 'cil', 'CiPaw.01G097200' => 'cil', 'CiPaw.01G098300' => 'cil', 'CiPaw.01G110200' => 'cil', 'CiPaw.01G118700' => 'cil', 'CiPaw.01G121200' => 'cil', 'CiPaw.01G132500' => 'cil', 'CiPaw.01G146900' => 'cil', 'CiPaw.01G174000' => 'cil', 'CiPaw.01G179900' => 'cil', 'CiPaw.01G183400' => 'cil', 'CiPaw.01G240000' => 'cil', 'CiPaw.01G283500' => 'cil', 'CiPaw.01G307400' => 'cil', 'CiPaw.02G030800' => 'cil', 'CiPaw.02G047200' => 'cil', 'CiPaw.02G050500' => 'cil', 'CiPaw.02G069900' => 'cil', 'CiPaw.02G091600' => 'cil', 'CiPaw.02G095000' => 'cil', 'CiPaw.02G131900' => 'cil', 'CiPaw.03G043000' => 'cil', 'CiPaw.03G069900' => 'cil', 'CiPaw.03G088100' => 'cil', 'CiPaw.03G089300' => 'cil', 'CiPaw.03G093100' => 'cil', 'CiPaw.03G129800' => 'cil', 'CiPaw.03G131200' => 'cil', 'CiPaw.03G134500' => 'cil', 'CiPaw.03G152100' => 'cil', 'CiPaw.03G162700' => 'cil', 'CiPaw.03G172800' => 'cil', 'CiPaw.03G175800' => 'cil', 'CiPaw.03G181800' => 'cil', 'CiPaw.03G191400' => 'cil', 'CiPaw.03G198300' => 'cil', 'CiPaw.03G201300' => 'cil', 'CiPaw.03G224700' => 'cil', 'CiPaw.03G225000' => 'cil', 'CiPaw.04G065100' => 'cil', 'CiPaw.04G080400' => 'cil', 'CiPaw.04G113500' => 'cil', 'CiPaw.04G121900' => 'cil', 'CiPaw.04G144100' => 'cil', 'CiPaw.04G176500' => 'cil', 'CiPaw.05G086200' => 'cil', 'CiPaw.05G100200' => 'cil', 'CiPaw.05G114200' => 'cil', 'CiPaw.05G126800' => 'cil', 'CiPaw.05G228800' => 'cil', 'CiPaw.05G230600' => 'cil', 'CiPaw.05G236500' => 'cil', 'CiPaw.05G244800' => 'cil', 'CiPaw.06G026600' => 'cil', 'CiPaw.06G027900' => 'cil', 'CiPaw.06G051800' => 'cil', 'CiPaw.06G128500' => 'cil', 'CiPaw.06G165900' => 'cil', 'CiPaw.07G045400' => 'cil', 'CiPaw.07G048000' => 'cil', 'CiPaw.07G052000' => 'cil', 'CiPaw.07G073800' => 'cil', 'CiPaw.07G099700' => 'cil', 'CiPaw.07G108700' => 'cil', 'CiPaw.07G120000' => 'cil', 'CiPaw.07G134100' => 'cil', 'CiPaw.07G147000' => 'cil', 'CiPaw.07G149700' => 'cil', 'CiPaw.07G178300' => 'cil', 'CiPaw.07G184900' => 'cil', 'CiPaw.08G044500' => 'cil', 'CiPaw.08G046900' => 'cil', 'CiPaw.08G047300' => 'cil', 'CiPaw.08G115400' => 'cil', 'CiPaw.08G134700' => 'cil', 'CiPaw.08G157400' => 'cil', 'CiPaw.09G014300' => 'cil', 'CiPaw.09G088900' => 'cil', 'CiPaw.09G130900' => 'cil', 'CiPaw.09G133100' => 'cil', 'CiPaw.09G151300' => 'cil', 'CiPaw.09G172800' => 'cil', 'CiPaw.09G174900' => 'cil', 'CiPaw.09G175000' => 'cil', 'CiPaw.10G012800' => 'cil', 'CiPaw.10G028800' => 'cil', 'CiPaw.10G044700' => 'cil', 'CiPaw.10G067400' => 'cil', 'CiPaw.10G115900' => 'cil', 'CiPaw.10G126200' => 'cil', 'CiPaw.10G139700' => 'cil', 'CiPaw.10G155100' => 'cil', 'CiPaw.11G011300' => 'cil', 'CiPaw.11G025900' => 'cil', 'CiPaw.11G104100' => 'cil', 'CiPaw.11G142700' => 'cil', 'CiPaw.11G164500' => 'cil', 'CiPaw.11G189100' => 'cil', 'CiPaw.11G197100' => 'cil', 'CiPaw.12G006100' => 'cil', 'CiPaw.12G038500' => 'cil', 'CiPaw.12G041400' => 'cil', 'CiPaw.12G041600' => 'cil', 'CiPaw.12G051300' => 'cil', 'CiPaw.12G101800' => 'cil', 'CiPaw.12G107800' => 'cil', 'CiPaw.13G033200' => 'cil', 'CiPaw.13G129900' => 'cil', 'CiPaw.13G160200' => 'cil', 'CiPaw.14G018900' => 'cil', 'CiPaw.14G029000' => 'cil', 'CiPaw.14G031000' => 'cil', 'CiPaw.14G032000' => 'cil', 'CiPaw.14G032300' => 'cil', 'CiPaw.14G040600' => 'cil', 'CiPaw.14G060500' => 'cil', 'CiPaw.14G061500' => 'cil', 'CiPaw.14G077500' => 'cil', 'CiPaw.14G088300' => 'cil', 'CiPaw.14G108500' => 'cil', 'CiPaw.14G121300' => 'cil', 'CiPaw.14G133000' => 'cil', 'CiPaw.14G134600' => 'cil', 'CiPaw.15G027200' => 'cil', 'CiPaw.15G037700' => 'cil', 'CiPaw.15G050900' => 'cil', 'CiPaw.15G067200' => 'cil', 'CiPaw.15G072000' => 'cil', 'CiPaw.15G112900' => 'cil', 'CiPaw.15G133200' => 'cil', 'CiPaw.15G139500' => 'cil', 'CiPaw.15G155400' => 'cil', 'CiPaw.16G006000' => 'cil', 'CiPaw.16G013100' => 'cil', 'CiPaw.16G047100' => 'cil', 'CiPaw.16G048900' => 'cil', 'CiPaw.16G070300' => 'cil', 'CSS0000195' => 'camsi', 'CSS0001664' => 'camsi', 'CSS0002566' => 'camsi', 'CSS0003077' => 'camsi', 'CSS0004257' => 'camsi', 'CSS0004495' => 'camsi', 'CSS0004599' => 'camsi', 'CSS0004943' => 'camsi', 'CSS0005302' => 'camsi', 'CSS0006274' => 'camsi', 'CSS0006547' => 'camsi', 'CSS0006860' => 'camsi', 'CSS0008814' => 'camsi', 'CSS0008946' => 'camsi', 'CSS0009093' => 'camsi', 'CSS0010221' => 'camsi', 'CSS0010296' => 'camsi', 'CSS0010386' => 'camsi', 'CSS0010831' => 'camsi', 'CSS0011061' => 'camsi', 'CSS0012008' => 'camsi', 'CSS0012194' => 'camsi', 'CSS0013580' => 'camsi', 'CSS0014176' => 'camsi', 'CSS0014280' => 'camsi', 'CSS0014799' => 'camsi', 'CSS0015368' => 'camsi', 'CSS0017473' => 'camsi', 'CSS0019281' => 'camsi', 'CSS0021320' => 'camsi', 'CSS0021750' => 'camsi', 'CSS0023642' => 'camsi', 'CSS0023792' => 'camsi', 'CSS0031528' => 'camsi', 'CSS0033894' => 'camsi', 'CSS0034959' => 'camsi', 'CSS0035632' => 'camsi', 'CSS0038450' => 'camsi', 'CSS0039293' => 'camsi', 'CSS0041053' => 'camsi', 'CSS0041981' => 'camsi', 'CSS0042573' => 'camsi', 'CSS0042927' => 'camsi', 'CSS0047725' => 'camsi', 'CSS0049636' => 'camsi', 'CSS0050513' => 'camsi', 'DCAR_030203' => 'dca', 'Dinv07939' => 'din', 'FAN01G0456' => 'fan', 'FAN02G3001' => 'fan', 'FAN04G2781' => 'fan', 'FAN05G1385' => 'fan', 'FAN05G3062' => 'fan', 'FAN08G2267' => 'fan', 'FAN10G0481' => 'fan', 'FAN10G1257' => 'fan', 'FAN14G0954' => 'fan', 'FAN14G2347' => 'fan', 'FAN15G0187' => 'fan', 'FAN25G2214' => 'fan', 'FvH4_1g21031' => 'fve', 'FvH4_3g16231' => 'fve', 'FvH4_3g26413' => 'fve', 'FvH4_3g29014' => 'fve', 'FvH4_3g31921' => 'fve', 'FvH4_4g19882' => 'fve', 'FvH4_5g21960' => 'fve', 'FvH4_5g29683' => 'fve', 'FvH4_7g13271' => 'fve', 'Glyma.01G062500' => 'gma', 'Glyma.07G140900' => 'gma', 'Glyma.09G140900' => 'gma', 'Glyma.12G112700' => 'gma', 'Glyma.17G168800' => 'gma', 'HanXRQChr01g0027001' => 'han', 'HanXRQChr04g0120511' => 'han', 'HanXRQChr08g0232381' => 'han', 'HanXRQChr09g0265661' => 'han', 'HanXRQChr13g0416031' => 'han', 'Haze_05835' => 'cav', 'Haze_06597' => 'cav', 'Haze_07921' => 'cav', 'Haze_08599' => 'cav', 'Haze_10686' => 'cav', 'Haze_12994' => 'cav', 'Haze_13466' => 'cav', 'Haze_16101' => 'cav', 'Haze_17766' => 'cav', 'Haze_18456' => 'cav', 'Haze_20229' => 'cav', 'Hma1.2p1_0324F.1_g125640' => 'hma', 'Hma1.2p1_0733F.1_g210230' => 'hma', 'Hma1.2p1_0921F.1_g236870' => 'hma', 'Hma1.2p1_1313F.1_g274940' => 'hma', 'Hma1.2p1_3059F.1_g332230' => 'hma', 'Hund15925' => 'sun', 'Hund19562' => 'sun', 'Hund21925' => 'sun', 'MD03G1177400' => 'mdo', 'MD07G1026100' => 'mdo', 'MD17G1218600' => 'mdo', 'Medtr0867s0010' => 'mtr', 'Medtr6g081150' => 'mtr', 'Os01g0527900' => 'osa', 'Os02g0463725' => 'osa', 'Os02g0785600' => 'osa', 'Os03g0433733' => 'osa', 'Os04g0286500' => 'osa', 'Os05g0227800' => 'osa', 'Os06g0521000' => 'osa', 'Os06g0635500' => 'osa', 'Os06g0660650' => 'osa', 'Os07g0554400' => 'osa', 'Os08g0225900' => 'osa', 'Os08g0561000' => 'osa', 'Os09g0241700' => 'osa', 'Os09g0351900' => 'osa', 'Os11g0220700' => 'osa', 'Os11g0282700' => 'osa', 'Os12g0169300' => 'osa', 'Os12g0228500' => 'osa', 'Os12g0543800' => 'osa', 'PGR044G1547' => 'pgr', 'Potri.005G239150' => 'ptr', 'Potri.010G014250' => 'ptr', 'Prupe.1G172500' => 'ppe', 'Prupe.1G196800' => 'ppe', 'Prupe.1G279700' => 'ppe', 'Prupe.2G026400' => 'ppe', 'Prupe.3G094000' => 'ppe', 'Prupe.4G287300' => 'ppe', 'QL01p022166' => 'qlo', 'QL01p051890' => 'qlo', 'QL02p009469' => 'qlo', 'QL02p046053' => 'qlo', 'QL02p057958' => 'qlo', 'QL02p093127' => 'qlo', 'QL03p006855' => 'qlo', 'QL03p071586' => 'qlo', 'QL04p000022' => 'qlo', 'QL04p000024' => 'qlo', 'QL04p003192' => 'qlo', 'QL05p011416' => 'qlo', 'QL06p039590' => 'qlo', 'QL06p052750' => 'qlo', 'QL06p053821' => 'qlo', 'QL07p025287' => 'qlo', 'QL09p033218' => 'qlo', 'QL09p040841' => 'qlo', 'QL10p020337' => 'qlo', 'QL10p027209' => 'qlo', 'QL10p027969' => 'qlo', 'QL10p048988' => 'qlo', 'QL11p001241' => 'qlo', 'QL11p028487' => 'qlo', 'RcHm_v2.0_Chr2g0105031' => 'rch', 'RcHm_v2.0_Chr2g0117811' => 'rch', 'RcHm_v2.0_Chr6g0270241' => 'rch', 'RcHm_v2.0_Chr7g0215961' => 'rch', 'RcHm_v2.0_Chr7g0231991' => 'rch', 'Rhsim01G0041500' => 'rsi', 'Rhsim01G0115000' => 'rsi', 'Rhsim01G0115400' => 'rsi', 'Rhsim01G0133600' => 'rsi', 'Rhsim01G0159900' => 'rsi', 'Rhsim02G0189400' => 'rsi', 'Rhsim03G0135600' => 'rsi', 'Rhsim03G0149900' => 'rsi', 'Rhsim04G0125600' => 'rsi', 'Rhsim05G0091700' => 'rsi', 'Rhsim05G0092900' => 'rsi', 'Rhsim06G0075000' => 'rsi', 'Rhsim07G0066400' => 'rsi', 'Rhsim07G0156400' => 'rsi', 'Rhsim07G0182200' => 'rsi', 'Rhsim07G0182300' => 'rsi', 'Rhsim08G0180400' => 'rsi', 'Rhsim09G0056800' => 'rsi', 'Rhsim10G0153300' => 'rsi', 'Rhsim11G0012700' => 'rsi', 'Rhsim12G0031800' => 'rsi', 'Rhsim12G0055400' => 'rsi', 'Rhsim12G0091400' => 'rsi', 'Rhsim13G0070800' => 'rsi', 'Rhsim13G0193300' => 'rsi', 'RhsimUnG0111600' => 'rsi', 'RhsimUnG0137500' => 'rsi', 'RhsimUnG0172900' => 'rsi', 'SGA_v2.0_scaffold11G05878' => 'sas', 'SGA_v2.0_scaffold167G38458' => 'sas', 'SGA_v2.0_scaffold19G08588' => 'sas', 'SGA_v2.0_scaffold239G43990' => 'sas', 'SGA_v2.0_scaffold260G45865' => 'sas', 'SGA_v2.0_scaffold309G48177' => 'sas', 'SGA_v2.0_scaffold76G25122' => 'sas', 'SGA_v2.0_scaffold85G26708' => 'sas', 'SHI13914' => 'shi', 'SHI30402' => 'shi', 'TWI09G0020' => 'twi', 'TWI09G0456' => 'twi', 'TWI09G1572' => 'twi', 'TWI12G0266' => 'twi', 'TWI12G1451' => 'twi', 'TWI14G0851' => 'twi', 'TWI15G0796' => 'twi', 'TWI18G0820' => 'twi', 'TWI18G1152' => 'twi', 'TWI23G0007' => 'twi', 'TWI23G0314' => 'twi', 'TWI31G0674' => 'twi', 'TWI31G0938' => 'twi', 'TWI34G0641' => 'twi', 'TWI34G1527' => 'twi', 'TWI36G0193' => 'twi', 'TWI36G0405' => 'twi', 'TWI38G0892' => 'twi', 'TWI38G0936' => 'twi', 'TWI38G2218' => 'twi', 'TWI53G0679' => 'twi', 'TWI53G0863' => 'twi', 'TWI53G1133' => 'twi', 'TWI60G0823' => 'twi', 'TWI63G0919' => 'twi', 'TWI63G1436' => 'twi', 'TWI73G0140' => 'twi', 'TWI73G0419' => 'twi', 'TWI73G0420' => 'twi', 'TWI73G1276' => 'twi', 'TWI74G0405' => 'twi', 'TWI74G0837' => 'twi', 'TWI75G0594' => 'twi', 'TWI75G1615' => 'twi', 'TWI77G0816' => 'twi', 'vmacro03831' => 'vma', 'vmacro13746' => 'vma', 'vmacro16089' => 'vma', 'vmacro22863' => 'vma', 'Zm00001eb085790' => 'zma', 'Zm00001eb114250' => 'zma', 'Zm00001eb138070' => 'zma', 'Zm00001eb167560' => 'zma', 'Zm00001eb199990' => 'zma', 'Zm00001eb368180' => 'zma', 'Zm00001eb382470' => 'zma' ) $gf_id = 'HOM05D001576' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001576' ) $data_identifier = 'HOM05D001576' $data_type = 'gf_id' $species_gene_counts = array( 'aox' => (int) 9, 'acertr' => (int) 3, 'cansat' => (int) 1, 'ccl' => (int) 4, 'cil' => (int) 145, 'camsi' => (int) 46, 'dca' => (int) 1, 'din' => (int) 1, 'fan' => (int) 12, 'fve' => (int) 9, 'gma' => (int) 5, 'han' => (int) 5, 'cav' => (int) 11, 'hma' => (int) 5, 'sun' => (int) 3, 'mdo' => (int) 3, 'mtr' => (int) 2, 'osa' => (int) 19, 'pgr' => (int) 1, 'ptr' => (int) 2, 'ppe' => (int) 6, 'qlo' => (int) 24, 'rch' => (int) 5, 'rsi' => (int) 28, 'sas' => (int) 8, 'shi' => (int) 2, 'twi' => (int) 35, 'vma' => (int) 4, 'zma' => (int) 7 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb382470' $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' => 'HOM05D001576', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '406', 'num_species' => '29' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'Aqoxy1G01456' => 'aox', 'Aqoxy1G02949' => 'aox', 'Aqoxy3G01274' => 'aox', 'Aqoxy3G02110' => 'aox', 'Aqoxy3G02268' => 'aox', 'Aqoxy5G02702' => 'aox', 'Aqoxy5G02988' => 'aox', 'Aqoxy5G03427' => 'aox', 'Aqoxy6G02363' => 'aox', 'Atru.chr1.3225' => 'acertr', 'Atru.chr8.1198' => 'acertr', 'Atru.chr9.790' => 'acertr', 'CANSAT01G3197' => 'cansat', 'Ciclev10003979m.g' => 'ccl', 'Ciclev10017471m.g' => 'ccl', 'Ciclev10018206m.g' => 'ccl', 'Ciclev10033751m.g' => 'ccl', 'CiPaw.01G000900' => 'cil', 'CiPaw.01G001000' => 'cil', 'CiPaw.01G033500' => 'cil', 'CiPaw.01G060300' => 'cil', 'CiPaw.01G070200' => 'cil', 'CiPaw.01G075100' => 'cil', 'CiPaw.01G084700' => 'cil', 'CiPaw.01G087900' => 'cil', 'CiPaw.01G092600' => 'cil', 'CiPaw.01G097200' => 'cil', 'CiPaw.01G098300' => 'cil', 'CiPaw.01G110200' => 'cil', 'CiPaw.01G118700' => 'cil', 'CiPaw.01G121200' => 'cil', 'CiPaw.01G132500' => 'cil', 'CiPaw.01G146900' => 'cil', 'CiPaw.01G174000' => 'cil', 'CiPaw.01G179900' => 'cil', 'CiPaw.01G183400' => 'cil', 'CiPaw.01G240000' => 'cil', 'CiPaw.01G283500' => 'cil', 'CiPaw.01G307400' => 'cil', 'CiPaw.02G030800' => 'cil', 'CiPaw.02G047200' => 'cil', 'CiPaw.02G050500' => 'cil', 'CiPaw.02G069900' => 'cil', 'CiPaw.02G091600' => 'cil', 'CiPaw.02G095000' => 'cil', 'CiPaw.02G131900' => 'cil', 'CiPaw.03G043000' => 'cil', 'CiPaw.03G069900' => 'cil', 'CiPaw.03G088100' => 'cil', 'CiPaw.03G089300' => 'cil', 'CiPaw.03G093100' => 'cil', 'CiPaw.03G129800' => 'cil', 'CiPaw.03G131200' => 'cil', 'CiPaw.03G134500' => 'cil', 'CiPaw.03G152100' => 'cil', 'CiPaw.03G162700' => 'cil', 'CiPaw.03G172800' => 'cil', 'CiPaw.03G175800' => 'cil', 'CiPaw.03G181800' => 'cil', 'CiPaw.03G191400' => 'cil', 'CiPaw.03G198300' => 'cil', 'CiPaw.03G201300' => 'cil', 'CiPaw.03G224700' => 'cil', 'CiPaw.03G225000' => 'cil', 'CiPaw.04G065100' => 'cil', 'CiPaw.04G080400' => 'cil', 'CiPaw.04G113500' => 'cil', 'CiPaw.04G121900' => 'cil', 'CiPaw.04G144100' => 'cil', 'CiPaw.04G176500' => 'cil', 'CiPaw.05G086200' => 'cil', 'CiPaw.05G100200' => 'cil', 'CiPaw.05G114200' => 'cil', 'CiPaw.05G126800' => 'cil', 'CiPaw.05G228800' => 'cil', 'CiPaw.05G230600' => 'cil', 'CiPaw.05G236500' => 'cil', 'CiPaw.05G244800' => 'cil', 'CiPaw.06G026600' => 'cil', 'CiPaw.06G027900' => 'cil', 'CiPaw.06G051800' => 'cil', 'CiPaw.06G128500' => 'cil', 'CiPaw.06G165900' => 'cil', 'CiPaw.07G045400' => 'cil', 'CiPaw.07G048000' => 'cil', 'CiPaw.07G052000' => 'cil', 'CiPaw.07G073800' => 'cil', 'CiPaw.07G099700' => 'cil', 'CiPaw.07G108700' => 'cil', 'CiPaw.07G120000' => 'cil', 'CiPaw.07G134100' => 'cil', 'CiPaw.07G147000' => 'cil', 'CiPaw.07G149700' => 'cil', 'CiPaw.07G178300' => 'cil', 'CiPaw.07G184900' => 'cil', 'CiPaw.08G044500' => 'cil', 'CiPaw.08G046900' => 'cil', 'CiPaw.08G047300' => 'cil', 'CiPaw.08G115400' => 'cil', 'CiPaw.08G134700' => 'cil', 'CiPaw.08G157400' => 'cil', 'CiPaw.09G014300' => 'cil', 'CiPaw.09G088900' => 'cil', 'CiPaw.09G130900' => 'cil', 'CiPaw.09G133100' => 'cil', 'CiPaw.09G151300' => 'cil', 'CiPaw.09G172800' => 'cil', 'CiPaw.09G174900' => 'cil', 'CiPaw.09G175000' => 'cil', 'CiPaw.10G012800' => 'cil', 'CiPaw.10G028800' => 'cil', 'CiPaw.10G044700' => 'cil', 'CiPaw.10G067400' => 'cil', 'CiPaw.10G115900' => 'cil', 'CiPaw.10G126200' => 'cil', 'CiPaw.10G139700' => 'cil', 'CiPaw.10G155100' => 'cil', 'CiPaw.11G011300' => 'cil', 'CiPaw.11G025900' => 'cil', 'CiPaw.11G104100' => 'cil', 'CiPaw.11G142700' => 'cil', 'CiPaw.11G164500' => 'cil', 'CiPaw.11G189100' => 'cil', 'CiPaw.11G197100' => 'cil', 'CiPaw.12G006100' => 'cil', 'CiPaw.12G038500' => 'cil', 'CiPaw.12G041400' => 'cil', 'CiPaw.12G041600' => 'cil', 'CiPaw.12G051300' => 'cil', 'CiPaw.12G101800' => 'cil', 'CiPaw.12G107800' => 'cil', 'CiPaw.13G033200' => 'cil', 'CiPaw.13G129900' => 'cil', 'CiPaw.13G160200' => 'cil', 'CiPaw.14G018900' => 'cil', 'CiPaw.14G029000' => 'cil', 'CiPaw.14G031000' => 'cil', 'CiPaw.14G032000' => 'cil', 'CiPaw.14G032300' => 'cil', 'CiPaw.14G040600' => 'cil', 'CiPaw.14G060500' => 'cil', 'CiPaw.14G061500' => 'cil', 'CiPaw.14G077500' => 'cil', 'CiPaw.14G088300' => 'cil', 'CiPaw.14G108500' => 'cil', 'CiPaw.14G121300' => 'cil', 'CiPaw.14G133000' => 'cil', 'CiPaw.14G134600' => 'cil', 'CiPaw.15G027200' => 'cil', 'CiPaw.15G037700' => 'cil', 'CiPaw.15G050900' => 'cil', 'CiPaw.15G067200' => 'cil', 'CiPaw.15G072000' => 'cil', 'CiPaw.15G112900' => 'cil', 'CiPaw.15G133200' => 'cil', 'CiPaw.15G139500' => 'cil', 'CiPaw.15G155400' => 'cil', 'CiPaw.16G006000' => 'cil', 'CiPaw.16G013100' => 'cil', 'CiPaw.16G047100' => 'cil', 'CiPaw.16G048900' => 'cil', 'CiPaw.16G070300' => 'cil', 'CSS0000195' => 'camsi', 'CSS0001664' => 'camsi', 'CSS0002566' => 'camsi', 'CSS0003077' => 'camsi', 'CSS0004257' => 'camsi', 'CSS0004495' => 'camsi', 'CSS0004599' => 'camsi', 'CSS0004943' => 'camsi', 'CSS0005302' => 'camsi', 'CSS0006274' => 'camsi', 'CSS0006547' => 'camsi', 'CSS0006860' => 'camsi', 'CSS0008814' => 'camsi', 'CSS0008946' => 'camsi', 'CSS0009093' => 'camsi', 'CSS0010221' => 'camsi', 'CSS0010296' => 'camsi', 'CSS0010386' => 'camsi', 'CSS0010831' => 'camsi', 'CSS0011061' => 'camsi', 'CSS0012008' => 'camsi', 'CSS0012194' => 'camsi', 'CSS0013580' => 'camsi', 'CSS0014176' => 'camsi', 'CSS0014280' => 'camsi', 'CSS0014799' => 'camsi', 'CSS0015368' => 'camsi', 'CSS0017473' => 'camsi', 'CSS0019281' => 'camsi', 'CSS0021320' => 'camsi', 'CSS0021750' => 'camsi', 'CSS0023642' => 'camsi', 'CSS0023792' => 'camsi', 'CSS0031528' => 'camsi', 'CSS0033894' => 'camsi', 'CSS0034959' => 'camsi', 'CSS0035632' => 'camsi', 'CSS0038450' => 'camsi', 'CSS0039293' => 'camsi', 'CSS0041053' => 'camsi', 'CSS0041981' => 'camsi', 'CSS0042573' => 'camsi', 'CSS0042927' => 'camsi', 'CSS0047725' => 'camsi', 'CSS0049636' => 'camsi', 'CSS0050513' => 'camsi', 'DCAR_030203' => 'dca', 'Dinv07939' => 'din', 'FAN01G0456' => 'fan', 'FAN02G3001' => 'fan', 'FAN04G2781' => 'fan', 'FAN05G1385' => 'fan', 'FAN05G3062' => 'fan', 'FAN08G2267' => 'fan', 'FAN10G0481' => 'fan', 'FAN10G1257' => 'fan', 'FAN14G0954' => 'fan', 'FAN14G2347' => 'fan', 'FAN15G0187' => 'fan', 'FAN25G2214' => 'fan', 'FvH4_1g21031' => 'fve', 'FvH4_3g16231' => 'fve', 'FvH4_3g26413' => 'fve', 'FvH4_3g29014' => 'fve', 'FvH4_3g31921' => 'fve', 'FvH4_4g19882' => 'fve', 'FvH4_5g21960' => 'fve', 'FvH4_5g29683' => 'fve', 'FvH4_7g13271' => 'fve', 'Glyma.01G062500' => 'gma', 'Glyma.07G140900' => 'gma', 'Glyma.09G140900' => 'gma', 'Glyma.12G112700' => 'gma', 'Glyma.17G168800' => 'gma', 'HanXRQChr01g0027001' => 'han', 'HanXRQChr04g0120511' => 'han', 'HanXRQChr08g0232381' => 'han', 'HanXRQChr09g0265661' => 'han', 'HanXRQChr13g0416031' => 'han', 'Haze_05835' => 'cav', 'Haze_06597' => 'cav', 'Haze_07921' => 'cav', 'Haze_08599' => 'cav', 'Haze_10686' => 'cav', 'Haze_12994' => 'cav', 'Haze_13466' => 'cav', 'Haze_16101' => 'cav', 'Haze_17766' => 'cav', 'Haze_18456' => 'cav', 'Haze_20229' => 'cav', 'Hma1.2p1_0324F.1_g125640' => 'hma', 'Hma1.2p1_0733F.1_g210230' => 'hma', 'Hma1.2p1_0921F.1_g236870' => 'hma', 'Hma1.2p1_1313F.1_g274940' => 'hma', 'Hma1.2p1_3059F.1_g332230' => 'hma', 'Hund15925' => 'sun', 'Hund19562' => 'sun', 'Hund21925' => 'sun', 'MD03G1177400' => 'mdo', 'MD07G1026100' => 'mdo', 'MD17G1218600' => 'mdo', 'Medtr0867s0010' => 'mtr', 'Medtr6g081150' => 'mtr', 'Os01g0527900' => 'osa', 'Os02g0463725' => 'osa', 'Os02g0785600' => 'osa', 'Os03g0433733' => 'osa', 'Os04g0286500' => 'osa', 'Os05g0227800' => 'osa', 'Os06g0521000' => 'osa', 'Os06g0635500' => 'osa', 'Os06g0660650' => 'osa', 'Os07g0554400' => 'osa', 'Os08g0225900' => 'osa', 'Os08g0561000' => 'osa', 'Os09g0241700' => 'osa', 'Os09g0351900' => 'osa', 'Os11g0220700' => 'osa', 'Os11g0282700' => 'osa', 'Os12g0169300' => 'osa', 'Os12g0228500' => 'osa', 'Os12g0543800' => 'osa', 'PGR044G1547' => 'pgr', 'Potri.005G239150' => 'ptr', 'Potri.010G014250' => 'ptr', 'Prupe.1G172500' => 'ppe', 'Prupe.1G196800' => 'ppe', 'Prupe.1G279700' => 'ppe', 'Prupe.2G026400' => 'ppe', 'Prupe.3G094000' => 'ppe', 'Prupe.4G287300' => 'ppe', 'QL01p022166' => 'qlo', 'QL01p051890' => 'qlo', 'QL02p009469' => 'qlo', 'QL02p046053' => 'qlo', 'QL02p057958' => 'qlo', 'QL02p093127' => 'qlo', 'QL03p006855' => 'qlo', 'QL03p071586' => 'qlo', 'QL04p000022' => 'qlo', 'QL04p000024' => 'qlo', 'QL04p003192' => 'qlo', 'QL05p011416' => 'qlo', 'QL06p039590' => 'qlo', 'QL06p052750' => 'qlo', 'QL06p053821' => 'qlo', 'QL07p025287' => 'qlo', 'QL09p033218' => 'qlo', 'QL09p040841' => 'qlo', 'QL10p020337' => 'qlo', 'QL10p027209' => 'qlo', 'QL10p027969' => 'qlo', 'QL10p048988' => 'qlo', 'QL11p001241' => 'qlo', 'QL11p028487' => 'qlo', 'RcHm_v2.0_Chr2g0105031' => 'rch', 'RcHm_v2.0_Chr2g0117811' => 'rch', 'RcHm_v2.0_Chr6g0270241' => 'rch', 'RcHm_v2.0_Chr7g0215961' => 'rch', 'RcHm_v2.0_Chr7g0231991' => 'rch', 'Rhsim01G0041500' => 'rsi', 'Rhsim01G0115000' => 'rsi', 'Rhsim01G0115400' => 'rsi', 'Rhsim01G0133600' => 'rsi', 'Rhsim01G0159900' => 'rsi', 'Rhsim02G0189400' => 'rsi', 'Rhsim03G0135600' => 'rsi', 'Rhsim03G0149900' => 'rsi', 'Rhsim04G0125600' => 'rsi', 'Rhsim05G0091700' => 'rsi', 'Rhsim05G0092900' => 'rsi', 'Rhsim06G0075000' => 'rsi', 'Rhsim07G0066400' => 'rsi', 'Rhsim07G0156400' => 'rsi', 'Rhsim07G0182200' => 'rsi', 'Rhsim07G0182300' => 'rsi', 'Rhsim08G0180400' => 'rsi', 'Rhsim09G0056800' => 'rsi', 'Rhsim10G0153300' => 'rsi', 'Rhsim11G0012700' => 'rsi', 'Rhsim12G0031800' => 'rsi', 'Rhsim12G0055400' => 'rsi', 'Rhsim12G0091400' => 'rsi', 'Rhsim13G0070800' => 'rsi', 'Rhsim13G0193300' => 'rsi', 'RhsimUnG0111600' => 'rsi', 'RhsimUnG0137500' => 'rsi', 'RhsimUnG0172900' => 'rsi', 'SGA_v2.0_scaffold11G05878' => 'sas', 'SGA_v2.0_scaffold167G38458' => 'sas', 'SGA_v2.0_scaffold19G08588' => 'sas', 'SGA_v2.0_scaffold239G43990' => 'sas', 'SGA_v2.0_scaffold260G45865' => 'sas', 'SGA_v2.0_scaffold309G48177' => 'sas', 'SGA_v2.0_scaffold76G25122' => 'sas', 'SGA_v2.0_scaffold85G26708' => 'sas', 'SHI13914' => 'shi', 'SHI30402' => 'shi', 'TWI09G0020' => 'twi', 'TWI09G0456' => 'twi', 'TWI09G1572' => 'twi', 'TWI12G0266' => 'twi', 'TWI12G1451' => 'twi', 'TWI14G0851' => 'twi', 'TWI15G0796' => 'twi', 'TWI18G0820' => 'twi', 'TWI18G1152' => 'twi', 'TWI23G0007' => 'twi', 'TWI23G0314' => 'twi', 'TWI31G0674' => 'twi', 'TWI31G0938' => 'twi', 'TWI34G0641' => 'twi', 'TWI34G1527' => 'twi', 'TWI36G0193' => 'twi', 'TWI36G0405' => 'twi', 'TWI38G0892' => 'twi', 'TWI38G0936' => 'twi', 'TWI38G2218' => 'twi', 'TWI53G0679' => 'twi', 'TWI53G0863' => 'twi', 'TWI53G1133' => 'twi', 'TWI60G0823' => 'twi', 'TWI63G0919' => 'twi', 'TWI63G1436' => 'twi', 'TWI73G0140' => 'twi', 'TWI73G0419' => 'twi', 'TWI73G0420' => 'twi', 'TWI73G1276' => 'twi', 'TWI74G0405' => 'twi', 'TWI74G0837' => 'twi', 'TWI75G0594' => 'twi', 'TWI75G1615' => 'twi', 'TWI77G0816' => 'twi', 'vmacro03831' => 'vma', 'vmacro13746' => 'vma', 'vmacro16089' => 'vma', 'vmacro22863' => 'vma', 'Zm00001eb085790' => 'zma', 'Zm00001eb114250' => 'zma', 'Zm00001eb138070' => 'zma', 'Zm00001eb167560' => 'zma', 'Zm00001eb199990' => 'zma', 'Zm00001eb368180' => 'zma', 'Zm00001eb382470' => 'zma' ), 'gf_id' => 'HOM05D001576', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001576' ), 'data_identifier' => 'HOM05D001576', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001576', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '406', 'num_species' => '29' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'Aqoxy1G01456' => 'aox', 'Aqoxy1G02949' => 'aox', 'Aqoxy3G01274' => 'aox', 'Aqoxy3G02110' => 'aox', 'Aqoxy3G02268' => 'aox', 'Aqoxy5G02702' => 'aox', 'Aqoxy5G02988' => 'aox', 'Aqoxy5G03427' => 'aox', 'Aqoxy6G02363' => 'aox', 'Atru.chr1.3225' => 'acertr', 'Atru.chr8.1198' => 'acertr', 'Atru.chr9.790' => 'acertr', 'CANSAT01G3197' => 'cansat', 'Ciclev10003979m.g' => 'ccl', 'Ciclev10017471m.g' => 'ccl', 'Ciclev10018206m.g' => 'ccl', 'Ciclev10033751m.g' => 'ccl', 'CiPaw.01G000900' => 'cil', 'CiPaw.01G001000' => 'cil', 'CiPaw.01G033500' => 'cil', 'CiPaw.01G060300' => 'cil', 'CiPaw.01G070200' => 'cil', 'CiPaw.01G075100' => 'cil', 'CiPaw.01G084700' => 'cil', 'CiPaw.01G087900' => 'cil', 'CiPaw.01G092600' => 'cil', 'CiPaw.01G097200' => 'cil', 'CiPaw.01G098300' => 'cil', 'CiPaw.01G110200' => 'cil', 'CiPaw.01G118700' => 'cil', 'CiPaw.01G121200' => 'cil', 'CiPaw.01G132500' => 'cil', 'CiPaw.01G146900' => 'cil', 'CiPaw.01G174000' => 'cil', 'CiPaw.01G179900' => 'cil', 'CiPaw.01G183400' => 'cil', 'CiPaw.01G240000' => 'cil', 'CiPaw.01G283500' => 'cil', 'CiPaw.01G307400' => 'cil', 'CiPaw.02G030800' => 'cil', 'CiPaw.02G047200' => 'cil', 'CiPaw.02G050500' => 'cil', 'CiPaw.02G069900' => 'cil', 'CiPaw.02G091600' => 'cil', 'CiPaw.02G095000' => 'cil', 'CiPaw.02G131900' => 'cil', 'CiPaw.03G043000' => 'cil', 'CiPaw.03G069900' => 'cil', 'CiPaw.03G088100' => 'cil', 'CiPaw.03G089300' => 'cil', 'CiPaw.03G093100' => 'cil', 'CiPaw.03G129800' => 'cil', 'CiPaw.03G131200' => 'cil', 'CiPaw.03G134500' => 'cil', 'CiPaw.03G152100' => 'cil', 'CiPaw.03G162700' => 'cil', 'CiPaw.03G172800' => 'cil', 'CiPaw.03G175800' => 'cil', 'CiPaw.03G181800' => 'cil', 'CiPaw.03G191400' => 'cil', 'CiPaw.03G198300' => 'cil', 'CiPaw.03G201300' => 'cil', 'CiPaw.03G224700' => 'cil', 'CiPaw.03G225000' => 'cil', 'CiPaw.04G065100' => 'cil', 'CiPaw.04G080400' => 'cil', 'CiPaw.04G113500' => 'cil', 'CiPaw.04G121900' => 'cil', 'CiPaw.04G144100' => 'cil', 'CiPaw.04G176500' => 'cil', 'CiPaw.05G086200' => 'cil', 'CiPaw.05G100200' => 'cil', 'CiPaw.05G114200' => 'cil', 'CiPaw.05G126800' => 'cil', 'CiPaw.05G228800' => 'cil', 'CiPaw.05G230600' => 'cil', 'CiPaw.05G236500' => 'cil', 'CiPaw.05G244800' => 'cil', 'CiPaw.06G026600' => 'cil', 'CiPaw.06G027900' => 'cil', 'CiPaw.06G051800' => 'cil', 'CiPaw.06G128500' => 'cil', 'CiPaw.06G165900' => 'cil', 'CiPaw.07G045400' => 'cil', 'CiPaw.07G048000' => 'cil', 'CiPaw.07G052000' => 'cil', 'CiPaw.07G073800' => 'cil', 'CiPaw.07G099700' => 'cil', 'CiPaw.07G108700' => 'cil', 'CiPaw.07G120000' => 'cil', 'CiPaw.07G134100' => 'cil', 'CiPaw.07G147000' => 'cil', 'CiPaw.07G149700' => 'cil', 'CiPaw.07G178300' => 'cil', 'CiPaw.07G184900' => 'cil', 'CiPaw.08G044500' => 'cil', 'CiPaw.08G046900' => 'cil', 'CiPaw.08G047300' => 'cil', 'CiPaw.08G115400' => 'cil', 'CiPaw.08G134700' => 'cil', 'CiPaw.08G157400' => 'cil', 'CiPaw.09G014300' => 'cil', 'CiPaw.09G088900' => 'cil', 'CiPaw.09G130900' => 'cil', 'CiPaw.09G133100' => 'cil', 'CiPaw.09G151300' => 'cil', 'CiPaw.09G172800' => 'cil', 'CiPaw.09G174900' => 'cil', 'CiPaw.09G175000' => 'cil', 'CiPaw.10G012800' => 'cil', 'CiPaw.10G028800' => 'cil', 'CiPaw.10G044700' => 'cil', 'CiPaw.10G067400' => 'cil', 'CiPaw.10G115900' => 'cil', 'CiPaw.10G126200' => 'cil', 'CiPaw.10G139700' => 'cil', 'CiPaw.10G155100' => 'cil', 'CiPaw.11G011300' => 'cil', 'CiPaw.11G025900' => 'cil', 'CiPaw.11G104100' => 'cil', 'CiPaw.11G142700' => 'cil', 'CiPaw.11G164500' => 'cil', 'CiPaw.11G189100' => 'cil', 'CiPaw.11G197100' => 'cil', 'CiPaw.12G006100' => 'cil', 'CiPaw.12G038500' => 'cil', 'CiPaw.12G041400' => 'cil', 'CiPaw.12G041600' => 'cil', 'CiPaw.12G051300' => 'cil', 'CiPaw.12G101800' => 'cil', 'CiPaw.12G107800' => 'cil', 'CiPaw.13G033200' => 'cil', 'CiPaw.13G129900' => 'cil', 'CiPaw.13G160200' => 'cil', 'CiPaw.14G018900' => 'cil', 'CiPaw.14G029000' => 'cil', 'CiPaw.14G031000' => 'cil', 'CiPaw.14G032000' => 'cil', 'CiPaw.14G032300' => 'cil', 'CiPaw.14G040600' => 'cil', 'CiPaw.14G060500' => 'cil', 'CiPaw.14G061500' => 'cil', 'CiPaw.14G077500' => 'cil', 'CiPaw.14G088300' => 'cil', 'CiPaw.14G108500' => 'cil', 'CiPaw.14G121300' => 'cil', 'CiPaw.14G133000' => 'cil', 'CiPaw.14G134600' => 'cil', 'CiPaw.15G027200' => 'cil', 'CiPaw.15G037700' => 'cil', 'CiPaw.15G050900' => 'cil', 'CiPaw.15G067200' => 'cil', 'CiPaw.15G072000' => 'cil', 'CiPaw.15G112900' => 'cil', 'CiPaw.15G133200' => 'cil', 'CiPaw.15G139500' => 'cil', 'CiPaw.15G155400' => 'cil', 'CiPaw.16G006000' => 'cil', 'CiPaw.16G013100' => 'cil', 'CiPaw.16G047100' => 'cil', 'CiPaw.16G048900' => 'cil', 'CiPaw.16G070300' => 'cil', 'CSS0000195' => 'camsi', 'CSS0001664' => 'camsi', 'CSS0002566' => 'camsi', 'CSS0003077' => 'camsi', 'CSS0004257' => 'camsi', 'CSS0004495' => 'camsi', 'CSS0004599' => 'camsi', 'CSS0004943' => 'camsi', 'CSS0005302' => 'camsi', 'CSS0006274' => 'camsi', 'CSS0006547' => 'camsi', 'CSS0006860' => 'camsi', 'CSS0008814' => 'camsi', 'CSS0008946' => 'camsi', 'CSS0009093' => 'camsi', 'CSS0010221' => 'camsi', 'CSS0010296' => 'camsi', 'CSS0010386' => 'camsi', 'CSS0010831' => 'camsi', 'CSS0011061' => 'camsi', 'CSS0012008' => 'camsi', 'CSS0012194' => 'camsi', 'CSS0013580' => 'camsi', 'CSS0014176' => 'camsi', 'CSS0014280' => 'camsi', 'CSS0014799' => 'camsi', 'CSS0015368' => 'camsi', 'CSS0017473' => 'camsi', 'CSS0019281' => 'camsi', 'CSS0021320' => 'camsi', 'CSS0021750' => 'camsi', 'CSS0023642' => 'camsi', 'CSS0023792' => 'camsi', 'CSS0031528' => 'camsi', 'CSS0033894' => 'camsi', 'CSS0034959' => 'camsi', 'CSS0035632' => 'camsi', 'CSS0038450' => 'camsi', 'CSS0039293' => 'camsi', 'CSS0041053' => 'camsi', 'CSS0041981' => 'camsi', 'CSS0042573' => 'camsi', 'CSS0042927' => 'camsi', 'CSS0047725' => 'camsi', 'CSS0049636' => 'camsi', 'CSS0050513' => 'camsi', 'DCAR_030203' => 'dca', 'Dinv07939' => 'din', 'FAN01G0456' => 'fan', 'FAN02G3001' => 'fan', 'FAN04G2781' => 'fan', 'FAN05G1385' => 'fan', 'FAN05G3062' => 'fan', 'FAN08G2267' => 'fan', 'FAN10G0481' => 'fan', 'FAN10G1257' => 'fan', 'FAN14G0954' => 'fan', 'FAN14G2347' => 'fan', 'FAN15G0187' => 'fan', 'FAN25G2214' => 'fan', 'FvH4_1g21031' => 'fve', 'FvH4_3g16231' => 'fve', 'FvH4_3g26413' => 'fve', 'FvH4_3g29014' => 'fve', 'FvH4_3g31921' => 'fve', 'FvH4_4g19882' => 'fve', 'FvH4_5g21960' => 'fve', 'FvH4_5g29683' => 'fve', 'FvH4_7g13271' => 'fve', 'Glyma.01G062500' => 'gma', 'Glyma.07G140900' => 'gma', 'Glyma.09G140900' => 'gma', 'Glyma.12G112700' => 'gma', 'Glyma.17G168800' => 'gma', 'HanXRQChr01g0027001' => 'han', 'HanXRQChr04g0120511' => 'han', 'HanXRQChr08g0232381' => 'han', 'HanXRQChr09g0265661' => 'han', 'HanXRQChr13g0416031' => 'han', 'Haze_05835' => 'cav', 'Haze_06597' => 'cav', 'Haze_07921' => 'cav', 'Haze_08599' => 'cav', 'Haze_10686' => 'cav', 'Haze_12994' => 'cav', 'Haze_13466' => 'cav', 'Haze_16101' => 'cav', 'Haze_17766' => 'cav', 'Haze_18456' => 'cav', 'Haze_20229' => 'cav', 'Hma1.2p1_0324F.1_g125640' => 'hma', 'Hma1.2p1_0733F.1_g210230' => 'hma', 'Hma1.2p1_0921F.1_g236870' => 'hma', 'Hma1.2p1_1313F.1_g274940' => 'hma', 'Hma1.2p1_3059F.1_g332230' => 'hma', 'Hund15925' => 'sun', 'Hund19562' => 'sun', 'Hund21925' => 'sun', 'MD03G1177400' => 'mdo', 'MD07G1026100' => 'mdo', 'MD17G1218600' => 'mdo', 'Medtr0867s0010' => 'mtr', 'Medtr6g081150' => 'mtr', 'Os01g0527900' => 'osa', 'Os02g0463725' => 'osa', 'Os02g0785600' => 'osa', 'Os03g0433733' => 'osa', 'Os04g0286500' => 'osa', 'Os05g0227800' => 'osa', 'Os06g0521000' => 'osa', 'Os06g0635500' => 'osa', 'Os06g0660650' => 'osa', 'Os07g0554400' => 'osa', 'Os08g0225900' => 'osa', 'Os08g0561000' => 'osa', 'Os09g0241700' => 'osa', 'Os09g0351900' => 'osa', 'Os11g0220700' => 'osa', 'Os11g0282700' => 'osa', 'Os12g0169300' => 'osa', 'Os12g0228500' => 'osa', 'Os12g0543800' => 'osa', 'PGR044G1547' => 'pgr', 'Potri.005G239150' => 'ptr', 'Potri.010G014250' => 'ptr', 'Prupe.1G172500' => 'ppe', 'Prupe.1G196800' => 'ppe', 'Prupe.1G279700' => 'ppe', 'Prupe.2G026400' => 'ppe', 'Prupe.3G094000' => 'ppe', 'Prupe.4G287300' => 'ppe', 'QL01p022166' => 'qlo', 'QL01p051890' => 'qlo', 'QL02p009469' => 'qlo', 'QL02p046053' => 'qlo', 'QL02p057958' => 'qlo', 'QL02p093127' => 'qlo', 'QL03p006855' => 'qlo', 'QL03p071586' => 'qlo', 'QL04p000022' => 'qlo', 'QL04p000024' => 'qlo', 'QL04p003192' => 'qlo', 'QL05p011416' => 'qlo', 'QL06p039590' => 'qlo', 'QL06p052750' => 'qlo', 'QL06p053821' => 'qlo', 'QL07p025287' => 'qlo', 'QL09p033218' => 'qlo', 'QL09p040841' => 'qlo', 'QL10p020337' => 'qlo', 'QL10p027209' => 'qlo', 'QL10p027969' => 'qlo', 'QL10p048988' => 'qlo', 'QL11p001241' => 'qlo', 'QL11p028487' => 'qlo', 'RcHm_v2.0_Chr2g0105031' => 'rch', 'RcHm_v2.0_Chr2g0117811' => 'rch', 'RcHm_v2.0_Chr6g0270241' => 'rch', 'RcHm_v2.0_Chr7g0215961' => 'rch', 'RcHm_v2.0_Chr7g0231991' => 'rch', 'Rhsim01G0041500' => 'rsi', 'Rhsim01G0115000' => 'rsi', 'Rhsim01G0115400' => 'rsi', 'Rhsim01G0133600' => 'rsi', 'Rhsim01G0159900' => 'rsi', 'Rhsim02G0189400' => 'rsi', 'Rhsim03G0135600' => 'rsi', 'Rhsim03G0149900' => 'rsi', 'Rhsim04G0125600' => 'rsi', 'Rhsim05G0091700' => 'rsi', 'Rhsim05G0092900' => 'rsi', 'Rhsim06G0075000' => 'rsi', 'Rhsim07G0066400' => 'rsi', 'Rhsim07G0156400' => 'rsi', 'Rhsim07G0182200' => 'rsi', 'Rhsim07G0182300' => 'rsi', 'Rhsim08G0180400' => 'rsi', 'Rhsim09G0056800' => 'rsi', 'Rhsim10G0153300' => 'rsi', 'Rhsim11G0012700' => 'rsi', 'Rhsim12G0031800' => 'rsi', 'Rhsim12G0055400' => 'rsi', 'Rhsim12G0091400' => 'rsi', 'Rhsim13G0070800' => 'rsi', 'Rhsim13G0193300' => 'rsi', 'RhsimUnG0111600' => 'rsi', 'RhsimUnG0137500' => 'rsi', 'RhsimUnG0172900' => 'rsi', 'SGA_v2.0_scaffold11G05878' => 'sas', 'SGA_v2.0_scaffold167G38458' => 'sas', 'SGA_v2.0_scaffold19G08588' => 'sas', 'SGA_v2.0_scaffold239G43990' => 'sas', 'SGA_v2.0_scaffold260G45865' => 'sas', 'SGA_v2.0_scaffold309G48177' => 'sas', 'SGA_v2.0_scaffold76G25122' => 'sas', 'SGA_v2.0_scaffold85G26708' => 'sas', 'SHI13914' => 'shi', 'SHI30402' => 'shi', 'TWI09G0020' => 'twi', 'TWI09G0456' => 'twi', 'TWI09G1572' => 'twi', 'TWI12G0266' => 'twi', 'TWI12G1451' => 'twi', 'TWI14G0851' => 'twi', 'TWI15G0796' => 'twi', 'TWI18G0820' => 'twi', 'TWI18G1152' => 'twi', 'TWI23G0007' => 'twi', 'TWI23G0314' => 'twi', 'TWI31G0674' => 'twi', 'TWI31G0938' => 'twi', 'TWI34G0641' => 'twi', 'TWI34G1527' => 'twi', 'TWI36G0193' => 'twi', 'TWI36G0405' => 'twi', 'TWI38G0892' => 'twi', 'TWI38G0936' => 'twi', 'TWI38G2218' => 'twi', 'TWI53G0679' => 'twi', 'TWI53G0863' => 'twi', 'TWI53G1133' => 'twi', 'TWI60G0823' => 'twi', 'TWI63G0919' => 'twi', 'TWI63G1436' => 'twi', 'TWI73G0140' => 'twi', 'TWI73G0419' => 'twi', 'TWI73G0420' => 'twi', 'TWI73G1276' => 'twi', 'TWI74G0405' => 'twi', 'TWI74G0837' => 'twi', 'TWI75G0594' => 'twi', 'TWI75G1615' => 'twi', 'TWI77G0816' => 'twi', 'vmacro03831' => 'vma', 'vmacro13746' => 'vma', 'vmacro16089' => 'vma', 'vmacro22863' => 'vma', 'Zm00001eb085790' => 'zma', 'Zm00001eb114250' => 'zma', 'Zm00001eb138070' => 'zma', 'Zm00001eb167560' => 'zma', 'Zm00001eb199990' => 'zma', 'Zm00001eb368180' => 'zma', 'Zm00001eb382470' => 'zma' ) $gf_id = 'HOM05D001576' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001576' ) $data_identifier = 'HOM05D001576' $data_type = 'gf_id' $species_gene_counts = array( 'aox' => (int) 9, 'acertr' => (int) 3, 'cansat' => (int) 1, 'ccl' => (int) 4, 'cil' => (int) 145, 'camsi' => (int) 46, 'dca' => (int) 1, 'din' => (int) 1, 'fan' => (int) 12, 'fve' => (int) 9, 'gma' => (int) 5, 'han' => (int) 5, 'cav' => (int) 11, 'hma' => (int) 5, 'sun' => (int) 3, 'mdo' => (int) 3, 'mtr' => (int) 2, 'osa' => (int) 19, 'pgr' => (int) 1, 'ptr' => (int) 2, 'ppe' => (int) 6, 'qlo' => (int) 24, 'rch' => (int) 5, 'rsi' => (int) 28, 'sas' => (int) 8, 'shi' => (int) 2, 'twi' => (int) 35, 'vma' => (int) 4, 'zma' => (int) 7 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb382470' $species_info = array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ) $local_species = 'han' $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' => 'HOM05D001576', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '406', 'num_species' => '29' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'Aqoxy1G01456' => 'aox', 'Aqoxy1G02949' => 'aox', 'Aqoxy3G01274' => 'aox', 'Aqoxy3G02110' => 'aox', 'Aqoxy3G02268' => 'aox', 'Aqoxy5G02702' => 'aox', 'Aqoxy5G02988' => 'aox', 'Aqoxy5G03427' => 'aox', 'Aqoxy6G02363' => 'aox', 'Atru.chr1.3225' => 'acertr', 'Atru.chr8.1198' => 'acertr', 'Atru.chr9.790' => 'acertr', 'CANSAT01G3197' => 'cansat', 'Ciclev10003979m.g' => 'ccl', 'Ciclev10017471m.g' => 'ccl', 'Ciclev10018206m.g' => 'ccl', 'Ciclev10033751m.g' => 'ccl', 'CiPaw.01G000900' => 'cil', 'CiPaw.01G001000' => 'cil', 'CiPaw.01G033500' => 'cil', 'CiPaw.01G060300' => 'cil', 'CiPaw.01G070200' => 'cil', 'CiPaw.01G075100' => 'cil', 'CiPaw.01G084700' => 'cil', 'CiPaw.01G087900' => 'cil', 'CiPaw.01G092600' => 'cil', 'CiPaw.01G097200' => 'cil', 'CiPaw.01G098300' => 'cil', 'CiPaw.01G110200' => 'cil', 'CiPaw.01G118700' => 'cil', 'CiPaw.01G121200' => 'cil', 'CiPaw.01G132500' => 'cil', 'CiPaw.01G146900' => 'cil', 'CiPaw.01G174000' => 'cil', 'CiPaw.01G179900' => 'cil', 'CiPaw.01G183400' => 'cil', 'CiPaw.01G240000' => 'cil', 'CiPaw.01G283500' => 'cil', 'CiPaw.01G307400' => 'cil', 'CiPaw.02G030800' => 'cil', 'CiPaw.02G047200' => 'cil', 'CiPaw.02G050500' => 'cil', 'CiPaw.02G069900' => 'cil', 'CiPaw.02G091600' => 'cil', 'CiPaw.02G095000' => 'cil', 'CiPaw.02G131900' => 'cil', 'CiPaw.03G043000' => 'cil', 'CiPaw.03G069900' => 'cil', 'CiPaw.03G088100' => 'cil', 'CiPaw.03G089300' => 'cil', 'CiPaw.03G093100' => 'cil', 'CiPaw.03G129800' => 'cil', 'CiPaw.03G131200' => 'cil', 'CiPaw.03G134500' => 'cil', 'CiPaw.03G152100' => 'cil', 'CiPaw.03G162700' => 'cil', 'CiPaw.03G172800' => 'cil', 'CiPaw.03G175800' => 'cil', 'CiPaw.03G181800' => 'cil', 'CiPaw.03G191400' => 'cil', 'CiPaw.03G198300' => 'cil', 'CiPaw.03G201300' => 'cil', 'CiPaw.03G224700' => 'cil', 'CiPaw.03G225000' => 'cil', 'CiPaw.04G065100' => 'cil', 'CiPaw.04G080400' => 'cil', 'CiPaw.04G113500' => 'cil', 'CiPaw.04G121900' => 'cil', 'CiPaw.04G144100' => 'cil', 'CiPaw.04G176500' => 'cil', 'CiPaw.05G086200' => 'cil', 'CiPaw.05G100200' => 'cil', 'CiPaw.05G114200' => 'cil', 'CiPaw.05G126800' => 'cil', 'CiPaw.05G228800' => 'cil', 'CiPaw.05G230600' => 'cil', 'CiPaw.05G236500' => 'cil', 'CiPaw.05G244800' => 'cil', 'CiPaw.06G026600' => 'cil', 'CiPaw.06G027900' => 'cil', 'CiPaw.06G051800' => 'cil', 'CiPaw.06G128500' => 'cil', 'CiPaw.06G165900' => 'cil', 'CiPaw.07G045400' => 'cil', 'CiPaw.07G048000' => 'cil', 'CiPaw.07G052000' => 'cil', 'CiPaw.07G073800' => 'cil', 'CiPaw.07G099700' => 'cil', 'CiPaw.07G108700' => 'cil', 'CiPaw.07G120000' => 'cil', 'CiPaw.07G134100' => 'cil', 'CiPaw.07G147000' => 'cil', 'CiPaw.07G149700' => 'cil', 'CiPaw.07G178300' => 'cil', 'CiPaw.07G184900' => 'cil', 'CiPaw.08G044500' => 'cil', 'CiPaw.08G046900' => 'cil', 'CiPaw.08G047300' => 'cil', 'CiPaw.08G115400' => 'cil', 'CiPaw.08G134700' => 'cil', 'CiPaw.08G157400' => 'cil', 'CiPaw.09G014300' => 'cil', 'CiPaw.09G088900' => 'cil', 'CiPaw.09G130900' => 'cil', 'CiPaw.09G133100' => 'cil', 'CiPaw.09G151300' => 'cil', 'CiPaw.09G172800' => 'cil', 'CiPaw.09G174900' => 'cil', 'CiPaw.09G175000' => 'cil', 'CiPaw.10G012800' => 'cil', 'CiPaw.10G028800' => 'cil', 'CiPaw.10G044700' => 'cil', 'CiPaw.10G067400' => 'cil', 'CiPaw.10G115900' => 'cil', 'CiPaw.10G126200' => 'cil', 'CiPaw.10G139700' => 'cil', 'CiPaw.10G155100' => 'cil', 'CiPaw.11G011300' => 'cil', 'CiPaw.11G025900' => 'cil', 'CiPaw.11G104100' => 'cil', 'CiPaw.11G142700' => 'cil', 'CiPaw.11G164500' => 'cil', 'CiPaw.11G189100' => 'cil', 'CiPaw.11G197100' => 'cil', 'CiPaw.12G006100' => 'cil', 'CiPaw.12G038500' => 'cil', 'CiPaw.12G041400' => 'cil', 'CiPaw.12G041600' => 'cil', 'CiPaw.12G051300' => 'cil', 'CiPaw.12G101800' => 'cil', 'CiPaw.12G107800' => 'cil', 'CiPaw.13G033200' => 'cil', 'CiPaw.13G129900' => 'cil', 'CiPaw.13G160200' => 'cil', 'CiPaw.14G018900' => 'cil', 'CiPaw.14G029000' => 'cil', 'CiPaw.14G031000' => 'cil', 'CiPaw.14G032000' => 'cil', 'CiPaw.14G032300' => 'cil', 'CiPaw.14G040600' => 'cil', 'CiPaw.14G060500' => 'cil', 'CiPaw.14G061500' => 'cil', 'CiPaw.14G077500' => 'cil', 'CiPaw.14G088300' => 'cil', 'CiPaw.14G108500' => 'cil', 'CiPaw.14G121300' => 'cil', 'CiPaw.14G133000' => 'cil', 'CiPaw.14G134600' => 'cil', 'CiPaw.15G027200' => 'cil', 'CiPaw.15G037700' => 'cil', 'CiPaw.15G050900' => 'cil', 'CiPaw.15G067200' => 'cil', 'CiPaw.15G072000' => 'cil', 'CiPaw.15G112900' => 'cil', 'CiPaw.15G133200' => 'cil', 'CiPaw.15G139500' => 'cil', 'CiPaw.15G155400' => 'cil', 'CiPaw.16G006000' => 'cil', 'CiPaw.16G013100' => 'cil', 'CiPaw.16G047100' => 'cil', 'CiPaw.16G048900' => 'cil', 'CiPaw.16G070300' => 'cil', 'CSS0000195' => 'camsi', 'CSS0001664' => 'camsi', 'CSS0002566' => 'camsi', 'CSS0003077' => 'camsi', 'CSS0004257' => 'camsi', 'CSS0004495' => 'camsi', 'CSS0004599' => 'camsi', 'CSS0004943' => 'camsi', 'CSS0005302' => 'camsi', 'CSS0006274' => 'camsi', 'CSS0006547' => 'camsi', 'CSS0006860' => 'camsi', 'CSS0008814' => 'camsi', 'CSS0008946' => 'camsi', 'CSS0009093' => 'camsi', 'CSS0010221' => 'camsi', 'CSS0010296' => 'camsi', 'CSS0010386' => 'camsi', 'CSS0010831' => 'camsi', 'CSS0011061' => 'camsi', 'CSS0012008' => 'camsi', 'CSS0012194' => 'camsi', 'CSS0013580' => 'camsi', 'CSS0014176' => 'camsi', 'CSS0014280' => 'camsi', 'CSS0014799' => 'camsi', 'CSS0015368' => 'camsi', 'CSS0017473' => 'camsi', 'CSS0019281' => 'camsi', 'CSS0021320' => 'camsi', 'CSS0021750' => 'camsi', 'CSS0023642' => 'camsi', 'CSS0023792' => 'camsi', 'CSS0031528' => 'camsi', 'CSS0033894' => 'camsi', 'CSS0034959' => 'camsi', 'CSS0035632' => 'camsi', 'CSS0038450' => 'camsi', 'CSS0039293' => 'camsi', 'CSS0041053' => 'camsi', 'CSS0041981' => 'camsi', 'CSS0042573' => 'camsi', 'CSS0042927' => 'camsi', 'CSS0047725' => 'camsi', 'CSS0049636' => 'camsi', 'CSS0050513' => 'camsi', 'DCAR_030203' => 'dca', 'Dinv07939' => 'din', 'FAN01G0456' => 'fan', 'FAN02G3001' => 'fan', 'FAN04G2781' => 'fan', 'FAN05G1385' => 'fan', 'FAN05G3062' => 'fan', 'FAN08G2267' => 'fan', 'FAN10G0481' => 'fan', 'FAN10G1257' => 'fan', 'FAN14G0954' => 'fan', 'FAN14G2347' => 'fan', 'FAN15G0187' => 'fan', 'FAN25G2214' => 'fan', 'FvH4_1g21031' => 'fve', 'FvH4_3g16231' => 'fve', 'FvH4_3g26413' => 'fve', 'FvH4_3g29014' => 'fve', 'FvH4_3g31921' => 'fve', 'FvH4_4g19882' => 'fve', 'FvH4_5g21960' => 'fve', 'FvH4_5g29683' => 'fve', 'FvH4_7g13271' => 'fve', 'Glyma.01G062500' => 'gma', 'Glyma.07G140900' => 'gma', 'Glyma.09G140900' => 'gma', 'Glyma.12G112700' => 'gma', 'Glyma.17G168800' => 'gma', 'HanXRQChr01g0027001' => 'han', 'HanXRQChr04g0120511' => 'han', 'HanXRQChr08g0232381' => 'han', 'HanXRQChr09g0265661' => 'han', 'HanXRQChr13g0416031' => 'han', 'Haze_05835' => 'cav', 'Haze_06597' => 'cav', 'Haze_07921' => 'cav', 'Haze_08599' => 'cav', 'Haze_10686' => 'cav', 'Haze_12994' => 'cav', 'Haze_13466' => 'cav', 'Haze_16101' => 'cav', 'Haze_17766' => 'cav', 'Haze_18456' => 'cav', 'Haze_20229' => 'cav', 'Hma1.2p1_0324F.1_g125640' => 'hma', 'Hma1.2p1_0733F.1_g210230' => 'hma', 'Hma1.2p1_0921F.1_g236870' => 'hma', 'Hma1.2p1_1313F.1_g274940' => 'hma', 'Hma1.2p1_3059F.1_g332230' => 'hma', 'Hund15925' => 'sun', 'Hund19562' => 'sun', 'Hund21925' => 'sun', 'MD03G1177400' => 'mdo', 'MD07G1026100' => 'mdo', 'MD17G1218600' => 'mdo', 'Medtr0867s0010' => 'mtr', 'Medtr6g081150' => 'mtr', 'Os01g0527900' => 'osa', 'Os02g0463725' => 'osa', 'Os02g0785600' => 'osa', 'Os03g0433733' => 'osa', 'Os04g0286500' => 'osa', 'Os05g0227800' => 'osa', 'Os06g0521000' => 'osa', 'Os06g0635500' => 'osa', 'Os06g0660650' => 'osa', 'Os07g0554400' => 'osa', 'Os08g0225900' => 'osa', 'Os08g0561000' => 'osa', 'Os09g0241700' => 'osa', 'Os09g0351900' => 'osa', 'Os11g0220700' => 'osa', 'Os11g0282700' => 'osa', 'Os12g0169300' => 'osa', 'Os12g0228500' => 'osa', 'Os12g0543800' => 'osa', 'PGR044G1547' => 'pgr', 'Potri.005G239150' => 'ptr', 'Potri.010G014250' => 'ptr', 'Prupe.1G172500' => 'ppe', 'Prupe.1G196800' => 'ppe', 'Prupe.1G279700' => 'ppe', 'Prupe.2G026400' => 'ppe', 'Prupe.3G094000' => 'ppe', 'Prupe.4G287300' => 'ppe', 'QL01p022166' => 'qlo', 'QL01p051890' => 'qlo', 'QL02p009469' => 'qlo', 'QL02p046053' => 'qlo', 'QL02p057958' => 'qlo', 'QL02p093127' => 'qlo', 'QL03p006855' => 'qlo', 'QL03p071586' => 'qlo', 'QL04p000022' => 'qlo', 'QL04p000024' => 'qlo', 'QL04p003192' => 'qlo', 'QL05p011416' => 'qlo', 'QL06p039590' => 'qlo', 'QL06p052750' => 'qlo', 'QL06p053821' => 'qlo', 'QL07p025287' => 'qlo', 'QL09p033218' => 'qlo', 'QL09p040841' => 'qlo', 'QL10p020337' => 'qlo', 'QL10p027209' => 'qlo', 'QL10p027969' => 'qlo', 'QL10p048988' => 'qlo', 'QL11p001241' => 'qlo', 'QL11p028487' => 'qlo', 'RcHm_v2.0_Chr2g0105031' => 'rch', 'RcHm_v2.0_Chr2g0117811' => 'rch', 'RcHm_v2.0_Chr6g0270241' => 'rch', 'RcHm_v2.0_Chr7g0215961' => 'rch', 'RcHm_v2.0_Chr7g0231991' => 'rch', 'Rhsim01G0041500' => 'rsi', 'Rhsim01G0115000' => 'rsi', 'Rhsim01G0115400' => 'rsi', 'Rhsim01G0133600' => 'rsi', 'Rhsim01G0159900' => 'rsi', 'Rhsim02G0189400' => 'rsi', 'Rhsim03G0135600' => 'rsi', 'Rhsim03G0149900' => 'rsi', 'Rhsim04G0125600' => 'rsi', 'Rhsim05G0091700' => 'rsi', 'Rhsim05G0092900' => 'rsi', 'Rhsim06G0075000' => 'rsi', 'Rhsim07G0066400' => 'rsi', 'Rhsim07G0156400' => 'rsi', 'Rhsim07G0182200' => 'rsi', 'Rhsim07G0182300' => 'rsi', 'Rhsim08G0180400' => 'rsi', 'Rhsim09G0056800' => 'rsi', 'Rhsim10G0153300' => 'rsi', 'Rhsim11G0012700' => 'rsi', 'Rhsim12G0031800' => 'rsi', 'Rhsim12G0055400' => 'rsi', 'Rhsim12G0091400' => 'rsi', 'Rhsim13G0070800' => 'rsi', 'Rhsim13G0193300' => 'rsi', 'RhsimUnG0111600' => 'rsi', 'RhsimUnG0137500' => 'rsi', 'RhsimUnG0172900' => 'rsi', 'SGA_v2.0_scaffold11G05878' => 'sas', 'SGA_v2.0_scaffold167G38458' => 'sas', 'SGA_v2.0_scaffold19G08588' => 'sas', 'SGA_v2.0_scaffold239G43990' => 'sas', 'SGA_v2.0_scaffold260G45865' => 'sas', 'SGA_v2.0_scaffold309G48177' => 'sas', 'SGA_v2.0_scaffold76G25122' => 'sas', 'SGA_v2.0_scaffold85G26708' => 'sas', 'SHI13914' => 'shi', 'SHI30402' => 'shi', 'TWI09G0020' => 'twi', 'TWI09G0456' => 'twi', 'TWI09G1572' => 'twi', 'TWI12G0266' => 'twi', 'TWI12G1451' => 'twi', 'TWI14G0851' => 'twi', 'TWI15G0796' => 'twi', 'TWI18G0820' => 'twi', 'TWI18G1152' => 'twi', 'TWI23G0007' => 'twi', 'TWI23G0314' => 'twi', 'TWI31G0674' => 'twi', 'TWI31G0938' => 'twi', 'TWI34G0641' => 'twi', 'TWI34G1527' => 'twi', 'TWI36G0193' => 'twi', 'TWI36G0405' => 'twi', 'TWI38G0892' => 'twi', 'TWI38G0936' => 'twi', 'TWI38G2218' => 'twi', 'TWI53G0679' => 'twi', 'TWI53G0863' => 'twi', 'TWI53G1133' => 'twi', 'TWI60G0823' => 'twi', 'TWI63G0919' => 'twi', 'TWI63G1436' => 'twi', 'TWI73G0140' => 'twi', 'TWI73G0419' => 'twi', 'TWI73G0420' => 'twi', 'TWI73G1276' => 'twi', 'TWI74G0405' => 'twi', 'TWI74G0837' => 'twi', 'TWI75G0594' => 'twi', 'TWI75G1615' => 'twi', 'TWI77G0816' => 'twi', 'vmacro03831' => 'vma', 'vmacro13746' => 'vma', 'vmacro16089' => 'vma', 'vmacro22863' => 'vma', 'Zm00001eb085790' => 'zma', 'Zm00001eb114250' => 'zma', 'Zm00001eb138070' => 'zma', 'Zm00001eb167560' => 'zma', 'Zm00001eb199990' => 'zma', 'Zm00001eb368180' => 'zma', 'Zm00001eb382470' => 'zma' ), 'gf_id' => 'HOM05D001576', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001576' ), 'data_identifier' => 'HOM05D001576', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001576', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '406', 'num_species' => '29' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'Aqoxy1G01456' => 'aox', 'Aqoxy1G02949' => 'aox', 'Aqoxy3G01274' => 'aox', 'Aqoxy3G02110' => 'aox', 'Aqoxy3G02268' => 'aox', 'Aqoxy5G02702' => 'aox', 'Aqoxy5G02988' => 'aox', 'Aqoxy5G03427' => 'aox', 'Aqoxy6G02363' => 'aox', 'Atru.chr1.3225' => 'acertr', 'Atru.chr8.1198' => 'acertr', 'Atru.chr9.790' => 'acertr', 'CANSAT01G3197' => 'cansat', 'Ciclev10003979m.g' => 'ccl', 'Ciclev10017471m.g' => 'ccl', 'Ciclev10018206m.g' => 'ccl', 'Ciclev10033751m.g' => 'ccl', 'CiPaw.01G000900' => 'cil', 'CiPaw.01G001000' => 'cil', 'CiPaw.01G033500' => 'cil', 'CiPaw.01G060300' => 'cil', 'CiPaw.01G070200' => 'cil', 'CiPaw.01G075100' => 'cil', 'CiPaw.01G084700' => 'cil', 'CiPaw.01G087900' => 'cil', 'CiPaw.01G092600' => 'cil', 'CiPaw.01G097200' => 'cil', 'CiPaw.01G098300' => 'cil', 'CiPaw.01G110200' => 'cil', 'CiPaw.01G118700' => 'cil', 'CiPaw.01G121200' => 'cil', 'CiPaw.01G132500' => 'cil', 'CiPaw.01G146900' => 'cil', 'CiPaw.01G174000' => 'cil', 'CiPaw.01G179900' => 'cil', 'CiPaw.01G183400' => 'cil', 'CiPaw.01G240000' => 'cil', 'CiPaw.01G283500' => 'cil', 'CiPaw.01G307400' => 'cil', 'CiPaw.02G030800' => 'cil', 'CiPaw.02G047200' => 'cil', 'CiPaw.02G050500' => 'cil', 'CiPaw.02G069900' => 'cil', 'CiPaw.02G091600' => 'cil', 'CiPaw.02G095000' => 'cil', 'CiPaw.02G131900' => 'cil', 'CiPaw.03G043000' => 'cil', 'CiPaw.03G069900' => 'cil', 'CiPaw.03G088100' => 'cil', 'CiPaw.03G089300' => 'cil', 'CiPaw.03G093100' => 'cil', 'CiPaw.03G129800' => 'cil', 'CiPaw.03G131200' => 'cil', 'CiPaw.03G134500' => 'cil', 'CiPaw.03G152100' => 'cil', 'CiPaw.03G162700' => 'cil', 'CiPaw.03G172800' => 'cil', 'CiPaw.03G175800' => 'cil', 'CiPaw.03G181800' => 'cil', 'CiPaw.03G191400' => 'cil', 'CiPaw.03G198300' => 'cil', 'CiPaw.03G201300' => 'cil', 'CiPaw.03G224700' => 'cil', 'CiPaw.03G225000' => 'cil', 'CiPaw.04G065100' => 'cil', 'CiPaw.04G080400' => 'cil', 'CiPaw.04G113500' => 'cil', 'CiPaw.04G121900' => 'cil', 'CiPaw.04G144100' => 'cil', 'CiPaw.04G176500' => 'cil', 'CiPaw.05G086200' => 'cil', 'CiPaw.05G100200' => 'cil', 'CiPaw.05G114200' => 'cil', 'CiPaw.05G126800' => 'cil', 'CiPaw.05G228800' => 'cil', 'CiPaw.05G230600' => 'cil', 'CiPaw.05G236500' => 'cil', 'CiPaw.05G244800' => 'cil', 'CiPaw.06G026600' => 'cil', 'CiPaw.06G027900' => 'cil', 'CiPaw.06G051800' => 'cil', 'CiPaw.06G128500' => 'cil', 'CiPaw.06G165900' => 'cil', 'CiPaw.07G045400' => 'cil', 'CiPaw.07G048000' => 'cil', 'CiPaw.07G052000' => 'cil', 'CiPaw.07G073800' => 'cil', 'CiPaw.07G099700' => 'cil', 'CiPaw.07G108700' => 'cil', 'CiPaw.07G120000' => 'cil', 'CiPaw.07G134100' => 'cil', 'CiPaw.07G147000' => 'cil', 'CiPaw.07G149700' => 'cil', 'CiPaw.07G178300' => 'cil', 'CiPaw.07G184900' => 'cil', 'CiPaw.08G044500' => 'cil', 'CiPaw.08G046900' => 'cil', 'CiPaw.08G047300' => 'cil', 'CiPaw.08G115400' => 'cil', 'CiPaw.08G134700' => 'cil', 'CiPaw.08G157400' => 'cil', 'CiPaw.09G014300' => 'cil', 'CiPaw.09G088900' => 'cil', 'CiPaw.09G130900' => 'cil', 'CiPaw.09G133100' => 'cil', 'CiPaw.09G151300' => 'cil', 'CiPaw.09G172800' => 'cil', 'CiPaw.09G174900' => 'cil', 'CiPaw.09G175000' => 'cil', 'CiPaw.10G012800' => 'cil', 'CiPaw.10G028800' => 'cil', 'CiPaw.10G044700' => 'cil', 'CiPaw.10G067400' => 'cil', 'CiPaw.10G115900' => 'cil', 'CiPaw.10G126200' => 'cil', 'CiPaw.10G139700' => 'cil', 'CiPaw.10G155100' => 'cil', 'CiPaw.11G011300' => 'cil', 'CiPaw.11G025900' => 'cil', 'CiPaw.11G104100' => 'cil', 'CiPaw.11G142700' => 'cil', 'CiPaw.11G164500' => 'cil', 'CiPaw.11G189100' => 'cil', 'CiPaw.11G197100' => 'cil', 'CiPaw.12G006100' => 'cil', 'CiPaw.12G038500' => 'cil', 'CiPaw.12G041400' => 'cil', 'CiPaw.12G041600' => 'cil', 'CiPaw.12G051300' => 'cil', 'CiPaw.12G101800' => 'cil', 'CiPaw.12G107800' => 'cil', 'CiPaw.13G033200' => 'cil', 'CiPaw.13G129900' => 'cil', 'CiPaw.13G160200' => 'cil', 'CiPaw.14G018900' => 'cil', 'CiPaw.14G029000' => 'cil', 'CiPaw.14G031000' => 'cil', 'CiPaw.14G032000' => 'cil', 'CiPaw.14G032300' => 'cil', 'CiPaw.14G040600' => 'cil', 'CiPaw.14G060500' => 'cil', 'CiPaw.14G061500' => 'cil', 'CiPaw.14G077500' => 'cil', 'CiPaw.14G088300' => 'cil', 'CiPaw.14G108500' => 'cil', 'CiPaw.14G121300' => 'cil', 'CiPaw.14G133000' => 'cil', 'CiPaw.14G134600' => 'cil', 'CiPaw.15G027200' => 'cil', 'CiPaw.15G037700' => 'cil', 'CiPaw.15G050900' => 'cil', 'CiPaw.15G067200' => 'cil', 'CiPaw.15G072000' => 'cil', 'CiPaw.15G112900' => 'cil', 'CiPaw.15G133200' => 'cil', 'CiPaw.15G139500' => 'cil', 'CiPaw.15G155400' => 'cil', 'CiPaw.16G006000' => 'cil', 'CiPaw.16G013100' => 'cil', 'CiPaw.16G047100' => 'cil', 'CiPaw.16G048900' => 'cil', 'CiPaw.16G070300' => 'cil', 'CSS0000195' => 'camsi', 'CSS0001664' => 'camsi', 'CSS0002566' => 'camsi', 'CSS0003077' => 'camsi', 'CSS0004257' => 'camsi', 'CSS0004495' => 'camsi', 'CSS0004599' => 'camsi', 'CSS0004943' => 'camsi', 'CSS0005302' => 'camsi', 'CSS0006274' => 'camsi', 'CSS0006547' => 'camsi', 'CSS0006860' => 'camsi', 'CSS0008814' => 'camsi', 'CSS0008946' => 'camsi', 'CSS0009093' => 'camsi', 'CSS0010221' => 'camsi', 'CSS0010296' => 'camsi', 'CSS0010386' => 'camsi', 'CSS0010831' => 'camsi', 'CSS0011061' => 'camsi', 'CSS0012008' => 'camsi', 'CSS0012194' => 'camsi', 'CSS0013580' => 'camsi', 'CSS0014176' => 'camsi', 'CSS0014280' => 'camsi', 'CSS0014799' => 'camsi', 'CSS0015368' => 'camsi', 'CSS0017473' => 'camsi', 'CSS0019281' => 'camsi', 'CSS0021320' => 'camsi', 'CSS0021750' => 'camsi', 'CSS0023642' => 'camsi', 'CSS0023792' => 'camsi', 'CSS0031528' => 'camsi', 'CSS0033894' => 'camsi', 'CSS0034959' => 'camsi', 'CSS0035632' => 'camsi', 'CSS0038450' => 'camsi', 'CSS0039293' => 'camsi', 'CSS0041053' => 'camsi', 'CSS0041981' => 'camsi', 'CSS0042573' => 'camsi', 'CSS0042927' => 'camsi', 'CSS0047725' => 'camsi', 'CSS0049636' => 'camsi', 'CSS0050513' => 'camsi', 'DCAR_030203' => 'dca', 'Dinv07939' => 'din', 'FAN01G0456' => 'fan', 'FAN02G3001' => 'fan', 'FAN04G2781' => 'fan', 'FAN05G1385' => 'fan', 'FAN05G3062' => 'fan', 'FAN08G2267' => 'fan', 'FAN10G0481' => 'fan', 'FAN10G1257' => 'fan', 'FAN14G0954' => 'fan', 'FAN14G2347' => 'fan', 'FAN15G0187' => 'fan', 'FAN25G2214' => 'fan', 'FvH4_1g21031' => 'fve', 'FvH4_3g16231' => 'fve', 'FvH4_3g26413' => 'fve', 'FvH4_3g29014' => 'fve', 'FvH4_3g31921' => 'fve', 'FvH4_4g19882' => 'fve', 'FvH4_5g21960' => 'fve', 'FvH4_5g29683' => 'fve', 'FvH4_7g13271' => 'fve', 'Glyma.01G062500' => 'gma', 'Glyma.07G140900' => 'gma', 'Glyma.09G140900' => 'gma', 'Glyma.12G112700' => 'gma', 'Glyma.17G168800' => 'gma', 'HanXRQChr01g0027001' => 'han', 'HanXRQChr04g0120511' => 'han', 'HanXRQChr08g0232381' => 'han', 'HanXRQChr09g0265661' => 'han', 'HanXRQChr13g0416031' => 'han', 'Haze_05835' => 'cav', 'Haze_06597' => 'cav', 'Haze_07921' => 'cav', 'Haze_08599' => 'cav', 'Haze_10686' => 'cav', 'Haze_12994' => 'cav', 'Haze_13466' => 'cav', 'Haze_16101' => 'cav', 'Haze_17766' => 'cav', 'Haze_18456' => 'cav', 'Haze_20229' => 'cav', 'Hma1.2p1_0324F.1_g125640' => 'hma', 'Hma1.2p1_0733F.1_g210230' => 'hma', 'Hma1.2p1_0921F.1_g236870' => 'hma', 'Hma1.2p1_1313F.1_g274940' => 'hma', 'Hma1.2p1_3059F.1_g332230' => 'hma', 'Hund15925' => 'sun', 'Hund19562' => 'sun', 'Hund21925' => 'sun', 'MD03G1177400' => 'mdo', 'MD07G1026100' => 'mdo', 'MD17G1218600' => 'mdo', 'Medtr0867s0010' => 'mtr', 'Medtr6g081150' => 'mtr', 'Os01g0527900' => 'osa', 'Os02g0463725' => 'osa', 'Os02g0785600' => 'osa', 'Os03g0433733' => 'osa', 'Os04g0286500' => 'osa', 'Os05g0227800' => 'osa', 'Os06g0521000' => 'osa', 'Os06g0635500' => 'osa', 'Os06g0660650' => 'osa', 'Os07g0554400' => 'osa', 'Os08g0225900' => 'osa', 'Os08g0561000' => 'osa', 'Os09g0241700' => 'osa', 'Os09g0351900' => 'osa', 'Os11g0220700' => 'osa', 'Os11g0282700' => 'osa', 'Os12g0169300' => 'osa', 'Os12g0228500' => 'osa', 'Os12g0543800' => 'osa', 'PGR044G1547' => 'pgr', 'Potri.005G239150' => 'ptr', 'Potri.010G014250' => 'ptr', 'Prupe.1G172500' => 'ppe', 'Prupe.1G196800' => 'ppe', 'Prupe.1G279700' => 'ppe', 'Prupe.2G026400' => 'ppe', 'Prupe.3G094000' => 'ppe', 'Prupe.4G287300' => 'ppe', 'QL01p022166' => 'qlo', 'QL01p051890' => 'qlo', 'QL02p009469' => 'qlo', 'QL02p046053' => 'qlo', 'QL02p057958' => 'qlo', 'QL02p093127' => 'qlo', 'QL03p006855' => 'qlo', 'QL03p071586' => 'qlo', 'QL04p000022' => 'qlo', 'QL04p000024' => 'qlo', 'QL04p003192' => 'qlo', 'QL05p011416' => 'qlo', 'QL06p039590' => 'qlo', 'QL06p052750' => 'qlo', 'QL06p053821' => 'qlo', 'QL07p025287' => 'qlo', 'QL09p033218' => 'qlo', 'QL09p040841' => 'qlo', 'QL10p020337' => 'qlo', 'QL10p027209' => 'qlo', 'QL10p027969' => 'qlo', 'QL10p048988' => 'qlo', 'QL11p001241' => 'qlo', 'QL11p028487' => 'qlo', 'RcHm_v2.0_Chr2g0105031' => 'rch', 'RcHm_v2.0_Chr2g0117811' => 'rch', 'RcHm_v2.0_Chr6g0270241' => 'rch', 'RcHm_v2.0_Chr7g0215961' => 'rch', 'RcHm_v2.0_Chr7g0231991' => 'rch', 'Rhsim01G0041500' => 'rsi', 'Rhsim01G0115000' => 'rsi', 'Rhsim01G0115400' => 'rsi', 'Rhsim01G0133600' => 'rsi', 'Rhsim01G0159900' => 'rsi', 'Rhsim02G0189400' => 'rsi', 'Rhsim03G0135600' => 'rsi', 'Rhsim03G0149900' => 'rsi', 'Rhsim04G0125600' => 'rsi', 'Rhsim05G0091700' => 'rsi', 'Rhsim05G0092900' => 'rsi', 'Rhsim06G0075000' => 'rsi', 'Rhsim07G0066400' => 'rsi', 'Rhsim07G0156400' => 'rsi', 'Rhsim07G0182200' => 'rsi', 'Rhsim07G0182300' => 'rsi', 'Rhsim08G0180400' => 'rsi', 'Rhsim09G0056800' => 'rsi', 'Rhsim10G0153300' => 'rsi', 'Rhsim11G0012700' => 'rsi', 'Rhsim12G0031800' => 'rsi', 'Rhsim12G0055400' => 'rsi', 'Rhsim12G0091400' => 'rsi', 'Rhsim13G0070800' => 'rsi', 'Rhsim13G0193300' => 'rsi', 'RhsimUnG0111600' => 'rsi', 'RhsimUnG0137500' => 'rsi', 'RhsimUnG0172900' => 'rsi', 'SGA_v2.0_scaffold11G05878' => 'sas', 'SGA_v2.0_scaffold167G38458' => 'sas', 'SGA_v2.0_scaffold19G08588' => 'sas', 'SGA_v2.0_scaffold239G43990' => 'sas', 'SGA_v2.0_scaffold260G45865' => 'sas', 'SGA_v2.0_scaffold309G48177' => 'sas', 'SGA_v2.0_scaffold76G25122' => 'sas', 'SGA_v2.0_scaffold85G26708' => 'sas', 'SHI13914' => 'shi', 'SHI30402' => 'shi', 'TWI09G0020' => 'twi', 'TWI09G0456' => 'twi', 'TWI09G1572' => 'twi', 'TWI12G0266' => 'twi', 'TWI12G1451' => 'twi', 'TWI14G0851' => 'twi', 'TWI15G0796' => 'twi', 'TWI18G0820' => 'twi', 'TWI18G1152' => 'twi', 'TWI23G0007' => 'twi', 'TWI23G0314' => 'twi', 'TWI31G0674' => 'twi', 'TWI31G0938' => 'twi', 'TWI34G0641' => 'twi', 'TWI34G1527' => 'twi', 'TWI36G0193' => 'twi', 'TWI36G0405' => 'twi', 'TWI38G0892' => 'twi', 'TWI38G0936' => 'twi', 'TWI38G2218' => 'twi', 'TWI53G0679' => 'twi', 'TWI53G0863' => 'twi', 'TWI53G1133' => 'twi', 'TWI60G0823' => 'twi', 'TWI63G0919' => 'twi', 'TWI63G1436' => 'twi', 'TWI73G0140' => 'twi', 'TWI73G0419' => 'twi', 'TWI73G0420' => 'twi', 'TWI73G1276' => 'twi', 'TWI74G0405' => 'twi', 'TWI74G0837' => 'twi', 'TWI75G0594' => 'twi', 'TWI75G1615' => 'twi', 'TWI77G0816' => 'twi', 'vmacro03831' => 'vma', 'vmacro13746' => 'vma', 'vmacro16089' => 'vma', 'vmacro22863' => 'vma', 'Zm00001eb085790' => 'zma', 'Zm00001eb114250' => 'zma', 'Zm00001eb138070' => 'zma', 'Zm00001eb167560' => 'zma', 'Zm00001eb199990' => 'zma', 'Zm00001eb368180' => 'zma', 'Zm00001eb382470' => 'zma' ) $gf_id = 'HOM05D001576' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001576' ) $data_identifier = 'HOM05D001576' $data_type = 'gf_id' $species_gene_counts = array( 'aox' => (int) 9, 'acertr' => (int) 3, 'cansat' => (int) 1, 'ccl' => (int) 4, 'cil' => (int) 145, 'camsi' => (int) 46, 'dca' => (int) 1, 'din' => (int) 1, 'fan' => (int) 12, 'fve' => (int) 9, 'gma' => (int) 5, 'han' => (int) 5, 'cav' => (int) 11, 'hma' => (int) 5, 'sun' => (int) 3, 'mdo' => (int) 3, 'mtr' => (int) 2, 'osa' => (int) 19, 'pgr' => (int) 1, 'ptr' => (int) 2, 'ppe' => (int) 6, 'qlo' => (int) 24, 'rch' => (int) 5, 'rsi' => (int) 28, 'sas' => (int) 8, 'shi' => (int) 2, 'twi' => (int) 35, 'vma' => (int) 4, 'zma' => (int) 7 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb382470' $species_info = array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ) $local_species = 'han' $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' => 'HOM05D001576', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '406', 'num_species' => '29' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'Aqoxy1G01456' => 'aox', 'Aqoxy1G02949' => 'aox', 'Aqoxy3G01274' => 'aox', 'Aqoxy3G02110' => 'aox', 'Aqoxy3G02268' => 'aox', 'Aqoxy5G02702' => 'aox', 'Aqoxy5G02988' => 'aox', 'Aqoxy5G03427' => 'aox', 'Aqoxy6G02363' => 'aox', 'Atru.chr1.3225' => 'acertr', 'Atru.chr8.1198' => 'acertr', 'Atru.chr9.790' => 'acertr', 'CANSAT01G3197' => 'cansat', 'Ciclev10003979m.g' => 'ccl', 'Ciclev10017471m.g' => 'ccl', 'Ciclev10018206m.g' => 'ccl', 'Ciclev10033751m.g' => 'ccl', 'CiPaw.01G000900' => 'cil', 'CiPaw.01G001000' => 'cil', 'CiPaw.01G033500' => 'cil', 'CiPaw.01G060300' => 'cil', 'CiPaw.01G070200' => 'cil', 'CiPaw.01G075100' => 'cil', 'CiPaw.01G084700' => 'cil', 'CiPaw.01G087900' => 'cil', 'CiPaw.01G092600' => 'cil', 'CiPaw.01G097200' => 'cil', 'CiPaw.01G098300' => 'cil', 'CiPaw.01G110200' => 'cil', 'CiPaw.01G118700' => 'cil', 'CiPaw.01G121200' => 'cil', 'CiPaw.01G132500' => 'cil', 'CiPaw.01G146900' => 'cil', 'CiPaw.01G174000' => 'cil', 'CiPaw.01G179900' => 'cil', 'CiPaw.01G183400' => 'cil', 'CiPaw.01G240000' => 'cil', 'CiPaw.01G283500' => 'cil', 'CiPaw.01G307400' => 'cil', 'CiPaw.02G030800' => 'cil', 'CiPaw.02G047200' => 'cil', 'CiPaw.02G050500' => 'cil', 'CiPaw.02G069900' => 'cil', 'CiPaw.02G091600' => 'cil', 'CiPaw.02G095000' => 'cil', 'CiPaw.02G131900' => 'cil', 'CiPaw.03G043000' => 'cil', 'CiPaw.03G069900' => 'cil', 'CiPaw.03G088100' => 'cil', 'CiPaw.03G089300' => 'cil', 'CiPaw.03G093100' => 'cil', 'CiPaw.03G129800' => 'cil', 'CiPaw.03G131200' => 'cil', 'CiPaw.03G134500' => 'cil', 'CiPaw.03G152100' => 'cil', 'CiPaw.03G162700' => 'cil', 'CiPaw.03G172800' => 'cil', 'CiPaw.03G175800' => 'cil', 'CiPaw.03G181800' => 'cil', 'CiPaw.03G191400' => 'cil', 'CiPaw.03G198300' => 'cil', 'CiPaw.03G201300' => 'cil', 'CiPaw.03G224700' => 'cil', 'CiPaw.03G225000' => 'cil', 'CiPaw.04G065100' => 'cil', 'CiPaw.04G080400' => 'cil', 'CiPaw.04G113500' => 'cil', 'CiPaw.04G121900' => 'cil', 'CiPaw.04G144100' => 'cil', 'CiPaw.04G176500' => 'cil', 'CiPaw.05G086200' => 'cil', 'CiPaw.05G100200' => 'cil', 'CiPaw.05G114200' => 'cil', 'CiPaw.05G126800' => 'cil', 'CiPaw.05G228800' => 'cil', 'CiPaw.05G230600' => 'cil', 'CiPaw.05G236500' => 'cil', 'CiPaw.05G244800' => 'cil', 'CiPaw.06G026600' => 'cil', 'CiPaw.06G027900' => 'cil', 'CiPaw.06G051800' => 'cil', 'CiPaw.06G128500' => 'cil', 'CiPaw.06G165900' => 'cil', 'CiPaw.07G045400' => 'cil', 'CiPaw.07G048000' => 'cil', 'CiPaw.07G052000' => 'cil', 'CiPaw.07G073800' => 'cil', 'CiPaw.07G099700' => 'cil', 'CiPaw.07G108700' => 'cil', 'CiPaw.07G120000' => 'cil', 'CiPaw.07G134100' => 'cil', 'CiPaw.07G147000' => 'cil', 'CiPaw.07G149700' => 'cil', 'CiPaw.07G178300' => 'cil', 'CiPaw.07G184900' => 'cil', 'CiPaw.08G044500' => 'cil', 'CiPaw.08G046900' => 'cil', 'CiPaw.08G047300' => 'cil', 'CiPaw.08G115400' => 'cil', 'CiPaw.08G134700' => 'cil', 'CiPaw.08G157400' => 'cil', 'CiPaw.09G014300' => 'cil', 'CiPaw.09G088900' => 'cil', 'CiPaw.09G130900' => 'cil', 'CiPaw.09G133100' => 'cil', 'CiPaw.09G151300' => 'cil', 'CiPaw.09G172800' => 'cil', 'CiPaw.09G174900' => 'cil', 'CiPaw.09G175000' => 'cil', 'CiPaw.10G012800' => 'cil', 'CiPaw.10G028800' => 'cil', 'CiPaw.10G044700' => 'cil', 'CiPaw.10G067400' => 'cil', 'CiPaw.10G115900' => 'cil', 'CiPaw.10G126200' => 'cil', 'CiPaw.10G139700' => 'cil', 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=> 'qlo', 'QL07p025287' => 'qlo', 'QL09p033218' => 'qlo', 'QL09p040841' => 'qlo', 'QL10p020337' => 'qlo', 'QL10p027209' => 'qlo', 'QL10p027969' => 'qlo', 'QL10p048988' => 'qlo', 'QL11p001241' => 'qlo', 'QL11p028487' => 'qlo', 'RcHm_v2.0_Chr2g0105031' => 'rch', 'RcHm_v2.0_Chr2g0117811' => 'rch', 'RcHm_v2.0_Chr6g0270241' => 'rch', 'RcHm_v2.0_Chr7g0215961' => 'rch', 'RcHm_v2.0_Chr7g0231991' => 'rch', 'Rhsim01G0041500' => 'rsi', 'Rhsim01G0115000' => 'rsi', 'Rhsim01G0115400' => 'rsi', 'Rhsim01G0133600' => 'rsi', 'Rhsim01G0159900' => 'rsi', 'Rhsim02G0189400' => 'rsi', 'Rhsim03G0135600' => 'rsi', 'Rhsim03G0149900' => 'rsi', 'Rhsim04G0125600' => 'rsi', 'Rhsim05G0091700' => 'rsi', 'Rhsim05G0092900' => 'rsi', 'Rhsim06G0075000' => 'rsi', 'Rhsim07G0066400' => 'rsi', 'Rhsim07G0156400' => 'rsi', 'Rhsim07G0182200' => 'rsi', 'Rhsim07G0182300' => 'rsi', 'Rhsim08G0180400' => 'rsi', 'Rhsim09G0056800' => 'rsi', 'Rhsim10G0153300' => 'rsi', 'Rhsim11G0012700' => 'rsi', 'Rhsim12G0031800' => 'rsi', 'Rhsim12G0055400' => 'rsi', 'Rhsim12G0091400' => 'rsi', 'Rhsim13G0070800' => 'rsi', 'Rhsim13G0193300' => 'rsi', 'RhsimUnG0111600' => 'rsi', 'RhsimUnG0137500' => 'rsi', 'RhsimUnG0172900' => 'rsi', 'SGA_v2.0_scaffold11G05878' => 'sas', 'SGA_v2.0_scaffold167G38458' => 'sas', 'SGA_v2.0_scaffold19G08588' => 'sas', 'SGA_v2.0_scaffold239G43990' => 'sas', 'SGA_v2.0_scaffold260G45865' => 'sas', 'SGA_v2.0_scaffold309G48177' => 'sas', 'SGA_v2.0_scaffold76G25122' => 'sas', 'SGA_v2.0_scaffold85G26708' => 'sas', 'SHI13914' => 'shi', 'SHI30402' => 'shi', 'TWI09G0020' => 'twi', 'TWI09G0456' => 'twi', 'TWI09G1572' => 'twi', 'TWI12G0266' => 'twi', 'TWI12G1451' => 'twi', 'TWI14G0851' => 'twi', 'TWI15G0796' => 'twi', 'TWI18G0820' => 'twi', 'TWI18G1152' => 'twi', 'TWI23G0007' => 'twi', 'TWI23G0314' => 'twi', 'TWI31G0674' => 'twi', 'TWI31G0938' => 'twi', 'TWI34G0641' => 'twi', 'TWI34G1527' => 'twi', 'TWI36G0193' => 'twi', 'TWI36G0405' => 'twi', 'TWI38G0892' => 'twi', 'TWI38G0936' => 'twi', 'TWI38G2218' => 'twi', 'TWI53G0679' => 'twi', 'TWI53G0863' => 'twi', 'TWI53G1133' => 'twi', 'TWI60G0823' => 'twi', 'TWI63G0919' => 'twi', 'TWI63G1436' => 'twi', 'TWI73G0140' => 'twi', 'TWI73G0419' => 'twi', 'TWI73G0420' => 'twi', 'TWI73G1276' => 'twi', 'TWI74G0405' => 'twi', 'TWI74G0837' => 'twi', 'TWI75G0594' => 'twi', 'TWI75G1615' => 'twi', 'TWI77G0816' => 'twi', 'vmacro03831' => 'vma', 'vmacro13746' => 'vma', 'vmacro16089' => 'vma', 'vmacro22863' => 'vma', 'Zm00001eb085790' => 'zma', 'Zm00001eb114250' => 'zma', 'Zm00001eb138070' => 'zma', 'Zm00001eb167560' => 'zma', 'Zm00001eb199990' => 'zma', 'Zm00001eb368180' => 'zma', 'Zm00001eb382470' => 'zma' ), 'gf_id' => 'HOM05D001576', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001576' ), 'data_identifier' => 'HOM05D001576', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001576', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '406', 'num_species' => '29' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'Aqoxy1G01456' => 'aox', 'Aqoxy1G02949' => 'aox', 'Aqoxy3G01274' => 'aox', 'Aqoxy3G02110' => 'aox', 'Aqoxy3G02268' => 'aox', 'Aqoxy5G02702' => 'aox', 'Aqoxy5G02988' => 'aox', 'Aqoxy5G03427' => 'aox', 'Aqoxy6G02363' => 'aox', 'Atru.chr1.3225' => 'acertr', 'Atru.chr8.1198' => 'acertr', 'Atru.chr9.790' => 'acertr', 'CANSAT01G3197' => 'cansat', 'Ciclev10003979m.g' => 'ccl', 'Ciclev10017471m.g' => 'ccl', 'Ciclev10018206m.g' => 'ccl', 'Ciclev10033751m.g' => 'ccl', 'CiPaw.01G000900' => 'cil', 'CiPaw.01G001000' => 'cil', 'CiPaw.01G033500' => 'cil', 'CiPaw.01G060300' => 'cil', 'CiPaw.01G070200' => 'cil', 'CiPaw.01G075100' => 'cil', 'CiPaw.01G084700' => 'cil', 'CiPaw.01G087900' => 'cil', 'CiPaw.01G092600' => 'cil', 'CiPaw.01G097200' => 'cil', 'CiPaw.01G098300' => 'cil', 'CiPaw.01G110200' => 'cil', 'CiPaw.01G118700' => 'cil', 'CiPaw.01G121200' => 'cil', 'CiPaw.01G132500' => 'cil', 'CiPaw.01G146900' => 'cil', 'CiPaw.01G174000' => 'cil', 'CiPaw.01G179900' => 'cil', 'CiPaw.01G183400' => 'cil', 'CiPaw.01G240000' => 'cil', 'CiPaw.01G283500' => 'cil', 'CiPaw.01G307400' => 'cil', 'CiPaw.02G030800' => 'cil', 'CiPaw.02G047200' => 'cil', 'CiPaw.02G050500' => 'cil', 'CiPaw.02G069900' => 'cil', 'CiPaw.02G091600' => 'cil', 'CiPaw.02G095000' => 'cil', 'CiPaw.02G131900' => 'cil', 'CiPaw.03G043000' => 'cil', 'CiPaw.03G069900' => 'cil', 'CiPaw.03G088100' => 'cil', 'CiPaw.03G089300' => 'cil', 'CiPaw.03G093100' => 'cil', 'CiPaw.03G129800' => 'cil', 'CiPaw.03G131200' => 'cil', 'CiPaw.03G134500' => 'cil', 'CiPaw.03G152100' => 'cil', 'CiPaw.03G162700' => 'cil', 'CiPaw.03G172800' => 'cil', 'CiPaw.03G175800' => 'cil', 'CiPaw.03G181800' => 'cil', 'CiPaw.03G191400' => 'cil', 'CiPaw.03G198300' => 'cil', 'CiPaw.03G201300' => 'cil', 'CiPaw.03G224700' => 'cil', 'CiPaw.03G225000' => 'cil', 'CiPaw.04G065100' => 'cil', 'CiPaw.04G080400' => 'cil', 'CiPaw.04G113500' => 'cil', 'CiPaw.04G121900' => 'cil', 'CiPaw.04G144100' => 'cil', 'CiPaw.04G176500' => 'cil', 'CiPaw.05G086200' => 'cil', 'CiPaw.05G100200' => 'cil', 'CiPaw.05G114200' => 'cil', 'CiPaw.05G126800' => 'cil', 'CiPaw.05G228800' => 'cil', 'CiPaw.05G230600' => 'cil', 'CiPaw.05G236500' => 'cil', 'CiPaw.05G244800' => 'cil', 'CiPaw.06G026600' => 'cil', 'CiPaw.06G027900' => 'cil', 'CiPaw.06G051800' => 'cil', 'CiPaw.06G128500' => 'cil', 'CiPaw.06G165900' => 'cil', 'CiPaw.07G045400' => 'cil', 'CiPaw.07G048000' => 'cil', 'CiPaw.07G052000' => 'cil', 'CiPaw.07G073800' => 'cil', 'CiPaw.07G099700' => 'cil', 'CiPaw.07G108700' => 'cil', 'CiPaw.07G120000' => 'cil', 'CiPaw.07G134100' => 'cil', 'CiPaw.07G147000' => 'cil', 'CiPaw.07G149700' => 'cil', 'CiPaw.07G178300' => 'cil', 'CiPaw.07G184900' => 'cil', 'CiPaw.08G044500' => 'cil', 'CiPaw.08G046900' => 'cil', 'CiPaw.08G047300' => 'cil', 'CiPaw.08G115400' => 'cil', 'CiPaw.08G134700' => 'cil', 'CiPaw.08G157400' => 'cil', 'CiPaw.09G014300' => 'cil', 'CiPaw.09G088900' => 'cil', 'CiPaw.09G130900' => 'cil', 'CiPaw.09G133100' => 'cil', 'CiPaw.09G151300' => 'cil', 'CiPaw.09G172800' => 'cil', 'CiPaw.09G174900' => 'cil', 'CiPaw.09G175000' => 'cil', 'CiPaw.10G012800' => 'cil', 'CiPaw.10G028800' => 'cil', 'CiPaw.10G044700' => 'cil', 'CiPaw.10G067400' => 'cil', 'CiPaw.10G115900' => 'cil', 'CiPaw.10G126200' => 'cil', 'CiPaw.10G139700' => 'cil', 'CiPaw.10G155100' => 'cil', 'CiPaw.11G011300' => 'cil', 'CiPaw.11G025900' => 'cil', 'CiPaw.11G104100' => 'cil', 'CiPaw.11G142700' => 'cil', 'CiPaw.11G164500' => 'cil', 'CiPaw.11G189100' => 'cil', 'CiPaw.11G197100' => 'cil', 'CiPaw.12G006100' => 'cil', 'CiPaw.12G038500' => 'cil', 'CiPaw.12G041400' => 'cil', 'CiPaw.12G041600' => 'cil', 'CiPaw.12G051300' => 'cil', 'CiPaw.12G101800' => 'cil', 'CiPaw.12G107800' => 'cil', 'CiPaw.13G033200' => 'cil', 'CiPaw.13G129900' => 'cil', 'CiPaw.13G160200' => 'cil', 'CiPaw.14G018900' => 'cil', 'CiPaw.14G029000' => 'cil', 'CiPaw.14G031000' => 'cil', 'CiPaw.14G032000' => 'cil', 'CiPaw.14G032300' => 'cil', 'CiPaw.14G040600' => 'cil', 'CiPaw.14G060500' => 'cil', 'CiPaw.14G061500' => 'cil', 'CiPaw.14G077500' => 'cil', 'CiPaw.14G088300' => 'cil', 'CiPaw.14G108500' => 'cil', 'CiPaw.14G121300' => 'cil', 'CiPaw.14G133000' => 'cil', 'CiPaw.14G134600' => 'cil', 'CiPaw.15G027200' => 'cil', 'CiPaw.15G037700' => 'cil', 'CiPaw.15G050900' => 'cil', 'CiPaw.15G067200' => 'cil', 'CiPaw.15G072000' => 'cil', 'CiPaw.15G112900' => 'cil', 'CiPaw.15G133200' => 'cil', 'CiPaw.15G139500' => 'cil', 'CiPaw.15G155400' => 'cil', 'CiPaw.16G006000' => 'cil', 'CiPaw.16G013100' => 'cil', 'CiPaw.16G047100' => 'cil', 'CiPaw.16G048900' => 'cil', 'CiPaw.16G070300' => 'cil', 'CSS0000195' => 'camsi', 'CSS0001664' => 'camsi', 'CSS0002566' => 'camsi', 'CSS0003077' => 'camsi', 'CSS0004257' => 'camsi', 'CSS0004495' => 'camsi', 'CSS0004599' => 'camsi', 'CSS0004943' => 'camsi', 'CSS0005302' => 'camsi', 'CSS0006274' => 'camsi', 'CSS0006547' => 'camsi', 'CSS0006860' => 'camsi', 'CSS0008814' => 'camsi', 'CSS0008946' => 'camsi', 'CSS0009093' => 'camsi', 'CSS0010221' => 'camsi', 'CSS0010296' => 'camsi', 'CSS0010386' => 'camsi', 'CSS0010831' => 'camsi', 'CSS0011061' => 'camsi', 'CSS0012008' => 'camsi', 'CSS0012194' => 'camsi', 'CSS0013580' => 'camsi', 'CSS0014176' => 'camsi', 'CSS0014280' => 'camsi', 'CSS0014799' => 'camsi', 'CSS0015368' => 'camsi', 'CSS0017473' => 'camsi', 'CSS0019281' => 'camsi', 'CSS0021320' => 'camsi', 'CSS0021750' => 'camsi', 'CSS0023642' => 'camsi', 'CSS0023792' => 'camsi', 'CSS0031528' => 'camsi', 'CSS0033894' => 'camsi', 'CSS0034959' => 'camsi', 'CSS0035632' => 'camsi', 'CSS0038450' => 'camsi', 'CSS0039293' => 'camsi', 'CSS0041053' => 'camsi', 'CSS0041981' => 'camsi', 'CSS0042573' => 'camsi', 'CSS0042927' => 'camsi', 'CSS0047725' => 'camsi', 'CSS0049636' => 'camsi', 'CSS0050513' => 'camsi', 'DCAR_030203' => 'dca', 'Dinv07939' => 'din', 'FAN01G0456' => 'fan', 'FAN02G3001' => 'fan', 'FAN04G2781' => 'fan', 'FAN05G1385' => 'fan', 'FAN05G3062' => 'fan', 'FAN08G2267' => 'fan', 'FAN10G0481' => 'fan', 'FAN10G1257' => 'fan', 'FAN14G0954' => 'fan', 'FAN14G2347' => 'fan', 'FAN15G0187' => 'fan', 'FAN25G2214' => 'fan', 'FvH4_1g21031' => 'fve', 'FvH4_3g16231' => 'fve', 'FvH4_3g26413' => 'fve', 'FvH4_3g29014' => 'fve', 'FvH4_3g31921' => 'fve', 'FvH4_4g19882' => 'fve', 'FvH4_5g21960' => 'fve', 'FvH4_5g29683' => 'fve', 'FvH4_7g13271' => 'fve', 'Glyma.01G062500' => 'gma', 'Glyma.07G140900' => 'gma', 'Glyma.09G140900' => 'gma', 'Glyma.12G112700' => 'gma', 'Glyma.17G168800' => 'gma', 'HanXRQChr01g0027001' => 'han', 'HanXRQChr04g0120511' => 'han', 'HanXRQChr08g0232381' => 'han', 'HanXRQChr09g0265661' => 'han', 'HanXRQChr13g0416031' => 'han', 'Haze_05835' => 'cav', 'Haze_06597' => 'cav', 'Haze_07921' => 'cav', 'Haze_08599' => 'cav', 'Haze_10686' => 'cav', 'Haze_12994' => 'cav', 'Haze_13466' => 'cav', 'Haze_16101' => 'cav', 'Haze_17766' => 'cav', 'Haze_18456' => 'cav', 'Haze_20229' => 'cav', 'Hma1.2p1_0324F.1_g125640' => 'hma', 'Hma1.2p1_0733F.1_g210230' => 'hma', 'Hma1.2p1_0921F.1_g236870' => 'hma', 'Hma1.2p1_1313F.1_g274940' => 'hma', 'Hma1.2p1_3059F.1_g332230' => 'hma', 'Hund15925' => 'sun', 'Hund19562' => 'sun', 'Hund21925' => 'sun', 'MD03G1177400' => 'mdo', 'MD07G1026100' => 'mdo', 'MD17G1218600' => 'mdo', 'Medtr0867s0010' => 'mtr', 'Medtr6g081150' => 'mtr', 'Os01g0527900' => 'osa', 'Os02g0463725' => 'osa', 'Os02g0785600' => 'osa', 'Os03g0433733' => 'osa', 'Os04g0286500' => 'osa', 'Os05g0227800' => 'osa', 'Os06g0521000' => 'osa', 'Os06g0635500' => 'osa', 'Os06g0660650' => 'osa', 'Os07g0554400' => 'osa', 'Os08g0225900' => 'osa', 'Os08g0561000' => 'osa', 'Os09g0241700' => 'osa', 'Os09g0351900' => 'osa', 'Os11g0220700' => 'osa', 'Os11g0282700' => 'osa', 'Os12g0169300' => 'osa', 'Os12g0228500' => 'osa', 'Os12g0543800' => 'osa', 'PGR044G1547' => 'pgr', 'Potri.005G239150' => 'ptr', 'Potri.010G014250' => 'ptr', 'Prupe.1G172500' => 'ppe', 'Prupe.1G196800' => 'ppe', 'Prupe.1G279700' => 'ppe', 'Prupe.2G026400' => 'ppe', 'Prupe.3G094000' => 'ppe', 'Prupe.4G287300' => 'ppe', 'QL01p022166' => 'qlo', 'QL01p051890' => 'qlo', 'QL02p009469' => 'qlo', 'QL02p046053' => 'qlo', 'QL02p057958' => 'qlo', 'QL02p093127' => 'qlo', 'QL03p006855' => 'qlo', 'QL03p071586' => 'qlo', 'QL04p000022' => 'qlo', 'QL04p000024' => 'qlo', 'QL04p003192' => 'qlo', 'QL05p011416' => 'qlo', 'QL06p039590' => 'qlo', 'QL06p052750' => 'qlo', 'QL06p053821' => 'qlo', 'QL07p025287' => 'qlo', 'QL09p033218' => 'qlo', 'QL09p040841' => 'qlo', 'QL10p020337' => 'qlo', 'QL10p027209' => 'qlo', 'QL10p027969' => 'qlo', 'QL10p048988' => 'qlo', 'QL11p001241' => 'qlo', 'QL11p028487' => 'qlo', 'RcHm_v2.0_Chr2g0105031' => 'rch', 'RcHm_v2.0_Chr2g0117811' => 'rch', 'RcHm_v2.0_Chr6g0270241' => 'rch', 'RcHm_v2.0_Chr7g0215961' => 'rch', 'RcHm_v2.0_Chr7g0231991' => 'rch', 'Rhsim01G0041500' => 'rsi', 'Rhsim01G0115000' => 'rsi', 'Rhsim01G0115400' => 'rsi', 'Rhsim01G0133600' => 'rsi', 'Rhsim01G0159900' => 'rsi', 'Rhsim02G0189400' => 'rsi', 'Rhsim03G0135600' => 'rsi', 'Rhsim03G0149900' => 'rsi', 'Rhsim04G0125600' => 'rsi', 'Rhsim05G0091700' => 'rsi', 'Rhsim05G0092900' => 'rsi', 'Rhsim06G0075000' => 'rsi', 'Rhsim07G0066400' => 'rsi', 'Rhsim07G0156400' => 'rsi', 'Rhsim07G0182200' => 'rsi', 'Rhsim07G0182300' => 'rsi', 'Rhsim08G0180400' => 'rsi', 'Rhsim09G0056800' => 'rsi', 'Rhsim10G0153300' => 'rsi', 'Rhsim11G0012700' => 'rsi', 'Rhsim12G0031800' => 'rsi', 'Rhsim12G0055400' => 'rsi', 'Rhsim12G0091400' => 'rsi', 'Rhsim13G0070800' => 'rsi', 'Rhsim13G0193300' => 'rsi', 'RhsimUnG0111600' => 'rsi', 'RhsimUnG0137500' => 'rsi', 'RhsimUnG0172900' => 'rsi', 'SGA_v2.0_scaffold11G05878' => 'sas', 'SGA_v2.0_scaffold167G38458' => 'sas', 'SGA_v2.0_scaffold19G08588' => 'sas', 'SGA_v2.0_scaffold239G43990' => 'sas', 'SGA_v2.0_scaffold260G45865' => 'sas', 'SGA_v2.0_scaffold309G48177' => 'sas', 'SGA_v2.0_scaffold76G25122' => 'sas', 'SGA_v2.0_scaffold85G26708' => 'sas', 'SHI13914' => 'shi', 'SHI30402' => 'shi', 'TWI09G0020' => 'twi', 'TWI09G0456' => 'twi', 'TWI09G1572' => 'twi', 'TWI12G0266' => 'twi', 'TWI12G1451' => 'twi', 'TWI14G0851' => 'twi', 'TWI15G0796' => 'twi', 'TWI18G0820' => 'twi', 'TWI18G1152' => 'twi', 'TWI23G0007' => 'twi', 'TWI23G0314' => 'twi', 'TWI31G0674' => 'twi', 'TWI31G0938' => 'twi', 'TWI34G0641' => 'twi', 'TWI34G1527' => 'twi', 'TWI36G0193' => 'twi', 'TWI36G0405' => 'twi', 'TWI38G0892' => 'twi', 'TWI38G0936' => 'twi', 'TWI38G2218' => 'twi', 'TWI53G0679' => 'twi', 'TWI53G0863' => 'twi', 'TWI53G1133' => 'twi', 'TWI60G0823' => 'twi', 'TWI63G0919' => 'twi', 'TWI63G1436' => 'twi', 'TWI73G0140' => 'twi', 'TWI73G0419' => 'twi', 'TWI73G0420' => 'twi', 'TWI73G1276' => 'twi', 'TWI74G0405' => 'twi', 'TWI74G0837' => 'twi', 'TWI75G0594' => 'twi', 'TWI75G1615' => 'twi', 'TWI77G0816' => 'twi', 'vmacro03831' => 'vma', 'vmacro13746' => 'vma', 'vmacro16089' => 'vma', 'vmacro22863' => 'vma', 'Zm00001eb085790' => 'zma', 'Zm00001eb114250' => 'zma', 'Zm00001eb138070' => 'zma', 'Zm00001eb167560' => 'zma', 'Zm00001eb199990' => 'zma', 'Zm00001eb368180' => 'zma', 'Zm00001eb382470' => 'zma' ) $gf_id = 'HOM05D001576' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001576' ) $data_identifier = 'HOM05D001576' $data_type = 'gf_id' $species_gene_counts = array( 'aox' => (int) 9, 'acertr' => (int) 3, 'cansat' => (int) 1, 'ccl' => (int) 4, 'cil' => (int) 145, 'camsi' => (int) 46, 'dca' => (int) 1, 'din' => (int) 1, 'fan' => (int) 12, 'fve' => (int) 9, 'gma' => (int) 5, 'han' => (int) 5, 'cav' => (int) 11, 'hma' => (int) 5, 'sun' => (int) 3, 'mdo' => (int) 3, 'mtr' => (int) 2, 'osa' => (int) 19, 'pgr' => (int) 1, 'ptr' => (int) 2, 'ppe' => (int) 6, 'qlo' => (int) 24, 'rch' => (int) 5, 'rsi' => (int) 28, 'sas' => (int) 8, 'shi' => (int) 2, 'twi' => (int) 35, 'vma' => (int) 4, 'zma' => (int) 7 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb382470' $species_info = array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ) $local_species = 'hma' $disabled = '' $selected = '' $num_hits = (int) 1include - APP/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp, line 33 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933 View::_renderElement() - CORE/Cake/View/View.php, line 1224 View::element() - CORE/Cake/View/View.php, line 418 include - APP/View/Elements/analysis/phylogenetics_module/gf_data_settings.ctp, line 37 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933 View::_renderElement() - CORE/Cake/View/View.php, line 1224 View::element() - CORE/Cake/View/View.php, line 418 include - APP/View/Elements/analysis/phylogenetics_module/parameter_selection.ctp, line 64 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933 View::_renderElement() - CORE/Cake/View/View.php, line 1224 View::element() - CORE/Cake/View/View.php, line 418 include - APP/View/Analysis/custom_tree_creation.ctp, line 27 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933
$viewFile = '/www/bioinformatics01_ro/plaza/_dev_instances/feedback/app/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp' $dataForView = array( 'sidebar_info' => array( 'gf_id' => 'HOM05D001576', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '406', 'num_species' => '29' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'Aqoxy1G01456' => 'aox', 'Aqoxy1G02949' => 'aox', 'Aqoxy3G01274' => 'aox', 'Aqoxy3G02110' => 'aox', 'Aqoxy3G02268' => 'aox', 'Aqoxy5G02702' => 'aox', 'Aqoxy5G02988' => 'aox', 'Aqoxy5G03427' => 'aox', 'Aqoxy6G02363' => 'aox', 'Atru.chr1.3225' => 'acertr', 'Atru.chr8.1198' => 'acertr', 'Atru.chr9.790' => 'acertr', 'CANSAT01G3197' => 'cansat', 'Ciclev10003979m.g' => 'ccl', 'Ciclev10017471m.g' => 'ccl', 'Ciclev10018206m.g' => 'ccl', 'Ciclev10033751m.g' => 'ccl', 'CiPaw.01G000900' => 'cil', 'CiPaw.01G001000' => 'cil', 'CiPaw.01G033500' => 'cil', 'CiPaw.01G060300' => 'cil', 'CiPaw.01G070200' => 'cil', 'CiPaw.01G075100' => 'cil', 'CiPaw.01G084700' => 'cil', 'CiPaw.01G087900' => 'cil', 'CiPaw.01G092600' => 'cil', 'CiPaw.01G097200' => 'cil', 'CiPaw.01G098300' => 'cil', 'CiPaw.01G110200' => 'cil', 'CiPaw.01G118700' => 'cil', 'CiPaw.01G121200' => 'cil', 'CiPaw.01G132500' => 'cil', 'CiPaw.01G146900' => 'cil', 'CiPaw.01G174000' => 'cil', 'CiPaw.01G179900' => 'cil', 'CiPaw.01G183400' => 'cil', 'CiPaw.01G240000' => 'cil', 'CiPaw.01G283500' => 'cil', 'CiPaw.01G307400' => 'cil', 'CiPaw.02G030800' => 'cil', 'CiPaw.02G047200' => 'cil', 'CiPaw.02G050500' => 'cil', 'CiPaw.02G069900' => 'cil', 'CiPaw.02G091600' => 'cil', 'CiPaw.02G095000' => 'cil', 'CiPaw.02G131900' => 'cil', 'CiPaw.03G043000' => 'cil', 'CiPaw.03G069900' => 'cil', 'CiPaw.03G088100' => 'cil', 'CiPaw.03G089300' => 'cil', 'CiPaw.03G093100' => 'cil', 'CiPaw.03G129800' => 'cil', 'CiPaw.03G131200' => 'cil', 'CiPaw.03G134500' => 'cil', 'CiPaw.03G152100' => 'cil', 'CiPaw.03G162700' => 'cil', 'CiPaw.03G172800' => 'cil', 'CiPaw.03G175800' => 'cil', 'CiPaw.03G181800' => 'cil', 'CiPaw.03G191400' => 'cil', 'CiPaw.03G198300' => 'cil', 'CiPaw.03G201300' => 'cil', 'CiPaw.03G224700' => 'cil', 'CiPaw.03G225000' => 'cil', 'CiPaw.04G065100' => 'cil', 'CiPaw.04G080400' => 'cil', 'CiPaw.04G113500' => 'cil', 'CiPaw.04G121900' => 'cil', 'CiPaw.04G144100' => 'cil', 'CiPaw.04G176500' => 'cil', 'CiPaw.05G086200' => 'cil', 'CiPaw.05G100200' => 'cil', 'CiPaw.05G114200' => 'cil', 'CiPaw.05G126800' => 'cil', 'CiPaw.05G228800' => 'cil', 'CiPaw.05G230600' => 'cil', 'CiPaw.05G236500' => 'cil', 'CiPaw.05G244800' => 'cil', 'CiPaw.06G026600' => 'cil', 'CiPaw.06G027900' => 'cil', 'CiPaw.06G051800' => 'cil', 'CiPaw.06G128500' => 'cil', 'CiPaw.06G165900' => 'cil', 'CiPaw.07G045400' => 'cil', 'CiPaw.07G048000' => 'cil', 'CiPaw.07G052000' => 'cil', 'CiPaw.07G073800' => 'cil', 'CiPaw.07G099700' => 'cil', 'CiPaw.07G108700' => 'cil', 'CiPaw.07G120000' => 'cil', 'CiPaw.07G134100' => 'cil', 'CiPaw.07G147000' => 'cil', 'CiPaw.07G149700' => 'cil', 'CiPaw.07G178300' => 'cil', 'CiPaw.07G184900' => 'cil', 'CiPaw.08G044500' => 'cil', 'CiPaw.08G046900' => 'cil', 'CiPaw.08G047300' => 'cil', 'CiPaw.08G115400' => 'cil', 'CiPaw.08G134700' => 'cil', 'CiPaw.08G157400' => 'cil', 'CiPaw.09G014300' => 'cil', 'CiPaw.09G088900' => 'cil', 'CiPaw.09G130900' => 'cil', 'CiPaw.09G133100' => 'cil', 'CiPaw.09G151300' => 'cil', 'CiPaw.09G172800' => 'cil', 'CiPaw.09G174900' => 'cil', 'CiPaw.09G175000' => 'cil', 'CiPaw.10G012800' => 'cil', 'CiPaw.10G028800' => 'cil', 'CiPaw.10G044700' => 'cil', 'CiPaw.10G067400' => 'cil', 'CiPaw.10G115900' => 'cil', 'CiPaw.10G126200' => 'cil', 'CiPaw.10G139700' => 'cil', 'CiPaw.10G155100' => 'cil', 'CiPaw.11G011300' => 'cil', 'CiPaw.11G025900' => 'cil', 'CiPaw.11G104100' => 'cil', 'CiPaw.11G142700' => 'cil', 'CiPaw.11G164500' => 'cil', 'CiPaw.11G189100' => 'cil', 'CiPaw.11G197100' => 'cil', 'CiPaw.12G006100' => 'cil', 'CiPaw.12G038500' => 'cil', 'CiPaw.12G041400' => 'cil', 'CiPaw.12G041600' => 'cil', 'CiPaw.12G051300' => 'cil', 'CiPaw.12G101800' => 'cil', 'CiPaw.12G107800' => 'cil', 'CiPaw.13G033200' => 'cil', 'CiPaw.13G129900' => 'cil', 'CiPaw.13G160200' => 'cil', 'CiPaw.14G018900' => 'cil', 'CiPaw.14G029000' => 'cil', 'CiPaw.14G031000' => 'cil', 'CiPaw.14G032000' => 'cil', 'CiPaw.14G032300' => 'cil', 'CiPaw.14G040600' => 'cil', 'CiPaw.14G060500' => 'cil', 'CiPaw.14G061500' => 'cil', 'CiPaw.14G077500' => 'cil', 'CiPaw.14G088300' => 'cil', 'CiPaw.14G108500' => 'cil', 'CiPaw.14G121300' => 'cil', 'CiPaw.14G133000' => 'cil', 'CiPaw.14G134600' => 'cil', 'CiPaw.15G027200' => 'cil', 'CiPaw.15G037700' => 'cil', 'CiPaw.15G050900' => 'cil', 'CiPaw.15G067200' => 'cil', 'CiPaw.15G072000' => 'cil', 'CiPaw.15G112900' => 'cil', 'CiPaw.15G133200' => 'cil', 'CiPaw.15G139500' => 'cil', 'CiPaw.15G155400' => 'cil', 'CiPaw.16G006000' => 'cil', 'CiPaw.16G013100' => 'cil', 'CiPaw.16G047100' => 'cil', 'CiPaw.16G048900' => 'cil', 'CiPaw.16G070300' => 'cil', 'CSS0000195' => 'camsi', 'CSS0001664' => 'camsi', 'CSS0002566' => 'camsi', 'CSS0003077' => 'camsi', 'CSS0004257' => 'camsi', 'CSS0004495' => 'camsi', 'CSS0004599' => 'camsi', 'CSS0004943' => 'camsi', 'CSS0005302' => 'camsi', 'CSS0006274' => 'camsi', 'CSS0006547' => 'camsi', 'CSS0006860' => 'camsi', 'CSS0008814' => 'camsi', 'CSS0008946' => 'camsi', 'CSS0009093' => 'camsi', 'CSS0010221' => 'camsi', 'CSS0010296' => 'camsi', 'CSS0010386' => 'camsi', 'CSS0010831' => 'camsi', 'CSS0011061' => 'camsi', 'CSS0012008' => 'camsi', 'CSS0012194' => 'camsi', 'CSS0013580' => 'camsi', 'CSS0014176' => 'camsi', 'CSS0014280' => 'camsi', 'CSS0014799' => 'camsi', 'CSS0015368' => 'camsi', 'CSS0017473' => 'camsi', 'CSS0019281' => 'camsi', 'CSS0021320' => 'camsi', 'CSS0021750' => 'camsi', 'CSS0023642' => 'camsi', 'CSS0023792' => 'camsi', 'CSS0031528' => 'camsi', 'CSS0033894' => 'camsi', 'CSS0034959' => 'camsi', 'CSS0035632' => 'camsi', 'CSS0038450' => 'camsi', 'CSS0039293' => 'camsi', 'CSS0041053' => 'camsi', 'CSS0041981' => 'camsi', 'CSS0042573' => 'camsi', 'CSS0042927' => 'camsi', 'CSS0047725' => 'camsi', 'CSS0049636' => 'camsi', 'CSS0050513' => 'camsi', 'DCAR_030203' => 'dca', 'Dinv07939' => 'din', 'FAN01G0456' => 'fan', 'FAN02G3001' => 'fan', 'FAN04G2781' => 'fan', 'FAN05G1385' => 'fan', 'FAN05G3062' => 'fan', 'FAN08G2267' => 'fan', 'FAN10G0481' => 'fan', 'FAN10G1257' => 'fan', 'FAN14G0954' => 'fan', 'FAN14G2347' => 'fan', 'FAN15G0187' => 'fan', 'FAN25G2214' => 'fan', 'FvH4_1g21031' => 'fve', 'FvH4_3g16231' => 'fve', 'FvH4_3g26413' => 'fve', 'FvH4_3g29014' => 'fve', 'FvH4_3g31921' => 'fve', 'FvH4_4g19882' => 'fve', 'FvH4_5g21960' => 'fve', 'FvH4_5g29683' => 'fve', 'FvH4_7g13271' => 'fve', 'Glyma.01G062500' => 'gma', 'Glyma.07G140900' => 'gma', 'Glyma.09G140900' => 'gma', 'Glyma.12G112700' => 'gma', 'Glyma.17G168800' => 'gma', 'HanXRQChr01g0027001' => 'han', 'HanXRQChr04g0120511' => 'han', 'HanXRQChr08g0232381' => 'han', 'HanXRQChr09g0265661' => 'han', 'HanXRQChr13g0416031' => 'han', 'Haze_05835' => 'cav', 'Haze_06597' => 'cav', 'Haze_07921' => 'cav', 'Haze_08599' => 'cav', 'Haze_10686' => 'cav', 'Haze_12994' => 'cav', 'Haze_13466' => 'cav', 'Haze_16101' => 'cav', 'Haze_17766' => 'cav', 'Haze_18456' => 'cav', 'Haze_20229' => 'cav', 'Hma1.2p1_0324F.1_g125640' => 'hma', 'Hma1.2p1_0733F.1_g210230' => 'hma', 'Hma1.2p1_0921F.1_g236870' => 'hma', 'Hma1.2p1_1313F.1_g274940' => 'hma', 'Hma1.2p1_3059F.1_g332230' => 'hma', 'Hund15925' => 'sun', 'Hund19562' => 'sun', 'Hund21925' => 'sun', 'MD03G1177400' => 'mdo', 'MD07G1026100' => 'mdo', 'MD17G1218600' => 'mdo', 'Medtr0867s0010' => 'mtr', 'Medtr6g081150' => 'mtr', 'Os01g0527900' => 'osa', 'Os02g0463725' => 'osa', 'Os02g0785600' => 'osa', 'Os03g0433733' => 'osa', 'Os04g0286500' => 'osa', 'Os05g0227800' => 'osa', 'Os06g0521000' => 'osa', 'Os06g0635500' => 'osa', 'Os06g0660650' => 'osa', 'Os07g0554400' => 'osa', 'Os08g0225900' => 'osa', 'Os08g0561000' => 'osa', 'Os09g0241700' => 'osa', 'Os09g0351900' => 'osa', 'Os11g0220700' => 'osa', 'Os11g0282700' => 'osa', 'Os12g0169300' => 'osa', 'Os12g0228500' => 'osa', 'Os12g0543800' => 'osa', 'PGR044G1547' => 'pgr', 'Potri.005G239150' => 'ptr', 'Potri.010G014250' => 'ptr', 'Prupe.1G172500' => 'ppe', 'Prupe.1G196800' => 'ppe', 'Prupe.1G279700' => 'ppe', 'Prupe.2G026400' => 'ppe', 'Prupe.3G094000' => 'ppe', 'Prupe.4G287300' => 'ppe', 'QL01p022166' => 'qlo', 'QL01p051890' => 'qlo', 'QL02p009469' => 'qlo', 'QL02p046053' => 'qlo', 'QL02p057958' => 'qlo', 'QL02p093127' => 'qlo', 'QL03p006855' => 'qlo', 'QL03p071586' => 'qlo', 'QL04p000022' => 'qlo', 'QL04p000024' => 'qlo', 'QL04p003192' => 'qlo', 'QL05p011416' => 'qlo', 'QL06p039590' => 'qlo', 'QL06p052750' => 'qlo', 'QL06p053821' => 'qlo', 'QL07p025287' => 'qlo', 'QL09p033218' => 'qlo', 'QL09p040841' => 'qlo', 'QL10p020337' => 'qlo', 'QL10p027209' => 'qlo', 'QL10p027969' => 'qlo', 'QL10p048988' => 'qlo', 'QL11p001241' => 'qlo', 'QL11p028487' => 'qlo', 'RcHm_v2.0_Chr2g0105031' => 'rch', 'RcHm_v2.0_Chr2g0117811' => 'rch', 'RcHm_v2.0_Chr6g0270241' => 'rch', 'RcHm_v2.0_Chr7g0215961' => 'rch', 'RcHm_v2.0_Chr7g0231991' => 'rch', 'Rhsim01G0041500' => 'rsi', 'Rhsim01G0115000' => 'rsi', 'Rhsim01G0115400' => 'rsi', 'Rhsim01G0133600' => 'rsi', 'Rhsim01G0159900' => 'rsi', 'Rhsim02G0189400' => 'rsi', 'Rhsim03G0135600' => 'rsi', 'Rhsim03G0149900' => 'rsi', 'Rhsim04G0125600' => 'rsi', 'Rhsim05G0091700' => 'rsi', 'Rhsim05G0092900' => 'rsi', 'Rhsim06G0075000' => 'rsi', 'Rhsim07G0066400' => 'rsi', 'Rhsim07G0156400' => 'rsi', 'Rhsim07G0182200' => 'rsi', 'Rhsim07G0182300' => 'rsi', 'Rhsim08G0180400' => 'rsi', 'Rhsim09G0056800' => 'rsi', 'Rhsim10G0153300' => 'rsi', 'Rhsim11G0012700' => 'rsi', 'Rhsim12G0031800' => 'rsi', 'Rhsim12G0055400' => 'rsi', 'Rhsim12G0091400' => 'rsi', 'Rhsim13G0070800' => 'rsi', 'Rhsim13G0193300' => 'rsi', 'RhsimUnG0111600' => 'rsi', 'RhsimUnG0137500' => 'rsi', 'RhsimUnG0172900' => 'rsi', 'SGA_v2.0_scaffold11G05878' => 'sas', 'SGA_v2.0_scaffold167G38458' => 'sas', 'SGA_v2.0_scaffold19G08588' => 'sas', 'SGA_v2.0_scaffold239G43990' => 'sas', 'SGA_v2.0_scaffold260G45865' => 'sas', 'SGA_v2.0_scaffold309G48177' => 'sas', 'SGA_v2.0_scaffold76G25122' => 'sas', 'SGA_v2.0_scaffold85G26708' => 'sas', 'SHI13914' => 'shi', 'SHI30402' => 'shi', 'TWI09G0020' => 'twi', 'TWI09G0456' => 'twi', 'TWI09G1572' => 'twi', 'TWI12G0266' => 'twi', 'TWI12G1451' => 'twi', 'TWI14G0851' => 'twi', 'TWI15G0796' => 'twi', 'TWI18G0820' => 'twi', 'TWI18G1152' => 'twi', 'TWI23G0007' => 'twi', 'TWI23G0314' => 'twi', 'TWI31G0674' => 'twi', 'TWI31G0938' => 'twi', 'TWI34G0641' => 'twi', 'TWI34G1527' => 'twi', 'TWI36G0193' => 'twi', 'TWI36G0405' => 'twi', 'TWI38G0892' => 'twi', 'TWI38G0936' => 'twi', 'TWI38G2218' => 'twi', 'TWI53G0679' => 'twi', 'TWI53G0863' => 'twi', 'TWI53G1133' => 'twi', 'TWI60G0823' => 'twi', 'TWI63G0919' => 'twi', 'TWI63G1436' => 'twi', 'TWI73G0140' => 'twi', 'TWI73G0419' => 'twi', 'TWI73G0420' => 'twi', 'TWI73G1276' => 'twi', 'TWI74G0405' => 'twi', 'TWI74G0837' => 'twi', 'TWI75G0594' => 'twi', 'TWI75G1615' => 'twi', 'TWI77G0816' => 'twi', 'vmacro03831' => 'vma', 'vmacro13746' => 'vma', 'vmacro16089' => 'vma', 'vmacro22863' => 'vma', 'Zm00001eb085790' => 'zma', 'Zm00001eb114250' => 'zma', 'Zm00001eb138070' => 'zma', 'Zm00001eb167560' => 'zma', 'Zm00001eb199990' => 'zma', 'Zm00001eb368180' => 'zma', 'Zm00001eb382470' => 'zma' ), 'gf_id' => 'HOM05D001576', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001576' ), 'data_identifier' => 'HOM05D001576', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001576', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '406', 'num_species' => '29' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'Aqoxy1G01456' => 'aox', 'Aqoxy1G02949' => 'aox', 'Aqoxy3G01274' => 'aox', 'Aqoxy3G02110' => 'aox', 'Aqoxy3G02268' => 'aox', 'Aqoxy5G02702' => 'aox', 'Aqoxy5G02988' => 'aox', 'Aqoxy5G03427' => 'aox', 'Aqoxy6G02363' => 'aox', 'Atru.chr1.3225' => 'acertr', 'Atru.chr8.1198' => 'acertr', 'Atru.chr9.790' => 'acertr', 'CANSAT01G3197' => 'cansat', 'Ciclev10003979m.g' => 'ccl', 'Ciclev10017471m.g' => 'ccl', 'Ciclev10018206m.g' => 'ccl', 'Ciclev10033751m.g' => 'ccl', 'CiPaw.01G000900' => 'cil', 'CiPaw.01G001000' => 'cil', 'CiPaw.01G033500' => 'cil', 'CiPaw.01G060300' => 'cil', 'CiPaw.01G070200' => 'cil', 'CiPaw.01G075100' => 'cil', 'CiPaw.01G084700' => 'cil', 'CiPaw.01G087900' => 'cil', 'CiPaw.01G092600' => 'cil', 'CiPaw.01G097200' => 'cil', 'CiPaw.01G098300' => 'cil', 'CiPaw.01G110200' => 'cil', 'CiPaw.01G118700' => 'cil', 'CiPaw.01G121200' => 'cil', 'CiPaw.01G132500' => 'cil', 'CiPaw.01G146900' => 'cil', 'CiPaw.01G174000' => 'cil', 'CiPaw.01G179900' => 'cil', 'CiPaw.01G183400' => 'cil', 'CiPaw.01G240000' => 'cil', 'CiPaw.01G283500' => 'cil', 'CiPaw.01G307400' => 'cil', 'CiPaw.02G030800' => 'cil', 'CiPaw.02G047200' => 'cil', 'CiPaw.02G050500' => 'cil', 'CiPaw.02G069900' => 'cil', 'CiPaw.02G091600' => 'cil', 'CiPaw.02G095000' => 'cil', 'CiPaw.02G131900' => 'cil', 'CiPaw.03G043000' => 'cil', 'CiPaw.03G069900' => 'cil', 'CiPaw.03G088100' => 'cil', 'CiPaw.03G089300' => 'cil', 'CiPaw.03G093100' => 'cil', 'CiPaw.03G129800' => 'cil', 'CiPaw.03G131200' => 'cil', 'CiPaw.03G134500' => 'cil', 'CiPaw.03G152100' => 'cil', 'CiPaw.03G162700' => 'cil', 'CiPaw.03G172800' => 'cil', 'CiPaw.03G175800' => 'cil', 'CiPaw.03G181800' => 'cil', 'CiPaw.03G191400' => 'cil', 'CiPaw.03G198300' => 'cil', 'CiPaw.03G201300' => 'cil', 'CiPaw.03G224700' => 'cil', 'CiPaw.03G225000' => 'cil', 'CiPaw.04G065100' => 'cil', 'CiPaw.04G080400' => 'cil', 'CiPaw.04G113500' => 'cil', 'CiPaw.04G121900' => 'cil', 'CiPaw.04G144100' => 'cil', 'CiPaw.04G176500' => 'cil', 'CiPaw.05G086200' => 'cil', 'CiPaw.05G100200' => 'cil', 'CiPaw.05G114200' => 'cil', 'CiPaw.05G126800' => 'cil', 'CiPaw.05G228800' => 'cil', 'CiPaw.05G230600' => 'cil', 'CiPaw.05G236500' => 'cil', 'CiPaw.05G244800' => 'cil', 'CiPaw.06G026600' => 'cil', 'CiPaw.06G027900' => 'cil', 'CiPaw.06G051800' => 'cil', 'CiPaw.06G128500' => 'cil', 'CiPaw.06G165900' => 'cil', 'CiPaw.07G045400' => 'cil', 'CiPaw.07G048000' => 'cil', 'CiPaw.07G052000' => 'cil', 'CiPaw.07G073800' => 'cil', 'CiPaw.07G099700' => 'cil', 'CiPaw.07G108700' => 'cil', 'CiPaw.07G120000' => 'cil', 'CiPaw.07G134100' => 'cil', 'CiPaw.07G147000' => 'cil', 'CiPaw.07G149700' => 'cil', 'CiPaw.07G178300' => 'cil', 'CiPaw.07G184900' => 'cil', 'CiPaw.08G044500' => 'cil', 'CiPaw.08G046900' => 'cil', 'CiPaw.08G047300' => 'cil', 'CiPaw.08G115400' => 'cil', 'CiPaw.08G134700' => 'cil', 'CiPaw.08G157400' => 'cil', 'CiPaw.09G014300' => 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'CiPaw.14G032000' => 'cil', 'CiPaw.14G032300' => 'cil', 'CiPaw.14G040600' => 'cil', 'CiPaw.14G060500' => 'cil', 'CiPaw.14G061500' => 'cil', 'CiPaw.14G077500' => 'cil', 'CiPaw.14G088300' => 'cil', 'CiPaw.14G108500' => 'cil', 'CiPaw.14G121300' => 'cil', 'CiPaw.14G133000' => 'cil', 'CiPaw.14G134600' => 'cil', 'CiPaw.15G027200' => 'cil', 'CiPaw.15G037700' => 'cil', 'CiPaw.15G050900' => 'cil', 'CiPaw.15G067200' => 'cil', 'CiPaw.15G072000' => 'cil', 'CiPaw.15G112900' => 'cil', 'CiPaw.15G133200' => 'cil', 'CiPaw.15G139500' => 'cil', 'CiPaw.15G155400' => 'cil', 'CiPaw.16G006000' => 'cil', 'CiPaw.16G013100' => 'cil', 'CiPaw.16G047100' => 'cil', 'CiPaw.16G048900' => 'cil', 'CiPaw.16G070300' => 'cil', 'CSS0000195' => 'camsi', 'CSS0001664' => 'camsi', 'CSS0002566' => 'camsi', 'CSS0003077' => 'camsi', 'CSS0004257' => 'camsi', 'CSS0004495' => 'camsi', 'CSS0004599' => 'camsi', 'CSS0004943' => 'camsi', 'CSS0005302' => 'camsi', 'CSS0006274' => 'camsi', 'CSS0006547' => 'camsi', 'CSS0006860' => 'camsi', 'CSS0008814' => 'camsi', 'CSS0008946' => 'camsi', 'CSS0009093' => 'camsi', 'CSS0010221' => 'camsi', 'CSS0010296' => 'camsi', 'CSS0010386' => 'camsi', 'CSS0010831' => 'camsi', 'CSS0011061' => 'camsi', 'CSS0012008' => 'camsi', 'CSS0012194' => 'camsi', 'CSS0013580' => 'camsi', 'CSS0014176' => 'camsi', 'CSS0014280' => 'camsi', 'CSS0014799' => 'camsi', 'CSS0015368' => 'camsi', 'CSS0017473' => 'camsi', 'CSS0019281' => 'camsi', 'CSS0021320' => 'camsi', 'CSS0021750' => 'camsi', 'CSS0023642' => 'camsi', 'CSS0023792' => 'camsi', 'CSS0031528' => 'camsi', 'CSS0033894' => 'camsi', 'CSS0034959' => 'camsi', 'CSS0035632' => 'camsi', 'CSS0038450' => 'camsi', 'CSS0039293' => 'camsi', 'CSS0041053' => 'camsi', 'CSS0041981' => 'camsi', 'CSS0042573' => 'camsi', 'CSS0042927' => 'camsi', 'CSS0047725' => 'camsi', 'CSS0049636' => 'camsi', 'CSS0050513' => 'camsi', 'DCAR_030203' => 'dca', 'Dinv07939' => 'din', 'FAN01G0456' => 'fan', 'FAN02G3001' => 'fan', 'FAN04G2781' => 'fan', 'FAN05G1385' => 'fan', 'FAN05G3062' => 'fan', 'FAN08G2267' => 'fan', 'FAN10G0481' => 'fan', 'FAN10G1257' => 'fan', 'FAN14G0954' => 'fan', 'FAN14G2347' => 'fan', 'FAN15G0187' => 'fan', 'FAN25G2214' => 'fan', 'FvH4_1g21031' => 'fve', 'FvH4_3g16231' => 'fve', 'FvH4_3g26413' => 'fve', 'FvH4_3g29014' => 'fve', 'FvH4_3g31921' => 'fve', 'FvH4_4g19882' => 'fve', 'FvH4_5g21960' => 'fve', 'FvH4_5g29683' => 'fve', 'FvH4_7g13271' => 'fve', 'Glyma.01G062500' => 'gma', 'Glyma.07G140900' => 'gma', 'Glyma.09G140900' => 'gma', 'Glyma.12G112700' => 'gma', 'Glyma.17G168800' => 'gma', 'HanXRQChr01g0027001' => 'han', 'HanXRQChr04g0120511' => 'han', 'HanXRQChr08g0232381' => 'han', 'HanXRQChr09g0265661' => 'han', 'HanXRQChr13g0416031' => 'han', 'Haze_05835' => 'cav', 'Haze_06597' => 'cav', 'Haze_07921' => 'cav', 'Haze_08599' => 'cav', 'Haze_10686' => 'cav', 'Haze_12994' => 'cav', 'Haze_13466' => 'cav', 'Haze_16101' => 'cav', 'Haze_17766' => 'cav', 'Haze_18456' => 'cav', 'Haze_20229' => 'cav', 'Hma1.2p1_0324F.1_g125640' => 'hma', 'Hma1.2p1_0733F.1_g210230' => 'hma', 'Hma1.2p1_0921F.1_g236870' => 'hma', 'Hma1.2p1_1313F.1_g274940' => 'hma', 'Hma1.2p1_3059F.1_g332230' => 'hma', 'Hund15925' => 'sun', 'Hund19562' => 'sun', 'Hund21925' => 'sun', 'MD03G1177400' => 'mdo', 'MD07G1026100' => 'mdo', 'MD17G1218600' => 'mdo', 'Medtr0867s0010' => 'mtr', 'Medtr6g081150' => 'mtr', 'Os01g0527900' => 'osa', 'Os02g0463725' => 'osa', 'Os02g0785600' => 'osa', 'Os03g0433733' => 'osa', 'Os04g0286500' => 'osa', 'Os05g0227800' => 'osa', 'Os06g0521000' => 'osa', 'Os06g0635500' => 'osa', 'Os06g0660650' => 'osa', 'Os07g0554400' => 'osa', 'Os08g0225900' => 'osa', 'Os08g0561000' => 'osa', 'Os09g0241700' => 'osa', 'Os09g0351900' => 'osa', 'Os11g0220700' => 'osa', 'Os11g0282700' => 'osa', 'Os12g0169300' => 'osa', 'Os12g0228500' => 'osa', 'Os12g0543800' => 'osa', 'PGR044G1547' => 'pgr', 'Potri.005G239150' => 'ptr', 'Potri.010G014250' => 'ptr', 'Prupe.1G172500' => 'ppe', 'Prupe.1G196800' => 'ppe', 'Prupe.1G279700' => 'ppe', 'Prupe.2G026400' => 'ppe', 'Prupe.3G094000' => 'ppe', 'Prupe.4G287300' => 'ppe', 'QL01p022166' => 'qlo', 'QL01p051890' => 'qlo', 'QL02p009469' => 'qlo', 'QL02p046053' => 'qlo', 'QL02p057958' => 'qlo', 'QL02p093127' => 'qlo', 'QL03p006855' => 'qlo', 'QL03p071586' => 'qlo', 'QL04p000022' => 'qlo', 'QL04p000024' => 'qlo', 'QL04p003192' => 'qlo', 'QL05p011416' => 'qlo', 'QL06p039590' => 'qlo', 'QL06p052750' => 'qlo', 'QL06p053821' => 'qlo', 'QL07p025287' => 'qlo', 'QL09p033218' => 'qlo', 'QL09p040841' => 'qlo', 'QL10p020337' => 'qlo', 'QL10p027209' => 'qlo', 'QL10p027969' => 'qlo', 'QL10p048988' => 'qlo', 'QL11p001241' => 'qlo', 'QL11p028487' => 'qlo', 'RcHm_v2.0_Chr2g0105031' => 'rch', 'RcHm_v2.0_Chr2g0117811' => 'rch', 'RcHm_v2.0_Chr6g0270241' => 'rch', 'RcHm_v2.0_Chr7g0215961' => 'rch', 'RcHm_v2.0_Chr7g0231991' => 'rch', 'Rhsim01G0041500' => 'rsi', 'Rhsim01G0115000' => 'rsi', 'Rhsim01G0115400' => 'rsi', 'Rhsim01G0133600' => 'rsi', 'Rhsim01G0159900' => 'rsi', 'Rhsim02G0189400' => 'rsi', 'Rhsim03G0135600' => 'rsi', 'Rhsim03G0149900' => 'rsi', 'Rhsim04G0125600' => 'rsi', 'Rhsim05G0091700' => 'rsi', 'Rhsim05G0092900' => 'rsi', 'Rhsim06G0075000' => 'rsi', 'Rhsim07G0066400' => 'rsi', 'Rhsim07G0156400' => 'rsi', 'Rhsim07G0182200' => 'rsi', 'Rhsim07G0182300' => 'rsi', 'Rhsim08G0180400' => 'rsi', 'Rhsim09G0056800' => 'rsi', 'Rhsim10G0153300' => 'rsi', 'Rhsim11G0012700' => 'rsi', 'Rhsim12G0031800' => 'rsi', 'Rhsim12G0055400' => 'rsi', 'Rhsim12G0091400' => 'rsi', 'Rhsim13G0070800' => 'rsi', 'Rhsim13G0193300' => 'rsi', 'RhsimUnG0111600' => 'rsi', 'RhsimUnG0137500' => 'rsi', 'RhsimUnG0172900' => 'rsi', 'SGA_v2.0_scaffold11G05878' => 'sas', 'SGA_v2.0_scaffold167G38458' => 'sas', 'SGA_v2.0_scaffold19G08588' => 'sas', 'SGA_v2.0_scaffold239G43990' => 'sas', 'SGA_v2.0_scaffold260G45865' => 'sas', 'SGA_v2.0_scaffold309G48177' => 'sas', 'SGA_v2.0_scaffold76G25122' => 'sas', 'SGA_v2.0_scaffold85G26708' => 'sas', 'SHI13914' => 'shi', 'SHI30402' => 'shi', 'TWI09G0020' => 'twi', 'TWI09G0456' => 'twi', 'TWI09G1572' => 'twi', 'TWI12G0266' => 'twi', 'TWI12G1451' => 'twi', 'TWI14G0851' => 'twi', 'TWI15G0796' => 'twi', 'TWI18G0820' => 'twi', 'TWI18G1152' => 'twi', 'TWI23G0007' => 'twi', 'TWI23G0314' => 'twi', 'TWI31G0674' => 'twi', 'TWI31G0938' => 'twi', 'TWI34G0641' => 'twi', 'TWI34G1527' => 'twi', 'TWI36G0193' => 'twi', 'TWI36G0405' => 'twi', 'TWI38G0892' => 'twi', 'TWI38G0936' => 'twi', 'TWI38G2218' => 'twi', 'TWI53G0679' => 'twi', 'TWI53G0863' => 'twi', 'TWI53G1133' => 'twi', 'TWI60G0823' => 'twi', 'TWI63G0919' => 'twi', 'TWI63G1436' => 'twi', 'TWI73G0140' => 'twi', 'TWI73G0419' => 'twi', 'TWI73G0420' => 'twi', 'TWI73G1276' => 'twi', 'TWI74G0405' => 'twi', 'TWI74G0837' => 'twi', 'TWI75G0594' => 'twi', 'TWI75G1615' => 'twi', 'TWI77G0816' => 'twi', 'vmacro03831' => 'vma', 'vmacro13746' => 'vma', 'vmacro16089' => 'vma', 'vmacro22863' => 'vma', 'Zm00001eb085790' => 'zma', 'Zm00001eb114250' => 'zma', 'Zm00001eb138070' => 'zma', 'Zm00001eb167560' => 'zma', 'Zm00001eb199990' => 'zma', 'Zm00001eb368180' => 'zma', 'Zm00001eb382470' => 'zma' ) $gf_id = 'HOM05D001576' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001576' ) $data_identifier = 'HOM05D001576' $data_type = 'gf_id' $species_gene_counts = array( 'aox' => (int) 9, 'acertr' => (int) 3, 'cansat' => (int) 1, 'ccl' => (int) 4, 'cil' => (int) 145, 'camsi' => (int) 46, 'dca' => (int) 1, 'din' => (int) 1, 'fan' => (int) 12, 'fve' => (int) 9, 'gma' => (int) 5, 'han' => (int) 5, 'cav' => (int) 11, 'hma' => (int) 5, 'sun' => (int) 3, 'mdo' => (int) 3, 'mtr' => (int) 2, 'osa' => (int) 19, 'pgr' => (int) 1, 'ptr' => (int) 2, 'ppe' => (int) 6, 'qlo' => (int) 24, 'rch' => (int) 5, 'rsi' => (int) 28, 'sas' => (int) 8, 'shi' => (int) 2, 'twi' => (int) 35, 'vma' => (int) 4, 'zma' => (int) 7 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb382470' $species_info = array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ) $local_species = 'hma' $disabled = '' $selected = '' $num_hits = (int) 1
Warning (2): count(): Parameter must be an array or an object that implements Countable [APP/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp, line 33]Code Context $disabled = (!array_key_exists($local_species,$species_gene_counts))?"disabled":""; $selected = (isset($selected_species) && array_key_exists($local_species,$selected_species))?"checked='checked'":""; $num_hits = (array_key_exists($local_species,$species_gene_counts))?count($species_gene_counts[$local_species]):0; $viewFile = '/www/bioinformatics01_ro/plaza/_dev_instances/feedback/app/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp' $dataForView = array( 'sidebar_info' => array( 'gf_id' => 'HOM05D001576', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '406', 'num_species' => '29' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'Aqoxy1G01456' => 'aox', 'Aqoxy1G02949' => 'aox', 'Aqoxy3G01274' => 'aox', 'Aqoxy3G02110' => 'aox', 'Aqoxy3G02268' => 'aox', 'Aqoxy5G02702' => 'aox', 'Aqoxy5G02988' => 'aox', 'Aqoxy5G03427' => 'aox', 'Aqoxy6G02363' => 'aox', 'Atru.chr1.3225' => 'acertr', 'Atru.chr8.1198' => 'acertr', 'Atru.chr9.790' => 'acertr', 'CANSAT01G3197' => 'cansat', 'Ciclev10003979m.g' => 'ccl', 'Ciclev10017471m.g' => 'ccl', 'Ciclev10018206m.g' => 'ccl', 'Ciclev10033751m.g' => 'ccl', 'CiPaw.01G000900' => 'cil', 'CiPaw.01G001000' => 'cil', 'CiPaw.01G033500' => 'cil', 'CiPaw.01G060300' => 'cil', 'CiPaw.01G070200' => 'cil', 'CiPaw.01G075100' => 'cil', 'CiPaw.01G084700' => 'cil', 'CiPaw.01G087900' => 'cil', 'CiPaw.01G092600' => 'cil', 'CiPaw.01G097200' => 'cil', 'CiPaw.01G098300' => 'cil', 'CiPaw.01G110200' => 'cil', 'CiPaw.01G118700' => 'cil', 'CiPaw.01G121200' => 'cil', 'CiPaw.01G132500' => 'cil', 'CiPaw.01G146900' => 'cil', 'CiPaw.01G174000' => 'cil', 'CiPaw.01G179900' => 'cil', 'CiPaw.01G183400' => 'cil', 'CiPaw.01G240000' => 'cil', 'CiPaw.01G283500' => 'cil', 'CiPaw.01G307400' => 'cil', 'CiPaw.02G030800' => 'cil', 'CiPaw.02G047200' => 'cil', 'CiPaw.02G050500' => 'cil', 'CiPaw.02G069900' => 'cil', 'CiPaw.02G091600' => 'cil', 'CiPaw.02G095000' => 'cil', 'CiPaw.02G131900' => 'cil', 'CiPaw.03G043000' => 'cil', 'CiPaw.03G069900' => 'cil', 'CiPaw.03G088100' => 'cil', 'CiPaw.03G089300' => 'cil', 'CiPaw.03G093100' => 'cil', 'CiPaw.03G129800' => 'cil', 'CiPaw.03G131200' => 'cil', 'CiPaw.03G134500' => 'cil', 'CiPaw.03G152100' => 'cil', 'CiPaw.03G162700' => 'cil', 'CiPaw.03G172800' => 'cil', 'CiPaw.03G175800' => 'cil', 'CiPaw.03G181800' => 'cil', 'CiPaw.03G191400' => 'cil', 'CiPaw.03G198300' => 'cil', 'CiPaw.03G201300' => 'cil', 'CiPaw.03G224700' => 'cil', 'CiPaw.03G225000' => 'cil', 'CiPaw.04G065100' => 'cil', 'CiPaw.04G080400' => 'cil', 'CiPaw.04G113500' => 'cil', 'CiPaw.04G121900' => 'cil', 'CiPaw.04G144100' => 'cil', 'CiPaw.04G176500' => 'cil', 'CiPaw.05G086200' => 'cil', 'CiPaw.05G100200' => 'cil', 'CiPaw.05G114200' => 'cil', 'CiPaw.05G126800' => 'cil', 'CiPaw.05G228800' => 'cil', 'CiPaw.05G230600' => 'cil', 'CiPaw.05G236500' => 'cil', 'CiPaw.05G244800' => 'cil', 'CiPaw.06G026600' => 'cil', 'CiPaw.06G027900' => 'cil', 'CiPaw.06G051800' => 'cil', 'CiPaw.06G128500' => 'cil', 'CiPaw.06G165900' => 'cil', 'CiPaw.07G045400' => 'cil', 'CiPaw.07G048000' => 'cil', 'CiPaw.07G052000' => 'cil', 'CiPaw.07G073800' => 'cil', 'CiPaw.07G099700' => 'cil', 'CiPaw.07G108700' => 'cil', 'CiPaw.07G120000' => 'cil', 'CiPaw.07G134100' => 'cil', 'CiPaw.07G147000' => 'cil', 'CiPaw.07G149700' => 'cil', 'CiPaw.07G178300' => 'cil', 'CiPaw.07G184900' => 'cil', 'CiPaw.08G044500' => 'cil', 'CiPaw.08G046900' => 'cil', 'CiPaw.08G047300' => 'cil', 'CiPaw.08G115400' => 'cil', 'CiPaw.08G134700' => 'cil', 'CiPaw.08G157400' => 'cil', 'CiPaw.09G014300' => 'cil', 'CiPaw.09G088900' => 'cil', 'CiPaw.09G130900' => 'cil', 'CiPaw.09G133100' => 'cil', 'CiPaw.09G151300' => 'cil', 'CiPaw.09G172800' => 'cil', 'CiPaw.09G174900' => 'cil', 'CiPaw.09G175000' => 'cil', 'CiPaw.10G012800' => 'cil', 'CiPaw.10G028800' => 'cil', 'CiPaw.10G044700' => 'cil', 'CiPaw.10G067400' => 'cil', 'CiPaw.10G115900' => 'cil', 'CiPaw.10G126200' => 'cil', 'CiPaw.10G139700' => 'cil', 'CiPaw.10G155100' => 'cil', 'CiPaw.11G011300' => 'cil', 'CiPaw.11G025900' => 'cil', 'CiPaw.11G104100' => 'cil', 'CiPaw.11G142700' => 'cil', 'CiPaw.11G164500' => 'cil', 'CiPaw.11G189100' => 'cil', 'CiPaw.11G197100' => 'cil', 'CiPaw.12G006100' => 'cil', 'CiPaw.12G038500' => 'cil', 'CiPaw.12G041400' => 'cil', 'CiPaw.12G041600' => 'cil', 'CiPaw.12G051300' => 'cil', 'CiPaw.12G101800' => 'cil', 'CiPaw.12G107800' => 'cil', 'CiPaw.13G033200' => 'cil', 'CiPaw.13G129900' => 'cil', 'CiPaw.13G160200' => 'cil', 'CiPaw.14G018900' => 'cil', 'CiPaw.14G029000' => 'cil', 'CiPaw.14G031000' => 'cil', 'CiPaw.14G032000' => 'cil', 'CiPaw.14G032300' => 'cil', 'CiPaw.14G040600' => 'cil', 'CiPaw.14G060500' => 'cil', 'CiPaw.14G061500' => 'cil', 'CiPaw.14G077500' => 'cil', 'CiPaw.14G088300' => 'cil', 'CiPaw.14G108500' => 'cil', 'CiPaw.14G121300' => 'cil', 'CiPaw.14G133000' => 'cil', 'CiPaw.14G134600' => 'cil', 'CiPaw.15G027200' => 'cil', 'CiPaw.15G037700' => 'cil', 'CiPaw.15G050900' => 'cil', 'CiPaw.15G067200' => 'cil', 'CiPaw.15G072000' => 'cil', 'CiPaw.15G112900' => 'cil', 'CiPaw.15G133200' => 'cil', 'CiPaw.15G139500' => 'cil', 'CiPaw.15G155400' => 'cil', 'CiPaw.16G006000' => 'cil', 'CiPaw.16G013100' => 'cil', 'CiPaw.16G047100' => 'cil', 'CiPaw.16G048900' => 'cil', 'CiPaw.16G070300' => 'cil', 'CSS0000195' => 'camsi', 'CSS0001664' => 'camsi', 'CSS0002566' => 'camsi', 'CSS0003077' => 'camsi', 'CSS0004257' => 'camsi', 'CSS0004495' => 'camsi', 'CSS0004599' => 'camsi', 'CSS0004943' => 'camsi', 'CSS0005302' => 'camsi', 'CSS0006274' => 'camsi', 'CSS0006547' => 'camsi', 'CSS0006860' => 'camsi', 'CSS0008814' => 'camsi', 'CSS0008946' => 'camsi', 'CSS0009093' => 'camsi', 'CSS0010221' => 'camsi', 'CSS0010296' => 'camsi', 'CSS0010386' => 'camsi', 'CSS0010831' => 'camsi', 'CSS0011061' => 'camsi', 'CSS0012008' => 'camsi', 'CSS0012194' => 'camsi', 'CSS0013580' => 'camsi', 'CSS0014176' => 'camsi', 'CSS0014280' => 'camsi', 'CSS0014799' => 'camsi', 'CSS0015368' => 'camsi', 'CSS0017473' => 'camsi', 'CSS0019281' => 'camsi', 'CSS0021320' => 'camsi', 'CSS0021750' => 'camsi', 'CSS0023642' => 'camsi', 'CSS0023792' => 'camsi', 'CSS0031528' => 'camsi', 'CSS0033894' => 'camsi', 'CSS0034959' => 'camsi', 'CSS0035632' => 'camsi', 'CSS0038450' => 'camsi', 'CSS0039293' => 'camsi', 'CSS0041053' => 'camsi', 'CSS0041981' => 'camsi', 'CSS0042573' => 'camsi', 'CSS0042927' => 'camsi', 'CSS0047725' => 'camsi', 'CSS0049636' => 'camsi', 'CSS0050513' => 'camsi', 'DCAR_030203' => 'dca', 'Dinv07939' => 'din', 'FAN01G0456' => 'fan', 'FAN02G3001' => 'fan', 'FAN04G2781' => 'fan', 'FAN05G1385' => 'fan', 'FAN05G3062' => 'fan', 'FAN08G2267' => 'fan', 'FAN10G0481' => 'fan', 'FAN10G1257' => 'fan', 'FAN14G0954' => 'fan', 'FAN14G2347' => 'fan', 'FAN15G0187' => 'fan', 'FAN25G2214' => 'fan', 'FvH4_1g21031' => 'fve', 'FvH4_3g16231' => 'fve', 'FvH4_3g26413' => 'fve', 'FvH4_3g29014' => 'fve', 'FvH4_3g31921' => 'fve', 'FvH4_4g19882' => 'fve', 'FvH4_5g21960' => 'fve', 'FvH4_5g29683' => 'fve', 'FvH4_7g13271' => 'fve', 'Glyma.01G062500' => 'gma', 'Glyma.07G140900' => 'gma', 'Glyma.09G140900' => 'gma', 'Glyma.12G112700' => 'gma', 'Glyma.17G168800' => 'gma', 'HanXRQChr01g0027001' => 'han', 'HanXRQChr04g0120511' => 'han', 'HanXRQChr08g0232381' => 'han', 'HanXRQChr09g0265661' => 'han', 'HanXRQChr13g0416031' => 'han', 'Haze_05835' => 'cav', 'Haze_06597' => 'cav', 'Haze_07921' => 'cav', 'Haze_08599' => 'cav', 'Haze_10686' => 'cav', 'Haze_12994' => 'cav', 'Haze_13466' => 'cav', 'Haze_16101' => 'cav', 'Haze_17766' => 'cav', 'Haze_18456' => 'cav', 'Haze_20229' => 'cav', 'Hma1.2p1_0324F.1_g125640' => 'hma', 'Hma1.2p1_0733F.1_g210230' => 'hma', 'Hma1.2p1_0921F.1_g236870' => 'hma', 'Hma1.2p1_1313F.1_g274940' => 'hma', 'Hma1.2p1_3059F.1_g332230' => 'hma', 'Hund15925' => 'sun', 'Hund19562' => 'sun', 'Hund21925' => 'sun', 'MD03G1177400' => 'mdo', 'MD07G1026100' => 'mdo', 'MD17G1218600' => 'mdo', 'Medtr0867s0010' => 'mtr', 'Medtr6g081150' => 'mtr', 'Os01g0527900' => 'osa', 'Os02g0463725' => 'osa', 'Os02g0785600' => 'osa', 'Os03g0433733' => 'osa', 'Os04g0286500' => 'osa', 'Os05g0227800' => 'osa', 'Os06g0521000' => 'osa', 'Os06g0635500' => 'osa', 'Os06g0660650' => 'osa', 'Os07g0554400' => 'osa', 'Os08g0225900' => 'osa', 'Os08g0561000' => 'osa', 'Os09g0241700' => 'osa', 'Os09g0351900' => 'osa', 'Os11g0220700' => 'osa', 'Os11g0282700' => 'osa', 'Os12g0169300' => 'osa', 'Os12g0228500' => 'osa', 'Os12g0543800' => 'osa', 'PGR044G1547' => 'pgr', 'Potri.005G239150' => 'ptr', 'Potri.010G014250' => 'ptr', 'Prupe.1G172500' => 'ppe', 'Prupe.1G196800' => 'ppe', 'Prupe.1G279700' => 'ppe', 'Prupe.2G026400' => 'ppe', 'Prupe.3G094000' => 'ppe', 'Prupe.4G287300' => 'ppe', 'QL01p022166' => 'qlo', 'QL01p051890' => 'qlo', 'QL02p009469' => 'qlo', 'QL02p046053' => 'qlo', 'QL02p057958' => 'qlo', 'QL02p093127' => 'qlo', 'QL03p006855' => 'qlo', 'QL03p071586' => 'qlo', 'QL04p000022' => 'qlo', 'QL04p000024' => 'qlo', 'QL04p003192' => 'qlo', 'QL05p011416' => 'qlo', 'QL06p039590' => 'qlo', 'QL06p052750' => 'qlo', 'QL06p053821' => 'qlo', 'QL07p025287' => 'qlo', 'QL09p033218' => 'qlo', 'QL09p040841' => 'qlo', 'QL10p020337' => 'qlo', 'QL10p027209' => 'qlo', 'QL10p027969' => 'qlo', 'QL10p048988' => 'qlo', 'QL11p001241' => 'qlo', 'QL11p028487' => 'qlo', 'RcHm_v2.0_Chr2g0105031' => 'rch', 'RcHm_v2.0_Chr2g0117811' => 'rch', 'RcHm_v2.0_Chr6g0270241' => 'rch', 'RcHm_v2.0_Chr7g0215961' => 'rch', 'RcHm_v2.0_Chr7g0231991' => 'rch', 'Rhsim01G0041500' => 'rsi', 'Rhsim01G0115000' => 'rsi', 'Rhsim01G0115400' => 'rsi', 'Rhsim01G0133600' => 'rsi', 'Rhsim01G0159900' => 'rsi', 'Rhsim02G0189400' => 'rsi', 'Rhsim03G0135600' => 'rsi', 'Rhsim03G0149900' => 'rsi', 'Rhsim04G0125600' => 'rsi', 'Rhsim05G0091700' => 'rsi', 'Rhsim05G0092900' => 'rsi', 'Rhsim06G0075000' => 'rsi', 'Rhsim07G0066400' => 'rsi', 'Rhsim07G0156400' => 'rsi', 'Rhsim07G0182200' => 'rsi', 'Rhsim07G0182300' => 'rsi', 'Rhsim08G0180400' => 'rsi', 'Rhsim09G0056800' => 'rsi', 'Rhsim10G0153300' => 'rsi', 'Rhsim11G0012700' => 'rsi', 'Rhsim12G0031800' => 'rsi', 'Rhsim12G0055400' => 'rsi', 'Rhsim12G0091400' => 'rsi', 'Rhsim13G0070800' => 'rsi', 'Rhsim13G0193300' => 'rsi', 'RhsimUnG0111600' => 'rsi', 'RhsimUnG0137500' => 'rsi', 'RhsimUnG0172900' => 'rsi', 'SGA_v2.0_scaffold11G05878' => 'sas', 'SGA_v2.0_scaffold167G38458' => 'sas', 'SGA_v2.0_scaffold19G08588' => 'sas', 'SGA_v2.0_scaffold239G43990' => 'sas', 'SGA_v2.0_scaffold260G45865' => 'sas', 'SGA_v2.0_scaffold309G48177' => 'sas', 'SGA_v2.0_scaffold76G25122' => 'sas', 'SGA_v2.0_scaffold85G26708' => 'sas', 'SHI13914' => 'shi', 'SHI30402' => 'shi', 'TWI09G0020' => 'twi', 'TWI09G0456' => 'twi', 'TWI09G1572' => 'twi', 'TWI12G0266' => 'twi', 'TWI12G1451' => 'twi', 'TWI14G0851' => 'twi', 'TWI15G0796' => 'twi', 'TWI18G0820' => 'twi', 'TWI18G1152' => 'twi', 'TWI23G0007' => 'twi', 'TWI23G0314' => 'twi', 'TWI31G0674' => 'twi', 'TWI31G0938' => 'twi', 'TWI34G0641' => 'twi', 'TWI34G1527' => 'twi', 'TWI36G0193' => 'twi', 'TWI36G0405' => 'twi', 'TWI38G0892' => 'twi', 'TWI38G0936' => 'twi', 'TWI38G2218' => 'twi', 'TWI53G0679' => 'twi', 'TWI53G0863' => 'twi', 'TWI53G1133' => 'twi', 'TWI60G0823' => 'twi', 'TWI63G0919' => 'twi', 'TWI63G1436' => 'twi', 'TWI73G0140' => 'twi', 'TWI73G0419' => 'twi', 'TWI73G0420' => 'twi', 'TWI73G1276' => 'twi', 'TWI74G0405' => 'twi', 'TWI74G0837' => 'twi', 'TWI75G0594' => 'twi', 'TWI75G1615' => 'twi', 'TWI77G0816' => 'twi', 'vmacro03831' => 'vma', 'vmacro13746' => 'vma', 'vmacro16089' => 'vma', 'vmacro22863' => 'vma', 'Zm00001eb085790' => 'zma', 'Zm00001eb114250' => 'zma', 'Zm00001eb138070' => 'zma', 'Zm00001eb167560' => 'zma', 'Zm00001eb199990' => 'zma', 'Zm00001eb368180' => 'zma', 'Zm00001eb382470' => 'zma' ), 'gf_id' => 'HOM05D001576', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001576' ), 'data_identifier' => 'HOM05D001576', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001576', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '406', 'num_species' => '29' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'Aqoxy1G01456' => 'aox', 'Aqoxy1G02949' => 'aox', 'Aqoxy3G01274' => 'aox', 'Aqoxy3G02110' => 'aox', 'Aqoxy3G02268' => 'aox', 'Aqoxy5G02702' => 'aox', 'Aqoxy5G02988' => 'aox', 'Aqoxy5G03427' => 'aox', 'Aqoxy6G02363' => 'aox', 'Atru.chr1.3225' => 'acertr', 'Atru.chr8.1198' => 'acertr', 'Atru.chr9.790' => 'acertr', 'CANSAT01G3197' => 'cansat', 'Ciclev10003979m.g' => 'ccl', 'Ciclev10017471m.g' => 'ccl', 'Ciclev10018206m.g' => 'ccl', 'Ciclev10033751m.g' => 'ccl', 'CiPaw.01G000900' => 'cil', 'CiPaw.01G001000' => 'cil', 'CiPaw.01G033500' => 'cil', 'CiPaw.01G060300' => 'cil', 'CiPaw.01G070200' => 'cil', 'CiPaw.01G075100' => 'cil', 'CiPaw.01G084700' => 'cil', 'CiPaw.01G087900' => 'cil', 'CiPaw.01G092600' => 'cil', 'CiPaw.01G097200' => 'cil', 'CiPaw.01G098300' => 'cil', 'CiPaw.01G110200' => 'cil', 'CiPaw.01G118700' => 'cil', 'CiPaw.01G121200' => 'cil', 'CiPaw.01G132500' => 'cil', 'CiPaw.01G146900' => 'cil', 'CiPaw.01G174000' => 'cil', 'CiPaw.01G179900' => 'cil', 'CiPaw.01G183400' => 'cil', 'CiPaw.01G240000' => 'cil', 'CiPaw.01G283500' => 'cil', 'CiPaw.01G307400' => 'cil', 'CiPaw.02G030800' => 'cil', 'CiPaw.02G047200' => 'cil', 'CiPaw.02G050500' => 'cil', 'CiPaw.02G069900' => 'cil', 'CiPaw.02G091600' => 'cil', 'CiPaw.02G095000' => 'cil', 'CiPaw.02G131900' => 'cil', 'CiPaw.03G043000' => 'cil', 'CiPaw.03G069900' => 'cil', 'CiPaw.03G088100' => 'cil', 'CiPaw.03G089300' => 'cil', 'CiPaw.03G093100' => 'cil', 'CiPaw.03G129800' => 'cil', 'CiPaw.03G131200' => 'cil', 'CiPaw.03G134500' => 'cil', 'CiPaw.03G152100' => 'cil', 'CiPaw.03G162700' => 'cil', 'CiPaw.03G172800' => 'cil', 'CiPaw.03G175800' => 'cil', 'CiPaw.03G181800' => 'cil', 'CiPaw.03G191400' => 'cil', 'CiPaw.03G198300' => 'cil', 'CiPaw.03G201300' => 'cil', 'CiPaw.03G224700' => 'cil', 'CiPaw.03G225000' => 'cil', 'CiPaw.04G065100' => 'cil', 'CiPaw.04G080400' => 'cil', 'CiPaw.04G113500' => 'cil', 'CiPaw.04G121900' => 'cil', 'CiPaw.04G144100' => 'cil', 'CiPaw.04G176500' => 'cil', 'CiPaw.05G086200' => 'cil', 'CiPaw.05G100200' => 'cil', 'CiPaw.05G114200' => 'cil', 'CiPaw.05G126800' => 'cil', 'CiPaw.05G228800' => 'cil', 'CiPaw.05G230600' => 'cil', 'CiPaw.05G236500' => 'cil', 'CiPaw.05G244800' => 'cil', 'CiPaw.06G026600' => 'cil', 'CiPaw.06G027900' => 'cil', 'CiPaw.06G051800' => 'cil', 'CiPaw.06G128500' => 'cil', 'CiPaw.06G165900' => 'cil', 'CiPaw.07G045400' => 'cil', 'CiPaw.07G048000' => 'cil', 'CiPaw.07G052000' => 'cil', 'CiPaw.07G073800' => 'cil', 'CiPaw.07G099700' => 'cil', 'CiPaw.07G108700' => 'cil', 'CiPaw.07G120000' => 'cil', 'CiPaw.07G134100' => 'cil', 'CiPaw.07G147000' => 'cil', 'CiPaw.07G149700' => 'cil', 'CiPaw.07G178300' => 'cil', 'CiPaw.07G184900' => 'cil', 'CiPaw.08G044500' => 'cil', 'CiPaw.08G046900' => 'cil', 'CiPaw.08G047300' => 'cil', 'CiPaw.08G115400' => 'cil', 'CiPaw.08G134700' => 'cil', 'CiPaw.08G157400' => 'cil', 'CiPaw.09G014300' => 'cil', 'CiPaw.09G088900' => 'cil', 'CiPaw.09G130900' => 'cil', 'CiPaw.09G133100' => 'cil', 'CiPaw.09G151300' => 'cil', 'CiPaw.09G172800' => 'cil', 'CiPaw.09G174900' => 'cil', 'CiPaw.09G175000' => 'cil', 'CiPaw.10G012800' => 'cil', 'CiPaw.10G028800' => 'cil', 'CiPaw.10G044700' => 'cil', 'CiPaw.10G067400' => 'cil', 'CiPaw.10G115900' => 'cil', 'CiPaw.10G126200' => 'cil', 'CiPaw.10G139700' => 'cil', 'CiPaw.10G155100' => 'cil', 'CiPaw.11G011300' => 'cil', 'CiPaw.11G025900' => 'cil', 'CiPaw.11G104100' => 'cil', 'CiPaw.11G142700' => 'cil', 'CiPaw.11G164500' => 'cil', 'CiPaw.11G189100' => 'cil', 'CiPaw.11G197100' => 'cil', 'CiPaw.12G006100' => 'cil', 'CiPaw.12G038500' => 'cil', 'CiPaw.12G041400' => 'cil', 'CiPaw.12G041600' => 'cil', 'CiPaw.12G051300' => 'cil', 'CiPaw.12G101800' => 'cil', 'CiPaw.12G107800' => 'cil', 'CiPaw.13G033200' => 'cil', 'CiPaw.13G129900' => 'cil', 'CiPaw.13G160200' => 'cil', 'CiPaw.14G018900' => 'cil', 'CiPaw.14G029000' => 'cil', 'CiPaw.14G031000' => 'cil', 'CiPaw.14G032000' => 'cil', 'CiPaw.14G032300' => 'cil', 'CiPaw.14G040600' => 'cil', 'CiPaw.14G060500' => 'cil', 'CiPaw.14G061500' => 'cil', 'CiPaw.14G077500' => 'cil', 'CiPaw.14G088300' => 'cil', 'CiPaw.14G108500' => 'cil', 'CiPaw.14G121300' => 'cil', 'CiPaw.14G133000' => 'cil', 'CiPaw.14G134600' => 'cil', 'CiPaw.15G027200' => 'cil', 'CiPaw.15G037700' => 'cil', 'CiPaw.15G050900' => 'cil', 'CiPaw.15G067200' => 'cil', 'CiPaw.15G072000' => 'cil', 'CiPaw.15G112900' => 'cil', 'CiPaw.15G133200' => 'cil', 'CiPaw.15G139500' => 'cil', 'CiPaw.15G155400' => 'cil', 'CiPaw.16G006000' => 'cil', 'CiPaw.16G013100' => 'cil', 'CiPaw.16G047100' => 'cil', 'CiPaw.16G048900' => 'cil', 'CiPaw.16G070300' => 'cil', 'CSS0000195' => 'camsi', 'CSS0001664' => 'camsi', 'CSS0002566' => 'camsi', 'CSS0003077' => 'camsi', 'CSS0004257' => 'camsi', 'CSS0004495' => 'camsi', 'CSS0004599' => 'camsi', 'CSS0004943' => 'camsi', 'CSS0005302' => 'camsi', 'CSS0006274' => 'camsi', 'CSS0006547' => 'camsi', 'CSS0006860' => 'camsi', 'CSS0008814' => 'camsi', 'CSS0008946' => 'camsi', 'CSS0009093' => 'camsi', 'CSS0010221' => 'camsi', 'CSS0010296' => 'camsi', 'CSS0010386' => 'camsi', 'CSS0010831' => 'camsi', 'CSS0011061' => 'camsi', 'CSS0012008' => 'camsi', 'CSS0012194' => 'camsi', 'CSS0013580' => 'camsi', 'CSS0014176' => 'camsi', 'CSS0014280' => 'camsi', 'CSS0014799' => 'camsi', 'CSS0015368' => 'camsi', 'CSS0017473' => 'camsi', 'CSS0019281' => 'camsi', 'CSS0021320' => 'camsi', 'CSS0021750' => 'camsi', 'CSS0023642' => 'camsi', 'CSS0023792' => 'camsi', 'CSS0031528' => 'camsi', 'CSS0033894' => 'camsi', 'CSS0034959' => 'camsi', 'CSS0035632' => 'camsi', 'CSS0038450' => 'camsi', 'CSS0039293' => 'camsi', 'CSS0041053' => 'camsi', 'CSS0041981' => 'camsi', 'CSS0042573' => 'camsi', 'CSS0042927' => 'camsi', 'CSS0047725' => 'camsi', 'CSS0049636' => 'camsi', 'CSS0050513' => 'camsi', 'DCAR_030203' => 'dca', 'Dinv07939' => 'din', 'FAN01G0456' => 'fan', 'FAN02G3001' => 'fan', 'FAN04G2781' => 'fan', 'FAN05G1385' => 'fan', 'FAN05G3062' => 'fan', 'FAN08G2267' => 'fan', 'FAN10G0481' => 'fan', 'FAN10G1257' => 'fan', 'FAN14G0954' => 'fan', 'FAN14G2347' => 'fan', 'FAN15G0187' => 'fan', 'FAN25G2214' => 'fan', 'FvH4_1g21031' => 'fve', 'FvH4_3g16231' => 'fve', 'FvH4_3g26413' => 'fve', 'FvH4_3g29014' => 'fve', 'FvH4_3g31921' => 'fve', 'FvH4_4g19882' => 'fve', 'FvH4_5g21960' => 'fve', 'FvH4_5g29683' => 'fve', 'FvH4_7g13271' => 'fve', 'Glyma.01G062500' => 'gma', 'Glyma.07G140900' => 'gma', 'Glyma.09G140900' => 'gma', 'Glyma.12G112700' => 'gma', 'Glyma.17G168800' => 'gma', 'HanXRQChr01g0027001' => 'han', 'HanXRQChr04g0120511' => 'han', 'HanXRQChr08g0232381' => 'han', 'HanXRQChr09g0265661' => 'han', 'HanXRQChr13g0416031' => 'han', 'Haze_05835' => 'cav', 'Haze_06597' => 'cav', 'Haze_07921' => 'cav', 'Haze_08599' => 'cav', 'Haze_10686' => 'cav', 'Haze_12994' => 'cav', 'Haze_13466' => 'cav', 'Haze_16101' => 'cav', 'Haze_17766' => 'cav', 'Haze_18456' => 'cav', 'Haze_20229' => 'cav', 'Hma1.2p1_0324F.1_g125640' => 'hma', 'Hma1.2p1_0733F.1_g210230' => 'hma', 'Hma1.2p1_0921F.1_g236870' => 'hma', 'Hma1.2p1_1313F.1_g274940' => 'hma', 'Hma1.2p1_3059F.1_g332230' => 'hma', 'Hund15925' => 'sun', 'Hund19562' => 'sun', 'Hund21925' => 'sun', 'MD03G1177400' => 'mdo', 'MD07G1026100' => 'mdo', 'MD17G1218600' => 'mdo', 'Medtr0867s0010' => 'mtr', 'Medtr6g081150' => 'mtr', 'Os01g0527900' => 'osa', 'Os02g0463725' => 'osa', 'Os02g0785600' => 'osa', 'Os03g0433733' => 'osa', 'Os04g0286500' => 'osa', 'Os05g0227800' => 'osa', 'Os06g0521000' => 'osa', 'Os06g0635500' => 'osa', 'Os06g0660650' => 'osa', 'Os07g0554400' => 'osa', 'Os08g0225900' => 'osa', 'Os08g0561000' => 'osa', 'Os09g0241700' => 'osa', 'Os09g0351900' => 'osa', 'Os11g0220700' => 'osa', 'Os11g0282700' => 'osa', 'Os12g0169300' => 'osa', 'Os12g0228500' => 'osa', 'Os12g0543800' => 'osa', 'PGR044G1547' => 'pgr', 'Potri.005G239150' => 'ptr', 'Potri.010G014250' => 'ptr', 'Prupe.1G172500' => 'ppe', 'Prupe.1G196800' => 'ppe', 'Prupe.1G279700' => 'ppe', 'Prupe.2G026400' => 'ppe', 'Prupe.3G094000' => 'ppe', 'Prupe.4G287300' => 'ppe', 'QL01p022166' => 'qlo', 'QL01p051890' => 'qlo', 'QL02p009469' => 'qlo', 'QL02p046053' => 'qlo', 'QL02p057958' => 'qlo', 'QL02p093127' => 'qlo', 'QL03p006855' => 'qlo', 'QL03p071586' => 'qlo', 'QL04p000022' => 'qlo', 'QL04p000024' => 'qlo', 'QL04p003192' => 'qlo', 'QL05p011416' => 'qlo', 'QL06p039590' => 'qlo', 'QL06p052750' => 'qlo', 'QL06p053821' => 'qlo', 'QL07p025287' => 'qlo', 'QL09p033218' => 'qlo', 'QL09p040841' => 'qlo', 'QL10p020337' => 'qlo', 'QL10p027209' => 'qlo', 'QL10p027969' => 'qlo', 'QL10p048988' => 'qlo', 'QL11p001241' => 'qlo', 'QL11p028487' => 'qlo', 'RcHm_v2.0_Chr2g0105031' => 'rch', 'RcHm_v2.0_Chr2g0117811' => 'rch', 'RcHm_v2.0_Chr6g0270241' => 'rch', 'RcHm_v2.0_Chr7g0215961' => 'rch', 'RcHm_v2.0_Chr7g0231991' => 'rch', 'Rhsim01G0041500' => 'rsi', 'Rhsim01G0115000' => 'rsi', 'Rhsim01G0115400' => 'rsi', 'Rhsim01G0133600' => 'rsi', 'Rhsim01G0159900' => 'rsi', 'Rhsim02G0189400' => 'rsi', 'Rhsim03G0135600' => 'rsi', 'Rhsim03G0149900' => 'rsi', 'Rhsim04G0125600' => 'rsi', 'Rhsim05G0091700' => 'rsi', 'Rhsim05G0092900' => 'rsi', 'Rhsim06G0075000' => 'rsi', 'Rhsim07G0066400' => 'rsi', 'Rhsim07G0156400' => 'rsi', 'Rhsim07G0182200' => 'rsi', 'Rhsim07G0182300' => 'rsi', 'Rhsim08G0180400' => 'rsi', 'Rhsim09G0056800' => 'rsi', 'Rhsim10G0153300' => 'rsi', 'Rhsim11G0012700' => 'rsi', 'Rhsim12G0031800' => 'rsi', 'Rhsim12G0055400' => 'rsi', 'Rhsim12G0091400' => 'rsi', 'Rhsim13G0070800' => 'rsi', 'Rhsim13G0193300' => 'rsi', 'RhsimUnG0111600' => 'rsi', 'RhsimUnG0137500' => 'rsi', 'RhsimUnG0172900' => 'rsi', 'SGA_v2.0_scaffold11G05878' => 'sas', 'SGA_v2.0_scaffold167G38458' => 'sas', 'SGA_v2.0_scaffold19G08588' => 'sas', 'SGA_v2.0_scaffold239G43990' => 'sas', 'SGA_v2.0_scaffold260G45865' => 'sas', 'SGA_v2.0_scaffold309G48177' => 'sas', 'SGA_v2.0_scaffold76G25122' => 'sas', 'SGA_v2.0_scaffold85G26708' => 'sas', 'SHI13914' => 'shi', 'SHI30402' => 'shi', 'TWI09G0020' => 'twi', 'TWI09G0456' => 'twi', 'TWI09G1572' => 'twi', 'TWI12G0266' => 'twi', 'TWI12G1451' => 'twi', 'TWI14G0851' => 'twi', 'TWI15G0796' => 'twi', 'TWI18G0820' => 'twi', 'TWI18G1152' => 'twi', 'TWI23G0007' => 'twi', 'TWI23G0314' => 'twi', 'TWI31G0674' => 'twi', 'TWI31G0938' => 'twi', 'TWI34G0641' => 'twi', 'TWI34G1527' => 'twi', 'TWI36G0193' => 'twi', 'TWI36G0405' => 'twi', 'TWI38G0892' => 'twi', 'TWI38G0936' => 'twi', 'TWI38G2218' => 'twi', 'TWI53G0679' => 'twi', 'TWI53G0863' => 'twi', 'TWI53G1133' => 'twi', 'TWI60G0823' => 'twi', 'TWI63G0919' => 'twi', 'TWI63G1436' => 'twi', 'TWI73G0140' => 'twi', 'TWI73G0419' => 'twi', 'TWI73G0420' => 'twi', 'TWI73G1276' => 'twi', 'TWI74G0405' => 'twi', 'TWI74G0837' => 'twi', 'TWI75G0594' => 'twi', 'TWI75G1615' => 'twi', 'TWI77G0816' => 'twi', 'vmacro03831' => 'vma', 'vmacro13746' => 'vma', 'vmacro16089' => 'vma', 'vmacro22863' => 'vma', 'Zm00001eb085790' => 'zma', 'Zm00001eb114250' => 'zma', 'Zm00001eb138070' => 'zma', 'Zm00001eb167560' => 'zma', 'Zm00001eb199990' => 'zma', 'Zm00001eb368180' => 'zma', 'Zm00001eb382470' => 'zma' ) $gf_id = 'HOM05D001576' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001576' ) $data_identifier = 'HOM05D001576' $data_type = 'gf_id' $species_gene_counts = array( 'aox' => (int) 9, 'acertr' => (int) 3, 'cansat' => (int) 1, 'ccl' => (int) 4, 'cil' => (int) 145, 'camsi' => (int) 46, 'dca' => (int) 1, 'din' => (int) 1, 'fan' => (int) 12, 'fve' => (int) 9, 'gma' => (int) 5, 'han' => (int) 5, 'cav' => (int) 11, 'hma' => (int) 5, 'sun' => (int) 3, 'mdo' => (int) 3, 'mtr' => (int) 2, 'osa' => (int) 19, 'pgr' => (int) 1, 'ptr' => (int) 2, 'ppe' => (int) 6, 'qlo' => (int) 24, 'rch' => (int) 5, 'rsi' => (int) 28, 'sas' => (int) 8, 'shi' => (int) 2, 'twi' => (int) 35, 'vma' => (int) 4, 'zma' => (int) 7 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb382470' $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' => 'HOM05D001576', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '406', 'num_species' => '29' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'Aqoxy1G01456' => 'aox', 'Aqoxy1G02949' => 'aox', 'Aqoxy3G01274' => 'aox', 'Aqoxy3G02110' => 'aox', 'Aqoxy3G02268' => 'aox', 'Aqoxy5G02702' => 'aox', 'Aqoxy5G02988' => 'aox', 'Aqoxy5G03427' => 'aox', 'Aqoxy6G02363' => 'aox', 'Atru.chr1.3225' => 'acertr', 'Atru.chr8.1198' => 'acertr', 'Atru.chr9.790' => 'acertr', 'CANSAT01G3197' => 'cansat', 'Ciclev10003979m.g' => 'ccl', 'Ciclev10017471m.g' => 'ccl', 'Ciclev10018206m.g' => 'ccl', 'Ciclev10033751m.g' => 'ccl', 'CiPaw.01G000900' => 'cil', 'CiPaw.01G001000' => 'cil', 'CiPaw.01G033500' => 'cil', 'CiPaw.01G060300' => 'cil', 'CiPaw.01G070200' => 'cil', 'CiPaw.01G075100' => 'cil', 'CiPaw.01G084700' => 'cil', 'CiPaw.01G087900' => 'cil', 'CiPaw.01G092600' => 'cil', 'CiPaw.01G097200' => 'cil', 'CiPaw.01G098300' => 'cil', 'CiPaw.01G110200' => 'cil', 'CiPaw.01G118700' => 'cil', 'CiPaw.01G121200' => 'cil', 'CiPaw.01G132500' => 'cil', 'CiPaw.01G146900' => 'cil', 'CiPaw.01G174000' => 'cil', 'CiPaw.01G179900' => 'cil', 'CiPaw.01G183400' => 'cil', 'CiPaw.01G240000' => 'cil', 'CiPaw.01G283500' => 'cil', 'CiPaw.01G307400' => 'cil', 'CiPaw.02G030800' => 'cil', 'CiPaw.02G047200' => 'cil', 'CiPaw.02G050500' => 'cil', 'CiPaw.02G069900' => 'cil', 'CiPaw.02G091600' => 'cil', 'CiPaw.02G095000' => 'cil', 'CiPaw.02G131900' => 'cil', 'CiPaw.03G043000' => 'cil', 'CiPaw.03G069900' => 'cil', 'CiPaw.03G088100' => 'cil', 'CiPaw.03G089300' => 'cil', 'CiPaw.03G093100' => 'cil', 'CiPaw.03G129800' => 'cil', 'CiPaw.03G131200' => 'cil', 'CiPaw.03G134500' => 'cil', 'CiPaw.03G152100' => 'cil', 'CiPaw.03G162700' => 'cil', 'CiPaw.03G172800' => 'cil', 'CiPaw.03G175800' => 'cil', 'CiPaw.03G181800' => 'cil', 'CiPaw.03G191400' => 'cil', 'CiPaw.03G198300' => 'cil', 'CiPaw.03G201300' => 'cil', 'CiPaw.03G224700' => 'cil', 'CiPaw.03G225000' => 'cil', 'CiPaw.04G065100' => 'cil', 'CiPaw.04G080400' => 'cil', 'CiPaw.04G113500' => 'cil', 'CiPaw.04G121900' => 'cil', 'CiPaw.04G144100' => 'cil', 'CiPaw.04G176500' => 'cil', 'CiPaw.05G086200' => 'cil', 'CiPaw.05G100200' => 'cil', 'CiPaw.05G114200' => 'cil', 'CiPaw.05G126800' => 'cil', 'CiPaw.05G228800' => 'cil', 'CiPaw.05G230600' => 'cil', 'CiPaw.05G236500' => 'cil', 'CiPaw.05G244800' => 'cil', 'CiPaw.06G026600' => 'cil', 'CiPaw.06G027900' => 'cil', 'CiPaw.06G051800' => 'cil', 'CiPaw.06G128500' => 'cil', 'CiPaw.06G165900' => 'cil', 'CiPaw.07G045400' => 'cil', 'CiPaw.07G048000' => 'cil', 'CiPaw.07G052000' => 'cil', 'CiPaw.07G073800' => 'cil', 'CiPaw.07G099700' => 'cil', 'CiPaw.07G108700' => 'cil', 'CiPaw.07G120000' => 'cil', 'CiPaw.07G134100' => 'cil', 'CiPaw.07G147000' => 'cil', 'CiPaw.07G149700' => 'cil', 'CiPaw.07G178300' => 'cil', 'CiPaw.07G184900' => 'cil', 'CiPaw.08G044500' => 'cil', 'CiPaw.08G046900' => 'cil', 'CiPaw.08G047300' => 'cil', 'CiPaw.08G115400' => 'cil', 'CiPaw.08G134700' => 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'TWI09G0020' => 'twi', 'TWI09G0456' => 'twi', 'TWI09G1572' => 'twi', 'TWI12G0266' => 'twi', 'TWI12G1451' => 'twi', 'TWI14G0851' => 'twi', 'TWI15G0796' => 'twi', 'TWI18G0820' => 'twi', 'TWI18G1152' => 'twi', 'TWI23G0007' => 'twi', 'TWI23G0314' => 'twi', 'TWI31G0674' => 'twi', 'TWI31G0938' => 'twi', 'TWI34G0641' => 'twi', 'TWI34G1527' => 'twi', 'TWI36G0193' => 'twi', 'TWI36G0405' => 'twi', 'TWI38G0892' => 'twi', 'TWI38G0936' => 'twi', 'TWI38G2218' => 'twi', 'TWI53G0679' => 'twi', 'TWI53G0863' => 'twi', 'TWI53G1133' => 'twi', 'TWI60G0823' => 'twi', 'TWI63G0919' => 'twi', 'TWI63G1436' => 'twi', 'TWI73G0140' => 'twi', 'TWI73G0419' => 'twi', 'TWI73G0420' => 'twi', 'TWI73G1276' => 'twi', 'TWI74G0405' => 'twi', 'TWI74G0837' => 'twi', 'TWI75G0594' => 'twi', 'TWI75G1615' => 'twi', 'TWI77G0816' => 'twi', 'vmacro03831' => 'vma', 'vmacro13746' => 'vma', 'vmacro16089' => 'vma', 'vmacro22863' => 'vma', 'Zm00001eb085790' => 'zma', 'Zm00001eb114250' => 'zma', 'Zm00001eb138070' => 'zma', 'Zm00001eb167560' => 'zma', 'Zm00001eb199990' => 'zma', 'Zm00001eb368180' => 'zma', 'Zm00001eb382470' => 'zma' ), 'gf_id' => 'HOM05D001576', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001576' ), 'data_identifier' => 'HOM05D001576', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001576', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '406', 'num_species' => '29' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'Aqoxy1G01456' => 'aox', 'Aqoxy1G02949' => 'aox', 'Aqoxy3G01274' => 'aox', 'Aqoxy3G02110' => 'aox', 'Aqoxy3G02268' => 'aox', 'Aqoxy5G02702' => 'aox', 'Aqoxy5G02988' => 'aox', 'Aqoxy5G03427' => 'aox', 'Aqoxy6G02363' => 'aox', 'Atru.chr1.3225' => 'acertr', 'Atru.chr8.1198' => 'acertr', 'Atru.chr9.790' => 'acertr', 'CANSAT01G3197' => 'cansat', 'Ciclev10003979m.g' => 'ccl', 'Ciclev10017471m.g' => 'ccl', 'Ciclev10018206m.g' => 'ccl', 'Ciclev10033751m.g' => 'ccl', 'CiPaw.01G000900' => 'cil', 'CiPaw.01G001000' => 'cil', 'CiPaw.01G033500' => 'cil', 'CiPaw.01G060300' => 'cil', 'CiPaw.01G070200' => 'cil', 'CiPaw.01G075100' => 'cil', 'CiPaw.01G084700' => 'cil', 'CiPaw.01G087900' => 'cil', 'CiPaw.01G092600' => 'cil', 'CiPaw.01G097200' => 'cil', 'CiPaw.01G098300' => 'cil', 'CiPaw.01G110200' => 'cil', 'CiPaw.01G118700' => 'cil', 'CiPaw.01G121200' => 'cil', 'CiPaw.01G132500' => 'cil', 'CiPaw.01G146900' => 'cil', 'CiPaw.01G174000' => 'cil', 'CiPaw.01G179900' => 'cil', 'CiPaw.01G183400' => 'cil', 'CiPaw.01G240000' => 'cil', 'CiPaw.01G283500' => 'cil', 'CiPaw.01G307400' => 'cil', 'CiPaw.02G030800' => 'cil', 'CiPaw.02G047200' => 'cil', 'CiPaw.02G050500' => 'cil', 'CiPaw.02G069900' => 'cil', 'CiPaw.02G091600' => 'cil', 'CiPaw.02G095000' => 'cil', 'CiPaw.02G131900' => 'cil', 'CiPaw.03G043000' => 'cil', 'CiPaw.03G069900' => 'cil', 'CiPaw.03G088100' => 'cil', 'CiPaw.03G089300' => 'cil', 'CiPaw.03G093100' => 'cil', 'CiPaw.03G129800' => 'cil', 'CiPaw.03G131200' => 'cil', 'CiPaw.03G134500' => 'cil', 'CiPaw.03G152100' => 'cil', 'CiPaw.03G162700' => 'cil', 'CiPaw.03G172800' => 'cil', 'CiPaw.03G175800' => 'cil', 'CiPaw.03G181800' => 'cil', 'CiPaw.03G191400' => 'cil', 'CiPaw.03G198300' => 'cil', 'CiPaw.03G201300' => 'cil', 'CiPaw.03G224700' => 'cil', 'CiPaw.03G225000' => 'cil', 'CiPaw.04G065100' => 'cil', 'CiPaw.04G080400' => 'cil', 'CiPaw.04G113500' => 'cil', 'CiPaw.04G121900' => 'cil', 'CiPaw.04G144100' => 'cil', 'CiPaw.04G176500' => 'cil', 'CiPaw.05G086200' => 'cil', 'CiPaw.05G100200' => 'cil', 'CiPaw.05G114200' => 'cil', 'CiPaw.05G126800' => 'cil', 'CiPaw.05G228800' => 'cil', 'CiPaw.05G230600' => 'cil', 'CiPaw.05G236500' => 'cil', 'CiPaw.05G244800' => 'cil', 'CiPaw.06G026600' => 'cil', 'CiPaw.06G027900' => 'cil', 'CiPaw.06G051800' => 'cil', 'CiPaw.06G128500' => 'cil', 'CiPaw.06G165900' => 'cil', 'CiPaw.07G045400' => 'cil', 'CiPaw.07G048000' => 'cil', 'CiPaw.07G052000' => 'cil', 'CiPaw.07G073800' => 'cil', 'CiPaw.07G099700' => 'cil', 'CiPaw.07G108700' => 'cil', 'CiPaw.07G120000' => 'cil', 'CiPaw.07G134100' => 'cil', 'CiPaw.07G147000' => 'cil', 'CiPaw.07G149700' => 'cil', 'CiPaw.07G178300' => 'cil', 'CiPaw.07G184900' => 'cil', 'CiPaw.08G044500' => 'cil', 'CiPaw.08G046900' => 'cil', 'CiPaw.08G047300' => 'cil', 'CiPaw.08G115400' => 'cil', 'CiPaw.08G134700' => 'cil', 'CiPaw.08G157400' => 'cil', 'CiPaw.09G014300' => 'cil', 'CiPaw.09G088900' => 'cil', 'CiPaw.09G130900' => 'cil', 'CiPaw.09G133100' => 'cil', 'CiPaw.09G151300' => 'cil', 'CiPaw.09G172800' => 'cil', 'CiPaw.09G174900' => 'cil', 'CiPaw.09G175000' => 'cil', 'CiPaw.10G012800' => 'cil', 'CiPaw.10G028800' => 'cil', 'CiPaw.10G044700' => 'cil', 'CiPaw.10G067400' => 'cil', 'CiPaw.10G115900' => 'cil', 'CiPaw.10G126200' => 'cil', 'CiPaw.10G139700' => 'cil', 'CiPaw.10G155100' => 'cil', 'CiPaw.11G011300' => 'cil', 'CiPaw.11G025900' => 'cil', 'CiPaw.11G104100' => 'cil', 'CiPaw.11G142700' => 'cil', 'CiPaw.11G164500' => 'cil', 'CiPaw.11G189100' => 'cil', 'CiPaw.11G197100' => 'cil', 'CiPaw.12G006100' => 'cil', 'CiPaw.12G038500' => 'cil', 'CiPaw.12G041400' => 'cil', 'CiPaw.12G041600' => 'cil', 'CiPaw.12G051300' => 'cil', 'CiPaw.12G101800' => 'cil', 'CiPaw.12G107800' => 'cil', 'CiPaw.13G033200' => 'cil', 'CiPaw.13G129900' => 'cil', 'CiPaw.13G160200' => 'cil', 'CiPaw.14G018900' => 'cil', 'CiPaw.14G029000' => 'cil', 'CiPaw.14G031000' => 'cil', 'CiPaw.14G032000' => 'cil', 'CiPaw.14G032300' => 'cil', 'CiPaw.14G040600' => 'cil', 'CiPaw.14G060500' => 'cil', 'CiPaw.14G061500' => 'cil', 'CiPaw.14G077500' => 'cil', 'CiPaw.14G088300' => 'cil', 'CiPaw.14G108500' => 'cil', 'CiPaw.14G121300' => 'cil', 'CiPaw.14G133000' => 'cil', 'CiPaw.14G134600' => 'cil', 'CiPaw.15G027200' => 'cil', 'CiPaw.15G037700' => 'cil', 'CiPaw.15G050900' => 'cil', 'CiPaw.15G067200' => 'cil', 'CiPaw.15G072000' => 'cil', 'CiPaw.15G112900' => 'cil', 'CiPaw.15G133200' => 'cil', 'CiPaw.15G139500' => 'cil', 'CiPaw.15G155400' => 'cil', 'CiPaw.16G006000' => 'cil', 'CiPaw.16G013100' => 'cil', 'CiPaw.16G047100' => 'cil', 'CiPaw.16G048900' => 'cil', 'CiPaw.16G070300' => 'cil', 'CSS0000195' => 'camsi', 'CSS0001664' => 'camsi', 'CSS0002566' => 'camsi', 'CSS0003077' => 'camsi', 'CSS0004257' => 'camsi', 'CSS0004495' => 'camsi', 'CSS0004599' => 'camsi', 'CSS0004943' => 'camsi', 'CSS0005302' => 'camsi', 'CSS0006274' => 'camsi', 'CSS0006547' => 'camsi', 'CSS0006860' => 'camsi', 'CSS0008814' => 'camsi', 'CSS0008946' => 'camsi', 'CSS0009093' => 'camsi', 'CSS0010221' => 'camsi', 'CSS0010296' => 'camsi', 'CSS0010386' => 'camsi', 'CSS0010831' => 'camsi', 'CSS0011061' => 'camsi', 'CSS0012008' => 'camsi', 'CSS0012194' => 'camsi', 'CSS0013580' => 'camsi', 'CSS0014176' => 'camsi', 'CSS0014280' => 'camsi', 'CSS0014799' => 'camsi', 'CSS0015368' => 'camsi', 'CSS0017473' => 'camsi', 'CSS0019281' => 'camsi', 'CSS0021320' => 'camsi', 'CSS0021750' => 'camsi', 'CSS0023642' => 'camsi', 'CSS0023792' => 'camsi', 'CSS0031528' => 'camsi', 'CSS0033894' => 'camsi', 'CSS0034959' => 'camsi', 'CSS0035632' => 'camsi', 'CSS0038450' => 'camsi', 'CSS0039293' => 'camsi', 'CSS0041053' => 'camsi', 'CSS0041981' => 'camsi', 'CSS0042573' => 'camsi', 'CSS0042927' => 'camsi', 'CSS0047725' => 'camsi', 'CSS0049636' => 'camsi', 'CSS0050513' => 'camsi', 'DCAR_030203' => 'dca', 'Dinv07939' => 'din', 'FAN01G0456' => 'fan', 'FAN02G3001' => 'fan', 'FAN04G2781' => 'fan', 'FAN05G1385' => 'fan', 'FAN05G3062' => 'fan', 'FAN08G2267' => 'fan', 'FAN10G0481' => 'fan', 'FAN10G1257' => 'fan', 'FAN14G0954' => 'fan', 'FAN14G2347' => 'fan', 'FAN15G0187' => 'fan', 'FAN25G2214' => 'fan', 'FvH4_1g21031' => 'fve', 'FvH4_3g16231' => 'fve', 'FvH4_3g26413' => 'fve', 'FvH4_3g29014' => 'fve', 'FvH4_3g31921' => 'fve', 'FvH4_4g19882' => 'fve', 'FvH4_5g21960' => 'fve', 'FvH4_5g29683' => 'fve', 'FvH4_7g13271' => 'fve', 'Glyma.01G062500' => 'gma', 'Glyma.07G140900' => 'gma', 'Glyma.09G140900' => 'gma', 'Glyma.12G112700' => 'gma', 'Glyma.17G168800' => 'gma', 'HanXRQChr01g0027001' => 'han', 'HanXRQChr04g0120511' => 'han', 'HanXRQChr08g0232381' => 'han', 'HanXRQChr09g0265661' => 'han', 'HanXRQChr13g0416031' => 'han', 'Haze_05835' => 'cav', 'Haze_06597' => 'cav', 'Haze_07921' => 'cav', 'Haze_08599' => 'cav', 'Haze_10686' => 'cav', 'Haze_12994' => 'cav', 'Haze_13466' => 'cav', 'Haze_16101' => 'cav', 'Haze_17766' => 'cav', 'Haze_18456' => 'cav', 'Haze_20229' => 'cav', 'Hma1.2p1_0324F.1_g125640' => 'hma', 'Hma1.2p1_0733F.1_g210230' => 'hma', 'Hma1.2p1_0921F.1_g236870' => 'hma', 'Hma1.2p1_1313F.1_g274940' => 'hma', 'Hma1.2p1_3059F.1_g332230' => 'hma', 'Hund15925' => 'sun', 'Hund19562' => 'sun', 'Hund21925' => 'sun', 'MD03G1177400' => 'mdo', 'MD07G1026100' => 'mdo', 'MD17G1218600' => 'mdo', 'Medtr0867s0010' => 'mtr', 'Medtr6g081150' => 'mtr', 'Os01g0527900' => 'osa', 'Os02g0463725' => 'osa', 'Os02g0785600' => 'osa', 'Os03g0433733' => 'osa', 'Os04g0286500' => 'osa', 'Os05g0227800' => 'osa', 'Os06g0521000' => 'osa', 'Os06g0635500' => 'osa', 'Os06g0660650' => 'osa', 'Os07g0554400' => 'osa', 'Os08g0225900' => 'osa', 'Os08g0561000' => 'osa', 'Os09g0241700' => 'osa', 'Os09g0351900' => 'osa', 'Os11g0220700' => 'osa', 'Os11g0282700' => 'osa', 'Os12g0169300' => 'osa', 'Os12g0228500' => 'osa', 'Os12g0543800' => 'osa', 'PGR044G1547' => 'pgr', 'Potri.005G239150' => 'ptr', 'Potri.010G014250' => 'ptr', 'Prupe.1G172500' => 'ppe', 'Prupe.1G196800' => 'ppe', 'Prupe.1G279700' => 'ppe', 'Prupe.2G026400' => 'ppe', 'Prupe.3G094000' => 'ppe', 'Prupe.4G287300' => 'ppe', 'QL01p022166' => 'qlo', 'QL01p051890' => 'qlo', 'QL02p009469' => 'qlo', 'QL02p046053' => 'qlo', 'QL02p057958' => 'qlo', 'QL02p093127' => 'qlo', 'QL03p006855' => 'qlo', 'QL03p071586' => 'qlo', 'QL04p000022' => 'qlo', 'QL04p000024' => 'qlo', 'QL04p003192' => 'qlo', 'QL05p011416' => 'qlo', 'QL06p039590' => 'qlo', 'QL06p052750' => 'qlo', 'QL06p053821' => 'qlo', 'QL07p025287' => 'qlo', 'QL09p033218' => 'qlo', 'QL09p040841' => 'qlo', 'QL10p020337' => 'qlo', 'QL10p027209' => 'qlo', 'QL10p027969' => 'qlo', 'QL10p048988' => 'qlo', 'QL11p001241' => 'qlo', 'QL11p028487' => 'qlo', 'RcHm_v2.0_Chr2g0105031' => 'rch', 'RcHm_v2.0_Chr2g0117811' => 'rch', 'RcHm_v2.0_Chr6g0270241' => 'rch', 'RcHm_v2.0_Chr7g0215961' => 'rch', 'RcHm_v2.0_Chr7g0231991' => 'rch', 'Rhsim01G0041500' => 'rsi', 'Rhsim01G0115000' => 'rsi', 'Rhsim01G0115400' => 'rsi', 'Rhsim01G0133600' => 'rsi', 'Rhsim01G0159900' => 'rsi', 'Rhsim02G0189400' => 'rsi', 'Rhsim03G0135600' => 'rsi', 'Rhsim03G0149900' => 'rsi', 'Rhsim04G0125600' => 'rsi', 'Rhsim05G0091700' => 'rsi', 'Rhsim05G0092900' => 'rsi', 'Rhsim06G0075000' => 'rsi', 'Rhsim07G0066400' => 'rsi', 'Rhsim07G0156400' => 'rsi', 'Rhsim07G0182200' => 'rsi', 'Rhsim07G0182300' => 'rsi', 'Rhsim08G0180400' => 'rsi', 'Rhsim09G0056800' => 'rsi', 'Rhsim10G0153300' => 'rsi', 'Rhsim11G0012700' => 'rsi', 'Rhsim12G0031800' => 'rsi', 'Rhsim12G0055400' => 'rsi', 'Rhsim12G0091400' => 'rsi', 'Rhsim13G0070800' => 'rsi', 'Rhsim13G0193300' => 'rsi', 'RhsimUnG0111600' => 'rsi', 'RhsimUnG0137500' => 'rsi', 'RhsimUnG0172900' => 'rsi', 'SGA_v2.0_scaffold11G05878' => 'sas', 'SGA_v2.0_scaffold167G38458' => 'sas', 'SGA_v2.0_scaffold19G08588' => 'sas', 'SGA_v2.0_scaffold239G43990' => 'sas', 'SGA_v2.0_scaffold260G45865' => 'sas', 'SGA_v2.0_scaffold309G48177' => 'sas', 'SGA_v2.0_scaffold76G25122' => 'sas', 'SGA_v2.0_scaffold85G26708' => 'sas', 'SHI13914' => 'shi', 'SHI30402' => 'shi', 'TWI09G0020' => 'twi', 'TWI09G0456' => 'twi', 'TWI09G1572' => 'twi', 'TWI12G0266' => 'twi', 'TWI12G1451' => 'twi', 'TWI14G0851' => 'twi', 'TWI15G0796' => 'twi', 'TWI18G0820' => 'twi', 'TWI18G1152' => 'twi', 'TWI23G0007' => 'twi', 'TWI23G0314' => 'twi', 'TWI31G0674' => 'twi', 'TWI31G0938' => 'twi', 'TWI34G0641' => 'twi', 'TWI34G1527' => 'twi', 'TWI36G0193' => 'twi', 'TWI36G0405' => 'twi', 'TWI38G0892' => 'twi', 'TWI38G0936' => 'twi', 'TWI38G2218' => 'twi', 'TWI53G0679' => 'twi', 'TWI53G0863' => 'twi', 'TWI53G1133' => 'twi', 'TWI60G0823' => 'twi', 'TWI63G0919' => 'twi', 'TWI63G1436' => 'twi', 'TWI73G0140' => 'twi', 'TWI73G0419' => 'twi', 'TWI73G0420' => 'twi', 'TWI73G1276' => 'twi', 'TWI74G0405' => 'twi', 'TWI74G0837' => 'twi', 'TWI75G0594' => 'twi', 'TWI75G1615' => 'twi', 'TWI77G0816' => 'twi', 'vmacro03831' => 'vma', 'vmacro13746' => 'vma', 'vmacro16089' => 'vma', 'vmacro22863' => 'vma', 'Zm00001eb085790' => 'zma', 'Zm00001eb114250' => 'zma', 'Zm00001eb138070' => 'zma', 'Zm00001eb167560' => 'zma', 'Zm00001eb199990' => 'zma', 'Zm00001eb368180' => 'zma', 'Zm00001eb382470' => 'zma' ) $gf_id = 'HOM05D001576' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001576' ) $data_identifier = 'HOM05D001576' $data_type = 'gf_id' $species_gene_counts = array( 'aox' => (int) 9, 'acertr' => (int) 3, 'cansat' => (int) 1, 'ccl' => (int) 4, 'cil' => (int) 145, 'camsi' => (int) 46, 'dca' => (int) 1, 'din' => (int) 1, 'fan' => (int) 12, 'fve' => (int) 9, 'gma' => (int) 5, 'han' => (int) 5, 'cav' => (int) 11, 'hma' => (int) 5, 'sun' => (int) 3, 'mdo' => (int) 3, 'mtr' => (int) 2, 'osa' => (int) 19, 'pgr' => (int) 1, 'ptr' => (int) 2, 'ppe' => (int) 6, 'qlo' => (int) 24, 'rch' => (int) 5, 'rsi' => (int) 28, 'sas' => (int) 8, 'shi' => (int) 2, 'twi' => (int) 35, 'vma' => (int) 4, 'zma' => (int) 7 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb382470' $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' => 'HOM05D001576', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '406', 'num_species' => '29' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'Aqoxy1G01456' => 'aox', 'Aqoxy1G02949' => 'aox', 'Aqoxy3G01274' => 'aox', 'Aqoxy3G02110' => 'aox', 'Aqoxy3G02268' => 'aox', 'Aqoxy5G02702' => 'aox', 'Aqoxy5G02988' => 'aox', 'Aqoxy5G03427' => 'aox', 'Aqoxy6G02363' => 'aox', 'Atru.chr1.3225' => 'acertr', 'Atru.chr8.1198' => 'acertr', 'Atru.chr9.790' => 'acertr', 'CANSAT01G3197' => 'cansat', 'Ciclev10003979m.g' => 'ccl', 'Ciclev10017471m.g' => 'ccl', 'Ciclev10018206m.g' => 'ccl', 'Ciclev10033751m.g' => 'ccl', 'CiPaw.01G000900' => 'cil', 'CiPaw.01G001000' => 'cil', 'CiPaw.01G033500' => 'cil', 'CiPaw.01G060300' => 'cil', 'CiPaw.01G070200' => 'cil', 'CiPaw.01G075100' => 'cil', 'CiPaw.01G084700' => 'cil', 'CiPaw.01G087900' => 'cil', 'CiPaw.01G092600' => 'cil', 'CiPaw.01G097200' => 'cil', 'CiPaw.01G098300' => 'cil', 'CiPaw.01G110200' => 'cil', 'CiPaw.01G118700' => 'cil', 'CiPaw.01G121200' => 'cil', 'CiPaw.01G132500' => 'cil', 'CiPaw.01G146900' => 'cil', 'CiPaw.01G174000' => 'cil', 'CiPaw.01G179900' => 'cil', 'CiPaw.01G183400' => 'cil', 'CiPaw.01G240000' => 'cil', 'CiPaw.01G283500' => 'cil', 'CiPaw.01G307400' => 'cil', 'CiPaw.02G030800' => 'cil', 'CiPaw.02G047200' => 'cil', 'CiPaw.02G050500' => 'cil', 'CiPaw.02G069900' => 'cil', 'CiPaw.02G091600' => 'cil', 'CiPaw.02G095000' => 'cil', 'CiPaw.02G131900' => 'cil', 'CiPaw.03G043000' => 'cil', 'CiPaw.03G069900' => 'cil', 'CiPaw.03G088100' => 'cil', 'CiPaw.03G089300' => 'cil', 'CiPaw.03G093100' => 'cil', 'CiPaw.03G129800' => 'cil', 'CiPaw.03G131200' => 'cil', 'CiPaw.03G134500' => 'cil', 'CiPaw.03G152100' => 'cil', 'CiPaw.03G162700' => 'cil', 'CiPaw.03G172800' => 'cil', 'CiPaw.03G175800' => 'cil', 'CiPaw.03G181800' => 'cil', 'CiPaw.03G191400' => 'cil', 'CiPaw.03G198300' => 'cil', 'CiPaw.03G201300' => 'cil', 'CiPaw.03G224700' => 'cil', 'CiPaw.03G225000' => 'cil', 'CiPaw.04G065100' => 'cil', 'CiPaw.04G080400' => 'cil', 'CiPaw.04G113500' => 'cil', 'CiPaw.04G121900' => 'cil', 'CiPaw.04G144100' => 'cil', 'CiPaw.04G176500' => 'cil', 'CiPaw.05G086200' => 'cil', 'CiPaw.05G100200' => 'cil', 'CiPaw.05G114200' => 'cil', 'CiPaw.05G126800' => 'cil', 'CiPaw.05G228800' => 'cil', 'CiPaw.05G230600' => 'cil', 'CiPaw.05G236500' => 'cil', 'CiPaw.05G244800' => 'cil', 'CiPaw.06G026600' => 'cil', 'CiPaw.06G027900' => 'cil', 'CiPaw.06G051800' => 'cil', 'CiPaw.06G128500' => 'cil', 'CiPaw.06G165900' => 'cil', 'CiPaw.07G045400' => 'cil', 'CiPaw.07G048000' => 'cil', 'CiPaw.07G052000' => 'cil', 'CiPaw.07G073800' => 'cil', 'CiPaw.07G099700' => 'cil', 'CiPaw.07G108700' => 'cil', 'CiPaw.07G120000' => 'cil', 'CiPaw.07G134100' => 'cil', 'CiPaw.07G147000' => 'cil', 'CiPaw.07G149700' => 'cil', 'CiPaw.07G178300' => 'cil', 'CiPaw.07G184900' => 'cil', 'CiPaw.08G044500' => 'cil', 'CiPaw.08G046900' => 'cil', 'CiPaw.08G047300' => 'cil', 'CiPaw.08G115400' => 'cil', 'CiPaw.08G134700' => 'cil', 'CiPaw.08G157400' => 'cil', 'CiPaw.09G014300' => 'cil', 'CiPaw.09G088900' => 'cil', 'CiPaw.09G130900' => 'cil', 'CiPaw.09G133100' => 'cil', 'CiPaw.09G151300' => 'cil', 'CiPaw.09G172800' => 'cil', 'CiPaw.09G174900' => 'cil', 'CiPaw.09G175000' => 'cil', 'CiPaw.10G012800' => 'cil', 'CiPaw.10G028800' => 'cil', 'CiPaw.10G044700' => 'cil', 'CiPaw.10G067400' => 'cil', 'CiPaw.10G115900' => 'cil', 'CiPaw.10G126200' => 'cil', 'CiPaw.10G139700' => 'cil', 'CiPaw.10G155100' => 'cil', 'CiPaw.11G011300' => 'cil', 'CiPaw.11G025900' => 'cil', 'CiPaw.11G104100' => 'cil', 'CiPaw.11G142700' => 'cil', 'CiPaw.11G164500' => 'cil', 'CiPaw.11G189100' => 'cil', 'CiPaw.11G197100' => 'cil', 'CiPaw.12G006100' => 'cil', 'CiPaw.12G038500' => 'cil', 'CiPaw.12G041400' => 'cil', 'CiPaw.12G041600' => 'cil', 'CiPaw.12G051300' => 'cil', 'CiPaw.12G101800' => 'cil', 'CiPaw.12G107800' => 'cil', 'CiPaw.13G033200' => 'cil', 'CiPaw.13G129900' => 'cil', 'CiPaw.13G160200' => 'cil', 'CiPaw.14G018900' => 'cil', 'CiPaw.14G029000' => 'cil', 'CiPaw.14G031000' => 'cil', 'CiPaw.14G032000' => 'cil', 'CiPaw.14G032300' => 'cil', 'CiPaw.14G040600' => 'cil', 'CiPaw.14G060500' => 'cil', 'CiPaw.14G061500' => 'cil', 'CiPaw.14G077500' => 'cil', 'CiPaw.14G088300' => 'cil', 'CiPaw.14G108500' => 'cil', 'CiPaw.14G121300' => 'cil', 'CiPaw.14G133000' => 'cil', 'CiPaw.14G134600' => 'cil', 'CiPaw.15G027200' => 'cil', 'CiPaw.15G037700' => 'cil', 'CiPaw.15G050900' => 'cil', 'CiPaw.15G067200' => 'cil', 'CiPaw.15G072000' => 'cil', 'CiPaw.15G112900' => 'cil', 'CiPaw.15G133200' => 'cil', 'CiPaw.15G139500' => 'cil', 'CiPaw.15G155400' => 'cil', 'CiPaw.16G006000' => 'cil', 'CiPaw.16G013100' => 'cil', 'CiPaw.16G047100' => 'cil', 'CiPaw.16G048900' => 'cil', 'CiPaw.16G070300' => 'cil', 'CSS0000195' => 'camsi', 'CSS0001664' => 'camsi', 'CSS0002566' => 'camsi', 'CSS0003077' => 'camsi', 'CSS0004257' => 'camsi', 'CSS0004495' => 'camsi', 'CSS0004599' => 'camsi', 'CSS0004943' => 'camsi', 'CSS0005302' => 'camsi', 'CSS0006274' => 'camsi', 'CSS0006547' => 'camsi', 'CSS0006860' => 'camsi', 'CSS0008814' => 'camsi', 'CSS0008946' => 'camsi', 'CSS0009093' => 'camsi', 'CSS0010221' => 'camsi', 'CSS0010296' => 'camsi', 'CSS0010386' => 'camsi', 'CSS0010831' => 'camsi', 'CSS0011061' => 'camsi', 'CSS0012008' => 'camsi', 'CSS0012194' => 'camsi', 'CSS0013580' => 'camsi', 'CSS0014176' => 'camsi', 'CSS0014280' => 'camsi', 'CSS0014799' => 'camsi', 'CSS0015368' => 'camsi', 'CSS0017473' => 'camsi', 'CSS0019281' => 'camsi', 'CSS0021320' => 'camsi', 'CSS0021750' => 'camsi', 'CSS0023642' => 'camsi', 'CSS0023792' => 'camsi', 'CSS0031528' => 'camsi', 'CSS0033894' => 'camsi', 'CSS0034959' => 'camsi', 'CSS0035632' => 'camsi', 'CSS0038450' => 'camsi', 'CSS0039293' => 'camsi', 'CSS0041053' => 'camsi', 'CSS0041981' => 'camsi', 'CSS0042573' => 'camsi', 'CSS0042927' => 'camsi', 'CSS0047725' => 'camsi', 'CSS0049636' => 'camsi', 'CSS0050513' => 'camsi', 'DCAR_030203' => 'dca', 'Dinv07939' => 'din', 'FAN01G0456' => 'fan', 'FAN02G3001' => 'fan', 'FAN04G2781' => 'fan', 'FAN05G1385' => 'fan', 'FAN05G3062' => 'fan', 'FAN08G2267' => 'fan', 'FAN10G0481' => 'fan', 'FAN10G1257' => 'fan', 'FAN14G0954' => 'fan', 'FAN14G2347' => 'fan', 'FAN15G0187' => 'fan', 'FAN25G2214' => 'fan', 'FvH4_1g21031' => 'fve', 'FvH4_3g16231' => 'fve', 'FvH4_3g26413' => 'fve', 'FvH4_3g29014' => 'fve', 'FvH4_3g31921' => 'fve', 'FvH4_4g19882' => 'fve', 'FvH4_5g21960' => 'fve', 'FvH4_5g29683' => 'fve', 'FvH4_7g13271' => 'fve', 'Glyma.01G062500' => 'gma', 'Glyma.07G140900' => 'gma', 'Glyma.09G140900' => 'gma', 'Glyma.12G112700' => 'gma', 'Glyma.17G168800' => 'gma', 'HanXRQChr01g0027001' => 'han', 'HanXRQChr04g0120511' => 'han', 'HanXRQChr08g0232381' => 'han', 'HanXRQChr09g0265661' => 'han', 'HanXRQChr13g0416031' => 'han', 'Haze_05835' => 'cav', 'Haze_06597' => 'cav', 'Haze_07921' => 'cav', 'Haze_08599' => 'cav', 'Haze_10686' => 'cav', 'Haze_12994' => 'cav', 'Haze_13466' => 'cav', 'Haze_16101' => 'cav', 'Haze_17766' => 'cav', 'Haze_18456' => 'cav', 'Haze_20229' => 'cav', 'Hma1.2p1_0324F.1_g125640' => 'hma', 'Hma1.2p1_0733F.1_g210230' => 'hma', 'Hma1.2p1_0921F.1_g236870' => 'hma', 'Hma1.2p1_1313F.1_g274940' => 'hma', 'Hma1.2p1_3059F.1_g332230' => 'hma', 'Hund15925' => 'sun', 'Hund19562' => 'sun', 'Hund21925' => 'sun', 'MD03G1177400' => 'mdo', 'MD07G1026100' => 'mdo', 'MD17G1218600' => 'mdo', 'Medtr0867s0010' => 'mtr', 'Medtr6g081150' => 'mtr', 'Os01g0527900' => 'osa', 'Os02g0463725' => 'osa', 'Os02g0785600' => 'osa', 'Os03g0433733' => 'osa', 'Os04g0286500' => 'osa', 'Os05g0227800' => 'osa', 'Os06g0521000' => 'osa', 'Os06g0635500' => 'osa', 'Os06g0660650' => 'osa', 'Os07g0554400' => 'osa', 'Os08g0225900' => 'osa', 'Os08g0561000' => 'osa', 'Os09g0241700' => 'osa', 'Os09g0351900' => 'osa', 'Os11g0220700' => 'osa', 'Os11g0282700' => 'osa', 'Os12g0169300' => 'osa', 'Os12g0228500' => 'osa', 'Os12g0543800' => 'osa', 'PGR044G1547' => 'pgr', 'Potri.005G239150' => 'ptr', 'Potri.010G014250' => 'ptr', 'Prupe.1G172500' => 'ppe', 'Prupe.1G196800' => 'ppe', 'Prupe.1G279700' => 'ppe', 'Prupe.2G026400' => 'ppe', 'Prupe.3G094000' => 'ppe', 'Prupe.4G287300' => 'ppe', 'QL01p022166' => 'qlo', 'QL01p051890' => 'qlo', 'QL02p009469' => 'qlo', 'QL02p046053' => 'qlo', 'QL02p057958' => 'qlo', 'QL02p093127' => 'qlo', 'QL03p006855' => 'qlo', 'QL03p071586' => 'qlo', 'QL04p000022' => 'qlo', 'QL04p000024' => 'qlo', 'QL04p003192' => 'qlo', 'QL05p011416' => 'qlo', 'QL06p039590' => 'qlo', 'QL06p052750' => 'qlo', 'QL06p053821' => 'qlo', 'QL07p025287' => 'qlo', 'QL09p033218' => 'qlo', 'QL09p040841' => 'qlo', 'QL10p020337' => 'qlo', 'QL10p027209' => 'qlo', 'QL10p027969' => 'qlo', 'QL10p048988' => 'qlo', 'QL11p001241' => 'qlo', 'QL11p028487' => 'qlo', 'RcHm_v2.0_Chr2g0105031' => 'rch', 'RcHm_v2.0_Chr2g0117811' => 'rch', 'RcHm_v2.0_Chr6g0270241' => 'rch', 'RcHm_v2.0_Chr7g0215961' => 'rch', 'RcHm_v2.0_Chr7g0231991' => 'rch', 'Rhsim01G0041500' => 'rsi', 'Rhsim01G0115000' => 'rsi', 'Rhsim01G0115400' => 'rsi', 'Rhsim01G0133600' => 'rsi', 'Rhsim01G0159900' => 'rsi', 'Rhsim02G0189400' => 'rsi', 'Rhsim03G0135600' => 'rsi', 'Rhsim03G0149900' => 'rsi', 'Rhsim04G0125600' => 'rsi', 'Rhsim05G0091700' => 'rsi', 'Rhsim05G0092900' => 'rsi', 'Rhsim06G0075000' => 'rsi', 'Rhsim07G0066400' => 'rsi', 'Rhsim07G0156400' => 'rsi', 'Rhsim07G0182200' => 'rsi', 'Rhsim07G0182300' => 'rsi', 'Rhsim08G0180400' => 'rsi', 'Rhsim09G0056800' => 'rsi', 'Rhsim10G0153300' => 'rsi', 'Rhsim11G0012700' => 'rsi', 'Rhsim12G0031800' => 'rsi', 'Rhsim12G0055400' => 'rsi', 'Rhsim12G0091400' => 'rsi', 'Rhsim13G0070800' => 'rsi', 'Rhsim13G0193300' => 'rsi', 'RhsimUnG0111600' => 'rsi', 'RhsimUnG0137500' => 'rsi', 'RhsimUnG0172900' => 'rsi', 'SGA_v2.0_scaffold11G05878' => 'sas', 'SGA_v2.0_scaffold167G38458' => 'sas', 'SGA_v2.0_scaffold19G08588' => 'sas', 'SGA_v2.0_scaffold239G43990' => 'sas', 'SGA_v2.0_scaffold260G45865' => 'sas', 'SGA_v2.0_scaffold309G48177' => 'sas', 'SGA_v2.0_scaffold76G25122' => 'sas', 'SGA_v2.0_scaffold85G26708' => 'sas', 'SHI13914' => 'shi', 'SHI30402' => 'shi', 'TWI09G0020' => 'twi', 'TWI09G0456' => 'twi', 'TWI09G1572' => 'twi', 'TWI12G0266' => 'twi', 'TWI12G1451' => 'twi', 'TWI14G0851' => 'twi', 'TWI15G0796' => 'twi', 'TWI18G0820' => 'twi', 'TWI18G1152' => 'twi', 'TWI23G0007' => 'twi', 'TWI23G0314' => 'twi', 'TWI31G0674' => 'twi', 'TWI31G0938' => 'twi', 'TWI34G0641' => 'twi', 'TWI34G1527' => 'twi', 'TWI36G0193' => 'twi', 'TWI36G0405' => 'twi', 'TWI38G0892' => 'twi', 'TWI38G0936' => 'twi', 'TWI38G2218' => 'twi', 'TWI53G0679' => 'twi', 'TWI53G0863' => 'twi', 'TWI53G1133' => 'twi', 'TWI60G0823' => 'twi', 'TWI63G0919' => 'twi', 'TWI63G1436' => 'twi', 'TWI73G0140' => 'twi', 'TWI73G0419' => 'twi', 'TWI73G0420' => 'twi', 'TWI73G1276' => 'twi', 'TWI74G0405' => 'twi', 'TWI74G0837' => 'twi', 'TWI75G0594' => 'twi', 'TWI75G1615' => 'twi', 'TWI77G0816' => 'twi', 'vmacro03831' => 'vma', 'vmacro13746' => 'vma', 'vmacro16089' => 'vma', 'vmacro22863' => 'vma', 'Zm00001eb085790' => 'zma', 'Zm00001eb114250' => 'zma', 'Zm00001eb138070' => 'zma', 'Zm00001eb167560' => 'zma', 'Zm00001eb199990' => 'zma', 'Zm00001eb368180' => 'zma', 'Zm00001eb382470' => 'zma' ), 'gf_id' => 'HOM05D001576', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001576' ), 'data_identifier' => 'HOM05D001576', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001576', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '406', 'num_species' => '29' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'Aqoxy1G01456' => 'aox', 'Aqoxy1G02949' => 'aox', 'Aqoxy3G01274' => 'aox', 'Aqoxy3G02110' => 'aox', 'Aqoxy3G02268' => 'aox', 'Aqoxy5G02702' => 'aox', 'Aqoxy5G02988' => 'aox', 'Aqoxy5G03427' => 'aox', 'Aqoxy6G02363' => 'aox', 'Atru.chr1.3225' => 'acertr', 'Atru.chr8.1198' => 'acertr', 'Atru.chr9.790' => 'acertr', 'CANSAT01G3197' => 'cansat', 'Ciclev10003979m.g' => 'ccl', 'Ciclev10017471m.g' => 'ccl', 'Ciclev10018206m.g' => 'ccl', 'Ciclev10033751m.g' => 'ccl', 'CiPaw.01G000900' => 'cil', 'CiPaw.01G001000' => 'cil', 'CiPaw.01G033500' => 'cil', 'CiPaw.01G060300' => 'cil', 'CiPaw.01G070200' => 'cil', 'CiPaw.01G075100' => 'cil', 'CiPaw.01G084700' => 'cil', 'CiPaw.01G087900' => 'cil', 'CiPaw.01G092600' => 'cil', 'CiPaw.01G097200' => 'cil', 'CiPaw.01G098300' => 'cil', 'CiPaw.01G110200' => 'cil', 'CiPaw.01G118700' => 'cil', 'CiPaw.01G121200' => 'cil', 'CiPaw.01G132500' => 'cil', 'CiPaw.01G146900' => 'cil', 'CiPaw.01G174000' => 'cil', 'CiPaw.01G179900' => 'cil', 'CiPaw.01G183400' => 'cil', 'CiPaw.01G240000' => 'cil', 'CiPaw.01G283500' => 'cil', 'CiPaw.01G307400' => 'cil', 'CiPaw.02G030800' => 'cil', 'CiPaw.02G047200' => 'cil', 'CiPaw.02G050500' => 'cil', 'CiPaw.02G069900' => 'cil', 'CiPaw.02G091600' => 'cil', 'CiPaw.02G095000' => 'cil', 'CiPaw.02G131900' => 'cil', 'CiPaw.03G043000' => 'cil', 'CiPaw.03G069900' => 'cil', 'CiPaw.03G088100' => 'cil', 'CiPaw.03G089300' => 'cil', 'CiPaw.03G093100' => 'cil', 'CiPaw.03G129800' => 'cil', 'CiPaw.03G131200' => 'cil', 'CiPaw.03G134500' => 'cil', 'CiPaw.03G152100' => 'cil', 'CiPaw.03G162700' => 'cil', 'CiPaw.03G172800' => 'cil', 'CiPaw.03G175800' => 'cil', 'CiPaw.03G181800' => 'cil', 'CiPaw.03G191400' => 'cil', 'CiPaw.03G198300' => 'cil', 'CiPaw.03G201300' => 'cil', 'CiPaw.03G224700' => 'cil', 'CiPaw.03G225000' => 'cil', 'CiPaw.04G065100' => 'cil', 'CiPaw.04G080400' => 'cil', 'CiPaw.04G113500' => 'cil', 'CiPaw.04G121900' => 'cil', 'CiPaw.04G144100' => 'cil', 'CiPaw.04G176500' => 'cil', 'CiPaw.05G086200' => 'cil', 'CiPaw.05G100200' => 'cil', 'CiPaw.05G114200' => 'cil', 'CiPaw.05G126800' => 'cil', 'CiPaw.05G228800' => 'cil', 'CiPaw.05G230600' => 'cil', 'CiPaw.05G236500' => 'cil', 'CiPaw.05G244800' => 'cil', 'CiPaw.06G026600' => 'cil', 'CiPaw.06G027900' => 'cil', 'CiPaw.06G051800' => 'cil', 'CiPaw.06G128500' => 'cil', 'CiPaw.06G165900' => 'cil', 'CiPaw.07G045400' => 'cil', 'CiPaw.07G048000' => 'cil', 'CiPaw.07G052000' => 'cil', 'CiPaw.07G073800' => 'cil', 'CiPaw.07G099700' => 'cil', 'CiPaw.07G108700' => 'cil', 'CiPaw.07G120000' => 'cil', 'CiPaw.07G134100' => 'cil', 'CiPaw.07G147000' => 'cil', 'CiPaw.07G149700' => 'cil', 'CiPaw.07G178300' => 'cil', 'CiPaw.07G184900' => 'cil', 'CiPaw.08G044500' => 'cil', 'CiPaw.08G046900' => 'cil', 'CiPaw.08G047300' => 'cil', 'CiPaw.08G115400' => 'cil', 'CiPaw.08G134700' => 'cil', 'CiPaw.08G157400' => 'cil', 'CiPaw.09G014300' => 'cil', 'CiPaw.09G088900' => 'cil', 'CiPaw.09G130900' => 'cil', 'CiPaw.09G133100' => 'cil', 'CiPaw.09G151300' => 'cil', 'CiPaw.09G172800' => 'cil', 'CiPaw.09G174900' => 'cil', 'CiPaw.09G175000' => 'cil', 'CiPaw.10G012800' => 'cil', 'CiPaw.10G028800' => 'cil', 'CiPaw.10G044700' => 'cil', 'CiPaw.10G067400' => 'cil', 'CiPaw.10G115900' => 'cil', 'CiPaw.10G126200' => 'cil', 'CiPaw.10G139700' => 'cil', 'CiPaw.10G155100' => 'cil', 'CiPaw.11G011300' => 'cil', 'CiPaw.11G025900' => 'cil', 'CiPaw.11G104100' => 'cil', 'CiPaw.11G142700' => 'cil', 'CiPaw.11G164500' => 'cil', 'CiPaw.11G189100' => 'cil', 'CiPaw.11G197100' => 'cil', 'CiPaw.12G006100' => 'cil', 'CiPaw.12G038500' => 'cil', 'CiPaw.12G041400' => 'cil', 'CiPaw.12G041600' => 'cil', 'CiPaw.12G051300' => 'cil', 'CiPaw.12G101800' => 'cil', 'CiPaw.12G107800' => 'cil', 'CiPaw.13G033200' => 'cil', 'CiPaw.13G129900' => 'cil', 'CiPaw.13G160200' => 'cil', 'CiPaw.14G018900' => 'cil', 'CiPaw.14G029000' => 'cil', 'CiPaw.14G031000' => 'cil', 'CiPaw.14G032000' => 'cil', 'CiPaw.14G032300' => 'cil', 'CiPaw.14G040600' => 'cil', 'CiPaw.14G060500' => 'cil', 'CiPaw.14G061500' => 'cil', 'CiPaw.14G077500' => 'cil', 'CiPaw.14G088300' => 'cil', 'CiPaw.14G108500' => 'cil', 'CiPaw.14G121300' => 'cil', 'CiPaw.14G133000' => 'cil', 'CiPaw.14G134600' => 'cil', 'CiPaw.15G027200' => 'cil', 'CiPaw.15G037700' => 'cil', 'CiPaw.15G050900' => 'cil', 'CiPaw.15G067200' => 'cil', 'CiPaw.15G072000' => 'cil', 'CiPaw.15G112900' => 'cil', 'CiPaw.15G133200' => 'cil', 'CiPaw.15G139500' => 'cil', 'CiPaw.15G155400' => 'cil', 'CiPaw.16G006000' => 'cil', 'CiPaw.16G013100' => 'cil', 'CiPaw.16G047100' => 'cil', 'CiPaw.16G048900' => 'cil', 'CiPaw.16G070300' => 'cil', 'CSS0000195' => 'camsi', 'CSS0001664' => 'camsi', 'CSS0002566' => 'camsi', 'CSS0003077' => 'camsi', 'CSS0004257' => 'camsi', 'CSS0004495' => 'camsi', 'CSS0004599' => 'camsi', 'CSS0004943' => 'camsi', 'CSS0005302' => 'camsi', 'CSS0006274' => 'camsi', 'CSS0006547' => 'camsi', 'CSS0006860' => 'camsi', 'CSS0008814' => 'camsi', 'CSS0008946' => 'camsi', 'CSS0009093' => 'camsi', 'CSS0010221' => 'camsi', 'CSS0010296' => 'camsi', 'CSS0010386' => 'camsi', 'CSS0010831' => 'camsi', 'CSS0011061' => 'camsi', 'CSS0012008' => 'camsi', 'CSS0012194' => 'camsi', 'CSS0013580' => 'camsi', 'CSS0014176' => 'camsi', 'CSS0014280' => 'camsi', 'CSS0014799' => 'camsi', 'CSS0015368' => 'camsi', 'CSS0017473' => 'camsi', 'CSS0019281' => 'camsi', 'CSS0021320' => 'camsi', 'CSS0021750' => 'camsi', 'CSS0023642' => 'camsi', 'CSS0023792' => 'camsi', 'CSS0031528' => 'camsi', 'CSS0033894' => 'camsi', 'CSS0034959' => 'camsi', 'CSS0035632' => 'camsi', 'CSS0038450' => 'camsi', 'CSS0039293' => 'camsi', 'CSS0041053' => 'camsi', 'CSS0041981' => 'camsi', 'CSS0042573' => 'camsi', 'CSS0042927' => 'camsi', 'CSS0047725' => 'camsi', 'CSS0049636' => 'camsi', 'CSS0050513' => 'camsi', 'DCAR_030203' => 'dca', 'Dinv07939' => 'din', 'FAN01G0456' => 'fan', 'FAN02G3001' => 'fan', 'FAN04G2781' => 'fan', 'FAN05G1385' => 'fan', 'FAN05G3062' => 'fan', 'FAN08G2267' => 'fan', 'FAN10G0481' => 'fan', 'FAN10G1257' => 'fan', 'FAN14G0954' => 'fan', 'FAN14G2347' => 'fan', 'FAN15G0187' => 'fan', 'FAN25G2214' => 'fan', 'FvH4_1g21031' => 'fve', 'FvH4_3g16231' => 'fve', 'FvH4_3g26413' => 'fve', 'FvH4_3g29014' => 'fve', 'FvH4_3g31921' => 'fve', 'FvH4_4g19882' => 'fve', 'FvH4_5g21960' => 'fve', 'FvH4_5g29683' => 'fve', 'FvH4_7g13271' => 'fve', 'Glyma.01G062500' => 'gma', 'Glyma.07G140900' => 'gma', 'Glyma.09G140900' => 'gma', 'Glyma.12G112700' => 'gma', 'Glyma.17G168800' => 'gma', 'HanXRQChr01g0027001' => 'han', 'HanXRQChr04g0120511' => 'han', 'HanXRQChr08g0232381' => 'han', 'HanXRQChr09g0265661' => 'han', 'HanXRQChr13g0416031' => 'han', 'Haze_05835' => 'cav', 'Haze_06597' => 'cav', 'Haze_07921' => 'cav', 'Haze_08599' => 'cav', 'Haze_10686' => 'cav', 'Haze_12994' => 'cav', 'Haze_13466' => 'cav', 'Haze_16101' => 'cav', 'Haze_17766' => 'cav', 'Haze_18456' => 'cav', 'Haze_20229' => 'cav', 'Hma1.2p1_0324F.1_g125640' => 'hma', 'Hma1.2p1_0733F.1_g210230' => 'hma', 'Hma1.2p1_0921F.1_g236870' => 'hma', 'Hma1.2p1_1313F.1_g274940' => 'hma', 'Hma1.2p1_3059F.1_g332230' => 'hma', 'Hund15925' => 'sun', 'Hund19562' => 'sun', 'Hund21925' => 'sun', 'MD03G1177400' => 'mdo', 'MD07G1026100' => 'mdo', 'MD17G1218600' => 'mdo', 'Medtr0867s0010' => 'mtr', 'Medtr6g081150' => 'mtr', 'Os01g0527900' => 'osa', 'Os02g0463725' => 'osa', 'Os02g0785600' => 'osa', 'Os03g0433733' => 'osa', 'Os04g0286500' => 'osa', 'Os05g0227800' => 'osa', 'Os06g0521000' => 'osa', 'Os06g0635500' => 'osa', 'Os06g0660650' => 'osa', 'Os07g0554400' => 'osa', 'Os08g0225900' => 'osa', 'Os08g0561000' => 'osa', 'Os09g0241700' => 'osa', 'Os09g0351900' => 'osa', 'Os11g0220700' => 'osa', 'Os11g0282700' => 'osa', 'Os12g0169300' => 'osa', 'Os12g0228500' => 'osa', 'Os12g0543800' => 'osa', 'PGR044G1547' => 'pgr', 'Potri.005G239150' => 'ptr', 'Potri.010G014250' => 'ptr', 'Prupe.1G172500' => 'ppe', 'Prupe.1G196800' => 'ppe', 'Prupe.1G279700' => 'ppe', 'Prupe.2G026400' => 'ppe', 'Prupe.3G094000' => 'ppe', 'Prupe.4G287300' => 'ppe', 'QL01p022166' => 'qlo', 'QL01p051890' => 'qlo', 'QL02p009469' => 'qlo', 'QL02p046053' => 'qlo', 'QL02p057958' => 'qlo', 'QL02p093127' => 'qlo', 'QL03p006855' => 'qlo', 'QL03p071586' => 'qlo', 'QL04p000022' => 'qlo', 'QL04p000024' => 'qlo', 'QL04p003192' => 'qlo', 'QL05p011416' => 'qlo', 'QL06p039590' => 'qlo', 'QL06p052750' => 'qlo', 'QL06p053821' => 'qlo', 'QL07p025287' => 'qlo', 'QL09p033218' => 'qlo', 'QL09p040841' => 'qlo', 'QL10p020337' => 'qlo', 'QL10p027209' => 'qlo', 'QL10p027969' => 'qlo', 'QL10p048988' => 'qlo', 'QL11p001241' => 'qlo', 'QL11p028487' => 'qlo', 'RcHm_v2.0_Chr2g0105031' => 'rch', 'RcHm_v2.0_Chr2g0117811' => 'rch', 'RcHm_v2.0_Chr6g0270241' => 'rch', 'RcHm_v2.0_Chr7g0215961' => 'rch', 'RcHm_v2.0_Chr7g0231991' => 'rch', 'Rhsim01G0041500' => 'rsi', 'Rhsim01G0115000' => 'rsi', 'Rhsim01G0115400' => 'rsi', 'Rhsim01G0133600' => 'rsi', 'Rhsim01G0159900' => 'rsi', 'Rhsim02G0189400' => 'rsi', 'Rhsim03G0135600' => 'rsi', 'Rhsim03G0149900' => 'rsi', 'Rhsim04G0125600' => 'rsi', 'Rhsim05G0091700' => 'rsi', 'Rhsim05G0092900' => 'rsi', 'Rhsim06G0075000' => 'rsi', 'Rhsim07G0066400' => 'rsi', 'Rhsim07G0156400' => 'rsi', 'Rhsim07G0182200' => 'rsi', 'Rhsim07G0182300' => 'rsi', 'Rhsim08G0180400' => 'rsi', 'Rhsim09G0056800' => 'rsi', 'Rhsim10G0153300' => 'rsi', 'Rhsim11G0012700' => 'rsi', 'Rhsim12G0031800' => 'rsi', 'Rhsim12G0055400' => 'rsi', 'Rhsim12G0091400' => 'rsi', 'Rhsim13G0070800' => 'rsi', 'Rhsim13G0193300' => 'rsi', 'RhsimUnG0111600' => 'rsi', 'RhsimUnG0137500' => 'rsi', 'RhsimUnG0172900' => 'rsi', 'SGA_v2.0_scaffold11G05878' => 'sas', 'SGA_v2.0_scaffold167G38458' => 'sas', 'SGA_v2.0_scaffold19G08588' => 'sas', 'SGA_v2.0_scaffold239G43990' => 'sas', 'SGA_v2.0_scaffold260G45865' => 'sas', 'SGA_v2.0_scaffold309G48177' => 'sas', 'SGA_v2.0_scaffold76G25122' => 'sas', 'SGA_v2.0_scaffold85G26708' => 'sas', 'SHI13914' => 'shi', 'SHI30402' => 'shi', 'TWI09G0020' => 'twi', 'TWI09G0456' => 'twi', 'TWI09G1572' => 'twi', 'TWI12G0266' => 'twi', 'TWI12G1451' => 'twi', 'TWI14G0851' => 'twi', 'TWI15G0796' => 'twi', 'TWI18G0820' => 'twi', 'TWI18G1152' => 'twi', 'TWI23G0007' => 'twi', 'TWI23G0314' => 'twi', 'TWI31G0674' => 'twi', 'TWI31G0938' => 'twi', 'TWI34G0641' => 'twi', 'TWI34G1527' => 'twi', 'TWI36G0193' => 'twi', 'TWI36G0405' => 'twi', 'TWI38G0892' => 'twi', 'TWI38G0936' => 'twi', 'TWI38G2218' => 'twi', 'TWI53G0679' => 'twi', 'TWI53G0863' => 'twi', 'TWI53G1133' => 'twi', 'TWI60G0823' => 'twi', 'TWI63G0919' => 'twi', 'TWI63G1436' => 'twi', 'TWI73G0140' => 'twi', 'TWI73G0419' => 'twi', 'TWI73G0420' => 'twi', 'TWI73G1276' => 'twi', 'TWI74G0405' => 'twi', 'TWI74G0837' => 'twi', 'TWI75G0594' => 'twi', 'TWI75G1615' => 'twi', 'TWI77G0816' => 'twi', 'vmacro03831' => 'vma', 'vmacro13746' => 'vma', 'vmacro16089' => 'vma', 'vmacro22863' => 'vma', 'Zm00001eb085790' => 'zma', 'Zm00001eb114250' => 'zma', 'Zm00001eb138070' => 'zma', 'Zm00001eb167560' => 'zma', 'Zm00001eb199990' => 'zma', 'Zm00001eb368180' => 'zma', 'Zm00001eb382470' => 'zma' ) $gf_id = 'HOM05D001576' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001576' ) $data_identifier = 'HOM05D001576' $data_type = 'gf_id' $species_gene_counts = array( 'aox' => (int) 9, 'acertr' => (int) 3, 'cansat' => (int) 1, 'ccl' => (int) 4, 'cil' => (int) 145, 'camsi' => (int) 46, 'dca' => (int) 1, 'din' => (int) 1, 'fan' => (int) 12, 'fve' => (int) 9, 'gma' => (int) 5, 'han' => (int) 5, 'cav' => (int) 11, 'hma' => (int) 5, 'sun' => (int) 3, 'mdo' => (int) 3, 'mtr' => (int) 2, 'osa' => (int) 19, 'pgr' => (int) 1, 'ptr' => (int) 2, 'ppe' => (int) 6, 'qlo' => (int) 24, 'rch' => (int) 5, 'rsi' => (int) 28, 'sas' => (int) 8, 'shi' => (int) 2, 'twi' => (int) 35, 'vma' => (int) 4, 'zma' => (int) 7 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb382470' $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' => 'HOM05D001576', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '406', 'num_species' => '29' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'Aqoxy1G01456' => 'aox', 'Aqoxy1G02949' => 'aox', 'Aqoxy3G01274' => 'aox', 'Aqoxy3G02110' => 'aox', 'Aqoxy3G02268' => 'aox', 'Aqoxy5G02702' => 'aox', 'Aqoxy5G02988' => 'aox', 'Aqoxy5G03427' => 'aox', 'Aqoxy6G02363' => 'aox', 'Atru.chr1.3225' => 'acertr', 'Atru.chr8.1198' => 'acertr', 'Atru.chr9.790' => 'acertr', 'CANSAT01G3197' => 'cansat', 'Ciclev10003979m.g' => 'ccl', 'Ciclev10017471m.g' => 'ccl', 'Ciclev10018206m.g' => 'ccl', 'Ciclev10033751m.g' => 'ccl', 'CiPaw.01G000900' => 'cil', 'CiPaw.01G001000' => 'cil', 'CiPaw.01G033500' => 'cil', 'CiPaw.01G060300' => 'cil', 'CiPaw.01G070200' => 'cil', 'CiPaw.01G075100' => 'cil', 'CiPaw.01G084700' => 'cil', 'CiPaw.01G087900' => 'cil', 'CiPaw.01G092600' => 'cil', 'CiPaw.01G097200' => 'cil', 'CiPaw.01G098300' => 'cil', 'CiPaw.01G110200' => 'cil', 'CiPaw.01G118700' => 'cil', 'CiPaw.01G121200' => 'cil', 'CiPaw.01G132500' => 'cil', 'CiPaw.01G146900' => 'cil', 'CiPaw.01G174000' => 'cil', 'CiPaw.01G179900' => 'cil', 'CiPaw.01G183400' => 'cil', 'CiPaw.01G240000' => 'cil', 'CiPaw.01G283500' => 'cil', 'CiPaw.01G307400' => 'cil', 'CiPaw.02G030800' => 'cil', 'CiPaw.02G047200' => 'cil', 'CiPaw.02G050500' => 'cil', 'CiPaw.02G069900' => 'cil', 'CiPaw.02G091600' => 'cil', 'CiPaw.02G095000' => 'cil', 'CiPaw.02G131900' => 'cil', 'CiPaw.03G043000' => 'cil', 'CiPaw.03G069900' => 'cil', 'CiPaw.03G088100' => 'cil', 'CiPaw.03G089300' => 'cil', 'CiPaw.03G093100' => 'cil', 'CiPaw.03G129800' => 'cil', 'CiPaw.03G131200' => 'cil', 'CiPaw.03G134500' => 'cil', 'CiPaw.03G152100' => 'cil', 'CiPaw.03G162700' => 'cil', 'CiPaw.03G172800' => 'cil', 'CiPaw.03G175800' => 'cil', 'CiPaw.03G181800' => 'cil', 'CiPaw.03G191400' => 'cil', 'CiPaw.03G198300' => 'cil', 'CiPaw.03G201300' => 'cil', 'CiPaw.03G224700' => 'cil', 'CiPaw.03G225000' => 'cil', 'CiPaw.04G065100' => 'cil', 'CiPaw.04G080400' => 'cil', 'CiPaw.04G113500' => 'cil', 'CiPaw.04G121900' => 'cil', 'CiPaw.04G144100' => 'cil', 'CiPaw.04G176500' => 'cil', 'CiPaw.05G086200' => 'cil', 'CiPaw.05G100200' => 'cil', 'CiPaw.05G114200' => 'cil', 'CiPaw.05G126800' => 'cil', 'CiPaw.05G228800' => 'cil', 'CiPaw.05G230600' => 'cil', 'CiPaw.05G236500' => 'cil', 'CiPaw.05G244800' => 'cil', 'CiPaw.06G026600' => 'cil', 'CiPaw.06G027900' => 'cil', 'CiPaw.06G051800' => 'cil', 'CiPaw.06G128500' => 'cil', 'CiPaw.06G165900' => 'cil', 'CiPaw.07G045400' => 'cil', 'CiPaw.07G048000' => 'cil', 'CiPaw.07G052000' => 'cil', 'CiPaw.07G073800' => 'cil', 'CiPaw.07G099700' => 'cil', 'CiPaw.07G108700' => 'cil', 'CiPaw.07G120000' => 'cil', 'CiPaw.07G134100' => 'cil', 'CiPaw.07G147000' => 'cil', 'CiPaw.07G149700' => 'cil', 'CiPaw.07G178300' => 'cil', 'CiPaw.07G184900' => 'cil', 'CiPaw.08G044500' => 'cil', 'CiPaw.08G046900' => 'cil', 'CiPaw.08G047300' => 'cil', 'CiPaw.08G115400' => 'cil', 'CiPaw.08G134700' => 'cil', 'CiPaw.08G157400' => 'cil', 'CiPaw.09G014300' => 'cil', 'CiPaw.09G088900' => 'cil', 'CiPaw.09G130900' => 'cil', 'CiPaw.09G133100' => 'cil', 'CiPaw.09G151300' => 'cil', 'CiPaw.09G172800' => 'cil', 'CiPaw.09G174900' => 'cil', 'CiPaw.09G175000' => 'cil', 'CiPaw.10G012800' => 'cil', 'CiPaw.10G028800' => 'cil', 'CiPaw.10G044700' => 'cil', 'CiPaw.10G067400' => 'cil', 'CiPaw.10G115900' => 'cil', 'CiPaw.10G126200' => 'cil', 'CiPaw.10G139700' => 'cil', 'CiPaw.10G155100' => 'cil', 'CiPaw.11G011300' => 'cil', 'CiPaw.11G025900' => 'cil', 'CiPaw.11G104100' => 'cil', 'CiPaw.11G142700' => 'cil', 'CiPaw.11G164500' => 'cil', 'CiPaw.11G189100' => 'cil', 'CiPaw.11G197100' => 'cil', 'CiPaw.12G006100' => 'cil', 'CiPaw.12G038500' => 'cil', 'CiPaw.12G041400' => 'cil', 'CiPaw.12G041600' => 'cil', 'CiPaw.12G051300' => 'cil', 'CiPaw.12G101800' => 'cil', 'CiPaw.12G107800' => 'cil', 'CiPaw.13G033200' => 'cil', 'CiPaw.13G129900' => 'cil', 'CiPaw.13G160200' => 'cil', 'CiPaw.14G018900' => 'cil', 'CiPaw.14G029000' => 'cil', 'CiPaw.14G031000' => 'cil', 'CiPaw.14G032000' => 'cil', 'CiPaw.14G032300' => 'cil', 'CiPaw.14G040600' => 'cil', 'CiPaw.14G060500' => 'cil', 'CiPaw.14G061500' => 'cil', 'CiPaw.14G077500' => 'cil', 'CiPaw.14G088300' => 'cil', 'CiPaw.14G108500' => 'cil', 'CiPaw.14G121300' => 'cil', 'CiPaw.14G133000' => 'cil', 'CiPaw.14G134600' => 'cil', 'CiPaw.15G027200' => 'cil', 'CiPaw.15G037700' => 'cil', 'CiPaw.15G050900' => 'cil', 'CiPaw.15G067200' => 'cil', 'CiPaw.15G072000' => 'cil', 'CiPaw.15G112900' => 'cil', 'CiPaw.15G133200' => 'cil', 'CiPaw.15G139500' => 'cil', 'CiPaw.15G155400' => 'cil', 'CiPaw.16G006000' => 'cil', 'CiPaw.16G013100' => 'cil', 'CiPaw.16G047100' => 'cil', 'CiPaw.16G048900' => 'cil', 'CiPaw.16G070300' => 'cil', 'CSS0000195' => 'camsi', 'CSS0001664' => 'camsi', 'CSS0002566' => 'camsi', 'CSS0003077' => 'camsi', 'CSS0004257' => 'camsi', 'CSS0004495' => 'camsi', 'CSS0004599' => 'camsi', 'CSS0004943' => 'camsi', 'CSS0005302' => 'camsi', 'CSS0006274' => 'camsi', 'CSS0006547' => 'camsi', 'CSS0006860' => 'camsi', 'CSS0008814' => 'camsi', 'CSS0008946' => 'camsi', 'CSS0009093' => 'camsi', 'CSS0010221' => 'camsi', 'CSS0010296' => 'camsi', 'CSS0010386' => 'camsi', 'CSS0010831' => 'camsi', 'CSS0011061' => 'camsi', 'CSS0012008' => 'camsi', 'CSS0012194' => 'camsi', 'CSS0013580' => 'camsi', 'CSS0014176' => 'camsi', 'CSS0014280' => 'camsi', 'CSS0014799' => 'camsi', 'CSS0015368' => 'camsi', 'CSS0017473' => 'camsi', 'CSS0019281' => 'camsi', 'CSS0021320' => 'camsi', 'CSS0021750' => 'camsi', 'CSS0023642' => 'camsi', 'CSS0023792' => 'camsi', 'CSS0031528' => 'camsi', 'CSS0033894' => 'camsi', 'CSS0034959' => 'camsi', 'CSS0035632' => 'camsi', 'CSS0038450' => 'camsi', 'CSS0039293' => 'camsi', 'CSS0041053' => 'camsi', 'CSS0041981' => 'camsi', 'CSS0042573' => 'camsi', 'CSS0042927' => 'camsi', 'CSS0047725' => 'camsi', 'CSS0049636' => 'camsi', 'CSS0050513' => 'camsi', 'DCAR_030203' => 'dca', 'Dinv07939' => 'din', 'FAN01G0456' => 'fan', 'FAN02G3001' => 'fan', 'FAN04G2781' => 'fan', 'FAN05G1385' => 'fan', 'FAN05G3062' => 'fan', 'FAN08G2267' => 'fan', 'FAN10G0481' => 'fan', 'FAN10G1257' => 'fan', 'FAN14G0954' => 'fan', 'FAN14G2347' => 'fan', 'FAN15G0187' => 'fan', 'FAN25G2214' => 'fan', 'FvH4_1g21031' => 'fve', 'FvH4_3g16231' => 'fve', 'FvH4_3g26413' => 'fve', 'FvH4_3g29014' => 'fve', 'FvH4_3g31921' => 'fve', 'FvH4_4g19882' => 'fve', 'FvH4_5g21960' => 'fve', 'FvH4_5g29683' => 'fve', 'FvH4_7g13271' => 'fve', 'Glyma.01G062500' => 'gma', 'Glyma.07G140900' => 'gma', 'Glyma.09G140900' => 'gma', 'Glyma.12G112700' => 'gma', 'Glyma.17G168800' => 'gma', 'HanXRQChr01g0027001' => 'han', 'HanXRQChr04g0120511' => 'han', 'HanXRQChr08g0232381' => 'han', 'HanXRQChr09g0265661' => 'han', 'HanXRQChr13g0416031' => 'han', 'Haze_05835' => 'cav', 'Haze_06597' => 'cav', 'Haze_07921' => 'cav', 'Haze_08599' => 'cav', 'Haze_10686' => 'cav', 'Haze_12994' => 'cav', 'Haze_13466' => 'cav', 'Haze_16101' => 'cav', 'Haze_17766' => 'cav', 'Haze_18456' => 'cav', 'Haze_20229' => 'cav', 'Hma1.2p1_0324F.1_g125640' => 'hma', 'Hma1.2p1_0733F.1_g210230' => 'hma', 'Hma1.2p1_0921F.1_g236870' => 'hma', 'Hma1.2p1_1313F.1_g274940' => 'hma', 'Hma1.2p1_3059F.1_g332230' => 'hma', 'Hund15925' => 'sun', 'Hund19562' => 'sun', 'Hund21925' => 'sun', 'MD03G1177400' => 'mdo', 'MD07G1026100' => 'mdo', 'MD17G1218600' => 'mdo', 'Medtr0867s0010' => 'mtr', 'Medtr6g081150' => 'mtr', 'Os01g0527900' => 'osa', 'Os02g0463725' => 'osa', 'Os02g0785600' => 'osa', 'Os03g0433733' => 'osa', 'Os04g0286500' => 'osa', 'Os05g0227800' => 'osa', 'Os06g0521000' => 'osa', 'Os06g0635500' => 'osa', 'Os06g0660650' => 'osa', 'Os07g0554400' => 'osa', 'Os08g0225900' => 'osa', 'Os08g0561000' => 'osa', 'Os09g0241700' => 'osa', 'Os09g0351900' => 'osa', 'Os11g0220700' => 'osa', 'Os11g0282700' => 'osa', 'Os12g0169300' => 'osa', 'Os12g0228500' => 'osa', 'Os12g0543800' => 'osa', 'PGR044G1547' => 'pgr', 'Potri.005G239150' => 'ptr', 'Potri.010G014250' => 'ptr', 'Prupe.1G172500' => 'ppe', 'Prupe.1G196800' => 'ppe', 'Prupe.1G279700' => 'ppe', 'Prupe.2G026400' => 'ppe', 'Prupe.3G094000' => 'ppe', 'Prupe.4G287300' => 'ppe', 'QL01p022166' => 'qlo', 'QL01p051890' => 'qlo', 'QL02p009469' => 'qlo', 'QL02p046053' => 'qlo', 'QL02p057958' => 'qlo', 'QL02p093127' => 'qlo', 'QL03p006855' => 'qlo', 'QL03p071586' => 'qlo', 'QL04p000022' => 'qlo', 'QL04p000024' => 'qlo', 'QL04p003192' => 'qlo', 'QL05p011416' => 'qlo', 'QL06p039590' => 'qlo', 'QL06p052750' => 'qlo', 'QL06p053821' => 'qlo', 'QL07p025287' => 'qlo', 'QL09p033218' => 'qlo', 'QL09p040841' => 'qlo', 'QL10p020337' => 'qlo', 'QL10p027209' => 'qlo', 'QL10p027969' => 'qlo', 'QL10p048988' => 'qlo', 'QL11p001241' => 'qlo', 'QL11p028487' => 'qlo', 'RcHm_v2.0_Chr2g0105031' => 'rch', 'RcHm_v2.0_Chr2g0117811' => 'rch', 'RcHm_v2.0_Chr6g0270241' => 'rch', 'RcHm_v2.0_Chr7g0215961' => 'rch', 'RcHm_v2.0_Chr7g0231991' => 'rch', 'Rhsim01G0041500' => 'rsi', 'Rhsim01G0115000' => 'rsi', 'Rhsim01G0115400' => 'rsi', 'Rhsim01G0133600' => 'rsi', 'Rhsim01G0159900' => 'rsi', 'Rhsim02G0189400' => 'rsi', 'Rhsim03G0135600' => 'rsi', 'Rhsim03G0149900' => 'rsi', 'Rhsim04G0125600' => 'rsi', 'Rhsim05G0091700' => 'rsi', 'Rhsim05G0092900' => 'rsi', 'Rhsim06G0075000' => 'rsi', 'Rhsim07G0066400' => 'rsi', 'Rhsim07G0156400' => 'rsi', 'Rhsim07G0182200' => 'rsi', 'Rhsim07G0182300' => 'rsi', 'Rhsim08G0180400' => 'rsi', 'Rhsim09G0056800' => 'rsi', 'Rhsim10G0153300' => 'rsi', 'Rhsim11G0012700' => 'rsi', 'Rhsim12G0031800' => 'rsi', 'Rhsim12G0055400' => 'rsi', 'Rhsim12G0091400' => 'rsi', 'Rhsim13G0070800' => 'rsi', 'Rhsim13G0193300' => 'rsi', 'RhsimUnG0111600' => 'rsi', 'RhsimUnG0137500' => 'rsi', 'RhsimUnG0172900' => 'rsi', 'SGA_v2.0_scaffold11G05878' => 'sas', 'SGA_v2.0_scaffold167G38458' => 'sas', 'SGA_v2.0_scaffold19G08588' => 'sas', 'SGA_v2.0_scaffold239G43990' => 'sas', 'SGA_v2.0_scaffold260G45865' => 'sas', 'SGA_v2.0_scaffold309G48177' => 'sas', 'SGA_v2.0_scaffold76G25122' => 'sas', 'SGA_v2.0_scaffold85G26708' => 'sas', 'SHI13914' => 'shi', 'SHI30402' => 'shi', 'TWI09G0020' => 'twi', 'TWI09G0456' => 'twi', 'TWI09G1572' => 'twi', 'TWI12G0266' => 'twi', 'TWI12G1451' => 'twi', 'TWI14G0851' => 'twi', 'TWI15G0796' => 'twi', 'TWI18G0820' => 'twi', 'TWI18G1152' => 'twi', 'TWI23G0007' => 'twi', 'TWI23G0314' => 'twi', 'TWI31G0674' => 'twi', 'TWI31G0938' => 'twi', 'TWI34G0641' => 'twi', 'TWI34G1527' => 'twi', 'TWI36G0193' => 'twi', 'TWI36G0405' => 'twi', 'TWI38G0892' => 'twi', 'TWI38G0936' => 'twi', 'TWI38G2218' => 'twi', 'TWI53G0679' => 'twi', 'TWI53G0863' => 'twi', 'TWI53G1133' => 'twi', 'TWI60G0823' => 'twi', 'TWI63G0919' => 'twi', 'TWI63G1436' => 'twi', 'TWI73G0140' => 'twi', 'TWI73G0419' => 'twi', 'TWI73G0420' => 'twi', 'TWI73G1276' => 'twi', 'TWI74G0405' => 'twi', 'TWI74G0837' => 'twi', 'TWI75G0594' => 'twi', 'TWI75G1615' => 'twi', 'TWI77G0816' => 'twi', 'vmacro03831' => 'vma', 'vmacro13746' => 'vma', 'vmacro16089' => 'vma', 'vmacro22863' => 'vma', 'Zm00001eb085790' => 'zma', 'Zm00001eb114250' => 'zma', 'Zm00001eb138070' => 'zma', 'Zm00001eb167560' => 'zma', 'Zm00001eb199990' => 'zma', 'Zm00001eb368180' => 'zma', 'Zm00001eb382470' => 'zma' ), 'gf_id' => 'HOM05D001576', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001576' ), 'data_identifier' => 'HOM05D001576', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001576', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '406', 'num_species' => '29' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'Aqoxy1G01456' => 'aox', 'Aqoxy1G02949' => 'aox', 'Aqoxy3G01274' => 'aox', 'Aqoxy3G02110' => 'aox', 'Aqoxy3G02268' => 'aox', 'Aqoxy5G02702' => 'aox', 'Aqoxy5G02988' => 'aox', 'Aqoxy5G03427' => 'aox', 'Aqoxy6G02363' => 'aox', 'Atru.chr1.3225' => 'acertr', 'Atru.chr8.1198' => 'acertr', 'Atru.chr9.790' => 'acertr', 'CANSAT01G3197' => 'cansat', 'Ciclev10003979m.g' => 'ccl', 'Ciclev10017471m.g' => 'ccl', 'Ciclev10018206m.g' => 'ccl', 'Ciclev10033751m.g' => 'ccl', 'CiPaw.01G000900' => 'cil', 'CiPaw.01G001000' => 'cil', 'CiPaw.01G033500' => 'cil', 'CiPaw.01G060300' => 'cil', 'CiPaw.01G070200' => 'cil', 'CiPaw.01G075100' => 'cil', 'CiPaw.01G084700' => 'cil', 'CiPaw.01G087900' => 'cil', 'CiPaw.01G092600' => 'cil', 'CiPaw.01G097200' => 'cil', 'CiPaw.01G098300' => 'cil', 'CiPaw.01G110200' => 'cil', 'CiPaw.01G118700' => 'cil', 'CiPaw.01G121200' => 'cil', 'CiPaw.01G132500' => 'cil', 'CiPaw.01G146900' => 'cil', 'CiPaw.01G174000' => 'cil', 'CiPaw.01G179900' => 'cil', 'CiPaw.01G183400' => 'cil', 'CiPaw.01G240000' => 'cil', 'CiPaw.01G283500' => 'cil', 'CiPaw.01G307400' => 'cil', 'CiPaw.02G030800' => 'cil', 'CiPaw.02G047200' => 'cil', 'CiPaw.02G050500' => 'cil', 'CiPaw.02G069900' => 'cil', 'CiPaw.02G091600' => 'cil', 'CiPaw.02G095000' => 'cil', 'CiPaw.02G131900' => 'cil', 'CiPaw.03G043000' => 'cil', 'CiPaw.03G069900' => 'cil', 'CiPaw.03G088100' => 'cil', 'CiPaw.03G089300' => 'cil', 'CiPaw.03G093100' => 'cil', 'CiPaw.03G129800' => 'cil', 'CiPaw.03G131200' => 'cil', 'CiPaw.03G134500' => 'cil', 'CiPaw.03G152100' => 'cil', 'CiPaw.03G162700' => 'cil', 'CiPaw.03G172800' => 'cil', 'CiPaw.03G175800' => 'cil', 'CiPaw.03G181800' => 'cil', 'CiPaw.03G191400' => 'cil', 'CiPaw.03G198300' => 'cil', 'CiPaw.03G201300' => 'cil', 'CiPaw.03G224700' => 'cil', 'CiPaw.03G225000' => 'cil', 'CiPaw.04G065100' => 'cil', 'CiPaw.04G080400' => 'cil', 'CiPaw.04G113500' => 'cil', 'CiPaw.04G121900' => 'cil', 'CiPaw.04G144100' => 'cil', 'CiPaw.04G176500' => 'cil', 'CiPaw.05G086200' => 'cil', 'CiPaw.05G100200' => 'cil', 'CiPaw.05G114200' => 'cil', 'CiPaw.05G126800' => 'cil', 'CiPaw.05G228800' => 'cil', 'CiPaw.05G230600' => 'cil', 'CiPaw.05G236500' => 'cil', 'CiPaw.05G244800' => 'cil', 'CiPaw.06G026600' => 'cil', 'CiPaw.06G027900' => 'cil', 'CiPaw.06G051800' => 'cil', 'CiPaw.06G128500' => 'cil', 'CiPaw.06G165900' => 'cil', 'CiPaw.07G045400' => 'cil', 'CiPaw.07G048000' => 'cil', 'CiPaw.07G052000' => 'cil', 'CiPaw.07G073800' => 'cil', 'CiPaw.07G099700' => 'cil', 'CiPaw.07G108700' => 'cil', 'CiPaw.07G120000' => 'cil', 'CiPaw.07G134100' => 'cil', 'CiPaw.07G147000' => 'cil', 'CiPaw.07G149700' => 'cil', 'CiPaw.07G178300' => 'cil', 'CiPaw.07G184900' => 'cil', 'CiPaw.08G044500' => 'cil', 'CiPaw.08G046900' => 'cil', 'CiPaw.08G047300' => 'cil', 'CiPaw.08G115400' => 'cil', 'CiPaw.08G134700' => 'cil', 'CiPaw.08G157400' => 'cil', 'CiPaw.09G014300' => 'cil', 'CiPaw.09G088900' => 'cil', 'CiPaw.09G130900' => 'cil', 'CiPaw.09G133100' => 'cil', 'CiPaw.09G151300' => 'cil', 'CiPaw.09G172800' => 'cil', 'CiPaw.09G174900' => 'cil', 'CiPaw.09G175000' => 'cil', 'CiPaw.10G012800' => 'cil', 'CiPaw.10G028800' => 'cil', 'CiPaw.10G044700' => 'cil', 'CiPaw.10G067400' => 'cil', 'CiPaw.10G115900' => 'cil', 'CiPaw.10G126200' => 'cil', 'CiPaw.10G139700' => 'cil', 'CiPaw.10G155100' => 'cil', 'CiPaw.11G011300' => 'cil', 'CiPaw.11G025900' => 'cil', 'CiPaw.11G104100' => 'cil', 'CiPaw.11G142700' => 'cil', 'CiPaw.11G164500' => 'cil', 'CiPaw.11G189100' => 'cil', 'CiPaw.11G197100' => 'cil', 'CiPaw.12G006100' => 'cil', 'CiPaw.12G038500' => 'cil', 'CiPaw.12G041400' => 'cil', 'CiPaw.12G041600' => 'cil', 'CiPaw.12G051300' => 'cil', 'CiPaw.12G101800' => 'cil', 'CiPaw.12G107800' => 'cil', 'CiPaw.13G033200' => 'cil', 'CiPaw.13G129900' => 'cil', 'CiPaw.13G160200' => 'cil', 'CiPaw.14G018900' => 'cil', 'CiPaw.14G029000' => 'cil', 'CiPaw.14G031000' => 'cil', 'CiPaw.14G032000' => 'cil', 'CiPaw.14G032300' => 'cil', 'CiPaw.14G040600' => 'cil', 'CiPaw.14G060500' => 'cil', 'CiPaw.14G061500' => 'cil', 'CiPaw.14G077500' => 'cil', 'CiPaw.14G088300' => 'cil', 'CiPaw.14G108500' => 'cil', 'CiPaw.14G121300' => 'cil', 'CiPaw.14G133000' => 'cil', 'CiPaw.14G134600' => 'cil', 'CiPaw.15G027200' => 'cil', 'CiPaw.15G037700' => 'cil', 'CiPaw.15G050900' => 'cil', 'CiPaw.15G067200' => 'cil', 'CiPaw.15G072000' => 'cil', 'CiPaw.15G112900' => 'cil', 'CiPaw.15G133200' => 'cil', 'CiPaw.15G139500' => 'cil', 'CiPaw.15G155400' => 'cil', 'CiPaw.16G006000' => 'cil', 'CiPaw.16G013100' => 'cil', 'CiPaw.16G047100' => 'cil', 'CiPaw.16G048900' => 'cil', 'CiPaw.16G070300' => 'cil', 'CSS0000195' => 'camsi', 'CSS0001664' => 'camsi', 'CSS0002566' => 'camsi', 'CSS0003077' => 'camsi', 'CSS0004257' => 'camsi', 'CSS0004495' => 'camsi', 'CSS0004599' => 'camsi', 'CSS0004943' => 'camsi', 'CSS0005302' => 'camsi', 'CSS0006274' => 'camsi', 'CSS0006547' => 'camsi', 'CSS0006860' => 'camsi', 'CSS0008814' => 'camsi', 'CSS0008946' => 'camsi', 'CSS0009093' => 'camsi', 'CSS0010221' => 'camsi', 'CSS0010296' => 'camsi', 'CSS0010386' => 'camsi', 'CSS0010831' => 'camsi', 'CSS0011061' => 'camsi', 'CSS0012008' => 'camsi', 'CSS0012194' => 'camsi', 'CSS0013580' => 'camsi', 'CSS0014176' => 'camsi', 'CSS0014280' => 'camsi', 'CSS0014799' => 'camsi', 'CSS0015368' => 'camsi', 'CSS0017473' => 'camsi', 'CSS0019281' => 'camsi', 'CSS0021320' => 'camsi', 'CSS0021750' => 'camsi', 'CSS0023642' => 'camsi', 'CSS0023792' => 'camsi', 'CSS0031528' => 'camsi', 'CSS0033894' => 'camsi', 'CSS0034959' => 'camsi', 'CSS0035632' => 'camsi', 'CSS0038450' => 'camsi', 'CSS0039293' => 'camsi', 'CSS0041053' => 'camsi', 'CSS0041981' => 'camsi', 'CSS0042573' => 'camsi', 'CSS0042927' => 'camsi', 'CSS0047725' => 'camsi', 'CSS0049636' => 'camsi', 'CSS0050513' => 'camsi', 'DCAR_030203' => 'dca', 'Dinv07939' => 'din', 'FAN01G0456' => 'fan', 'FAN02G3001' => 'fan', 'FAN04G2781' => 'fan', 'FAN05G1385' => 'fan', 'FAN05G3062' => 'fan', 'FAN08G2267' => 'fan', 'FAN10G0481' => 'fan', 'FAN10G1257' => 'fan', 'FAN14G0954' => 'fan', 'FAN14G2347' => 'fan', 'FAN15G0187' => 'fan', 'FAN25G2214' => 'fan', 'FvH4_1g21031' => 'fve', 'FvH4_3g16231' => 'fve', 'FvH4_3g26413' => 'fve', 'FvH4_3g29014' => 'fve', 'FvH4_3g31921' => 'fve', 'FvH4_4g19882' => 'fve', 'FvH4_5g21960' => 'fve', 'FvH4_5g29683' => 'fve', 'FvH4_7g13271' => 'fve', 'Glyma.01G062500' => 'gma', 'Glyma.07G140900' => 'gma', 'Glyma.09G140900' => 'gma', 'Glyma.12G112700' => 'gma', 'Glyma.17G168800' => 'gma', 'HanXRQChr01g0027001' => 'han', 'HanXRQChr04g0120511' => 'han', 'HanXRQChr08g0232381' => 'han', 'HanXRQChr09g0265661' => 'han', 'HanXRQChr13g0416031' => 'han', 'Haze_05835' => 'cav', 'Haze_06597' => 'cav', 'Haze_07921' => 'cav', 'Haze_08599' => 'cav', 'Haze_10686' => 'cav', 'Haze_12994' => 'cav', 'Haze_13466' => 'cav', 'Haze_16101' => 'cav', 'Haze_17766' => 'cav', 'Haze_18456' => 'cav', 'Haze_20229' => 'cav', 'Hma1.2p1_0324F.1_g125640' => 'hma', 'Hma1.2p1_0733F.1_g210230' => 'hma', 'Hma1.2p1_0921F.1_g236870' => 'hma', 'Hma1.2p1_1313F.1_g274940' => 'hma', 'Hma1.2p1_3059F.1_g332230' => 'hma', 'Hund15925' => 'sun', 'Hund19562' => 'sun', 'Hund21925' => 'sun', 'MD03G1177400' => 'mdo', 'MD07G1026100' => 'mdo', 'MD17G1218600' => 'mdo', 'Medtr0867s0010' => 'mtr', 'Medtr6g081150' => 'mtr', 'Os01g0527900' => 'osa', 'Os02g0463725' => 'osa', 'Os02g0785600' => 'osa', 'Os03g0433733' => 'osa', 'Os04g0286500' => 'osa', 'Os05g0227800' => 'osa', 'Os06g0521000' => 'osa', 'Os06g0635500' => 'osa', 'Os06g0660650' => 'osa', 'Os07g0554400' => 'osa', 'Os08g0225900' => 'osa', 'Os08g0561000' => 'osa', 'Os09g0241700' => 'osa', 'Os09g0351900' => 'osa', 'Os11g0220700' => 'osa', 'Os11g0282700' => 'osa', 'Os12g0169300' => 'osa', 'Os12g0228500' => 'osa', 'Os12g0543800' => 'osa', 'PGR044G1547' => 'pgr', 'Potri.005G239150' => 'ptr', 'Potri.010G014250' => 'ptr', 'Prupe.1G172500' => 'ppe', 'Prupe.1G196800' => 'ppe', 'Prupe.1G279700' => 'ppe', 'Prupe.2G026400' => 'ppe', 'Prupe.3G094000' => 'ppe', 'Prupe.4G287300' => 'ppe', 'QL01p022166' => 'qlo', 'QL01p051890' => 'qlo', 'QL02p009469' => 'qlo', 'QL02p046053' => 'qlo', 'QL02p057958' => 'qlo', 'QL02p093127' => 'qlo', 'QL03p006855' => 'qlo', 'QL03p071586' => 'qlo', 'QL04p000022' => 'qlo', 'QL04p000024' => 'qlo', 'QL04p003192' => 'qlo', 'QL05p011416' => 'qlo', 'QL06p039590' => 'qlo', 'QL06p052750' => 'qlo', 'QL06p053821' => 'qlo', 'QL07p025287' => 'qlo', 'QL09p033218' => 'qlo', 'QL09p040841' => 'qlo', 'QL10p020337' => 'qlo', 'QL10p027209' => 'qlo', 'QL10p027969' => 'qlo', 'QL10p048988' => 'qlo', 'QL11p001241' => 'qlo', 'QL11p028487' => 'qlo', 'RcHm_v2.0_Chr2g0105031' => 'rch', 'RcHm_v2.0_Chr2g0117811' => 'rch', 'RcHm_v2.0_Chr6g0270241' => 'rch', 'RcHm_v2.0_Chr7g0215961' => 'rch', 'RcHm_v2.0_Chr7g0231991' => 'rch', 'Rhsim01G0041500' => 'rsi', 'Rhsim01G0115000' => 'rsi', 'Rhsim01G0115400' => 'rsi', 'Rhsim01G0133600' => 'rsi', 'Rhsim01G0159900' => 'rsi', 'Rhsim02G0189400' => 'rsi', 'Rhsim03G0135600' => 'rsi', 'Rhsim03G0149900' => 'rsi', 'Rhsim04G0125600' => 'rsi', 'Rhsim05G0091700' => 'rsi', 'Rhsim05G0092900' => 'rsi', 'Rhsim06G0075000' => 'rsi', 'Rhsim07G0066400' => 'rsi', 'Rhsim07G0156400' => 'rsi', 'Rhsim07G0182200' => 'rsi', 'Rhsim07G0182300' => 'rsi', 'Rhsim08G0180400' => 'rsi', 'Rhsim09G0056800' => 'rsi', 'Rhsim10G0153300' => 'rsi', 'Rhsim11G0012700' => 'rsi', 'Rhsim12G0031800' => 'rsi', 'Rhsim12G0055400' => 'rsi', 'Rhsim12G0091400' => 'rsi', 'Rhsim13G0070800' => 'rsi', 'Rhsim13G0193300' => 'rsi', 'RhsimUnG0111600' => 'rsi', 'RhsimUnG0137500' => 'rsi', 'RhsimUnG0172900' => 'rsi', 'SGA_v2.0_scaffold11G05878' => 'sas', 'SGA_v2.0_scaffold167G38458' => 'sas', 'SGA_v2.0_scaffold19G08588' => 'sas', 'SGA_v2.0_scaffold239G43990' => 'sas', 'SGA_v2.0_scaffold260G45865' => 'sas', 'SGA_v2.0_scaffold309G48177' => 'sas', 'SGA_v2.0_scaffold76G25122' => 'sas', 'SGA_v2.0_scaffold85G26708' => 'sas', 'SHI13914' => 'shi', 'SHI30402' => 'shi', 'TWI09G0020' => 'twi', 'TWI09G0456' => 'twi', 'TWI09G1572' => 'twi', 'TWI12G0266' => 'twi', 'TWI12G1451' => 'twi', 'TWI14G0851' => 'twi', 'TWI15G0796' => 'twi', 'TWI18G0820' => 'twi', 'TWI18G1152' => 'twi', 'TWI23G0007' => 'twi', 'TWI23G0314' => 'twi', 'TWI31G0674' => 'twi', 'TWI31G0938' => 'twi', 'TWI34G0641' => 'twi', 'TWI34G1527' => 'twi', 'TWI36G0193' => 'twi', 'TWI36G0405' => 'twi', 'TWI38G0892' => 'twi', 'TWI38G0936' => 'twi', 'TWI38G2218' => 'twi', 'TWI53G0679' => 'twi', 'TWI53G0863' => 'twi', 'TWI53G1133' => 'twi', 'TWI60G0823' => 'twi', 'TWI63G0919' => 'twi', 'TWI63G1436' => 'twi', 'TWI73G0140' => 'twi', 'TWI73G0419' => 'twi', 'TWI73G0420' => 'twi', 'TWI73G1276' => 'twi', 'TWI74G0405' => 'twi', 'TWI74G0837' => 'twi', 'TWI75G0594' => 'twi', 'TWI75G1615' => 'twi', 'TWI77G0816' => 'twi', 'vmacro03831' => 'vma', 'vmacro13746' => 'vma', 'vmacro16089' => 'vma', 'vmacro22863' => 'vma', 'Zm00001eb085790' => 'zma', 'Zm00001eb114250' => 'zma', 'Zm00001eb138070' => 'zma', 'Zm00001eb167560' => 'zma', 'Zm00001eb199990' => 'zma', 'Zm00001eb368180' => 'zma', 'Zm00001eb382470' => 'zma' ) $gf_id = 'HOM05D001576' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001576' ) $data_identifier = 'HOM05D001576' $data_type = 'gf_id' $species_gene_counts = array( 'aox' => (int) 9, 'acertr' => (int) 3, 'cansat' => (int) 1, 'ccl' => (int) 4, 'cil' => (int) 145, 'camsi' => (int) 46, 'dca' => (int) 1, 'din' => (int) 1, 'fan' => (int) 12, 'fve' => (int) 9, 'gma' => (int) 5, 'han' => (int) 5, 'cav' => (int) 11, 'hma' => (int) 5, 'sun' => (int) 3, 'mdo' => (int) 3, 'mtr' => (int) 2, 'osa' => (int) 19, 'pgr' => (int) 1, 'ptr' => (int) 2, 'ppe' => (int) 6, 'qlo' => (int) 24, 'rch' => (int) 5, 'rsi' => (int) 28, 'sas' => (int) 8, 'shi' => (int) 2, 'twi' => (int) 35, 'vma' => (int) 4, 'zma' => (int) 7 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb382470' $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' => 'HOM05D001576', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '406', 'num_species' => '29' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'Aqoxy1G01456' => 'aox', 'Aqoxy1G02949' => 'aox', 'Aqoxy3G01274' => 'aox', 'Aqoxy3G02110' => 'aox', 'Aqoxy3G02268' => 'aox', 'Aqoxy5G02702' => 'aox', 'Aqoxy5G02988' => 'aox', 'Aqoxy5G03427' => 'aox', 'Aqoxy6G02363' => 'aox', 'Atru.chr1.3225' => 'acertr', 'Atru.chr8.1198' => 'acertr', 'Atru.chr9.790' => 'acertr', 'CANSAT01G3197' => 'cansat', 'Ciclev10003979m.g' => 'ccl', 'Ciclev10017471m.g' => 'ccl', 'Ciclev10018206m.g' => 'ccl', 'Ciclev10033751m.g' => 'ccl', 'CiPaw.01G000900' => 'cil', 'CiPaw.01G001000' => 'cil', 'CiPaw.01G033500' => 'cil', 'CiPaw.01G060300' => 'cil', 'CiPaw.01G070200' => 'cil', 'CiPaw.01G075100' => 'cil', 'CiPaw.01G084700' => 'cil', 'CiPaw.01G087900' => 'cil', 'CiPaw.01G092600' => 'cil', 'CiPaw.01G097200' => 'cil', 'CiPaw.01G098300' => 'cil', 'CiPaw.01G110200' => 'cil', 'CiPaw.01G118700' => 'cil', 'CiPaw.01G121200' => 'cil', 'CiPaw.01G132500' => 'cil', 'CiPaw.01G146900' => 'cil', 'CiPaw.01G174000' => 'cil', 'CiPaw.01G179900' => 'cil', 'CiPaw.01G183400' => 'cil', 'CiPaw.01G240000' => 'cil', 'CiPaw.01G283500' => 'cil', 'CiPaw.01G307400' => 'cil', 'CiPaw.02G030800' => 'cil', 'CiPaw.02G047200' => 'cil', 'CiPaw.02G050500' => 'cil', 'CiPaw.02G069900' => 'cil', 'CiPaw.02G091600' => 'cil', 'CiPaw.02G095000' => 'cil', 'CiPaw.02G131900' => 'cil', 'CiPaw.03G043000' => 'cil', 'CiPaw.03G069900' => 'cil', 'CiPaw.03G088100' => 'cil', 'CiPaw.03G089300' => 'cil', 'CiPaw.03G093100' => 'cil', 'CiPaw.03G129800' => 'cil', 'CiPaw.03G131200' => 'cil', 'CiPaw.03G134500' => 'cil', 'CiPaw.03G152100' => 'cil', 'CiPaw.03G162700' => 'cil', 'CiPaw.03G172800' => 'cil', 'CiPaw.03G175800' => 'cil', 'CiPaw.03G181800' => 'cil', 'CiPaw.03G191400' => 'cil', 'CiPaw.03G198300' => 'cil', 'CiPaw.03G201300' => 'cil', 'CiPaw.03G224700' => 'cil', 'CiPaw.03G225000' => 'cil', 'CiPaw.04G065100' => 'cil', 'CiPaw.04G080400' => 'cil', 'CiPaw.04G113500' => 'cil', 'CiPaw.04G121900' => 'cil', 'CiPaw.04G144100' => 'cil', 'CiPaw.04G176500' => 'cil', 'CiPaw.05G086200' => 'cil', 'CiPaw.05G100200' => 'cil', 'CiPaw.05G114200' => 'cil', 'CiPaw.05G126800' => 'cil', 'CiPaw.05G228800' => 'cil', 'CiPaw.05G230600' => 'cil', 'CiPaw.05G236500' => 'cil', 'CiPaw.05G244800' => 'cil', 'CiPaw.06G026600' => 'cil', 'CiPaw.06G027900' => 'cil', 'CiPaw.06G051800' => 'cil', 'CiPaw.06G128500' => 'cil', 'CiPaw.06G165900' => 'cil', 'CiPaw.07G045400' => 'cil', 'CiPaw.07G048000' => 'cil', 'CiPaw.07G052000' => 'cil', 'CiPaw.07G073800' => 'cil', 'CiPaw.07G099700' => 'cil', 'CiPaw.07G108700' => 'cil', 'CiPaw.07G120000' => 'cil', 'CiPaw.07G134100' => 'cil', 'CiPaw.07G147000' => 'cil', 'CiPaw.07G149700' => 'cil', 'CiPaw.07G178300' => 'cil', 'CiPaw.07G184900' => 'cil', 'CiPaw.08G044500' => 'cil', 'CiPaw.08G046900' => 'cil', 'CiPaw.08G047300' => 'cil', 'CiPaw.08G115400' => 'cil', 'CiPaw.08G134700' => 'cil', 'CiPaw.08G157400' => 'cil', 'CiPaw.09G014300' => 'cil', 'CiPaw.09G088900' => 'cil', 'CiPaw.09G130900' => 'cil', 'CiPaw.09G133100' => 'cil', 'CiPaw.09G151300' => 'cil', 'CiPaw.09G172800' => 'cil', 'CiPaw.09G174900' => 'cil', 'CiPaw.09G175000' => 'cil', 'CiPaw.10G012800' => 'cil', 'CiPaw.10G028800' => 'cil', 'CiPaw.10G044700' => 'cil', 'CiPaw.10G067400' => 'cil', 'CiPaw.10G115900' => 'cil', 'CiPaw.10G126200' => 'cil', 'CiPaw.10G139700' => 'cil', 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=> 'qlo', 'QL07p025287' => 'qlo', 'QL09p033218' => 'qlo', 'QL09p040841' => 'qlo', 'QL10p020337' => 'qlo', 'QL10p027209' => 'qlo', 'QL10p027969' => 'qlo', 'QL10p048988' => 'qlo', 'QL11p001241' => 'qlo', 'QL11p028487' => 'qlo', 'RcHm_v2.0_Chr2g0105031' => 'rch', 'RcHm_v2.0_Chr2g0117811' => 'rch', 'RcHm_v2.0_Chr6g0270241' => 'rch', 'RcHm_v2.0_Chr7g0215961' => 'rch', 'RcHm_v2.0_Chr7g0231991' => 'rch', 'Rhsim01G0041500' => 'rsi', 'Rhsim01G0115000' => 'rsi', 'Rhsim01G0115400' => 'rsi', 'Rhsim01G0133600' => 'rsi', 'Rhsim01G0159900' => 'rsi', 'Rhsim02G0189400' => 'rsi', 'Rhsim03G0135600' => 'rsi', 'Rhsim03G0149900' => 'rsi', 'Rhsim04G0125600' => 'rsi', 'Rhsim05G0091700' => 'rsi', 'Rhsim05G0092900' => 'rsi', 'Rhsim06G0075000' => 'rsi', 'Rhsim07G0066400' => 'rsi', 'Rhsim07G0156400' => 'rsi', 'Rhsim07G0182200' => 'rsi', 'Rhsim07G0182300' => 'rsi', 'Rhsim08G0180400' => 'rsi', 'Rhsim09G0056800' => 'rsi', 'Rhsim10G0153300' => 'rsi', 'Rhsim11G0012700' => 'rsi', 'Rhsim12G0031800' => 'rsi', 'Rhsim12G0055400' => 'rsi', 'Rhsim12G0091400' => 'rsi', 'Rhsim13G0070800' => 'rsi', 'Rhsim13G0193300' => 'rsi', 'RhsimUnG0111600' => 'rsi', 'RhsimUnG0137500' => 'rsi', 'RhsimUnG0172900' => 'rsi', 'SGA_v2.0_scaffold11G05878' => 'sas', 'SGA_v2.0_scaffold167G38458' => 'sas', 'SGA_v2.0_scaffold19G08588' => 'sas', 'SGA_v2.0_scaffold239G43990' => 'sas', 'SGA_v2.0_scaffold260G45865' => 'sas', 'SGA_v2.0_scaffold309G48177' => 'sas', 'SGA_v2.0_scaffold76G25122' => 'sas', 'SGA_v2.0_scaffold85G26708' => 'sas', 'SHI13914' => 'shi', 'SHI30402' => 'shi', 'TWI09G0020' => 'twi', 'TWI09G0456' => 'twi', 'TWI09G1572' => 'twi', 'TWI12G0266' => 'twi', 'TWI12G1451' => 'twi', 'TWI14G0851' => 'twi', 'TWI15G0796' => 'twi', 'TWI18G0820' => 'twi', 'TWI18G1152' => 'twi', 'TWI23G0007' => 'twi', 'TWI23G0314' => 'twi', 'TWI31G0674' => 'twi', 'TWI31G0938' => 'twi', 'TWI34G0641' => 'twi', 'TWI34G1527' => 'twi', 'TWI36G0193' => 'twi', 'TWI36G0405' => 'twi', 'TWI38G0892' => 'twi', 'TWI38G0936' => 'twi', 'TWI38G2218' => 'twi', 'TWI53G0679' => 'twi', 'TWI53G0863' => 'twi', 'TWI53G1133' => 'twi', 'TWI60G0823' => 'twi', 'TWI63G0919' => 'twi', 'TWI63G1436' => 'twi', 'TWI73G0140' => 'twi', 'TWI73G0419' => 'twi', 'TWI73G0420' => 'twi', 'TWI73G1276' => 'twi', 'TWI74G0405' => 'twi', 'TWI74G0837' => 'twi', 'TWI75G0594' => 'twi', 'TWI75G1615' => 'twi', 'TWI77G0816' => 'twi', 'vmacro03831' => 'vma', 'vmacro13746' => 'vma', 'vmacro16089' => 'vma', 'vmacro22863' => 'vma', 'Zm00001eb085790' => 'zma', 'Zm00001eb114250' => 'zma', 'Zm00001eb138070' => 'zma', 'Zm00001eb167560' => 'zma', 'Zm00001eb199990' => 'zma', 'Zm00001eb368180' => 'zma', 'Zm00001eb382470' => 'zma' ), 'gf_id' => 'HOM05D001576', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001576' ), 'data_identifier' => 'HOM05D001576', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001576', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '406', 'num_species' => '29' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'Aqoxy1G01456' => 'aox', 'Aqoxy1G02949' => 'aox', 'Aqoxy3G01274' => 'aox', 'Aqoxy3G02110' => 'aox', 'Aqoxy3G02268' => 'aox', 'Aqoxy5G02702' => 'aox', 'Aqoxy5G02988' => 'aox', 'Aqoxy5G03427' => 'aox', 'Aqoxy6G02363' => 'aox', 'Atru.chr1.3225' => 'acertr', 'Atru.chr8.1198' => 'acertr', 'Atru.chr9.790' => 'acertr', 'CANSAT01G3197' => 'cansat', 'Ciclev10003979m.g' => 'ccl', 'Ciclev10017471m.g' => 'ccl', 'Ciclev10018206m.g' => 'ccl', 'Ciclev10033751m.g' => 'ccl', 'CiPaw.01G000900' => 'cil', 'CiPaw.01G001000' => 'cil', 'CiPaw.01G033500' => 'cil', 'CiPaw.01G060300' => 'cil', 'CiPaw.01G070200' => 'cil', 'CiPaw.01G075100' => 'cil', 'CiPaw.01G084700' => 'cil', 'CiPaw.01G087900' => 'cil', 'CiPaw.01G092600' => 'cil', 'CiPaw.01G097200' => 'cil', 'CiPaw.01G098300' => 'cil', 'CiPaw.01G110200' => 'cil', 'CiPaw.01G118700' => 'cil', 'CiPaw.01G121200' => 'cil', 'CiPaw.01G132500' => 'cil', 'CiPaw.01G146900' => 'cil', 'CiPaw.01G174000' => 'cil', 'CiPaw.01G179900' => 'cil', 'CiPaw.01G183400' => 'cil', 'CiPaw.01G240000' => 'cil', 'CiPaw.01G283500' => 'cil', 'CiPaw.01G307400' => 'cil', 'CiPaw.02G030800' => 'cil', 'CiPaw.02G047200' => 'cil', 'CiPaw.02G050500' => 'cil', 'CiPaw.02G069900' => 'cil', 'CiPaw.02G091600' => 'cil', 'CiPaw.02G095000' => 'cil', 'CiPaw.02G131900' => 'cil', 'CiPaw.03G043000' => 'cil', 'CiPaw.03G069900' => 'cil', 'CiPaw.03G088100' => 'cil', 'CiPaw.03G089300' => 'cil', 'CiPaw.03G093100' => 'cil', 'CiPaw.03G129800' => 'cil', 'CiPaw.03G131200' => 'cil', 'CiPaw.03G134500' => 'cil', 'CiPaw.03G152100' => 'cil', 'CiPaw.03G162700' => 'cil', 'CiPaw.03G172800' => 'cil', 'CiPaw.03G175800' => 'cil', 'CiPaw.03G181800' => 'cil', 'CiPaw.03G191400' => 'cil', 'CiPaw.03G198300' => 'cil', 'CiPaw.03G201300' => 'cil', 'CiPaw.03G224700' => 'cil', 'CiPaw.03G225000' => 'cil', 'CiPaw.04G065100' => 'cil', 'CiPaw.04G080400' => 'cil', 'CiPaw.04G113500' => 'cil', 'CiPaw.04G121900' => 'cil', 'CiPaw.04G144100' => 'cil', 'CiPaw.04G176500' => 'cil', 'CiPaw.05G086200' => 'cil', 'CiPaw.05G100200' => 'cil', 'CiPaw.05G114200' => 'cil', 'CiPaw.05G126800' => 'cil', 'CiPaw.05G228800' => 'cil', 'CiPaw.05G230600' => 'cil', 'CiPaw.05G236500' => 'cil', 'CiPaw.05G244800' => 'cil', 'CiPaw.06G026600' => 'cil', 'CiPaw.06G027900' => 'cil', 'CiPaw.06G051800' => 'cil', 'CiPaw.06G128500' => 'cil', 'CiPaw.06G165900' => 'cil', 'CiPaw.07G045400' => 'cil', 'CiPaw.07G048000' => 'cil', 'CiPaw.07G052000' => 'cil', 'CiPaw.07G073800' => 'cil', 'CiPaw.07G099700' => 'cil', 'CiPaw.07G108700' => 'cil', 'CiPaw.07G120000' => 'cil', 'CiPaw.07G134100' => 'cil', 'CiPaw.07G147000' => 'cil', 'CiPaw.07G149700' => 'cil', 'CiPaw.07G178300' => 'cil', 'CiPaw.07G184900' => 'cil', 'CiPaw.08G044500' => 'cil', 'CiPaw.08G046900' => 'cil', 'CiPaw.08G047300' => 'cil', 'CiPaw.08G115400' => 'cil', 'CiPaw.08G134700' => 'cil', 'CiPaw.08G157400' => 'cil', 'CiPaw.09G014300' => 'cil', 'CiPaw.09G088900' => 'cil', 'CiPaw.09G130900' => 'cil', 'CiPaw.09G133100' => 'cil', 'CiPaw.09G151300' => 'cil', 'CiPaw.09G172800' => 'cil', 'CiPaw.09G174900' => 'cil', 'CiPaw.09G175000' => 'cil', 'CiPaw.10G012800' => 'cil', 'CiPaw.10G028800' => 'cil', 'CiPaw.10G044700' => 'cil', 'CiPaw.10G067400' => 'cil', 'CiPaw.10G115900' => 'cil', 'CiPaw.10G126200' => 'cil', 'CiPaw.10G139700' => 'cil', 'CiPaw.10G155100' => 'cil', 'CiPaw.11G011300' => 'cil', 'CiPaw.11G025900' => 'cil', 'CiPaw.11G104100' => 'cil', 'CiPaw.11G142700' => 'cil', 'CiPaw.11G164500' => 'cil', 'CiPaw.11G189100' => 'cil', 'CiPaw.11G197100' => 'cil', 'CiPaw.12G006100' => 'cil', 'CiPaw.12G038500' => 'cil', 'CiPaw.12G041400' => 'cil', 'CiPaw.12G041600' => 'cil', 'CiPaw.12G051300' => 'cil', 'CiPaw.12G101800' => 'cil', 'CiPaw.12G107800' => 'cil', 'CiPaw.13G033200' => 'cil', 'CiPaw.13G129900' => 'cil', 'CiPaw.13G160200' => 'cil', 'CiPaw.14G018900' => 'cil', 'CiPaw.14G029000' => 'cil', 'CiPaw.14G031000' => 'cil', 'CiPaw.14G032000' => 'cil', 'CiPaw.14G032300' => 'cil', 'CiPaw.14G040600' => 'cil', 'CiPaw.14G060500' => 'cil', 'CiPaw.14G061500' => 'cil', 'CiPaw.14G077500' => 'cil', 'CiPaw.14G088300' => 'cil', 'CiPaw.14G108500' => 'cil', 'CiPaw.14G121300' => 'cil', 'CiPaw.14G133000' => 'cil', 'CiPaw.14G134600' => 'cil', 'CiPaw.15G027200' => 'cil', 'CiPaw.15G037700' => 'cil', 'CiPaw.15G050900' => 'cil', 'CiPaw.15G067200' => 'cil', 'CiPaw.15G072000' => 'cil', 'CiPaw.15G112900' => 'cil', 'CiPaw.15G133200' => 'cil', 'CiPaw.15G139500' => 'cil', 'CiPaw.15G155400' => 'cil', 'CiPaw.16G006000' => 'cil', 'CiPaw.16G013100' => 'cil', 'CiPaw.16G047100' => 'cil', 'CiPaw.16G048900' => 'cil', 'CiPaw.16G070300' => 'cil', 'CSS0000195' => 'camsi', 'CSS0001664' => 'camsi', 'CSS0002566' => 'camsi', 'CSS0003077' => 'camsi', 'CSS0004257' => 'camsi', 'CSS0004495' => 'camsi', 'CSS0004599' => 'camsi', 'CSS0004943' => 'camsi', 'CSS0005302' => 'camsi', 'CSS0006274' => 'camsi', 'CSS0006547' => 'camsi', 'CSS0006860' => 'camsi', 'CSS0008814' => 'camsi', 'CSS0008946' => 'camsi', 'CSS0009093' => 'camsi', 'CSS0010221' => 'camsi', 'CSS0010296' => 'camsi', 'CSS0010386' => 'camsi', 'CSS0010831' => 'camsi', 'CSS0011061' => 'camsi', 'CSS0012008' => 'camsi', 'CSS0012194' => 'camsi', 'CSS0013580' => 'camsi', 'CSS0014176' => 'camsi', 'CSS0014280' => 'camsi', 'CSS0014799' => 'camsi', 'CSS0015368' => 'camsi', 'CSS0017473' => 'camsi', 'CSS0019281' => 'camsi', 'CSS0021320' => 'camsi', 'CSS0021750' => 'camsi', 'CSS0023642' => 'camsi', 'CSS0023792' => 'camsi', 'CSS0031528' => 'camsi', 'CSS0033894' => 'camsi', 'CSS0034959' => 'camsi', 'CSS0035632' => 'camsi', 'CSS0038450' => 'camsi', 'CSS0039293' => 'camsi', 'CSS0041053' => 'camsi', 'CSS0041981' => 'camsi', 'CSS0042573' => 'camsi', 'CSS0042927' => 'camsi', 'CSS0047725' => 'camsi', 'CSS0049636' => 'camsi', 'CSS0050513' => 'camsi', 'DCAR_030203' => 'dca', 'Dinv07939' => 'din', 'FAN01G0456' => 'fan', 'FAN02G3001' => 'fan', 'FAN04G2781' => 'fan', 'FAN05G1385' => 'fan', 'FAN05G3062' => 'fan', 'FAN08G2267' => 'fan', 'FAN10G0481' => 'fan', 'FAN10G1257' => 'fan', 'FAN14G0954' => 'fan', 'FAN14G2347' => 'fan', 'FAN15G0187' => 'fan', 'FAN25G2214' => 'fan', 'FvH4_1g21031' => 'fve', 'FvH4_3g16231' => 'fve', 'FvH4_3g26413' => 'fve', 'FvH4_3g29014' => 'fve', 'FvH4_3g31921' => 'fve', 'FvH4_4g19882' => 'fve', 'FvH4_5g21960' => 'fve', 'FvH4_5g29683' => 'fve', 'FvH4_7g13271' => 'fve', 'Glyma.01G062500' => 'gma', 'Glyma.07G140900' => 'gma', 'Glyma.09G140900' => 'gma', 'Glyma.12G112700' => 'gma', 'Glyma.17G168800' => 'gma', 'HanXRQChr01g0027001' => 'han', 'HanXRQChr04g0120511' => 'han', 'HanXRQChr08g0232381' => 'han', 'HanXRQChr09g0265661' => 'han', 'HanXRQChr13g0416031' => 'han', 'Haze_05835' => 'cav', 'Haze_06597' => 'cav', 'Haze_07921' => 'cav', 'Haze_08599' => 'cav', 'Haze_10686' => 'cav', 'Haze_12994' => 'cav', 'Haze_13466' => 'cav', 'Haze_16101' => 'cav', 'Haze_17766' => 'cav', 'Haze_18456' => 'cav', 'Haze_20229' => 'cav', 'Hma1.2p1_0324F.1_g125640' => 'hma', 'Hma1.2p1_0733F.1_g210230' => 'hma', 'Hma1.2p1_0921F.1_g236870' => 'hma', 'Hma1.2p1_1313F.1_g274940' => 'hma', 'Hma1.2p1_3059F.1_g332230' => 'hma', 'Hund15925' => 'sun', 'Hund19562' => 'sun', 'Hund21925' => 'sun', 'MD03G1177400' => 'mdo', 'MD07G1026100' => 'mdo', 'MD17G1218600' => 'mdo', 'Medtr0867s0010' => 'mtr', 'Medtr6g081150' => 'mtr', 'Os01g0527900' => 'osa', 'Os02g0463725' => 'osa', 'Os02g0785600' => 'osa', 'Os03g0433733' => 'osa', 'Os04g0286500' => 'osa', 'Os05g0227800' => 'osa', 'Os06g0521000' => 'osa', 'Os06g0635500' => 'osa', 'Os06g0660650' => 'osa', 'Os07g0554400' => 'osa', 'Os08g0225900' => 'osa', 'Os08g0561000' => 'osa', 'Os09g0241700' => 'osa', 'Os09g0351900' => 'osa', 'Os11g0220700' => 'osa', 'Os11g0282700' => 'osa', 'Os12g0169300' => 'osa', 'Os12g0228500' => 'osa', 'Os12g0543800' => 'osa', 'PGR044G1547' => 'pgr', 'Potri.005G239150' => 'ptr', 'Potri.010G014250' => 'ptr', 'Prupe.1G172500' => 'ppe', 'Prupe.1G196800' => 'ppe', 'Prupe.1G279700' => 'ppe', 'Prupe.2G026400' => 'ppe', 'Prupe.3G094000' => 'ppe', 'Prupe.4G287300' => 'ppe', 'QL01p022166' => 'qlo', 'QL01p051890' => 'qlo', 'QL02p009469' => 'qlo', 'QL02p046053' => 'qlo', 'QL02p057958' => 'qlo', 'QL02p093127' => 'qlo', 'QL03p006855' => 'qlo', 'QL03p071586' => 'qlo', 'QL04p000022' => 'qlo', 'QL04p000024' => 'qlo', 'QL04p003192' => 'qlo', 'QL05p011416' => 'qlo', 'QL06p039590' => 'qlo', 'QL06p052750' => 'qlo', 'QL06p053821' => 'qlo', 'QL07p025287' => 'qlo', 'QL09p033218' => 'qlo', 'QL09p040841' => 'qlo', 'QL10p020337' => 'qlo', 'QL10p027209' => 'qlo', 'QL10p027969' => 'qlo', 'QL10p048988' => 'qlo', 'QL11p001241' => 'qlo', 'QL11p028487' => 'qlo', 'RcHm_v2.0_Chr2g0105031' => 'rch', 'RcHm_v2.0_Chr2g0117811' => 'rch', 'RcHm_v2.0_Chr6g0270241' => 'rch', 'RcHm_v2.0_Chr7g0215961' => 'rch', 'RcHm_v2.0_Chr7g0231991' => 'rch', 'Rhsim01G0041500' => 'rsi', 'Rhsim01G0115000' => 'rsi', 'Rhsim01G0115400' => 'rsi', 'Rhsim01G0133600' => 'rsi', 'Rhsim01G0159900' => 'rsi', 'Rhsim02G0189400' => 'rsi', 'Rhsim03G0135600' => 'rsi', 'Rhsim03G0149900' => 'rsi', 'Rhsim04G0125600' => 'rsi', 'Rhsim05G0091700' => 'rsi', 'Rhsim05G0092900' => 'rsi', 'Rhsim06G0075000' => 'rsi', 'Rhsim07G0066400' => 'rsi', 'Rhsim07G0156400' => 'rsi', 'Rhsim07G0182200' => 'rsi', 'Rhsim07G0182300' => 'rsi', 'Rhsim08G0180400' => 'rsi', 'Rhsim09G0056800' => 'rsi', 'Rhsim10G0153300' => 'rsi', 'Rhsim11G0012700' => 'rsi', 'Rhsim12G0031800' => 'rsi', 'Rhsim12G0055400' => 'rsi', 'Rhsim12G0091400' => 'rsi', 'Rhsim13G0070800' => 'rsi', 'Rhsim13G0193300' => 'rsi', 'RhsimUnG0111600' => 'rsi', 'RhsimUnG0137500' => 'rsi', 'RhsimUnG0172900' => 'rsi', 'SGA_v2.0_scaffold11G05878' => 'sas', 'SGA_v2.0_scaffold167G38458' => 'sas', 'SGA_v2.0_scaffold19G08588' => 'sas', 'SGA_v2.0_scaffold239G43990' => 'sas', 'SGA_v2.0_scaffold260G45865' => 'sas', 'SGA_v2.0_scaffold309G48177' => 'sas', 'SGA_v2.0_scaffold76G25122' => 'sas', 'SGA_v2.0_scaffold85G26708' => 'sas', 'SHI13914' => 'shi', 'SHI30402' => 'shi', 'TWI09G0020' => 'twi', 'TWI09G0456' => 'twi', 'TWI09G1572' => 'twi', 'TWI12G0266' => 'twi', 'TWI12G1451' => 'twi', 'TWI14G0851' => 'twi', 'TWI15G0796' => 'twi', 'TWI18G0820' => 'twi', 'TWI18G1152' => 'twi', 'TWI23G0007' => 'twi', 'TWI23G0314' => 'twi', 'TWI31G0674' => 'twi', 'TWI31G0938' => 'twi', 'TWI34G0641' => 'twi', 'TWI34G1527' => 'twi', 'TWI36G0193' => 'twi', 'TWI36G0405' => 'twi', 'TWI38G0892' => 'twi', 'TWI38G0936' => 'twi', 'TWI38G2218' => 'twi', 'TWI53G0679' => 'twi', 'TWI53G0863' => 'twi', 'TWI53G1133' => 'twi', 'TWI60G0823' => 'twi', 'TWI63G0919' => 'twi', 'TWI63G1436' => 'twi', 'TWI73G0140' => 'twi', 'TWI73G0419' => 'twi', 'TWI73G0420' => 'twi', 'TWI73G1276' => 'twi', 'TWI74G0405' => 'twi', 'TWI74G0837' => 'twi', 'TWI75G0594' => 'twi', 'TWI75G1615' => 'twi', 'TWI77G0816' => 'twi', 'vmacro03831' => 'vma', 'vmacro13746' => 'vma', 'vmacro16089' => 'vma', 'vmacro22863' => 'vma', 'Zm00001eb085790' => 'zma', 'Zm00001eb114250' => 'zma', 'Zm00001eb138070' => 'zma', 'Zm00001eb167560' => 'zma', 'Zm00001eb199990' => 'zma', 'Zm00001eb368180' => 'zma', 'Zm00001eb382470' => 'zma' ) $gf_id = 'HOM05D001576' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001576' ) $data_identifier = 'HOM05D001576' $data_type = 'gf_id' $species_gene_counts = array( 'aox' => (int) 9, 'acertr' => (int) 3, 'cansat' => (int) 1, 'ccl' => (int) 4, 'cil' => (int) 145, 'camsi' => (int) 46, 'dca' => (int) 1, 'din' => (int) 1, 'fan' => (int) 12, 'fve' => (int) 9, 'gma' => (int) 5, 'han' => (int) 5, 'cav' => (int) 11, 'hma' => (int) 5, 'sun' => (int) 3, 'mdo' => (int) 3, 'mtr' => (int) 2, 'osa' => (int) 19, 'pgr' => (int) 1, 'ptr' => (int) 2, 'ppe' => (int) 6, 'qlo' => (int) 24, 'rch' => (int) 5, 'rsi' => (int) 28, 'sas' => (int) 8, 'shi' => (int) 2, 'twi' => (int) 35, 'vma' => (int) 4, 'zma' => (int) 7 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb382470' $species_info = array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ) $local_species = 'osa' $disabled = '' $selected = '' $num_hits = (int) 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' => 'HOM05D001576', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '406', 'num_species' => '29' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'Aqoxy1G01456' => 'aox', 'Aqoxy1G02949' => 'aox', 'Aqoxy3G01274' => 'aox', 'Aqoxy3G02110' => 'aox', 'Aqoxy3G02268' => 'aox', 'Aqoxy5G02702' => 'aox', 'Aqoxy5G02988' => 'aox', 'Aqoxy5G03427' => 'aox', 'Aqoxy6G02363' => 'aox', 'Atru.chr1.3225' => 'acertr', 'Atru.chr8.1198' => 'acertr', 'Atru.chr9.790' => 'acertr', 'CANSAT01G3197' => 'cansat', 'Ciclev10003979m.g' => 'ccl', 'Ciclev10017471m.g' => 'ccl', 'Ciclev10018206m.g' => 'ccl', 'Ciclev10033751m.g' => 'ccl', 'CiPaw.01G000900' => 'cil', 'CiPaw.01G001000' => 'cil', 'CiPaw.01G033500' => 'cil', 'CiPaw.01G060300' => 'cil', 'CiPaw.01G070200' => 'cil', 'CiPaw.01G075100' => 'cil', 'CiPaw.01G084700' => 'cil', 'CiPaw.01G087900' => 'cil', 'CiPaw.01G092600' => 'cil', 'CiPaw.01G097200' => 'cil', 'CiPaw.01G098300' => 'cil', 'CiPaw.01G110200' => 'cil', 'CiPaw.01G118700' => 'cil', 'CiPaw.01G121200' => 'cil', 'CiPaw.01G132500' => 'cil', 'CiPaw.01G146900' => 'cil', 'CiPaw.01G174000' => 'cil', 'CiPaw.01G179900' => 'cil', 'CiPaw.01G183400' => 'cil', 'CiPaw.01G240000' => 'cil', 'CiPaw.01G283500' => 'cil', 'CiPaw.01G307400' => 'cil', 'CiPaw.02G030800' => 'cil', 'CiPaw.02G047200' => 'cil', 'CiPaw.02G050500' => 'cil', 'CiPaw.02G069900' => 'cil', 'CiPaw.02G091600' => 'cil', 'CiPaw.02G095000' => 'cil', 'CiPaw.02G131900' => 'cil', 'CiPaw.03G043000' => 'cil', 'CiPaw.03G069900' => 'cil', 'CiPaw.03G088100' => 'cil', 'CiPaw.03G089300' => 'cil', 'CiPaw.03G093100' => 'cil', 'CiPaw.03G129800' => 'cil', 'CiPaw.03G131200' => 'cil', 'CiPaw.03G134500' => 'cil', 'CiPaw.03G152100' => 'cil', 'CiPaw.03G162700' => 'cil', 'CiPaw.03G172800' => 'cil', 'CiPaw.03G175800' => 'cil', 'CiPaw.03G181800' => 'cil', 'CiPaw.03G191400' => 'cil', 'CiPaw.03G198300' => 'cil', 'CiPaw.03G201300' => 'cil', 'CiPaw.03G224700' => 'cil', 'CiPaw.03G225000' => 'cil', 'CiPaw.04G065100' => 'cil', 'CiPaw.04G080400' => 'cil', 'CiPaw.04G113500' => 'cil', 'CiPaw.04G121900' => 'cil', 'CiPaw.04G144100' => 'cil', 'CiPaw.04G176500' => 'cil', 'CiPaw.05G086200' => 'cil', 'CiPaw.05G100200' => 'cil', 'CiPaw.05G114200' => 'cil', 'CiPaw.05G126800' => 'cil', 'CiPaw.05G228800' => 'cil', 'CiPaw.05G230600' => 'cil', 'CiPaw.05G236500' => 'cil', 'CiPaw.05G244800' => 'cil', 'CiPaw.06G026600' => 'cil', 'CiPaw.06G027900' => 'cil', 'CiPaw.06G051800' => 'cil', 'CiPaw.06G128500' => 'cil', 'CiPaw.06G165900' => 'cil', 'CiPaw.07G045400' => 'cil', 'CiPaw.07G048000' => 'cil', 'CiPaw.07G052000' => 'cil', 'CiPaw.07G073800' => 'cil', 'CiPaw.07G099700' => 'cil', 'CiPaw.07G108700' => 'cil', 'CiPaw.07G120000' => 'cil', 'CiPaw.07G134100' => 'cil', 'CiPaw.07G147000' => 'cil', 'CiPaw.07G149700' => 'cil', 'CiPaw.07G178300' => 'cil', 'CiPaw.07G184900' => 'cil', 'CiPaw.08G044500' => 'cil', 'CiPaw.08G046900' => 'cil', 'CiPaw.08G047300' => 'cil', 'CiPaw.08G115400' => 'cil', 'CiPaw.08G134700' => 'cil', 'CiPaw.08G157400' => 'cil', 'CiPaw.09G014300' => 'cil', 'CiPaw.09G088900' => 'cil', 'CiPaw.09G130900' => 'cil', 'CiPaw.09G133100' => 'cil', 'CiPaw.09G151300' => 'cil', 'CiPaw.09G172800' => 'cil', 'CiPaw.09G174900' => 'cil', 'CiPaw.09G175000' => 'cil', 'CiPaw.10G012800' => 'cil', 'CiPaw.10G028800' => 'cil', 'CiPaw.10G044700' => 'cil', 'CiPaw.10G067400' => 'cil', 'CiPaw.10G115900' => 'cil', 'CiPaw.10G126200' => 'cil', 'CiPaw.10G139700' => 'cil', 'CiPaw.10G155100' => 'cil', 'CiPaw.11G011300' => 'cil', 'CiPaw.11G025900' => 'cil', 'CiPaw.11G104100' => 'cil', 'CiPaw.11G142700' => 'cil', 'CiPaw.11G164500' => 'cil', 'CiPaw.11G189100' => 'cil', 'CiPaw.11G197100' => 'cil', 'CiPaw.12G006100' => 'cil', 'CiPaw.12G038500' => 'cil', 'CiPaw.12G041400' => 'cil', 'CiPaw.12G041600' => 'cil', 'CiPaw.12G051300' => 'cil', 'CiPaw.12G101800' => 'cil', 'CiPaw.12G107800' => 'cil', 'CiPaw.13G033200' => 'cil', 'CiPaw.13G129900' => 'cil', 'CiPaw.13G160200' => 'cil', 'CiPaw.14G018900' => 'cil', 'CiPaw.14G029000' => 'cil', 'CiPaw.14G031000' => 'cil', 'CiPaw.14G032000' => 'cil', 'CiPaw.14G032300' => 'cil', 'CiPaw.14G040600' => 'cil', 'CiPaw.14G060500' => 'cil', 'CiPaw.14G061500' => 'cil', 'CiPaw.14G077500' => 'cil', 'CiPaw.14G088300' => 'cil', 'CiPaw.14G108500' => 'cil', 'CiPaw.14G121300' => 'cil', 'CiPaw.14G133000' => 'cil', 'CiPaw.14G134600' => 'cil', 'CiPaw.15G027200' => 'cil', 'CiPaw.15G037700' => 'cil', 'CiPaw.15G050900' => 'cil', 'CiPaw.15G067200' => 'cil', 'CiPaw.15G072000' => 'cil', 'CiPaw.15G112900' => 'cil', 'CiPaw.15G133200' => 'cil', 'CiPaw.15G139500' => 'cil', 'CiPaw.15G155400' => 'cil', 'CiPaw.16G006000' => 'cil', 'CiPaw.16G013100' => 'cil', 'CiPaw.16G047100' => 'cil', 'CiPaw.16G048900' => 'cil', 'CiPaw.16G070300' => 'cil', 'CSS0000195' => 'camsi', 'CSS0001664' => 'camsi', 'CSS0002566' => 'camsi', 'CSS0003077' => 'camsi', 'CSS0004257' => 'camsi', 'CSS0004495' => 'camsi', 'CSS0004599' => 'camsi', 'CSS0004943' => 'camsi', 'CSS0005302' => 'camsi', 'CSS0006274' => 'camsi', 'CSS0006547' => 'camsi', 'CSS0006860' => 'camsi', 'CSS0008814' => 'camsi', 'CSS0008946' => 'camsi', 'CSS0009093' => 'camsi', 'CSS0010221' => 'camsi', 'CSS0010296' => 'camsi', 'CSS0010386' => 'camsi', 'CSS0010831' => 'camsi', 'CSS0011061' => 'camsi', 'CSS0012008' => 'camsi', 'CSS0012194' => 'camsi', 'CSS0013580' => 'camsi', 'CSS0014176' => 'camsi', 'CSS0014280' => 'camsi', 'CSS0014799' => 'camsi', 'CSS0015368' => 'camsi', 'CSS0017473' => 'camsi', 'CSS0019281' => 'camsi', 'CSS0021320' => 'camsi', 'CSS0021750' => 'camsi', 'CSS0023642' => 'camsi', 'CSS0023792' => 'camsi', 'CSS0031528' => 'camsi', 'CSS0033894' => 'camsi', 'CSS0034959' => 'camsi', 'CSS0035632' => 'camsi', 'CSS0038450' => 'camsi', 'CSS0039293' => 'camsi', 'CSS0041053' => 'camsi', 'CSS0041981' => 'camsi', 'CSS0042573' => 'camsi', 'CSS0042927' => 'camsi', 'CSS0047725' => 'camsi', 'CSS0049636' => 'camsi', 'CSS0050513' => 'camsi', 'DCAR_030203' => 'dca', 'Dinv07939' => 'din', 'FAN01G0456' => 'fan', 'FAN02G3001' => 'fan', 'FAN04G2781' => 'fan', 'FAN05G1385' => 'fan', 'FAN05G3062' => 'fan', 'FAN08G2267' => 'fan', 'FAN10G0481' => 'fan', 'FAN10G1257' => 'fan', 'FAN14G0954' => 'fan', 'FAN14G2347' => 'fan', 'FAN15G0187' => 'fan', 'FAN25G2214' => 'fan', 'FvH4_1g21031' => 'fve', 'FvH4_3g16231' => 'fve', 'FvH4_3g26413' => 'fve', 'FvH4_3g29014' => 'fve', 'FvH4_3g31921' => 'fve', 'FvH4_4g19882' => 'fve', 'FvH4_5g21960' => 'fve', 'FvH4_5g29683' => 'fve', 'FvH4_7g13271' => 'fve', 'Glyma.01G062500' => 'gma', 'Glyma.07G140900' => 'gma', 'Glyma.09G140900' => 'gma', 'Glyma.12G112700' => 'gma', 'Glyma.17G168800' => 'gma', 'HanXRQChr01g0027001' => 'han', 'HanXRQChr04g0120511' => 'han', 'HanXRQChr08g0232381' => 'han', 'HanXRQChr09g0265661' => 'han', 'HanXRQChr13g0416031' => 'han', 'Haze_05835' => 'cav', 'Haze_06597' => 'cav', 'Haze_07921' => 'cav', 'Haze_08599' => 'cav', 'Haze_10686' => 'cav', 'Haze_12994' => 'cav', 'Haze_13466' => 'cav', 'Haze_16101' => 'cav', 'Haze_17766' => 'cav', 'Haze_18456' => 'cav', 'Haze_20229' => 'cav', 'Hma1.2p1_0324F.1_g125640' => 'hma', 'Hma1.2p1_0733F.1_g210230' => 'hma', 'Hma1.2p1_0921F.1_g236870' => 'hma', 'Hma1.2p1_1313F.1_g274940' => 'hma', 'Hma1.2p1_3059F.1_g332230' => 'hma', 'Hund15925' => 'sun', 'Hund19562' => 'sun', 'Hund21925' => 'sun', 'MD03G1177400' => 'mdo', 'MD07G1026100' => 'mdo', 'MD17G1218600' => 'mdo', 'Medtr0867s0010' => 'mtr', 'Medtr6g081150' => 'mtr', 'Os01g0527900' => 'osa', 'Os02g0463725' => 'osa', 'Os02g0785600' => 'osa', 'Os03g0433733' => 'osa', 'Os04g0286500' => 'osa', 'Os05g0227800' => 'osa', 'Os06g0521000' => 'osa', 'Os06g0635500' => 'osa', 'Os06g0660650' => 'osa', 'Os07g0554400' => 'osa', 'Os08g0225900' => 'osa', 'Os08g0561000' => 'osa', 'Os09g0241700' => 'osa', 'Os09g0351900' => 'osa', 'Os11g0220700' => 'osa', 'Os11g0282700' => 'osa', 'Os12g0169300' => 'osa', 'Os12g0228500' => 'osa', 'Os12g0543800' => 'osa', 'PGR044G1547' => 'pgr', 'Potri.005G239150' => 'ptr', 'Potri.010G014250' => 'ptr', 'Prupe.1G172500' => 'ppe', 'Prupe.1G196800' => 'ppe', 'Prupe.1G279700' => 'ppe', 'Prupe.2G026400' => 'ppe', 'Prupe.3G094000' => 'ppe', 'Prupe.4G287300' => 'ppe', 'QL01p022166' => 'qlo', 'QL01p051890' => 'qlo', 'QL02p009469' => 'qlo', 'QL02p046053' => 'qlo', 'QL02p057958' => 'qlo', 'QL02p093127' => 'qlo', 'QL03p006855' => 'qlo', 'QL03p071586' => 'qlo', 'QL04p000022' => 'qlo', 'QL04p000024' => 'qlo', 'QL04p003192' => 'qlo', 'QL05p011416' => 'qlo', 'QL06p039590' => 'qlo', 'QL06p052750' => 'qlo', 'QL06p053821' => 'qlo', 'QL07p025287' => 'qlo', 'QL09p033218' => 'qlo', 'QL09p040841' => 'qlo', 'QL10p020337' => 'qlo', 'QL10p027209' => 'qlo', 'QL10p027969' => 'qlo', 'QL10p048988' => 'qlo', 'QL11p001241' => 'qlo', 'QL11p028487' => 'qlo', 'RcHm_v2.0_Chr2g0105031' => 'rch', 'RcHm_v2.0_Chr2g0117811' => 'rch', 'RcHm_v2.0_Chr6g0270241' => 'rch', 'RcHm_v2.0_Chr7g0215961' => 'rch', 'RcHm_v2.0_Chr7g0231991' => 'rch', 'Rhsim01G0041500' => 'rsi', 'Rhsim01G0115000' => 'rsi', 'Rhsim01G0115400' => 'rsi', 'Rhsim01G0133600' => 'rsi', 'Rhsim01G0159900' => 'rsi', 'Rhsim02G0189400' => 'rsi', 'Rhsim03G0135600' => 'rsi', 'Rhsim03G0149900' => 'rsi', 'Rhsim04G0125600' => 'rsi', 'Rhsim05G0091700' => 'rsi', 'Rhsim05G0092900' => 'rsi', 'Rhsim06G0075000' => 'rsi', 'Rhsim07G0066400' => 'rsi', 'Rhsim07G0156400' => 'rsi', 'Rhsim07G0182200' => 'rsi', 'Rhsim07G0182300' => 'rsi', 'Rhsim08G0180400' => 'rsi', 'Rhsim09G0056800' => 'rsi', 'Rhsim10G0153300' => 'rsi', 'Rhsim11G0012700' => 'rsi', 'Rhsim12G0031800' => 'rsi', 'Rhsim12G0055400' => 'rsi', 'Rhsim12G0091400' => 'rsi', 'Rhsim13G0070800' => 'rsi', 'Rhsim13G0193300' => 'rsi', 'RhsimUnG0111600' => 'rsi', 'RhsimUnG0137500' => 'rsi', 'RhsimUnG0172900' => 'rsi', 'SGA_v2.0_scaffold11G05878' => 'sas', 'SGA_v2.0_scaffold167G38458' => 'sas', 'SGA_v2.0_scaffold19G08588' => 'sas', 'SGA_v2.0_scaffold239G43990' => 'sas', 'SGA_v2.0_scaffold260G45865' => 'sas', 'SGA_v2.0_scaffold309G48177' => 'sas', 'SGA_v2.0_scaffold76G25122' => 'sas', 'SGA_v2.0_scaffold85G26708' => 'sas', 'SHI13914' => 'shi', 'SHI30402' => 'shi', 'TWI09G0020' => 'twi', 'TWI09G0456' => 'twi', 'TWI09G1572' => 'twi', 'TWI12G0266' => 'twi', 'TWI12G1451' => 'twi', 'TWI14G0851' => 'twi', 'TWI15G0796' => 'twi', 'TWI18G0820' => 'twi', 'TWI18G1152' => 'twi', 'TWI23G0007' => 'twi', 'TWI23G0314' => 'twi', 'TWI31G0674' => 'twi', 'TWI31G0938' => 'twi', 'TWI34G0641' => 'twi', 'TWI34G1527' => 'twi', 'TWI36G0193' => 'twi', 'TWI36G0405' => 'twi', 'TWI38G0892' => 'twi', 'TWI38G0936' => 'twi', 'TWI38G2218' => 'twi', 'TWI53G0679' => 'twi', 'TWI53G0863' => 'twi', 'TWI53G1133' => 'twi', 'TWI60G0823' => 'twi', 'TWI63G0919' => 'twi', 'TWI63G1436' => 'twi', 'TWI73G0140' => 'twi', 'TWI73G0419' => 'twi', 'TWI73G0420' => 'twi', 'TWI73G1276' => 'twi', 'TWI74G0405' => 'twi', 'TWI74G0837' => 'twi', 'TWI75G0594' => 'twi', 'TWI75G1615' => 'twi', 'TWI77G0816' => 'twi', 'vmacro03831' => 'vma', 'vmacro13746' => 'vma', 'vmacro16089' => 'vma', 'vmacro22863' => 'vma', 'Zm00001eb085790' => 'zma', 'Zm00001eb114250' => 'zma', 'Zm00001eb138070' => 'zma', 'Zm00001eb167560' => 'zma', 'Zm00001eb199990' => 'zma', 'Zm00001eb368180' => 'zma', 'Zm00001eb382470' => 'zma' ), 'gf_id' => 'HOM05D001576', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001576' ), 'data_identifier' => 'HOM05D001576', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001576', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '406', 'num_species' => '29' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'Aqoxy1G01456' => 'aox', 'Aqoxy1G02949' => 'aox', 'Aqoxy3G01274' => 'aox', 'Aqoxy3G02110' => 'aox', 'Aqoxy3G02268' => 'aox', 'Aqoxy5G02702' => 'aox', 'Aqoxy5G02988' => 'aox', 'Aqoxy5G03427' => 'aox', 'Aqoxy6G02363' => 'aox', 'Atru.chr1.3225' => 'acertr', 'Atru.chr8.1198' => 'acertr', 'Atru.chr9.790' => 'acertr', 'CANSAT01G3197' => 'cansat', 'Ciclev10003979m.g' => 'ccl', 'Ciclev10017471m.g' => 'ccl', 'Ciclev10018206m.g' => 'ccl', 'Ciclev10033751m.g' => 'ccl', 'CiPaw.01G000900' => 'cil', 'CiPaw.01G001000' => 'cil', 'CiPaw.01G033500' => 'cil', 'CiPaw.01G060300' => 'cil', 'CiPaw.01G070200' => 'cil', 'CiPaw.01G075100' => 'cil', 'CiPaw.01G084700' => 'cil', 'CiPaw.01G087900' => 'cil', 'CiPaw.01G092600' => 'cil', 'CiPaw.01G097200' => 'cil', 'CiPaw.01G098300' => 'cil', 'CiPaw.01G110200' => 'cil', 'CiPaw.01G118700' => 'cil', 'CiPaw.01G121200' => 'cil', 'CiPaw.01G132500' => 'cil', 'CiPaw.01G146900' => 'cil', 'CiPaw.01G174000' => 'cil', 'CiPaw.01G179900' => 'cil', 'CiPaw.01G183400' => 'cil', 'CiPaw.01G240000' => 'cil', 'CiPaw.01G283500' => 'cil', 'CiPaw.01G307400' => 'cil', 'CiPaw.02G030800' => 'cil', 'CiPaw.02G047200' => 'cil', 'CiPaw.02G050500' => 'cil', 'CiPaw.02G069900' => 'cil', 'CiPaw.02G091600' => 'cil', 'CiPaw.02G095000' => 'cil', 'CiPaw.02G131900' => 'cil', 'CiPaw.03G043000' => 'cil', 'CiPaw.03G069900' => 'cil', 'CiPaw.03G088100' => 'cil', 'CiPaw.03G089300' => 'cil', 'CiPaw.03G093100' => 'cil', 'CiPaw.03G129800' => 'cil', 'CiPaw.03G131200' => 'cil', 'CiPaw.03G134500' => 'cil', 'CiPaw.03G152100' => 'cil', 'CiPaw.03G162700' => 'cil', 'CiPaw.03G172800' => 'cil', 'CiPaw.03G175800' => 'cil', 'CiPaw.03G181800' => 'cil', 'CiPaw.03G191400' => 'cil', 'CiPaw.03G198300' => 'cil', 'CiPaw.03G201300' => 'cil', 'CiPaw.03G224700' => 'cil', 'CiPaw.03G225000' => 'cil', 'CiPaw.04G065100' => 'cil', 'CiPaw.04G080400' => 'cil', 'CiPaw.04G113500' => 'cil', 'CiPaw.04G121900' => 'cil', 'CiPaw.04G144100' => 'cil', 'CiPaw.04G176500' => 'cil', 'CiPaw.05G086200' => 'cil', 'CiPaw.05G100200' => 'cil', 'CiPaw.05G114200' => 'cil', 'CiPaw.05G126800' => 'cil', 'CiPaw.05G228800' => 'cil', 'CiPaw.05G230600' => 'cil', 'CiPaw.05G236500' => 'cil', 'CiPaw.05G244800' => 'cil', 'CiPaw.06G026600' => 'cil', 'CiPaw.06G027900' => 'cil', 'CiPaw.06G051800' => 'cil', 'CiPaw.06G128500' => 'cil', 'CiPaw.06G165900' => 'cil', 'CiPaw.07G045400' => 'cil', 'CiPaw.07G048000' => 'cil', 'CiPaw.07G052000' => 'cil', 'CiPaw.07G073800' => 'cil', 'CiPaw.07G099700' => 'cil', 'CiPaw.07G108700' => 'cil', 'CiPaw.07G120000' => 'cil', 'CiPaw.07G134100' => 'cil', 'CiPaw.07G147000' => 'cil', 'CiPaw.07G149700' => 'cil', 'CiPaw.07G178300' => 'cil', 'CiPaw.07G184900' => 'cil', 'CiPaw.08G044500' => 'cil', 'CiPaw.08G046900' => 'cil', 'CiPaw.08G047300' => 'cil', 'CiPaw.08G115400' => 'cil', 'CiPaw.08G134700' => 'cil', 'CiPaw.08G157400' => 'cil', 'CiPaw.09G014300' => 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'CiPaw.14G032000' => 'cil', 'CiPaw.14G032300' => 'cil', 'CiPaw.14G040600' => 'cil', 'CiPaw.14G060500' => 'cil', 'CiPaw.14G061500' => 'cil', 'CiPaw.14G077500' => 'cil', 'CiPaw.14G088300' => 'cil', 'CiPaw.14G108500' => 'cil', 'CiPaw.14G121300' => 'cil', 'CiPaw.14G133000' => 'cil', 'CiPaw.14G134600' => 'cil', 'CiPaw.15G027200' => 'cil', 'CiPaw.15G037700' => 'cil', 'CiPaw.15G050900' => 'cil', 'CiPaw.15G067200' => 'cil', 'CiPaw.15G072000' => 'cil', 'CiPaw.15G112900' => 'cil', 'CiPaw.15G133200' => 'cil', 'CiPaw.15G139500' => 'cil', 'CiPaw.15G155400' => 'cil', 'CiPaw.16G006000' => 'cil', 'CiPaw.16G013100' => 'cil', 'CiPaw.16G047100' => 'cil', 'CiPaw.16G048900' => 'cil', 'CiPaw.16G070300' => 'cil', 'CSS0000195' => 'camsi', 'CSS0001664' => 'camsi', 'CSS0002566' => 'camsi', 'CSS0003077' => 'camsi', 'CSS0004257' => 'camsi', 'CSS0004495' => 'camsi', 'CSS0004599' => 'camsi', 'CSS0004943' => 'camsi', 'CSS0005302' => 'camsi', 'CSS0006274' => 'camsi', 'CSS0006547' => 'camsi', 'CSS0006860' => 'camsi', 'CSS0008814' => 'camsi', 'CSS0008946' => 'camsi', 'CSS0009093' => 'camsi', 'CSS0010221' => 'camsi', 'CSS0010296' => 'camsi', 'CSS0010386' => 'camsi', 'CSS0010831' => 'camsi', 'CSS0011061' => 'camsi', 'CSS0012008' => 'camsi', 'CSS0012194' => 'camsi', 'CSS0013580' => 'camsi', 'CSS0014176' => 'camsi', 'CSS0014280' => 'camsi', 'CSS0014799' => 'camsi', 'CSS0015368' => 'camsi', 'CSS0017473' => 'camsi', 'CSS0019281' => 'camsi', 'CSS0021320' => 'camsi', 'CSS0021750' => 'camsi', 'CSS0023642' => 'camsi', 'CSS0023792' => 'camsi', 'CSS0031528' => 'camsi', 'CSS0033894' => 'camsi', 'CSS0034959' => 'camsi', 'CSS0035632' => 'camsi', 'CSS0038450' => 'camsi', 'CSS0039293' => 'camsi', 'CSS0041053' => 'camsi', 'CSS0041981' => 'camsi', 'CSS0042573' => 'camsi', 'CSS0042927' => 'camsi', 'CSS0047725' => 'camsi', 'CSS0049636' => 'camsi', 'CSS0050513' => 'camsi', 'DCAR_030203' => 'dca', 'Dinv07939' => 'din', 'FAN01G0456' => 'fan', 'FAN02G3001' => 'fan', 'FAN04G2781' => 'fan', 'FAN05G1385' => 'fan', 'FAN05G3062' => 'fan', 'FAN08G2267' => 'fan', 'FAN10G0481' => 'fan', 'FAN10G1257' => 'fan', 'FAN14G0954' => 'fan', 'FAN14G2347' => 'fan', 'FAN15G0187' => 'fan', 'FAN25G2214' => 'fan', 'FvH4_1g21031' => 'fve', 'FvH4_3g16231' => 'fve', 'FvH4_3g26413' => 'fve', 'FvH4_3g29014' => 'fve', 'FvH4_3g31921' => 'fve', 'FvH4_4g19882' => 'fve', 'FvH4_5g21960' => 'fve', 'FvH4_5g29683' => 'fve', 'FvH4_7g13271' => 'fve', 'Glyma.01G062500' => 'gma', 'Glyma.07G140900' => 'gma', 'Glyma.09G140900' => 'gma', 'Glyma.12G112700' => 'gma', 'Glyma.17G168800' => 'gma', 'HanXRQChr01g0027001' => 'han', 'HanXRQChr04g0120511' => 'han', 'HanXRQChr08g0232381' => 'han', 'HanXRQChr09g0265661' => 'han', 'HanXRQChr13g0416031' => 'han', 'Haze_05835' => 'cav', 'Haze_06597' => 'cav', 'Haze_07921' => 'cav', 'Haze_08599' => 'cav', 'Haze_10686' => 'cav', 'Haze_12994' => 'cav', 'Haze_13466' => 'cav', 'Haze_16101' => 'cav', 'Haze_17766' => 'cav', 'Haze_18456' => 'cav', 'Haze_20229' => 'cav', 'Hma1.2p1_0324F.1_g125640' => 'hma', 'Hma1.2p1_0733F.1_g210230' => 'hma', 'Hma1.2p1_0921F.1_g236870' => 'hma', 'Hma1.2p1_1313F.1_g274940' => 'hma', 'Hma1.2p1_3059F.1_g332230' => 'hma', 'Hund15925' => 'sun', 'Hund19562' => 'sun', 'Hund21925' => 'sun', 'MD03G1177400' => 'mdo', 'MD07G1026100' => 'mdo', 'MD17G1218600' => 'mdo', 'Medtr0867s0010' => 'mtr', 'Medtr6g081150' => 'mtr', 'Os01g0527900' => 'osa', 'Os02g0463725' => 'osa', 'Os02g0785600' => 'osa', 'Os03g0433733' => 'osa', 'Os04g0286500' => 'osa', 'Os05g0227800' => 'osa', 'Os06g0521000' => 'osa', 'Os06g0635500' => 'osa', 'Os06g0660650' => 'osa', 'Os07g0554400' => 'osa', 'Os08g0225900' => 'osa', 'Os08g0561000' => 'osa', 'Os09g0241700' => 'osa', 'Os09g0351900' => 'osa', 'Os11g0220700' => 'osa', 'Os11g0282700' => 'osa', 'Os12g0169300' => 'osa', 'Os12g0228500' => 'osa', 'Os12g0543800' => 'osa', 'PGR044G1547' => 'pgr', 'Potri.005G239150' => 'ptr', 'Potri.010G014250' => 'ptr', 'Prupe.1G172500' => 'ppe', 'Prupe.1G196800' => 'ppe', 'Prupe.1G279700' => 'ppe', 'Prupe.2G026400' => 'ppe', 'Prupe.3G094000' => 'ppe', 'Prupe.4G287300' => 'ppe', 'QL01p022166' => 'qlo', 'QL01p051890' => 'qlo', 'QL02p009469' => 'qlo', 'QL02p046053' => 'qlo', 'QL02p057958' => 'qlo', 'QL02p093127' => 'qlo', 'QL03p006855' => 'qlo', 'QL03p071586' => 'qlo', 'QL04p000022' => 'qlo', 'QL04p000024' => 'qlo', 'QL04p003192' => 'qlo', 'QL05p011416' => 'qlo', 'QL06p039590' => 'qlo', 'QL06p052750' => 'qlo', 'QL06p053821' => 'qlo', 'QL07p025287' => 'qlo', 'QL09p033218' => 'qlo', 'QL09p040841' => 'qlo', 'QL10p020337' => 'qlo', 'QL10p027209' => 'qlo', 'QL10p027969' => 'qlo', 'QL10p048988' => 'qlo', 'QL11p001241' => 'qlo', 'QL11p028487' => 'qlo', 'RcHm_v2.0_Chr2g0105031' => 'rch', 'RcHm_v2.0_Chr2g0117811' => 'rch', 'RcHm_v2.0_Chr6g0270241' => 'rch', 'RcHm_v2.0_Chr7g0215961' => 'rch', 'RcHm_v2.0_Chr7g0231991' => 'rch', 'Rhsim01G0041500' => 'rsi', 'Rhsim01G0115000' => 'rsi', 'Rhsim01G0115400' => 'rsi', 'Rhsim01G0133600' => 'rsi', 'Rhsim01G0159900' => 'rsi', 'Rhsim02G0189400' => 'rsi', 'Rhsim03G0135600' => 'rsi', 'Rhsim03G0149900' => 'rsi', 'Rhsim04G0125600' => 'rsi', 'Rhsim05G0091700' => 'rsi', 'Rhsim05G0092900' => 'rsi', 'Rhsim06G0075000' => 'rsi', 'Rhsim07G0066400' => 'rsi', 'Rhsim07G0156400' => 'rsi', 'Rhsim07G0182200' => 'rsi', 'Rhsim07G0182300' => 'rsi', 'Rhsim08G0180400' => 'rsi', 'Rhsim09G0056800' => 'rsi', 'Rhsim10G0153300' => 'rsi', 'Rhsim11G0012700' => 'rsi', 'Rhsim12G0031800' => 'rsi', 'Rhsim12G0055400' => 'rsi', 'Rhsim12G0091400' => 'rsi', 'Rhsim13G0070800' => 'rsi', 'Rhsim13G0193300' => 'rsi', 'RhsimUnG0111600' => 'rsi', 'RhsimUnG0137500' => 'rsi', 'RhsimUnG0172900' => 'rsi', 'SGA_v2.0_scaffold11G05878' => 'sas', 'SGA_v2.0_scaffold167G38458' => 'sas', 'SGA_v2.0_scaffold19G08588' => 'sas', 'SGA_v2.0_scaffold239G43990' => 'sas', 'SGA_v2.0_scaffold260G45865' => 'sas', 'SGA_v2.0_scaffold309G48177' => 'sas', 'SGA_v2.0_scaffold76G25122' => 'sas', 'SGA_v2.0_scaffold85G26708' => 'sas', 'SHI13914' => 'shi', 'SHI30402' => 'shi', 'TWI09G0020' => 'twi', 'TWI09G0456' => 'twi', 'TWI09G1572' => 'twi', 'TWI12G0266' => 'twi', 'TWI12G1451' => 'twi', 'TWI14G0851' => 'twi', 'TWI15G0796' => 'twi', 'TWI18G0820' => 'twi', 'TWI18G1152' => 'twi', 'TWI23G0007' => 'twi', 'TWI23G0314' => 'twi', 'TWI31G0674' => 'twi', 'TWI31G0938' => 'twi', 'TWI34G0641' => 'twi', 'TWI34G1527' => 'twi', 'TWI36G0193' => 'twi', 'TWI36G0405' => 'twi', 'TWI38G0892' => 'twi', 'TWI38G0936' => 'twi', 'TWI38G2218' => 'twi', 'TWI53G0679' => 'twi', 'TWI53G0863' => 'twi', 'TWI53G1133' => 'twi', 'TWI60G0823' => 'twi', 'TWI63G0919' => 'twi', 'TWI63G1436' => 'twi', 'TWI73G0140' => 'twi', 'TWI73G0419' => 'twi', 'TWI73G0420' => 'twi', 'TWI73G1276' => 'twi', 'TWI74G0405' => 'twi', 'TWI74G0837' => 'twi', 'TWI75G0594' => 'twi', 'TWI75G1615' => 'twi', 'TWI77G0816' => 'twi', 'vmacro03831' => 'vma', 'vmacro13746' => 'vma', 'vmacro16089' => 'vma', 'vmacro22863' => 'vma', 'Zm00001eb085790' => 'zma', 'Zm00001eb114250' => 'zma', 'Zm00001eb138070' => 'zma', 'Zm00001eb167560' => 'zma', 'Zm00001eb199990' => 'zma', 'Zm00001eb368180' => 'zma', 'Zm00001eb382470' => 'zma' ) $gf_id = 'HOM05D001576' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001576' ) $data_identifier = 'HOM05D001576' $data_type = 'gf_id' $species_gene_counts = array( 'aox' => (int) 9, 'acertr' => (int) 3, 'cansat' => (int) 1, 'ccl' => (int) 4, 'cil' => (int) 145, 'camsi' => (int) 46, 'dca' => (int) 1, 'din' => (int) 1, 'fan' => (int) 12, 'fve' => (int) 9, 'gma' => (int) 5, 'han' => (int) 5, 'cav' => (int) 11, 'hma' => (int) 5, 'sun' => (int) 3, 'mdo' => (int) 3, 'mtr' => (int) 2, 'osa' => (int) 19, 'pgr' => (int) 1, 'ptr' => (int) 2, 'ppe' => (int) 6, 'qlo' => (int) 24, 'rch' => (int) 5, 'rsi' => (int) 28, 'sas' => (int) 8, 'shi' => (int) 2, 'twi' => (int) 35, 'vma' => (int) 4, 'zma' => (int) 7 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb382470' $species_info = array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ) $local_species = 'osa' $disabled = '' $selected = '' $num_hits = (int) 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' => 'HOM05D001576', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '406', 'num_species' => '29' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'Aqoxy1G01456' => 'aox', 'Aqoxy1G02949' => 'aox', 'Aqoxy3G01274' => 'aox', 'Aqoxy3G02110' => 'aox', 'Aqoxy3G02268' => 'aox', 'Aqoxy5G02702' => 'aox', 'Aqoxy5G02988' => 'aox', 'Aqoxy5G03427' => 'aox', 'Aqoxy6G02363' => 'aox', 'Atru.chr1.3225' => 'acertr', 'Atru.chr8.1198' => 'acertr', 'Atru.chr9.790' => 'acertr', 'CANSAT01G3197' => 'cansat', 'Ciclev10003979m.g' => 'ccl', 'Ciclev10017471m.g' => 'ccl', 'Ciclev10018206m.g' => 'ccl', 'Ciclev10033751m.g' => 'ccl', 'CiPaw.01G000900' => 'cil', 'CiPaw.01G001000' => 'cil', 'CiPaw.01G033500' => 'cil', 'CiPaw.01G060300' => 'cil', 'CiPaw.01G070200' => 'cil', 'CiPaw.01G075100' => 'cil', 'CiPaw.01G084700' => 'cil', 'CiPaw.01G087900' => 'cil', 'CiPaw.01G092600' => 'cil', 'CiPaw.01G097200' => 'cil', 'CiPaw.01G098300' => 'cil', 'CiPaw.01G110200' => 'cil', 'CiPaw.01G118700' => 'cil', 'CiPaw.01G121200' => 'cil', 'CiPaw.01G132500' => 'cil', 'CiPaw.01G146900' => 'cil', 'CiPaw.01G174000' => 'cil', 'CiPaw.01G179900' => 'cil', 'CiPaw.01G183400' => 'cil', 'CiPaw.01G240000' => 'cil', 'CiPaw.01G283500' => 'cil', 'CiPaw.01G307400' => 'cil', 'CiPaw.02G030800' => 'cil', 'CiPaw.02G047200' => 'cil', 'CiPaw.02G050500' => 'cil', 'CiPaw.02G069900' => 'cil', 'CiPaw.02G091600' => 'cil', 'CiPaw.02G095000' => 'cil', 'CiPaw.02G131900' => 'cil', 'CiPaw.03G043000' => 'cil', 'CiPaw.03G069900' => 'cil', 'CiPaw.03G088100' => 'cil', 'CiPaw.03G089300' => 'cil', 'CiPaw.03G093100' => 'cil', 'CiPaw.03G129800' => 'cil', 'CiPaw.03G131200' => 'cil', 'CiPaw.03G134500' => 'cil', 'CiPaw.03G152100' => 'cil', 'CiPaw.03G162700' => 'cil', 'CiPaw.03G172800' => 'cil', 'CiPaw.03G175800' => 'cil', 'CiPaw.03G181800' => 'cil', 'CiPaw.03G191400' => 'cil', 'CiPaw.03G198300' => 'cil', 'CiPaw.03G201300' => 'cil', 'CiPaw.03G224700' => 'cil', 'CiPaw.03G225000' => 'cil', 'CiPaw.04G065100' => 'cil', 'CiPaw.04G080400' => 'cil', 'CiPaw.04G113500' => 'cil', 'CiPaw.04G121900' => 'cil', 'CiPaw.04G144100' => 'cil', 'CiPaw.04G176500' => 'cil', 'CiPaw.05G086200' => 'cil', 'CiPaw.05G100200' => 'cil', 'CiPaw.05G114200' => 'cil', 'CiPaw.05G126800' => 'cil', 'CiPaw.05G228800' => 'cil', 'CiPaw.05G230600' => 'cil', 'CiPaw.05G236500' => 'cil', 'CiPaw.05G244800' => 'cil', 'CiPaw.06G026600' => 'cil', 'CiPaw.06G027900' => 'cil', 'CiPaw.06G051800' => 'cil', 'CiPaw.06G128500' => 'cil', 'CiPaw.06G165900' => 'cil', 'CiPaw.07G045400' => 'cil', 'CiPaw.07G048000' => 'cil', 'CiPaw.07G052000' => 'cil', 'CiPaw.07G073800' => 'cil', 'CiPaw.07G099700' => 'cil', 'CiPaw.07G108700' => 'cil', 'CiPaw.07G120000' => 'cil', 'CiPaw.07G134100' => 'cil', 'CiPaw.07G147000' => 'cil', 'CiPaw.07G149700' => 'cil', 'CiPaw.07G178300' => 'cil', 'CiPaw.07G184900' => 'cil', 'CiPaw.08G044500' => 'cil', 'CiPaw.08G046900' => 'cil', 'CiPaw.08G047300' => 'cil', 'CiPaw.08G115400' => 'cil', 'CiPaw.08G134700' => 'cil', 'CiPaw.08G157400' => 'cil', 'CiPaw.09G014300' => 'cil', 'CiPaw.09G088900' => 'cil', 'CiPaw.09G130900' => 'cil', 'CiPaw.09G133100' => 'cil', 'CiPaw.09G151300' => 'cil', 'CiPaw.09G172800' => 'cil', 'CiPaw.09G174900' => 'cil', 'CiPaw.09G175000' => 'cil', 'CiPaw.10G012800' => 'cil', 'CiPaw.10G028800' => 'cil', 'CiPaw.10G044700' => 'cil', 'CiPaw.10G067400' => 'cil', 'CiPaw.10G115900' => 'cil', 'CiPaw.10G126200' => 'cil', 'CiPaw.10G139700' => 'cil', 'CiPaw.10G155100' => 'cil', 'CiPaw.11G011300' => 'cil', 'CiPaw.11G025900' => 'cil', 'CiPaw.11G104100' => 'cil', 'CiPaw.11G142700' => 'cil', 'CiPaw.11G164500' => 'cil', 'CiPaw.11G189100' => 'cil', 'CiPaw.11G197100' => 'cil', 'CiPaw.12G006100' => 'cil', 'CiPaw.12G038500' => 'cil', 'CiPaw.12G041400' => 'cil', 'CiPaw.12G041600' => 'cil', 'CiPaw.12G051300' => 'cil', 'CiPaw.12G101800' => 'cil', 'CiPaw.12G107800' => 'cil', 'CiPaw.13G033200' => 'cil', 'CiPaw.13G129900' => 'cil', 'CiPaw.13G160200' => 'cil', 'CiPaw.14G018900' => 'cil', 'CiPaw.14G029000' => 'cil', 'CiPaw.14G031000' => 'cil', 'CiPaw.14G032000' => 'cil', 'CiPaw.14G032300' => 'cil', 'CiPaw.14G040600' => 'cil', 'CiPaw.14G060500' => 'cil', 'CiPaw.14G061500' => 'cil', 'CiPaw.14G077500' => 'cil', 'CiPaw.14G088300' => 'cil', 'CiPaw.14G108500' => 'cil', 'CiPaw.14G121300' => 'cil', 'CiPaw.14G133000' => 'cil', 'CiPaw.14G134600' => 'cil', 'CiPaw.15G027200' => 'cil', 'CiPaw.15G037700' => 'cil', 'CiPaw.15G050900' => 'cil', 'CiPaw.15G067200' => 'cil', 'CiPaw.15G072000' => 'cil', 'CiPaw.15G112900' => 'cil', 'CiPaw.15G133200' => 'cil', 'CiPaw.15G139500' => 'cil', 'CiPaw.15G155400' => 'cil', 'CiPaw.16G006000' => 'cil', 'CiPaw.16G013100' => 'cil', 'CiPaw.16G047100' => 'cil', 'CiPaw.16G048900' => 'cil', 'CiPaw.16G070300' => 'cil', 'CSS0000195' => 'camsi', 'CSS0001664' => 'camsi', 'CSS0002566' => 'camsi', 'CSS0003077' => 'camsi', 'CSS0004257' => 'camsi', 'CSS0004495' => 'camsi', 'CSS0004599' => 'camsi', 'CSS0004943' => 'camsi', 'CSS0005302' => 'camsi', 'CSS0006274' => 'camsi', 'CSS0006547' => 'camsi', 'CSS0006860' => 'camsi', 'CSS0008814' => 'camsi', 'CSS0008946' => 'camsi', 'CSS0009093' => 'camsi', 'CSS0010221' => 'camsi', 'CSS0010296' => 'camsi', 'CSS0010386' => 'camsi', 'CSS0010831' => 'camsi', 'CSS0011061' => 'camsi', 'CSS0012008' => 'camsi', 'CSS0012194' => 'camsi', 'CSS0013580' => 'camsi', 'CSS0014176' => 'camsi', 'CSS0014280' => 'camsi', 'CSS0014799' => 'camsi', 'CSS0015368' => 'camsi', 'CSS0017473' => 'camsi', 'CSS0019281' => 'camsi', 'CSS0021320' => 'camsi', 'CSS0021750' => 'camsi', 'CSS0023642' => 'camsi', 'CSS0023792' => 'camsi', 'CSS0031528' => 'camsi', 'CSS0033894' => 'camsi', 'CSS0034959' => 'camsi', 'CSS0035632' => 'camsi', 'CSS0038450' => 'camsi', 'CSS0039293' => 'camsi', 'CSS0041053' => 'camsi', 'CSS0041981' => 'camsi', 'CSS0042573' => 'camsi', 'CSS0042927' => 'camsi', 'CSS0047725' => 'camsi', 'CSS0049636' => 'camsi', 'CSS0050513' => 'camsi', 'DCAR_030203' => 'dca', 'Dinv07939' => 'din', 'FAN01G0456' => 'fan', 'FAN02G3001' => 'fan', 'FAN04G2781' => 'fan', 'FAN05G1385' => 'fan', 'FAN05G3062' => 'fan', 'FAN08G2267' => 'fan', 'FAN10G0481' => 'fan', 'FAN10G1257' => 'fan', 'FAN14G0954' => 'fan', 'FAN14G2347' => 'fan', 'FAN15G0187' => 'fan', 'FAN25G2214' => 'fan', 'FvH4_1g21031' => 'fve', 'FvH4_3g16231' => 'fve', 'FvH4_3g26413' => 'fve', 'FvH4_3g29014' => 'fve', 'FvH4_3g31921' => 'fve', 'FvH4_4g19882' => 'fve', 'FvH4_5g21960' => 'fve', 'FvH4_5g29683' => 'fve', 'FvH4_7g13271' => 'fve', 'Glyma.01G062500' => 'gma', 'Glyma.07G140900' => 'gma', 'Glyma.09G140900' => 'gma', 'Glyma.12G112700' => 'gma', 'Glyma.17G168800' => 'gma', 'HanXRQChr01g0027001' => 'han', 'HanXRQChr04g0120511' => 'han', 'HanXRQChr08g0232381' => 'han', 'HanXRQChr09g0265661' => 'han', 'HanXRQChr13g0416031' => 'han', 'Haze_05835' => 'cav', 'Haze_06597' => 'cav', 'Haze_07921' => 'cav', 'Haze_08599' => 'cav', 'Haze_10686' => 'cav', 'Haze_12994' => 'cav', 'Haze_13466' => 'cav', 'Haze_16101' => 'cav', 'Haze_17766' => 'cav', 'Haze_18456' => 'cav', 'Haze_20229' => 'cav', 'Hma1.2p1_0324F.1_g125640' => 'hma', 'Hma1.2p1_0733F.1_g210230' => 'hma', 'Hma1.2p1_0921F.1_g236870' => 'hma', 'Hma1.2p1_1313F.1_g274940' => 'hma', 'Hma1.2p1_3059F.1_g332230' => 'hma', 'Hund15925' => 'sun', 'Hund19562' => 'sun', 'Hund21925' => 'sun', 'MD03G1177400' => 'mdo', 'MD07G1026100' => 'mdo', 'MD17G1218600' => 'mdo', 'Medtr0867s0010' => 'mtr', 'Medtr6g081150' => 'mtr', 'Os01g0527900' => 'osa', 'Os02g0463725' => 'osa', 'Os02g0785600' => 'osa', 'Os03g0433733' => 'osa', 'Os04g0286500' => 'osa', 'Os05g0227800' => 'osa', 'Os06g0521000' => 'osa', 'Os06g0635500' => 'osa', 'Os06g0660650' => 'osa', 'Os07g0554400' => 'osa', 'Os08g0225900' => 'osa', 'Os08g0561000' => 'osa', 'Os09g0241700' => 'osa', 'Os09g0351900' => 'osa', 'Os11g0220700' => 'osa', 'Os11g0282700' => 'osa', 'Os12g0169300' => 'osa', 'Os12g0228500' => 'osa', 'Os12g0543800' => 'osa', 'PGR044G1547' => 'pgr', 'Potri.005G239150' => 'ptr', 'Potri.010G014250' => 'ptr', 'Prupe.1G172500' => 'ppe', 'Prupe.1G196800' => 'ppe', 'Prupe.1G279700' => 'ppe', 'Prupe.2G026400' => 'ppe', 'Prupe.3G094000' => 'ppe', 'Prupe.4G287300' => 'ppe', 'QL01p022166' => 'qlo', 'QL01p051890' => 'qlo', 'QL02p009469' => 'qlo', 'QL02p046053' => 'qlo', 'QL02p057958' => 'qlo', 'QL02p093127' => 'qlo', 'QL03p006855' => 'qlo', 'QL03p071586' => 'qlo', 'QL04p000022' => 'qlo', 'QL04p000024' => 'qlo', 'QL04p003192' => 'qlo', 'QL05p011416' => 'qlo', 'QL06p039590' => 'qlo', 'QL06p052750' => 'qlo', 'QL06p053821' => 'qlo', 'QL07p025287' => 'qlo', 'QL09p033218' => 'qlo', 'QL09p040841' => 'qlo', 'QL10p020337' => 'qlo', 'QL10p027209' => 'qlo', 'QL10p027969' => 'qlo', 'QL10p048988' => 'qlo', 'QL11p001241' => 'qlo', 'QL11p028487' => 'qlo', 'RcHm_v2.0_Chr2g0105031' => 'rch', 'RcHm_v2.0_Chr2g0117811' => 'rch', 'RcHm_v2.0_Chr6g0270241' => 'rch', 'RcHm_v2.0_Chr7g0215961' => 'rch', 'RcHm_v2.0_Chr7g0231991' => 'rch', 'Rhsim01G0041500' => 'rsi', 'Rhsim01G0115000' => 'rsi', 'Rhsim01G0115400' => 'rsi', 'Rhsim01G0133600' => 'rsi', 'Rhsim01G0159900' => 'rsi', 'Rhsim02G0189400' => 'rsi', 'Rhsim03G0135600' => 'rsi', 'Rhsim03G0149900' => 'rsi', 'Rhsim04G0125600' => 'rsi', 'Rhsim05G0091700' => 'rsi', 'Rhsim05G0092900' => 'rsi', 'Rhsim06G0075000' => 'rsi', 'Rhsim07G0066400' => 'rsi', 'Rhsim07G0156400' => 'rsi', 'Rhsim07G0182200' => 'rsi', 'Rhsim07G0182300' => 'rsi', 'Rhsim08G0180400' => 'rsi', 'Rhsim09G0056800' => 'rsi', 'Rhsim10G0153300' => 'rsi', 'Rhsim11G0012700' => 'rsi', 'Rhsim12G0031800' => 'rsi', 'Rhsim12G0055400' => 'rsi', 'Rhsim12G0091400' => 'rsi', 'Rhsim13G0070800' => 'rsi', 'Rhsim13G0193300' => 'rsi', 'RhsimUnG0111600' => 'rsi', 'RhsimUnG0137500' => 'rsi', 'RhsimUnG0172900' => 'rsi', 'SGA_v2.0_scaffold11G05878' => 'sas', 'SGA_v2.0_scaffold167G38458' => 'sas', 'SGA_v2.0_scaffold19G08588' => 'sas', 'SGA_v2.0_scaffold239G43990' => 'sas', 'SGA_v2.0_scaffold260G45865' => 'sas', 'SGA_v2.0_scaffold309G48177' => 'sas', 'SGA_v2.0_scaffold76G25122' => 'sas', 'SGA_v2.0_scaffold85G26708' => 'sas', 'SHI13914' => 'shi', 'SHI30402' => 'shi', 'TWI09G0020' => 'twi', 'TWI09G0456' => 'twi', 'TWI09G1572' => 'twi', 'TWI12G0266' => 'twi', 'TWI12G1451' => 'twi', 'TWI14G0851' => 'twi', 'TWI15G0796' => 'twi', 'TWI18G0820' => 'twi', 'TWI18G1152' => 'twi', 'TWI23G0007' => 'twi', 'TWI23G0314' => 'twi', 'TWI31G0674' => 'twi', 'TWI31G0938' => 'twi', 'TWI34G0641' => 'twi', 'TWI34G1527' => 'twi', 'TWI36G0193' => 'twi', 'TWI36G0405' => 'twi', 'TWI38G0892' => 'twi', 'TWI38G0936' => 'twi', 'TWI38G2218' => 'twi', 'TWI53G0679' => 'twi', 'TWI53G0863' => 'twi', 'TWI53G1133' => 'twi', 'TWI60G0823' => 'twi', 'TWI63G0919' => 'twi', 'TWI63G1436' => 'twi', 'TWI73G0140' => 'twi', 'TWI73G0419' => 'twi', 'TWI73G0420' => 'twi', 'TWI73G1276' => 'twi', 'TWI74G0405' => 'twi', 'TWI74G0837' => 'twi', 'TWI75G0594' => 'twi', 'TWI75G1615' => 'twi', 'TWI77G0816' => 'twi', 'vmacro03831' => 'vma', 'vmacro13746' => 'vma', 'vmacro16089' => 'vma', 'vmacro22863' => 'vma', 'Zm00001eb085790' => 'zma', 'Zm00001eb114250' => 'zma', 'Zm00001eb138070' => 'zma', 'Zm00001eb167560' => 'zma', 'Zm00001eb199990' => 'zma', 'Zm00001eb368180' => 'zma', 'Zm00001eb382470' => 'zma' ), 'gf_id' => 'HOM05D001576', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001576' ), 'data_identifier' => 'HOM05D001576', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001576', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '406', 'num_species' => '29' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'Aqoxy1G01456' => 'aox', 'Aqoxy1G02949' => 'aox', 'Aqoxy3G01274' => 'aox', 'Aqoxy3G02110' => 'aox', 'Aqoxy3G02268' => 'aox', 'Aqoxy5G02702' => 'aox', 'Aqoxy5G02988' => 'aox', 'Aqoxy5G03427' => 'aox', 'Aqoxy6G02363' => 'aox', 'Atru.chr1.3225' => 'acertr', 'Atru.chr8.1198' => 'acertr', 'Atru.chr9.790' => 'acertr', 'CANSAT01G3197' => 'cansat', 'Ciclev10003979m.g' => 'ccl', 'Ciclev10017471m.g' => 'ccl', 'Ciclev10018206m.g' => 'ccl', 'Ciclev10033751m.g' => 'ccl', 'CiPaw.01G000900' => 'cil', 'CiPaw.01G001000' => 'cil', 'CiPaw.01G033500' => 'cil', 'CiPaw.01G060300' => 'cil', 'CiPaw.01G070200' => 'cil', 'CiPaw.01G075100' => 'cil', 'CiPaw.01G084700' => 'cil', 'CiPaw.01G087900' => 'cil', 'CiPaw.01G092600' => 'cil', 'CiPaw.01G097200' => 'cil', 'CiPaw.01G098300' => 'cil', 'CiPaw.01G110200' => 'cil', 'CiPaw.01G118700' => 'cil', 'CiPaw.01G121200' => 'cil', 'CiPaw.01G132500' => 'cil', 'CiPaw.01G146900' => 'cil', 'CiPaw.01G174000' => 'cil', 'CiPaw.01G179900' => 'cil', 'CiPaw.01G183400' => 'cil', 'CiPaw.01G240000' => 'cil', 'CiPaw.01G283500' => 'cil', 'CiPaw.01G307400' => 'cil', 'CiPaw.02G030800' => 'cil', 'CiPaw.02G047200' => 'cil', 'CiPaw.02G050500' => 'cil', 'CiPaw.02G069900' => 'cil', 'CiPaw.02G091600' => 'cil', 'CiPaw.02G095000' => 'cil', 'CiPaw.02G131900' => 'cil', 'CiPaw.03G043000' => 'cil', 'CiPaw.03G069900' => 'cil', 'CiPaw.03G088100' => 'cil', 'CiPaw.03G089300' => 'cil', 'CiPaw.03G093100' => 'cil', 'CiPaw.03G129800' => 'cil', 'CiPaw.03G131200' => 'cil', 'CiPaw.03G134500' => 'cil', 'CiPaw.03G152100' => 'cil', 'CiPaw.03G162700' => 'cil', 'CiPaw.03G172800' => 'cil', 'CiPaw.03G175800' => 'cil', 'CiPaw.03G181800' => 'cil', 'CiPaw.03G191400' => 'cil', 'CiPaw.03G198300' => 'cil', 'CiPaw.03G201300' => 'cil', 'CiPaw.03G224700' => 'cil', 'CiPaw.03G225000' => 'cil', 'CiPaw.04G065100' => 'cil', 'CiPaw.04G080400' => 'cil', 'CiPaw.04G113500' => 'cil', 'CiPaw.04G121900' => 'cil', 'CiPaw.04G144100' => 'cil', 'CiPaw.04G176500' => 'cil', 'CiPaw.05G086200' => 'cil', 'CiPaw.05G100200' => 'cil', 'CiPaw.05G114200' => 'cil', 'CiPaw.05G126800' => 'cil', 'CiPaw.05G228800' => 'cil', 'CiPaw.05G230600' => 'cil', 'CiPaw.05G236500' => 'cil', 'CiPaw.05G244800' => 'cil', 'CiPaw.06G026600' => 'cil', 'CiPaw.06G027900' => 'cil', 'CiPaw.06G051800' => 'cil', 'CiPaw.06G128500' => 'cil', 'CiPaw.06G165900' => 'cil', 'CiPaw.07G045400' => 'cil', 'CiPaw.07G048000' => 'cil', 'CiPaw.07G052000' => 'cil', 'CiPaw.07G073800' => 'cil', 'CiPaw.07G099700' => 'cil', 'CiPaw.07G108700' => 'cil', 'CiPaw.07G120000' => 'cil', 'CiPaw.07G134100' => 'cil', 'CiPaw.07G147000' => 'cil', 'CiPaw.07G149700' => 'cil', 'CiPaw.07G178300' => 'cil', 'CiPaw.07G184900' => 'cil', 'CiPaw.08G044500' => 'cil', 'CiPaw.08G046900' => 'cil', 'CiPaw.08G047300' => 'cil', 'CiPaw.08G115400' => 'cil', 'CiPaw.08G134700' => 'cil', 'CiPaw.08G157400' => 'cil', 'CiPaw.09G014300' => 'cil', 'CiPaw.09G088900' => 'cil', 'CiPaw.09G130900' => 'cil', 'CiPaw.09G133100' => 'cil', 'CiPaw.09G151300' => 'cil', 'CiPaw.09G172800' => 'cil', 'CiPaw.09G174900' => 'cil', 'CiPaw.09G175000' => 'cil', 'CiPaw.10G012800' => 'cil', 'CiPaw.10G028800' => 'cil', 'CiPaw.10G044700' => 'cil', 'CiPaw.10G067400' => 'cil', 'CiPaw.10G115900' => 'cil', 'CiPaw.10G126200' => 'cil', 'CiPaw.10G139700' => 'cil', 'CiPaw.10G155100' => 'cil', 'CiPaw.11G011300' => 'cil', 'CiPaw.11G025900' => 'cil', 'CiPaw.11G104100' => 'cil', 'CiPaw.11G142700' => 'cil', 'CiPaw.11G164500' => 'cil', 'CiPaw.11G189100' => 'cil', 'CiPaw.11G197100' => 'cil', 'CiPaw.12G006100' => 'cil', 'CiPaw.12G038500' => 'cil', 'CiPaw.12G041400' => 'cil', 'CiPaw.12G041600' => 'cil', 'CiPaw.12G051300' => 'cil', 'CiPaw.12G101800' => 'cil', 'CiPaw.12G107800' => 'cil', 'CiPaw.13G033200' => 'cil', 'CiPaw.13G129900' => 'cil', 'CiPaw.13G160200' => 'cil', 'CiPaw.14G018900' => 'cil', 'CiPaw.14G029000' => 'cil', 'CiPaw.14G031000' => 'cil', 'CiPaw.14G032000' => 'cil', 'CiPaw.14G032300' => 'cil', 'CiPaw.14G040600' => 'cil', 'CiPaw.14G060500' => 'cil', 'CiPaw.14G061500' => 'cil', 'CiPaw.14G077500' => 'cil', 'CiPaw.14G088300' => 'cil', 'CiPaw.14G108500' => 'cil', 'CiPaw.14G121300' => 'cil', 'CiPaw.14G133000' => 'cil', 'CiPaw.14G134600' => 'cil', 'CiPaw.15G027200' => 'cil', 'CiPaw.15G037700' => 'cil', 'CiPaw.15G050900' => 'cil', 'CiPaw.15G067200' => 'cil', 'CiPaw.15G072000' => 'cil', 'CiPaw.15G112900' => 'cil', 'CiPaw.15G133200' => 'cil', 'CiPaw.15G139500' => 'cil', 'CiPaw.15G155400' => 'cil', 'CiPaw.16G006000' => 'cil', 'CiPaw.16G013100' => 'cil', 'CiPaw.16G047100' => 'cil', 'CiPaw.16G048900' => 'cil', 'CiPaw.16G070300' => 'cil', 'CSS0000195' => 'camsi', 'CSS0001664' => 'camsi', 'CSS0002566' => 'camsi', 'CSS0003077' => 'camsi', 'CSS0004257' => 'camsi', 'CSS0004495' => 'camsi', 'CSS0004599' => 'camsi', 'CSS0004943' => 'camsi', 'CSS0005302' => 'camsi', 'CSS0006274' => 'camsi', 'CSS0006547' => 'camsi', 'CSS0006860' => 'camsi', 'CSS0008814' => 'camsi', 'CSS0008946' => 'camsi', 'CSS0009093' => 'camsi', 'CSS0010221' => 'camsi', 'CSS0010296' => 'camsi', 'CSS0010386' => 'camsi', 'CSS0010831' => 'camsi', 'CSS0011061' => 'camsi', 'CSS0012008' => 'camsi', 'CSS0012194' => 'camsi', 'CSS0013580' => 'camsi', 'CSS0014176' => 'camsi', 'CSS0014280' => 'camsi', 'CSS0014799' => 'camsi', 'CSS0015368' => 'camsi', 'CSS0017473' => 'camsi', 'CSS0019281' => 'camsi', 'CSS0021320' => 'camsi', 'CSS0021750' => 'camsi', 'CSS0023642' => 'camsi', 'CSS0023792' => 'camsi', 'CSS0031528' => 'camsi', 'CSS0033894' => 'camsi', 'CSS0034959' => 'camsi', 'CSS0035632' => 'camsi', 'CSS0038450' => 'camsi', 'CSS0039293' => 'camsi', 'CSS0041053' => 'camsi', 'CSS0041981' => 'camsi', 'CSS0042573' => 'camsi', 'CSS0042927' => 'camsi', 'CSS0047725' => 'camsi', 'CSS0049636' => 'camsi', 'CSS0050513' => 'camsi', 'DCAR_030203' => 'dca', 'Dinv07939' => 'din', 'FAN01G0456' => 'fan', 'FAN02G3001' => 'fan', 'FAN04G2781' => 'fan', 'FAN05G1385' => 'fan', 'FAN05G3062' => 'fan', 'FAN08G2267' => 'fan', 'FAN10G0481' => 'fan', 'FAN10G1257' => 'fan', 'FAN14G0954' => 'fan', 'FAN14G2347' => 'fan', 'FAN15G0187' => 'fan', 'FAN25G2214' => 'fan', 'FvH4_1g21031' => 'fve', 'FvH4_3g16231' => 'fve', 'FvH4_3g26413' => 'fve', 'FvH4_3g29014' => 'fve', 'FvH4_3g31921' => 'fve', 'FvH4_4g19882' => 'fve', 'FvH4_5g21960' => 'fve', 'FvH4_5g29683' => 'fve', 'FvH4_7g13271' => 'fve', 'Glyma.01G062500' => 'gma', 'Glyma.07G140900' => 'gma', 'Glyma.09G140900' => 'gma', 'Glyma.12G112700' => 'gma', 'Glyma.17G168800' => 'gma', 'HanXRQChr01g0027001' => 'han', 'HanXRQChr04g0120511' => 'han', 'HanXRQChr08g0232381' => 'han', 'HanXRQChr09g0265661' => 'han', 'HanXRQChr13g0416031' => 'han', 'Haze_05835' => 'cav', 'Haze_06597' => 'cav', 'Haze_07921' => 'cav', 'Haze_08599' => 'cav', 'Haze_10686' => 'cav', 'Haze_12994' => 'cav', 'Haze_13466' => 'cav', 'Haze_16101' => 'cav', 'Haze_17766' => 'cav', 'Haze_18456' => 'cav', 'Haze_20229' => 'cav', 'Hma1.2p1_0324F.1_g125640' => 'hma', 'Hma1.2p1_0733F.1_g210230' => 'hma', 'Hma1.2p1_0921F.1_g236870' => 'hma', 'Hma1.2p1_1313F.1_g274940' => 'hma', 'Hma1.2p1_3059F.1_g332230' => 'hma', 'Hund15925' => 'sun', 'Hund19562' => 'sun', 'Hund21925' => 'sun', 'MD03G1177400' => 'mdo', 'MD07G1026100' => 'mdo', 'MD17G1218600' => 'mdo', 'Medtr0867s0010' => 'mtr', 'Medtr6g081150' => 'mtr', 'Os01g0527900' => 'osa', 'Os02g0463725' => 'osa', 'Os02g0785600' => 'osa', 'Os03g0433733' => 'osa', 'Os04g0286500' => 'osa', 'Os05g0227800' => 'osa', 'Os06g0521000' => 'osa', 'Os06g0635500' => 'osa', 'Os06g0660650' => 'osa', 'Os07g0554400' => 'osa', 'Os08g0225900' => 'osa', 'Os08g0561000' => 'osa', 'Os09g0241700' => 'osa', 'Os09g0351900' => 'osa', 'Os11g0220700' => 'osa', 'Os11g0282700' => 'osa', 'Os12g0169300' => 'osa', 'Os12g0228500' => 'osa', 'Os12g0543800' => 'osa', 'PGR044G1547' => 'pgr', 'Potri.005G239150' => 'ptr', 'Potri.010G014250' => 'ptr', 'Prupe.1G172500' => 'ppe', 'Prupe.1G196800' => 'ppe', 'Prupe.1G279700' => 'ppe', 'Prupe.2G026400' => 'ppe', 'Prupe.3G094000' => 'ppe', 'Prupe.4G287300' => 'ppe', 'QL01p022166' => 'qlo', 'QL01p051890' => 'qlo', 'QL02p009469' => 'qlo', 'QL02p046053' => 'qlo', 'QL02p057958' => 'qlo', 'QL02p093127' => 'qlo', 'QL03p006855' => 'qlo', 'QL03p071586' => 'qlo', 'QL04p000022' => 'qlo', 'QL04p000024' => 'qlo', 'QL04p003192' => 'qlo', 'QL05p011416' => 'qlo', 'QL06p039590' => 'qlo', 'QL06p052750' => 'qlo', 'QL06p053821' => 'qlo', 'QL07p025287' => 'qlo', 'QL09p033218' => 'qlo', 'QL09p040841' => 'qlo', 'QL10p020337' => 'qlo', 'QL10p027209' => 'qlo', 'QL10p027969' => 'qlo', 'QL10p048988' => 'qlo', 'QL11p001241' => 'qlo', 'QL11p028487' => 'qlo', 'RcHm_v2.0_Chr2g0105031' => 'rch', 'RcHm_v2.0_Chr2g0117811' => 'rch', 'RcHm_v2.0_Chr6g0270241' => 'rch', 'RcHm_v2.0_Chr7g0215961' => 'rch', 'RcHm_v2.0_Chr7g0231991' => 'rch', 'Rhsim01G0041500' => 'rsi', 'Rhsim01G0115000' => 'rsi', 'Rhsim01G0115400' => 'rsi', 'Rhsim01G0133600' => 'rsi', 'Rhsim01G0159900' => 'rsi', 'Rhsim02G0189400' => 'rsi', 'Rhsim03G0135600' => 'rsi', 'Rhsim03G0149900' => 'rsi', 'Rhsim04G0125600' => 'rsi', 'Rhsim05G0091700' => 'rsi', 'Rhsim05G0092900' => 'rsi', 'Rhsim06G0075000' => 'rsi', 'Rhsim07G0066400' => 'rsi', 'Rhsim07G0156400' => 'rsi', 'Rhsim07G0182200' => 'rsi', 'Rhsim07G0182300' => 'rsi', 'Rhsim08G0180400' => 'rsi', 'Rhsim09G0056800' => 'rsi', 'Rhsim10G0153300' => 'rsi', 'Rhsim11G0012700' => 'rsi', 'Rhsim12G0031800' => 'rsi', 'Rhsim12G0055400' => 'rsi', 'Rhsim12G0091400' => 'rsi', 'Rhsim13G0070800' => 'rsi', 'Rhsim13G0193300' => 'rsi', 'RhsimUnG0111600' => 'rsi', 'RhsimUnG0137500' => 'rsi', 'RhsimUnG0172900' => 'rsi', 'SGA_v2.0_scaffold11G05878' => 'sas', 'SGA_v2.0_scaffold167G38458' => 'sas', 'SGA_v2.0_scaffold19G08588' => 'sas', 'SGA_v2.0_scaffold239G43990' => 'sas', 'SGA_v2.0_scaffold260G45865' => 'sas', 'SGA_v2.0_scaffold309G48177' => 'sas', 'SGA_v2.0_scaffold76G25122' => 'sas', 'SGA_v2.0_scaffold85G26708' => 'sas', 'SHI13914' => 'shi', 'SHI30402' => 'shi', 'TWI09G0020' => 'twi', 'TWI09G0456' => 'twi', 'TWI09G1572' => 'twi', 'TWI12G0266' => 'twi', 'TWI12G1451' => 'twi', 'TWI14G0851' => 'twi', 'TWI15G0796' => 'twi', 'TWI18G0820' => 'twi', 'TWI18G1152' => 'twi', 'TWI23G0007' => 'twi', 'TWI23G0314' => 'twi', 'TWI31G0674' => 'twi', 'TWI31G0938' => 'twi', 'TWI34G0641' => 'twi', 'TWI34G1527' => 'twi', 'TWI36G0193' => 'twi', 'TWI36G0405' => 'twi', 'TWI38G0892' => 'twi', 'TWI38G0936' => 'twi', 'TWI38G2218' => 'twi', 'TWI53G0679' => 'twi', 'TWI53G0863' => 'twi', 'TWI53G1133' => 'twi', 'TWI60G0823' => 'twi', 'TWI63G0919' => 'twi', 'TWI63G1436' => 'twi', 'TWI73G0140' => 'twi', 'TWI73G0419' => 'twi', 'TWI73G0420' => 'twi', 'TWI73G1276' => 'twi', 'TWI74G0405' => 'twi', 'TWI74G0837' => 'twi', 'TWI75G0594' => 'twi', 'TWI75G1615' => 'twi', 'TWI77G0816' => 'twi', 'vmacro03831' => 'vma', 'vmacro13746' => 'vma', 'vmacro16089' => 'vma', 'vmacro22863' => 'vma', 'Zm00001eb085790' => 'zma', 'Zm00001eb114250' => 'zma', 'Zm00001eb138070' => 'zma', 'Zm00001eb167560' => 'zma', 'Zm00001eb199990' => 'zma', 'Zm00001eb368180' => 'zma', 'Zm00001eb382470' => 'zma' ) $gf_id = 'HOM05D001576' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001576' ) $data_identifier = 'HOM05D001576' $data_type = 'gf_id' $species_gene_counts = array( 'aox' => (int) 9, 'acertr' => (int) 3, 'cansat' => (int) 1, 'ccl' => (int) 4, 'cil' => (int) 145, 'camsi' => (int) 46, 'dca' => (int) 1, 'din' => (int) 1, 'fan' => (int) 12, 'fve' => (int) 9, 'gma' => (int) 5, 'han' => (int) 5, 'cav' => (int) 11, 'hma' => (int) 5, 'sun' => (int) 3, 'mdo' => (int) 3, 'mtr' => (int) 2, 'osa' => (int) 19, 'pgr' => (int) 1, 'ptr' => (int) 2, 'ppe' => (int) 6, 'qlo' => (int) 24, 'rch' => (int) 5, 'rsi' => (int) 28, 'sas' => (int) 8, 'shi' => (int) 2, 'twi' => (int) 35, 'vma' => (int) 4, 'zma' => (int) 7 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb382470' $species_info = array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ) $local_species = 'ptr' $disabled = '' $selected = '' $num_hits = (int) 0include - APP/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp, line 33 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933 View::_renderElement() - CORE/Cake/View/View.php, line 1224 View::element() - CORE/Cake/View/View.php, line 418 include - APP/View/Elements/analysis/phylogenetics_module/gf_data_settings.ctp, line 37 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933 View::_renderElement() - CORE/Cake/View/View.php, line 1224 View::element() - CORE/Cake/View/View.php, line 418 include - APP/View/Elements/analysis/phylogenetics_module/parameter_selection.ctp, line 64 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933 View::_renderElement() - CORE/Cake/View/View.php, line 1224 View::element() - CORE/Cake/View/View.php, line 418 include - APP/View/Analysis/custom_tree_creation.ctp, line 27 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933
$viewFile = '/www/bioinformatics01_ro/plaza/_dev_instances/feedback/app/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp' $dataForView = array( 'sidebar_info' => array( 'gf_id' => 'HOM05D001576', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '406', 'num_species' => '29' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'Aqoxy1G01456' => 'aox', 'Aqoxy1G02949' => 'aox', 'Aqoxy3G01274' => 'aox', 'Aqoxy3G02110' => 'aox', 'Aqoxy3G02268' => 'aox', 'Aqoxy5G02702' => 'aox', 'Aqoxy5G02988' => 'aox', 'Aqoxy5G03427' => 'aox', 'Aqoxy6G02363' => 'aox', 'Atru.chr1.3225' => 'acertr', 'Atru.chr8.1198' => 'acertr', 'Atru.chr9.790' => 'acertr', 'CANSAT01G3197' => 'cansat', 'Ciclev10003979m.g' => 'ccl', 'Ciclev10017471m.g' => 'ccl', 'Ciclev10018206m.g' => 'ccl', 'Ciclev10033751m.g' => 'ccl', 'CiPaw.01G000900' => 'cil', 'CiPaw.01G001000' => 'cil', 'CiPaw.01G033500' => 'cil', 'CiPaw.01G060300' => 'cil', 'CiPaw.01G070200' => 'cil', 'CiPaw.01G075100' => 'cil', 'CiPaw.01G084700' => 'cil', 'CiPaw.01G087900' => 'cil', 'CiPaw.01G092600' => 'cil', 'CiPaw.01G097200' => 'cil', 'CiPaw.01G098300' => 'cil', 'CiPaw.01G110200' => 'cil', 'CiPaw.01G118700' => 'cil', 'CiPaw.01G121200' => 'cil', 'CiPaw.01G132500' => 'cil', 'CiPaw.01G146900' => 'cil', 'CiPaw.01G174000' => 'cil', 'CiPaw.01G179900' => 'cil', 'CiPaw.01G183400' => 'cil', 'CiPaw.01G240000' => 'cil', 'CiPaw.01G283500' => 'cil', 'CiPaw.01G307400' => 'cil', 'CiPaw.02G030800' => 'cil', 'CiPaw.02G047200' => 'cil', 'CiPaw.02G050500' => 'cil', 'CiPaw.02G069900' => 'cil', 'CiPaw.02G091600' => 'cil', 'CiPaw.02G095000' => 'cil', 'CiPaw.02G131900' => 'cil', 'CiPaw.03G043000' => 'cil', 'CiPaw.03G069900' => 'cil', 'CiPaw.03G088100' => 'cil', 'CiPaw.03G089300' => 'cil', 'CiPaw.03G093100' => 'cil', 'CiPaw.03G129800' => 'cil', 'CiPaw.03G131200' => 'cil', 'CiPaw.03G134500' => 'cil', 'CiPaw.03G152100' => 'cil', 'CiPaw.03G162700' => 'cil', 'CiPaw.03G172800' => 'cil', 'CiPaw.03G175800' => 'cil', 'CiPaw.03G181800' => 'cil', 'CiPaw.03G191400' => 'cil', 'CiPaw.03G198300' => 'cil', 'CiPaw.03G201300' => 'cil', 'CiPaw.03G224700' => 'cil', 'CiPaw.03G225000' => 'cil', 'CiPaw.04G065100' => 'cil', 'CiPaw.04G080400' => 'cil', 'CiPaw.04G113500' => 'cil', 'CiPaw.04G121900' => 'cil', 'CiPaw.04G144100' => 'cil', 'CiPaw.04G176500' => 'cil', 'CiPaw.05G086200' => 'cil', 'CiPaw.05G100200' => 'cil', 'CiPaw.05G114200' => 'cil', 'CiPaw.05G126800' => 'cil', 'CiPaw.05G228800' => 'cil', 'CiPaw.05G230600' => 'cil', 'CiPaw.05G236500' => 'cil', 'CiPaw.05G244800' => 'cil', 'CiPaw.06G026600' => 'cil', 'CiPaw.06G027900' => 'cil', 'CiPaw.06G051800' => 'cil', 'CiPaw.06G128500' => 'cil', 'CiPaw.06G165900' => 'cil', 'CiPaw.07G045400' => 'cil', 'CiPaw.07G048000' => 'cil', 'CiPaw.07G052000' => 'cil', 'CiPaw.07G073800' => 'cil', 'CiPaw.07G099700' => 'cil', 'CiPaw.07G108700' => 'cil', 'CiPaw.07G120000' => 'cil', 'CiPaw.07G134100' => 'cil', 'CiPaw.07G147000' => 'cil', 'CiPaw.07G149700' => 'cil', 'CiPaw.07G178300' => 'cil', 'CiPaw.07G184900' => 'cil', 'CiPaw.08G044500' => 'cil', 'CiPaw.08G046900' => 'cil', 'CiPaw.08G047300' => 'cil', 'CiPaw.08G115400' => 'cil', 'CiPaw.08G134700' => 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'TWI09G0020' => 'twi', 'TWI09G0456' => 'twi', 'TWI09G1572' => 'twi', 'TWI12G0266' => 'twi', 'TWI12G1451' => 'twi', 'TWI14G0851' => 'twi', 'TWI15G0796' => 'twi', 'TWI18G0820' => 'twi', 'TWI18G1152' => 'twi', 'TWI23G0007' => 'twi', 'TWI23G0314' => 'twi', 'TWI31G0674' => 'twi', 'TWI31G0938' => 'twi', 'TWI34G0641' => 'twi', 'TWI34G1527' => 'twi', 'TWI36G0193' => 'twi', 'TWI36G0405' => 'twi', 'TWI38G0892' => 'twi', 'TWI38G0936' => 'twi', 'TWI38G2218' => 'twi', 'TWI53G0679' => 'twi', 'TWI53G0863' => 'twi', 'TWI53G1133' => 'twi', 'TWI60G0823' => 'twi', 'TWI63G0919' => 'twi', 'TWI63G1436' => 'twi', 'TWI73G0140' => 'twi', 'TWI73G0419' => 'twi', 'TWI73G0420' => 'twi', 'TWI73G1276' => 'twi', 'TWI74G0405' => 'twi', 'TWI74G0837' => 'twi', 'TWI75G0594' => 'twi', 'TWI75G1615' => 'twi', 'TWI77G0816' => 'twi', 'vmacro03831' => 'vma', 'vmacro13746' => 'vma', 'vmacro16089' => 'vma', 'vmacro22863' => 'vma', 'Zm00001eb085790' => 'zma', 'Zm00001eb114250' => 'zma', 'Zm00001eb138070' => 'zma', 'Zm00001eb167560' => 'zma', 'Zm00001eb199990' => 'zma', 'Zm00001eb368180' => 'zma', 'Zm00001eb382470' => 'zma' ), 'gf_id' => 'HOM05D001576', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001576' ), 'data_identifier' => 'HOM05D001576', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001576', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '406', 'num_species' => '29' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'Aqoxy1G01456' => 'aox', 'Aqoxy1G02949' => 'aox', 'Aqoxy3G01274' => 'aox', 'Aqoxy3G02110' => 'aox', 'Aqoxy3G02268' => 'aox', 'Aqoxy5G02702' => 'aox', 'Aqoxy5G02988' => 'aox', 'Aqoxy5G03427' => 'aox', 'Aqoxy6G02363' => 'aox', 'Atru.chr1.3225' => 'acertr', 'Atru.chr8.1198' => 'acertr', 'Atru.chr9.790' => 'acertr', 'CANSAT01G3197' => 'cansat', 'Ciclev10003979m.g' => 'ccl', 'Ciclev10017471m.g' => 'ccl', 'Ciclev10018206m.g' => 'ccl', 'Ciclev10033751m.g' => 'ccl', 'CiPaw.01G000900' => 'cil', 'CiPaw.01G001000' => 'cil', 'CiPaw.01G033500' => 'cil', 'CiPaw.01G060300' => 'cil', 'CiPaw.01G070200' => 'cil', 'CiPaw.01G075100' => 'cil', 'CiPaw.01G084700' => 'cil', 'CiPaw.01G087900' => 'cil', 'CiPaw.01G092600' => 'cil', 'CiPaw.01G097200' => 'cil', 'CiPaw.01G098300' => 'cil', 'CiPaw.01G110200' => 'cil', 'CiPaw.01G118700' => 'cil', 'CiPaw.01G121200' => 'cil', 'CiPaw.01G132500' => 'cil', 'CiPaw.01G146900' => 'cil', 'CiPaw.01G174000' => 'cil', 'CiPaw.01G179900' => 'cil', 'CiPaw.01G183400' => 'cil', 'CiPaw.01G240000' => 'cil', 'CiPaw.01G283500' => 'cil', 'CiPaw.01G307400' => 'cil', 'CiPaw.02G030800' => 'cil', 'CiPaw.02G047200' => 'cil', 'CiPaw.02G050500' => 'cil', 'CiPaw.02G069900' => 'cil', 'CiPaw.02G091600' => 'cil', 'CiPaw.02G095000' => 'cil', 'CiPaw.02G131900' => 'cil', 'CiPaw.03G043000' => 'cil', 'CiPaw.03G069900' => 'cil', 'CiPaw.03G088100' => 'cil', 'CiPaw.03G089300' => 'cil', 'CiPaw.03G093100' => 'cil', 'CiPaw.03G129800' => 'cil', 'CiPaw.03G131200' => 'cil', 'CiPaw.03G134500' => 'cil', 'CiPaw.03G152100' => 'cil', 'CiPaw.03G162700' => 'cil', 'CiPaw.03G172800' => 'cil', 'CiPaw.03G175800' => 'cil', 'CiPaw.03G181800' => 'cil', 'CiPaw.03G191400' => 'cil', 'CiPaw.03G198300' => 'cil', 'CiPaw.03G201300' => 'cil', 'CiPaw.03G224700' => 'cil', 'CiPaw.03G225000' => 'cil', 'CiPaw.04G065100' => 'cil', 'CiPaw.04G080400' => 'cil', 'CiPaw.04G113500' => 'cil', 'CiPaw.04G121900' => 'cil', 'CiPaw.04G144100' => 'cil', 'CiPaw.04G176500' => 'cil', 'CiPaw.05G086200' => 'cil', 'CiPaw.05G100200' => 'cil', 'CiPaw.05G114200' => 'cil', 'CiPaw.05G126800' => 'cil', 'CiPaw.05G228800' => 'cil', 'CiPaw.05G230600' => 'cil', 'CiPaw.05G236500' => 'cil', 'CiPaw.05G244800' => 'cil', 'CiPaw.06G026600' => 'cil', 'CiPaw.06G027900' => 'cil', 'CiPaw.06G051800' => 'cil', 'CiPaw.06G128500' => 'cil', 'CiPaw.06G165900' => 'cil', 'CiPaw.07G045400' => 'cil', 'CiPaw.07G048000' => 'cil', 'CiPaw.07G052000' => 'cil', 'CiPaw.07G073800' => 'cil', 'CiPaw.07G099700' => 'cil', 'CiPaw.07G108700' => 'cil', 'CiPaw.07G120000' => 'cil', 'CiPaw.07G134100' => 'cil', 'CiPaw.07G147000' => 'cil', 'CiPaw.07G149700' => 'cil', 'CiPaw.07G178300' => 'cil', 'CiPaw.07G184900' => 'cil', 'CiPaw.08G044500' => 'cil', 'CiPaw.08G046900' => 'cil', 'CiPaw.08G047300' => 'cil', 'CiPaw.08G115400' => 'cil', 'CiPaw.08G134700' => 'cil', 'CiPaw.08G157400' => 'cil', 'CiPaw.09G014300' => 'cil', 'CiPaw.09G088900' => 'cil', 'CiPaw.09G130900' => 'cil', 'CiPaw.09G133100' => 'cil', 'CiPaw.09G151300' => 'cil', 'CiPaw.09G172800' => 'cil', 'CiPaw.09G174900' => 'cil', 'CiPaw.09G175000' => 'cil', 'CiPaw.10G012800' => 'cil', 'CiPaw.10G028800' => 'cil', 'CiPaw.10G044700' => 'cil', 'CiPaw.10G067400' => 'cil', 'CiPaw.10G115900' => 'cil', 'CiPaw.10G126200' => 'cil', 'CiPaw.10G139700' => 'cil', 'CiPaw.10G155100' => 'cil', 'CiPaw.11G011300' => 'cil', 'CiPaw.11G025900' => 'cil', 'CiPaw.11G104100' => 'cil', 'CiPaw.11G142700' => 'cil', 'CiPaw.11G164500' => 'cil', 'CiPaw.11G189100' => 'cil', 'CiPaw.11G197100' => 'cil', 'CiPaw.12G006100' => 'cil', 'CiPaw.12G038500' => 'cil', 'CiPaw.12G041400' => 'cil', 'CiPaw.12G041600' => 'cil', 'CiPaw.12G051300' => 'cil', 'CiPaw.12G101800' => 'cil', 'CiPaw.12G107800' => 'cil', 'CiPaw.13G033200' => 'cil', 'CiPaw.13G129900' => 'cil', 'CiPaw.13G160200' => 'cil', 'CiPaw.14G018900' => 'cil', 'CiPaw.14G029000' => 'cil', 'CiPaw.14G031000' => 'cil', 'CiPaw.14G032000' => 'cil', 'CiPaw.14G032300' => 'cil', 'CiPaw.14G040600' => 'cil', 'CiPaw.14G060500' => 'cil', 'CiPaw.14G061500' => 'cil', 'CiPaw.14G077500' => 'cil', 'CiPaw.14G088300' => 'cil', 'CiPaw.14G108500' => 'cil', 'CiPaw.14G121300' => 'cil', 'CiPaw.14G133000' => 'cil', 'CiPaw.14G134600' => 'cil', 'CiPaw.15G027200' => 'cil', 'CiPaw.15G037700' => 'cil', 'CiPaw.15G050900' => 'cil', 'CiPaw.15G067200' => 'cil', 'CiPaw.15G072000' => 'cil', 'CiPaw.15G112900' => 'cil', 'CiPaw.15G133200' => 'cil', 'CiPaw.15G139500' => 'cil', 'CiPaw.15G155400' => 'cil', 'CiPaw.16G006000' => 'cil', 'CiPaw.16G013100' => 'cil', 'CiPaw.16G047100' => 'cil', 'CiPaw.16G048900' => 'cil', 'CiPaw.16G070300' => 'cil', 'CSS0000195' => 'camsi', 'CSS0001664' => 'camsi', 'CSS0002566' => 'camsi', 'CSS0003077' => 'camsi', 'CSS0004257' => 'camsi', 'CSS0004495' => 'camsi', 'CSS0004599' => 'camsi', 'CSS0004943' => 'camsi', 'CSS0005302' => 'camsi', 'CSS0006274' => 'camsi', 'CSS0006547' => 'camsi', 'CSS0006860' => 'camsi', 'CSS0008814' => 'camsi', 'CSS0008946' => 'camsi', 'CSS0009093' => 'camsi', 'CSS0010221' => 'camsi', 'CSS0010296' => 'camsi', 'CSS0010386' => 'camsi', 'CSS0010831' => 'camsi', 'CSS0011061' => 'camsi', 'CSS0012008' => 'camsi', 'CSS0012194' => 'camsi', 'CSS0013580' => 'camsi', 'CSS0014176' => 'camsi', 'CSS0014280' => 'camsi', 'CSS0014799' => 'camsi', 'CSS0015368' => 'camsi', 'CSS0017473' => 'camsi', 'CSS0019281' => 'camsi', 'CSS0021320' => 'camsi', 'CSS0021750' => 'camsi', 'CSS0023642' => 'camsi', 'CSS0023792' => 'camsi', 'CSS0031528' => 'camsi', 'CSS0033894' => 'camsi', 'CSS0034959' => 'camsi', 'CSS0035632' => 'camsi', 'CSS0038450' => 'camsi', 'CSS0039293' => 'camsi', 'CSS0041053' => 'camsi', 'CSS0041981' => 'camsi', 'CSS0042573' => 'camsi', 'CSS0042927' => 'camsi', 'CSS0047725' => 'camsi', 'CSS0049636' => 'camsi', 'CSS0050513' => 'camsi', 'DCAR_030203' => 'dca', 'Dinv07939' => 'din', 'FAN01G0456' => 'fan', 'FAN02G3001' => 'fan', 'FAN04G2781' => 'fan', 'FAN05G1385' => 'fan', 'FAN05G3062' => 'fan', 'FAN08G2267' => 'fan', 'FAN10G0481' => 'fan', 'FAN10G1257' => 'fan', 'FAN14G0954' => 'fan', 'FAN14G2347' => 'fan', 'FAN15G0187' => 'fan', 'FAN25G2214' => 'fan', 'FvH4_1g21031' => 'fve', 'FvH4_3g16231' => 'fve', 'FvH4_3g26413' => 'fve', 'FvH4_3g29014' => 'fve', 'FvH4_3g31921' => 'fve', 'FvH4_4g19882' => 'fve', 'FvH4_5g21960' => 'fve', 'FvH4_5g29683' => 'fve', 'FvH4_7g13271' => 'fve', 'Glyma.01G062500' => 'gma', 'Glyma.07G140900' => 'gma', 'Glyma.09G140900' => 'gma', 'Glyma.12G112700' => 'gma', 'Glyma.17G168800' => 'gma', 'HanXRQChr01g0027001' => 'han', 'HanXRQChr04g0120511' => 'han', 'HanXRQChr08g0232381' => 'han', 'HanXRQChr09g0265661' => 'han', 'HanXRQChr13g0416031' => 'han', 'Haze_05835' => 'cav', 'Haze_06597' => 'cav', 'Haze_07921' => 'cav', 'Haze_08599' => 'cav', 'Haze_10686' => 'cav', 'Haze_12994' => 'cav', 'Haze_13466' => 'cav', 'Haze_16101' => 'cav', 'Haze_17766' => 'cav', 'Haze_18456' => 'cav', 'Haze_20229' => 'cav', 'Hma1.2p1_0324F.1_g125640' => 'hma', 'Hma1.2p1_0733F.1_g210230' => 'hma', 'Hma1.2p1_0921F.1_g236870' => 'hma', 'Hma1.2p1_1313F.1_g274940' => 'hma', 'Hma1.2p1_3059F.1_g332230' => 'hma', 'Hund15925' => 'sun', 'Hund19562' => 'sun', 'Hund21925' => 'sun', 'MD03G1177400' => 'mdo', 'MD07G1026100' => 'mdo', 'MD17G1218600' => 'mdo', 'Medtr0867s0010' => 'mtr', 'Medtr6g081150' => 'mtr', 'Os01g0527900' => 'osa', 'Os02g0463725' => 'osa', 'Os02g0785600' => 'osa', 'Os03g0433733' => 'osa', 'Os04g0286500' => 'osa', 'Os05g0227800' => 'osa', 'Os06g0521000' => 'osa', 'Os06g0635500' => 'osa', 'Os06g0660650' => 'osa', 'Os07g0554400' => 'osa', 'Os08g0225900' => 'osa', 'Os08g0561000' => 'osa', 'Os09g0241700' => 'osa', 'Os09g0351900' => 'osa', 'Os11g0220700' => 'osa', 'Os11g0282700' => 'osa', 'Os12g0169300' => 'osa', 'Os12g0228500' => 'osa', 'Os12g0543800' => 'osa', 'PGR044G1547' => 'pgr', 'Potri.005G239150' => 'ptr', 'Potri.010G014250' => 'ptr', 'Prupe.1G172500' => 'ppe', 'Prupe.1G196800' => 'ppe', 'Prupe.1G279700' => 'ppe', 'Prupe.2G026400' => 'ppe', 'Prupe.3G094000' => 'ppe', 'Prupe.4G287300' => 'ppe', 'QL01p022166' => 'qlo', 'QL01p051890' => 'qlo', 'QL02p009469' => 'qlo', 'QL02p046053' => 'qlo', 'QL02p057958' => 'qlo', 'QL02p093127' => 'qlo', 'QL03p006855' => 'qlo', 'QL03p071586' => 'qlo', 'QL04p000022' => 'qlo', 'QL04p000024' => 'qlo', 'QL04p003192' => 'qlo', 'QL05p011416' => 'qlo', 'QL06p039590' => 'qlo', 'QL06p052750' => 'qlo', 'QL06p053821' => 'qlo', 'QL07p025287' => 'qlo', 'QL09p033218' => 'qlo', 'QL09p040841' => 'qlo', 'QL10p020337' => 'qlo', 'QL10p027209' => 'qlo', 'QL10p027969' => 'qlo', 'QL10p048988' => 'qlo', 'QL11p001241' => 'qlo', 'QL11p028487' => 'qlo', 'RcHm_v2.0_Chr2g0105031' => 'rch', 'RcHm_v2.0_Chr2g0117811' => 'rch', 'RcHm_v2.0_Chr6g0270241' => 'rch', 'RcHm_v2.0_Chr7g0215961' => 'rch', 'RcHm_v2.0_Chr7g0231991' => 'rch', 'Rhsim01G0041500' => 'rsi', 'Rhsim01G0115000' => 'rsi', 'Rhsim01G0115400' => 'rsi', 'Rhsim01G0133600' => 'rsi', 'Rhsim01G0159900' => 'rsi', 'Rhsim02G0189400' => 'rsi', 'Rhsim03G0135600' => 'rsi', 'Rhsim03G0149900' => 'rsi', 'Rhsim04G0125600' => 'rsi', 'Rhsim05G0091700' => 'rsi', 'Rhsim05G0092900' => 'rsi', 'Rhsim06G0075000' => 'rsi', 'Rhsim07G0066400' => 'rsi', 'Rhsim07G0156400' => 'rsi', 'Rhsim07G0182200' => 'rsi', 'Rhsim07G0182300' => 'rsi', 'Rhsim08G0180400' => 'rsi', 'Rhsim09G0056800' => 'rsi', 'Rhsim10G0153300' => 'rsi', 'Rhsim11G0012700' => 'rsi', 'Rhsim12G0031800' => 'rsi', 'Rhsim12G0055400' => 'rsi', 'Rhsim12G0091400' => 'rsi', 'Rhsim13G0070800' => 'rsi', 'Rhsim13G0193300' => 'rsi', 'RhsimUnG0111600' => 'rsi', 'RhsimUnG0137500' => 'rsi', 'RhsimUnG0172900' => 'rsi', 'SGA_v2.0_scaffold11G05878' => 'sas', 'SGA_v2.0_scaffold167G38458' => 'sas', 'SGA_v2.0_scaffold19G08588' => 'sas', 'SGA_v2.0_scaffold239G43990' => 'sas', 'SGA_v2.0_scaffold260G45865' => 'sas', 'SGA_v2.0_scaffold309G48177' => 'sas', 'SGA_v2.0_scaffold76G25122' => 'sas', 'SGA_v2.0_scaffold85G26708' => 'sas', 'SHI13914' => 'shi', 'SHI30402' => 'shi', 'TWI09G0020' => 'twi', 'TWI09G0456' => 'twi', 'TWI09G1572' => 'twi', 'TWI12G0266' => 'twi', 'TWI12G1451' => 'twi', 'TWI14G0851' => 'twi', 'TWI15G0796' => 'twi', 'TWI18G0820' => 'twi', 'TWI18G1152' => 'twi', 'TWI23G0007' => 'twi', 'TWI23G0314' => 'twi', 'TWI31G0674' => 'twi', 'TWI31G0938' => 'twi', 'TWI34G0641' => 'twi', 'TWI34G1527' => 'twi', 'TWI36G0193' => 'twi', 'TWI36G0405' => 'twi', 'TWI38G0892' => 'twi', 'TWI38G0936' => 'twi', 'TWI38G2218' => 'twi', 'TWI53G0679' => 'twi', 'TWI53G0863' => 'twi', 'TWI53G1133' => 'twi', 'TWI60G0823' => 'twi', 'TWI63G0919' => 'twi', 'TWI63G1436' => 'twi', 'TWI73G0140' => 'twi', 'TWI73G0419' => 'twi', 'TWI73G0420' => 'twi', 'TWI73G1276' => 'twi', 'TWI74G0405' => 'twi', 'TWI74G0837' => 'twi', 'TWI75G0594' => 'twi', 'TWI75G1615' => 'twi', 'TWI77G0816' => 'twi', 'vmacro03831' => 'vma', 'vmacro13746' => 'vma', 'vmacro16089' => 'vma', 'vmacro22863' => 'vma', 'Zm00001eb085790' => 'zma', 'Zm00001eb114250' => 'zma', 'Zm00001eb138070' => 'zma', 'Zm00001eb167560' => 'zma', 'Zm00001eb199990' => 'zma', 'Zm00001eb368180' => 'zma', 'Zm00001eb382470' => 'zma' ) $gf_id = 'HOM05D001576' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001576' ) $data_identifier = 'HOM05D001576' $data_type = 'gf_id' $species_gene_counts = array( 'aox' => (int) 9, 'acertr' => (int) 3, 'cansat' => (int) 1, 'ccl' => (int) 4, 'cil' => (int) 145, 'camsi' => (int) 46, 'dca' => (int) 1, 'din' => (int) 1, 'fan' => (int) 12, 'fve' => (int) 9, 'gma' => (int) 5, 'han' => (int) 5, 'cav' => (int) 11, 'hma' => (int) 5, 'sun' => (int) 3, 'mdo' => (int) 3, 'mtr' => (int) 2, 'osa' => (int) 19, 'pgr' => (int) 1, 'ptr' => (int) 2, 'ppe' => (int) 6, 'qlo' => (int) 24, 'rch' => (int) 5, 'rsi' => (int) 28, 'sas' => (int) 8, 'shi' => (int) 2, 'twi' => (int) 35, 'vma' => (int) 4, 'zma' => (int) 7 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb382470' $species_info = array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ) $local_species = 'ptr' $disabled = '' $selected = '' $num_hits = (int) 0
Warning (2): count(): Parameter must be an array or an object that implements Countable [APP/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp, line 33]Code Context $disabled = (!array_key_exists($local_species,$species_gene_counts))?"disabled":""; $selected = (isset($selected_species) && array_key_exists($local_species,$selected_species))?"checked='checked'":""; $num_hits = (array_key_exists($local_species,$species_gene_counts))?count($species_gene_counts[$local_species]):0; $viewFile = '/www/bioinformatics01_ro/plaza/_dev_instances/feedback/app/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp' $dataForView = array( 'sidebar_info' => array( 'gf_id' => 'HOM05D001576', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '406', 'num_species' => '29' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'Aqoxy1G01456' => 'aox', 'Aqoxy1G02949' => 'aox', 'Aqoxy3G01274' => 'aox', 'Aqoxy3G02110' => 'aox', 'Aqoxy3G02268' => 'aox', 'Aqoxy5G02702' => 'aox', 'Aqoxy5G02988' => 'aox', 'Aqoxy5G03427' => 'aox', 'Aqoxy6G02363' => 'aox', 'Atru.chr1.3225' => 'acertr', 'Atru.chr8.1198' => 'acertr', 'Atru.chr9.790' => 'acertr', 'CANSAT01G3197' => 'cansat', 'Ciclev10003979m.g' => 'ccl', 'Ciclev10017471m.g' => 'ccl', 'Ciclev10018206m.g' => 'ccl', 'Ciclev10033751m.g' => 'ccl', 'CiPaw.01G000900' => 'cil', 'CiPaw.01G001000' => 'cil', 'CiPaw.01G033500' => 'cil', 'CiPaw.01G060300' => 'cil', 'CiPaw.01G070200' => 'cil', 'CiPaw.01G075100' => 'cil', 'CiPaw.01G084700' => 'cil', 'CiPaw.01G087900' => 'cil', 'CiPaw.01G092600' => 'cil', 'CiPaw.01G097200' => 'cil', 'CiPaw.01G098300' => 'cil', 'CiPaw.01G110200' => 'cil', 'CiPaw.01G118700' => 'cil', 'CiPaw.01G121200' => 'cil', 'CiPaw.01G132500' => 'cil', 'CiPaw.01G146900' => 'cil', 'CiPaw.01G174000' => 'cil', 'CiPaw.01G179900' => 'cil', 'CiPaw.01G183400' => 'cil', 'CiPaw.01G240000' => 'cil', 'CiPaw.01G283500' => 'cil', 'CiPaw.01G307400' => 'cil', 'CiPaw.02G030800' => 'cil', 'CiPaw.02G047200' => 'cil', 'CiPaw.02G050500' => 'cil', 'CiPaw.02G069900' => 'cil', 'CiPaw.02G091600' => 'cil', 'CiPaw.02G095000' => 'cil', 'CiPaw.02G131900' => 'cil', 'CiPaw.03G043000' => 'cil', 'CiPaw.03G069900' => 'cil', 'CiPaw.03G088100' => 'cil', 'CiPaw.03G089300' => 'cil', 'CiPaw.03G093100' => 'cil', 'CiPaw.03G129800' => 'cil', 'CiPaw.03G131200' => 'cil', 'CiPaw.03G134500' => 'cil', 'CiPaw.03G152100' => 'cil', 'CiPaw.03G162700' => 'cil', 'CiPaw.03G172800' => 'cil', 'CiPaw.03G175800' => 'cil', 'CiPaw.03G181800' => 'cil', 'CiPaw.03G191400' => 'cil', 'CiPaw.03G198300' => 'cil', 'CiPaw.03G201300' => 'cil', 'CiPaw.03G224700' => 'cil', 'CiPaw.03G225000' => 'cil', 'CiPaw.04G065100' => 'cil', 'CiPaw.04G080400' => 'cil', 'CiPaw.04G113500' => 'cil', 'CiPaw.04G121900' => 'cil', 'CiPaw.04G144100' => 'cil', 'CiPaw.04G176500' => 'cil', 'CiPaw.05G086200' => 'cil', 'CiPaw.05G100200' => 'cil', 'CiPaw.05G114200' => 'cil', 'CiPaw.05G126800' => 'cil', 'CiPaw.05G228800' => 'cil', 'CiPaw.05G230600' => 'cil', 'CiPaw.05G236500' => 'cil', 'CiPaw.05G244800' => 'cil', 'CiPaw.06G026600' => 'cil', 'CiPaw.06G027900' => 'cil', 'CiPaw.06G051800' => 'cil', 'CiPaw.06G128500' => 'cil', 'CiPaw.06G165900' => 'cil', 'CiPaw.07G045400' => 'cil', 'CiPaw.07G048000' => 'cil', 'CiPaw.07G052000' => 'cil', 'CiPaw.07G073800' => 'cil', 'CiPaw.07G099700' => 'cil', 'CiPaw.07G108700' => 'cil', 'CiPaw.07G120000' => 'cil', 'CiPaw.07G134100' => 'cil', 'CiPaw.07G147000' => 'cil', 'CiPaw.07G149700' => 'cil', 'CiPaw.07G178300' => 'cil', 'CiPaw.07G184900' => 'cil', 'CiPaw.08G044500' => 'cil', 'CiPaw.08G046900' => 'cil', 'CiPaw.08G047300' => 'cil', 'CiPaw.08G115400' => 'cil', 'CiPaw.08G134700' => 'cil', 'CiPaw.08G157400' => 'cil', 'CiPaw.09G014300' => 'cil', 'CiPaw.09G088900' => 'cil', 'CiPaw.09G130900' => 'cil', 'CiPaw.09G133100' => 'cil', 'CiPaw.09G151300' => 'cil', 'CiPaw.09G172800' => 'cil', 'CiPaw.09G174900' => 'cil', 'CiPaw.09G175000' => 'cil', 'CiPaw.10G012800' => 'cil', 'CiPaw.10G028800' => 'cil', 'CiPaw.10G044700' => 'cil', 'CiPaw.10G067400' => 'cil', 'CiPaw.10G115900' => 'cil', 'CiPaw.10G126200' => 'cil', 'CiPaw.10G139700' => 'cil', 'CiPaw.10G155100' => 'cil', 'CiPaw.11G011300' => 'cil', 'CiPaw.11G025900' => 'cil', 'CiPaw.11G104100' => 'cil', 'CiPaw.11G142700' => 'cil', 'CiPaw.11G164500' => 'cil', 'CiPaw.11G189100' => 'cil', 'CiPaw.11G197100' => 'cil', 'CiPaw.12G006100' => 'cil', 'CiPaw.12G038500' => 'cil', 'CiPaw.12G041400' => 'cil', 'CiPaw.12G041600' => 'cil', 'CiPaw.12G051300' => 'cil', 'CiPaw.12G101800' => 'cil', 'CiPaw.12G107800' => 'cil', 'CiPaw.13G033200' => 'cil', 'CiPaw.13G129900' => 'cil', 'CiPaw.13G160200' => 'cil', 'CiPaw.14G018900' => 'cil', 'CiPaw.14G029000' => 'cil', 'CiPaw.14G031000' => 'cil', 'CiPaw.14G032000' => 'cil', 'CiPaw.14G032300' => 'cil', 'CiPaw.14G040600' => 'cil', 'CiPaw.14G060500' => 'cil', 'CiPaw.14G061500' => 'cil', 'CiPaw.14G077500' => 'cil', 'CiPaw.14G088300' => 'cil', 'CiPaw.14G108500' => 'cil', 'CiPaw.14G121300' => 'cil', 'CiPaw.14G133000' => 'cil', 'CiPaw.14G134600' => 'cil', 'CiPaw.15G027200' => 'cil', 'CiPaw.15G037700' => 'cil', 'CiPaw.15G050900' => 'cil', 'CiPaw.15G067200' => 'cil', 'CiPaw.15G072000' => 'cil', 'CiPaw.15G112900' => 'cil', 'CiPaw.15G133200' => 'cil', 'CiPaw.15G139500' => 'cil', 'CiPaw.15G155400' => 'cil', 'CiPaw.16G006000' => 'cil', 'CiPaw.16G013100' => 'cil', 'CiPaw.16G047100' => 'cil', 'CiPaw.16G048900' => 'cil', 'CiPaw.16G070300' => 'cil', 'CSS0000195' => 'camsi', 'CSS0001664' => 'camsi', 'CSS0002566' => 'camsi', 'CSS0003077' => 'camsi', 'CSS0004257' => 'camsi', 'CSS0004495' => 'camsi', 'CSS0004599' => 'camsi', 'CSS0004943' => 'camsi', 'CSS0005302' => 'camsi', 'CSS0006274' => 'camsi', 'CSS0006547' => 'camsi', 'CSS0006860' => 'camsi', 'CSS0008814' => 'camsi', 'CSS0008946' => 'camsi', 'CSS0009093' => 'camsi', 'CSS0010221' => 'camsi', 'CSS0010296' => 'camsi', 'CSS0010386' => 'camsi', 'CSS0010831' => 'camsi', 'CSS0011061' => 'camsi', 'CSS0012008' => 'camsi', 'CSS0012194' => 'camsi', 'CSS0013580' => 'camsi', 'CSS0014176' => 'camsi', 'CSS0014280' => 'camsi', 'CSS0014799' => 'camsi', 'CSS0015368' => 'camsi', 'CSS0017473' => 'camsi', 'CSS0019281' => 'camsi', 'CSS0021320' => 'camsi', 'CSS0021750' => 'camsi', 'CSS0023642' => 'camsi', 'CSS0023792' => 'camsi', 'CSS0031528' => 'camsi', 'CSS0033894' => 'camsi', 'CSS0034959' => 'camsi', 'CSS0035632' => 'camsi', 'CSS0038450' => 'camsi', 'CSS0039293' => 'camsi', 'CSS0041053' => 'camsi', 'CSS0041981' => 'camsi', 'CSS0042573' => 'camsi', 'CSS0042927' => 'camsi', 'CSS0047725' => 'camsi', 'CSS0049636' => 'camsi', 'CSS0050513' => 'camsi', 'DCAR_030203' => 'dca', 'Dinv07939' => 'din', 'FAN01G0456' => 'fan', 'FAN02G3001' => 'fan', 'FAN04G2781' => 'fan', 'FAN05G1385' => 'fan', 'FAN05G3062' => 'fan', 'FAN08G2267' => 'fan', 'FAN10G0481' => 'fan', 'FAN10G1257' => 'fan', 'FAN14G0954' => 'fan', 'FAN14G2347' => 'fan', 'FAN15G0187' => 'fan', 'FAN25G2214' => 'fan', 'FvH4_1g21031' => 'fve', 'FvH4_3g16231' => 'fve', 'FvH4_3g26413' => 'fve', 'FvH4_3g29014' => 'fve', 'FvH4_3g31921' => 'fve', 'FvH4_4g19882' => 'fve', 'FvH4_5g21960' => 'fve', 'FvH4_5g29683' => 'fve', 'FvH4_7g13271' => 'fve', 'Glyma.01G062500' => 'gma', 'Glyma.07G140900' => 'gma', 'Glyma.09G140900' => 'gma', 'Glyma.12G112700' => 'gma', 'Glyma.17G168800' => 'gma', 'HanXRQChr01g0027001' => 'han', 'HanXRQChr04g0120511' => 'han', 'HanXRQChr08g0232381' => 'han', 'HanXRQChr09g0265661' => 'han', 'HanXRQChr13g0416031' => 'han', 'Haze_05835' => 'cav', 'Haze_06597' => 'cav', 'Haze_07921' => 'cav', 'Haze_08599' => 'cav', 'Haze_10686' => 'cav', 'Haze_12994' => 'cav', 'Haze_13466' => 'cav', 'Haze_16101' => 'cav', 'Haze_17766' => 'cav', 'Haze_18456' => 'cav', 'Haze_20229' => 'cav', 'Hma1.2p1_0324F.1_g125640' => 'hma', 'Hma1.2p1_0733F.1_g210230' => 'hma', 'Hma1.2p1_0921F.1_g236870' => 'hma', 'Hma1.2p1_1313F.1_g274940' => 'hma', 'Hma1.2p1_3059F.1_g332230' => 'hma', 'Hund15925' => 'sun', 'Hund19562' => 'sun', 'Hund21925' => 'sun', 'MD03G1177400' => 'mdo', 'MD07G1026100' => 'mdo', 'MD17G1218600' => 'mdo', 'Medtr0867s0010' => 'mtr', 'Medtr6g081150' => 'mtr', 'Os01g0527900' => 'osa', 'Os02g0463725' => 'osa', 'Os02g0785600' => 'osa', 'Os03g0433733' => 'osa', 'Os04g0286500' => 'osa', 'Os05g0227800' => 'osa', 'Os06g0521000' => 'osa', 'Os06g0635500' => 'osa', 'Os06g0660650' => 'osa', 'Os07g0554400' => 'osa', 'Os08g0225900' => 'osa', 'Os08g0561000' => 'osa', 'Os09g0241700' => 'osa', 'Os09g0351900' => 'osa', 'Os11g0220700' => 'osa', 'Os11g0282700' => 'osa', 'Os12g0169300' => 'osa', 'Os12g0228500' => 'osa', 'Os12g0543800' => 'osa', 'PGR044G1547' => 'pgr', 'Potri.005G239150' => 'ptr', 'Potri.010G014250' => 'ptr', 'Prupe.1G172500' => 'ppe', 'Prupe.1G196800' => 'ppe', 'Prupe.1G279700' => 'ppe', 'Prupe.2G026400' => 'ppe', 'Prupe.3G094000' => 'ppe', 'Prupe.4G287300' => 'ppe', 'QL01p022166' => 'qlo', 'QL01p051890' => 'qlo', 'QL02p009469' => 'qlo', 'QL02p046053' => 'qlo', 'QL02p057958' => 'qlo', 'QL02p093127' => 'qlo', 'QL03p006855' => 'qlo', 'QL03p071586' => 'qlo', 'QL04p000022' => 'qlo', 'QL04p000024' => 'qlo', 'QL04p003192' => 'qlo', 'QL05p011416' => 'qlo', 'QL06p039590' => 'qlo', 'QL06p052750' => 'qlo', 'QL06p053821' => 'qlo', 'QL07p025287' => 'qlo', 'QL09p033218' => 'qlo', 'QL09p040841' => 'qlo', 'QL10p020337' => 'qlo', 'QL10p027209' => 'qlo', 'QL10p027969' => 'qlo', 'QL10p048988' => 'qlo', 'QL11p001241' => 'qlo', 'QL11p028487' => 'qlo', 'RcHm_v2.0_Chr2g0105031' => 'rch', 'RcHm_v2.0_Chr2g0117811' => 'rch', 'RcHm_v2.0_Chr6g0270241' => 'rch', 'RcHm_v2.0_Chr7g0215961' => 'rch', 'RcHm_v2.0_Chr7g0231991' => 'rch', 'Rhsim01G0041500' => 'rsi', 'Rhsim01G0115000' => 'rsi', 'Rhsim01G0115400' => 'rsi', 'Rhsim01G0133600' => 'rsi', 'Rhsim01G0159900' => 'rsi', 'Rhsim02G0189400' => 'rsi', 'Rhsim03G0135600' => 'rsi', 'Rhsim03G0149900' => 'rsi', 'Rhsim04G0125600' => 'rsi', 'Rhsim05G0091700' => 'rsi', 'Rhsim05G0092900' => 'rsi', 'Rhsim06G0075000' => 'rsi', 'Rhsim07G0066400' => 'rsi', 'Rhsim07G0156400' => 'rsi', 'Rhsim07G0182200' => 'rsi', 'Rhsim07G0182300' => 'rsi', 'Rhsim08G0180400' => 'rsi', 'Rhsim09G0056800' => 'rsi', 'Rhsim10G0153300' => 'rsi', 'Rhsim11G0012700' => 'rsi', 'Rhsim12G0031800' => 'rsi', 'Rhsim12G0055400' => 'rsi', 'Rhsim12G0091400' => 'rsi', 'Rhsim13G0070800' => 'rsi', 'Rhsim13G0193300' => 'rsi', 'RhsimUnG0111600' => 'rsi', 'RhsimUnG0137500' => 'rsi', 'RhsimUnG0172900' => 'rsi', 'SGA_v2.0_scaffold11G05878' => 'sas', 'SGA_v2.0_scaffold167G38458' => 'sas', 'SGA_v2.0_scaffold19G08588' => 'sas', 'SGA_v2.0_scaffold239G43990' => 'sas', 'SGA_v2.0_scaffold260G45865' => 'sas', 'SGA_v2.0_scaffold309G48177' => 'sas', 'SGA_v2.0_scaffold76G25122' => 'sas', 'SGA_v2.0_scaffold85G26708' => 'sas', 'SHI13914' => 'shi', 'SHI30402' => 'shi', 'TWI09G0020' => 'twi', 'TWI09G0456' => 'twi', 'TWI09G1572' => 'twi', 'TWI12G0266' => 'twi', 'TWI12G1451' => 'twi', 'TWI14G0851' => 'twi', 'TWI15G0796' => 'twi', 'TWI18G0820' => 'twi', 'TWI18G1152' => 'twi', 'TWI23G0007' => 'twi', 'TWI23G0314' => 'twi', 'TWI31G0674' => 'twi', 'TWI31G0938' => 'twi', 'TWI34G0641' => 'twi', 'TWI34G1527' => 'twi', 'TWI36G0193' => 'twi', 'TWI36G0405' => 'twi', 'TWI38G0892' => 'twi', 'TWI38G0936' => 'twi', 'TWI38G2218' => 'twi', 'TWI53G0679' => 'twi', 'TWI53G0863' => 'twi', 'TWI53G1133' => 'twi', 'TWI60G0823' => 'twi', 'TWI63G0919' => 'twi', 'TWI63G1436' => 'twi', 'TWI73G0140' => 'twi', 'TWI73G0419' => 'twi', 'TWI73G0420' => 'twi', 'TWI73G1276' => 'twi', 'TWI74G0405' => 'twi', 'TWI74G0837' => 'twi', 'TWI75G0594' => 'twi', 'TWI75G1615' => 'twi', 'TWI77G0816' => 'twi', 'vmacro03831' => 'vma', 'vmacro13746' => 'vma', 'vmacro16089' => 'vma', 'vmacro22863' => 'vma', 'Zm00001eb085790' => 'zma', 'Zm00001eb114250' => 'zma', 'Zm00001eb138070' => 'zma', 'Zm00001eb167560' => 'zma', 'Zm00001eb199990' => 'zma', 'Zm00001eb368180' => 'zma', 'Zm00001eb382470' => 'zma' ), 'gf_id' => 'HOM05D001576', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001576' ), 'data_identifier' => 'HOM05D001576', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001576', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '406', 'num_species' => '29' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'Aqoxy1G01456' => 'aox', 'Aqoxy1G02949' => 'aox', 'Aqoxy3G01274' => 'aox', 'Aqoxy3G02110' => 'aox', 'Aqoxy3G02268' => 'aox', 'Aqoxy5G02702' => 'aox', 'Aqoxy5G02988' => 'aox', 'Aqoxy5G03427' => 'aox', 'Aqoxy6G02363' => 'aox', 'Atru.chr1.3225' => 'acertr', 'Atru.chr8.1198' => 'acertr', 'Atru.chr9.790' => 'acertr', 'CANSAT01G3197' => 'cansat', 'Ciclev10003979m.g' => 'ccl', 'Ciclev10017471m.g' => 'ccl', 'Ciclev10018206m.g' => 'ccl', 'Ciclev10033751m.g' => 'ccl', 'CiPaw.01G000900' => 'cil', 'CiPaw.01G001000' => 'cil', 'CiPaw.01G033500' => 'cil', 'CiPaw.01G060300' => 'cil', 'CiPaw.01G070200' => 'cil', 'CiPaw.01G075100' => 'cil', 'CiPaw.01G084700' => 'cil', 'CiPaw.01G087900' => 'cil', 'CiPaw.01G092600' => 'cil', 'CiPaw.01G097200' => 'cil', 'CiPaw.01G098300' => 'cil', 'CiPaw.01G110200' => 'cil', 'CiPaw.01G118700' => 'cil', 'CiPaw.01G121200' => 'cil', 'CiPaw.01G132500' => 'cil', 'CiPaw.01G146900' => 'cil', 'CiPaw.01G174000' => 'cil', 'CiPaw.01G179900' => 'cil', 'CiPaw.01G183400' => 'cil', 'CiPaw.01G240000' => 'cil', 'CiPaw.01G283500' => 'cil', 'CiPaw.01G307400' => 'cil', 'CiPaw.02G030800' => 'cil', 'CiPaw.02G047200' => 'cil', 'CiPaw.02G050500' => 'cil', 'CiPaw.02G069900' => 'cil', 'CiPaw.02G091600' => 'cil', 'CiPaw.02G095000' => 'cil', 'CiPaw.02G131900' => 'cil', 'CiPaw.03G043000' => 'cil', 'CiPaw.03G069900' => 'cil', 'CiPaw.03G088100' => 'cil', 'CiPaw.03G089300' => 'cil', 'CiPaw.03G093100' => 'cil', 'CiPaw.03G129800' => 'cil', 'CiPaw.03G131200' => 'cil', 'CiPaw.03G134500' => 'cil', 'CiPaw.03G152100' => 'cil', 'CiPaw.03G162700' => 'cil', 'CiPaw.03G172800' => 'cil', 'CiPaw.03G175800' => 'cil', 'CiPaw.03G181800' => 'cil', 'CiPaw.03G191400' => 'cil', 'CiPaw.03G198300' => 'cil', 'CiPaw.03G201300' => 'cil', 'CiPaw.03G224700' => 'cil', 'CiPaw.03G225000' => 'cil', 'CiPaw.04G065100' => 'cil', 'CiPaw.04G080400' => 'cil', 'CiPaw.04G113500' => 'cil', 'CiPaw.04G121900' => 'cil', 'CiPaw.04G144100' => 'cil', 'CiPaw.04G176500' => 'cil', 'CiPaw.05G086200' => 'cil', 'CiPaw.05G100200' => 'cil', 'CiPaw.05G114200' => 'cil', 'CiPaw.05G126800' => 'cil', 'CiPaw.05G228800' => 'cil', 'CiPaw.05G230600' => 'cil', 'CiPaw.05G236500' => 'cil', 'CiPaw.05G244800' => 'cil', 'CiPaw.06G026600' => 'cil', 'CiPaw.06G027900' => 'cil', 'CiPaw.06G051800' => 'cil', 'CiPaw.06G128500' => 'cil', 'CiPaw.06G165900' => 'cil', 'CiPaw.07G045400' => 'cil', 'CiPaw.07G048000' => 'cil', 'CiPaw.07G052000' => 'cil', 'CiPaw.07G073800' => 'cil', 'CiPaw.07G099700' => 'cil', 'CiPaw.07G108700' => 'cil', 'CiPaw.07G120000' => 'cil', 'CiPaw.07G134100' => 'cil', 'CiPaw.07G147000' => 'cil', 'CiPaw.07G149700' => 'cil', 'CiPaw.07G178300' => 'cil', 'CiPaw.07G184900' => 'cil', 'CiPaw.08G044500' => 'cil', 'CiPaw.08G046900' => 'cil', 'CiPaw.08G047300' => 'cil', 'CiPaw.08G115400' => 'cil', 'CiPaw.08G134700' => 'cil', 'CiPaw.08G157400' => 'cil', 'CiPaw.09G014300' => 'cil', 'CiPaw.09G088900' => 'cil', 'CiPaw.09G130900' => 'cil', 'CiPaw.09G133100' => 'cil', 'CiPaw.09G151300' => 'cil', 'CiPaw.09G172800' => 'cil', 'CiPaw.09G174900' => 'cil', 'CiPaw.09G175000' => 'cil', 'CiPaw.10G012800' => 'cil', 'CiPaw.10G028800' => 'cil', 'CiPaw.10G044700' => 'cil', 'CiPaw.10G067400' => 'cil', 'CiPaw.10G115900' => 'cil', 'CiPaw.10G126200' => 'cil', 'CiPaw.10G139700' => 'cil', 'CiPaw.10G155100' => 'cil', 'CiPaw.11G011300' => 'cil', 'CiPaw.11G025900' => 'cil', 'CiPaw.11G104100' => 'cil', 'CiPaw.11G142700' => 'cil', 'CiPaw.11G164500' => 'cil', 'CiPaw.11G189100' => 'cil', 'CiPaw.11G197100' => 'cil', 'CiPaw.12G006100' => 'cil', 'CiPaw.12G038500' => 'cil', 'CiPaw.12G041400' => 'cil', 'CiPaw.12G041600' => 'cil', 'CiPaw.12G051300' => 'cil', 'CiPaw.12G101800' => 'cil', 'CiPaw.12G107800' => 'cil', 'CiPaw.13G033200' => 'cil', 'CiPaw.13G129900' => 'cil', 'CiPaw.13G160200' => 'cil', 'CiPaw.14G018900' => 'cil', 'CiPaw.14G029000' => 'cil', 'CiPaw.14G031000' => 'cil', 'CiPaw.14G032000' => 'cil', 'CiPaw.14G032300' => 'cil', 'CiPaw.14G040600' => 'cil', 'CiPaw.14G060500' => 'cil', 'CiPaw.14G061500' => 'cil', 'CiPaw.14G077500' => 'cil', 'CiPaw.14G088300' => 'cil', 'CiPaw.14G108500' => 'cil', 'CiPaw.14G121300' => 'cil', 'CiPaw.14G133000' => 'cil', 'CiPaw.14G134600' => 'cil', 'CiPaw.15G027200' => 'cil', 'CiPaw.15G037700' => 'cil', 'CiPaw.15G050900' => 'cil', 'CiPaw.15G067200' => 'cil', 'CiPaw.15G072000' => 'cil', 'CiPaw.15G112900' => 'cil', 'CiPaw.15G133200' => 'cil', 'CiPaw.15G139500' => 'cil', 'CiPaw.15G155400' => 'cil', 'CiPaw.16G006000' => 'cil', 'CiPaw.16G013100' => 'cil', 'CiPaw.16G047100' => 'cil', 'CiPaw.16G048900' => 'cil', 'CiPaw.16G070300' => 'cil', 'CSS0000195' => 'camsi', 'CSS0001664' => 'camsi', 'CSS0002566' => 'camsi', 'CSS0003077' => 'camsi', 'CSS0004257' => 'camsi', 'CSS0004495' => 'camsi', 'CSS0004599' => 'camsi', 'CSS0004943' => 'camsi', 'CSS0005302' => 'camsi', 'CSS0006274' => 'camsi', 'CSS0006547' => 'camsi', 'CSS0006860' => 'camsi', 'CSS0008814' => 'camsi', 'CSS0008946' => 'camsi', 'CSS0009093' => 'camsi', 'CSS0010221' => 'camsi', 'CSS0010296' => 'camsi', 'CSS0010386' => 'camsi', 'CSS0010831' => 'camsi', 'CSS0011061' => 'camsi', 'CSS0012008' => 'camsi', 'CSS0012194' => 'camsi', 'CSS0013580' => 'camsi', 'CSS0014176' => 'camsi', 'CSS0014280' => 'camsi', 'CSS0014799' => 'camsi', 'CSS0015368' => 'camsi', 'CSS0017473' => 'camsi', 'CSS0019281' => 'camsi', 'CSS0021320' => 'camsi', 'CSS0021750' => 'camsi', 'CSS0023642' => 'camsi', 'CSS0023792' => 'camsi', 'CSS0031528' => 'camsi', 'CSS0033894' => 'camsi', 'CSS0034959' => 'camsi', 'CSS0035632' => 'camsi', 'CSS0038450' => 'camsi', 'CSS0039293' => 'camsi', 'CSS0041053' => 'camsi', 'CSS0041981' => 'camsi', 'CSS0042573' => 'camsi', 'CSS0042927' => 'camsi', 'CSS0047725' => 'camsi', 'CSS0049636' => 'camsi', 'CSS0050513' => 'camsi', 'DCAR_030203' => 'dca', 'Dinv07939' => 'din', 'FAN01G0456' => 'fan', 'FAN02G3001' => 'fan', 'FAN04G2781' => 'fan', 'FAN05G1385' => 'fan', 'FAN05G3062' => 'fan', 'FAN08G2267' => 'fan', 'FAN10G0481' => 'fan', 'FAN10G1257' => 'fan', 'FAN14G0954' => 'fan', 'FAN14G2347' => 'fan', 'FAN15G0187' => 'fan', 'FAN25G2214' => 'fan', 'FvH4_1g21031' => 'fve', 'FvH4_3g16231' => 'fve', 'FvH4_3g26413' => 'fve', 'FvH4_3g29014' => 'fve', 'FvH4_3g31921' => 'fve', 'FvH4_4g19882' => 'fve', 'FvH4_5g21960' => 'fve', 'FvH4_5g29683' => 'fve', 'FvH4_7g13271' => 'fve', 'Glyma.01G062500' => 'gma', 'Glyma.07G140900' => 'gma', 'Glyma.09G140900' => 'gma', 'Glyma.12G112700' => 'gma', 'Glyma.17G168800' => 'gma', 'HanXRQChr01g0027001' => 'han', 'HanXRQChr04g0120511' => 'han', 'HanXRQChr08g0232381' => 'han', 'HanXRQChr09g0265661' => 'han', 'HanXRQChr13g0416031' => 'han', 'Haze_05835' => 'cav', 'Haze_06597' => 'cav', 'Haze_07921' => 'cav', 'Haze_08599' => 'cav', 'Haze_10686' => 'cav', 'Haze_12994' => 'cav', 'Haze_13466' => 'cav', 'Haze_16101' => 'cav', 'Haze_17766' => 'cav', 'Haze_18456' => 'cav', 'Haze_20229' => 'cav', 'Hma1.2p1_0324F.1_g125640' => 'hma', 'Hma1.2p1_0733F.1_g210230' => 'hma', 'Hma1.2p1_0921F.1_g236870' => 'hma', 'Hma1.2p1_1313F.1_g274940' => 'hma', 'Hma1.2p1_3059F.1_g332230' => 'hma', 'Hund15925' => 'sun', 'Hund19562' => 'sun', 'Hund21925' => 'sun', 'MD03G1177400' => 'mdo', 'MD07G1026100' => 'mdo', 'MD17G1218600' => 'mdo', 'Medtr0867s0010' => 'mtr', 'Medtr6g081150' => 'mtr', 'Os01g0527900' => 'osa', 'Os02g0463725' => 'osa', 'Os02g0785600' => 'osa', 'Os03g0433733' => 'osa', 'Os04g0286500' => 'osa', 'Os05g0227800' => 'osa', 'Os06g0521000' => 'osa', 'Os06g0635500' => 'osa', 'Os06g0660650' => 'osa', 'Os07g0554400' => 'osa', 'Os08g0225900' => 'osa', 'Os08g0561000' => 'osa', 'Os09g0241700' => 'osa', 'Os09g0351900' => 'osa', 'Os11g0220700' => 'osa', 'Os11g0282700' => 'osa', 'Os12g0169300' => 'osa', 'Os12g0228500' => 'osa', 'Os12g0543800' => 'osa', 'PGR044G1547' => 'pgr', 'Potri.005G239150' => 'ptr', 'Potri.010G014250' => 'ptr', 'Prupe.1G172500' => 'ppe', 'Prupe.1G196800' => 'ppe', 'Prupe.1G279700' => 'ppe', 'Prupe.2G026400' => 'ppe', 'Prupe.3G094000' => 'ppe', 'Prupe.4G287300' => 'ppe', 'QL01p022166' => 'qlo', 'QL01p051890' => 'qlo', 'QL02p009469' => 'qlo', 'QL02p046053' => 'qlo', 'QL02p057958' => 'qlo', 'QL02p093127' => 'qlo', 'QL03p006855' => 'qlo', 'QL03p071586' => 'qlo', 'QL04p000022' => 'qlo', 'QL04p000024' => 'qlo', 'QL04p003192' => 'qlo', 'QL05p011416' => 'qlo', 'QL06p039590' => 'qlo', 'QL06p052750' => 'qlo', 'QL06p053821' => 'qlo', 'QL07p025287' => 'qlo', 'QL09p033218' => 'qlo', 'QL09p040841' => 'qlo', 'QL10p020337' => 'qlo', 'QL10p027209' => 'qlo', 'QL10p027969' => 'qlo', 'QL10p048988' => 'qlo', 'QL11p001241' => 'qlo', 'QL11p028487' => 'qlo', 'RcHm_v2.0_Chr2g0105031' => 'rch', 'RcHm_v2.0_Chr2g0117811' => 'rch', 'RcHm_v2.0_Chr6g0270241' => 'rch', 'RcHm_v2.0_Chr7g0215961' => 'rch', 'RcHm_v2.0_Chr7g0231991' => 'rch', 'Rhsim01G0041500' => 'rsi', 'Rhsim01G0115000' => 'rsi', 'Rhsim01G0115400' => 'rsi', 'Rhsim01G0133600' => 'rsi', 'Rhsim01G0159900' => 'rsi', 'Rhsim02G0189400' => 'rsi', 'Rhsim03G0135600' => 'rsi', 'Rhsim03G0149900' => 'rsi', 'Rhsim04G0125600' => 'rsi', 'Rhsim05G0091700' => 'rsi', 'Rhsim05G0092900' => 'rsi', 'Rhsim06G0075000' => 'rsi', 'Rhsim07G0066400' => 'rsi', 'Rhsim07G0156400' => 'rsi', 'Rhsim07G0182200' => 'rsi', 'Rhsim07G0182300' => 'rsi', 'Rhsim08G0180400' => 'rsi', 'Rhsim09G0056800' => 'rsi', 'Rhsim10G0153300' => 'rsi', 'Rhsim11G0012700' => 'rsi', 'Rhsim12G0031800' => 'rsi', 'Rhsim12G0055400' => 'rsi', 'Rhsim12G0091400' => 'rsi', 'Rhsim13G0070800' => 'rsi', 'Rhsim13G0193300' => 'rsi', 'RhsimUnG0111600' => 'rsi', 'RhsimUnG0137500' => 'rsi', 'RhsimUnG0172900' => 'rsi', 'SGA_v2.0_scaffold11G05878' => 'sas', 'SGA_v2.0_scaffold167G38458' => 'sas', 'SGA_v2.0_scaffold19G08588' => 'sas', 'SGA_v2.0_scaffold239G43990' => 'sas', 'SGA_v2.0_scaffold260G45865' => 'sas', 'SGA_v2.0_scaffold309G48177' => 'sas', 'SGA_v2.0_scaffold76G25122' => 'sas', 'SGA_v2.0_scaffold85G26708' => 'sas', 'SHI13914' => 'shi', 'SHI30402' => 'shi', 'TWI09G0020' => 'twi', 'TWI09G0456' => 'twi', 'TWI09G1572' => 'twi', 'TWI12G0266' => 'twi', 'TWI12G1451' => 'twi', 'TWI14G0851' => 'twi', 'TWI15G0796' => 'twi', 'TWI18G0820' => 'twi', 'TWI18G1152' => 'twi', 'TWI23G0007' => 'twi', 'TWI23G0314' => 'twi', 'TWI31G0674' => 'twi', 'TWI31G0938' => 'twi', 'TWI34G0641' => 'twi', 'TWI34G1527' => 'twi', 'TWI36G0193' => 'twi', 'TWI36G0405' => 'twi', 'TWI38G0892' => 'twi', 'TWI38G0936' => 'twi', 'TWI38G2218' => 'twi', 'TWI53G0679' => 'twi', 'TWI53G0863' => 'twi', 'TWI53G1133' => 'twi', 'TWI60G0823' => 'twi', 'TWI63G0919' => 'twi', 'TWI63G1436' => 'twi', 'TWI73G0140' => 'twi', 'TWI73G0419' => 'twi', 'TWI73G0420' => 'twi', 'TWI73G1276' => 'twi', 'TWI74G0405' => 'twi', 'TWI74G0837' => 'twi', 'TWI75G0594' => 'twi', 'TWI75G1615' => 'twi', 'TWI77G0816' => 'twi', 'vmacro03831' => 'vma', 'vmacro13746' => 'vma', 'vmacro16089' => 'vma', 'vmacro22863' => 'vma', 'Zm00001eb085790' => 'zma', 'Zm00001eb114250' => 'zma', 'Zm00001eb138070' => 'zma', 'Zm00001eb167560' => 'zma', 'Zm00001eb199990' => 'zma', 'Zm00001eb368180' => 'zma', 'Zm00001eb382470' => 'zma' ) $gf_id = 'HOM05D001576' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001576' ) $data_identifier = 'HOM05D001576' $data_type = 'gf_id' $species_gene_counts = array( 'aox' => (int) 9, 'acertr' => (int) 3, 'cansat' => (int) 1, 'ccl' => (int) 4, 'cil' => (int) 145, 'camsi' => (int) 46, 'dca' => (int) 1, 'din' => (int) 1, 'fan' => (int) 12, 'fve' => (int) 9, 'gma' => (int) 5, 'han' => (int) 5, 'cav' => (int) 11, 'hma' => (int) 5, 'sun' => (int) 3, 'mdo' => (int) 3, 'mtr' => (int) 2, 'osa' => (int) 19, 'pgr' => (int) 1, 'ptr' => (int) 2, 'ppe' => (int) 6, 'qlo' => (int) 24, 'rch' => (int) 5, 'rsi' => (int) 28, 'sas' => (int) 8, 'shi' => (int) 2, 'twi' => (int) 35, 'vma' => (int) 4, 'zma' => (int) 7 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb382470' $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' => 'HOM05D001576', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '406', 'num_species' => '29' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'Aqoxy1G01456' => 'aox', 'Aqoxy1G02949' => 'aox', 'Aqoxy3G01274' => 'aox', 'Aqoxy3G02110' => 'aox', 'Aqoxy3G02268' => 'aox', 'Aqoxy5G02702' => 'aox', 'Aqoxy5G02988' => 'aox', 'Aqoxy5G03427' => 'aox', 'Aqoxy6G02363' => 'aox', 'Atru.chr1.3225' => 'acertr', 'Atru.chr8.1198' => 'acertr', 'Atru.chr9.790' => 'acertr', 'CANSAT01G3197' => 'cansat', 'Ciclev10003979m.g' => 'ccl', 'Ciclev10017471m.g' => 'ccl', 'Ciclev10018206m.g' => 'ccl', 'Ciclev10033751m.g' => 'ccl', 'CiPaw.01G000900' => 'cil', 'CiPaw.01G001000' => 'cil', 'CiPaw.01G033500' => 'cil', 'CiPaw.01G060300' => 'cil', 'CiPaw.01G070200' => 'cil', 'CiPaw.01G075100' => 'cil', 'CiPaw.01G084700' => 'cil', 'CiPaw.01G087900' => 'cil', 'CiPaw.01G092600' => 'cil', 'CiPaw.01G097200' => 'cil', 'CiPaw.01G098300' => 'cil', 'CiPaw.01G110200' => 'cil', 'CiPaw.01G118700' => 'cil', 'CiPaw.01G121200' => 'cil', 'CiPaw.01G132500' => 'cil', 'CiPaw.01G146900' => 'cil', 'CiPaw.01G174000' => 'cil', 'CiPaw.01G179900' => 'cil', 'CiPaw.01G183400' => 'cil', 'CiPaw.01G240000' => 'cil', 'CiPaw.01G283500' => 'cil', 'CiPaw.01G307400' => 'cil', 'CiPaw.02G030800' => 'cil', 'CiPaw.02G047200' => 'cil', 'CiPaw.02G050500' => 'cil', 'CiPaw.02G069900' => 'cil', 'CiPaw.02G091600' => 'cil', 'CiPaw.02G095000' => 'cil', 'CiPaw.02G131900' => 'cil', 'CiPaw.03G043000' => 'cil', 'CiPaw.03G069900' => 'cil', 'CiPaw.03G088100' => 'cil', 'CiPaw.03G089300' => 'cil', 'CiPaw.03G093100' => 'cil', 'CiPaw.03G129800' => 'cil', 'CiPaw.03G131200' => 'cil', 'CiPaw.03G134500' => 'cil', 'CiPaw.03G152100' => 'cil', 'CiPaw.03G162700' => 'cil', 'CiPaw.03G172800' => 'cil', 'CiPaw.03G175800' => 'cil', 'CiPaw.03G181800' => 'cil', 'CiPaw.03G191400' => 'cil', 'CiPaw.03G198300' => 'cil', 'CiPaw.03G201300' => 'cil', 'CiPaw.03G224700' => 'cil', 'CiPaw.03G225000' => 'cil', 'CiPaw.04G065100' => 'cil', 'CiPaw.04G080400' => 'cil', 'CiPaw.04G113500' => 'cil', 'CiPaw.04G121900' => 'cil', 'CiPaw.04G144100' => 'cil', 'CiPaw.04G176500' => 'cil', 'CiPaw.05G086200' => 'cil', 'CiPaw.05G100200' => 'cil', 'CiPaw.05G114200' => 'cil', 'CiPaw.05G126800' => 'cil', 'CiPaw.05G228800' => 'cil', 'CiPaw.05G230600' => 'cil', 'CiPaw.05G236500' => 'cil', 'CiPaw.05G244800' => 'cil', 'CiPaw.06G026600' => 'cil', 'CiPaw.06G027900' => 'cil', 'CiPaw.06G051800' => 'cil', 'CiPaw.06G128500' => 'cil', 'CiPaw.06G165900' => 'cil', 'CiPaw.07G045400' => 'cil', 'CiPaw.07G048000' => 'cil', 'CiPaw.07G052000' => 'cil', 'CiPaw.07G073800' => 'cil', 'CiPaw.07G099700' => 'cil', 'CiPaw.07G108700' => 'cil', 'CiPaw.07G120000' => 'cil', 'CiPaw.07G134100' => 'cil', 'CiPaw.07G147000' => 'cil', 'CiPaw.07G149700' => 'cil', 'CiPaw.07G178300' => 'cil', 'CiPaw.07G184900' => 'cil', 'CiPaw.08G044500' => 'cil', 'CiPaw.08G046900' => 'cil', 'CiPaw.08G047300' => 'cil', 'CiPaw.08G115400' => 'cil', 'CiPaw.08G134700' => 'cil', 'CiPaw.08G157400' => 'cil', 'CiPaw.09G014300' => 'cil', 'CiPaw.09G088900' => 'cil', 'CiPaw.09G130900' => 'cil', 'CiPaw.09G133100' => 'cil', 'CiPaw.09G151300' => 'cil', 'CiPaw.09G172800' => 'cil', 'CiPaw.09G174900' => 'cil', 'CiPaw.09G175000' => 'cil', 'CiPaw.10G012800' => 'cil', 'CiPaw.10G028800' => 'cil', 'CiPaw.10G044700' => 'cil', 'CiPaw.10G067400' => 'cil', 'CiPaw.10G115900' => 'cil', 'CiPaw.10G126200' => 'cil', 'CiPaw.10G139700' => 'cil', 'CiPaw.10G155100' => 'cil', 'CiPaw.11G011300' => 'cil', 'CiPaw.11G025900' => 'cil', 'CiPaw.11G104100' => 'cil', 'CiPaw.11G142700' => 'cil', 'CiPaw.11G164500' => 'cil', 'CiPaw.11G189100' => 'cil', 'CiPaw.11G197100' => 'cil', 'CiPaw.12G006100' => 'cil', 'CiPaw.12G038500' => 'cil', 'CiPaw.12G041400' => 'cil', 'CiPaw.12G041600' => 'cil', 'CiPaw.12G051300' => 'cil', 'CiPaw.12G101800' => 'cil', 'CiPaw.12G107800' => 'cil', 'CiPaw.13G033200' => 'cil', 'CiPaw.13G129900' => 'cil', 'CiPaw.13G160200' => 'cil', 'CiPaw.14G018900' => 'cil', 'CiPaw.14G029000' => 'cil', 'CiPaw.14G031000' => 'cil', 'CiPaw.14G032000' => 'cil', 'CiPaw.14G032300' => 'cil', 'CiPaw.14G040600' => 'cil', 'CiPaw.14G060500' => 'cil', 'CiPaw.14G061500' => 'cil', 'CiPaw.14G077500' => 'cil', 'CiPaw.14G088300' => 'cil', 'CiPaw.14G108500' => 'cil', 'CiPaw.14G121300' => 'cil', 'CiPaw.14G133000' => 'cil', 'CiPaw.14G134600' => 'cil', 'CiPaw.15G027200' => 'cil', 'CiPaw.15G037700' => 'cil', 'CiPaw.15G050900' => 'cil', 'CiPaw.15G067200' => 'cil', 'CiPaw.15G072000' => 'cil', 'CiPaw.15G112900' => 'cil', 'CiPaw.15G133200' => 'cil', 'CiPaw.15G139500' => 'cil', 'CiPaw.15G155400' => 'cil', 'CiPaw.16G006000' => 'cil', 'CiPaw.16G013100' => 'cil', 'CiPaw.16G047100' => 'cil', 'CiPaw.16G048900' => 'cil', 'CiPaw.16G070300' => 'cil', 'CSS0000195' => 'camsi', 'CSS0001664' => 'camsi', 'CSS0002566' => 'camsi', 'CSS0003077' => 'camsi', 'CSS0004257' => 'camsi', 'CSS0004495' => 'camsi', 'CSS0004599' => 'camsi', 'CSS0004943' => 'camsi', 'CSS0005302' => 'camsi', 'CSS0006274' => 'camsi', 'CSS0006547' => 'camsi', 'CSS0006860' => 'camsi', 'CSS0008814' => 'camsi', 'CSS0008946' => 'camsi', 'CSS0009093' => 'camsi', 'CSS0010221' => 'camsi', 'CSS0010296' => 'camsi', 'CSS0010386' => 'camsi', 'CSS0010831' => 'camsi', 'CSS0011061' => 'camsi', 'CSS0012008' => 'camsi', 'CSS0012194' => 'camsi', 'CSS0013580' => 'camsi', 'CSS0014176' => 'camsi', 'CSS0014280' => 'camsi', 'CSS0014799' => 'camsi', 'CSS0015368' => 'camsi', 'CSS0017473' => 'camsi', 'CSS0019281' => 'camsi', 'CSS0021320' => 'camsi', 'CSS0021750' => 'camsi', 'CSS0023642' => 'camsi', 'CSS0023792' => 'camsi', 'CSS0031528' => 'camsi', 'CSS0033894' => 'camsi', 'CSS0034959' => 'camsi', 'CSS0035632' => 'camsi', 'CSS0038450' => 'camsi', 'CSS0039293' => 'camsi', 'CSS0041053' => 'camsi', 'CSS0041981' => 'camsi', 'CSS0042573' => 'camsi', 'CSS0042927' => 'camsi', 'CSS0047725' => 'camsi', 'CSS0049636' => 'camsi', 'CSS0050513' => 'camsi', 'DCAR_030203' => 'dca', 'Dinv07939' => 'din', 'FAN01G0456' => 'fan', 'FAN02G3001' => 'fan', 'FAN04G2781' => 'fan', 'FAN05G1385' => 'fan', 'FAN05G3062' => 'fan', 'FAN08G2267' => 'fan', 'FAN10G0481' => 'fan', 'FAN10G1257' => 'fan', 'FAN14G0954' => 'fan', 'FAN14G2347' => 'fan', 'FAN15G0187' => 'fan', 'FAN25G2214' => 'fan', 'FvH4_1g21031' => 'fve', 'FvH4_3g16231' => 'fve', 'FvH4_3g26413' => 'fve', 'FvH4_3g29014' => 'fve', 'FvH4_3g31921' => 'fve', 'FvH4_4g19882' => 'fve', 'FvH4_5g21960' => 'fve', 'FvH4_5g29683' => 'fve', 'FvH4_7g13271' => 'fve', 'Glyma.01G062500' => 'gma', 'Glyma.07G140900' => 'gma', 'Glyma.09G140900' => 'gma', 'Glyma.12G112700' => 'gma', 'Glyma.17G168800' => 'gma', 'HanXRQChr01g0027001' => 'han', 'HanXRQChr04g0120511' => 'han', 'HanXRQChr08g0232381' => 'han', 'HanXRQChr09g0265661' => 'han', 'HanXRQChr13g0416031' => 'han', 'Haze_05835' => 'cav', 'Haze_06597' => 'cav', 'Haze_07921' => 'cav', 'Haze_08599' => 'cav', 'Haze_10686' => 'cav', 'Haze_12994' => 'cav', 'Haze_13466' => 'cav', 'Haze_16101' => 'cav', 'Haze_17766' => 'cav', 'Haze_18456' => 'cav', 'Haze_20229' => 'cav', 'Hma1.2p1_0324F.1_g125640' => 'hma', 'Hma1.2p1_0733F.1_g210230' => 'hma', 'Hma1.2p1_0921F.1_g236870' => 'hma', 'Hma1.2p1_1313F.1_g274940' => 'hma', 'Hma1.2p1_3059F.1_g332230' => 'hma', 'Hund15925' => 'sun', 'Hund19562' => 'sun', 'Hund21925' => 'sun', 'MD03G1177400' => 'mdo', 'MD07G1026100' => 'mdo', 'MD17G1218600' => 'mdo', 'Medtr0867s0010' => 'mtr', 'Medtr6g081150' => 'mtr', 'Os01g0527900' => 'osa', 'Os02g0463725' => 'osa', 'Os02g0785600' => 'osa', 'Os03g0433733' => 'osa', 'Os04g0286500' => 'osa', 'Os05g0227800' => 'osa', 'Os06g0521000' => 'osa', 'Os06g0635500' => 'osa', 'Os06g0660650' => 'osa', 'Os07g0554400' => 'osa', 'Os08g0225900' => 'osa', 'Os08g0561000' => 'osa', 'Os09g0241700' => 'osa', 'Os09g0351900' => 'osa', 'Os11g0220700' => 'osa', 'Os11g0282700' => 'osa', 'Os12g0169300' => 'osa', 'Os12g0228500' => 'osa', 'Os12g0543800' => 'osa', 'PGR044G1547' => 'pgr', 'Potri.005G239150' => 'ptr', 'Potri.010G014250' => 'ptr', 'Prupe.1G172500' => 'ppe', 'Prupe.1G196800' => 'ppe', 'Prupe.1G279700' => 'ppe', 'Prupe.2G026400' => 'ppe', 'Prupe.3G094000' => 'ppe', 'Prupe.4G287300' => 'ppe', 'QL01p022166' => 'qlo', 'QL01p051890' => 'qlo', 'QL02p009469' => 'qlo', 'QL02p046053' => 'qlo', 'QL02p057958' => 'qlo', 'QL02p093127' => 'qlo', 'QL03p006855' => 'qlo', 'QL03p071586' => 'qlo', 'QL04p000022' => 'qlo', 'QL04p000024' => 'qlo', 'QL04p003192' => 'qlo', 'QL05p011416' => 'qlo', 'QL06p039590' => 'qlo', 'QL06p052750' => 'qlo', 'QL06p053821' => 'qlo', 'QL07p025287' => 'qlo', 'QL09p033218' => 'qlo', 'QL09p040841' => 'qlo', 'QL10p020337' => 'qlo', 'QL10p027209' => 'qlo', 'QL10p027969' => 'qlo', 'QL10p048988' => 'qlo', 'QL11p001241' => 'qlo', 'QL11p028487' => 'qlo', 'RcHm_v2.0_Chr2g0105031' => 'rch', 'RcHm_v2.0_Chr2g0117811' => 'rch', 'RcHm_v2.0_Chr6g0270241' => 'rch', 'RcHm_v2.0_Chr7g0215961' => 'rch', 'RcHm_v2.0_Chr7g0231991' => 'rch', 'Rhsim01G0041500' => 'rsi', 'Rhsim01G0115000' => 'rsi', 'Rhsim01G0115400' => 'rsi', 'Rhsim01G0133600' => 'rsi', 'Rhsim01G0159900' => 'rsi', 'Rhsim02G0189400' => 'rsi', 'Rhsim03G0135600' => 'rsi', 'Rhsim03G0149900' => 'rsi', 'Rhsim04G0125600' => 'rsi', 'Rhsim05G0091700' => 'rsi', 'Rhsim05G0092900' => 'rsi', 'Rhsim06G0075000' => 'rsi', 'Rhsim07G0066400' => 'rsi', 'Rhsim07G0156400' => 'rsi', 'Rhsim07G0182200' => 'rsi', 'Rhsim07G0182300' => 'rsi', 'Rhsim08G0180400' => 'rsi', 'Rhsim09G0056800' => 'rsi', 'Rhsim10G0153300' => 'rsi', 'Rhsim11G0012700' => 'rsi', 'Rhsim12G0031800' => 'rsi', 'Rhsim12G0055400' => 'rsi', 'Rhsim12G0091400' => 'rsi', 'Rhsim13G0070800' => 'rsi', 'Rhsim13G0193300' => 'rsi', 'RhsimUnG0111600' => 'rsi', 'RhsimUnG0137500' => 'rsi', 'RhsimUnG0172900' => 'rsi', 'SGA_v2.0_scaffold11G05878' => 'sas', 'SGA_v2.0_scaffold167G38458' => 'sas', 'SGA_v2.0_scaffold19G08588' => 'sas', 'SGA_v2.0_scaffold239G43990' => 'sas', 'SGA_v2.0_scaffold260G45865' => 'sas', 'SGA_v2.0_scaffold309G48177' => 'sas', 'SGA_v2.0_scaffold76G25122' => 'sas', 'SGA_v2.0_scaffold85G26708' => 'sas', 'SHI13914' => 'shi', 'SHI30402' => 'shi', 'TWI09G0020' => 'twi', 'TWI09G0456' => 'twi', 'TWI09G1572' => 'twi', 'TWI12G0266' => 'twi', 'TWI12G1451' => 'twi', 'TWI14G0851' => 'twi', 'TWI15G0796' => 'twi', 'TWI18G0820' => 'twi', 'TWI18G1152' => 'twi', 'TWI23G0007' => 'twi', 'TWI23G0314' => 'twi', 'TWI31G0674' => 'twi', 'TWI31G0938' => 'twi', 'TWI34G0641' => 'twi', 'TWI34G1527' => 'twi', 'TWI36G0193' => 'twi', 'TWI36G0405' => 'twi', 'TWI38G0892' => 'twi', 'TWI38G0936' => 'twi', 'TWI38G2218' => 'twi', 'TWI53G0679' => 'twi', 'TWI53G0863' => 'twi', 'TWI53G1133' => 'twi', 'TWI60G0823' => 'twi', 'TWI63G0919' => 'twi', 'TWI63G1436' => 'twi', 'TWI73G0140' => 'twi', 'TWI73G0419' => 'twi', 'TWI73G0420' => 'twi', 'TWI73G1276' => 'twi', 'TWI74G0405' => 'twi', 'TWI74G0837' => 'twi', 'TWI75G0594' => 'twi', 'TWI75G1615' => 'twi', 'TWI77G0816' => 'twi', 'vmacro03831' => 'vma', 'vmacro13746' => 'vma', 'vmacro16089' => 'vma', 'vmacro22863' => 'vma', 'Zm00001eb085790' => 'zma', 'Zm00001eb114250' => 'zma', 'Zm00001eb138070' => 'zma', 'Zm00001eb167560' => 'zma', 'Zm00001eb199990' => 'zma', 'Zm00001eb368180' => 'zma', 'Zm00001eb382470' => 'zma' ), 'gf_id' => 'HOM05D001576', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001576' ), 'data_identifier' => 'HOM05D001576', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001576', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '406', 'num_species' => '29' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'Aqoxy1G01456' => 'aox', 'Aqoxy1G02949' => 'aox', 'Aqoxy3G01274' => 'aox', 'Aqoxy3G02110' => 'aox', 'Aqoxy3G02268' => 'aox', 'Aqoxy5G02702' => 'aox', 'Aqoxy5G02988' => 'aox', 'Aqoxy5G03427' => 'aox', 'Aqoxy6G02363' => 'aox', 'Atru.chr1.3225' => 'acertr', 'Atru.chr8.1198' => 'acertr', 'Atru.chr9.790' => 'acertr', 'CANSAT01G3197' => 'cansat', 'Ciclev10003979m.g' => 'ccl', 'Ciclev10017471m.g' => 'ccl', 'Ciclev10018206m.g' => 'ccl', 'Ciclev10033751m.g' => 'ccl', 'CiPaw.01G000900' => 'cil', 'CiPaw.01G001000' => 'cil', 'CiPaw.01G033500' => 'cil', 'CiPaw.01G060300' => 'cil', 'CiPaw.01G070200' => 'cil', 'CiPaw.01G075100' => 'cil', 'CiPaw.01G084700' => 'cil', 'CiPaw.01G087900' => 'cil', 'CiPaw.01G092600' => 'cil', 'CiPaw.01G097200' => 'cil', 'CiPaw.01G098300' => 'cil', 'CiPaw.01G110200' => 'cil', 'CiPaw.01G118700' => 'cil', 'CiPaw.01G121200' => 'cil', 'CiPaw.01G132500' => 'cil', 'CiPaw.01G146900' => 'cil', 'CiPaw.01G174000' => 'cil', 'CiPaw.01G179900' => 'cil', 'CiPaw.01G183400' => 'cil', 'CiPaw.01G240000' => 'cil', 'CiPaw.01G283500' => 'cil', 'CiPaw.01G307400' => 'cil', 'CiPaw.02G030800' => 'cil', 'CiPaw.02G047200' => 'cil', 'CiPaw.02G050500' => 'cil', 'CiPaw.02G069900' => 'cil', 'CiPaw.02G091600' => 'cil', 'CiPaw.02G095000' => 'cil', 'CiPaw.02G131900' => 'cil', 'CiPaw.03G043000' => 'cil', 'CiPaw.03G069900' => 'cil', 'CiPaw.03G088100' => 'cil', 'CiPaw.03G089300' => 'cil', 'CiPaw.03G093100' => 'cil', 'CiPaw.03G129800' => 'cil', 'CiPaw.03G131200' => 'cil', 'CiPaw.03G134500' => 'cil', 'CiPaw.03G152100' => 'cil', 'CiPaw.03G162700' => 'cil', 'CiPaw.03G172800' => 'cil', 'CiPaw.03G175800' => 'cil', 'CiPaw.03G181800' => 'cil', 'CiPaw.03G191400' => 'cil', 'CiPaw.03G198300' => 'cil', 'CiPaw.03G201300' => 'cil', 'CiPaw.03G224700' => 'cil', 'CiPaw.03G225000' => 'cil', 'CiPaw.04G065100' => 'cil', 'CiPaw.04G080400' => 'cil', 'CiPaw.04G113500' => 'cil', 'CiPaw.04G121900' => 'cil', 'CiPaw.04G144100' => 'cil', 'CiPaw.04G176500' => 'cil', 'CiPaw.05G086200' => 'cil', 'CiPaw.05G100200' => 'cil', 'CiPaw.05G114200' => 'cil', 'CiPaw.05G126800' => 'cil', 'CiPaw.05G228800' => 'cil', 'CiPaw.05G230600' => 'cil', 'CiPaw.05G236500' => 'cil', 'CiPaw.05G244800' => 'cil', 'CiPaw.06G026600' => 'cil', 'CiPaw.06G027900' => 'cil', 'CiPaw.06G051800' => 'cil', 'CiPaw.06G128500' => 'cil', 'CiPaw.06G165900' => 'cil', 'CiPaw.07G045400' => 'cil', 'CiPaw.07G048000' => 'cil', 'CiPaw.07G052000' => 'cil', 'CiPaw.07G073800' => 'cil', 'CiPaw.07G099700' => 'cil', 'CiPaw.07G108700' => 'cil', 'CiPaw.07G120000' => 'cil', 'CiPaw.07G134100' => 'cil', 'CiPaw.07G147000' => 'cil', 'CiPaw.07G149700' => 'cil', 'CiPaw.07G178300' => 'cil', 'CiPaw.07G184900' => 'cil', 'CiPaw.08G044500' => 'cil', 'CiPaw.08G046900' => 'cil', 'CiPaw.08G047300' => 'cil', 'CiPaw.08G115400' => 'cil', 'CiPaw.08G134700' => 'cil', 'CiPaw.08G157400' => 'cil', 'CiPaw.09G014300' => 'cil', 'CiPaw.09G088900' => 'cil', 'CiPaw.09G130900' => 'cil', 'CiPaw.09G133100' => 'cil', 'CiPaw.09G151300' => 'cil', 'CiPaw.09G172800' => 'cil', 'CiPaw.09G174900' => 'cil', 'CiPaw.09G175000' => 'cil', 'CiPaw.10G012800' => 'cil', 'CiPaw.10G028800' => 'cil', 'CiPaw.10G044700' => 'cil', 'CiPaw.10G067400' => 'cil', 'CiPaw.10G115900' => 'cil', 'CiPaw.10G126200' => 'cil', 'CiPaw.10G139700' => 'cil', 'CiPaw.10G155100' => 'cil', 'CiPaw.11G011300' => 'cil', 'CiPaw.11G025900' => 'cil', 'CiPaw.11G104100' => 'cil', 'CiPaw.11G142700' => 'cil', 'CiPaw.11G164500' => 'cil', 'CiPaw.11G189100' => 'cil', 'CiPaw.11G197100' => 'cil', 'CiPaw.12G006100' => 'cil', 'CiPaw.12G038500' => 'cil', 'CiPaw.12G041400' => 'cil', 'CiPaw.12G041600' => 'cil', 'CiPaw.12G051300' => 'cil', 'CiPaw.12G101800' => 'cil', 'CiPaw.12G107800' => 'cil', 'CiPaw.13G033200' => 'cil', 'CiPaw.13G129900' => 'cil', 'CiPaw.13G160200' => 'cil', 'CiPaw.14G018900' => 'cil', 'CiPaw.14G029000' => 'cil', 'CiPaw.14G031000' => 'cil', 'CiPaw.14G032000' => 'cil', 'CiPaw.14G032300' => 'cil', 'CiPaw.14G040600' => 'cil', 'CiPaw.14G060500' => 'cil', 'CiPaw.14G061500' => 'cil', 'CiPaw.14G077500' => 'cil', 'CiPaw.14G088300' => 'cil', 'CiPaw.14G108500' => 'cil', 'CiPaw.14G121300' => 'cil', 'CiPaw.14G133000' => 'cil', 'CiPaw.14G134600' => 'cil', 'CiPaw.15G027200' => 'cil', 'CiPaw.15G037700' => 'cil', 'CiPaw.15G050900' => 'cil', 'CiPaw.15G067200' => 'cil', 'CiPaw.15G072000' => 'cil', 'CiPaw.15G112900' => 'cil', 'CiPaw.15G133200' => 'cil', 'CiPaw.15G139500' => 'cil', 'CiPaw.15G155400' => 'cil', 'CiPaw.16G006000' => 'cil', 'CiPaw.16G013100' => 'cil', 'CiPaw.16G047100' => 'cil', 'CiPaw.16G048900' => 'cil', 'CiPaw.16G070300' => 'cil', 'CSS0000195' => 'camsi', 'CSS0001664' => 'camsi', 'CSS0002566' => 'camsi', 'CSS0003077' => 'camsi', 'CSS0004257' => 'camsi', 'CSS0004495' => 'camsi', 'CSS0004599' => 'camsi', 'CSS0004943' => 'camsi', 'CSS0005302' => 'camsi', 'CSS0006274' => 'camsi', 'CSS0006547' => 'camsi', 'CSS0006860' => 'camsi', 'CSS0008814' => 'camsi', 'CSS0008946' => 'camsi', 'CSS0009093' => 'camsi', 'CSS0010221' => 'camsi', 'CSS0010296' => 'camsi', 'CSS0010386' => 'camsi', 'CSS0010831' => 'camsi', 'CSS0011061' => 'camsi', 'CSS0012008' => 'camsi', 'CSS0012194' => 'camsi', 'CSS0013580' => 'camsi', 'CSS0014176' => 'camsi', 'CSS0014280' => 'camsi', 'CSS0014799' => 'camsi', 'CSS0015368' => 'camsi', 'CSS0017473' => 'camsi', 'CSS0019281' => 'camsi', 'CSS0021320' => 'camsi', 'CSS0021750' => 'camsi', 'CSS0023642' => 'camsi', 'CSS0023792' => 'camsi', 'CSS0031528' => 'camsi', 'CSS0033894' => 'camsi', 'CSS0034959' => 'camsi', 'CSS0035632' => 'camsi', 'CSS0038450' => 'camsi', 'CSS0039293' => 'camsi', 'CSS0041053' => 'camsi', 'CSS0041981' => 'camsi', 'CSS0042573' => 'camsi', 'CSS0042927' => 'camsi', 'CSS0047725' => 'camsi', 'CSS0049636' => 'camsi', 'CSS0050513' => 'camsi', 'DCAR_030203' => 'dca', 'Dinv07939' => 'din', 'FAN01G0456' => 'fan', 'FAN02G3001' => 'fan', 'FAN04G2781' => 'fan', 'FAN05G1385' => 'fan', 'FAN05G3062' => 'fan', 'FAN08G2267' => 'fan', 'FAN10G0481' => 'fan', 'FAN10G1257' => 'fan', 'FAN14G0954' => 'fan', 'FAN14G2347' => 'fan', 'FAN15G0187' => 'fan', 'FAN25G2214' => 'fan', 'FvH4_1g21031' => 'fve', 'FvH4_3g16231' => 'fve', 'FvH4_3g26413' => 'fve', 'FvH4_3g29014' => 'fve', 'FvH4_3g31921' => 'fve', 'FvH4_4g19882' => 'fve', 'FvH4_5g21960' => 'fve', 'FvH4_5g29683' => 'fve', 'FvH4_7g13271' => 'fve', 'Glyma.01G062500' => 'gma', 'Glyma.07G140900' => 'gma', 'Glyma.09G140900' => 'gma', 'Glyma.12G112700' => 'gma', 'Glyma.17G168800' => 'gma', 'HanXRQChr01g0027001' => 'han', 'HanXRQChr04g0120511' => 'han', 'HanXRQChr08g0232381' => 'han', 'HanXRQChr09g0265661' => 'han', 'HanXRQChr13g0416031' => 'han', 'Haze_05835' => 'cav', 'Haze_06597' => 'cav', 'Haze_07921' => 'cav', 'Haze_08599' => 'cav', 'Haze_10686' => 'cav', 'Haze_12994' => 'cav', 'Haze_13466' => 'cav', 'Haze_16101' => 'cav', 'Haze_17766' => 'cav', 'Haze_18456' => 'cav', 'Haze_20229' => 'cav', 'Hma1.2p1_0324F.1_g125640' => 'hma', 'Hma1.2p1_0733F.1_g210230' => 'hma', 'Hma1.2p1_0921F.1_g236870' => 'hma', 'Hma1.2p1_1313F.1_g274940' => 'hma', 'Hma1.2p1_3059F.1_g332230' => 'hma', 'Hund15925' => 'sun', 'Hund19562' => 'sun', 'Hund21925' => 'sun', 'MD03G1177400' => 'mdo', 'MD07G1026100' => 'mdo', 'MD17G1218600' => 'mdo', 'Medtr0867s0010' => 'mtr', 'Medtr6g081150' => 'mtr', 'Os01g0527900' => 'osa', 'Os02g0463725' => 'osa', 'Os02g0785600' => 'osa', 'Os03g0433733' => 'osa', 'Os04g0286500' => 'osa', 'Os05g0227800' => 'osa', 'Os06g0521000' => 'osa', 'Os06g0635500' => 'osa', 'Os06g0660650' => 'osa', 'Os07g0554400' => 'osa', 'Os08g0225900' => 'osa', 'Os08g0561000' => 'osa', 'Os09g0241700' => 'osa', 'Os09g0351900' => 'osa', 'Os11g0220700' => 'osa', 'Os11g0282700' => 'osa', 'Os12g0169300' => 'osa', 'Os12g0228500' => 'osa', 'Os12g0543800' => 'osa', 'PGR044G1547' => 'pgr', 'Potri.005G239150' => 'ptr', 'Potri.010G014250' => 'ptr', 'Prupe.1G172500' => 'ppe', 'Prupe.1G196800' => 'ppe', 'Prupe.1G279700' => 'ppe', 'Prupe.2G026400' => 'ppe', 'Prupe.3G094000' => 'ppe', 'Prupe.4G287300' => 'ppe', 'QL01p022166' => 'qlo', 'QL01p051890' => 'qlo', 'QL02p009469' => 'qlo', 'QL02p046053' => 'qlo', 'QL02p057958' => 'qlo', 'QL02p093127' => 'qlo', 'QL03p006855' => 'qlo', 'QL03p071586' => 'qlo', 'QL04p000022' => 'qlo', 'QL04p000024' => 'qlo', 'QL04p003192' => 'qlo', 'QL05p011416' => 'qlo', 'QL06p039590' => 'qlo', 'QL06p052750' => 'qlo', 'QL06p053821' => 'qlo', 'QL07p025287' => 'qlo', 'QL09p033218' => 'qlo', 'QL09p040841' => 'qlo', 'QL10p020337' => 'qlo', 'QL10p027209' => 'qlo', 'QL10p027969' => 'qlo', 'QL10p048988' => 'qlo', 'QL11p001241' => 'qlo', 'QL11p028487' => 'qlo', 'RcHm_v2.0_Chr2g0105031' => 'rch', 'RcHm_v2.0_Chr2g0117811' => 'rch', 'RcHm_v2.0_Chr6g0270241' => 'rch', 'RcHm_v2.0_Chr7g0215961' => 'rch', 'RcHm_v2.0_Chr7g0231991' => 'rch', 'Rhsim01G0041500' => 'rsi', 'Rhsim01G0115000' => 'rsi', 'Rhsim01G0115400' => 'rsi', 'Rhsim01G0133600' => 'rsi', 'Rhsim01G0159900' => 'rsi', 'Rhsim02G0189400' => 'rsi', 'Rhsim03G0135600' => 'rsi', 'Rhsim03G0149900' => 'rsi', 'Rhsim04G0125600' => 'rsi', 'Rhsim05G0091700' => 'rsi', 'Rhsim05G0092900' => 'rsi', 'Rhsim06G0075000' => 'rsi', 'Rhsim07G0066400' => 'rsi', 'Rhsim07G0156400' => 'rsi', 'Rhsim07G0182200' => 'rsi', 'Rhsim07G0182300' => 'rsi', 'Rhsim08G0180400' => 'rsi', 'Rhsim09G0056800' => 'rsi', 'Rhsim10G0153300' => 'rsi', 'Rhsim11G0012700' => 'rsi', 'Rhsim12G0031800' => 'rsi', 'Rhsim12G0055400' => 'rsi', 'Rhsim12G0091400' => 'rsi', 'Rhsim13G0070800' => 'rsi', 'Rhsim13G0193300' => 'rsi', 'RhsimUnG0111600' => 'rsi', 'RhsimUnG0137500' => 'rsi', 'RhsimUnG0172900' => 'rsi', 'SGA_v2.0_scaffold11G05878' => 'sas', 'SGA_v2.0_scaffold167G38458' => 'sas', 'SGA_v2.0_scaffold19G08588' => 'sas', 'SGA_v2.0_scaffold239G43990' => 'sas', 'SGA_v2.0_scaffold260G45865' => 'sas', 'SGA_v2.0_scaffold309G48177' => 'sas', 'SGA_v2.0_scaffold76G25122' => 'sas', 'SGA_v2.0_scaffold85G26708' => 'sas', 'SHI13914' => 'shi', 'SHI30402' => 'shi', 'TWI09G0020' => 'twi', 'TWI09G0456' => 'twi', 'TWI09G1572' => 'twi', 'TWI12G0266' => 'twi', 'TWI12G1451' => 'twi', 'TWI14G0851' => 'twi', 'TWI15G0796' => 'twi', 'TWI18G0820' => 'twi', 'TWI18G1152' => 'twi', 'TWI23G0007' => 'twi', 'TWI23G0314' => 'twi', 'TWI31G0674' => 'twi', 'TWI31G0938' => 'twi', 'TWI34G0641' => 'twi', 'TWI34G1527' => 'twi', 'TWI36G0193' => 'twi', 'TWI36G0405' => 'twi', 'TWI38G0892' => 'twi', 'TWI38G0936' => 'twi', 'TWI38G2218' => 'twi', 'TWI53G0679' => 'twi', 'TWI53G0863' => 'twi', 'TWI53G1133' => 'twi', 'TWI60G0823' => 'twi', 'TWI63G0919' => 'twi', 'TWI63G1436' => 'twi', 'TWI73G0140' => 'twi', 'TWI73G0419' => 'twi', 'TWI73G0420' => 'twi', 'TWI73G1276' => 'twi', 'TWI74G0405' => 'twi', 'TWI74G0837' => 'twi', 'TWI75G0594' => 'twi', 'TWI75G1615' => 'twi', 'TWI77G0816' => 'twi', 'vmacro03831' => 'vma', 'vmacro13746' => 'vma', 'vmacro16089' => 'vma', 'vmacro22863' => 'vma', 'Zm00001eb085790' => 'zma', 'Zm00001eb114250' => 'zma', 'Zm00001eb138070' => 'zma', 'Zm00001eb167560' => 'zma', 'Zm00001eb199990' => 'zma', 'Zm00001eb368180' => 'zma', 'Zm00001eb382470' => 'zma' ) $gf_id = 'HOM05D001576' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001576' ) $data_identifier = 'HOM05D001576' $data_type = 'gf_id' $species_gene_counts = array( 'aox' => (int) 9, 'acertr' => (int) 3, 'cansat' => (int) 1, 'ccl' => (int) 4, 'cil' => (int) 145, 'camsi' => (int) 46, 'dca' => (int) 1, 'din' => (int) 1, 'fan' => (int) 12, 'fve' => (int) 9, 'gma' => (int) 5, 'han' => (int) 5, 'cav' => (int) 11, 'hma' => (int) 5, 'sun' => (int) 3, 'mdo' => (int) 3, 'mtr' => (int) 2, 'osa' => (int) 19, 'pgr' => (int) 1, 'ptr' => (int) 2, 'ppe' => (int) 6, 'qlo' => (int) 24, 'rch' => (int) 5, 'rsi' => (int) 28, 'sas' => (int) 8, 'shi' => (int) 2, 'twi' => (int) 35, 'vma' => (int) 4, 'zma' => (int) 7 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb382470' $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' => 'HOM05D001576', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '406', 'num_species' => '29' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'Aqoxy1G01456' => 'aox', 'Aqoxy1G02949' => 'aox', 'Aqoxy3G01274' => 'aox', 'Aqoxy3G02110' => 'aox', 'Aqoxy3G02268' => 'aox', 'Aqoxy5G02702' => 'aox', 'Aqoxy5G02988' => 'aox', 'Aqoxy5G03427' => 'aox', 'Aqoxy6G02363' => 'aox', 'Atru.chr1.3225' => 'acertr', 'Atru.chr8.1198' => 'acertr', 'Atru.chr9.790' => 'acertr', 'CANSAT01G3197' => 'cansat', 'Ciclev10003979m.g' => 'ccl', 'Ciclev10017471m.g' => 'ccl', 'Ciclev10018206m.g' => 'ccl', 'Ciclev10033751m.g' => 'ccl', 'CiPaw.01G000900' => 'cil', 'CiPaw.01G001000' => 'cil', 'CiPaw.01G033500' => 'cil', 'CiPaw.01G060300' => 'cil', 'CiPaw.01G070200' => 'cil', 'CiPaw.01G075100' => 'cil', 'CiPaw.01G084700' => 'cil', 'CiPaw.01G087900' => 'cil', 'CiPaw.01G092600' => 'cil', 'CiPaw.01G097200' => 'cil', 'CiPaw.01G098300' => 'cil', 'CiPaw.01G110200' => 'cil', 'CiPaw.01G118700' => 'cil', 'CiPaw.01G121200' => 'cil', 'CiPaw.01G132500' => 'cil', 'CiPaw.01G146900' => 'cil', 'CiPaw.01G174000' => 'cil', 'CiPaw.01G179900' => 'cil', 'CiPaw.01G183400' => 'cil', 'CiPaw.01G240000' => 'cil', 'CiPaw.01G283500' => 'cil', 'CiPaw.01G307400' => 'cil', 'CiPaw.02G030800' => 'cil', 'CiPaw.02G047200' => 'cil', 'CiPaw.02G050500' => 'cil', 'CiPaw.02G069900' => 'cil', 'CiPaw.02G091600' => 'cil', 'CiPaw.02G095000' => 'cil', 'CiPaw.02G131900' => 'cil', 'CiPaw.03G043000' => 'cil', 'CiPaw.03G069900' => 'cil', 'CiPaw.03G088100' => 'cil', 'CiPaw.03G089300' => 'cil', 'CiPaw.03G093100' => 'cil', 'CiPaw.03G129800' => 'cil', 'CiPaw.03G131200' => 'cil', 'CiPaw.03G134500' => 'cil', 'CiPaw.03G152100' => 'cil', 'CiPaw.03G162700' => 'cil', 'CiPaw.03G172800' => 'cil', 'CiPaw.03G175800' => 'cil', 'CiPaw.03G181800' => 'cil', 'CiPaw.03G191400' => 'cil', 'CiPaw.03G198300' => 'cil', 'CiPaw.03G201300' => 'cil', 'CiPaw.03G224700' => 'cil', 'CiPaw.03G225000' => 'cil', 'CiPaw.04G065100' => 'cil', 'CiPaw.04G080400' => 'cil', 'CiPaw.04G113500' => 'cil', 'CiPaw.04G121900' => 'cil', 'CiPaw.04G144100' => 'cil', 'CiPaw.04G176500' => 'cil', 'CiPaw.05G086200' => 'cil', 'CiPaw.05G100200' => 'cil', 'CiPaw.05G114200' => 'cil', 'CiPaw.05G126800' => 'cil', 'CiPaw.05G228800' => 'cil', 'CiPaw.05G230600' => 'cil', 'CiPaw.05G236500' => 'cil', 'CiPaw.05G244800' => 'cil', 'CiPaw.06G026600' => 'cil', 'CiPaw.06G027900' => 'cil', 'CiPaw.06G051800' => 'cil', 'CiPaw.06G128500' => 'cil', 'CiPaw.06G165900' => 'cil', 'CiPaw.07G045400' => 'cil', 'CiPaw.07G048000' => 'cil', 'CiPaw.07G052000' => 'cil', 'CiPaw.07G073800' => 'cil', 'CiPaw.07G099700' => 'cil', 'CiPaw.07G108700' => 'cil', 'CiPaw.07G120000' => 'cil', 'CiPaw.07G134100' => 'cil', 'CiPaw.07G147000' => 'cil', 'CiPaw.07G149700' => 'cil', 'CiPaw.07G178300' => 'cil', 'CiPaw.07G184900' => 'cil', 'CiPaw.08G044500' => 'cil', 'CiPaw.08G046900' => 'cil', 'CiPaw.08G047300' => 'cil', 'CiPaw.08G115400' => 'cil', 'CiPaw.08G134700' => 'cil', 'CiPaw.08G157400' => 'cil', 'CiPaw.09G014300' => 'cil', 'CiPaw.09G088900' => 'cil', 'CiPaw.09G130900' => 'cil', 'CiPaw.09G133100' => 'cil', 'CiPaw.09G151300' => 'cil', 'CiPaw.09G172800' => 'cil', 'CiPaw.09G174900' => 'cil', 'CiPaw.09G175000' => 'cil', 'CiPaw.10G012800' => 'cil', 'CiPaw.10G028800' => 'cil', 'CiPaw.10G044700' => 'cil', 'CiPaw.10G067400' => 'cil', 'CiPaw.10G115900' => 'cil', 'CiPaw.10G126200' => 'cil', 'CiPaw.10G139700' => 'cil', 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=> 'qlo', 'QL07p025287' => 'qlo', 'QL09p033218' => 'qlo', 'QL09p040841' => 'qlo', 'QL10p020337' => 'qlo', 'QL10p027209' => 'qlo', 'QL10p027969' => 'qlo', 'QL10p048988' => 'qlo', 'QL11p001241' => 'qlo', 'QL11p028487' => 'qlo', 'RcHm_v2.0_Chr2g0105031' => 'rch', 'RcHm_v2.0_Chr2g0117811' => 'rch', 'RcHm_v2.0_Chr6g0270241' => 'rch', 'RcHm_v2.0_Chr7g0215961' => 'rch', 'RcHm_v2.0_Chr7g0231991' => 'rch', 'Rhsim01G0041500' => 'rsi', 'Rhsim01G0115000' => 'rsi', 'Rhsim01G0115400' => 'rsi', 'Rhsim01G0133600' => 'rsi', 'Rhsim01G0159900' => 'rsi', 'Rhsim02G0189400' => 'rsi', 'Rhsim03G0135600' => 'rsi', 'Rhsim03G0149900' => 'rsi', 'Rhsim04G0125600' => 'rsi', 'Rhsim05G0091700' => 'rsi', 'Rhsim05G0092900' => 'rsi', 'Rhsim06G0075000' => 'rsi', 'Rhsim07G0066400' => 'rsi', 'Rhsim07G0156400' => 'rsi', 'Rhsim07G0182200' => 'rsi', 'Rhsim07G0182300' => 'rsi', 'Rhsim08G0180400' => 'rsi', 'Rhsim09G0056800' => 'rsi', 'Rhsim10G0153300' => 'rsi', 'Rhsim11G0012700' => 'rsi', 'Rhsim12G0031800' => 'rsi', 'Rhsim12G0055400' => 'rsi', 'Rhsim12G0091400' => 'rsi', 'Rhsim13G0070800' => 'rsi', 'Rhsim13G0193300' => 'rsi', 'RhsimUnG0111600' => 'rsi', 'RhsimUnG0137500' => 'rsi', 'RhsimUnG0172900' => 'rsi', 'SGA_v2.0_scaffold11G05878' => 'sas', 'SGA_v2.0_scaffold167G38458' => 'sas', 'SGA_v2.0_scaffold19G08588' => 'sas', 'SGA_v2.0_scaffold239G43990' => 'sas', 'SGA_v2.0_scaffold260G45865' => 'sas', 'SGA_v2.0_scaffold309G48177' => 'sas', 'SGA_v2.0_scaffold76G25122' => 'sas', 'SGA_v2.0_scaffold85G26708' => 'sas', 'SHI13914' => 'shi', 'SHI30402' => 'shi', 'TWI09G0020' => 'twi', 'TWI09G0456' => 'twi', 'TWI09G1572' => 'twi', 'TWI12G0266' => 'twi', 'TWI12G1451' => 'twi', 'TWI14G0851' => 'twi', 'TWI15G0796' => 'twi', 'TWI18G0820' => 'twi', 'TWI18G1152' => 'twi', 'TWI23G0007' => 'twi', 'TWI23G0314' => 'twi', 'TWI31G0674' => 'twi', 'TWI31G0938' => 'twi', 'TWI34G0641' => 'twi', 'TWI34G1527' => 'twi', 'TWI36G0193' => 'twi', 'TWI36G0405' => 'twi', 'TWI38G0892' => 'twi', 'TWI38G0936' => 'twi', 'TWI38G2218' => 'twi', 'TWI53G0679' => 'twi', 'TWI53G0863' => 'twi', 'TWI53G1133' => 'twi', 'TWI60G0823' => 'twi', 'TWI63G0919' => 'twi', 'TWI63G1436' => 'twi', 'TWI73G0140' => 'twi', 'TWI73G0419' => 'twi', 'TWI73G0420' => 'twi', 'TWI73G1276' => 'twi', 'TWI74G0405' => 'twi', 'TWI74G0837' => 'twi', 'TWI75G0594' => 'twi', 'TWI75G1615' => 'twi', 'TWI77G0816' => 'twi', 'vmacro03831' => 'vma', 'vmacro13746' => 'vma', 'vmacro16089' => 'vma', 'vmacro22863' => 'vma', 'Zm00001eb085790' => 'zma', 'Zm00001eb114250' => 'zma', 'Zm00001eb138070' => 'zma', 'Zm00001eb167560' => 'zma', 'Zm00001eb199990' => 'zma', 'Zm00001eb368180' => 'zma', 'Zm00001eb382470' => 'zma' ), 'gf_id' => 'HOM05D001576', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001576' ), 'data_identifier' => 'HOM05D001576', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001576', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '406', 'num_species' => '29' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'Aqoxy1G01456' => 'aox', 'Aqoxy1G02949' => 'aox', 'Aqoxy3G01274' => 'aox', 'Aqoxy3G02110' => 'aox', 'Aqoxy3G02268' => 'aox', 'Aqoxy5G02702' => 'aox', 'Aqoxy5G02988' => 'aox', 'Aqoxy5G03427' => 'aox', 'Aqoxy6G02363' => 'aox', 'Atru.chr1.3225' => 'acertr', 'Atru.chr8.1198' => 'acertr', 'Atru.chr9.790' => 'acertr', 'CANSAT01G3197' => 'cansat', 'Ciclev10003979m.g' => 'ccl', 'Ciclev10017471m.g' => 'ccl', 'Ciclev10018206m.g' => 'ccl', 'Ciclev10033751m.g' => 'ccl', 'CiPaw.01G000900' => 'cil', 'CiPaw.01G001000' => 'cil', 'CiPaw.01G033500' => 'cil', 'CiPaw.01G060300' => 'cil', 'CiPaw.01G070200' => 'cil', 'CiPaw.01G075100' => 'cil', 'CiPaw.01G084700' => 'cil', 'CiPaw.01G087900' => 'cil', 'CiPaw.01G092600' => 'cil', 'CiPaw.01G097200' => 'cil', 'CiPaw.01G098300' => 'cil', 'CiPaw.01G110200' => 'cil', 'CiPaw.01G118700' => 'cil', 'CiPaw.01G121200' => 'cil', 'CiPaw.01G132500' => 'cil', 'CiPaw.01G146900' => 'cil', 'CiPaw.01G174000' => 'cil', 'CiPaw.01G179900' => 'cil', 'CiPaw.01G183400' => 'cil', 'CiPaw.01G240000' => 'cil', 'CiPaw.01G283500' => 'cil', 'CiPaw.01G307400' => 'cil', 'CiPaw.02G030800' => 'cil', 'CiPaw.02G047200' => 'cil', 'CiPaw.02G050500' => 'cil', 'CiPaw.02G069900' => 'cil', 'CiPaw.02G091600' => 'cil', 'CiPaw.02G095000' => 'cil', 'CiPaw.02G131900' => 'cil', 'CiPaw.03G043000' => 'cil', 'CiPaw.03G069900' => 'cil', 'CiPaw.03G088100' => 'cil', 'CiPaw.03G089300' => 'cil', 'CiPaw.03G093100' => 'cil', 'CiPaw.03G129800' => 'cil', 'CiPaw.03G131200' => 'cil', 'CiPaw.03G134500' => 'cil', 'CiPaw.03G152100' => 'cil', 'CiPaw.03G162700' => 'cil', 'CiPaw.03G172800' => 'cil', 'CiPaw.03G175800' => 'cil', 'CiPaw.03G181800' => 'cil', 'CiPaw.03G191400' => 'cil', 'CiPaw.03G198300' => 'cil', 'CiPaw.03G201300' => 'cil', 'CiPaw.03G224700' => 'cil', 'CiPaw.03G225000' => 'cil', 'CiPaw.04G065100' => 'cil', 'CiPaw.04G080400' => 'cil', 'CiPaw.04G113500' => 'cil', 'CiPaw.04G121900' => 'cil', 'CiPaw.04G144100' => 'cil', 'CiPaw.04G176500' => 'cil', 'CiPaw.05G086200' => 'cil', 'CiPaw.05G100200' => 'cil', 'CiPaw.05G114200' => 'cil', 'CiPaw.05G126800' => 'cil', 'CiPaw.05G228800' => 'cil', 'CiPaw.05G230600' => 'cil', 'CiPaw.05G236500' => 'cil', 'CiPaw.05G244800' => 'cil', 'CiPaw.06G026600' => 'cil', 'CiPaw.06G027900' => 'cil', 'CiPaw.06G051800' => 'cil', 'CiPaw.06G128500' => 'cil', 'CiPaw.06G165900' => 'cil', 'CiPaw.07G045400' => 'cil', 'CiPaw.07G048000' => 'cil', 'CiPaw.07G052000' => 'cil', 'CiPaw.07G073800' => 'cil', 'CiPaw.07G099700' => 'cil', 'CiPaw.07G108700' => 'cil', 'CiPaw.07G120000' => 'cil', 'CiPaw.07G134100' => 'cil', 'CiPaw.07G147000' => 'cil', 'CiPaw.07G149700' => 'cil', 'CiPaw.07G178300' => 'cil', 'CiPaw.07G184900' => 'cil', 'CiPaw.08G044500' => 'cil', 'CiPaw.08G046900' => 'cil', 'CiPaw.08G047300' => 'cil', 'CiPaw.08G115400' => 'cil', 'CiPaw.08G134700' => 'cil', 'CiPaw.08G157400' => 'cil', 'CiPaw.09G014300' => 'cil', 'CiPaw.09G088900' => 'cil', 'CiPaw.09G130900' => 'cil', 'CiPaw.09G133100' => 'cil', 'CiPaw.09G151300' => 'cil', 'CiPaw.09G172800' => 'cil', 'CiPaw.09G174900' => 'cil', 'CiPaw.09G175000' => 'cil', 'CiPaw.10G012800' => 'cil', 'CiPaw.10G028800' => 'cil', 'CiPaw.10G044700' => 'cil', 'CiPaw.10G067400' => 'cil', 'CiPaw.10G115900' => 'cil', 'CiPaw.10G126200' => 'cil', 'CiPaw.10G139700' => 'cil', 'CiPaw.10G155100' => 'cil', 'CiPaw.11G011300' => 'cil', 'CiPaw.11G025900' => 'cil', 'CiPaw.11G104100' => 'cil', 'CiPaw.11G142700' => 'cil', 'CiPaw.11G164500' => 'cil', 'CiPaw.11G189100' => 'cil', 'CiPaw.11G197100' => 'cil', 'CiPaw.12G006100' => 'cil', 'CiPaw.12G038500' => 'cil', 'CiPaw.12G041400' => 'cil', 'CiPaw.12G041600' => 'cil', 'CiPaw.12G051300' => 'cil', 'CiPaw.12G101800' => 'cil', 'CiPaw.12G107800' => 'cil', 'CiPaw.13G033200' => 'cil', 'CiPaw.13G129900' => 'cil', 'CiPaw.13G160200' => 'cil', 'CiPaw.14G018900' => 'cil', 'CiPaw.14G029000' => 'cil', 'CiPaw.14G031000' => 'cil', 'CiPaw.14G032000' => 'cil', 'CiPaw.14G032300' => 'cil', 'CiPaw.14G040600' => 'cil', 'CiPaw.14G060500' => 'cil', 'CiPaw.14G061500' => 'cil', 'CiPaw.14G077500' => 'cil', 'CiPaw.14G088300' => 'cil', 'CiPaw.14G108500' => 'cil', 'CiPaw.14G121300' => 'cil', 'CiPaw.14G133000' => 'cil', 'CiPaw.14G134600' => 'cil', 'CiPaw.15G027200' => 'cil', 'CiPaw.15G037700' => 'cil', 'CiPaw.15G050900' => 'cil', 'CiPaw.15G067200' => 'cil', 'CiPaw.15G072000' => 'cil', 'CiPaw.15G112900' => 'cil', 'CiPaw.15G133200' => 'cil', 'CiPaw.15G139500' => 'cil', 'CiPaw.15G155400' => 'cil', 'CiPaw.16G006000' => 'cil', 'CiPaw.16G013100' => 'cil', 'CiPaw.16G047100' => 'cil', 'CiPaw.16G048900' => 'cil', 'CiPaw.16G070300' => 'cil', 'CSS0000195' => 'camsi', 'CSS0001664' => 'camsi', 'CSS0002566' => 'camsi', 'CSS0003077' => 'camsi', 'CSS0004257' => 'camsi', 'CSS0004495' => 'camsi', 'CSS0004599' => 'camsi', 'CSS0004943' => 'camsi', 'CSS0005302' => 'camsi', 'CSS0006274' => 'camsi', 'CSS0006547' => 'camsi', 'CSS0006860' => 'camsi', 'CSS0008814' => 'camsi', 'CSS0008946' => 'camsi', 'CSS0009093' => 'camsi', 'CSS0010221' => 'camsi', 'CSS0010296' => 'camsi', 'CSS0010386' => 'camsi', 'CSS0010831' => 'camsi', 'CSS0011061' => 'camsi', 'CSS0012008' => 'camsi', 'CSS0012194' => 'camsi', 'CSS0013580' => 'camsi', 'CSS0014176' => 'camsi', 'CSS0014280' => 'camsi', 'CSS0014799' => 'camsi', 'CSS0015368' => 'camsi', 'CSS0017473' => 'camsi', 'CSS0019281' => 'camsi', 'CSS0021320' => 'camsi', 'CSS0021750' => 'camsi', 'CSS0023642' => 'camsi', 'CSS0023792' => 'camsi', 'CSS0031528' => 'camsi', 'CSS0033894' => 'camsi', 'CSS0034959' => 'camsi', 'CSS0035632' => 'camsi', 'CSS0038450' => 'camsi', 'CSS0039293' => 'camsi', 'CSS0041053' => 'camsi', 'CSS0041981' => 'camsi', 'CSS0042573' => 'camsi', 'CSS0042927' => 'camsi', 'CSS0047725' => 'camsi', 'CSS0049636' => 'camsi', 'CSS0050513' => 'camsi', 'DCAR_030203' => 'dca', 'Dinv07939' => 'din', 'FAN01G0456' => 'fan', 'FAN02G3001' => 'fan', 'FAN04G2781' => 'fan', 'FAN05G1385' => 'fan', 'FAN05G3062' => 'fan', 'FAN08G2267' => 'fan', 'FAN10G0481' => 'fan', 'FAN10G1257' => 'fan', 'FAN14G0954' => 'fan', 'FAN14G2347' => 'fan', 'FAN15G0187' => 'fan', 'FAN25G2214' => 'fan', 'FvH4_1g21031' => 'fve', 'FvH4_3g16231' => 'fve', 'FvH4_3g26413' => 'fve', 'FvH4_3g29014' => 'fve', 'FvH4_3g31921' => 'fve', 'FvH4_4g19882' => 'fve', 'FvH4_5g21960' => 'fve', 'FvH4_5g29683' => 'fve', 'FvH4_7g13271' => 'fve', 'Glyma.01G062500' => 'gma', 'Glyma.07G140900' => 'gma', 'Glyma.09G140900' => 'gma', 'Glyma.12G112700' => 'gma', 'Glyma.17G168800' => 'gma', 'HanXRQChr01g0027001' => 'han', 'HanXRQChr04g0120511' => 'han', 'HanXRQChr08g0232381' => 'han', 'HanXRQChr09g0265661' => 'han', 'HanXRQChr13g0416031' => 'han', 'Haze_05835' => 'cav', 'Haze_06597' => 'cav', 'Haze_07921' => 'cav', 'Haze_08599' => 'cav', 'Haze_10686' => 'cav', 'Haze_12994' => 'cav', 'Haze_13466' => 'cav', 'Haze_16101' => 'cav', 'Haze_17766' => 'cav', 'Haze_18456' => 'cav', 'Haze_20229' => 'cav', 'Hma1.2p1_0324F.1_g125640' => 'hma', 'Hma1.2p1_0733F.1_g210230' => 'hma', 'Hma1.2p1_0921F.1_g236870' => 'hma', 'Hma1.2p1_1313F.1_g274940' => 'hma', 'Hma1.2p1_3059F.1_g332230' => 'hma', 'Hund15925' => 'sun', 'Hund19562' => 'sun', 'Hund21925' => 'sun', 'MD03G1177400' => 'mdo', 'MD07G1026100' => 'mdo', 'MD17G1218600' => 'mdo', 'Medtr0867s0010' => 'mtr', 'Medtr6g081150' => 'mtr', 'Os01g0527900' => 'osa', 'Os02g0463725' => 'osa', 'Os02g0785600' => 'osa', 'Os03g0433733' => 'osa', 'Os04g0286500' => 'osa', 'Os05g0227800' => 'osa', 'Os06g0521000' => 'osa', 'Os06g0635500' => 'osa', 'Os06g0660650' => 'osa', 'Os07g0554400' => 'osa', 'Os08g0225900' => 'osa', 'Os08g0561000' => 'osa', 'Os09g0241700' => 'osa', 'Os09g0351900' => 'osa', 'Os11g0220700' => 'osa', 'Os11g0282700' => 'osa', 'Os12g0169300' => 'osa', 'Os12g0228500' => 'osa', 'Os12g0543800' => 'osa', 'PGR044G1547' => 'pgr', 'Potri.005G239150' => 'ptr', 'Potri.010G014250' => 'ptr', 'Prupe.1G172500' => 'ppe', 'Prupe.1G196800' => 'ppe', 'Prupe.1G279700' => 'ppe', 'Prupe.2G026400' => 'ppe', 'Prupe.3G094000' => 'ppe', 'Prupe.4G287300' => 'ppe', 'QL01p022166' => 'qlo', 'QL01p051890' => 'qlo', 'QL02p009469' => 'qlo', 'QL02p046053' => 'qlo', 'QL02p057958' => 'qlo', 'QL02p093127' => 'qlo', 'QL03p006855' => 'qlo', 'QL03p071586' => 'qlo', 'QL04p000022' => 'qlo', 'QL04p000024' => 'qlo', 'QL04p003192' => 'qlo', 'QL05p011416' => 'qlo', 'QL06p039590' => 'qlo', 'QL06p052750' => 'qlo', 'QL06p053821' => 'qlo', 'QL07p025287' => 'qlo', 'QL09p033218' => 'qlo', 'QL09p040841' => 'qlo', 'QL10p020337' => 'qlo', 'QL10p027209' => 'qlo', 'QL10p027969' => 'qlo', 'QL10p048988' => 'qlo', 'QL11p001241' => 'qlo', 'QL11p028487' => 'qlo', 'RcHm_v2.0_Chr2g0105031' => 'rch', 'RcHm_v2.0_Chr2g0117811' => 'rch', 'RcHm_v2.0_Chr6g0270241' => 'rch', 'RcHm_v2.0_Chr7g0215961' => 'rch', 'RcHm_v2.0_Chr7g0231991' => 'rch', 'Rhsim01G0041500' => 'rsi', 'Rhsim01G0115000' => 'rsi', 'Rhsim01G0115400' => 'rsi', 'Rhsim01G0133600' => 'rsi', 'Rhsim01G0159900' => 'rsi', 'Rhsim02G0189400' => 'rsi', 'Rhsim03G0135600' => 'rsi', 'Rhsim03G0149900' => 'rsi', 'Rhsim04G0125600' => 'rsi', 'Rhsim05G0091700' => 'rsi', 'Rhsim05G0092900' => 'rsi', 'Rhsim06G0075000' => 'rsi', 'Rhsim07G0066400' => 'rsi', 'Rhsim07G0156400' => 'rsi', 'Rhsim07G0182200' => 'rsi', 'Rhsim07G0182300' => 'rsi', 'Rhsim08G0180400' => 'rsi', 'Rhsim09G0056800' => 'rsi', 'Rhsim10G0153300' => 'rsi', 'Rhsim11G0012700' => 'rsi', 'Rhsim12G0031800' => 'rsi', 'Rhsim12G0055400' => 'rsi', 'Rhsim12G0091400' => 'rsi', 'Rhsim13G0070800' => 'rsi', 'Rhsim13G0193300' => 'rsi', 'RhsimUnG0111600' => 'rsi', 'RhsimUnG0137500' => 'rsi', 'RhsimUnG0172900' => 'rsi', 'SGA_v2.0_scaffold11G05878' => 'sas', 'SGA_v2.0_scaffold167G38458' => 'sas', 'SGA_v2.0_scaffold19G08588' => 'sas', 'SGA_v2.0_scaffold239G43990' => 'sas', 'SGA_v2.0_scaffold260G45865' => 'sas', 'SGA_v2.0_scaffold309G48177' => 'sas', 'SGA_v2.0_scaffold76G25122' => 'sas', 'SGA_v2.0_scaffold85G26708' => 'sas', 'SHI13914' => 'shi', 'SHI30402' => 'shi', 'TWI09G0020' => 'twi', 'TWI09G0456' => 'twi', 'TWI09G1572' => 'twi', 'TWI12G0266' => 'twi', 'TWI12G1451' => 'twi', 'TWI14G0851' => 'twi', 'TWI15G0796' => 'twi', 'TWI18G0820' => 'twi', 'TWI18G1152' => 'twi', 'TWI23G0007' => 'twi', 'TWI23G0314' => 'twi', 'TWI31G0674' => 'twi', 'TWI31G0938' => 'twi', 'TWI34G0641' => 'twi', 'TWI34G1527' => 'twi', 'TWI36G0193' => 'twi', 'TWI36G0405' => 'twi', 'TWI38G0892' => 'twi', 'TWI38G0936' => 'twi', 'TWI38G2218' => 'twi', 'TWI53G0679' => 'twi', 'TWI53G0863' => 'twi', 'TWI53G1133' => 'twi', 'TWI60G0823' => 'twi', 'TWI63G0919' => 'twi', 'TWI63G1436' => 'twi', 'TWI73G0140' => 'twi', 'TWI73G0419' => 'twi', 'TWI73G0420' => 'twi', 'TWI73G1276' => 'twi', 'TWI74G0405' => 'twi', 'TWI74G0837' => 'twi', 'TWI75G0594' => 'twi', 'TWI75G1615' => 'twi', 'TWI77G0816' => 'twi', 'vmacro03831' => 'vma', 'vmacro13746' => 'vma', 'vmacro16089' => 'vma', 'vmacro22863' => 'vma', 'Zm00001eb085790' => 'zma', 'Zm00001eb114250' => 'zma', 'Zm00001eb138070' => 'zma', 'Zm00001eb167560' => 'zma', 'Zm00001eb199990' => 'zma', 'Zm00001eb368180' => 'zma', 'Zm00001eb382470' => 'zma' ) $gf_id = 'HOM05D001576' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001576' ) $data_identifier = 'HOM05D001576' $data_type = 'gf_id' $species_gene_counts = array( 'aox' => (int) 9, 'acertr' => (int) 3, 'cansat' => (int) 1, 'ccl' => (int) 4, 'cil' => (int) 145, 'camsi' => (int) 46, 'dca' => (int) 1, 'din' => (int) 1, 'fan' => (int) 12, 'fve' => (int) 9, 'gma' => (int) 5, 'han' => (int) 5, 'cav' => (int) 11, 'hma' => (int) 5, 'sun' => (int) 3, 'mdo' => (int) 3, 'mtr' => (int) 2, 'osa' => (int) 19, 'pgr' => (int) 1, 'ptr' => (int) 2, 'ppe' => (int) 6, 'qlo' => (int) 24, 'rch' => (int) 5, 'rsi' => (int) 28, 'sas' => (int) 8, 'shi' => (int) 2, 'twi' => (int) 35, 'vma' => (int) 4, 'zma' => (int) 7 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb382470' $species_info = array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ) $local_species = 'pgr' $disabled = '' $selected = '' $num_hits = (int) 1include - APP/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp, line 33 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933 View::_renderElement() - CORE/Cake/View/View.php, line 1224 View::element() - CORE/Cake/View/View.php, line 418 include - APP/View/Elements/analysis/phylogenetics_module/gf_data_settings.ctp, line 37 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933 View::_renderElement() - CORE/Cake/View/View.php, line 1224 View::element() - CORE/Cake/View/View.php, line 418 include - APP/View/Elements/analysis/phylogenetics_module/parameter_selection.ctp, line 64 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933 View::_renderElement() - CORE/Cake/View/View.php, line 1224 View::element() - CORE/Cake/View/View.php, line 418 include - APP/View/Analysis/custom_tree_creation.ctp, line 27 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933
$viewFile = '/www/bioinformatics01_ro/plaza/_dev_instances/feedback/app/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp' $dataForView = array( 'sidebar_info' => array( 'gf_id' => 'HOM05D001576', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '406', 'num_species' => '29' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'Aqoxy1G01456' => 'aox', 'Aqoxy1G02949' => 'aox', 'Aqoxy3G01274' => 'aox', 'Aqoxy3G02110' => 'aox', 'Aqoxy3G02268' => 'aox', 'Aqoxy5G02702' => 'aox', 'Aqoxy5G02988' => 'aox', 'Aqoxy5G03427' => 'aox', 'Aqoxy6G02363' => 'aox', 'Atru.chr1.3225' => 'acertr', 'Atru.chr8.1198' => 'acertr', 'Atru.chr9.790' => 'acertr', 'CANSAT01G3197' => 'cansat', 'Ciclev10003979m.g' => 'ccl', 'Ciclev10017471m.g' => 'ccl', 'Ciclev10018206m.g' => 'ccl', 'Ciclev10033751m.g' => 'ccl', 'CiPaw.01G000900' => 'cil', 'CiPaw.01G001000' => 'cil', 'CiPaw.01G033500' => 'cil', 'CiPaw.01G060300' => 'cil', 'CiPaw.01G070200' => 'cil', 'CiPaw.01G075100' => 'cil', 'CiPaw.01G084700' => 'cil', 'CiPaw.01G087900' => 'cil', 'CiPaw.01G092600' => 'cil', 'CiPaw.01G097200' => 'cil', 'CiPaw.01G098300' => 'cil', 'CiPaw.01G110200' => 'cil', 'CiPaw.01G118700' => 'cil', 'CiPaw.01G121200' => 'cil', 'CiPaw.01G132500' => 'cil', 'CiPaw.01G146900' => 'cil', 'CiPaw.01G174000' => 'cil', 'CiPaw.01G179900' => 'cil', 'CiPaw.01G183400' => 'cil', 'CiPaw.01G240000' => 'cil', 'CiPaw.01G283500' => 'cil', 'CiPaw.01G307400' => 'cil', 'CiPaw.02G030800' => 'cil', 'CiPaw.02G047200' => 'cil', 'CiPaw.02G050500' => 'cil', 'CiPaw.02G069900' => 'cil', 'CiPaw.02G091600' => 'cil', 'CiPaw.02G095000' => 'cil', 'CiPaw.02G131900' => 'cil', 'CiPaw.03G043000' => 'cil', 'CiPaw.03G069900' => 'cil', 'CiPaw.03G088100' => 'cil', 'CiPaw.03G089300' => 'cil', 'CiPaw.03G093100' => 'cil', 'CiPaw.03G129800' => 'cil', 'CiPaw.03G131200' => 'cil', 'CiPaw.03G134500' => 'cil', 'CiPaw.03G152100' => 'cil', 'CiPaw.03G162700' => 'cil', 'CiPaw.03G172800' => 'cil', 'CiPaw.03G175800' => 'cil', 'CiPaw.03G181800' => 'cil', 'CiPaw.03G191400' => 'cil', 'CiPaw.03G198300' => 'cil', 'CiPaw.03G201300' => 'cil', 'CiPaw.03G224700' => 'cil', 'CiPaw.03G225000' => 'cil', 'CiPaw.04G065100' => 'cil', 'CiPaw.04G080400' => 'cil', 'CiPaw.04G113500' => 'cil', 'CiPaw.04G121900' => 'cil', 'CiPaw.04G144100' => 'cil', 'CiPaw.04G176500' => 'cil', 'CiPaw.05G086200' => 'cil', 'CiPaw.05G100200' => 'cil', 'CiPaw.05G114200' => 'cil', 'CiPaw.05G126800' => 'cil', 'CiPaw.05G228800' => 'cil', 'CiPaw.05G230600' => 'cil', 'CiPaw.05G236500' => 'cil', 'CiPaw.05G244800' => 'cil', 'CiPaw.06G026600' => 'cil', 'CiPaw.06G027900' => 'cil', 'CiPaw.06G051800' => 'cil', 'CiPaw.06G128500' => 'cil', 'CiPaw.06G165900' => 'cil', 'CiPaw.07G045400' => 'cil', 'CiPaw.07G048000' => 'cil', 'CiPaw.07G052000' => 'cil', 'CiPaw.07G073800' => 'cil', 'CiPaw.07G099700' => 'cil', 'CiPaw.07G108700' => 'cil', 'CiPaw.07G120000' => 'cil', 'CiPaw.07G134100' => 'cil', 'CiPaw.07G147000' => 'cil', 'CiPaw.07G149700' => 'cil', 'CiPaw.07G178300' => 'cil', 'CiPaw.07G184900' => 'cil', 'CiPaw.08G044500' => 'cil', 'CiPaw.08G046900' => 'cil', 'CiPaw.08G047300' => 'cil', 'CiPaw.08G115400' => 'cil', 'CiPaw.08G134700' => 'cil', 'CiPaw.08G157400' => 'cil', 'CiPaw.09G014300' => 'cil', 'CiPaw.09G088900' => 'cil', 'CiPaw.09G130900' => 'cil', 'CiPaw.09G133100' => 'cil', 'CiPaw.09G151300' => 'cil', 'CiPaw.09G172800' => 'cil', 'CiPaw.09G174900' => 'cil', 'CiPaw.09G175000' => 'cil', 'CiPaw.10G012800' => 'cil', 'CiPaw.10G028800' => 'cil', 'CiPaw.10G044700' => 'cil', 'CiPaw.10G067400' => 'cil', 'CiPaw.10G115900' => 'cil', 'CiPaw.10G126200' => 'cil', 'CiPaw.10G139700' => 'cil', 'CiPaw.10G155100' => 'cil', 'CiPaw.11G011300' => 'cil', 'CiPaw.11G025900' => 'cil', 'CiPaw.11G104100' => 'cil', 'CiPaw.11G142700' => 'cil', 'CiPaw.11G164500' => 'cil', 'CiPaw.11G189100' => 'cil', 'CiPaw.11G197100' => 'cil', 'CiPaw.12G006100' => 'cil', 'CiPaw.12G038500' => 'cil', 'CiPaw.12G041400' => 'cil', 'CiPaw.12G041600' => 'cil', 'CiPaw.12G051300' => 'cil', 'CiPaw.12G101800' => 'cil', 'CiPaw.12G107800' => 'cil', 'CiPaw.13G033200' => 'cil', 'CiPaw.13G129900' => 'cil', 'CiPaw.13G160200' => 'cil', 'CiPaw.14G018900' => 'cil', 'CiPaw.14G029000' => 'cil', 'CiPaw.14G031000' => 'cil', 'CiPaw.14G032000' => 'cil', 'CiPaw.14G032300' => 'cil', 'CiPaw.14G040600' => 'cil', 'CiPaw.14G060500' => 'cil', 'CiPaw.14G061500' => 'cil', 'CiPaw.14G077500' => 'cil', 'CiPaw.14G088300' => 'cil', 'CiPaw.14G108500' => 'cil', 'CiPaw.14G121300' => 'cil', 'CiPaw.14G133000' => 'cil', 'CiPaw.14G134600' => 'cil', 'CiPaw.15G027200' => 'cil', 'CiPaw.15G037700' => 'cil', 'CiPaw.15G050900' => 'cil', 'CiPaw.15G067200' => 'cil', 'CiPaw.15G072000' => 'cil', 'CiPaw.15G112900' => 'cil', 'CiPaw.15G133200' => 'cil', 'CiPaw.15G139500' => 'cil', 'CiPaw.15G155400' => 'cil', 'CiPaw.16G006000' => 'cil', 'CiPaw.16G013100' => 'cil', 'CiPaw.16G047100' => 'cil', 'CiPaw.16G048900' => 'cil', 'CiPaw.16G070300' => 'cil', 'CSS0000195' => 'camsi', 'CSS0001664' => 'camsi', 'CSS0002566' => 'camsi', 'CSS0003077' => 'camsi', 'CSS0004257' => 'camsi', 'CSS0004495' => 'camsi', 'CSS0004599' => 'camsi', 'CSS0004943' => 'camsi', 'CSS0005302' => 'camsi', 'CSS0006274' => 'camsi', 'CSS0006547' => 'camsi', 'CSS0006860' => 'camsi', 'CSS0008814' => 'camsi', 'CSS0008946' => 'camsi', 'CSS0009093' => 'camsi', 'CSS0010221' => 'camsi', 'CSS0010296' => 'camsi', 'CSS0010386' => 'camsi', 'CSS0010831' => 'camsi', 'CSS0011061' => 'camsi', 'CSS0012008' => 'camsi', 'CSS0012194' => 'camsi', 'CSS0013580' => 'camsi', 'CSS0014176' => 'camsi', 'CSS0014280' => 'camsi', 'CSS0014799' => 'camsi', 'CSS0015368' => 'camsi', 'CSS0017473' => 'camsi', 'CSS0019281' => 'camsi', 'CSS0021320' => 'camsi', 'CSS0021750' => 'camsi', 'CSS0023642' => 'camsi', 'CSS0023792' => 'camsi', 'CSS0031528' => 'camsi', 'CSS0033894' => 'camsi', 'CSS0034959' => 'camsi', 'CSS0035632' => 'camsi', 'CSS0038450' => 'camsi', 'CSS0039293' => 'camsi', 'CSS0041053' => 'camsi', 'CSS0041981' => 'camsi', 'CSS0042573' => 'camsi', 'CSS0042927' => 'camsi', 'CSS0047725' => 'camsi', 'CSS0049636' => 'camsi', 'CSS0050513' => 'camsi', 'DCAR_030203' => 'dca', 'Dinv07939' => 'din', 'FAN01G0456' => 'fan', 'FAN02G3001' => 'fan', 'FAN04G2781' => 'fan', 'FAN05G1385' => 'fan', 'FAN05G3062' => 'fan', 'FAN08G2267' => 'fan', 'FAN10G0481' => 'fan', 'FAN10G1257' => 'fan', 'FAN14G0954' => 'fan', 'FAN14G2347' => 'fan', 'FAN15G0187' => 'fan', 'FAN25G2214' => 'fan', 'FvH4_1g21031' => 'fve', 'FvH4_3g16231' => 'fve', 'FvH4_3g26413' => 'fve', 'FvH4_3g29014' => 'fve', 'FvH4_3g31921' => 'fve', 'FvH4_4g19882' => 'fve', 'FvH4_5g21960' => 'fve', 'FvH4_5g29683' => 'fve', 'FvH4_7g13271' => 'fve', 'Glyma.01G062500' => 'gma', 'Glyma.07G140900' => 'gma', 'Glyma.09G140900' => 'gma', 'Glyma.12G112700' => 'gma', 'Glyma.17G168800' => 'gma', 'HanXRQChr01g0027001' => 'han', 'HanXRQChr04g0120511' => 'han', 'HanXRQChr08g0232381' => 'han', 'HanXRQChr09g0265661' => 'han', 'HanXRQChr13g0416031' => 'han', 'Haze_05835' => 'cav', 'Haze_06597' => 'cav', 'Haze_07921' => 'cav', 'Haze_08599' => 'cav', 'Haze_10686' => 'cav', 'Haze_12994' => 'cav', 'Haze_13466' => 'cav', 'Haze_16101' => 'cav', 'Haze_17766' => 'cav', 'Haze_18456' => 'cav', 'Haze_20229' => 'cav', 'Hma1.2p1_0324F.1_g125640' => 'hma', 'Hma1.2p1_0733F.1_g210230' => 'hma', 'Hma1.2p1_0921F.1_g236870' => 'hma', 'Hma1.2p1_1313F.1_g274940' => 'hma', 'Hma1.2p1_3059F.1_g332230' => 'hma', 'Hund15925' => 'sun', 'Hund19562' => 'sun', 'Hund21925' => 'sun', 'MD03G1177400' => 'mdo', 'MD07G1026100' => 'mdo', 'MD17G1218600' => 'mdo', 'Medtr0867s0010' => 'mtr', 'Medtr6g081150' => 'mtr', 'Os01g0527900' => 'osa', 'Os02g0463725' => 'osa', 'Os02g0785600' => 'osa', 'Os03g0433733' => 'osa', 'Os04g0286500' => 'osa', 'Os05g0227800' => 'osa', 'Os06g0521000' => 'osa', 'Os06g0635500' => 'osa', 'Os06g0660650' => 'osa', 'Os07g0554400' => 'osa', 'Os08g0225900' => 'osa', 'Os08g0561000' => 'osa', 'Os09g0241700' => 'osa', 'Os09g0351900' => 'osa', 'Os11g0220700' => 'osa', 'Os11g0282700' => 'osa', 'Os12g0169300' => 'osa', 'Os12g0228500' => 'osa', 'Os12g0543800' => 'osa', 'PGR044G1547' => 'pgr', 'Potri.005G239150' => 'ptr', 'Potri.010G014250' => 'ptr', 'Prupe.1G172500' => 'ppe', 'Prupe.1G196800' => 'ppe', 'Prupe.1G279700' => 'ppe', 'Prupe.2G026400' => 'ppe', 'Prupe.3G094000' => 'ppe', 'Prupe.4G287300' => 'ppe', 'QL01p022166' => 'qlo', 'QL01p051890' => 'qlo', 'QL02p009469' => 'qlo', 'QL02p046053' => 'qlo', 'QL02p057958' => 'qlo', 'QL02p093127' => 'qlo', 'QL03p006855' => 'qlo', 'QL03p071586' => 'qlo', 'QL04p000022' => 'qlo', 'QL04p000024' => 'qlo', 'QL04p003192' => 'qlo', 'QL05p011416' => 'qlo', 'QL06p039590' => 'qlo', 'QL06p052750' => 'qlo', 'QL06p053821' => 'qlo', 'QL07p025287' => 'qlo', 'QL09p033218' => 'qlo', 'QL09p040841' => 'qlo', 'QL10p020337' => 'qlo', 'QL10p027209' => 'qlo', 'QL10p027969' => 'qlo', 'QL10p048988' => 'qlo', 'QL11p001241' => 'qlo', 'QL11p028487' => 'qlo', 'RcHm_v2.0_Chr2g0105031' => 'rch', 'RcHm_v2.0_Chr2g0117811' => 'rch', 'RcHm_v2.0_Chr6g0270241' => 'rch', 'RcHm_v2.0_Chr7g0215961' => 'rch', 'RcHm_v2.0_Chr7g0231991' => 'rch', 'Rhsim01G0041500' => 'rsi', 'Rhsim01G0115000' => 'rsi', 'Rhsim01G0115400' => 'rsi', 'Rhsim01G0133600' => 'rsi', 'Rhsim01G0159900' => 'rsi', 'Rhsim02G0189400' => 'rsi', 'Rhsim03G0135600' => 'rsi', 'Rhsim03G0149900' => 'rsi', 'Rhsim04G0125600' => 'rsi', 'Rhsim05G0091700' => 'rsi', 'Rhsim05G0092900' => 'rsi', 'Rhsim06G0075000' => 'rsi', 'Rhsim07G0066400' => 'rsi', 'Rhsim07G0156400' => 'rsi', 'Rhsim07G0182200' => 'rsi', 'Rhsim07G0182300' => 'rsi', 'Rhsim08G0180400' => 'rsi', 'Rhsim09G0056800' => 'rsi', 'Rhsim10G0153300' => 'rsi', 'Rhsim11G0012700' => 'rsi', 'Rhsim12G0031800' => 'rsi', 'Rhsim12G0055400' => 'rsi', 'Rhsim12G0091400' => 'rsi', 'Rhsim13G0070800' => 'rsi', 'Rhsim13G0193300' => 'rsi', 'RhsimUnG0111600' => 'rsi', 'RhsimUnG0137500' => 'rsi', 'RhsimUnG0172900' => 'rsi', 'SGA_v2.0_scaffold11G05878' => 'sas', 'SGA_v2.0_scaffold167G38458' => 'sas', 'SGA_v2.0_scaffold19G08588' => 'sas', 'SGA_v2.0_scaffold239G43990' => 'sas', 'SGA_v2.0_scaffold260G45865' => 'sas', 'SGA_v2.0_scaffold309G48177' => 'sas', 'SGA_v2.0_scaffold76G25122' => 'sas', 'SGA_v2.0_scaffold85G26708' => 'sas', 'SHI13914' => 'shi', 'SHI30402' => 'shi', 'TWI09G0020' => 'twi', 'TWI09G0456' => 'twi', 'TWI09G1572' => 'twi', 'TWI12G0266' => 'twi', 'TWI12G1451' => 'twi', 'TWI14G0851' => 'twi', 'TWI15G0796' => 'twi', 'TWI18G0820' => 'twi', 'TWI18G1152' => 'twi', 'TWI23G0007' => 'twi', 'TWI23G0314' => 'twi', 'TWI31G0674' => 'twi', 'TWI31G0938' => 'twi', 'TWI34G0641' => 'twi', 'TWI34G1527' => 'twi', 'TWI36G0193' => 'twi', 'TWI36G0405' => 'twi', 'TWI38G0892' => 'twi', 'TWI38G0936' => 'twi', 'TWI38G2218' => 'twi', 'TWI53G0679' => 'twi', 'TWI53G0863' => 'twi', 'TWI53G1133' => 'twi', 'TWI60G0823' => 'twi', 'TWI63G0919' => 'twi', 'TWI63G1436' => 'twi', 'TWI73G0140' => 'twi', 'TWI73G0419' => 'twi', 'TWI73G0420' => 'twi', 'TWI73G1276' => 'twi', 'TWI74G0405' => 'twi', 'TWI74G0837' => 'twi', 'TWI75G0594' => 'twi', 'TWI75G1615' => 'twi', 'TWI77G0816' => 'twi', 'vmacro03831' => 'vma', 'vmacro13746' => 'vma', 'vmacro16089' => 'vma', 'vmacro22863' => 'vma', 'Zm00001eb085790' => 'zma', 'Zm00001eb114250' => 'zma', 'Zm00001eb138070' => 'zma', 'Zm00001eb167560' => 'zma', 'Zm00001eb199990' => 'zma', 'Zm00001eb368180' => 'zma', 'Zm00001eb382470' => 'zma' ), 'gf_id' => 'HOM05D001576', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001576' ), 'data_identifier' => 'HOM05D001576', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001576', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '406', 'num_species' => '29' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'Aqoxy1G01456' => 'aox', 'Aqoxy1G02949' => 'aox', 'Aqoxy3G01274' => 'aox', 'Aqoxy3G02110' => 'aox', 'Aqoxy3G02268' => 'aox', 'Aqoxy5G02702' => 'aox', 'Aqoxy5G02988' => 'aox', 'Aqoxy5G03427' => 'aox', 'Aqoxy6G02363' => 'aox', 'Atru.chr1.3225' => 'acertr', 'Atru.chr8.1198' => 'acertr', 'Atru.chr9.790' => 'acertr', 'CANSAT01G3197' => 'cansat', 'Ciclev10003979m.g' => 'ccl', 'Ciclev10017471m.g' => 'ccl', 'Ciclev10018206m.g' => 'ccl', 'Ciclev10033751m.g' => 'ccl', 'CiPaw.01G000900' => 'cil', 'CiPaw.01G001000' => 'cil', 'CiPaw.01G033500' => 'cil', 'CiPaw.01G060300' => 'cil', 'CiPaw.01G070200' => 'cil', 'CiPaw.01G075100' => 'cil', 'CiPaw.01G084700' => 'cil', 'CiPaw.01G087900' => 'cil', 'CiPaw.01G092600' => 'cil', 'CiPaw.01G097200' => 'cil', 'CiPaw.01G098300' => 'cil', 'CiPaw.01G110200' => 'cil', 'CiPaw.01G118700' => 'cil', 'CiPaw.01G121200' => 'cil', 'CiPaw.01G132500' => 'cil', 'CiPaw.01G146900' => 'cil', 'CiPaw.01G174000' => 'cil', 'CiPaw.01G179900' => 'cil', 'CiPaw.01G183400' => 'cil', 'CiPaw.01G240000' => 'cil', 'CiPaw.01G283500' => 'cil', 'CiPaw.01G307400' => 'cil', 'CiPaw.02G030800' => 'cil', 'CiPaw.02G047200' => 'cil', 'CiPaw.02G050500' => 'cil', 'CiPaw.02G069900' => 'cil', 'CiPaw.02G091600' => 'cil', 'CiPaw.02G095000' => 'cil', 'CiPaw.02G131900' => 'cil', 'CiPaw.03G043000' => 'cil', 'CiPaw.03G069900' => 'cil', 'CiPaw.03G088100' => 'cil', 'CiPaw.03G089300' => 'cil', 'CiPaw.03G093100' => 'cil', 'CiPaw.03G129800' => 'cil', 'CiPaw.03G131200' => 'cil', 'CiPaw.03G134500' => 'cil', 'CiPaw.03G152100' => 'cil', 'CiPaw.03G162700' => 'cil', 'CiPaw.03G172800' => 'cil', 'CiPaw.03G175800' => 'cil', 'CiPaw.03G181800' => 'cil', 'CiPaw.03G191400' => 'cil', 'CiPaw.03G198300' => 'cil', 'CiPaw.03G201300' => 'cil', 'CiPaw.03G224700' => 'cil', 'CiPaw.03G225000' => 'cil', 'CiPaw.04G065100' => 'cil', 'CiPaw.04G080400' => 'cil', 'CiPaw.04G113500' => 'cil', 'CiPaw.04G121900' => 'cil', 'CiPaw.04G144100' => 'cil', 'CiPaw.04G176500' => 'cil', 'CiPaw.05G086200' => 'cil', 'CiPaw.05G100200' => 'cil', 'CiPaw.05G114200' => 'cil', 'CiPaw.05G126800' => 'cil', 'CiPaw.05G228800' => 'cil', 'CiPaw.05G230600' => 'cil', 'CiPaw.05G236500' => 'cil', 'CiPaw.05G244800' => 'cil', 'CiPaw.06G026600' => 'cil', 'CiPaw.06G027900' => 'cil', 'CiPaw.06G051800' => 'cil', 'CiPaw.06G128500' => 'cil', 'CiPaw.06G165900' => 'cil', 'CiPaw.07G045400' => 'cil', 'CiPaw.07G048000' => 'cil', 'CiPaw.07G052000' => 'cil', 'CiPaw.07G073800' => 'cil', 'CiPaw.07G099700' => 'cil', 'CiPaw.07G108700' => 'cil', 'CiPaw.07G120000' => 'cil', 'CiPaw.07G134100' => 'cil', 'CiPaw.07G147000' => 'cil', 'CiPaw.07G149700' => 'cil', 'CiPaw.07G178300' => 'cil', 'CiPaw.07G184900' => 'cil', 'CiPaw.08G044500' => 'cil', 'CiPaw.08G046900' => 'cil', 'CiPaw.08G047300' => 'cil', 'CiPaw.08G115400' => 'cil', 'CiPaw.08G134700' => 'cil', 'CiPaw.08G157400' => 'cil', 'CiPaw.09G014300' => 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'CiPaw.14G032000' => 'cil', 'CiPaw.14G032300' => 'cil', 'CiPaw.14G040600' => 'cil', 'CiPaw.14G060500' => 'cil', 'CiPaw.14G061500' => 'cil', 'CiPaw.14G077500' => 'cil', 'CiPaw.14G088300' => 'cil', 'CiPaw.14G108500' => 'cil', 'CiPaw.14G121300' => 'cil', 'CiPaw.14G133000' => 'cil', 'CiPaw.14G134600' => 'cil', 'CiPaw.15G027200' => 'cil', 'CiPaw.15G037700' => 'cil', 'CiPaw.15G050900' => 'cil', 'CiPaw.15G067200' => 'cil', 'CiPaw.15G072000' => 'cil', 'CiPaw.15G112900' => 'cil', 'CiPaw.15G133200' => 'cil', 'CiPaw.15G139500' => 'cil', 'CiPaw.15G155400' => 'cil', 'CiPaw.16G006000' => 'cil', 'CiPaw.16G013100' => 'cil', 'CiPaw.16G047100' => 'cil', 'CiPaw.16G048900' => 'cil', 'CiPaw.16G070300' => 'cil', 'CSS0000195' => 'camsi', 'CSS0001664' => 'camsi', 'CSS0002566' => 'camsi', 'CSS0003077' => 'camsi', 'CSS0004257' => 'camsi', 'CSS0004495' => 'camsi', 'CSS0004599' => 'camsi', 'CSS0004943' => 'camsi', 'CSS0005302' => 'camsi', 'CSS0006274' => 'camsi', 'CSS0006547' => 'camsi', 'CSS0006860' => 'camsi', 'CSS0008814' => 'camsi', 'CSS0008946' => 'camsi', 'CSS0009093' => 'camsi', 'CSS0010221' => 'camsi', 'CSS0010296' => 'camsi', 'CSS0010386' => 'camsi', 'CSS0010831' => 'camsi', 'CSS0011061' => 'camsi', 'CSS0012008' => 'camsi', 'CSS0012194' => 'camsi', 'CSS0013580' => 'camsi', 'CSS0014176' => 'camsi', 'CSS0014280' => 'camsi', 'CSS0014799' => 'camsi', 'CSS0015368' => 'camsi', 'CSS0017473' => 'camsi', 'CSS0019281' => 'camsi', 'CSS0021320' => 'camsi', 'CSS0021750' => 'camsi', 'CSS0023642' => 'camsi', 'CSS0023792' => 'camsi', 'CSS0031528' => 'camsi', 'CSS0033894' => 'camsi', 'CSS0034959' => 'camsi', 'CSS0035632' => 'camsi', 'CSS0038450' => 'camsi', 'CSS0039293' => 'camsi', 'CSS0041053' => 'camsi', 'CSS0041981' => 'camsi', 'CSS0042573' => 'camsi', 'CSS0042927' => 'camsi', 'CSS0047725' => 'camsi', 'CSS0049636' => 'camsi', 'CSS0050513' => 'camsi', 'DCAR_030203' => 'dca', 'Dinv07939' => 'din', 'FAN01G0456' => 'fan', 'FAN02G3001' => 'fan', 'FAN04G2781' => 'fan', 'FAN05G1385' => 'fan', 'FAN05G3062' => 'fan', 'FAN08G2267' => 'fan', 'FAN10G0481' => 'fan', 'FAN10G1257' => 'fan', 'FAN14G0954' => 'fan', 'FAN14G2347' => 'fan', 'FAN15G0187' => 'fan', 'FAN25G2214' => 'fan', 'FvH4_1g21031' => 'fve', 'FvH4_3g16231' => 'fve', 'FvH4_3g26413' => 'fve', 'FvH4_3g29014' => 'fve', 'FvH4_3g31921' => 'fve', 'FvH4_4g19882' => 'fve', 'FvH4_5g21960' => 'fve', 'FvH4_5g29683' => 'fve', 'FvH4_7g13271' => 'fve', 'Glyma.01G062500' => 'gma', 'Glyma.07G140900' => 'gma', 'Glyma.09G140900' => 'gma', 'Glyma.12G112700' => 'gma', 'Glyma.17G168800' => 'gma', 'HanXRQChr01g0027001' => 'han', 'HanXRQChr04g0120511' => 'han', 'HanXRQChr08g0232381' => 'han', 'HanXRQChr09g0265661' => 'han', 'HanXRQChr13g0416031' => 'han', 'Haze_05835' => 'cav', 'Haze_06597' => 'cav', 'Haze_07921' => 'cav', 'Haze_08599' => 'cav', 'Haze_10686' => 'cav', 'Haze_12994' => 'cav', 'Haze_13466' => 'cav', 'Haze_16101' => 'cav', 'Haze_17766' => 'cav', 'Haze_18456' => 'cav', 'Haze_20229' => 'cav', 'Hma1.2p1_0324F.1_g125640' => 'hma', 'Hma1.2p1_0733F.1_g210230' => 'hma', 'Hma1.2p1_0921F.1_g236870' => 'hma', 'Hma1.2p1_1313F.1_g274940' => 'hma', 'Hma1.2p1_3059F.1_g332230' => 'hma', 'Hund15925' => 'sun', 'Hund19562' => 'sun', 'Hund21925' => 'sun', 'MD03G1177400' => 'mdo', 'MD07G1026100' => 'mdo', 'MD17G1218600' => 'mdo', 'Medtr0867s0010' => 'mtr', 'Medtr6g081150' => 'mtr', 'Os01g0527900' => 'osa', 'Os02g0463725' => 'osa', 'Os02g0785600' => 'osa', 'Os03g0433733' => 'osa', 'Os04g0286500' => 'osa', 'Os05g0227800' => 'osa', 'Os06g0521000' => 'osa', 'Os06g0635500' => 'osa', 'Os06g0660650' => 'osa', 'Os07g0554400' => 'osa', 'Os08g0225900' => 'osa', 'Os08g0561000' => 'osa', 'Os09g0241700' => 'osa', 'Os09g0351900' => 'osa', 'Os11g0220700' => 'osa', 'Os11g0282700' => 'osa', 'Os12g0169300' => 'osa', 'Os12g0228500' => 'osa', 'Os12g0543800' => 'osa', 'PGR044G1547' => 'pgr', 'Potri.005G239150' => 'ptr', 'Potri.010G014250' => 'ptr', 'Prupe.1G172500' => 'ppe', 'Prupe.1G196800' => 'ppe', 'Prupe.1G279700' => 'ppe', 'Prupe.2G026400' => 'ppe', 'Prupe.3G094000' => 'ppe', 'Prupe.4G287300' => 'ppe', 'QL01p022166' => 'qlo', 'QL01p051890' => 'qlo', 'QL02p009469' => 'qlo', 'QL02p046053' => 'qlo', 'QL02p057958' => 'qlo', 'QL02p093127' => 'qlo', 'QL03p006855' => 'qlo', 'QL03p071586' => 'qlo', 'QL04p000022' => 'qlo', 'QL04p000024' => 'qlo', 'QL04p003192' => 'qlo', 'QL05p011416' => 'qlo', 'QL06p039590' => 'qlo', 'QL06p052750' => 'qlo', 'QL06p053821' => 'qlo', 'QL07p025287' => 'qlo', 'QL09p033218' => 'qlo', 'QL09p040841' => 'qlo', 'QL10p020337' => 'qlo', 'QL10p027209' => 'qlo', 'QL10p027969' => 'qlo', 'QL10p048988' => 'qlo', 'QL11p001241' => 'qlo', 'QL11p028487' => 'qlo', 'RcHm_v2.0_Chr2g0105031' => 'rch', 'RcHm_v2.0_Chr2g0117811' => 'rch', 'RcHm_v2.0_Chr6g0270241' => 'rch', 'RcHm_v2.0_Chr7g0215961' => 'rch', 'RcHm_v2.0_Chr7g0231991' => 'rch', 'Rhsim01G0041500' => 'rsi', 'Rhsim01G0115000' => 'rsi', 'Rhsim01G0115400' => 'rsi', 'Rhsim01G0133600' => 'rsi', 'Rhsim01G0159900' => 'rsi', 'Rhsim02G0189400' => 'rsi', 'Rhsim03G0135600' => 'rsi', 'Rhsim03G0149900' => 'rsi', 'Rhsim04G0125600' => 'rsi', 'Rhsim05G0091700' => 'rsi', 'Rhsim05G0092900' => 'rsi', 'Rhsim06G0075000' => 'rsi', 'Rhsim07G0066400' => 'rsi', 'Rhsim07G0156400' => 'rsi', 'Rhsim07G0182200' => 'rsi', 'Rhsim07G0182300' => 'rsi', 'Rhsim08G0180400' => 'rsi', 'Rhsim09G0056800' => 'rsi', 'Rhsim10G0153300' => 'rsi', 'Rhsim11G0012700' => 'rsi', 'Rhsim12G0031800' => 'rsi', 'Rhsim12G0055400' => 'rsi', 'Rhsim12G0091400' => 'rsi', 'Rhsim13G0070800' => 'rsi', 'Rhsim13G0193300' => 'rsi', 'RhsimUnG0111600' => 'rsi', 'RhsimUnG0137500' => 'rsi', 'RhsimUnG0172900' => 'rsi', 'SGA_v2.0_scaffold11G05878' => 'sas', 'SGA_v2.0_scaffold167G38458' => 'sas', 'SGA_v2.0_scaffold19G08588' => 'sas', 'SGA_v2.0_scaffold239G43990' => 'sas', 'SGA_v2.0_scaffold260G45865' => 'sas', 'SGA_v2.0_scaffold309G48177' => 'sas', 'SGA_v2.0_scaffold76G25122' => 'sas', 'SGA_v2.0_scaffold85G26708' => 'sas', 'SHI13914' => 'shi', 'SHI30402' => 'shi', 'TWI09G0020' => 'twi', 'TWI09G0456' => 'twi', 'TWI09G1572' => 'twi', 'TWI12G0266' => 'twi', 'TWI12G1451' => 'twi', 'TWI14G0851' => 'twi', 'TWI15G0796' => 'twi', 'TWI18G0820' => 'twi', 'TWI18G1152' => 'twi', 'TWI23G0007' => 'twi', 'TWI23G0314' => 'twi', 'TWI31G0674' => 'twi', 'TWI31G0938' => 'twi', 'TWI34G0641' => 'twi', 'TWI34G1527' => 'twi', 'TWI36G0193' => 'twi', 'TWI36G0405' => 'twi', 'TWI38G0892' => 'twi', 'TWI38G0936' => 'twi', 'TWI38G2218' => 'twi', 'TWI53G0679' => 'twi', 'TWI53G0863' => 'twi', 'TWI53G1133' => 'twi', 'TWI60G0823' => 'twi', 'TWI63G0919' => 'twi', 'TWI63G1436' => 'twi', 'TWI73G0140' => 'twi', 'TWI73G0419' => 'twi', 'TWI73G0420' => 'twi', 'TWI73G1276' => 'twi', 'TWI74G0405' => 'twi', 'TWI74G0837' => 'twi', 'TWI75G0594' => 'twi', 'TWI75G1615' => 'twi', 'TWI77G0816' => 'twi', 'vmacro03831' => 'vma', 'vmacro13746' => 'vma', 'vmacro16089' => 'vma', 'vmacro22863' => 'vma', 'Zm00001eb085790' => 'zma', 'Zm00001eb114250' => 'zma', 'Zm00001eb138070' => 'zma', 'Zm00001eb167560' => 'zma', 'Zm00001eb199990' => 'zma', 'Zm00001eb368180' => 'zma', 'Zm00001eb382470' => 'zma' ) $gf_id = 'HOM05D001576' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001576' ) $data_identifier = 'HOM05D001576' $data_type = 'gf_id' $species_gene_counts = array( 'aox' => (int) 9, 'acertr' => (int) 3, 'cansat' => (int) 1, 'ccl' => (int) 4, 'cil' => (int) 145, 'camsi' => (int) 46, 'dca' => (int) 1, 'din' => (int) 1, 'fan' => (int) 12, 'fve' => (int) 9, 'gma' => (int) 5, 'han' => (int) 5, 'cav' => (int) 11, 'hma' => (int) 5, 'sun' => (int) 3, 'mdo' => (int) 3, 'mtr' => (int) 2, 'osa' => (int) 19, 'pgr' => (int) 1, 'ptr' => (int) 2, 'ppe' => (int) 6, 'qlo' => (int) 24, 'rch' => (int) 5, 'rsi' => (int) 28, 'sas' => (int) 8, 'shi' => (int) 2, 'twi' => (int) 35, 'vma' => (int) 4, 'zma' => (int) 7 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb382470' $species_info = array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ) $local_species = 'pgr' $disabled = '' $selected = '' $num_hits = (int) 1
Warning (2): count(): Parameter must be an array or an object that implements Countable [APP/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp, line 33]Code Context $disabled = (!array_key_exists($local_species,$species_gene_counts))?"disabled":""; $selected = (isset($selected_species) && array_key_exists($local_species,$selected_species))?"checked='checked'":""; $num_hits = (array_key_exists($local_species,$species_gene_counts))?count($species_gene_counts[$local_species]):0; $viewFile = '/www/bioinformatics01_ro/plaza/_dev_instances/feedback/app/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp' $dataForView = array( 'sidebar_info' => array( 'gf_id' => 'HOM05D001576', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '406', 'num_species' => '29' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'Aqoxy1G01456' => 'aox', 'Aqoxy1G02949' => 'aox', 'Aqoxy3G01274' => 'aox', 'Aqoxy3G02110' => 'aox', 'Aqoxy3G02268' => 'aox', 'Aqoxy5G02702' => 'aox', 'Aqoxy5G02988' => 'aox', 'Aqoxy5G03427' => 'aox', 'Aqoxy6G02363' => 'aox', 'Atru.chr1.3225' => 'acertr', 'Atru.chr8.1198' => 'acertr', 'Atru.chr9.790' => 'acertr', 'CANSAT01G3197' => 'cansat', 'Ciclev10003979m.g' => 'ccl', 'Ciclev10017471m.g' => 'ccl', 'Ciclev10018206m.g' => 'ccl', 'Ciclev10033751m.g' => 'ccl', 'CiPaw.01G000900' => 'cil', 'CiPaw.01G001000' => 'cil', 'CiPaw.01G033500' => 'cil', 'CiPaw.01G060300' => 'cil', 'CiPaw.01G070200' => 'cil', 'CiPaw.01G075100' => 'cil', 'CiPaw.01G084700' => 'cil', 'CiPaw.01G087900' => 'cil', 'CiPaw.01G092600' => 'cil', 'CiPaw.01G097200' => 'cil', 'CiPaw.01G098300' => 'cil', 'CiPaw.01G110200' => 'cil', 'CiPaw.01G118700' => 'cil', 'CiPaw.01G121200' => 'cil', 'CiPaw.01G132500' => 'cil', 'CiPaw.01G146900' => 'cil', 'CiPaw.01G174000' => 'cil', 'CiPaw.01G179900' => 'cil', 'CiPaw.01G183400' => 'cil', 'CiPaw.01G240000' => 'cil', 'CiPaw.01G283500' => 'cil', 'CiPaw.01G307400' => 'cil', 'CiPaw.02G030800' => 'cil', 'CiPaw.02G047200' => 'cil', 'CiPaw.02G050500' => 'cil', 'CiPaw.02G069900' => 'cil', 'CiPaw.02G091600' => 'cil', 'CiPaw.02G095000' => 'cil', 'CiPaw.02G131900' => 'cil', 'CiPaw.03G043000' => 'cil', 'CiPaw.03G069900' => 'cil', 'CiPaw.03G088100' => 'cil', 'CiPaw.03G089300' => 'cil', 'CiPaw.03G093100' => 'cil', 'CiPaw.03G129800' => 'cil', 'CiPaw.03G131200' => 'cil', 'CiPaw.03G134500' => 'cil', 'CiPaw.03G152100' => 'cil', 'CiPaw.03G162700' => 'cil', 'CiPaw.03G172800' => 'cil', 'CiPaw.03G175800' => 'cil', 'CiPaw.03G181800' => 'cil', 'CiPaw.03G191400' => 'cil', 'CiPaw.03G198300' => 'cil', 'CiPaw.03G201300' => 'cil', 'CiPaw.03G224700' => 'cil', 'CiPaw.03G225000' => 'cil', 'CiPaw.04G065100' => 'cil', 'CiPaw.04G080400' => 'cil', 'CiPaw.04G113500' => 'cil', 'CiPaw.04G121900' => 'cil', 'CiPaw.04G144100' => 'cil', 'CiPaw.04G176500' => 'cil', 'CiPaw.05G086200' => 'cil', 'CiPaw.05G100200' => 'cil', 'CiPaw.05G114200' => 'cil', 'CiPaw.05G126800' => 'cil', 'CiPaw.05G228800' => 'cil', 'CiPaw.05G230600' => 'cil', 'CiPaw.05G236500' => 'cil', 'CiPaw.05G244800' => 'cil', 'CiPaw.06G026600' => 'cil', 'CiPaw.06G027900' => 'cil', 'CiPaw.06G051800' => 'cil', 'CiPaw.06G128500' => 'cil', 'CiPaw.06G165900' => 'cil', 'CiPaw.07G045400' => 'cil', 'CiPaw.07G048000' => 'cil', 'CiPaw.07G052000' => 'cil', 'CiPaw.07G073800' => 'cil', 'CiPaw.07G099700' => 'cil', 'CiPaw.07G108700' => 'cil', 'CiPaw.07G120000' => 'cil', 'CiPaw.07G134100' => 'cil', 'CiPaw.07G147000' => 'cil', 'CiPaw.07G149700' => 'cil', 'CiPaw.07G178300' => 'cil', 'CiPaw.07G184900' => 'cil', 'CiPaw.08G044500' => 'cil', 'CiPaw.08G046900' => 'cil', 'CiPaw.08G047300' => 'cil', 'CiPaw.08G115400' => 'cil', 'CiPaw.08G134700' => 'cil', 'CiPaw.08G157400' => 'cil', 'CiPaw.09G014300' => 'cil', 'CiPaw.09G088900' => 'cil', 'CiPaw.09G130900' => 'cil', 'CiPaw.09G133100' => 'cil', 'CiPaw.09G151300' => 'cil', 'CiPaw.09G172800' => 'cil', 'CiPaw.09G174900' => 'cil', 'CiPaw.09G175000' => 'cil', 'CiPaw.10G012800' => 'cil', 'CiPaw.10G028800' => 'cil', 'CiPaw.10G044700' => 'cil', 'CiPaw.10G067400' => 'cil', 'CiPaw.10G115900' => 'cil', 'CiPaw.10G126200' => 'cil', 'CiPaw.10G139700' => 'cil', 'CiPaw.10G155100' => 'cil', 'CiPaw.11G011300' => 'cil', 'CiPaw.11G025900' => 'cil', 'CiPaw.11G104100' => 'cil', 'CiPaw.11G142700' => 'cil', 'CiPaw.11G164500' => 'cil', 'CiPaw.11G189100' => 'cil', 'CiPaw.11G197100' => 'cil', 'CiPaw.12G006100' => 'cil', 'CiPaw.12G038500' => 'cil', 'CiPaw.12G041400' => 'cil', 'CiPaw.12G041600' => 'cil', 'CiPaw.12G051300' => 'cil', 'CiPaw.12G101800' => 'cil', 'CiPaw.12G107800' => 'cil', 'CiPaw.13G033200' => 'cil', 'CiPaw.13G129900' => 'cil', 'CiPaw.13G160200' => 'cil', 'CiPaw.14G018900' => 'cil', 'CiPaw.14G029000' => 'cil', 'CiPaw.14G031000' => 'cil', 'CiPaw.14G032000' => 'cil', 'CiPaw.14G032300' => 'cil', 'CiPaw.14G040600' => 'cil', 'CiPaw.14G060500' => 'cil', 'CiPaw.14G061500' => 'cil', 'CiPaw.14G077500' => 'cil', 'CiPaw.14G088300' => 'cil', 'CiPaw.14G108500' => 'cil', 'CiPaw.14G121300' => 'cil', 'CiPaw.14G133000' => 'cil', 'CiPaw.14G134600' => 'cil', 'CiPaw.15G027200' => 'cil', 'CiPaw.15G037700' => 'cil', 'CiPaw.15G050900' => 'cil', 'CiPaw.15G067200' => 'cil', 'CiPaw.15G072000' => 'cil', 'CiPaw.15G112900' => 'cil', 'CiPaw.15G133200' => 'cil', 'CiPaw.15G139500' => 'cil', 'CiPaw.15G155400' => 'cil', 'CiPaw.16G006000' => 'cil', 'CiPaw.16G013100' => 'cil', 'CiPaw.16G047100' => 'cil', 'CiPaw.16G048900' => 'cil', 'CiPaw.16G070300' => 'cil', 'CSS0000195' => 'camsi', 'CSS0001664' => 'camsi', 'CSS0002566' => 'camsi', 'CSS0003077' => 'camsi', 'CSS0004257' => 'camsi', 'CSS0004495' => 'camsi', 'CSS0004599' => 'camsi', 'CSS0004943' => 'camsi', 'CSS0005302' => 'camsi', 'CSS0006274' => 'camsi', 'CSS0006547' => 'camsi', 'CSS0006860' => 'camsi', 'CSS0008814' => 'camsi', 'CSS0008946' => 'camsi', 'CSS0009093' => 'camsi', 'CSS0010221' => 'camsi', 'CSS0010296' => 'camsi', 'CSS0010386' => 'camsi', 'CSS0010831' => 'camsi', 'CSS0011061' => 'camsi', 'CSS0012008' => 'camsi', 'CSS0012194' => 'camsi', 'CSS0013580' => 'camsi', 'CSS0014176' => 'camsi', 'CSS0014280' => 'camsi', 'CSS0014799' => 'camsi', 'CSS0015368' => 'camsi', 'CSS0017473' => 'camsi', 'CSS0019281' => 'camsi', 'CSS0021320' => 'camsi', 'CSS0021750' => 'camsi', 'CSS0023642' => 'camsi', 'CSS0023792' => 'camsi', 'CSS0031528' => 'camsi', 'CSS0033894' => 'camsi', 'CSS0034959' => 'camsi', 'CSS0035632' => 'camsi', 'CSS0038450' => 'camsi', 'CSS0039293' => 'camsi', 'CSS0041053' => 'camsi', 'CSS0041981' => 'camsi', 'CSS0042573' => 'camsi', 'CSS0042927' => 'camsi', 'CSS0047725' => 'camsi', 'CSS0049636' => 'camsi', 'CSS0050513' => 'camsi', 'DCAR_030203' => 'dca', 'Dinv07939' => 'din', 'FAN01G0456' => 'fan', 'FAN02G3001' => 'fan', 'FAN04G2781' => 'fan', 'FAN05G1385' => 'fan', 'FAN05G3062' => 'fan', 'FAN08G2267' => 'fan', 'FAN10G0481' => 'fan', 'FAN10G1257' => 'fan', 'FAN14G0954' => 'fan', 'FAN14G2347' => 'fan', 'FAN15G0187' => 'fan', 'FAN25G2214' => 'fan', 'FvH4_1g21031' => 'fve', 'FvH4_3g16231' => 'fve', 'FvH4_3g26413' => 'fve', 'FvH4_3g29014' => 'fve', 'FvH4_3g31921' => 'fve', 'FvH4_4g19882' => 'fve', 'FvH4_5g21960' => 'fve', 'FvH4_5g29683' => 'fve', 'FvH4_7g13271' => 'fve', 'Glyma.01G062500' => 'gma', 'Glyma.07G140900' => 'gma', 'Glyma.09G140900' => 'gma', 'Glyma.12G112700' => 'gma', 'Glyma.17G168800' => 'gma', 'HanXRQChr01g0027001' => 'han', 'HanXRQChr04g0120511' => 'han', 'HanXRQChr08g0232381' => 'han', 'HanXRQChr09g0265661' => 'han', 'HanXRQChr13g0416031' => 'han', 'Haze_05835' => 'cav', 'Haze_06597' => 'cav', 'Haze_07921' => 'cav', 'Haze_08599' => 'cav', 'Haze_10686' => 'cav', 'Haze_12994' => 'cav', 'Haze_13466' => 'cav', 'Haze_16101' => 'cav', 'Haze_17766' => 'cav', 'Haze_18456' => 'cav', 'Haze_20229' => 'cav', 'Hma1.2p1_0324F.1_g125640' => 'hma', 'Hma1.2p1_0733F.1_g210230' => 'hma', 'Hma1.2p1_0921F.1_g236870' => 'hma', 'Hma1.2p1_1313F.1_g274940' => 'hma', 'Hma1.2p1_3059F.1_g332230' => 'hma', 'Hund15925' => 'sun', 'Hund19562' => 'sun', 'Hund21925' => 'sun', 'MD03G1177400' => 'mdo', 'MD07G1026100' => 'mdo', 'MD17G1218600' => 'mdo', 'Medtr0867s0010' => 'mtr', 'Medtr6g081150' => 'mtr', 'Os01g0527900' => 'osa', 'Os02g0463725' => 'osa', 'Os02g0785600' => 'osa', 'Os03g0433733' => 'osa', 'Os04g0286500' => 'osa', 'Os05g0227800' => 'osa', 'Os06g0521000' => 'osa', 'Os06g0635500' => 'osa', 'Os06g0660650' => 'osa', 'Os07g0554400' => 'osa', 'Os08g0225900' => 'osa', 'Os08g0561000' => 'osa', 'Os09g0241700' => 'osa', 'Os09g0351900' => 'osa', 'Os11g0220700' => 'osa', 'Os11g0282700' => 'osa', 'Os12g0169300' => 'osa', 'Os12g0228500' => 'osa', 'Os12g0543800' => 'osa', 'PGR044G1547' => 'pgr', 'Potri.005G239150' => 'ptr', 'Potri.010G014250' => 'ptr', 'Prupe.1G172500' => 'ppe', 'Prupe.1G196800' => 'ppe', 'Prupe.1G279700' => 'ppe', 'Prupe.2G026400' => 'ppe', 'Prupe.3G094000' => 'ppe', 'Prupe.4G287300' => 'ppe', 'QL01p022166' => 'qlo', 'QL01p051890' => 'qlo', 'QL02p009469' => 'qlo', 'QL02p046053' => 'qlo', 'QL02p057958' => 'qlo', 'QL02p093127' => 'qlo', 'QL03p006855' => 'qlo', 'QL03p071586' => 'qlo', 'QL04p000022' => 'qlo', 'QL04p000024' => 'qlo', 'QL04p003192' => 'qlo', 'QL05p011416' => 'qlo', 'QL06p039590' => 'qlo', 'QL06p052750' => 'qlo', 'QL06p053821' => 'qlo', 'QL07p025287' => 'qlo', 'QL09p033218' => 'qlo', 'QL09p040841' => 'qlo', 'QL10p020337' => 'qlo', 'QL10p027209' => 'qlo', 'QL10p027969' => 'qlo', 'QL10p048988' => 'qlo', 'QL11p001241' => 'qlo', 'QL11p028487' => 'qlo', 'RcHm_v2.0_Chr2g0105031' => 'rch', 'RcHm_v2.0_Chr2g0117811' => 'rch', 'RcHm_v2.0_Chr6g0270241' => 'rch', 'RcHm_v2.0_Chr7g0215961' => 'rch', 'RcHm_v2.0_Chr7g0231991' => 'rch', 'Rhsim01G0041500' => 'rsi', 'Rhsim01G0115000' => 'rsi', 'Rhsim01G0115400' => 'rsi', 'Rhsim01G0133600' => 'rsi', 'Rhsim01G0159900' => 'rsi', 'Rhsim02G0189400' => 'rsi', 'Rhsim03G0135600' => 'rsi', 'Rhsim03G0149900' => 'rsi', 'Rhsim04G0125600' => 'rsi', 'Rhsim05G0091700' => 'rsi', 'Rhsim05G0092900' => 'rsi', 'Rhsim06G0075000' => 'rsi', 'Rhsim07G0066400' => 'rsi', 'Rhsim07G0156400' => 'rsi', 'Rhsim07G0182200' => 'rsi', 'Rhsim07G0182300' => 'rsi', 'Rhsim08G0180400' => 'rsi', 'Rhsim09G0056800' => 'rsi', 'Rhsim10G0153300' => 'rsi', 'Rhsim11G0012700' => 'rsi', 'Rhsim12G0031800' => 'rsi', 'Rhsim12G0055400' => 'rsi', 'Rhsim12G0091400' => 'rsi', 'Rhsim13G0070800' => 'rsi', 'Rhsim13G0193300' => 'rsi', 'RhsimUnG0111600' => 'rsi', 'RhsimUnG0137500' => 'rsi', 'RhsimUnG0172900' => 'rsi', 'SGA_v2.0_scaffold11G05878' => 'sas', 'SGA_v2.0_scaffold167G38458' => 'sas', 'SGA_v2.0_scaffold19G08588' => 'sas', 'SGA_v2.0_scaffold239G43990' => 'sas', 'SGA_v2.0_scaffold260G45865' => 'sas', 'SGA_v2.0_scaffold309G48177' => 'sas', 'SGA_v2.0_scaffold76G25122' => 'sas', 'SGA_v2.0_scaffold85G26708' => 'sas', 'SHI13914' => 'shi', 'SHI30402' => 'shi', 'TWI09G0020' => 'twi', 'TWI09G0456' => 'twi', 'TWI09G1572' => 'twi', 'TWI12G0266' => 'twi', 'TWI12G1451' => 'twi', 'TWI14G0851' => 'twi', 'TWI15G0796' => 'twi', 'TWI18G0820' => 'twi', 'TWI18G1152' => 'twi', 'TWI23G0007' => 'twi', 'TWI23G0314' => 'twi', 'TWI31G0674' => 'twi', 'TWI31G0938' => 'twi', 'TWI34G0641' => 'twi', 'TWI34G1527' => 'twi', 'TWI36G0193' => 'twi', 'TWI36G0405' => 'twi', 'TWI38G0892' => 'twi', 'TWI38G0936' => 'twi', 'TWI38G2218' => 'twi', 'TWI53G0679' => 'twi', 'TWI53G0863' => 'twi', 'TWI53G1133' => 'twi', 'TWI60G0823' => 'twi', 'TWI63G0919' => 'twi', 'TWI63G1436' => 'twi', 'TWI73G0140' => 'twi', 'TWI73G0419' => 'twi', 'TWI73G0420' => 'twi', 'TWI73G1276' => 'twi', 'TWI74G0405' => 'twi', 'TWI74G0837' => 'twi', 'TWI75G0594' => 'twi', 'TWI75G1615' => 'twi', 'TWI77G0816' => 'twi', 'vmacro03831' => 'vma', 'vmacro13746' => 'vma', 'vmacro16089' => 'vma', 'vmacro22863' => 'vma', 'Zm00001eb085790' => 'zma', 'Zm00001eb114250' => 'zma', 'Zm00001eb138070' => 'zma', 'Zm00001eb167560' => 'zma', 'Zm00001eb199990' => 'zma', 'Zm00001eb368180' => 'zma', 'Zm00001eb382470' => 'zma' ), 'gf_id' => 'HOM05D001576', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001576' ), 'data_identifier' => 'HOM05D001576', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001576', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '406', 'num_species' => '29' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'Aqoxy1G01456' => 'aox', 'Aqoxy1G02949' => 'aox', 'Aqoxy3G01274' => 'aox', 'Aqoxy3G02110' => 'aox', 'Aqoxy3G02268' => 'aox', 'Aqoxy5G02702' => 'aox', 'Aqoxy5G02988' => 'aox', 'Aqoxy5G03427' => 'aox', 'Aqoxy6G02363' => 'aox', 'Atru.chr1.3225' => 'acertr', 'Atru.chr8.1198' => 'acertr', 'Atru.chr9.790' => 'acertr', 'CANSAT01G3197' => 'cansat', 'Ciclev10003979m.g' => 'ccl', 'Ciclev10017471m.g' => 'ccl', 'Ciclev10018206m.g' => 'ccl', 'Ciclev10033751m.g' => 'ccl', 'CiPaw.01G000900' => 'cil', 'CiPaw.01G001000' => 'cil', 'CiPaw.01G033500' => 'cil', 'CiPaw.01G060300' => 'cil', 'CiPaw.01G070200' => 'cil', 'CiPaw.01G075100' => 'cil', 'CiPaw.01G084700' => 'cil', 'CiPaw.01G087900' => 'cil', 'CiPaw.01G092600' => 'cil', 'CiPaw.01G097200' => 'cil', 'CiPaw.01G098300' => 'cil', 'CiPaw.01G110200' => 'cil', 'CiPaw.01G118700' => 'cil', 'CiPaw.01G121200' => 'cil', 'CiPaw.01G132500' => 'cil', 'CiPaw.01G146900' => 'cil', 'CiPaw.01G174000' => 'cil', 'CiPaw.01G179900' => 'cil', 'CiPaw.01G183400' => 'cil', 'CiPaw.01G240000' => 'cil', 'CiPaw.01G283500' => 'cil', 'CiPaw.01G307400' => 'cil', 'CiPaw.02G030800' => 'cil', 'CiPaw.02G047200' => 'cil', 'CiPaw.02G050500' => 'cil', 'CiPaw.02G069900' => 'cil', 'CiPaw.02G091600' => 'cil', 'CiPaw.02G095000' => 'cil', 'CiPaw.02G131900' => 'cil', 'CiPaw.03G043000' => 'cil', 'CiPaw.03G069900' => 'cil', 'CiPaw.03G088100' => 'cil', 'CiPaw.03G089300' => 'cil', 'CiPaw.03G093100' => 'cil', 'CiPaw.03G129800' => 'cil', 'CiPaw.03G131200' => 'cil', 'CiPaw.03G134500' => 'cil', 'CiPaw.03G152100' => 'cil', 'CiPaw.03G162700' => 'cil', 'CiPaw.03G172800' => 'cil', 'CiPaw.03G175800' => 'cil', 'CiPaw.03G181800' => 'cil', 'CiPaw.03G191400' => 'cil', 'CiPaw.03G198300' => 'cil', 'CiPaw.03G201300' => 'cil', 'CiPaw.03G224700' => 'cil', 'CiPaw.03G225000' => 'cil', 'CiPaw.04G065100' => 'cil', 'CiPaw.04G080400' => 'cil', 'CiPaw.04G113500' => 'cil', 'CiPaw.04G121900' => 'cil', 'CiPaw.04G144100' => 'cil', 'CiPaw.04G176500' => 'cil', 'CiPaw.05G086200' => 'cil', 'CiPaw.05G100200' => 'cil', 'CiPaw.05G114200' => 'cil', 'CiPaw.05G126800' => 'cil', 'CiPaw.05G228800' => 'cil', 'CiPaw.05G230600' => 'cil', 'CiPaw.05G236500' => 'cil', 'CiPaw.05G244800' => 'cil', 'CiPaw.06G026600' => 'cil', 'CiPaw.06G027900' => 'cil', 'CiPaw.06G051800' => 'cil', 'CiPaw.06G128500' => 'cil', 'CiPaw.06G165900' => 'cil', 'CiPaw.07G045400' => 'cil', 'CiPaw.07G048000' => 'cil', 'CiPaw.07G052000' => 'cil', 'CiPaw.07G073800' => 'cil', 'CiPaw.07G099700' => 'cil', 'CiPaw.07G108700' => 'cil', 'CiPaw.07G120000' => 'cil', 'CiPaw.07G134100' => 'cil', 'CiPaw.07G147000' => 'cil', 'CiPaw.07G149700' => 'cil', 'CiPaw.07G178300' => 'cil', 'CiPaw.07G184900' => 'cil', 'CiPaw.08G044500' => 'cil', 'CiPaw.08G046900' => 'cil', 'CiPaw.08G047300' => 'cil', 'CiPaw.08G115400' => 'cil', 'CiPaw.08G134700' => 'cil', 'CiPaw.08G157400' => 'cil', 'CiPaw.09G014300' => 'cil', 'CiPaw.09G088900' => 'cil', 'CiPaw.09G130900' => 'cil', 'CiPaw.09G133100' => 'cil', 'CiPaw.09G151300' => 'cil', 'CiPaw.09G172800' => 'cil', 'CiPaw.09G174900' => 'cil', 'CiPaw.09G175000' => 'cil', 'CiPaw.10G012800' => 'cil', 'CiPaw.10G028800' => 'cil', 'CiPaw.10G044700' => 'cil', 'CiPaw.10G067400' => 'cil', 'CiPaw.10G115900' => 'cil', 'CiPaw.10G126200' => 'cil', 'CiPaw.10G139700' => 'cil', 'CiPaw.10G155100' => 'cil', 'CiPaw.11G011300' => 'cil', 'CiPaw.11G025900' => 'cil', 'CiPaw.11G104100' => 'cil', 'CiPaw.11G142700' => 'cil', 'CiPaw.11G164500' => 'cil', 'CiPaw.11G189100' => 'cil', 'CiPaw.11G197100' => 'cil', 'CiPaw.12G006100' => 'cil', 'CiPaw.12G038500' => 'cil', 'CiPaw.12G041400' => 'cil', 'CiPaw.12G041600' => 'cil', 'CiPaw.12G051300' => 'cil', 'CiPaw.12G101800' => 'cil', 'CiPaw.12G107800' => 'cil', 'CiPaw.13G033200' => 'cil', 'CiPaw.13G129900' => 'cil', 'CiPaw.13G160200' => 'cil', 'CiPaw.14G018900' => 'cil', 'CiPaw.14G029000' => 'cil', 'CiPaw.14G031000' => 'cil', 'CiPaw.14G032000' => 'cil', 'CiPaw.14G032300' => 'cil', 'CiPaw.14G040600' => 'cil', 'CiPaw.14G060500' => 'cil', 'CiPaw.14G061500' => 'cil', 'CiPaw.14G077500' => 'cil', 'CiPaw.14G088300' => 'cil', 'CiPaw.14G108500' => 'cil', 'CiPaw.14G121300' => 'cil', 'CiPaw.14G133000' => 'cil', 'CiPaw.14G134600' => 'cil', 'CiPaw.15G027200' => 'cil', 'CiPaw.15G037700' => 'cil', 'CiPaw.15G050900' => 'cil', 'CiPaw.15G067200' => 'cil', 'CiPaw.15G072000' => 'cil', 'CiPaw.15G112900' => 'cil', 'CiPaw.15G133200' => 'cil', 'CiPaw.15G139500' => 'cil', 'CiPaw.15G155400' => 'cil', 'CiPaw.16G006000' => 'cil', 'CiPaw.16G013100' => 'cil', 'CiPaw.16G047100' => 'cil', 'CiPaw.16G048900' => 'cil', 'CiPaw.16G070300' => 'cil', 'CSS0000195' => 'camsi', 'CSS0001664' => 'camsi', 'CSS0002566' => 'camsi', 'CSS0003077' => 'camsi', 'CSS0004257' => 'camsi', 'CSS0004495' => 'camsi', 'CSS0004599' => 'camsi', 'CSS0004943' => 'camsi', 'CSS0005302' => 'camsi', 'CSS0006274' => 'camsi', 'CSS0006547' => 'camsi', 'CSS0006860' => 'camsi', 'CSS0008814' => 'camsi', 'CSS0008946' => 'camsi', 'CSS0009093' => 'camsi', 'CSS0010221' => 'camsi', 'CSS0010296' => 'camsi', 'CSS0010386' => 'camsi', 'CSS0010831' => 'camsi', 'CSS0011061' => 'camsi', 'CSS0012008' => 'camsi', 'CSS0012194' => 'camsi', 'CSS0013580' => 'camsi', 'CSS0014176' => 'camsi', 'CSS0014280' => 'camsi', 'CSS0014799' => 'camsi', 'CSS0015368' => 'camsi', 'CSS0017473' => 'camsi', 'CSS0019281' => 'camsi', 'CSS0021320' => 'camsi', 'CSS0021750' => 'camsi', 'CSS0023642' => 'camsi', 'CSS0023792' => 'camsi', 'CSS0031528' => 'camsi', 'CSS0033894' => 'camsi', 'CSS0034959' => 'camsi', 'CSS0035632' => 'camsi', 'CSS0038450' => 'camsi', 'CSS0039293' => 'camsi', 'CSS0041053' => 'camsi', 'CSS0041981' => 'camsi', 'CSS0042573' => 'camsi', 'CSS0042927' => 'camsi', 'CSS0047725' => 'camsi', 'CSS0049636' => 'camsi', 'CSS0050513' => 'camsi', 'DCAR_030203' => 'dca', 'Dinv07939' => 'din', 'FAN01G0456' => 'fan', 'FAN02G3001' => 'fan', 'FAN04G2781' => 'fan', 'FAN05G1385' => 'fan', 'FAN05G3062' => 'fan', 'FAN08G2267' => 'fan', 'FAN10G0481' => 'fan', 'FAN10G1257' => 'fan', 'FAN14G0954' => 'fan', 'FAN14G2347' => 'fan', 'FAN15G0187' => 'fan', 'FAN25G2214' => 'fan', 'FvH4_1g21031' => 'fve', 'FvH4_3g16231' => 'fve', 'FvH4_3g26413' => 'fve', 'FvH4_3g29014' => 'fve', 'FvH4_3g31921' => 'fve', 'FvH4_4g19882' => 'fve', 'FvH4_5g21960' => 'fve', 'FvH4_5g29683' => 'fve', 'FvH4_7g13271' => 'fve', 'Glyma.01G062500' => 'gma', 'Glyma.07G140900' => 'gma', 'Glyma.09G140900' => 'gma', 'Glyma.12G112700' => 'gma', 'Glyma.17G168800' => 'gma', 'HanXRQChr01g0027001' => 'han', 'HanXRQChr04g0120511' => 'han', 'HanXRQChr08g0232381' => 'han', 'HanXRQChr09g0265661' => 'han', 'HanXRQChr13g0416031' => 'han', 'Haze_05835' => 'cav', 'Haze_06597' => 'cav', 'Haze_07921' => 'cav', 'Haze_08599' => 'cav', 'Haze_10686' => 'cav', 'Haze_12994' => 'cav', 'Haze_13466' => 'cav', 'Haze_16101' => 'cav', 'Haze_17766' => 'cav', 'Haze_18456' => 'cav', 'Haze_20229' => 'cav', 'Hma1.2p1_0324F.1_g125640' => 'hma', 'Hma1.2p1_0733F.1_g210230' => 'hma', 'Hma1.2p1_0921F.1_g236870' => 'hma', 'Hma1.2p1_1313F.1_g274940' => 'hma', 'Hma1.2p1_3059F.1_g332230' => 'hma', 'Hund15925' => 'sun', 'Hund19562' => 'sun', 'Hund21925' => 'sun', 'MD03G1177400' => 'mdo', 'MD07G1026100' => 'mdo', 'MD17G1218600' => 'mdo', 'Medtr0867s0010' => 'mtr', 'Medtr6g081150' => 'mtr', 'Os01g0527900' => 'osa', 'Os02g0463725' => 'osa', 'Os02g0785600' => 'osa', 'Os03g0433733' => 'osa', 'Os04g0286500' => 'osa', 'Os05g0227800' => 'osa', 'Os06g0521000' => 'osa', 'Os06g0635500' => 'osa', 'Os06g0660650' => 'osa', 'Os07g0554400' => 'osa', 'Os08g0225900' => 'osa', 'Os08g0561000' => 'osa', 'Os09g0241700' => 'osa', 'Os09g0351900' => 'osa', 'Os11g0220700' => 'osa', 'Os11g0282700' => 'osa', 'Os12g0169300' => 'osa', 'Os12g0228500' => 'osa', 'Os12g0543800' => 'osa', 'PGR044G1547' => 'pgr', 'Potri.005G239150' => 'ptr', 'Potri.010G014250' => 'ptr', 'Prupe.1G172500' => 'ppe', 'Prupe.1G196800' => 'ppe', 'Prupe.1G279700' => 'ppe', 'Prupe.2G026400' => 'ppe', 'Prupe.3G094000' => 'ppe', 'Prupe.4G287300' => 'ppe', 'QL01p022166' => 'qlo', 'QL01p051890' => 'qlo', 'QL02p009469' => 'qlo', 'QL02p046053' => 'qlo', 'QL02p057958' => 'qlo', 'QL02p093127' => 'qlo', 'QL03p006855' => 'qlo', 'QL03p071586' => 'qlo', 'QL04p000022' => 'qlo', 'QL04p000024' => 'qlo', 'QL04p003192' => 'qlo', 'QL05p011416' => 'qlo', 'QL06p039590' => 'qlo', 'QL06p052750' => 'qlo', 'QL06p053821' => 'qlo', 'QL07p025287' => 'qlo', 'QL09p033218' => 'qlo', 'QL09p040841' => 'qlo', 'QL10p020337' => 'qlo', 'QL10p027209' => 'qlo', 'QL10p027969' => 'qlo', 'QL10p048988' => 'qlo', 'QL11p001241' => 'qlo', 'QL11p028487' => 'qlo', 'RcHm_v2.0_Chr2g0105031' => 'rch', 'RcHm_v2.0_Chr2g0117811' => 'rch', 'RcHm_v2.0_Chr6g0270241' => 'rch', 'RcHm_v2.0_Chr7g0215961' => 'rch', 'RcHm_v2.0_Chr7g0231991' => 'rch', 'Rhsim01G0041500' => 'rsi', 'Rhsim01G0115000' => 'rsi', 'Rhsim01G0115400' => 'rsi', 'Rhsim01G0133600' => 'rsi', 'Rhsim01G0159900' => 'rsi', 'Rhsim02G0189400' => 'rsi', 'Rhsim03G0135600' => 'rsi', 'Rhsim03G0149900' => 'rsi', 'Rhsim04G0125600' => 'rsi', 'Rhsim05G0091700' => 'rsi', 'Rhsim05G0092900' => 'rsi', 'Rhsim06G0075000' => 'rsi', 'Rhsim07G0066400' => 'rsi', 'Rhsim07G0156400' => 'rsi', 'Rhsim07G0182200' => 'rsi', 'Rhsim07G0182300' => 'rsi', 'Rhsim08G0180400' => 'rsi', 'Rhsim09G0056800' => 'rsi', 'Rhsim10G0153300' => 'rsi', 'Rhsim11G0012700' => 'rsi', 'Rhsim12G0031800' => 'rsi', 'Rhsim12G0055400' => 'rsi', 'Rhsim12G0091400' => 'rsi', 'Rhsim13G0070800' => 'rsi', 'Rhsim13G0193300' => 'rsi', 'RhsimUnG0111600' => 'rsi', 'RhsimUnG0137500' => 'rsi', 'RhsimUnG0172900' => 'rsi', 'SGA_v2.0_scaffold11G05878' => 'sas', 'SGA_v2.0_scaffold167G38458' => 'sas', 'SGA_v2.0_scaffold19G08588' => 'sas', 'SGA_v2.0_scaffold239G43990' => 'sas', 'SGA_v2.0_scaffold260G45865' => 'sas', 'SGA_v2.0_scaffold309G48177' => 'sas', 'SGA_v2.0_scaffold76G25122' => 'sas', 'SGA_v2.0_scaffold85G26708' => 'sas', 'SHI13914' => 'shi', 'SHI30402' => 'shi', 'TWI09G0020' => 'twi', 'TWI09G0456' => 'twi', 'TWI09G1572' => 'twi', 'TWI12G0266' => 'twi', 'TWI12G1451' => 'twi', 'TWI14G0851' => 'twi', 'TWI15G0796' => 'twi', 'TWI18G0820' => 'twi', 'TWI18G1152' => 'twi', 'TWI23G0007' => 'twi', 'TWI23G0314' => 'twi', 'TWI31G0674' => 'twi', 'TWI31G0938' => 'twi', 'TWI34G0641' => 'twi', 'TWI34G1527' => 'twi', 'TWI36G0193' => 'twi', 'TWI36G0405' => 'twi', 'TWI38G0892' => 'twi', 'TWI38G0936' => 'twi', 'TWI38G2218' => 'twi', 'TWI53G0679' => 'twi', 'TWI53G0863' => 'twi', 'TWI53G1133' => 'twi', 'TWI60G0823' => 'twi', 'TWI63G0919' => 'twi', 'TWI63G1436' => 'twi', 'TWI73G0140' => 'twi', 'TWI73G0419' => 'twi', 'TWI73G0420' => 'twi', 'TWI73G1276' => 'twi', 'TWI74G0405' => 'twi', 'TWI74G0837' => 'twi', 'TWI75G0594' => 'twi', 'TWI75G1615' => 'twi', 'TWI77G0816' => 'twi', 'vmacro03831' => 'vma', 'vmacro13746' => 'vma', 'vmacro16089' => 'vma', 'vmacro22863' => 'vma', 'Zm00001eb085790' => 'zma', 'Zm00001eb114250' => 'zma', 'Zm00001eb138070' => 'zma', 'Zm00001eb167560' => 'zma', 'Zm00001eb199990' => 'zma', 'Zm00001eb368180' => 'zma', 'Zm00001eb382470' => 'zma' ) $gf_id = 'HOM05D001576' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001576' ) $data_identifier = 'HOM05D001576' $data_type = 'gf_id' $species_gene_counts = array( 'aox' => (int) 9, 'acertr' => (int) 3, 'cansat' => (int) 1, 'ccl' => (int) 4, 'cil' => (int) 145, 'camsi' => (int) 46, 'dca' => (int) 1, 'din' => (int) 1, 'fan' => (int) 12, 'fve' => (int) 9, 'gma' => (int) 5, 'han' => (int) 5, 'cav' => (int) 11, 'hma' => (int) 5, 'sun' => (int) 3, 'mdo' => (int) 3, 'mtr' => (int) 2, 'osa' => (int) 19, 'pgr' => (int) 1, 'ptr' => (int) 2, 'ppe' => (int) 6, 'qlo' => (int) 24, 'rch' => (int) 5, 'rsi' => (int) 28, 'sas' => (int) 8, 'shi' => (int) 2, 'twi' => (int) 35, 'vma' => (int) 4, 'zma' => (int) 7 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb382470' $species_info = array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ) $local_species = 'qlo' $disabled = '' $selected = '' $num_hits = (int) 1include - APP/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp, line 33 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933 View::_renderElement() - CORE/Cake/View/View.php, line 1224 View::element() - CORE/Cake/View/View.php, line 418 include - APP/View/Elements/analysis/phylogenetics_module/gf_data_settings.ctp, line 37 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933 View::_renderElement() - CORE/Cake/View/View.php, line 1224 View::element() - CORE/Cake/View/View.php, line 418 include - APP/View/Elements/analysis/phylogenetics_module/parameter_selection.ctp, line 64 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933 View::_renderElement() - CORE/Cake/View/View.php, line 1224 View::element() - CORE/Cake/View/View.php, line 418 include - APP/View/Analysis/custom_tree_creation.ctp, line 27 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933
$viewFile = '/www/bioinformatics01_ro/plaza/_dev_instances/feedback/app/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp' $dataForView = array( 'sidebar_info' => array( 'gf_id' => 'HOM05D001576', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '406', 'num_species' => '29' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'Aqoxy1G01456' => 'aox', 'Aqoxy1G02949' => 'aox', 'Aqoxy3G01274' => 'aox', 'Aqoxy3G02110' => 'aox', 'Aqoxy3G02268' => 'aox', 'Aqoxy5G02702' => 'aox', 'Aqoxy5G02988' => 'aox', 'Aqoxy5G03427' => 'aox', 'Aqoxy6G02363' => 'aox', 'Atru.chr1.3225' => 'acertr', 'Atru.chr8.1198' => 'acertr', 'Atru.chr9.790' => 'acertr', 'CANSAT01G3197' => 'cansat', 'Ciclev10003979m.g' => 'ccl', 'Ciclev10017471m.g' => 'ccl', 'Ciclev10018206m.g' => 'ccl', 'Ciclev10033751m.g' => 'ccl', 'CiPaw.01G000900' => 'cil', 'CiPaw.01G001000' => 'cil', 'CiPaw.01G033500' => 'cil', 'CiPaw.01G060300' => 'cil', 'CiPaw.01G070200' => 'cil', 'CiPaw.01G075100' => 'cil', 'CiPaw.01G084700' => 'cil', 'CiPaw.01G087900' => 'cil', 'CiPaw.01G092600' => 'cil', 'CiPaw.01G097200' => 'cil', 'CiPaw.01G098300' => 'cil', 'CiPaw.01G110200' => 'cil', 'CiPaw.01G118700' => 'cil', 'CiPaw.01G121200' => 'cil', 'CiPaw.01G132500' => 'cil', 'CiPaw.01G146900' => 'cil', 'CiPaw.01G174000' => 'cil', 'CiPaw.01G179900' => 'cil', 'CiPaw.01G183400' => 'cil', 'CiPaw.01G240000' => 'cil', 'CiPaw.01G283500' => 'cil', 'CiPaw.01G307400' => 'cil', 'CiPaw.02G030800' => 'cil', 'CiPaw.02G047200' => 'cil', 'CiPaw.02G050500' => 'cil', 'CiPaw.02G069900' => 'cil', 'CiPaw.02G091600' => 'cil', 'CiPaw.02G095000' => 'cil', 'CiPaw.02G131900' => 'cil', 'CiPaw.03G043000' => 'cil', 'CiPaw.03G069900' => 'cil', 'CiPaw.03G088100' => 'cil', 'CiPaw.03G089300' => 'cil', 'CiPaw.03G093100' => 'cil', 'CiPaw.03G129800' => 'cil', 'CiPaw.03G131200' => 'cil', 'CiPaw.03G134500' => 'cil', 'CiPaw.03G152100' => 'cil', 'CiPaw.03G162700' => 'cil', 'CiPaw.03G172800' => 'cil', 'CiPaw.03G175800' => 'cil', 'CiPaw.03G181800' => 'cil', 'CiPaw.03G191400' => 'cil', 'CiPaw.03G198300' => 'cil', 'CiPaw.03G201300' => 'cil', 'CiPaw.03G224700' => 'cil', 'CiPaw.03G225000' => 'cil', 'CiPaw.04G065100' => 'cil', 'CiPaw.04G080400' => 'cil', 'CiPaw.04G113500' => 'cil', 'CiPaw.04G121900' => 'cil', 'CiPaw.04G144100' => 'cil', 'CiPaw.04G176500' => 'cil', 'CiPaw.05G086200' => 'cil', 'CiPaw.05G100200' => 'cil', 'CiPaw.05G114200' => 'cil', 'CiPaw.05G126800' => 'cil', 'CiPaw.05G228800' => 'cil', 'CiPaw.05G230600' => 'cil', 'CiPaw.05G236500' => 'cil', 'CiPaw.05G244800' => 'cil', 'CiPaw.06G026600' => 'cil', 'CiPaw.06G027900' => 'cil', 'CiPaw.06G051800' => 'cil', 'CiPaw.06G128500' => 'cil', 'CiPaw.06G165900' => 'cil', 'CiPaw.07G045400' => 'cil', 'CiPaw.07G048000' => 'cil', 'CiPaw.07G052000' => 'cil', 'CiPaw.07G073800' => 'cil', 'CiPaw.07G099700' => 'cil', 'CiPaw.07G108700' => 'cil', 'CiPaw.07G120000' => 'cil', 'CiPaw.07G134100' => 'cil', 'CiPaw.07G147000' => 'cil', 'CiPaw.07G149700' => 'cil', 'CiPaw.07G178300' => 'cil', 'CiPaw.07G184900' => 'cil', 'CiPaw.08G044500' => 'cil', 'CiPaw.08G046900' => 'cil', 'CiPaw.08G047300' => 'cil', 'CiPaw.08G115400' => 'cil', 'CiPaw.08G134700' => 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'TWI09G0020' => 'twi', 'TWI09G0456' => 'twi', 'TWI09G1572' => 'twi', 'TWI12G0266' => 'twi', 'TWI12G1451' => 'twi', 'TWI14G0851' => 'twi', 'TWI15G0796' => 'twi', 'TWI18G0820' => 'twi', 'TWI18G1152' => 'twi', 'TWI23G0007' => 'twi', 'TWI23G0314' => 'twi', 'TWI31G0674' => 'twi', 'TWI31G0938' => 'twi', 'TWI34G0641' => 'twi', 'TWI34G1527' => 'twi', 'TWI36G0193' => 'twi', 'TWI36G0405' => 'twi', 'TWI38G0892' => 'twi', 'TWI38G0936' => 'twi', 'TWI38G2218' => 'twi', 'TWI53G0679' => 'twi', 'TWI53G0863' => 'twi', 'TWI53G1133' => 'twi', 'TWI60G0823' => 'twi', 'TWI63G0919' => 'twi', 'TWI63G1436' => 'twi', 'TWI73G0140' => 'twi', 'TWI73G0419' => 'twi', 'TWI73G0420' => 'twi', 'TWI73G1276' => 'twi', 'TWI74G0405' => 'twi', 'TWI74G0837' => 'twi', 'TWI75G0594' => 'twi', 'TWI75G1615' => 'twi', 'TWI77G0816' => 'twi', 'vmacro03831' => 'vma', 'vmacro13746' => 'vma', 'vmacro16089' => 'vma', 'vmacro22863' => 'vma', 'Zm00001eb085790' => 'zma', 'Zm00001eb114250' => 'zma', 'Zm00001eb138070' => 'zma', 'Zm00001eb167560' => 'zma', 'Zm00001eb199990' => 'zma', 'Zm00001eb368180' => 'zma', 'Zm00001eb382470' => 'zma' ), 'gf_id' => 'HOM05D001576', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001576' ), 'data_identifier' => 'HOM05D001576', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001576', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '406', 'num_species' => '29' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'Aqoxy1G01456' => 'aox', 'Aqoxy1G02949' => 'aox', 'Aqoxy3G01274' => 'aox', 'Aqoxy3G02110' => 'aox', 'Aqoxy3G02268' => 'aox', 'Aqoxy5G02702' => 'aox', 'Aqoxy5G02988' => 'aox', 'Aqoxy5G03427' => 'aox', 'Aqoxy6G02363' => 'aox', 'Atru.chr1.3225' => 'acertr', 'Atru.chr8.1198' => 'acertr', 'Atru.chr9.790' => 'acertr', 'CANSAT01G3197' => 'cansat', 'Ciclev10003979m.g' => 'ccl', 'Ciclev10017471m.g' => 'ccl', 'Ciclev10018206m.g' => 'ccl', 'Ciclev10033751m.g' => 'ccl', 'CiPaw.01G000900' => 'cil', 'CiPaw.01G001000' => 'cil', 'CiPaw.01G033500' => 'cil', 'CiPaw.01G060300' => 'cil', 'CiPaw.01G070200' => 'cil', 'CiPaw.01G075100' => 'cil', 'CiPaw.01G084700' => 'cil', 'CiPaw.01G087900' => 'cil', 'CiPaw.01G092600' => 'cil', 'CiPaw.01G097200' => 'cil', 'CiPaw.01G098300' => 'cil', 'CiPaw.01G110200' => 'cil', 'CiPaw.01G118700' => 'cil', 'CiPaw.01G121200' => 'cil', 'CiPaw.01G132500' => 'cil', 'CiPaw.01G146900' => 'cil', 'CiPaw.01G174000' => 'cil', 'CiPaw.01G179900' => 'cil', 'CiPaw.01G183400' => 'cil', 'CiPaw.01G240000' => 'cil', 'CiPaw.01G283500' => 'cil', 'CiPaw.01G307400' => 'cil', 'CiPaw.02G030800' => 'cil', 'CiPaw.02G047200' => 'cil', 'CiPaw.02G050500' => 'cil', 'CiPaw.02G069900' => 'cil', 'CiPaw.02G091600' => 'cil', 'CiPaw.02G095000' => 'cil', 'CiPaw.02G131900' => 'cil', 'CiPaw.03G043000' => 'cil', 'CiPaw.03G069900' => 'cil', 'CiPaw.03G088100' => 'cil', 'CiPaw.03G089300' => 'cil', 'CiPaw.03G093100' => 'cil', 'CiPaw.03G129800' => 'cil', 'CiPaw.03G131200' => 'cil', 'CiPaw.03G134500' => 'cil', 'CiPaw.03G152100' => 'cil', 'CiPaw.03G162700' => 'cil', 'CiPaw.03G172800' => 'cil', 'CiPaw.03G175800' => 'cil', 'CiPaw.03G181800' => 'cil', 'CiPaw.03G191400' => 'cil', 'CiPaw.03G198300' => 'cil', 'CiPaw.03G201300' => 'cil', 'CiPaw.03G224700' => 'cil', 'CiPaw.03G225000' => 'cil', 'CiPaw.04G065100' => 'cil', 'CiPaw.04G080400' => 'cil', 'CiPaw.04G113500' => 'cil', 'CiPaw.04G121900' => 'cil', 'CiPaw.04G144100' => 'cil', 'CiPaw.04G176500' => 'cil', 'CiPaw.05G086200' => 'cil', 'CiPaw.05G100200' => 'cil', 'CiPaw.05G114200' => 'cil', 'CiPaw.05G126800' => 'cil', 'CiPaw.05G228800' => 'cil', 'CiPaw.05G230600' => 'cil', 'CiPaw.05G236500' => 'cil', 'CiPaw.05G244800' => 'cil', 'CiPaw.06G026600' => 'cil', 'CiPaw.06G027900' => 'cil', 'CiPaw.06G051800' => 'cil', 'CiPaw.06G128500' => 'cil', 'CiPaw.06G165900' => 'cil', 'CiPaw.07G045400' => 'cil', 'CiPaw.07G048000' => 'cil', 'CiPaw.07G052000' => 'cil', 'CiPaw.07G073800' => 'cil', 'CiPaw.07G099700' => 'cil', 'CiPaw.07G108700' => 'cil', 'CiPaw.07G120000' => 'cil', 'CiPaw.07G134100' => 'cil', 'CiPaw.07G147000' => 'cil', 'CiPaw.07G149700' => 'cil', 'CiPaw.07G178300' => 'cil', 'CiPaw.07G184900' => 'cil', 'CiPaw.08G044500' => 'cil', 'CiPaw.08G046900' => 'cil', 'CiPaw.08G047300' => 'cil', 'CiPaw.08G115400' => 'cil', 'CiPaw.08G134700' => 'cil', 'CiPaw.08G157400' => 'cil', 'CiPaw.09G014300' => 'cil', 'CiPaw.09G088900' => 'cil', 'CiPaw.09G130900' => 'cil', 'CiPaw.09G133100' => 'cil', 'CiPaw.09G151300' => 'cil', 'CiPaw.09G172800' => 'cil', 'CiPaw.09G174900' => 'cil', 'CiPaw.09G175000' => 'cil', 'CiPaw.10G012800' => 'cil', 'CiPaw.10G028800' => 'cil', 'CiPaw.10G044700' => 'cil', 'CiPaw.10G067400' => 'cil', 'CiPaw.10G115900' => 'cil', 'CiPaw.10G126200' => 'cil', 'CiPaw.10G139700' => 'cil', 'CiPaw.10G155100' => 'cil', 'CiPaw.11G011300' => 'cil', 'CiPaw.11G025900' => 'cil', 'CiPaw.11G104100' => 'cil', 'CiPaw.11G142700' => 'cil', 'CiPaw.11G164500' => 'cil', 'CiPaw.11G189100' => 'cil', 'CiPaw.11G197100' => 'cil', 'CiPaw.12G006100' => 'cil', 'CiPaw.12G038500' => 'cil', 'CiPaw.12G041400' => 'cil', 'CiPaw.12G041600' => 'cil', 'CiPaw.12G051300' => 'cil', 'CiPaw.12G101800' => 'cil', 'CiPaw.12G107800' => 'cil', 'CiPaw.13G033200' => 'cil', 'CiPaw.13G129900' => 'cil', 'CiPaw.13G160200' => 'cil', 'CiPaw.14G018900' => 'cil', 'CiPaw.14G029000' => 'cil', 'CiPaw.14G031000' => 'cil', 'CiPaw.14G032000' => 'cil', 'CiPaw.14G032300' => 'cil', 'CiPaw.14G040600' => 'cil', 'CiPaw.14G060500' => 'cil', 'CiPaw.14G061500' => 'cil', 'CiPaw.14G077500' => 'cil', 'CiPaw.14G088300' => 'cil', 'CiPaw.14G108500' => 'cil', 'CiPaw.14G121300' => 'cil', 'CiPaw.14G133000' => 'cil', 'CiPaw.14G134600' => 'cil', 'CiPaw.15G027200' => 'cil', 'CiPaw.15G037700' => 'cil', 'CiPaw.15G050900' => 'cil', 'CiPaw.15G067200' => 'cil', 'CiPaw.15G072000' => 'cil', 'CiPaw.15G112900' => 'cil', 'CiPaw.15G133200' => 'cil', 'CiPaw.15G139500' => 'cil', 'CiPaw.15G155400' => 'cil', 'CiPaw.16G006000' => 'cil', 'CiPaw.16G013100' => 'cil', 'CiPaw.16G047100' => 'cil', 'CiPaw.16G048900' => 'cil', 'CiPaw.16G070300' => 'cil', 'CSS0000195' => 'camsi', 'CSS0001664' => 'camsi', 'CSS0002566' => 'camsi', 'CSS0003077' => 'camsi', 'CSS0004257' => 'camsi', 'CSS0004495' => 'camsi', 'CSS0004599' => 'camsi', 'CSS0004943' => 'camsi', 'CSS0005302' => 'camsi', 'CSS0006274' => 'camsi', 'CSS0006547' => 'camsi', 'CSS0006860' => 'camsi', 'CSS0008814' => 'camsi', 'CSS0008946' => 'camsi', 'CSS0009093' => 'camsi', 'CSS0010221' => 'camsi', 'CSS0010296' => 'camsi', 'CSS0010386' => 'camsi', 'CSS0010831' => 'camsi', 'CSS0011061' => 'camsi', 'CSS0012008' => 'camsi', 'CSS0012194' => 'camsi', 'CSS0013580' => 'camsi', 'CSS0014176' => 'camsi', 'CSS0014280' => 'camsi', 'CSS0014799' => 'camsi', 'CSS0015368' => 'camsi', 'CSS0017473' => 'camsi', 'CSS0019281' => 'camsi', 'CSS0021320' => 'camsi', 'CSS0021750' => 'camsi', 'CSS0023642' => 'camsi', 'CSS0023792' => 'camsi', 'CSS0031528' => 'camsi', 'CSS0033894' => 'camsi', 'CSS0034959' => 'camsi', 'CSS0035632' => 'camsi', 'CSS0038450' => 'camsi', 'CSS0039293' => 'camsi', 'CSS0041053' => 'camsi', 'CSS0041981' => 'camsi', 'CSS0042573' => 'camsi', 'CSS0042927' => 'camsi', 'CSS0047725' => 'camsi', 'CSS0049636' => 'camsi', 'CSS0050513' => 'camsi', 'DCAR_030203' => 'dca', 'Dinv07939' => 'din', 'FAN01G0456' => 'fan', 'FAN02G3001' => 'fan', 'FAN04G2781' => 'fan', 'FAN05G1385' => 'fan', 'FAN05G3062' => 'fan', 'FAN08G2267' => 'fan', 'FAN10G0481' => 'fan', 'FAN10G1257' => 'fan', 'FAN14G0954' => 'fan', 'FAN14G2347' => 'fan', 'FAN15G0187' => 'fan', 'FAN25G2214' => 'fan', 'FvH4_1g21031' => 'fve', 'FvH4_3g16231' => 'fve', 'FvH4_3g26413' => 'fve', 'FvH4_3g29014' => 'fve', 'FvH4_3g31921' => 'fve', 'FvH4_4g19882' => 'fve', 'FvH4_5g21960' => 'fve', 'FvH4_5g29683' => 'fve', 'FvH4_7g13271' => 'fve', 'Glyma.01G062500' => 'gma', 'Glyma.07G140900' => 'gma', 'Glyma.09G140900' => 'gma', 'Glyma.12G112700' => 'gma', 'Glyma.17G168800' => 'gma', 'HanXRQChr01g0027001' => 'han', 'HanXRQChr04g0120511' => 'han', 'HanXRQChr08g0232381' => 'han', 'HanXRQChr09g0265661' => 'han', 'HanXRQChr13g0416031' => 'han', 'Haze_05835' => 'cav', 'Haze_06597' => 'cav', 'Haze_07921' => 'cav', 'Haze_08599' => 'cav', 'Haze_10686' => 'cav', 'Haze_12994' => 'cav', 'Haze_13466' => 'cav', 'Haze_16101' => 'cav', 'Haze_17766' => 'cav', 'Haze_18456' => 'cav', 'Haze_20229' => 'cav', 'Hma1.2p1_0324F.1_g125640' => 'hma', 'Hma1.2p1_0733F.1_g210230' => 'hma', 'Hma1.2p1_0921F.1_g236870' => 'hma', 'Hma1.2p1_1313F.1_g274940' => 'hma', 'Hma1.2p1_3059F.1_g332230' => 'hma', 'Hund15925' => 'sun', 'Hund19562' => 'sun', 'Hund21925' => 'sun', 'MD03G1177400' => 'mdo', 'MD07G1026100' => 'mdo', 'MD17G1218600' => 'mdo', 'Medtr0867s0010' => 'mtr', 'Medtr6g081150' => 'mtr', 'Os01g0527900' => 'osa', 'Os02g0463725' => 'osa', 'Os02g0785600' => 'osa', 'Os03g0433733' => 'osa', 'Os04g0286500' => 'osa', 'Os05g0227800' => 'osa', 'Os06g0521000' => 'osa', 'Os06g0635500' => 'osa', 'Os06g0660650' => 'osa', 'Os07g0554400' => 'osa', 'Os08g0225900' => 'osa', 'Os08g0561000' => 'osa', 'Os09g0241700' => 'osa', 'Os09g0351900' => 'osa', 'Os11g0220700' => 'osa', 'Os11g0282700' => 'osa', 'Os12g0169300' => 'osa', 'Os12g0228500' => 'osa', 'Os12g0543800' => 'osa', 'PGR044G1547' => 'pgr', 'Potri.005G239150' => 'ptr', 'Potri.010G014250' => 'ptr', 'Prupe.1G172500' => 'ppe', 'Prupe.1G196800' => 'ppe', 'Prupe.1G279700' => 'ppe', 'Prupe.2G026400' => 'ppe', 'Prupe.3G094000' => 'ppe', 'Prupe.4G287300' => 'ppe', 'QL01p022166' => 'qlo', 'QL01p051890' => 'qlo', 'QL02p009469' => 'qlo', 'QL02p046053' => 'qlo', 'QL02p057958' => 'qlo', 'QL02p093127' => 'qlo', 'QL03p006855' => 'qlo', 'QL03p071586' => 'qlo', 'QL04p000022' => 'qlo', 'QL04p000024' => 'qlo', 'QL04p003192' => 'qlo', 'QL05p011416' => 'qlo', 'QL06p039590' => 'qlo', 'QL06p052750' => 'qlo', 'QL06p053821' => 'qlo', 'QL07p025287' => 'qlo', 'QL09p033218' => 'qlo', 'QL09p040841' => 'qlo', 'QL10p020337' => 'qlo', 'QL10p027209' => 'qlo', 'QL10p027969' => 'qlo', 'QL10p048988' => 'qlo', 'QL11p001241' => 'qlo', 'QL11p028487' => 'qlo', 'RcHm_v2.0_Chr2g0105031' => 'rch', 'RcHm_v2.0_Chr2g0117811' => 'rch', 'RcHm_v2.0_Chr6g0270241' => 'rch', 'RcHm_v2.0_Chr7g0215961' => 'rch', 'RcHm_v2.0_Chr7g0231991' => 'rch', 'Rhsim01G0041500' => 'rsi', 'Rhsim01G0115000' => 'rsi', 'Rhsim01G0115400' => 'rsi', 'Rhsim01G0133600' => 'rsi', 'Rhsim01G0159900' => 'rsi', 'Rhsim02G0189400' => 'rsi', 'Rhsim03G0135600' => 'rsi', 'Rhsim03G0149900' => 'rsi', 'Rhsim04G0125600' => 'rsi', 'Rhsim05G0091700' => 'rsi', 'Rhsim05G0092900' => 'rsi', 'Rhsim06G0075000' => 'rsi', 'Rhsim07G0066400' => 'rsi', 'Rhsim07G0156400' => 'rsi', 'Rhsim07G0182200' => 'rsi', 'Rhsim07G0182300' => 'rsi', 'Rhsim08G0180400' => 'rsi', 'Rhsim09G0056800' => 'rsi', 'Rhsim10G0153300' => 'rsi', 'Rhsim11G0012700' => 'rsi', 'Rhsim12G0031800' => 'rsi', 'Rhsim12G0055400' => 'rsi', 'Rhsim12G0091400' => 'rsi', 'Rhsim13G0070800' => 'rsi', 'Rhsim13G0193300' => 'rsi', 'RhsimUnG0111600' => 'rsi', 'RhsimUnG0137500' => 'rsi', 'RhsimUnG0172900' => 'rsi', 'SGA_v2.0_scaffold11G05878' => 'sas', 'SGA_v2.0_scaffold167G38458' => 'sas', 'SGA_v2.0_scaffold19G08588' => 'sas', 'SGA_v2.0_scaffold239G43990' => 'sas', 'SGA_v2.0_scaffold260G45865' => 'sas', 'SGA_v2.0_scaffold309G48177' => 'sas', 'SGA_v2.0_scaffold76G25122' => 'sas', 'SGA_v2.0_scaffold85G26708' => 'sas', 'SHI13914' => 'shi', 'SHI30402' => 'shi', 'TWI09G0020' => 'twi', 'TWI09G0456' => 'twi', 'TWI09G1572' => 'twi', 'TWI12G0266' => 'twi', 'TWI12G1451' => 'twi', 'TWI14G0851' => 'twi', 'TWI15G0796' => 'twi', 'TWI18G0820' => 'twi', 'TWI18G1152' => 'twi', 'TWI23G0007' => 'twi', 'TWI23G0314' => 'twi', 'TWI31G0674' => 'twi', 'TWI31G0938' => 'twi', 'TWI34G0641' => 'twi', 'TWI34G1527' => 'twi', 'TWI36G0193' => 'twi', 'TWI36G0405' => 'twi', 'TWI38G0892' => 'twi', 'TWI38G0936' => 'twi', 'TWI38G2218' => 'twi', 'TWI53G0679' => 'twi', 'TWI53G0863' => 'twi', 'TWI53G1133' => 'twi', 'TWI60G0823' => 'twi', 'TWI63G0919' => 'twi', 'TWI63G1436' => 'twi', 'TWI73G0140' => 'twi', 'TWI73G0419' => 'twi', 'TWI73G0420' => 'twi', 'TWI73G1276' => 'twi', 'TWI74G0405' => 'twi', 'TWI74G0837' => 'twi', 'TWI75G0594' => 'twi', 'TWI75G1615' => 'twi', 'TWI77G0816' => 'twi', 'vmacro03831' => 'vma', 'vmacro13746' => 'vma', 'vmacro16089' => 'vma', 'vmacro22863' => 'vma', 'Zm00001eb085790' => 'zma', 'Zm00001eb114250' => 'zma', 'Zm00001eb138070' => 'zma', 'Zm00001eb167560' => 'zma', 'Zm00001eb199990' => 'zma', 'Zm00001eb368180' => 'zma', 'Zm00001eb382470' => 'zma' ) $gf_id = 'HOM05D001576' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001576' ) $data_identifier = 'HOM05D001576' $data_type = 'gf_id' $species_gene_counts = array( 'aox' => (int) 9, 'acertr' => (int) 3, 'cansat' => (int) 1, 'ccl' => (int) 4, 'cil' => (int) 145, 'camsi' => (int) 46, 'dca' => (int) 1, 'din' => (int) 1, 'fan' => (int) 12, 'fve' => (int) 9, 'gma' => (int) 5, 'han' => (int) 5, 'cav' => (int) 11, 'hma' => (int) 5, 'sun' => (int) 3, 'mdo' => (int) 3, 'mtr' => (int) 2, 'osa' => (int) 19, 'pgr' => (int) 1, 'ptr' => (int) 2, 'ppe' => (int) 6, 'qlo' => (int) 24, 'rch' => (int) 5, 'rsi' => (int) 28, 'sas' => (int) 8, 'shi' => (int) 2, 'twi' => (int) 35, 'vma' => (int) 4, 'zma' => (int) 7 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb382470' $species_info = array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ) $local_species = 'qlo' $disabled = '' $selected = '' $num_hits = (int) 1
Warning (2): count(): Parameter must be an array or an object that implements Countable [APP/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp, line 33]Code Context $disabled = (!array_key_exists($local_species,$species_gene_counts))?"disabled":""; $selected = (isset($selected_species) && array_key_exists($local_species,$selected_species))?"checked='checked'":""; $num_hits = (array_key_exists($local_species,$species_gene_counts))?count($species_gene_counts[$local_species]):0; $viewFile = '/www/bioinformatics01_ro/plaza/_dev_instances/feedback/app/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp' $dataForView = array( 'sidebar_info' => array( 'gf_id' => 'HOM05D001576', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '406', 'num_species' => '29' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'Aqoxy1G01456' => 'aox', 'Aqoxy1G02949' => 'aox', 'Aqoxy3G01274' => 'aox', 'Aqoxy3G02110' => 'aox', 'Aqoxy3G02268' => 'aox', 'Aqoxy5G02702' => 'aox', 'Aqoxy5G02988' => 'aox', 'Aqoxy5G03427' => 'aox', 'Aqoxy6G02363' => 'aox', 'Atru.chr1.3225' => 'acertr', 'Atru.chr8.1198' => 'acertr', 'Atru.chr9.790' => 'acertr', 'CANSAT01G3197' => 'cansat', 'Ciclev10003979m.g' => 'ccl', 'Ciclev10017471m.g' => 'ccl', 'Ciclev10018206m.g' => 'ccl', 'Ciclev10033751m.g' => 'ccl', 'CiPaw.01G000900' => 'cil', 'CiPaw.01G001000' => 'cil', 'CiPaw.01G033500' => 'cil', 'CiPaw.01G060300' => 'cil', 'CiPaw.01G070200' => 'cil', 'CiPaw.01G075100' => 'cil', 'CiPaw.01G084700' => 'cil', 'CiPaw.01G087900' => 'cil', 'CiPaw.01G092600' => 'cil', 'CiPaw.01G097200' => 'cil', 'CiPaw.01G098300' => 'cil', 'CiPaw.01G110200' => 'cil', 'CiPaw.01G118700' => 'cil', 'CiPaw.01G121200' => 'cil', 'CiPaw.01G132500' => 'cil', 'CiPaw.01G146900' => 'cil', 'CiPaw.01G174000' => 'cil', 'CiPaw.01G179900' => 'cil', 'CiPaw.01G183400' => 'cil', 'CiPaw.01G240000' => 'cil', 'CiPaw.01G283500' => 'cil', 'CiPaw.01G307400' => 'cil', 'CiPaw.02G030800' => 'cil', 'CiPaw.02G047200' => 'cil', 'CiPaw.02G050500' => 'cil', 'CiPaw.02G069900' => 'cil', 'CiPaw.02G091600' => 'cil', 'CiPaw.02G095000' => 'cil', 'CiPaw.02G131900' => 'cil', 'CiPaw.03G043000' => 'cil', 'CiPaw.03G069900' => 'cil', 'CiPaw.03G088100' => 'cil', 'CiPaw.03G089300' => 'cil', 'CiPaw.03G093100' => 'cil', 'CiPaw.03G129800' => 'cil', 'CiPaw.03G131200' => 'cil', 'CiPaw.03G134500' => 'cil', 'CiPaw.03G152100' => 'cil', 'CiPaw.03G162700' => 'cil', 'CiPaw.03G172800' => 'cil', 'CiPaw.03G175800' => 'cil', 'CiPaw.03G181800' => 'cil', 'CiPaw.03G191400' => 'cil', 'CiPaw.03G198300' => 'cil', 'CiPaw.03G201300' => 'cil', 'CiPaw.03G224700' => 'cil', 'CiPaw.03G225000' => 'cil', 'CiPaw.04G065100' => 'cil', 'CiPaw.04G080400' => 'cil', 'CiPaw.04G113500' => 'cil', 'CiPaw.04G121900' => 'cil', 'CiPaw.04G144100' => 'cil', 'CiPaw.04G176500' => 'cil', 'CiPaw.05G086200' => 'cil', 'CiPaw.05G100200' => 'cil', 'CiPaw.05G114200' => 'cil', 'CiPaw.05G126800' => 'cil', 'CiPaw.05G228800' => 'cil', 'CiPaw.05G230600' => 'cil', 'CiPaw.05G236500' => 'cil', 'CiPaw.05G244800' => 'cil', 'CiPaw.06G026600' => 'cil', 'CiPaw.06G027900' => 'cil', 'CiPaw.06G051800' => 'cil', 'CiPaw.06G128500' => 'cil', 'CiPaw.06G165900' => 'cil', 'CiPaw.07G045400' => 'cil', 'CiPaw.07G048000' => 'cil', 'CiPaw.07G052000' => 'cil', 'CiPaw.07G073800' => 'cil', 'CiPaw.07G099700' => 'cil', 'CiPaw.07G108700' => 'cil', 'CiPaw.07G120000' => 'cil', 'CiPaw.07G134100' => 'cil', 'CiPaw.07G147000' => 'cil', 'CiPaw.07G149700' => 'cil', 'CiPaw.07G178300' => 'cil', 'CiPaw.07G184900' => 'cil', 'CiPaw.08G044500' => 'cil', 'CiPaw.08G046900' => 'cil', 'CiPaw.08G047300' => 'cil', 'CiPaw.08G115400' => 'cil', 'CiPaw.08G134700' => 'cil', 'CiPaw.08G157400' => 'cil', 'CiPaw.09G014300' => 'cil', 'CiPaw.09G088900' => 'cil', 'CiPaw.09G130900' => 'cil', 'CiPaw.09G133100' => 'cil', 'CiPaw.09G151300' => 'cil', 'CiPaw.09G172800' => 'cil', 'CiPaw.09G174900' => 'cil', 'CiPaw.09G175000' => 'cil', 'CiPaw.10G012800' => 'cil', 'CiPaw.10G028800' => 'cil', 'CiPaw.10G044700' => 'cil', 'CiPaw.10G067400' => 'cil', 'CiPaw.10G115900' => 'cil', 'CiPaw.10G126200' => 'cil', 'CiPaw.10G139700' => 'cil', 'CiPaw.10G155100' => 'cil', 'CiPaw.11G011300' => 'cil', 'CiPaw.11G025900' => 'cil', 'CiPaw.11G104100' => 'cil', 'CiPaw.11G142700' => 'cil', 'CiPaw.11G164500' => 'cil', 'CiPaw.11G189100' => 'cil', 'CiPaw.11G197100' => 'cil', 'CiPaw.12G006100' => 'cil', 'CiPaw.12G038500' => 'cil', 'CiPaw.12G041400' => 'cil', 'CiPaw.12G041600' => 'cil', 'CiPaw.12G051300' => 'cil', 'CiPaw.12G101800' => 'cil', 'CiPaw.12G107800' => 'cil', 'CiPaw.13G033200' => 'cil', 'CiPaw.13G129900' => 'cil', 'CiPaw.13G160200' => 'cil', 'CiPaw.14G018900' => 'cil', 'CiPaw.14G029000' => 'cil', 'CiPaw.14G031000' => 'cil', 'CiPaw.14G032000' => 'cil', 'CiPaw.14G032300' => 'cil', 'CiPaw.14G040600' => 'cil', 'CiPaw.14G060500' => 'cil', 'CiPaw.14G061500' => 'cil', 'CiPaw.14G077500' => 'cil', 'CiPaw.14G088300' => 'cil', 'CiPaw.14G108500' => 'cil', 'CiPaw.14G121300' => 'cil', 'CiPaw.14G133000' => 'cil', 'CiPaw.14G134600' => 'cil', 'CiPaw.15G027200' => 'cil', 'CiPaw.15G037700' => 'cil', 'CiPaw.15G050900' => 'cil', 'CiPaw.15G067200' => 'cil', 'CiPaw.15G072000' => 'cil', 'CiPaw.15G112900' => 'cil', 'CiPaw.15G133200' => 'cil', 'CiPaw.15G139500' => 'cil', 'CiPaw.15G155400' => 'cil', 'CiPaw.16G006000' => 'cil', 'CiPaw.16G013100' => 'cil', 'CiPaw.16G047100' => 'cil', 'CiPaw.16G048900' => 'cil', 'CiPaw.16G070300' => 'cil', 'CSS0000195' => 'camsi', 'CSS0001664' => 'camsi', 'CSS0002566' => 'camsi', 'CSS0003077' => 'camsi', 'CSS0004257' => 'camsi', 'CSS0004495' => 'camsi', 'CSS0004599' => 'camsi', 'CSS0004943' => 'camsi', 'CSS0005302' => 'camsi', 'CSS0006274' => 'camsi', 'CSS0006547' => 'camsi', 'CSS0006860' => 'camsi', 'CSS0008814' => 'camsi', 'CSS0008946' => 'camsi', 'CSS0009093' => 'camsi', 'CSS0010221' => 'camsi', 'CSS0010296' => 'camsi', 'CSS0010386' => 'camsi', 'CSS0010831' => 'camsi', 'CSS0011061' => 'camsi', 'CSS0012008' => 'camsi', 'CSS0012194' => 'camsi', 'CSS0013580' => 'camsi', 'CSS0014176' => 'camsi', 'CSS0014280' => 'camsi', 'CSS0014799' => 'camsi', 'CSS0015368' => 'camsi', 'CSS0017473' => 'camsi', 'CSS0019281' => 'camsi', 'CSS0021320' => 'camsi', 'CSS0021750' => 'camsi', 'CSS0023642' => 'camsi', 'CSS0023792' => 'camsi', 'CSS0031528' => 'camsi', 'CSS0033894' => 'camsi', 'CSS0034959' => 'camsi', 'CSS0035632' => 'camsi', 'CSS0038450' => 'camsi', 'CSS0039293' => 'camsi', 'CSS0041053' => 'camsi', 'CSS0041981' => 'camsi', 'CSS0042573' => 'camsi', 'CSS0042927' => 'camsi', 'CSS0047725' => 'camsi', 'CSS0049636' => 'camsi', 'CSS0050513' => 'camsi', 'DCAR_030203' => 'dca', 'Dinv07939' => 'din', 'FAN01G0456' => 'fan', 'FAN02G3001' => 'fan', 'FAN04G2781' => 'fan', 'FAN05G1385' => 'fan', 'FAN05G3062' => 'fan', 'FAN08G2267' => 'fan', 'FAN10G0481' => 'fan', 'FAN10G1257' => 'fan', 'FAN14G0954' => 'fan', 'FAN14G2347' => 'fan', 'FAN15G0187' => 'fan', 'FAN25G2214' => 'fan', 'FvH4_1g21031' => 'fve', 'FvH4_3g16231' => 'fve', 'FvH4_3g26413' => 'fve', 'FvH4_3g29014' => 'fve', 'FvH4_3g31921' => 'fve', 'FvH4_4g19882' => 'fve', 'FvH4_5g21960' => 'fve', 'FvH4_5g29683' => 'fve', 'FvH4_7g13271' => 'fve', 'Glyma.01G062500' => 'gma', 'Glyma.07G140900' => 'gma', 'Glyma.09G140900' => 'gma', 'Glyma.12G112700' => 'gma', 'Glyma.17G168800' => 'gma', 'HanXRQChr01g0027001' => 'han', 'HanXRQChr04g0120511' => 'han', 'HanXRQChr08g0232381' => 'han', 'HanXRQChr09g0265661' => 'han', 'HanXRQChr13g0416031' => 'han', 'Haze_05835' => 'cav', 'Haze_06597' => 'cav', 'Haze_07921' => 'cav', 'Haze_08599' => 'cav', 'Haze_10686' => 'cav', 'Haze_12994' => 'cav', 'Haze_13466' => 'cav', 'Haze_16101' => 'cav', 'Haze_17766' => 'cav', 'Haze_18456' => 'cav', 'Haze_20229' => 'cav', 'Hma1.2p1_0324F.1_g125640' => 'hma', 'Hma1.2p1_0733F.1_g210230' => 'hma', 'Hma1.2p1_0921F.1_g236870' => 'hma', 'Hma1.2p1_1313F.1_g274940' => 'hma', 'Hma1.2p1_3059F.1_g332230' => 'hma', 'Hund15925' => 'sun', 'Hund19562' => 'sun', 'Hund21925' => 'sun', 'MD03G1177400' => 'mdo', 'MD07G1026100' => 'mdo', 'MD17G1218600' => 'mdo', 'Medtr0867s0010' => 'mtr', 'Medtr6g081150' => 'mtr', 'Os01g0527900' => 'osa', 'Os02g0463725' => 'osa', 'Os02g0785600' => 'osa', 'Os03g0433733' => 'osa', 'Os04g0286500' => 'osa', 'Os05g0227800' => 'osa', 'Os06g0521000' => 'osa', 'Os06g0635500' => 'osa', 'Os06g0660650' => 'osa', 'Os07g0554400' => 'osa', 'Os08g0225900' => 'osa', 'Os08g0561000' => 'osa', 'Os09g0241700' => 'osa', 'Os09g0351900' => 'osa', 'Os11g0220700' => 'osa', 'Os11g0282700' => 'osa', 'Os12g0169300' => 'osa', 'Os12g0228500' => 'osa', 'Os12g0543800' => 'osa', 'PGR044G1547' => 'pgr', 'Potri.005G239150' => 'ptr', 'Potri.010G014250' => 'ptr', 'Prupe.1G172500' => 'ppe', 'Prupe.1G196800' => 'ppe', 'Prupe.1G279700' => 'ppe', 'Prupe.2G026400' => 'ppe', 'Prupe.3G094000' => 'ppe', 'Prupe.4G287300' => 'ppe', 'QL01p022166' => 'qlo', 'QL01p051890' => 'qlo', 'QL02p009469' => 'qlo', 'QL02p046053' => 'qlo', 'QL02p057958' => 'qlo', 'QL02p093127' => 'qlo', 'QL03p006855' => 'qlo', 'QL03p071586' => 'qlo', 'QL04p000022' => 'qlo', 'QL04p000024' => 'qlo', 'QL04p003192' => 'qlo', 'QL05p011416' => 'qlo', 'QL06p039590' => 'qlo', 'QL06p052750' => 'qlo', 'QL06p053821' => 'qlo', 'QL07p025287' => 'qlo', 'QL09p033218' => 'qlo', 'QL09p040841' => 'qlo', 'QL10p020337' => 'qlo', 'QL10p027209' => 'qlo', 'QL10p027969' => 'qlo', 'QL10p048988' => 'qlo', 'QL11p001241' => 'qlo', 'QL11p028487' => 'qlo', 'RcHm_v2.0_Chr2g0105031' => 'rch', 'RcHm_v2.0_Chr2g0117811' => 'rch', 'RcHm_v2.0_Chr6g0270241' => 'rch', 'RcHm_v2.0_Chr7g0215961' => 'rch', 'RcHm_v2.0_Chr7g0231991' => 'rch', 'Rhsim01G0041500' => 'rsi', 'Rhsim01G0115000' => 'rsi', 'Rhsim01G0115400' => 'rsi', 'Rhsim01G0133600' => 'rsi', 'Rhsim01G0159900' => 'rsi', 'Rhsim02G0189400' => 'rsi', 'Rhsim03G0135600' => 'rsi', 'Rhsim03G0149900' => 'rsi', 'Rhsim04G0125600' => 'rsi', 'Rhsim05G0091700' => 'rsi', 'Rhsim05G0092900' => 'rsi', 'Rhsim06G0075000' => 'rsi', 'Rhsim07G0066400' => 'rsi', 'Rhsim07G0156400' => 'rsi', 'Rhsim07G0182200' => 'rsi', 'Rhsim07G0182300' => 'rsi', 'Rhsim08G0180400' => 'rsi', 'Rhsim09G0056800' => 'rsi', 'Rhsim10G0153300' => 'rsi', 'Rhsim11G0012700' => 'rsi', 'Rhsim12G0031800' => 'rsi', 'Rhsim12G0055400' => 'rsi', 'Rhsim12G0091400' => 'rsi', 'Rhsim13G0070800' => 'rsi', 'Rhsim13G0193300' => 'rsi', 'RhsimUnG0111600' => 'rsi', 'RhsimUnG0137500' => 'rsi', 'RhsimUnG0172900' => 'rsi', 'SGA_v2.0_scaffold11G05878' => 'sas', 'SGA_v2.0_scaffold167G38458' => 'sas', 'SGA_v2.0_scaffold19G08588' => 'sas', 'SGA_v2.0_scaffold239G43990' => 'sas', 'SGA_v2.0_scaffold260G45865' => 'sas', 'SGA_v2.0_scaffold309G48177' => 'sas', 'SGA_v2.0_scaffold76G25122' => 'sas', 'SGA_v2.0_scaffold85G26708' => 'sas', 'SHI13914' => 'shi', 'SHI30402' => 'shi', 'TWI09G0020' => 'twi', 'TWI09G0456' => 'twi', 'TWI09G1572' => 'twi', 'TWI12G0266' => 'twi', 'TWI12G1451' => 'twi', 'TWI14G0851' => 'twi', 'TWI15G0796' => 'twi', 'TWI18G0820' => 'twi', 'TWI18G1152' => 'twi', 'TWI23G0007' => 'twi', 'TWI23G0314' => 'twi', 'TWI31G0674' => 'twi', 'TWI31G0938' => 'twi', 'TWI34G0641' => 'twi', 'TWI34G1527' => 'twi', 'TWI36G0193' => 'twi', 'TWI36G0405' => 'twi', 'TWI38G0892' => 'twi', 'TWI38G0936' => 'twi', 'TWI38G2218' => 'twi', 'TWI53G0679' => 'twi', 'TWI53G0863' => 'twi', 'TWI53G1133' => 'twi', 'TWI60G0823' => 'twi', 'TWI63G0919' => 'twi', 'TWI63G1436' => 'twi', 'TWI73G0140' => 'twi', 'TWI73G0419' => 'twi', 'TWI73G0420' => 'twi', 'TWI73G1276' => 'twi', 'TWI74G0405' => 'twi', 'TWI74G0837' => 'twi', 'TWI75G0594' => 'twi', 'TWI75G1615' => 'twi', 'TWI77G0816' => 'twi', 'vmacro03831' => 'vma', 'vmacro13746' => 'vma', 'vmacro16089' => 'vma', 'vmacro22863' => 'vma', 'Zm00001eb085790' => 'zma', 'Zm00001eb114250' => 'zma', 'Zm00001eb138070' => 'zma', 'Zm00001eb167560' => 'zma', 'Zm00001eb199990' => 'zma', 'Zm00001eb368180' => 'zma', 'Zm00001eb382470' => 'zma' ), 'gf_id' => 'HOM05D001576', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001576' ), 'data_identifier' => 'HOM05D001576', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001576', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '406', 'num_species' => '29' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'Aqoxy1G01456' => 'aox', 'Aqoxy1G02949' => 'aox', 'Aqoxy3G01274' => 'aox', 'Aqoxy3G02110' => 'aox', 'Aqoxy3G02268' => 'aox', 'Aqoxy5G02702' => 'aox', 'Aqoxy5G02988' => 'aox', 'Aqoxy5G03427' => 'aox', 'Aqoxy6G02363' => 'aox', 'Atru.chr1.3225' => 'acertr', 'Atru.chr8.1198' => 'acertr', 'Atru.chr9.790' => 'acertr', 'CANSAT01G3197' => 'cansat', 'Ciclev10003979m.g' => 'ccl', 'Ciclev10017471m.g' => 'ccl', 'Ciclev10018206m.g' => 'ccl', 'Ciclev10033751m.g' => 'ccl', 'CiPaw.01G000900' => 'cil', 'CiPaw.01G001000' => 'cil', 'CiPaw.01G033500' => 'cil', 'CiPaw.01G060300' => 'cil', 'CiPaw.01G070200' => 'cil', 'CiPaw.01G075100' => 'cil', 'CiPaw.01G084700' => 'cil', 'CiPaw.01G087900' => 'cil', 'CiPaw.01G092600' => 'cil', 'CiPaw.01G097200' => 'cil', 'CiPaw.01G098300' => 'cil', 'CiPaw.01G110200' => 'cil', 'CiPaw.01G118700' => 'cil', 'CiPaw.01G121200' => 'cil', 'CiPaw.01G132500' => 'cil', 'CiPaw.01G146900' => 'cil', 'CiPaw.01G174000' => 'cil', 'CiPaw.01G179900' => 'cil', 'CiPaw.01G183400' => 'cil', 'CiPaw.01G240000' => 'cil', 'CiPaw.01G283500' => 'cil', 'CiPaw.01G307400' => 'cil', 'CiPaw.02G030800' => 'cil', 'CiPaw.02G047200' => 'cil', 'CiPaw.02G050500' => 'cil', 'CiPaw.02G069900' => 'cil', 'CiPaw.02G091600' => 'cil', 'CiPaw.02G095000' => 'cil', 'CiPaw.02G131900' => 'cil', 'CiPaw.03G043000' => 'cil', 'CiPaw.03G069900' => 'cil', 'CiPaw.03G088100' => 'cil', 'CiPaw.03G089300' => 'cil', 'CiPaw.03G093100' => 'cil', 'CiPaw.03G129800' => 'cil', 'CiPaw.03G131200' => 'cil', 'CiPaw.03G134500' => 'cil', 'CiPaw.03G152100' => 'cil', 'CiPaw.03G162700' => 'cil', 'CiPaw.03G172800' => 'cil', 'CiPaw.03G175800' => 'cil', 'CiPaw.03G181800' => 'cil', 'CiPaw.03G191400' => 'cil', 'CiPaw.03G198300' => 'cil', 'CiPaw.03G201300' => 'cil', 'CiPaw.03G224700' => 'cil', 'CiPaw.03G225000' => 'cil', 'CiPaw.04G065100' => 'cil', 'CiPaw.04G080400' => 'cil', 'CiPaw.04G113500' => 'cil', 'CiPaw.04G121900' => 'cil', 'CiPaw.04G144100' => 'cil', 'CiPaw.04G176500' => 'cil', 'CiPaw.05G086200' => 'cil', 'CiPaw.05G100200' => 'cil', 'CiPaw.05G114200' => 'cil', 'CiPaw.05G126800' => 'cil', 'CiPaw.05G228800' => 'cil', 'CiPaw.05G230600' => 'cil', 'CiPaw.05G236500' => 'cil', 'CiPaw.05G244800' => 'cil', 'CiPaw.06G026600' => 'cil', 'CiPaw.06G027900' => 'cil', 'CiPaw.06G051800' => 'cil', 'CiPaw.06G128500' => 'cil', 'CiPaw.06G165900' => 'cil', 'CiPaw.07G045400' => 'cil', 'CiPaw.07G048000' => 'cil', 'CiPaw.07G052000' => 'cil', 'CiPaw.07G073800' => 'cil', 'CiPaw.07G099700' => 'cil', 'CiPaw.07G108700' => 'cil', 'CiPaw.07G120000' => 'cil', 'CiPaw.07G134100' => 'cil', 'CiPaw.07G147000' => 'cil', 'CiPaw.07G149700' => 'cil', 'CiPaw.07G178300' => 'cil', 'CiPaw.07G184900' => 'cil', 'CiPaw.08G044500' => 'cil', 'CiPaw.08G046900' => 'cil', 'CiPaw.08G047300' => 'cil', 'CiPaw.08G115400' => 'cil', 'CiPaw.08G134700' => 'cil', 'CiPaw.08G157400' => 'cil', 'CiPaw.09G014300' => 'cil', 'CiPaw.09G088900' => 'cil', 'CiPaw.09G130900' => 'cil', 'CiPaw.09G133100' => 'cil', 'CiPaw.09G151300' => 'cil', 'CiPaw.09G172800' => 'cil', 'CiPaw.09G174900' => 'cil', 'CiPaw.09G175000' => 'cil', 'CiPaw.10G012800' => 'cil', 'CiPaw.10G028800' => 'cil', 'CiPaw.10G044700' => 'cil', 'CiPaw.10G067400' => 'cil', 'CiPaw.10G115900' => 'cil', 'CiPaw.10G126200' => 'cil', 'CiPaw.10G139700' => 'cil', 'CiPaw.10G155100' => 'cil', 'CiPaw.11G011300' => 'cil', 'CiPaw.11G025900' => 'cil', 'CiPaw.11G104100' => 'cil', 'CiPaw.11G142700' => 'cil', 'CiPaw.11G164500' => 'cil', 'CiPaw.11G189100' => 'cil', 'CiPaw.11G197100' => 'cil', 'CiPaw.12G006100' => 'cil', 'CiPaw.12G038500' => 'cil', 'CiPaw.12G041400' => 'cil', 'CiPaw.12G041600' => 'cil', 'CiPaw.12G051300' => 'cil', 'CiPaw.12G101800' => 'cil', 'CiPaw.12G107800' => 'cil', 'CiPaw.13G033200' => 'cil', 'CiPaw.13G129900' => 'cil', 'CiPaw.13G160200' => 'cil', 'CiPaw.14G018900' => 'cil', 'CiPaw.14G029000' => 'cil', 'CiPaw.14G031000' => 'cil', 'CiPaw.14G032000' => 'cil', 'CiPaw.14G032300' => 'cil', 'CiPaw.14G040600' => 'cil', 'CiPaw.14G060500' => 'cil', 'CiPaw.14G061500' => 'cil', 'CiPaw.14G077500' => 'cil', 'CiPaw.14G088300' => 'cil', 'CiPaw.14G108500' => 'cil', 'CiPaw.14G121300' => 'cil', 'CiPaw.14G133000' => 'cil', 'CiPaw.14G134600' => 'cil', 'CiPaw.15G027200' => 'cil', 'CiPaw.15G037700' => 'cil', 'CiPaw.15G050900' => 'cil', 'CiPaw.15G067200' => 'cil', 'CiPaw.15G072000' => 'cil', 'CiPaw.15G112900' => 'cil', 'CiPaw.15G133200' => 'cil', 'CiPaw.15G139500' => 'cil', 'CiPaw.15G155400' => 'cil', 'CiPaw.16G006000' => 'cil', 'CiPaw.16G013100' => 'cil', 'CiPaw.16G047100' => 'cil', 'CiPaw.16G048900' => 'cil', 'CiPaw.16G070300' => 'cil', 'CSS0000195' => 'camsi', 'CSS0001664' => 'camsi', 'CSS0002566' => 'camsi', 'CSS0003077' => 'camsi', 'CSS0004257' => 'camsi', 'CSS0004495' => 'camsi', 'CSS0004599' => 'camsi', 'CSS0004943' => 'camsi', 'CSS0005302' => 'camsi', 'CSS0006274' => 'camsi', 'CSS0006547' => 'camsi', 'CSS0006860' => 'camsi', 'CSS0008814' => 'camsi', 'CSS0008946' => 'camsi', 'CSS0009093' => 'camsi', 'CSS0010221' => 'camsi', 'CSS0010296' => 'camsi', 'CSS0010386' => 'camsi', 'CSS0010831' => 'camsi', 'CSS0011061' => 'camsi', 'CSS0012008' => 'camsi', 'CSS0012194' => 'camsi', 'CSS0013580' => 'camsi', 'CSS0014176' => 'camsi', 'CSS0014280' => 'camsi', 'CSS0014799' => 'camsi', 'CSS0015368' => 'camsi', 'CSS0017473' => 'camsi', 'CSS0019281' => 'camsi', 'CSS0021320' => 'camsi', 'CSS0021750' => 'camsi', 'CSS0023642' => 'camsi', 'CSS0023792' => 'camsi', 'CSS0031528' => 'camsi', 'CSS0033894' => 'camsi', 'CSS0034959' => 'camsi', 'CSS0035632' => 'camsi', 'CSS0038450' => 'camsi', 'CSS0039293' => 'camsi', 'CSS0041053' => 'camsi', 'CSS0041981' => 'camsi', 'CSS0042573' => 'camsi', 'CSS0042927' => 'camsi', 'CSS0047725' => 'camsi', 'CSS0049636' => 'camsi', 'CSS0050513' => 'camsi', 'DCAR_030203' => 'dca', 'Dinv07939' => 'din', 'FAN01G0456' => 'fan', 'FAN02G3001' => 'fan', 'FAN04G2781' => 'fan', 'FAN05G1385' => 'fan', 'FAN05G3062' => 'fan', 'FAN08G2267' => 'fan', 'FAN10G0481' => 'fan', 'FAN10G1257' => 'fan', 'FAN14G0954' => 'fan', 'FAN14G2347' => 'fan', 'FAN15G0187' => 'fan', 'FAN25G2214' => 'fan', 'FvH4_1g21031' => 'fve', 'FvH4_3g16231' => 'fve', 'FvH4_3g26413' => 'fve', 'FvH4_3g29014' => 'fve', 'FvH4_3g31921' => 'fve', 'FvH4_4g19882' => 'fve', 'FvH4_5g21960' => 'fve', 'FvH4_5g29683' => 'fve', 'FvH4_7g13271' => 'fve', 'Glyma.01G062500' => 'gma', 'Glyma.07G140900' => 'gma', 'Glyma.09G140900' => 'gma', 'Glyma.12G112700' => 'gma', 'Glyma.17G168800' => 'gma', 'HanXRQChr01g0027001' => 'han', 'HanXRQChr04g0120511' => 'han', 'HanXRQChr08g0232381' => 'han', 'HanXRQChr09g0265661' => 'han', 'HanXRQChr13g0416031' => 'han', 'Haze_05835' => 'cav', 'Haze_06597' => 'cav', 'Haze_07921' => 'cav', 'Haze_08599' => 'cav', 'Haze_10686' => 'cav', 'Haze_12994' => 'cav', 'Haze_13466' => 'cav', 'Haze_16101' => 'cav', 'Haze_17766' => 'cav', 'Haze_18456' => 'cav', 'Haze_20229' => 'cav', 'Hma1.2p1_0324F.1_g125640' => 'hma', 'Hma1.2p1_0733F.1_g210230' => 'hma', 'Hma1.2p1_0921F.1_g236870' => 'hma', 'Hma1.2p1_1313F.1_g274940' => 'hma', 'Hma1.2p1_3059F.1_g332230' => 'hma', 'Hund15925' => 'sun', 'Hund19562' => 'sun', 'Hund21925' => 'sun', 'MD03G1177400' => 'mdo', 'MD07G1026100' => 'mdo', 'MD17G1218600' => 'mdo', 'Medtr0867s0010' => 'mtr', 'Medtr6g081150' => 'mtr', 'Os01g0527900' => 'osa', 'Os02g0463725' => 'osa', 'Os02g0785600' => 'osa', 'Os03g0433733' => 'osa', 'Os04g0286500' => 'osa', 'Os05g0227800' => 'osa', 'Os06g0521000' => 'osa', 'Os06g0635500' => 'osa', 'Os06g0660650' => 'osa', 'Os07g0554400' => 'osa', 'Os08g0225900' => 'osa', 'Os08g0561000' => 'osa', 'Os09g0241700' => 'osa', 'Os09g0351900' => 'osa', 'Os11g0220700' => 'osa', 'Os11g0282700' => 'osa', 'Os12g0169300' => 'osa', 'Os12g0228500' => 'osa', 'Os12g0543800' => 'osa', 'PGR044G1547' => 'pgr', 'Potri.005G239150' => 'ptr', 'Potri.010G014250' => 'ptr', 'Prupe.1G172500' => 'ppe', 'Prupe.1G196800' => 'ppe', 'Prupe.1G279700' => 'ppe', 'Prupe.2G026400' => 'ppe', 'Prupe.3G094000' => 'ppe', 'Prupe.4G287300' => 'ppe', 'QL01p022166' => 'qlo', 'QL01p051890' => 'qlo', 'QL02p009469' => 'qlo', 'QL02p046053' => 'qlo', 'QL02p057958' => 'qlo', 'QL02p093127' => 'qlo', 'QL03p006855' => 'qlo', 'QL03p071586' => 'qlo', 'QL04p000022' => 'qlo', 'QL04p000024' => 'qlo', 'QL04p003192' => 'qlo', 'QL05p011416' => 'qlo', 'QL06p039590' => 'qlo', 'QL06p052750' => 'qlo', 'QL06p053821' => 'qlo', 'QL07p025287' => 'qlo', 'QL09p033218' => 'qlo', 'QL09p040841' => 'qlo', 'QL10p020337' => 'qlo', 'QL10p027209' => 'qlo', 'QL10p027969' => 'qlo', 'QL10p048988' => 'qlo', 'QL11p001241' => 'qlo', 'QL11p028487' => 'qlo', 'RcHm_v2.0_Chr2g0105031' => 'rch', 'RcHm_v2.0_Chr2g0117811' => 'rch', 'RcHm_v2.0_Chr6g0270241' => 'rch', 'RcHm_v2.0_Chr7g0215961' => 'rch', 'RcHm_v2.0_Chr7g0231991' => 'rch', 'Rhsim01G0041500' => 'rsi', 'Rhsim01G0115000' => 'rsi', 'Rhsim01G0115400' => 'rsi', 'Rhsim01G0133600' => 'rsi', 'Rhsim01G0159900' => 'rsi', 'Rhsim02G0189400' => 'rsi', 'Rhsim03G0135600' => 'rsi', 'Rhsim03G0149900' => 'rsi', 'Rhsim04G0125600' => 'rsi', 'Rhsim05G0091700' => 'rsi', 'Rhsim05G0092900' => 'rsi', 'Rhsim06G0075000' => 'rsi', 'Rhsim07G0066400' => 'rsi', 'Rhsim07G0156400' => 'rsi', 'Rhsim07G0182200' => 'rsi', 'Rhsim07G0182300' => 'rsi', 'Rhsim08G0180400' => 'rsi', 'Rhsim09G0056800' => 'rsi', 'Rhsim10G0153300' => 'rsi', 'Rhsim11G0012700' => 'rsi', 'Rhsim12G0031800' => 'rsi', 'Rhsim12G0055400' => 'rsi', 'Rhsim12G0091400' => 'rsi', 'Rhsim13G0070800' => 'rsi', 'Rhsim13G0193300' => 'rsi', 'RhsimUnG0111600' => 'rsi', 'RhsimUnG0137500' => 'rsi', 'RhsimUnG0172900' => 'rsi', 'SGA_v2.0_scaffold11G05878' => 'sas', 'SGA_v2.0_scaffold167G38458' => 'sas', 'SGA_v2.0_scaffold19G08588' => 'sas', 'SGA_v2.0_scaffold239G43990' => 'sas', 'SGA_v2.0_scaffold260G45865' => 'sas', 'SGA_v2.0_scaffold309G48177' => 'sas', 'SGA_v2.0_scaffold76G25122' => 'sas', 'SGA_v2.0_scaffold85G26708' => 'sas', 'SHI13914' => 'shi', 'SHI30402' => 'shi', 'TWI09G0020' => 'twi', 'TWI09G0456' => 'twi', 'TWI09G1572' => 'twi', 'TWI12G0266' => 'twi', 'TWI12G1451' => 'twi', 'TWI14G0851' => 'twi', 'TWI15G0796' => 'twi', 'TWI18G0820' => 'twi', 'TWI18G1152' => 'twi', 'TWI23G0007' => 'twi', 'TWI23G0314' => 'twi', 'TWI31G0674' => 'twi', 'TWI31G0938' => 'twi', 'TWI34G0641' => 'twi', 'TWI34G1527' => 'twi', 'TWI36G0193' => 'twi', 'TWI36G0405' => 'twi', 'TWI38G0892' => 'twi', 'TWI38G0936' => 'twi', 'TWI38G2218' => 'twi', 'TWI53G0679' => 'twi', 'TWI53G0863' => 'twi', 'TWI53G1133' => 'twi', 'TWI60G0823' => 'twi', 'TWI63G0919' => 'twi', 'TWI63G1436' => 'twi', 'TWI73G0140' => 'twi', 'TWI73G0419' => 'twi', 'TWI73G0420' => 'twi', 'TWI73G1276' => 'twi', 'TWI74G0405' => 'twi', 'TWI74G0837' => 'twi', 'TWI75G0594' => 'twi', 'TWI75G1615' => 'twi', 'TWI77G0816' => 'twi', 'vmacro03831' => 'vma', 'vmacro13746' => 'vma', 'vmacro16089' => 'vma', 'vmacro22863' => 'vma', 'Zm00001eb085790' => 'zma', 'Zm00001eb114250' => 'zma', 'Zm00001eb138070' => 'zma', 'Zm00001eb167560' => 'zma', 'Zm00001eb199990' => 'zma', 'Zm00001eb368180' => 'zma', 'Zm00001eb382470' => 'zma' ) $gf_id = 'HOM05D001576' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001576' ) $data_identifier = 'HOM05D001576' $data_type = 'gf_id' $species_gene_counts = array( 'aox' => (int) 9, 'acertr' => (int) 3, 'cansat' => (int) 1, 'ccl' => (int) 4, 'cil' => (int) 145, 'camsi' => (int) 46, 'dca' => (int) 1, 'din' => (int) 1, 'fan' => (int) 12, 'fve' => (int) 9, 'gma' => (int) 5, 'han' => (int) 5, 'cav' => (int) 11, 'hma' => (int) 5, 'sun' => (int) 3, 'mdo' => (int) 3, 'mtr' => (int) 2, 'osa' => (int) 19, 'pgr' => (int) 1, 'ptr' => (int) 2, 'ppe' => (int) 6, 'qlo' => (int) 24, 'rch' => (int) 5, 'rsi' => (int) 28, 'sas' => (int) 8, 'shi' => (int) 2, 'twi' => (int) 35, 'vma' => (int) 4, 'zma' => (int) 7 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb382470' $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' => 'HOM05D001576', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '406', 'num_species' => '29' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'Aqoxy1G01456' => 'aox', 'Aqoxy1G02949' => 'aox', 'Aqoxy3G01274' => 'aox', 'Aqoxy3G02110' => 'aox', 'Aqoxy3G02268' => 'aox', 'Aqoxy5G02702' => 'aox', 'Aqoxy5G02988' => 'aox', 'Aqoxy5G03427' => 'aox', 'Aqoxy6G02363' => 'aox', 'Atru.chr1.3225' => 'acertr', 'Atru.chr8.1198' => 'acertr', 'Atru.chr9.790' => 'acertr', 'CANSAT01G3197' => 'cansat', 'Ciclev10003979m.g' => 'ccl', 'Ciclev10017471m.g' => 'ccl', 'Ciclev10018206m.g' => 'ccl', 'Ciclev10033751m.g' => 'ccl', 'CiPaw.01G000900' => 'cil', 'CiPaw.01G001000' => 'cil', 'CiPaw.01G033500' => 'cil', 'CiPaw.01G060300' => 'cil', 'CiPaw.01G070200' => 'cil', 'CiPaw.01G075100' => 'cil', 'CiPaw.01G084700' => 'cil', 'CiPaw.01G087900' => 'cil', 'CiPaw.01G092600' => 'cil', 'CiPaw.01G097200' => 'cil', 'CiPaw.01G098300' => 'cil', 'CiPaw.01G110200' => 'cil', 'CiPaw.01G118700' => 'cil', 'CiPaw.01G121200' => 'cil', 'CiPaw.01G132500' => 'cil', 'CiPaw.01G146900' => 'cil', 'CiPaw.01G174000' => 'cil', 'CiPaw.01G179900' => 'cil', 'CiPaw.01G183400' => 'cil', 'CiPaw.01G240000' => 'cil', 'CiPaw.01G283500' => 'cil', 'CiPaw.01G307400' => 'cil', 'CiPaw.02G030800' => 'cil', 'CiPaw.02G047200' => 'cil', 'CiPaw.02G050500' => 'cil', 'CiPaw.02G069900' => 'cil', 'CiPaw.02G091600' => 'cil', 'CiPaw.02G095000' => 'cil', 'CiPaw.02G131900' => 'cil', 'CiPaw.03G043000' => 'cil', 'CiPaw.03G069900' => 'cil', 'CiPaw.03G088100' => 'cil', 'CiPaw.03G089300' => 'cil', 'CiPaw.03G093100' => 'cil', 'CiPaw.03G129800' => 'cil', 'CiPaw.03G131200' => 'cil', 'CiPaw.03G134500' => 'cil', 'CiPaw.03G152100' => 'cil', 'CiPaw.03G162700' => 'cil', 'CiPaw.03G172800' => 'cil', 'CiPaw.03G175800' => 'cil', 'CiPaw.03G181800' => 'cil', 'CiPaw.03G191400' => 'cil', 'CiPaw.03G198300' => 'cil', 'CiPaw.03G201300' => 'cil', 'CiPaw.03G224700' => 'cil', 'CiPaw.03G225000' => 'cil', 'CiPaw.04G065100' => 'cil', 'CiPaw.04G080400' => 'cil', 'CiPaw.04G113500' => 'cil', 'CiPaw.04G121900' => 'cil', 'CiPaw.04G144100' => 'cil', 'CiPaw.04G176500' => 'cil', 'CiPaw.05G086200' => 'cil', 'CiPaw.05G100200' => 'cil', 'CiPaw.05G114200' => 'cil', 'CiPaw.05G126800' => 'cil', 'CiPaw.05G228800' => 'cil', 'CiPaw.05G230600' => 'cil', 'CiPaw.05G236500' => 'cil', 'CiPaw.05G244800' => 'cil', 'CiPaw.06G026600' => 'cil', 'CiPaw.06G027900' => 'cil', 'CiPaw.06G051800' => 'cil', 'CiPaw.06G128500' => 'cil', 'CiPaw.06G165900' => 'cil', 'CiPaw.07G045400' => 'cil', 'CiPaw.07G048000' => 'cil', 'CiPaw.07G052000' => 'cil', 'CiPaw.07G073800' => 'cil', 'CiPaw.07G099700' => 'cil', 'CiPaw.07G108700' => 'cil', 'CiPaw.07G120000' => 'cil', 'CiPaw.07G134100' => 'cil', 'CiPaw.07G147000' => 'cil', 'CiPaw.07G149700' => 'cil', 'CiPaw.07G178300' => 'cil', 'CiPaw.07G184900' => 'cil', 'CiPaw.08G044500' => 'cil', 'CiPaw.08G046900' => 'cil', 'CiPaw.08G047300' => 'cil', 'CiPaw.08G115400' => 'cil', 'CiPaw.08G134700' => 'cil', 'CiPaw.08G157400' => 'cil', 'CiPaw.09G014300' => 'cil', 'CiPaw.09G088900' => 'cil', 'CiPaw.09G130900' => 'cil', 'CiPaw.09G133100' => 'cil', 'CiPaw.09G151300' => 'cil', 'CiPaw.09G172800' => 'cil', 'CiPaw.09G174900' => 'cil', 'CiPaw.09G175000' => 'cil', 'CiPaw.10G012800' => 'cil', 'CiPaw.10G028800' => 'cil', 'CiPaw.10G044700' => 'cil', 'CiPaw.10G067400' => 'cil', 'CiPaw.10G115900' => 'cil', 'CiPaw.10G126200' => 'cil', 'CiPaw.10G139700' => 'cil', 'CiPaw.10G155100' => 'cil', 'CiPaw.11G011300' => 'cil', 'CiPaw.11G025900' => 'cil', 'CiPaw.11G104100' => 'cil', 'CiPaw.11G142700' => 'cil', 'CiPaw.11G164500' => 'cil', 'CiPaw.11G189100' => 'cil', 'CiPaw.11G197100' => 'cil', 'CiPaw.12G006100' => 'cil', 'CiPaw.12G038500' => 'cil', 'CiPaw.12G041400' => 'cil', 'CiPaw.12G041600' => 'cil', 'CiPaw.12G051300' => 'cil', 'CiPaw.12G101800' => 'cil', 'CiPaw.12G107800' => 'cil', 'CiPaw.13G033200' => 'cil', 'CiPaw.13G129900' => 'cil', 'CiPaw.13G160200' => 'cil', 'CiPaw.14G018900' => 'cil', 'CiPaw.14G029000' => 'cil', 'CiPaw.14G031000' => 'cil', 'CiPaw.14G032000' => 'cil', 'CiPaw.14G032300' => 'cil', 'CiPaw.14G040600' => 'cil', 'CiPaw.14G060500' => 'cil', 'CiPaw.14G061500' => 'cil', 'CiPaw.14G077500' => 'cil', 'CiPaw.14G088300' => 'cil', 'CiPaw.14G108500' => 'cil', 'CiPaw.14G121300' => 'cil', 'CiPaw.14G133000' => 'cil', 'CiPaw.14G134600' => 'cil', 'CiPaw.15G027200' => 'cil', 'CiPaw.15G037700' => 'cil', 'CiPaw.15G050900' => 'cil', 'CiPaw.15G067200' => 'cil', 'CiPaw.15G072000' => 'cil', 'CiPaw.15G112900' => 'cil', 'CiPaw.15G133200' => 'cil', 'CiPaw.15G139500' => 'cil', 'CiPaw.15G155400' => 'cil', 'CiPaw.16G006000' => 'cil', 'CiPaw.16G013100' => 'cil', 'CiPaw.16G047100' => 'cil', 'CiPaw.16G048900' => 'cil', 'CiPaw.16G070300' => 'cil', 'CSS0000195' => 'camsi', 'CSS0001664' => 'camsi', 'CSS0002566' => 'camsi', 'CSS0003077' => 'camsi', 'CSS0004257' => 'camsi', 'CSS0004495' => 'camsi', 'CSS0004599' => 'camsi', 'CSS0004943' => 'camsi', 'CSS0005302' => 'camsi', 'CSS0006274' => 'camsi', 'CSS0006547' => 'camsi', 'CSS0006860' => 'camsi', 'CSS0008814' => 'camsi', 'CSS0008946' => 'camsi', 'CSS0009093' => 'camsi', 'CSS0010221' => 'camsi', 'CSS0010296' => 'camsi', 'CSS0010386' => 'camsi', 'CSS0010831' => 'camsi', 'CSS0011061' => 'camsi', 'CSS0012008' => 'camsi', 'CSS0012194' => 'camsi', 'CSS0013580' => 'camsi', 'CSS0014176' => 'camsi', 'CSS0014280' => 'camsi', 'CSS0014799' => 'camsi', 'CSS0015368' => 'camsi', 'CSS0017473' => 'camsi', 'CSS0019281' => 'camsi', 'CSS0021320' => 'camsi', 'CSS0021750' => 'camsi', 'CSS0023642' => 'camsi', 'CSS0023792' => 'camsi', 'CSS0031528' => 'camsi', 'CSS0033894' => 'camsi', 'CSS0034959' => 'camsi', 'CSS0035632' => 'camsi', 'CSS0038450' => 'camsi', 'CSS0039293' => 'camsi', 'CSS0041053' => 'camsi', 'CSS0041981' => 'camsi', 'CSS0042573' => 'camsi', 'CSS0042927' => 'camsi', 'CSS0047725' => 'camsi', 'CSS0049636' => 'camsi', 'CSS0050513' => 'camsi', 'DCAR_030203' => 'dca', 'Dinv07939' => 'din', 'FAN01G0456' => 'fan', 'FAN02G3001' => 'fan', 'FAN04G2781' => 'fan', 'FAN05G1385' => 'fan', 'FAN05G3062' => 'fan', 'FAN08G2267' => 'fan', 'FAN10G0481' => 'fan', 'FAN10G1257' => 'fan', 'FAN14G0954' => 'fan', 'FAN14G2347' => 'fan', 'FAN15G0187' => 'fan', 'FAN25G2214' => 'fan', 'FvH4_1g21031' => 'fve', 'FvH4_3g16231' => 'fve', 'FvH4_3g26413' => 'fve', 'FvH4_3g29014' => 'fve', 'FvH4_3g31921' => 'fve', 'FvH4_4g19882' => 'fve', 'FvH4_5g21960' => 'fve', 'FvH4_5g29683' => 'fve', 'FvH4_7g13271' => 'fve', 'Glyma.01G062500' => 'gma', 'Glyma.07G140900' => 'gma', 'Glyma.09G140900' => 'gma', 'Glyma.12G112700' => 'gma', 'Glyma.17G168800' => 'gma', 'HanXRQChr01g0027001' => 'han', 'HanXRQChr04g0120511' => 'han', 'HanXRQChr08g0232381' => 'han', 'HanXRQChr09g0265661' => 'han', 'HanXRQChr13g0416031' => 'han', 'Haze_05835' => 'cav', 'Haze_06597' => 'cav', 'Haze_07921' => 'cav', 'Haze_08599' => 'cav', 'Haze_10686' => 'cav', 'Haze_12994' => 'cav', 'Haze_13466' => 'cav', 'Haze_16101' => 'cav', 'Haze_17766' => 'cav', 'Haze_18456' => 'cav', 'Haze_20229' => 'cav', 'Hma1.2p1_0324F.1_g125640' => 'hma', 'Hma1.2p1_0733F.1_g210230' => 'hma', 'Hma1.2p1_0921F.1_g236870' => 'hma', 'Hma1.2p1_1313F.1_g274940' => 'hma', 'Hma1.2p1_3059F.1_g332230' => 'hma', 'Hund15925' => 'sun', 'Hund19562' => 'sun', 'Hund21925' => 'sun', 'MD03G1177400' => 'mdo', 'MD07G1026100' => 'mdo', 'MD17G1218600' => 'mdo', 'Medtr0867s0010' => 'mtr', 'Medtr6g081150' => 'mtr', 'Os01g0527900' => 'osa', 'Os02g0463725' => 'osa', 'Os02g0785600' => 'osa', 'Os03g0433733' => 'osa', 'Os04g0286500' => 'osa', 'Os05g0227800' => 'osa', 'Os06g0521000' => 'osa', 'Os06g0635500' => 'osa', 'Os06g0660650' => 'osa', 'Os07g0554400' => 'osa', 'Os08g0225900' => 'osa', 'Os08g0561000' => 'osa', 'Os09g0241700' => 'osa', 'Os09g0351900' => 'osa', 'Os11g0220700' => 'osa', 'Os11g0282700' => 'osa', 'Os12g0169300' => 'osa', 'Os12g0228500' => 'osa', 'Os12g0543800' => 'osa', 'PGR044G1547' => 'pgr', 'Potri.005G239150' => 'ptr', 'Potri.010G014250' => 'ptr', 'Prupe.1G172500' => 'ppe', 'Prupe.1G196800' => 'ppe', 'Prupe.1G279700' => 'ppe', 'Prupe.2G026400' => 'ppe', 'Prupe.3G094000' => 'ppe', 'Prupe.4G287300' => 'ppe', 'QL01p022166' => 'qlo', 'QL01p051890' => 'qlo', 'QL02p009469' => 'qlo', 'QL02p046053' => 'qlo', 'QL02p057958' => 'qlo', 'QL02p093127' => 'qlo', 'QL03p006855' => 'qlo', 'QL03p071586' => 'qlo', 'QL04p000022' => 'qlo', 'QL04p000024' => 'qlo', 'QL04p003192' => 'qlo', 'QL05p011416' => 'qlo', 'QL06p039590' => 'qlo', 'QL06p052750' => 'qlo', 'QL06p053821' => 'qlo', 'QL07p025287' => 'qlo', 'QL09p033218' => 'qlo', 'QL09p040841' => 'qlo', 'QL10p020337' => 'qlo', 'QL10p027209' => 'qlo', 'QL10p027969' => 'qlo', 'QL10p048988' => 'qlo', 'QL11p001241' => 'qlo', 'QL11p028487' => 'qlo', 'RcHm_v2.0_Chr2g0105031' => 'rch', 'RcHm_v2.0_Chr2g0117811' => 'rch', 'RcHm_v2.0_Chr6g0270241' => 'rch', 'RcHm_v2.0_Chr7g0215961' => 'rch', 'RcHm_v2.0_Chr7g0231991' => 'rch', 'Rhsim01G0041500' => 'rsi', 'Rhsim01G0115000' => 'rsi', 'Rhsim01G0115400' => 'rsi', 'Rhsim01G0133600' => 'rsi', 'Rhsim01G0159900' => 'rsi', 'Rhsim02G0189400' => 'rsi', 'Rhsim03G0135600' => 'rsi', 'Rhsim03G0149900' => 'rsi', 'Rhsim04G0125600' => 'rsi', 'Rhsim05G0091700' => 'rsi', 'Rhsim05G0092900' => 'rsi', 'Rhsim06G0075000' => 'rsi', 'Rhsim07G0066400' => 'rsi', 'Rhsim07G0156400' => 'rsi', 'Rhsim07G0182200' => 'rsi', 'Rhsim07G0182300' => 'rsi', 'Rhsim08G0180400' => 'rsi', 'Rhsim09G0056800' => 'rsi', 'Rhsim10G0153300' => 'rsi', 'Rhsim11G0012700' => 'rsi', 'Rhsim12G0031800' => 'rsi', 'Rhsim12G0055400' => 'rsi', 'Rhsim12G0091400' => 'rsi', 'Rhsim13G0070800' => 'rsi', 'Rhsim13G0193300' => 'rsi', 'RhsimUnG0111600' => 'rsi', 'RhsimUnG0137500' => 'rsi', 'RhsimUnG0172900' => 'rsi', 'SGA_v2.0_scaffold11G05878' => 'sas', 'SGA_v2.0_scaffold167G38458' => 'sas', 'SGA_v2.0_scaffold19G08588' => 'sas', 'SGA_v2.0_scaffold239G43990' => 'sas', 'SGA_v2.0_scaffold260G45865' => 'sas', 'SGA_v2.0_scaffold309G48177' => 'sas', 'SGA_v2.0_scaffold76G25122' => 'sas', 'SGA_v2.0_scaffold85G26708' => 'sas', 'SHI13914' => 'shi', 'SHI30402' => 'shi', 'TWI09G0020' => 'twi', 'TWI09G0456' => 'twi', 'TWI09G1572' => 'twi', 'TWI12G0266' => 'twi', 'TWI12G1451' => 'twi', 'TWI14G0851' => 'twi', 'TWI15G0796' => 'twi', 'TWI18G0820' => 'twi', 'TWI18G1152' => 'twi', 'TWI23G0007' => 'twi', 'TWI23G0314' => 'twi', 'TWI31G0674' => 'twi', 'TWI31G0938' => 'twi', 'TWI34G0641' => 'twi', 'TWI34G1527' => 'twi', 'TWI36G0193' => 'twi', 'TWI36G0405' => 'twi', 'TWI38G0892' => 'twi', 'TWI38G0936' => 'twi', 'TWI38G2218' => 'twi', 'TWI53G0679' => 'twi', 'TWI53G0863' => 'twi', 'TWI53G1133' => 'twi', 'TWI60G0823' => 'twi', 'TWI63G0919' => 'twi', 'TWI63G1436' => 'twi', 'TWI73G0140' => 'twi', 'TWI73G0419' => 'twi', 'TWI73G0420' => 'twi', 'TWI73G1276' => 'twi', 'TWI74G0405' => 'twi', 'TWI74G0837' => 'twi', 'TWI75G0594' => 'twi', 'TWI75G1615' => 'twi', 'TWI77G0816' => 'twi', 'vmacro03831' => 'vma', 'vmacro13746' => 'vma', 'vmacro16089' => 'vma', 'vmacro22863' => 'vma', 'Zm00001eb085790' => 'zma', 'Zm00001eb114250' => 'zma', 'Zm00001eb138070' => 'zma', 'Zm00001eb167560' => 'zma', 'Zm00001eb199990' => 'zma', 'Zm00001eb368180' => 'zma', 'Zm00001eb382470' => 'zma' ), 'gf_id' => 'HOM05D001576', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001576' ), 'data_identifier' => 'HOM05D001576', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001576', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '406', 'num_species' => '29' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'Aqoxy1G01456' => 'aox', 'Aqoxy1G02949' => 'aox', 'Aqoxy3G01274' => 'aox', 'Aqoxy3G02110' => 'aox', 'Aqoxy3G02268' => 'aox', 'Aqoxy5G02702' => 'aox', 'Aqoxy5G02988' => 'aox', 'Aqoxy5G03427' => 'aox', 'Aqoxy6G02363' => 'aox', 'Atru.chr1.3225' => 'acertr', 'Atru.chr8.1198' => 'acertr', 'Atru.chr9.790' => 'acertr', 'CANSAT01G3197' => 'cansat', 'Ciclev10003979m.g' => 'ccl', 'Ciclev10017471m.g' => 'ccl', 'Ciclev10018206m.g' => 'ccl', 'Ciclev10033751m.g' => 'ccl', 'CiPaw.01G000900' => 'cil', 'CiPaw.01G001000' => 'cil', 'CiPaw.01G033500' => 'cil', 'CiPaw.01G060300' => 'cil', 'CiPaw.01G070200' => 'cil', 'CiPaw.01G075100' => 'cil', 'CiPaw.01G084700' => 'cil', 'CiPaw.01G087900' => 'cil', 'CiPaw.01G092600' => 'cil', 'CiPaw.01G097200' => 'cil', 'CiPaw.01G098300' => 'cil', 'CiPaw.01G110200' => 'cil', 'CiPaw.01G118700' => 'cil', 'CiPaw.01G121200' => 'cil', 'CiPaw.01G132500' => 'cil', 'CiPaw.01G146900' => 'cil', 'CiPaw.01G174000' => 'cil', 'CiPaw.01G179900' => 'cil', 'CiPaw.01G183400' => 'cil', 'CiPaw.01G240000' => 'cil', 'CiPaw.01G283500' => 'cil', 'CiPaw.01G307400' => 'cil', 'CiPaw.02G030800' => 'cil', 'CiPaw.02G047200' => 'cil', 'CiPaw.02G050500' => 'cil', 'CiPaw.02G069900' => 'cil', 'CiPaw.02G091600' => 'cil', 'CiPaw.02G095000' => 'cil', 'CiPaw.02G131900' => 'cil', 'CiPaw.03G043000' => 'cil', 'CiPaw.03G069900' => 'cil', 'CiPaw.03G088100' => 'cil', 'CiPaw.03G089300' => 'cil', 'CiPaw.03G093100' => 'cil', 'CiPaw.03G129800' => 'cil', 'CiPaw.03G131200' => 'cil', 'CiPaw.03G134500' => 'cil', 'CiPaw.03G152100' => 'cil', 'CiPaw.03G162700' => 'cil', 'CiPaw.03G172800' => 'cil', 'CiPaw.03G175800' => 'cil', 'CiPaw.03G181800' => 'cil', 'CiPaw.03G191400' => 'cil', 'CiPaw.03G198300' => 'cil', 'CiPaw.03G201300' => 'cil', 'CiPaw.03G224700' => 'cil', 'CiPaw.03G225000' => 'cil', 'CiPaw.04G065100' => 'cil', 'CiPaw.04G080400' => 'cil', 'CiPaw.04G113500' => 'cil', 'CiPaw.04G121900' => 'cil', 'CiPaw.04G144100' => 'cil', 'CiPaw.04G176500' => 'cil', 'CiPaw.05G086200' => 'cil', 'CiPaw.05G100200' => 'cil', 'CiPaw.05G114200' => 'cil', 'CiPaw.05G126800' => 'cil', 'CiPaw.05G228800' => 'cil', 'CiPaw.05G230600' => 'cil', 'CiPaw.05G236500' => 'cil', 'CiPaw.05G244800' => 'cil', 'CiPaw.06G026600' => 'cil', 'CiPaw.06G027900' => 'cil', 'CiPaw.06G051800' => 'cil', 'CiPaw.06G128500' => 'cil', 'CiPaw.06G165900' => 'cil', 'CiPaw.07G045400' => 'cil', 'CiPaw.07G048000' => 'cil', 'CiPaw.07G052000' => 'cil', 'CiPaw.07G073800' => 'cil', 'CiPaw.07G099700' => 'cil', 'CiPaw.07G108700' => 'cil', 'CiPaw.07G120000' => 'cil', 'CiPaw.07G134100' => 'cil', 'CiPaw.07G147000' => 'cil', 'CiPaw.07G149700' => 'cil', 'CiPaw.07G178300' => 'cil', 'CiPaw.07G184900' => 'cil', 'CiPaw.08G044500' => 'cil', 'CiPaw.08G046900' => 'cil', 'CiPaw.08G047300' => 'cil', 'CiPaw.08G115400' => 'cil', 'CiPaw.08G134700' => 'cil', 'CiPaw.08G157400' => 'cil', 'CiPaw.09G014300' => 'cil', 'CiPaw.09G088900' => 'cil', 'CiPaw.09G130900' => 'cil', 'CiPaw.09G133100' => 'cil', 'CiPaw.09G151300' => 'cil', 'CiPaw.09G172800' => 'cil', 'CiPaw.09G174900' => 'cil', 'CiPaw.09G175000' => 'cil', 'CiPaw.10G012800' => 'cil', 'CiPaw.10G028800' => 'cil', 'CiPaw.10G044700' => 'cil', 'CiPaw.10G067400' => 'cil', 'CiPaw.10G115900' => 'cil', 'CiPaw.10G126200' => 'cil', 'CiPaw.10G139700' => 'cil', 'CiPaw.10G155100' => 'cil', 'CiPaw.11G011300' => 'cil', 'CiPaw.11G025900' => 'cil', 'CiPaw.11G104100' => 'cil', 'CiPaw.11G142700' => 'cil', 'CiPaw.11G164500' => 'cil', 'CiPaw.11G189100' => 'cil', 'CiPaw.11G197100' => 'cil', 'CiPaw.12G006100' => 'cil', 'CiPaw.12G038500' => 'cil', 'CiPaw.12G041400' => 'cil', 'CiPaw.12G041600' => 'cil', 'CiPaw.12G051300' => 'cil', 'CiPaw.12G101800' => 'cil', 'CiPaw.12G107800' => 'cil', 'CiPaw.13G033200' => 'cil', 'CiPaw.13G129900' => 'cil', 'CiPaw.13G160200' => 'cil', 'CiPaw.14G018900' => 'cil', 'CiPaw.14G029000' => 'cil', 'CiPaw.14G031000' => 'cil', 'CiPaw.14G032000' => 'cil', 'CiPaw.14G032300' => 'cil', 'CiPaw.14G040600' => 'cil', 'CiPaw.14G060500' => 'cil', 'CiPaw.14G061500' => 'cil', 'CiPaw.14G077500' => 'cil', 'CiPaw.14G088300' => 'cil', 'CiPaw.14G108500' => 'cil', 'CiPaw.14G121300' => 'cil', 'CiPaw.14G133000' => 'cil', 'CiPaw.14G134600' => 'cil', 'CiPaw.15G027200' => 'cil', 'CiPaw.15G037700' => 'cil', 'CiPaw.15G050900' => 'cil', 'CiPaw.15G067200' => 'cil', 'CiPaw.15G072000' => 'cil', 'CiPaw.15G112900' => 'cil', 'CiPaw.15G133200' => 'cil', 'CiPaw.15G139500' => 'cil', 'CiPaw.15G155400' => 'cil', 'CiPaw.16G006000' => 'cil', 'CiPaw.16G013100' => 'cil', 'CiPaw.16G047100' => 'cil', 'CiPaw.16G048900' => 'cil', 'CiPaw.16G070300' => 'cil', 'CSS0000195' => 'camsi', 'CSS0001664' => 'camsi', 'CSS0002566' => 'camsi', 'CSS0003077' => 'camsi', 'CSS0004257' => 'camsi', 'CSS0004495' => 'camsi', 'CSS0004599' => 'camsi', 'CSS0004943' => 'camsi', 'CSS0005302' => 'camsi', 'CSS0006274' => 'camsi', 'CSS0006547' => 'camsi', 'CSS0006860' => 'camsi', 'CSS0008814' => 'camsi', 'CSS0008946' => 'camsi', 'CSS0009093' => 'camsi', 'CSS0010221' => 'camsi', 'CSS0010296' => 'camsi', 'CSS0010386' => 'camsi', 'CSS0010831' => 'camsi', 'CSS0011061' => 'camsi', 'CSS0012008' => 'camsi', 'CSS0012194' => 'camsi', 'CSS0013580' => 'camsi', 'CSS0014176' => 'camsi', 'CSS0014280' => 'camsi', 'CSS0014799' => 'camsi', 'CSS0015368' => 'camsi', 'CSS0017473' => 'camsi', 'CSS0019281' => 'camsi', 'CSS0021320' => 'camsi', 'CSS0021750' => 'camsi', 'CSS0023642' => 'camsi', 'CSS0023792' => 'camsi', 'CSS0031528' => 'camsi', 'CSS0033894' => 'camsi', 'CSS0034959' => 'camsi', 'CSS0035632' => 'camsi', 'CSS0038450' => 'camsi', 'CSS0039293' => 'camsi', 'CSS0041053' => 'camsi', 'CSS0041981' => 'camsi', 'CSS0042573' => 'camsi', 'CSS0042927' => 'camsi', 'CSS0047725' => 'camsi', 'CSS0049636' => 'camsi', 'CSS0050513' => 'camsi', 'DCAR_030203' => 'dca', 'Dinv07939' => 'din', 'FAN01G0456' => 'fan', 'FAN02G3001' => 'fan', 'FAN04G2781' => 'fan', 'FAN05G1385' => 'fan', 'FAN05G3062' => 'fan', 'FAN08G2267' => 'fan', 'FAN10G0481' => 'fan', 'FAN10G1257' => 'fan', 'FAN14G0954' => 'fan', 'FAN14G2347' => 'fan', 'FAN15G0187' => 'fan', 'FAN25G2214' => 'fan', 'FvH4_1g21031' => 'fve', 'FvH4_3g16231' => 'fve', 'FvH4_3g26413' => 'fve', 'FvH4_3g29014' => 'fve', 'FvH4_3g31921' => 'fve', 'FvH4_4g19882' => 'fve', 'FvH4_5g21960' => 'fve', 'FvH4_5g29683' => 'fve', 'FvH4_7g13271' => 'fve', 'Glyma.01G062500' => 'gma', 'Glyma.07G140900' => 'gma', 'Glyma.09G140900' => 'gma', 'Glyma.12G112700' => 'gma', 'Glyma.17G168800' => 'gma', 'HanXRQChr01g0027001' => 'han', 'HanXRQChr04g0120511' => 'han', 'HanXRQChr08g0232381' => 'han', 'HanXRQChr09g0265661' => 'han', 'HanXRQChr13g0416031' => 'han', 'Haze_05835' => 'cav', 'Haze_06597' => 'cav', 'Haze_07921' => 'cav', 'Haze_08599' => 'cav', 'Haze_10686' => 'cav', 'Haze_12994' => 'cav', 'Haze_13466' => 'cav', 'Haze_16101' => 'cav', 'Haze_17766' => 'cav', 'Haze_18456' => 'cav', 'Haze_20229' => 'cav', 'Hma1.2p1_0324F.1_g125640' => 'hma', 'Hma1.2p1_0733F.1_g210230' => 'hma', 'Hma1.2p1_0921F.1_g236870' => 'hma', 'Hma1.2p1_1313F.1_g274940' => 'hma', 'Hma1.2p1_3059F.1_g332230' => 'hma', 'Hund15925' => 'sun', 'Hund19562' => 'sun', 'Hund21925' => 'sun', 'MD03G1177400' => 'mdo', 'MD07G1026100' => 'mdo', 'MD17G1218600' => 'mdo', 'Medtr0867s0010' => 'mtr', 'Medtr6g081150' => 'mtr', 'Os01g0527900' => 'osa', 'Os02g0463725' => 'osa', 'Os02g0785600' => 'osa', 'Os03g0433733' => 'osa', 'Os04g0286500' => 'osa', 'Os05g0227800' => 'osa', 'Os06g0521000' => 'osa', 'Os06g0635500' => 'osa', 'Os06g0660650' => 'osa', 'Os07g0554400' => 'osa', 'Os08g0225900' => 'osa', 'Os08g0561000' => 'osa', 'Os09g0241700' => 'osa', 'Os09g0351900' => 'osa', 'Os11g0220700' => 'osa', 'Os11g0282700' => 'osa', 'Os12g0169300' => 'osa', 'Os12g0228500' => 'osa', 'Os12g0543800' => 'osa', 'PGR044G1547' => 'pgr', 'Potri.005G239150' => 'ptr', 'Potri.010G014250' => 'ptr', 'Prupe.1G172500' => 'ppe', 'Prupe.1G196800' => 'ppe', 'Prupe.1G279700' => 'ppe', 'Prupe.2G026400' => 'ppe', 'Prupe.3G094000' => 'ppe', 'Prupe.4G287300' => 'ppe', 'QL01p022166' => 'qlo', 'QL01p051890' => 'qlo', 'QL02p009469' => 'qlo', 'QL02p046053' => 'qlo', 'QL02p057958' => 'qlo', 'QL02p093127' => 'qlo', 'QL03p006855' => 'qlo', 'QL03p071586' => 'qlo', 'QL04p000022' => 'qlo', 'QL04p000024' => 'qlo', 'QL04p003192' => 'qlo', 'QL05p011416' => 'qlo', 'QL06p039590' => 'qlo', 'QL06p052750' => 'qlo', 'QL06p053821' => 'qlo', 'QL07p025287' => 'qlo', 'QL09p033218' => 'qlo', 'QL09p040841' => 'qlo', 'QL10p020337' => 'qlo', 'QL10p027209' => 'qlo', 'QL10p027969' => 'qlo', 'QL10p048988' => 'qlo', 'QL11p001241' => 'qlo', 'QL11p028487' => 'qlo', 'RcHm_v2.0_Chr2g0105031' => 'rch', 'RcHm_v2.0_Chr2g0117811' => 'rch', 'RcHm_v2.0_Chr6g0270241' => 'rch', 'RcHm_v2.0_Chr7g0215961' => 'rch', 'RcHm_v2.0_Chr7g0231991' => 'rch', 'Rhsim01G0041500' => 'rsi', 'Rhsim01G0115000' => 'rsi', 'Rhsim01G0115400' => 'rsi', 'Rhsim01G0133600' => 'rsi', 'Rhsim01G0159900' => 'rsi', 'Rhsim02G0189400' => 'rsi', 'Rhsim03G0135600' => 'rsi', 'Rhsim03G0149900' => 'rsi', 'Rhsim04G0125600' => 'rsi', 'Rhsim05G0091700' => 'rsi', 'Rhsim05G0092900' => 'rsi', 'Rhsim06G0075000' => 'rsi', 'Rhsim07G0066400' => 'rsi', 'Rhsim07G0156400' => 'rsi', 'Rhsim07G0182200' => 'rsi', 'Rhsim07G0182300' => 'rsi', 'Rhsim08G0180400' => 'rsi', 'Rhsim09G0056800' => 'rsi', 'Rhsim10G0153300' => 'rsi', 'Rhsim11G0012700' => 'rsi', 'Rhsim12G0031800' => 'rsi', 'Rhsim12G0055400' => 'rsi', 'Rhsim12G0091400' => 'rsi', 'Rhsim13G0070800' => 'rsi', 'Rhsim13G0193300' => 'rsi', 'RhsimUnG0111600' => 'rsi', 'RhsimUnG0137500' => 'rsi', 'RhsimUnG0172900' => 'rsi', 'SGA_v2.0_scaffold11G05878' => 'sas', 'SGA_v2.0_scaffold167G38458' => 'sas', 'SGA_v2.0_scaffold19G08588' => 'sas', 'SGA_v2.0_scaffold239G43990' => 'sas', 'SGA_v2.0_scaffold260G45865' => 'sas', 'SGA_v2.0_scaffold309G48177' => 'sas', 'SGA_v2.0_scaffold76G25122' => 'sas', 'SGA_v2.0_scaffold85G26708' => 'sas', 'SHI13914' => 'shi', 'SHI30402' => 'shi', 'TWI09G0020' => 'twi', 'TWI09G0456' => 'twi', 'TWI09G1572' => 'twi', 'TWI12G0266' => 'twi', 'TWI12G1451' => 'twi', 'TWI14G0851' => 'twi', 'TWI15G0796' => 'twi', 'TWI18G0820' => 'twi', 'TWI18G1152' => 'twi', 'TWI23G0007' => 'twi', 'TWI23G0314' => 'twi', 'TWI31G0674' => 'twi', 'TWI31G0938' => 'twi', 'TWI34G0641' => 'twi', 'TWI34G1527' => 'twi', 'TWI36G0193' => 'twi', 'TWI36G0405' => 'twi', 'TWI38G0892' => 'twi', 'TWI38G0936' => 'twi', 'TWI38G2218' => 'twi', 'TWI53G0679' => 'twi', 'TWI53G0863' => 'twi', 'TWI53G1133' => 'twi', 'TWI60G0823' => 'twi', 'TWI63G0919' => 'twi', 'TWI63G1436' => 'twi', 'TWI73G0140' => 'twi', 'TWI73G0419' => 'twi', 'TWI73G0420' => 'twi', 'TWI73G1276' => 'twi', 'TWI74G0405' => 'twi', 'TWI74G0837' => 'twi', 'TWI75G0594' => 'twi', 'TWI75G1615' => 'twi', 'TWI77G0816' => 'twi', 'vmacro03831' => 'vma', 'vmacro13746' => 'vma', 'vmacro16089' => 'vma', 'vmacro22863' => 'vma', 'Zm00001eb085790' => 'zma', 'Zm00001eb114250' => 'zma', 'Zm00001eb138070' => 'zma', 'Zm00001eb167560' => 'zma', 'Zm00001eb199990' => 'zma', 'Zm00001eb368180' => 'zma', 'Zm00001eb382470' => 'zma' ) $gf_id = 'HOM05D001576' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001576' ) $data_identifier = 'HOM05D001576' $data_type = 'gf_id' $species_gene_counts = array( 'aox' => (int) 9, 'acertr' => (int) 3, 'cansat' => (int) 1, 'ccl' => (int) 4, 'cil' => (int) 145, 'camsi' => (int) 46, 'dca' => (int) 1, 'din' => (int) 1, 'fan' => (int) 12, 'fve' => (int) 9, 'gma' => (int) 5, 'han' => (int) 5, 'cav' => (int) 11, 'hma' => (int) 5, 'sun' => (int) 3, 'mdo' => (int) 3, 'mtr' => (int) 2, 'osa' => (int) 19, 'pgr' => (int) 1, 'ptr' => (int) 2, 'ppe' => (int) 6, 'qlo' => (int) 24, 'rch' => (int) 5, 'rsi' => (int) 28, 'sas' => (int) 8, 'shi' => (int) 2, 'twi' => (int) 35, 'vma' => (int) 4, 'zma' => (int) 7 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb382470' $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' => 'HOM05D001576', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '406', 'num_species' => '29' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'Aqoxy1G01456' => 'aox', 'Aqoxy1G02949' => 'aox', 'Aqoxy3G01274' => 'aox', 'Aqoxy3G02110' => 'aox', 'Aqoxy3G02268' => 'aox', 'Aqoxy5G02702' => 'aox', 'Aqoxy5G02988' => 'aox', 'Aqoxy5G03427' => 'aox', 'Aqoxy6G02363' => 'aox', 'Atru.chr1.3225' => 'acertr', 'Atru.chr8.1198' => 'acertr', 'Atru.chr9.790' => 'acertr', 'CANSAT01G3197' => 'cansat', 'Ciclev10003979m.g' => 'ccl', 'Ciclev10017471m.g' => 'ccl', 'Ciclev10018206m.g' => 'ccl', 'Ciclev10033751m.g' => 'ccl', 'CiPaw.01G000900' => 'cil', 'CiPaw.01G001000' => 'cil', 'CiPaw.01G033500' => 'cil', 'CiPaw.01G060300' => 'cil', 'CiPaw.01G070200' => 'cil', 'CiPaw.01G075100' => 'cil', 'CiPaw.01G084700' => 'cil', 'CiPaw.01G087900' => 'cil', 'CiPaw.01G092600' => 'cil', 'CiPaw.01G097200' => 'cil', 'CiPaw.01G098300' => 'cil', 'CiPaw.01G110200' => 'cil', 'CiPaw.01G118700' => 'cil', 'CiPaw.01G121200' => 'cil', 'CiPaw.01G132500' => 'cil', 'CiPaw.01G146900' => 'cil', 'CiPaw.01G174000' => 'cil', 'CiPaw.01G179900' => 'cil', 'CiPaw.01G183400' => 'cil', 'CiPaw.01G240000' => 'cil', 'CiPaw.01G283500' => 'cil', 'CiPaw.01G307400' => 'cil', 'CiPaw.02G030800' => 'cil', 'CiPaw.02G047200' => 'cil', 'CiPaw.02G050500' => 'cil', 'CiPaw.02G069900' => 'cil', 'CiPaw.02G091600' => 'cil', 'CiPaw.02G095000' => 'cil', 'CiPaw.02G131900' => 'cil', 'CiPaw.03G043000' => 'cil', 'CiPaw.03G069900' => 'cil', 'CiPaw.03G088100' => 'cil', 'CiPaw.03G089300' => 'cil', 'CiPaw.03G093100' => 'cil', 'CiPaw.03G129800' => 'cil', 'CiPaw.03G131200' => 'cil', 'CiPaw.03G134500' => 'cil', 'CiPaw.03G152100' => 'cil', 'CiPaw.03G162700' => 'cil', 'CiPaw.03G172800' => 'cil', 'CiPaw.03G175800' => 'cil', 'CiPaw.03G181800' => 'cil', 'CiPaw.03G191400' => 'cil', 'CiPaw.03G198300' => 'cil', 'CiPaw.03G201300' => 'cil', 'CiPaw.03G224700' => 'cil', 'CiPaw.03G225000' => 'cil', 'CiPaw.04G065100' => 'cil', 'CiPaw.04G080400' => 'cil', 'CiPaw.04G113500' => 'cil', 'CiPaw.04G121900' => 'cil', 'CiPaw.04G144100' => 'cil', 'CiPaw.04G176500' => 'cil', 'CiPaw.05G086200' => 'cil', 'CiPaw.05G100200' => 'cil', 'CiPaw.05G114200' => 'cil', 'CiPaw.05G126800' => 'cil', 'CiPaw.05G228800' => 'cil', 'CiPaw.05G230600' => 'cil', 'CiPaw.05G236500' => 'cil', 'CiPaw.05G244800' => 'cil', 'CiPaw.06G026600' => 'cil', 'CiPaw.06G027900' => 'cil', 'CiPaw.06G051800' => 'cil', 'CiPaw.06G128500' => 'cil', 'CiPaw.06G165900' => 'cil', 'CiPaw.07G045400' => 'cil', 'CiPaw.07G048000' => 'cil', 'CiPaw.07G052000' => 'cil', 'CiPaw.07G073800' => 'cil', 'CiPaw.07G099700' => 'cil', 'CiPaw.07G108700' => 'cil', 'CiPaw.07G120000' => 'cil', 'CiPaw.07G134100' => 'cil', 'CiPaw.07G147000' => 'cil', 'CiPaw.07G149700' => 'cil', 'CiPaw.07G178300' => 'cil', 'CiPaw.07G184900' => 'cil', 'CiPaw.08G044500' => 'cil', 'CiPaw.08G046900' => 'cil', 'CiPaw.08G047300' => 'cil', 'CiPaw.08G115400' => 'cil', 'CiPaw.08G134700' => 'cil', 'CiPaw.08G157400' => 'cil', 'CiPaw.09G014300' => 'cil', 'CiPaw.09G088900' => 'cil', 'CiPaw.09G130900' => 'cil', 'CiPaw.09G133100' => 'cil', 'CiPaw.09G151300' => 'cil', 'CiPaw.09G172800' => 'cil', 'CiPaw.09G174900' => 'cil', 'CiPaw.09G175000' => 'cil', 'CiPaw.10G012800' => 'cil', 'CiPaw.10G028800' => 'cil', 'CiPaw.10G044700' => 'cil', 'CiPaw.10G067400' => 'cil', 'CiPaw.10G115900' => 'cil', 'CiPaw.10G126200' => 'cil', 'CiPaw.10G139700' => 'cil', 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=> 'qlo', 'QL07p025287' => 'qlo', 'QL09p033218' => 'qlo', 'QL09p040841' => 'qlo', 'QL10p020337' => 'qlo', 'QL10p027209' => 'qlo', 'QL10p027969' => 'qlo', 'QL10p048988' => 'qlo', 'QL11p001241' => 'qlo', 'QL11p028487' => 'qlo', 'RcHm_v2.0_Chr2g0105031' => 'rch', 'RcHm_v2.0_Chr2g0117811' => 'rch', 'RcHm_v2.0_Chr6g0270241' => 'rch', 'RcHm_v2.0_Chr7g0215961' => 'rch', 'RcHm_v2.0_Chr7g0231991' => 'rch', 'Rhsim01G0041500' => 'rsi', 'Rhsim01G0115000' => 'rsi', 'Rhsim01G0115400' => 'rsi', 'Rhsim01G0133600' => 'rsi', 'Rhsim01G0159900' => 'rsi', 'Rhsim02G0189400' => 'rsi', 'Rhsim03G0135600' => 'rsi', 'Rhsim03G0149900' => 'rsi', 'Rhsim04G0125600' => 'rsi', 'Rhsim05G0091700' => 'rsi', 'Rhsim05G0092900' => 'rsi', 'Rhsim06G0075000' => 'rsi', 'Rhsim07G0066400' => 'rsi', 'Rhsim07G0156400' => 'rsi', 'Rhsim07G0182200' => 'rsi', 'Rhsim07G0182300' => 'rsi', 'Rhsim08G0180400' => 'rsi', 'Rhsim09G0056800' => 'rsi', 'Rhsim10G0153300' => 'rsi', 'Rhsim11G0012700' => 'rsi', 'Rhsim12G0031800' => 'rsi', 'Rhsim12G0055400' => 'rsi', 'Rhsim12G0091400' => 'rsi', 'Rhsim13G0070800' => 'rsi', 'Rhsim13G0193300' => 'rsi', 'RhsimUnG0111600' => 'rsi', 'RhsimUnG0137500' => 'rsi', 'RhsimUnG0172900' => 'rsi', 'SGA_v2.0_scaffold11G05878' => 'sas', 'SGA_v2.0_scaffold167G38458' => 'sas', 'SGA_v2.0_scaffold19G08588' => 'sas', 'SGA_v2.0_scaffold239G43990' => 'sas', 'SGA_v2.0_scaffold260G45865' => 'sas', 'SGA_v2.0_scaffold309G48177' => 'sas', 'SGA_v2.0_scaffold76G25122' => 'sas', 'SGA_v2.0_scaffold85G26708' => 'sas', 'SHI13914' => 'shi', 'SHI30402' => 'shi', 'TWI09G0020' => 'twi', 'TWI09G0456' => 'twi', 'TWI09G1572' => 'twi', 'TWI12G0266' => 'twi', 'TWI12G1451' => 'twi', 'TWI14G0851' => 'twi', 'TWI15G0796' => 'twi', 'TWI18G0820' => 'twi', 'TWI18G1152' => 'twi', 'TWI23G0007' => 'twi', 'TWI23G0314' => 'twi', 'TWI31G0674' => 'twi', 'TWI31G0938' => 'twi', 'TWI34G0641' => 'twi', 'TWI34G1527' => 'twi', 'TWI36G0193' => 'twi', 'TWI36G0405' => 'twi', 'TWI38G0892' => 'twi', 'TWI38G0936' => 'twi', 'TWI38G2218' => 'twi', 'TWI53G0679' => 'twi', 'TWI53G0863' => 'twi', 'TWI53G1133' => 'twi', 'TWI60G0823' => 'twi', 'TWI63G0919' => 'twi', 'TWI63G1436' => 'twi', 'TWI73G0140' => 'twi', 'TWI73G0419' => 'twi', 'TWI73G0420' => 'twi', 'TWI73G1276' => 'twi', 'TWI74G0405' => 'twi', 'TWI74G0837' => 'twi', 'TWI75G0594' => 'twi', 'TWI75G1615' => 'twi', 'TWI77G0816' => 'twi', 'vmacro03831' => 'vma', 'vmacro13746' => 'vma', 'vmacro16089' => 'vma', 'vmacro22863' => 'vma', 'Zm00001eb085790' => 'zma', 'Zm00001eb114250' => 'zma', 'Zm00001eb138070' => 'zma', 'Zm00001eb167560' => 'zma', 'Zm00001eb199990' => 'zma', 'Zm00001eb368180' => 'zma', 'Zm00001eb382470' => 'zma' ), 'gf_id' => 'HOM05D001576', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001576' ), 'data_identifier' => 'HOM05D001576', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001576', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '406', 'num_species' => '29' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'Aqoxy1G01456' => 'aox', 'Aqoxy1G02949' => 'aox', 'Aqoxy3G01274' => 'aox', 'Aqoxy3G02110' => 'aox', 'Aqoxy3G02268' => 'aox', 'Aqoxy5G02702' => 'aox', 'Aqoxy5G02988' => 'aox', 'Aqoxy5G03427' => 'aox', 'Aqoxy6G02363' => 'aox', 'Atru.chr1.3225' => 'acertr', 'Atru.chr8.1198' => 'acertr', 'Atru.chr9.790' => 'acertr', 'CANSAT01G3197' => 'cansat', 'Ciclev10003979m.g' => 'ccl', 'Ciclev10017471m.g' => 'ccl', 'Ciclev10018206m.g' => 'ccl', 'Ciclev10033751m.g' => 'ccl', 'CiPaw.01G000900' => 'cil', 'CiPaw.01G001000' => 'cil', 'CiPaw.01G033500' => 'cil', 'CiPaw.01G060300' => 'cil', 'CiPaw.01G070200' => 'cil', 'CiPaw.01G075100' => 'cil', 'CiPaw.01G084700' => 'cil', 'CiPaw.01G087900' => 'cil', 'CiPaw.01G092600' => 'cil', 'CiPaw.01G097200' => 'cil', 'CiPaw.01G098300' => 'cil', 'CiPaw.01G110200' => 'cil', 'CiPaw.01G118700' => 'cil', 'CiPaw.01G121200' => 'cil', 'CiPaw.01G132500' => 'cil', 'CiPaw.01G146900' => 'cil', 'CiPaw.01G174000' => 'cil', 'CiPaw.01G179900' => 'cil', 'CiPaw.01G183400' => 'cil', 'CiPaw.01G240000' => 'cil', 'CiPaw.01G283500' => 'cil', 'CiPaw.01G307400' => 'cil', 'CiPaw.02G030800' => 'cil', 'CiPaw.02G047200' => 'cil', 'CiPaw.02G050500' => 'cil', 'CiPaw.02G069900' => 'cil', 'CiPaw.02G091600' => 'cil', 'CiPaw.02G095000' => 'cil', 'CiPaw.02G131900' => 'cil', 'CiPaw.03G043000' => 'cil', 'CiPaw.03G069900' => 'cil', 'CiPaw.03G088100' => 'cil', 'CiPaw.03G089300' => 'cil', 'CiPaw.03G093100' => 'cil', 'CiPaw.03G129800' => 'cil', 'CiPaw.03G131200' => 'cil', 'CiPaw.03G134500' => 'cil', 'CiPaw.03G152100' => 'cil', 'CiPaw.03G162700' => 'cil', 'CiPaw.03G172800' => 'cil', 'CiPaw.03G175800' => 'cil', 'CiPaw.03G181800' => 'cil', 'CiPaw.03G191400' => 'cil', 'CiPaw.03G198300' => 'cil', 'CiPaw.03G201300' => 'cil', 'CiPaw.03G224700' => 'cil', 'CiPaw.03G225000' => 'cil', 'CiPaw.04G065100' => 'cil', 'CiPaw.04G080400' => 'cil', 'CiPaw.04G113500' => 'cil', 'CiPaw.04G121900' => 'cil', 'CiPaw.04G144100' => 'cil', 'CiPaw.04G176500' => 'cil', 'CiPaw.05G086200' => 'cil', 'CiPaw.05G100200' => 'cil', 'CiPaw.05G114200' => 'cil', 'CiPaw.05G126800' => 'cil', 'CiPaw.05G228800' => 'cil', 'CiPaw.05G230600' => 'cil', 'CiPaw.05G236500' => 'cil', 'CiPaw.05G244800' => 'cil', 'CiPaw.06G026600' => 'cil', 'CiPaw.06G027900' => 'cil', 'CiPaw.06G051800' => 'cil', 'CiPaw.06G128500' => 'cil', 'CiPaw.06G165900' => 'cil', 'CiPaw.07G045400' => 'cil', 'CiPaw.07G048000' => 'cil', 'CiPaw.07G052000' => 'cil', 'CiPaw.07G073800' => 'cil', 'CiPaw.07G099700' => 'cil', 'CiPaw.07G108700' => 'cil', 'CiPaw.07G120000' => 'cil', 'CiPaw.07G134100' => 'cil', 'CiPaw.07G147000' => 'cil', 'CiPaw.07G149700' => 'cil', 'CiPaw.07G178300' => 'cil', 'CiPaw.07G184900' => 'cil', 'CiPaw.08G044500' => 'cil', 'CiPaw.08G046900' => 'cil', 'CiPaw.08G047300' => 'cil', 'CiPaw.08G115400' => 'cil', 'CiPaw.08G134700' => 'cil', 'CiPaw.08G157400' => 'cil', 'CiPaw.09G014300' => 'cil', 'CiPaw.09G088900' => 'cil', 'CiPaw.09G130900' => 'cil', 'CiPaw.09G133100' => 'cil', 'CiPaw.09G151300' => 'cil', 'CiPaw.09G172800' => 'cil', 'CiPaw.09G174900' => 'cil', 'CiPaw.09G175000' => 'cil', 'CiPaw.10G012800' => 'cil', 'CiPaw.10G028800' => 'cil', 'CiPaw.10G044700' => 'cil', 'CiPaw.10G067400' => 'cil', 'CiPaw.10G115900' => 'cil', 'CiPaw.10G126200' => 'cil', 'CiPaw.10G139700' => 'cil', 'CiPaw.10G155100' => 'cil', 'CiPaw.11G011300' => 'cil', 'CiPaw.11G025900' => 'cil', 'CiPaw.11G104100' => 'cil', 'CiPaw.11G142700' => 'cil', 'CiPaw.11G164500' => 'cil', 'CiPaw.11G189100' => 'cil', 'CiPaw.11G197100' => 'cil', 'CiPaw.12G006100' => 'cil', 'CiPaw.12G038500' => 'cil', 'CiPaw.12G041400' => 'cil', 'CiPaw.12G041600' => 'cil', 'CiPaw.12G051300' => 'cil', 'CiPaw.12G101800' => 'cil', 'CiPaw.12G107800' => 'cil', 'CiPaw.13G033200' => 'cil', 'CiPaw.13G129900' => 'cil', 'CiPaw.13G160200' => 'cil', 'CiPaw.14G018900' => 'cil', 'CiPaw.14G029000' => 'cil', 'CiPaw.14G031000' => 'cil', 'CiPaw.14G032000' => 'cil', 'CiPaw.14G032300' => 'cil', 'CiPaw.14G040600' => 'cil', 'CiPaw.14G060500' => 'cil', 'CiPaw.14G061500' => 'cil', 'CiPaw.14G077500' => 'cil', 'CiPaw.14G088300' => 'cil', 'CiPaw.14G108500' => 'cil', 'CiPaw.14G121300' => 'cil', 'CiPaw.14G133000' => 'cil', 'CiPaw.14G134600' => 'cil', 'CiPaw.15G027200' => 'cil', 'CiPaw.15G037700' => 'cil', 'CiPaw.15G050900' => 'cil', 'CiPaw.15G067200' => 'cil', 'CiPaw.15G072000' => 'cil', 'CiPaw.15G112900' => 'cil', 'CiPaw.15G133200' => 'cil', 'CiPaw.15G139500' => 'cil', 'CiPaw.15G155400' => 'cil', 'CiPaw.16G006000' => 'cil', 'CiPaw.16G013100' => 'cil', 'CiPaw.16G047100' => 'cil', 'CiPaw.16G048900' => 'cil', 'CiPaw.16G070300' => 'cil', 'CSS0000195' => 'camsi', 'CSS0001664' => 'camsi', 'CSS0002566' => 'camsi', 'CSS0003077' => 'camsi', 'CSS0004257' => 'camsi', 'CSS0004495' => 'camsi', 'CSS0004599' => 'camsi', 'CSS0004943' => 'camsi', 'CSS0005302' => 'camsi', 'CSS0006274' => 'camsi', 'CSS0006547' => 'camsi', 'CSS0006860' => 'camsi', 'CSS0008814' => 'camsi', 'CSS0008946' => 'camsi', 'CSS0009093' => 'camsi', 'CSS0010221' => 'camsi', 'CSS0010296' => 'camsi', 'CSS0010386' => 'camsi', 'CSS0010831' => 'camsi', 'CSS0011061' => 'camsi', 'CSS0012008' => 'camsi', 'CSS0012194' => 'camsi', 'CSS0013580' => 'camsi', 'CSS0014176' => 'camsi', 'CSS0014280' => 'camsi', 'CSS0014799' => 'camsi', 'CSS0015368' => 'camsi', 'CSS0017473' => 'camsi', 'CSS0019281' => 'camsi', 'CSS0021320' => 'camsi', 'CSS0021750' => 'camsi', 'CSS0023642' => 'camsi', 'CSS0023792' => 'camsi', 'CSS0031528' => 'camsi', 'CSS0033894' => 'camsi', 'CSS0034959' => 'camsi', 'CSS0035632' => 'camsi', 'CSS0038450' => 'camsi', 'CSS0039293' => 'camsi', 'CSS0041053' => 'camsi', 'CSS0041981' => 'camsi', 'CSS0042573' => 'camsi', 'CSS0042927' => 'camsi', 'CSS0047725' => 'camsi', 'CSS0049636' => 'camsi', 'CSS0050513' => 'camsi', 'DCAR_030203' => 'dca', 'Dinv07939' => 'din', 'FAN01G0456' => 'fan', 'FAN02G3001' => 'fan', 'FAN04G2781' => 'fan', 'FAN05G1385' => 'fan', 'FAN05G3062' => 'fan', 'FAN08G2267' => 'fan', 'FAN10G0481' => 'fan', 'FAN10G1257' => 'fan', 'FAN14G0954' => 'fan', 'FAN14G2347' => 'fan', 'FAN15G0187' => 'fan', 'FAN25G2214' => 'fan', 'FvH4_1g21031' => 'fve', 'FvH4_3g16231' => 'fve', 'FvH4_3g26413' => 'fve', 'FvH4_3g29014' => 'fve', 'FvH4_3g31921' => 'fve', 'FvH4_4g19882' => 'fve', 'FvH4_5g21960' => 'fve', 'FvH4_5g29683' => 'fve', 'FvH4_7g13271' => 'fve', 'Glyma.01G062500' => 'gma', 'Glyma.07G140900' => 'gma', 'Glyma.09G140900' => 'gma', 'Glyma.12G112700' => 'gma', 'Glyma.17G168800' => 'gma', 'HanXRQChr01g0027001' => 'han', 'HanXRQChr04g0120511' => 'han', 'HanXRQChr08g0232381' => 'han', 'HanXRQChr09g0265661' => 'han', 'HanXRQChr13g0416031' => 'han', 'Haze_05835' => 'cav', 'Haze_06597' => 'cav', 'Haze_07921' => 'cav', 'Haze_08599' => 'cav', 'Haze_10686' => 'cav', 'Haze_12994' => 'cav', 'Haze_13466' => 'cav', 'Haze_16101' => 'cav', 'Haze_17766' => 'cav', 'Haze_18456' => 'cav', 'Haze_20229' => 'cav', 'Hma1.2p1_0324F.1_g125640' => 'hma', 'Hma1.2p1_0733F.1_g210230' => 'hma', 'Hma1.2p1_0921F.1_g236870' => 'hma', 'Hma1.2p1_1313F.1_g274940' => 'hma', 'Hma1.2p1_3059F.1_g332230' => 'hma', 'Hund15925' => 'sun', 'Hund19562' => 'sun', 'Hund21925' => 'sun', 'MD03G1177400' => 'mdo', 'MD07G1026100' => 'mdo', 'MD17G1218600' => 'mdo', 'Medtr0867s0010' => 'mtr', 'Medtr6g081150' => 'mtr', 'Os01g0527900' => 'osa', 'Os02g0463725' => 'osa', 'Os02g0785600' => 'osa', 'Os03g0433733' => 'osa', 'Os04g0286500' => 'osa', 'Os05g0227800' => 'osa', 'Os06g0521000' => 'osa', 'Os06g0635500' => 'osa', 'Os06g0660650' => 'osa', 'Os07g0554400' => 'osa', 'Os08g0225900' => 'osa', 'Os08g0561000' => 'osa', 'Os09g0241700' => 'osa', 'Os09g0351900' => 'osa', 'Os11g0220700' => 'osa', 'Os11g0282700' => 'osa', 'Os12g0169300' => 'osa', 'Os12g0228500' => 'osa', 'Os12g0543800' => 'osa', 'PGR044G1547' => 'pgr', 'Potri.005G239150' => 'ptr', 'Potri.010G014250' => 'ptr', 'Prupe.1G172500' => 'ppe', 'Prupe.1G196800' => 'ppe', 'Prupe.1G279700' => 'ppe', 'Prupe.2G026400' => 'ppe', 'Prupe.3G094000' => 'ppe', 'Prupe.4G287300' => 'ppe', 'QL01p022166' => 'qlo', 'QL01p051890' => 'qlo', 'QL02p009469' => 'qlo', 'QL02p046053' => 'qlo', 'QL02p057958' => 'qlo', 'QL02p093127' => 'qlo', 'QL03p006855' => 'qlo', 'QL03p071586' => 'qlo', 'QL04p000022' => 'qlo', 'QL04p000024' => 'qlo', 'QL04p003192' => 'qlo', 'QL05p011416' => 'qlo', 'QL06p039590' => 'qlo', 'QL06p052750' => 'qlo', 'QL06p053821' => 'qlo', 'QL07p025287' => 'qlo', 'QL09p033218' => 'qlo', 'QL09p040841' => 'qlo', 'QL10p020337' => 'qlo', 'QL10p027209' => 'qlo', 'QL10p027969' => 'qlo', 'QL10p048988' => 'qlo', 'QL11p001241' => 'qlo', 'QL11p028487' => 'qlo', 'RcHm_v2.0_Chr2g0105031' => 'rch', 'RcHm_v2.0_Chr2g0117811' => 'rch', 'RcHm_v2.0_Chr6g0270241' => 'rch', 'RcHm_v2.0_Chr7g0215961' => 'rch', 'RcHm_v2.0_Chr7g0231991' => 'rch', 'Rhsim01G0041500' => 'rsi', 'Rhsim01G0115000' => 'rsi', 'Rhsim01G0115400' => 'rsi', 'Rhsim01G0133600' => 'rsi', 'Rhsim01G0159900' => 'rsi', 'Rhsim02G0189400' => 'rsi', 'Rhsim03G0135600' => 'rsi', 'Rhsim03G0149900' => 'rsi', 'Rhsim04G0125600' => 'rsi', 'Rhsim05G0091700' => 'rsi', 'Rhsim05G0092900' => 'rsi', 'Rhsim06G0075000' => 'rsi', 'Rhsim07G0066400' => 'rsi', 'Rhsim07G0156400' => 'rsi', 'Rhsim07G0182200' => 'rsi', 'Rhsim07G0182300' => 'rsi', 'Rhsim08G0180400' => 'rsi', 'Rhsim09G0056800' => 'rsi', 'Rhsim10G0153300' => 'rsi', 'Rhsim11G0012700' => 'rsi', 'Rhsim12G0031800' => 'rsi', 'Rhsim12G0055400' => 'rsi', 'Rhsim12G0091400' => 'rsi', 'Rhsim13G0070800' => 'rsi', 'Rhsim13G0193300' => 'rsi', 'RhsimUnG0111600' => 'rsi', 'RhsimUnG0137500' => 'rsi', 'RhsimUnG0172900' => 'rsi', 'SGA_v2.0_scaffold11G05878' => 'sas', 'SGA_v2.0_scaffold167G38458' => 'sas', 'SGA_v2.0_scaffold19G08588' => 'sas', 'SGA_v2.0_scaffold239G43990' => 'sas', 'SGA_v2.0_scaffold260G45865' => 'sas', 'SGA_v2.0_scaffold309G48177' => 'sas', 'SGA_v2.0_scaffold76G25122' => 'sas', 'SGA_v2.0_scaffold85G26708' => 'sas', 'SHI13914' => 'shi', 'SHI30402' => 'shi', 'TWI09G0020' => 'twi', 'TWI09G0456' => 'twi', 'TWI09G1572' => 'twi', 'TWI12G0266' => 'twi', 'TWI12G1451' => 'twi', 'TWI14G0851' => 'twi', 'TWI15G0796' => 'twi', 'TWI18G0820' => 'twi', 'TWI18G1152' => 'twi', 'TWI23G0007' => 'twi', 'TWI23G0314' => 'twi', 'TWI31G0674' => 'twi', 'TWI31G0938' => 'twi', 'TWI34G0641' => 'twi', 'TWI34G1527' => 'twi', 'TWI36G0193' => 'twi', 'TWI36G0405' => 'twi', 'TWI38G0892' => 'twi', 'TWI38G0936' => 'twi', 'TWI38G2218' => 'twi', 'TWI53G0679' => 'twi', 'TWI53G0863' => 'twi', 'TWI53G1133' => 'twi', 'TWI60G0823' => 'twi', 'TWI63G0919' => 'twi', 'TWI63G1436' => 'twi', 'TWI73G0140' => 'twi', 'TWI73G0419' => 'twi', 'TWI73G0420' => 'twi', 'TWI73G1276' => 'twi', 'TWI74G0405' => 'twi', 'TWI74G0837' => 'twi', 'TWI75G0594' => 'twi', 'TWI75G1615' => 'twi', 'TWI77G0816' => 'twi', 'vmacro03831' => 'vma', 'vmacro13746' => 'vma', 'vmacro16089' => 'vma', 'vmacro22863' => 'vma', 'Zm00001eb085790' => 'zma', 'Zm00001eb114250' => 'zma', 'Zm00001eb138070' => 'zma', 'Zm00001eb167560' => 'zma', 'Zm00001eb199990' => 'zma', 'Zm00001eb368180' => 'zma', 'Zm00001eb382470' => 'zma' ) $gf_id = 'HOM05D001576' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001576' ) $data_identifier = 'HOM05D001576' $data_type = 'gf_id' $species_gene_counts = array( 'aox' => (int) 9, 'acertr' => (int) 3, 'cansat' => (int) 1, 'ccl' => (int) 4, 'cil' => (int) 145, 'camsi' => (int) 46, 'dca' => (int) 1, 'din' => (int) 1, 'fan' => (int) 12, 'fve' => (int) 9, 'gma' => (int) 5, 'han' => (int) 5, 'cav' => (int) 11, 'hma' => (int) 5, 'sun' => (int) 3, 'mdo' => (int) 3, 'mtr' => (int) 2, 'osa' => (int) 19, 'pgr' => (int) 1, 'ptr' => (int) 2, 'ppe' => (int) 6, 'qlo' => (int) 24, 'rch' => (int) 5, 'rsi' => (int) 28, 'sas' => (int) 8, 'shi' => (int) 2, 'twi' => (int) 35, 'vma' => (int) 4, 'zma' => (int) 7 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb382470' $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' => 'HOM05D001576', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '406', 'num_species' => '29' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'Aqoxy1G01456' => 'aox', 'Aqoxy1G02949' => 'aox', 'Aqoxy3G01274' => 'aox', 'Aqoxy3G02110' => 'aox', 'Aqoxy3G02268' => 'aox', 'Aqoxy5G02702' => 'aox', 'Aqoxy5G02988' => 'aox', 'Aqoxy5G03427' => 'aox', 'Aqoxy6G02363' => 'aox', 'Atru.chr1.3225' => 'acertr', 'Atru.chr8.1198' => 'acertr', 'Atru.chr9.790' => 'acertr', 'CANSAT01G3197' => 'cansat', 'Ciclev10003979m.g' => 'ccl', 'Ciclev10017471m.g' => 'ccl', 'Ciclev10018206m.g' => 'ccl', 'Ciclev10033751m.g' => 'ccl', 'CiPaw.01G000900' => 'cil', 'CiPaw.01G001000' => 'cil', 'CiPaw.01G033500' => 'cil', 'CiPaw.01G060300' => 'cil', 'CiPaw.01G070200' => 'cil', 'CiPaw.01G075100' => 'cil', 'CiPaw.01G084700' => 'cil', 'CiPaw.01G087900' => 'cil', 'CiPaw.01G092600' => 'cil', 'CiPaw.01G097200' => 'cil', 'CiPaw.01G098300' => 'cil', 'CiPaw.01G110200' => 'cil', 'CiPaw.01G118700' => 'cil', 'CiPaw.01G121200' => 'cil', 'CiPaw.01G132500' => 'cil', 'CiPaw.01G146900' => 'cil', 'CiPaw.01G174000' => 'cil', 'CiPaw.01G179900' => 'cil', 'CiPaw.01G183400' => 'cil', 'CiPaw.01G240000' => 'cil', 'CiPaw.01G283500' => 'cil', 'CiPaw.01G307400' => 'cil', 'CiPaw.02G030800' => 'cil', 'CiPaw.02G047200' => 'cil', 'CiPaw.02G050500' => 'cil', 'CiPaw.02G069900' => 'cil', 'CiPaw.02G091600' => 'cil', 'CiPaw.02G095000' => 'cil', 'CiPaw.02G131900' => 'cil', 'CiPaw.03G043000' => 'cil', 'CiPaw.03G069900' => 'cil', 'CiPaw.03G088100' => 'cil', 'CiPaw.03G089300' => 'cil', 'CiPaw.03G093100' => 'cil', 'CiPaw.03G129800' => 'cil', 'CiPaw.03G131200' => 'cil', 'CiPaw.03G134500' => 'cil', 'CiPaw.03G152100' => 'cil', 'CiPaw.03G162700' => 'cil', 'CiPaw.03G172800' => 'cil', 'CiPaw.03G175800' => 'cil', 'CiPaw.03G181800' => 'cil', 'CiPaw.03G191400' => 'cil', 'CiPaw.03G198300' => 'cil', 'CiPaw.03G201300' => 'cil', 'CiPaw.03G224700' => 'cil', 'CiPaw.03G225000' => 'cil', 'CiPaw.04G065100' => 'cil', 'CiPaw.04G080400' => 'cil', 'CiPaw.04G113500' => 'cil', 'CiPaw.04G121900' => 'cil', 'CiPaw.04G144100' => 'cil', 'CiPaw.04G176500' => 'cil', 'CiPaw.05G086200' => 'cil', 'CiPaw.05G100200' => 'cil', 'CiPaw.05G114200' => 'cil', 'CiPaw.05G126800' => 'cil', 'CiPaw.05G228800' => 'cil', 'CiPaw.05G230600' => 'cil', 'CiPaw.05G236500' => 'cil', 'CiPaw.05G244800' => 'cil', 'CiPaw.06G026600' => 'cil', 'CiPaw.06G027900' => 'cil', 'CiPaw.06G051800' => 'cil', 'CiPaw.06G128500' => 'cil', 'CiPaw.06G165900' => 'cil', 'CiPaw.07G045400' => 'cil', 'CiPaw.07G048000' => 'cil', 'CiPaw.07G052000' => 'cil', 'CiPaw.07G073800' => 'cil', 'CiPaw.07G099700' => 'cil', 'CiPaw.07G108700' => 'cil', 'CiPaw.07G120000' => 'cil', 'CiPaw.07G134100' => 'cil', 'CiPaw.07G147000' => 'cil', 'CiPaw.07G149700' => 'cil', 'CiPaw.07G178300' => 'cil', 'CiPaw.07G184900' => 'cil', 'CiPaw.08G044500' => 'cil', 'CiPaw.08G046900' => 'cil', 'CiPaw.08G047300' => 'cil', 'CiPaw.08G115400' => 'cil', 'CiPaw.08G134700' => 'cil', 'CiPaw.08G157400' => 'cil', 'CiPaw.09G014300' => 'cil', 'CiPaw.09G088900' => 'cil', 'CiPaw.09G130900' => 'cil', 'CiPaw.09G133100' => 'cil', 'CiPaw.09G151300' => 'cil', 'CiPaw.09G172800' => 'cil', 'CiPaw.09G174900' => 'cil', 'CiPaw.09G175000' => 'cil', 'CiPaw.10G012800' => 'cil', 'CiPaw.10G028800' => 'cil', 'CiPaw.10G044700' => 'cil', 'CiPaw.10G067400' => 'cil', 'CiPaw.10G115900' => 'cil', 'CiPaw.10G126200' => 'cil', 'CiPaw.10G139700' => 'cil', 'CiPaw.10G155100' => 'cil', 'CiPaw.11G011300' => 'cil', 'CiPaw.11G025900' => 'cil', 'CiPaw.11G104100' => 'cil', 'CiPaw.11G142700' => 'cil', 'CiPaw.11G164500' => 'cil', 'CiPaw.11G189100' => 'cil', 'CiPaw.11G197100' => 'cil', 'CiPaw.12G006100' => 'cil', 'CiPaw.12G038500' => 'cil', 'CiPaw.12G041400' => 'cil', 'CiPaw.12G041600' => 'cil', 'CiPaw.12G051300' => 'cil', 'CiPaw.12G101800' => 'cil', 'CiPaw.12G107800' => 'cil', 'CiPaw.13G033200' => 'cil', 'CiPaw.13G129900' => 'cil', 'CiPaw.13G160200' => 'cil', 'CiPaw.14G018900' => 'cil', 'CiPaw.14G029000' => 'cil', 'CiPaw.14G031000' => 'cil', 'CiPaw.14G032000' => 'cil', 'CiPaw.14G032300' => 'cil', 'CiPaw.14G040600' => 'cil', 'CiPaw.14G060500' => 'cil', 'CiPaw.14G061500' => 'cil', 'CiPaw.14G077500' => 'cil', 'CiPaw.14G088300' => 'cil', 'CiPaw.14G108500' => 'cil', 'CiPaw.14G121300' => 'cil', 'CiPaw.14G133000' => 'cil', 'CiPaw.14G134600' => 'cil', 'CiPaw.15G027200' => 'cil', 'CiPaw.15G037700' => 'cil', 'CiPaw.15G050900' => 'cil', 'CiPaw.15G067200' => 'cil', 'CiPaw.15G072000' => 'cil', 'CiPaw.15G112900' => 'cil', 'CiPaw.15G133200' => 'cil', 'CiPaw.15G139500' => 'cil', 'CiPaw.15G155400' => 'cil', 'CiPaw.16G006000' => 'cil', 'CiPaw.16G013100' => 'cil', 'CiPaw.16G047100' => 'cil', 'CiPaw.16G048900' => 'cil', 'CiPaw.16G070300' => 'cil', 'CSS0000195' => 'camsi', 'CSS0001664' => 'camsi', 'CSS0002566' => 'camsi', 'CSS0003077' => 'camsi', 'CSS0004257' => 'camsi', 'CSS0004495' => 'camsi', 'CSS0004599' => 'camsi', 'CSS0004943' => 'camsi', 'CSS0005302' => 'camsi', 'CSS0006274' => 'camsi', 'CSS0006547' => 'camsi', 'CSS0006860' => 'camsi', 'CSS0008814' => 'camsi', 'CSS0008946' => 'camsi', 'CSS0009093' => 'camsi', 'CSS0010221' => 'camsi', 'CSS0010296' => 'camsi', 'CSS0010386' => 'camsi', 'CSS0010831' => 'camsi', 'CSS0011061' => 'camsi', 'CSS0012008' => 'camsi', 'CSS0012194' => 'camsi', 'CSS0013580' => 'camsi', 'CSS0014176' => 'camsi', 'CSS0014280' => 'camsi', 'CSS0014799' => 'camsi', 'CSS0015368' => 'camsi', 'CSS0017473' => 'camsi', 'CSS0019281' => 'camsi', 'CSS0021320' => 'camsi', 'CSS0021750' => 'camsi', 'CSS0023642' => 'camsi', 'CSS0023792' => 'camsi', 'CSS0031528' => 'camsi', 'CSS0033894' => 'camsi', 'CSS0034959' => 'camsi', 'CSS0035632' => 'camsi', 'CSS0038450' => 'camsi', 'CSS0039293' => 'camsi', 'CSS0041053' => 'camsi', 'CSS0041981' => 'camsi', 'CSS0042573' => 'camsi', 'CSS0042927' => 'camsi', 'CSS0047725' => 'camsi', 'CSS0049636' => 'camsi', 'CSS0050513' => 'camsi', 'DCAR_030203' => 'dca', 'Dinv07939' => 'din', 'FAN01G0456' => 'fan', 'FAN02G3001' => 'fan', 'FAN04G2781' => 'fan', 'FAN05G1385' => 'fan', 'FAN05G3062' => 'fan', 'FAN08G2267' => 'fan', 'FAN10G0481' => 'fan', 'FAN10G1257' => 'fan', 'FAN14G0954' => 'fan', 'FAN14G2347' => 'fan', 'FAN15G0187' => 'fan', 'FAN25G2214' => 'fan', 'FvH4_1g21031' => 'fve', 'FvH4_3g16231' => 'fve', 'FvH4_3g26413' => 'fve', 'FvH4_3g29014' => 'fve', 'FvH4_3g31921' => 'fve', 'FvH4_4g19882' => 'fve', 'FvH4_5g21960' => 'fve', 'FvH4_5g29683' => 'fve', 'FvH4_7g13271' => 'fve', 'Glyma.01G062500' => 'gma', 'Glyma.07G140900' => 'gma', 'Glyma.09G140900' => 'gma', 'Glyma.12G112700' => 'gma', 'Glyma.17G168800' => 'gma', 'HanXRQChr01g0027001' => 'han', 'HanXRQChr04g0120511' => 'han', 'HanXRQChr08g0232381' => 'han', 'HanXRQChr09g0265661' => 'han', 'HanXRQChr13g0416031' => 'han', 'Haze_05835' => 'cav', 'Haze_06597' => 'cav', 'Haze_07921' => 'cav', 'Haze_08599' => 'cav', 'Haze_10686' => 'cav', 'Haze_12994' => 'cav', 'Haze_13466' => 'cav', 'Haze_16101' => 'cav', 'Haze_17766' => 'cav', 'Haze_18456' => 'cav', 'Haze_20229' => 'cav', 'Hma1.2p1_0324F.1_g125640' => 'hma', 'Hma1.2p1_0733F.1_g210230' => 'hma', 'Hma1.2p1_0921F.1_g236870' => 'hma', 'Hma1.2p1_1313F.1_g274940' => 'hma', 'Hma1.2p1_3059F.1_g332230' => 'hma', 'Hund15925' => 'sun', 'Hund19562' => 'sun', 'Hund21925' => 'sun', 'MD03G1177400' => 'mdo', 'MD07G1026100' => 'mdo', 'MD17G1218600' => 'mdo', 'Medtr0867s0010' => 'mtr', 'Medtr6g081150' => 'mtr', 'Os01g0527900' => 'osa', 'Os02g0463725' => 'osa', 'Os02g0785600' => 'osa', 'Os03g0433733' => 'osa', 'Os04g0286500' => 'osa', 'Os05g0227800' => 'osa', 'Os06g0521000' => 'osa', 'Os06g0635500' => 'osa', 'Os06g0660650' => 'osa', 'Os07g0554400' => 'osa', 'Os08g0225900' => 'osa', 'Os08g0561000' => 'osa', 'Os09g0241700' => 'osa', 'Os09g0351900' => 'osa', 'Os11g0220700' => 'osa', 'Os11g0282700' => 'osa', 'Os12g0169300' => 'osa', 'Os12g0228500' => 'osa', 'Os12g0543800' => 'osa', 'PGR044G1547' => 'pgr', 'Potri.005G239150' => 'ptr', 'Potri.010G014250' => 'ptr', 'Prupe.1G172500' => 'ppe', 'Prupe.1G196800' => 'ppe', 'Prupe.1G279700' => 'ppe', 'Prupe.2G026400' => 'ppe', 'Prupe.3G094000' => 'ppe', 'Prupe.4G287300' => 'ppe', 'QL01p022166' => 'qlo', 'QL01p051890' => 'qlo', 'QL02p009469' => 'qlo', 'QL02p046053' => 'qlo', 'QL02p057958' => 'qlo', 'QL02p093127' => 'qlo', 'QL03p006855' => 'qlo', 'QL03p071586' => 'qlo', 'QL04p000022' => 'qlo', 'QL04p000024' => 'qlo', 'QL04p003192' => 'qlo', 'QL05p011416' => 'qlo', 'QL06p039590' => 'qlo', 'QL06p052750' => 'qlo', 'QL06p053821' => 'qlo', 'QL07p025287' => 'qlo', 'QL09p033218' => 'qlo', 'QL09p040841' => 'qlo', 'QL10p020337' => 'qlo', 'QL10p027209' => 'qlo', 'QL10p027969' => 'qlo', 'QL10p048988' => 'qlo', 'QL11p001241' => 'qlo', 'QL11p028487' => 'qlo', 'RcHm_v2.0_Chr2g0105031' => 'rch', 'RcHm_v2.0_Chr2g0117811' => 'rch', 'RcHm_v2.0_Chr6g0270241' => 'rch', 'RcHm_v2.0_Chr7g0215961' => 'rch', 'RcHm_v2.0_Chr7g0231991' => 'rch', 'Rhsim01G0041500' => 'rsi', 'Rhsim01G0115000' => 'rsi', 'Rhsim01G0115400' => 'rsi', 'Rhsim01G0133600' => 'rsi', 'Rhsim01G0159900' => 'rsi', 'Rhsim02G0189400' => 'rsi', 'Rhsim03G0135600' => 'rsi', 'Rhsim03G0149900' => 'rsi', 'Rhsim04G0125600' => 'rsi', 'Rhsim05G0091700' => 'rsi', 'Rhsim05G0092900' => 'rsi', 'Rhsim06G0075000' => 'rsi', 'Rhsim07G0066400' => 'rsi', 'Rhsim07G0156400' => 'rsi', 'Rhsim07G0182200' => 'rsi', 'Rhsim07G0182300' => 'rsi', 'Rhsim08G0180400' => 'rsi', 'Rhsim09G0056800' => 'rsi', 'Rhsim10G0153300' => 'rsi', 'Rhsim11G0012700' => 'rsi', 'Rhsim12G0031800' => 'rsi', 'Rhsim12G0055400' => 'rsi', 'Rhsim12G0091400' => 'rsi', 'Rhsim13G0070800' => 'rsi', 'Rhsim13G0193300' => 'rsi', 'RhsimUnG0111600' => 'rsi', 'RhsimUnG0137500' => 'rsi', 'RhsimUnG0172900' => 'rsi', 'SGA_v2.0_scaffold11G05878' => 'sas', 'SGA_v2.0_scaffold167G38458' => 'sas', 'SGA_v2.0_scaffold19G08588' => 'sas', 'SGA_v2.0_scaffold239G43990' => 'sas', 'SGA_v2.0_scaffold260G45865' => 'sas', 'SGA_v2.0_scaffold309G48177' => 'sas', 'SGA_v2.0_scaffold76G25122' => 'sas', 'SGA_v2.0_scaffold85G26708' => 'sas', 'SHI13914' => 'shi', 'SHI30402' => 'shi', 'TWI09G0020' => 'twi', 'TWI09G0456' => 'twi', 'TWI09G1572' => 'twi', 'TWI12G0266' => 'twi', 'TWI12G1451' => 'twi', 'TWI14G0851' => 'twi', 'TWI15G0796' => 'twi', 'TWI18G0820' => 'twi', 'TWI18G1152' => 'twi', 'TWI23G0007' => 'twi', 'TWI23G0314' => 'twi', 'TWI31G0674' => 'twi', 'TWI31G0938' => 'twi', 'TWI34G0641' => 'twi', 'TWI34G1527' => 'twi', 'TWI36G0193' => 'twi', 'TWI36G0405' => 'twi', 'TWI38G0892' => 'twi', 'TWI38G0936' => 'twi', 'TWI38G2218' => 'twi', 'TWI53G0679' => 'twi', 'TWI53G0863' => 'twi', 'TWI53G1133' => 'twi', 'TWI60G0823' => 'twi', 'TWI63G0919' => 'twi', 'TWI63G1436' => 'twi', 'TWI73G0140' => 'twi', 'TWI73G0419' => 'twi', 'TWI73G0420' => 'twi', 'TWI73G1276' => 'twi', 'TWI74G0405' => 'twi', 'TWI74G0837' => 'twi', 'TWI75G0594' => 'twi', 'TWI75G1615' => 'twi', 'TWI77G0816' => 'twi', 'vmacro03831' => 'vma', 'vmacro13746' => 'vma', 'vmacro16089' => 'vma', 'vmacro22863' => 'vma', 'Zm00001eb085790' => 'zma', 'Zm00001eb114250' => 'zma', 'Zm00001eb138070' => 'zma', 'Zm00001eb167560' => 'zma', 'Zm00001eb199990' => 'zma', 'Zm00001eb368180' => 'zma', 'Zm00001eb382470' => 'zma' ), 'gf_id' => 'HOM05D001576', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001576' ), 'data_identifier' => 'HOM05D001576', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001576', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '406', 'num_species' => '29' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'Aqoxy1G01456' => 'aox', 'Aqoxy1G02949' => 'aox', 'Aqoxy3G01274' => 'aox', 'Aqoxy3G02110' => 'aox', 'Aqoxy3G02268' => 'aox', 'Aqoxy5G02702' => 'aox', 'Aqoxy5G02988' => 'aox', 'Aqoxy5G03427' => 'aox', 'Aqoxy6G02363' => 'aox', 'Atru.chr1.3225' => 'acertr', 'Atru.chr8.1198' => 'acertr', 'Atru.chr9.790' => 'acertr', 'CANSAT01G3197' => 'cansat', 'Ciclev10003979m.g' => 'ccl', 'Ciclev10017471m.g' => 'ccl', 'Ciclev10018206m.g' => 'ccl', 'Ciclev10033751m.g' => 'ccl', 'CiPaw.01G000900' => 'cil', 'CiPaw.01G001000' => 'cil', 'CiPaw.01G033500' => 'cil', 'CiPaw.01G060300' => 'cil', 'CiPaw.01G070200' => 'cil', 'CiPaw.01G075100' => 'cil', 'CiPaw.01G084700' => 'cil', 'CiPaw.01G087900' => 'cil', 'CiPaw.01G092600' => 'cil', 'CiPaw.01G097200' => 'cil', 'CiPaw.01G098300' => 'cil', 'CiPaw.01G110200' => 'cil', 'CiPaw.01G118700' => 'cil', 'CiPaw.01G121200' => 'cil', 'CiPaw.01G132500' => 'cil', 'CiPaw.01G146900' => 'cil', 'CiPaw.01G174000' => 'cil', 'CiPaw.01G179900' => 'cil', 'CiPaw.01G183400' => 'cil', 'CiPaw.01G240000' => 'cil', 'CiPaw.01G283500' => 'cil', 'CiPaw.01G307400' => 'cil', 'CiPaw.02G030800' => 'cil', 'CiPaw.02G047200' => 'cil', 'CiPaw.02G050500' => 'cil', 'CiPaw.02G069900' => 'cil', 'CiPaw.02G091600' => 'cil', 'CiPaw.02G095000' => 'cil', 'CiPaw.02G131900' => 'cil', 'CiPaw.03G043000' => 'cil', 'CiPaw.03G069900' => 'cil', 'CiPaw.03G088100' => 'cil', 'CiPaw.03G089300' => 'cil', 'CiPaw.03G093100' => 'cil', 'CiPaw.03G129800' => 'cil', 'CiPaw.03G131200' => 'cil', 'CiPaw.03G134500' => 'cil', 'CiPaw.03G152100' => 'cil', 'CiPaw.03G162700' => 'cil', 'CiPaw.03G172800' => 'cil', 'CiPaw.03G175800' => 'cil', 'CiPaw.03G181800' => 'cil', 'CiPaw.03G191400' => 'cil', 'CiPaw.03G198300' => 'cil', 'CiPaw.03G201300' => 'cil', 'CiPaw.03G224700' => 'cil', 'CiPaw.03G225000' => 'cil', 'CiPaw.04G065100' => 'cil', 'CiPaw.04G080400' => 'cil', 'CiPaw.04G113500' => 'cil', 'CiPaw.04G121900' => 'cil', 'CiPaw.04G144100' => 'cil', 'CiPaw.04G176500' => 'cil', 'CiPaw.05G086200' => 'cil', 'CiPaw.05G100200' => 'cil', 'CiPaw.05G114200' => 'cil', 'CiPaw.05G126800' => 'cil', 'CiPaw.05G228800' => 'cil', 'CiPaw.05G230600' => 'cil', 'CiPaw.05G236500' => 'cil', 'CiPaw.05G244800' => 'cil', 'CiPaw.06G026600' => 'cil', 'CiPaw.06G027900' => 'cil', 'CiPaw.06G051800' => 'cil', 'CiPaw.06G128500' => 'cil', 'CiPaw.06G165900' => 'cil', 'CiPaw.07G045400' => 'cil', 'CiPaw.07G048000' => 'cil', 'CiPaw.07G052000' => 'cil', 'CiPaw.07G073800' => 'cil', 'CiPaw.07G099700' => 'cil', 'CiPaw.07G108700' => 'cil', 'CiPaw.07G120000' => 'cil', 'CiPaw.07G134100' => 'cil', 'CiPaw.07G147000' => 'cil', 'CiPaw.07G149700' => 'cil', 'CiPaw.07G178300' => 'cil', 'CiPaw.07G184900' => 'cil', 'CiPaw.08G044500' => 'cil', 'CiPaw.08G046900' => 'cil', 'CiPaw.08G047300' => 'cil', 'CiPaw.08G115400' => 'cil', 'CiPaw.08G134700' => 'cil', 'CiPaw.08G157400' => 'cil', 'CiPaw.09G014300' => 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'CiPaw.14G032000' => 'cil', 'CiPaw.14G032300' => 'cil', 'CiPaw.14G040600' => 'cil', 'CiPaw.14G060500' => 'cil', 'CiPaw.14G061500' => 'cil', 'CiPaw.14G077500' => 'cil', 'CiPaw.14G088300' => 'cil', 'CiPaw.14G108500' => 'cil', 'CiPaw.14G121300' => 'cil', 'CiPaw.14G133000' => 'cil', 'CiPaw.14G134600' => 'cil', 'CiPaw.15G027200' => 'cil', 'CiPaw.15G037700' => 'cil', 'CiPaw.15G050900' => 'cil', 'CiPaw.15G067200' => 'cil', 'CiPaw.15G072000' => 'cil', 'CiPaw.15G112900' => 'cil', 'CiPaw.15G133200' => 'cil', 'CiPaw.15G139500' => 'cil', 'CiPaw.15G155400' => 'cil', 'CiPaw.16G006000' => 'cil', 'CiPaw.16G013100' => 'cil', 'CiPaw.16G047100' => 'cil', 'CiPaw.16G048900' => 'cil', 'CiPaw.16G070300' => 'cil', 'CSS0000195' => 'camsi', 'CSS0001664' => 'camsi', 'CSS0002566' => 'camsi', 'CSS0003077' => 'camsi', 'CSS0004257' => 'camsi', 'CSS0004495' => 'camsi', 'CSS0004599' => 'camsi', 'CSS0004943' => 'camsi', 'CSS0005302' => 'camsi', 'CSS0006274' => 'camsi', 'CSS0006547' => 'camsi', 'CSS0006860' => 'camsi', 'CSS0008814' => 'camsi', 'CSS0008946' => 'camsi', 'CSS0009093' => 'camsi', 'CSS0010221' => 'camsi', 'CSS0010296' => 'camsi', 'CSS0010386' => 'camsi', 'CSS0010831' => 'camsi', 'CSS0011061' => 'camsi', 'CSS0012008' => 'camsi', 'CSS0012194' => 'camsi', 'CSS0013580' => 'camsi', 'CSS0014176' => 'camsi', 'CSS0014280' => 'camsi', 'CSS0014799' => 'camsi', 'CSS0015368' => 'camsi', 'CSS0017473' => 'camsi', 'CSS0019281' => 'camsi', 'CSS0021320' => 'camsi', 'CSS0021750' => 'camsi', 'CSS0023642' => 'camsi', 'CSS0023792' => 'camsi', 'CSS0031528' => 'camsi', 'CSS0033894' => 'camsi', 'CSS0034959' => 'camsi', 'CSS0035632' => 'camsi', 'CSS0038450' => 'camsi', 'CSS0039293' => 'camsi', 'CSS0041053' => 'camsi', 'CSS0041981' => 'camsi', 'CSS0042573' => 'camsi', 'CSS0042927' => 'camsi', 'CSS0047725' => 'camsi', 'CSS0049636' => 'camsi', 'CSS0050513' => 'camsi', 'DCAR_030203' => 'dca', 'Dinv07939' => 'din', 'FAN01G0456' => 'fan', 'FAN02G3001' => 'fan', 'FAN04G2781' => 'fan', 'FAN05G1385' => 'fan', 'FAN05G3062' => 'fan', 'FAN08G2267' => 'fan', 'FAN10G0481' => 'fan', 'FAN10G1257' => 'fan', 'FAN14G0954' => 'fan', 'FAN14G2347' => 'fan', 'FAN15G0187' => 'fan', 'FAN25G2214' => 'fan', 'FvH4_1g21031' => 'fve', 'FvH4_3g16231' => 'fve', 'FvH4_3g26413' => 'fve', 'FvH4_3g29014' => 'fve', 'FvH4_3g31921' => 'fve', 'FvH4_4g19882' => 'fve', 'FvH4_5g21960' => 'fve', 'FvH4_5g29683' => 'fve', 'FvH4_7g13271' => 'fve', 'Glyma.01G062500' => 'gma', 'Glyma.07G140900' => 'gma', 'Glyma.09G140900' => 'gma', 'Glyma.12G112700' => 'gma', 'Glyma.17G168800' => 'gma', 'HanXRQChr01g0027001' => 'han', 'HanXRQChr04g0120511' => 'han', 'HanXRQChr08g0232381' => 'han', 'HanXRQChr09g0265661' => 'han', 'HanXRQChr13g0416031' => 'han', 'Haze_05835' => 'cav', 'Haze_06597' => 'cav', 'Haze_07921' => 'cav', 'Haze_08599' => 'cav', 'Haze_10686' => 'cav', 'Haze_12994' => 'cav', 'Haze_13466' => 'cav', 'Haze_16101' => 'cav', 'Haze_17766' => 'cav', 'Haze_18456' => 'cav', 'Haze_20229' => 'cav', 'Hma1.2p1_0324F.1_g125640' => 'hma', 'Hma1.2p1_0733F.1_g210230' => 'hma', 'Hma1.2p1_0921F.1_g236870' => 'hma', 'Hma1.2p1_1313F.1_g274940' => 'hma', 'Hma1.2p1_3059F.1_g332230' => 'hma', 'Hund15925' => 'sun', 'Hund19562' => 'sun', 'Hund21925' => 'sun', 'MD03G1177400' => 'mdo', 'MD07G1026100' => 'mdo', 'MD17G1218600' => 'mdo', 'Medtr0867s0010' => 'mtr', 'Medtr6g081150' => 'mtr', 'Os01g0527900' => 'osa', 'Os02g0463725' => 'osa', 'Os02g0785600' => 'osa', 'Os03g0433733' => 'osa', 'Os04g0286500' => 'osa', 'Os05g0227800' => 'osa', 'Os06g0521000' => 'osa', 'Os06g0635500' => 'osa', 'Os06g0660650' => 'osa', 'Os07g0554400' => 'osa', 'Os08g0225900' => 'osa', 'Os08g0561000' => 'osa', 'Os09g0241700' => 'osa', 'Os09g0351900' => 'osa', 'Os11g0220700' => 'osa', 'Os11g0282700' => 'osa', 'Os12g0169300' => 'osa', 'Os12g0228500' => 'osa', 'Os12g0543800' => 'osa', 'PGR044G1547' => 'pgr', 'Potri.005G239150' => 'ptr', 'Potri.010G014250' => 'ptr', 'Prupe.1G172500' => 'ppe', 'Prupe.1G196800' => 'ppe', 'Prupe.1G279700' => 'ppe', 'Prupe.2G026400' => 'ppe', 'Prupe.3G094000' => 'ppe', 'Prupe.4G287300' => 'ppe', 'QL01p022166' => 'qlo', 'QL01p051890' => 'qlo', 'QL02p009469' => 'qlo', 'QL02p046053' => 'qlo', 'QL02p057958' => 'qlo', 'QL02p093127' => 'qlo', 'QL03p006855' => 'qlo', 'QL03p071586' => 'qlo', 'QL04p000022' => 'qlo', 'QL04p000024' => 'qlo', 'QL04p003192' => 'qlo', 'QL05p011416' => 'qlo', 'QL06p039590' => 'qlo', 'QL06p052750' => 'qlo', 'QL06p053821' => 'qlo', 'QL07p025287' => 'qlo', 'QL09p033218' => 'qlo', 'QL09p040841' => 'qlo', 'QL10p020337' => 'qlo', 'QL10p027209' => 'qlo', 'QL10p027969' => 'qlo', 'QL10p048988' => 'qlo', 'QL11p001241' => 'qlo', 'QL11p028487' => 'qlo', 'RcHm_v2.0_Chr2g0105031' => 'rch', 'RcHm_v2.0_Chr2g0117811' => 'rch', 'RcHm_v2.0_Chr6g0270241' => 'rch', 'RcHm_v2.0_Chr7g0215961' => 'rch', 'RcHm_v2.0_Chr7g0231991' => 'rch', 'Rhsim01G0041500' => 'rsi', 'Rhsim01G0115000' => 'rsi', 'Rhsim01G0115400' => 'rsi', 'Rhsim01G0133600' => 'rsi', 'Rhsim01G0159900' => 'rsi', 'Rhsim02G0189400' => 'rsi', 'Rhsim03G0135600' => 'rsi', 'Rhsim03G0149900' => 'rsi', 'Rhsim04G0125600' => 'rsi', 'Rhsim05G0091700' => 'rsi', 'Rhsim05G0092900' => 'rsi', 'Rhsim06G0075000' => 'rsi', 'Rhsim07G0066400' => 'rsi', 'Rhsim07G0156400' => 'rsi', 'Rhsim07G0182200' => 'rsi', 'Rhsim07G0182300' => 'rsi', 'Rhsim08G0180400' => 'rsi', 'Rhsim09G0056800' => 'rsi', 'Rhsim10G0153300' => 'rsi', 'Rhsim11G0012700' => 'rsi', 'Rhsim12G0031800' => 'rsi', 'Rhsim12G0055400' => 'rsi', 'Rhsim12G0091400' => 'rsi', 'Rhsim13G0070800' => 'rsi', 'Rhsim13G0193300' => 'rsi', 'RhsimUnG0111600' => 'rsi', 'RhsimUnG0137500' => 'rsi', 'RhsimUnG0172900' => 'rsi', 'SGA_v2.0_scaffold11G05878' => 'sas', 'SGA_v2.0_scaffold167G38458' => 'sas', 'SGA_v2.0_scaffold19G08588' => 'sas', 'SGA_v2.0_scaffold239G43990' => 'sas', 'SGA_v2.0_scaffold260G45865' => 'sas', 'SGA_v2.0_scaffold309G48177' => 'sas', 'SGA_v2.0_scaffold76G25122' => 'sas', 'SGA_v2.0_scaffold85G26708' => 'sas', 'SHI13914' => 'shi', 'SHI30402' => 'shi', 'TWI09G0020' => 'twi', 'TWI09G0456' => 'twi', 'TWI09G1572' => 'twi', 'TWI12G0266' => 'twi', 'TWI12G1451' => 'twi', 'TWI14G0851' => 'twi', 'TWI15G0796' => 'twi', 'TWI18G0820' => 'twi', 'TWI18G1152' => 'twi', 'TWI23G0007' => 'twi', 'TWI23G0314' => 'twi', 'TWI31G0674' => 'twi', 'TWI31G0938' => 'twi', 'TWI34G0641' => 'twi', 'TWI34G1527' => 'twi', 'TWI36G0193' => 'twi', 'TWI36G0405' => 'twi', 'TWI38G0892' => 'twi', 'TWI38G0936' => 'twi', 'TWI38G2218' => 'twi', 'TWI53G0679' => 'twi', 'TWI53G0863' => 'twi', 'TWI53G1133' => 'twi', 'TWI60G0823' => 'twi', 'TWI63G0919' => 'twi', 'TWI63G1436' => 'twi', 'TWI73G0140' => 'twi', 'TWI73G0419' => 'twi', 'TWI73G0420' => 'twi', 'TWI73G1276' => 'twi', 'TWI74G0405' => 'twi', 'TWI74G0837' => 'twi', 'TWI75G0594' => 'twi', 'TWI75G1615' => 'twi', 'TWI77G0816' => 'twi', 'vmacro03831' => 'vma', 'vmacro13746' => 'vma', 'vmacro16089' => 'vma', 'vmacro22863' => 'vma', 'Zm00001eb085790' => 'zma', 'Zm00001eb114250' => 'zma', 'Zm00001eb138070' => 'zma', 'Zm00001eb167560' => 'zma', 'Zm00001eb199990' => 'zma', 'Zm00001eb368180' => 'zma', 'Zm00001eb382470' => 'zma' ) $gf_id = 'HOM05D001576' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001576' ) $data_identifier = 'HOM05D001576' $data_type = 'gf_id' $species_gene_counts = array( 'aox' => (int) 9, 'acertr' => (int) 3, 'cansat' => (int) 1, 'ccl' => (int) 4, 'cil' => (int) 145, 'camsi' => (int) 46, 'dca' => (int) 1, 'din' => (int) 1, 'fan' => (int) 12, 'fve' => (int) 9, 'gma' => (int) 5, 'han' => (int) 5, 'cav' => (int) 11, 'hma' => (int) 5, 'sun' => (int) 3, 'mdo' => (int) 3, 'mtr' => (int) 2, 'osa' => (int) 19, 'pgr' => (int) 1, 'ptr' => (int) 2, 'ppe' => (int) 6, 'qlo' => (int) 24, 'rch' => (int) 5, 'rsi' => (int) 28, 'sas' => (int) 8, 'shi' => (int) 2, 'twi' => (int) 35, 'vma' => (int) 4, 'zma' => (int) 7 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb382470' $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' => 'HOM05D001576', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '406', 'num_species' => '29' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'Aqoxy1G01456' => 'aox', 'Aqoxy1G02949' => 'aox', 'Aqoxy3G01274' => 'aox', 'Aqoxy3G02110' => 'aox', 'Aqoxy3G02268' => 'aox', 'Aqoxy5G02702' => 'aox', 'Aqoxy5G02988' => 'aox', 'Aqoxy5G03427' => 'aox', 'Aqoxy6G02363' => 'aox', 'Atru.chr1.3225' => 'acertr', 'Atru.chr8.1198' => 'acertr', 'Atru.chr9.790' => 'acertr', 'CANSAT01G3197' => 'cansat', 'Ciclev10003979m.g' => 'ccl', 'Ciclev10017471m.g' => 'ccl', 'Ciclev10018206m.g' => 'ccl', 'Ciclev10033751m.g' => 'ccl', 'CiPaw.01G000900' => 'cil', 'CiPaw.01G001000' => 'cil', 'CiPaw.01G033500' => 'cil', 'CiPaw.01G060300' => 'cil', 'CiPaw.01G070200' => 'cil', 'CiPaw.01G075100' => 'cil', 'CiPaw.01G084700' => 'cil', 'CiPaw.01G087900' => 'cil', 'CiPaw.01G092600' => 'cil', 'CiPaw.01G097200' => 'cil', 'CiPaw.01G098300' => 'cil', 'CiPaw.01G110200' => 'cil', 'CiPaw.01G118700' => 'cil', 'CiPaw.01G121200' => 'cil', 'CiPaw.01G132500' => 'cil', 'CiPaw.01G146900' => 'cil', 'CiPaw.01G174000' => 'cil', 'CiPaw.01G179900' => 'cil', 'CiPaw.01G183400' => 'cil', 'CiPaw.01G240000' => 'cil', 'CiPaw.01G283500' => 'cil', 'CiPaw.01G307400' => 'cil', 'CiPaw.02G030800' => 'cil', 'CiPaw.02G047200' => 'cil', 'CiPaw.02G050500' => 'cil', 'CiPaw.02G069900' => 'cil', 'CiPaw.02G091600' => 'cil', 'CiPaw.02G095000' => 'cil', 'CiPaw.02G131900' => 'cil', 'CiPaw.03G043000' => 'cil', 'CiPaw.03G069900' => 'cil', 'CiPaw.03G088100' => 'cil', 'CiPaw.03G089300' => 'cil', 'CiPaw.03G093100' => 'cil', 'CiPaw.03G129800' => 'cil', 'CiPaw.03G131200' => 'cil', 'CiPaw.03G134500' => 'cil', 'CiPaw.03G152100' => 'cil', 'CiPaw.03G162700' => 'cil', 'CiPaw.03G172800' => 'cil', 'CiPaw.03G175800' => 'cil', 'CiPaw.03G181800' => 'cil', 'CiPaw.03G191400' => 'cil', 'CiPaw.03G198300' => 'cil', 'CiPaw.03G201300' => 'cil', 'CiPaw.03G224700' => 'cil', 'CiPaw.03G225000' => 'cil', 'CiPaw.04G065100' => 'cil', 'CiPaw.04G080400' => 'cil', 'CiPaw.04G113500' => 'cil', 'CiPaw.04G121900' => 'cil', 'CiPaw.04G144100' => 'cil', 'CiPaw.04G176500' => 'cil', 'CiPaw.05G086200' => 'cil', 'CiPaw.05G100200' => 'cil', 'CiPaw.05G114200' => 'cil', 'CiPaw.05G126800' => 'cil', 'CiPaw.05G228800' => 'cil', 'CiPaw.05G230600' => 'cil', 'CiPaw.05G236500' => 'cil', 'CiPaw.05G244800' => 'cil', 'CiPaw.06G026600' => 'cil', 'CiPaw.06G027900' => 'cil', 'CiPaw.06G051800' => 'cil', 'CiPaw.06G128500' => 'cil', 'CiPaw.06G165900' => 'cil', 'CiPaw.07G045400' => 'cil', 'CiPaw.07G048000' => 'cil', 'CiPaw.07G052000' => 'cil', 'CiPaw.07G073800' => 'cil', 'CiPaw.07G099700' => 'cil', 'CiPaw.07G108700' => 'cil', 'CiPaw.07G120000' => 'cil', 'CiPaw.07G134100' => 'cil', 'CiPaw.07G147000' => 'cil', 'CiPaw.07G149700' => 'cil', 'CiPaw.07G178300' => 'cil', 'CiPaw.07G184900' => 'cil', 'CiPaw.08G044500' => 'cil', 'CiPaw.08G046900' => 'cil', 'CiPaw.08G047300' => 'cil', 'CiPaw.08G115400' => 'cil', 'CiPaw.08G134700' => 'cil', 'CiPaw.08G157400' => 'cil', 'CiPaw.09G014300' => 'cil', 'CiPaw.09G088900' => 'cil', 'CiPaw.09G130900' => 'cil', 'CiPaw.09G133100' => 'cil', 'CiPaw.09G151300' => 'cil', 'CiPaw.09G172800' => 'cil', 'CiPaw.09G174900' => 'cil', 'CiPaw.09G175000' => 'cil', 'CiPaw.10G012800' => 'cil', 'CiPaw.10G028800' => 'cil', 'CiPaw.10G044700' => 'cil', 'CiPaw.10G067400' => 'cil', 'CiPaw.10G115900' => 'cil', 'CiPaw.10G126200' => 'cil', 'CiPaw.10G139700' => 'cil', 'CiPaw.10G155100' => 'cil', 'CiPaw.11G011300' => 'cil', 'CiPaw.11G025900' => 'cil', 'CiPaw.11G104100' => 'cil', 'CiPaw.11G142700' => 'cil', 'CiPaw.11G164500' => 'cil', 'CiPaw.11G189100' => 'cil', 'CiPaw.11G197100' => 'cil', 'CiPaw.12G006100' => 'cil', 'CiPaw.12G038500' => 'cil', 'CiPaw.12G041400' => 'cil', 'CiPaw.12G041600' => 'cil', 'CiPaw.12G051300' => 'cil', 'CiPaw.12G101800' => 'cil', 'CiPaw.12G107800' => 'cil', 'CiPaw.13G033200' => 'cil', 'CiPaw.13G129900' => 'cil', 'CiPaw.13G160200' => 'cil', 'CiPaw.14G018900' => 'cil', 'CiPaw.14G029000' => 'cil', 'CiPaw.14G031000' => 'cil', 'CiPaw.14G032000' => 'cil', 'CiPaw.14G032300' => 'cil', 'CiPaw.14G040600' => 'cil', 'CiPaw.14G060500' => 'cil', 'CiPaw.14G061500' => 'cil', 'CiPaw.14G077500' => 'cil', 'CiPaw.14G088300' => 'cil', 'CiPaw.14G108500' => 'cil', 'CiPaw.14G121300' => 'cil', 'CiPaw.14G133000' => 'cil', 'CiPaw.14G134600' => 'cil', 'CiPaw.15G027200' => 'cil', 'CiPaw.15G037700' => 'cil', 'CiPaw.15G050900' => 'cil', 'CiPaw.15G067200' => 'cil', 'CiPaw.15G072000' => 'cil', 'CiPaw.15G112900' => 'cil', 'CiPaw.15G133200' => 'cil', 'CiPaw.15G139500' => 'cil', 'CiPaw.15G155400' => 'cil', 'CiPaw.16G006000' => 'cil', 'CiPaw.16G013100' => 'cil', 'CiPaw.16G047100' => 'cil', 'CiPaw.16G048900' => 'cil', 'CiPaw.16G070300' => 'cil', 'CSS0000195' => 'camsi', 'CSS0001664' => 'camsi', 'CSS0002566' => 'camsi', 'CSS0003077' => 'camsi', 'CSS0004257' => 'camsi', 'CSS0004495' => 'camsi', 'CSS0004599' => 'camsi', 'CSS0004943' => 'camsi', 'CSS0005302' => 'camsi', 'CSS0006274' => 'camsi', 'CSS0006547' => 'camsi', 'CSS0006860' => 'camsi', 'CSS0008814' => 'camsi', 'CSS0008946' => 'camsi', 'CSS0009093' => 'camsi', 'CSS0010221' => 'camsi', 'CSS0010296' => 'camsi', 'CSS0010386' => 'camsi', 'CSS0010831' => 'camsi', 'CSS0011061' => 'camsi', 'CSS0012008' => 'camsi', 'CSS0012194' => 'camsi', 'CSS0013580' => 'camsi', 'CSS0014176' => 'camsi', 'CSS0014280' => 'camsi', 'CSS0014799' => 'camsi', 'CSS0015368' => 'camsi', 'CSS0017473' => 'camsi', 'CSS0019281' => 'camsi', 'CSS0021320' => 'camsi', 'CSS0021750' => 'camsi', 'CSS0023642' => 'camsi', 'CSS0023792' => 'camsi', 'CSS0031528' => 'camsi', 'CSS0033894' => 'camsi', 'CSS0034959' => 'camsi', 'CSS0035632' => 'camsi', 'CSS0038450' => 'camsi', 'CSS0039293' => 'camsi', 'CSS0041053' => 'camsi', 'CSS0041981' => 'camsi', 'CSS0042573' => 'camsi', 'CSS0042927' => 'camsi', 'CSS0047725' => 'camsi', 'CSS0049636' => 'camsi', 'CSS0050513' => 'camsi', 'DCAR_030203' => 'dca', 'Dinv07939' => 'din', 'FAN01G0456' => 'fan', 'FAN02G3001' => 'fan', 'FAN04G2781' => 'fan', 'FAN05G1385' => 'fan', 'FAN05G3062' => 'fan', 'FAN08G2267' => 'fan', 'FAN10G0481' => 'fan', 'FAN10G1257' => 'fan', 'FAN14G0954' => 'fan', 'FAN14G2347' => 'fan', 'FAN15G0187' => 'fan', 'FAN25G2214' => 'fan', 'FvH4_1g21031' => 'fve', 'FvH4_3g16231' => 'fve', 'FvH4_3g26413' => 'fve', 'FvH4_3g29014' => 'fve', 'FvH4_3g31921' => 'fve', 'FvH4_4g19882' => 'fve', 'FvH4_5g21960' => 'fve', 'FvH4_5g29683' => 'fve', 'FvH4_7g13271' => 'fve', 'Glyma.01G062500' => 'gma', 'Glyma.07G140900' => 'gma', 'Glyma.09G140900' => 'gma', 'Glyma.12G112700' => 'gma', 'Glyma.17G168800' => 'gma', 'HanXRQChr01g0027001' => 'han', 'HanXRQChr04g0120511' => 'han', 'HanXRQChr08g0232381' => 'han', 'HanXRQChr09g0265661' => 'han', 'HanXRQChr13g0416031' => 'han', 'Haze_05835' => 'cav', 'Haze_06597' => 'cav', 'Haze_07921' => 'cav', 'Haze_08599' => 'cav', 'Haze_10686' => 'cav', 'Haze_12994' => 'cav', 'Haze_13466' => 'cav', 'Haze_16101' => 'cav', 'Haze_17766' => 'cav', 'Haze_18456' => 'cav', 'Haze_20229' => 'cav', 'Hma1.2p1_0324F.1_g125640' => 'hma', 'Hma1.2p1_0733F.1_g210230' => 'hma', 'Hma1.2p1_0921F.1_g236870' => 'hma', 'Hma1.2p1_1313F.1_g274940' => 'hma', 'Hma1.2p1_3059F.1_g332230' => 'hma', 'Hund15925' => 'sun', 'Hund19562' => 'sun', 'Hund21925' => 'sun', 'MD03G1177400' => 'mdo', 'MD07G1026100' => 'mdo', 'MD17G1218600' => 'mdo', 'Medtr0867s0010' => 'mtr', 'Medtr6g081150' => 'mtr', 'Os01g0527900' => 'osa', 'Os02g0463725' => 'osa', 'Os02g0785600' => 'osa', 'Os03g0433733' => 'osa', 'Os04g0286500' => 'osa', 'Os05g0227800' => 'osa', 'Os06g0521000' => 'osa', 'Os06g0635500' => 'osa', 'Os06g0660650' => 'osa', 'Os07g0554400' => 'osa', 'Os08g0225900' => 'osa', 'Os08g0561000' => 'osa', 'Os09g0241700' => 'osa', 'Os09g0351900' => 'osa', 'Os11g0220700' => 'osa', 'Os11g0282700' => 'osa', 'Os12g0169300' => 'osa', 'Os12g0228500' => 'osa', 'Os12g0543800' => 'osa', 'PGR044G1547' => 'pgr', 'Potri.005G239150' => 'ptr', 'Potri.010G014250' => 'ptr', 'Prupe.1G172500' => 'ppe', 'Prupe.1G196800' => 'ppe', 'Prupe.1G279700' => 'ppe', 'Prupe.2G026400' => 'ppe', 'Prupe.3G094000' => 'ppe', 'Prupe.4G287300' => 'ppe', 'QL01p022166' => 'qlo', 'QL01p051890' => 'qlo', 'QL02p009469' => 'qlo', 'QL02p046053' => 'qlo', 'QL02p057958' => 'qlo', 'QL02p093127' => 'qlo', 'QL03p006855' => 'qlo', 'QL03p071586' => 'qlo', 'QL04p000022' => 'qlo', 'QL04p000024' => 'qlo', 'QL04p003192' => 'qlo', 'QL05p011416' => 'qlo', 'QL06p039590' => 'qlo', 'QL06p052750' => 'qlo', 'QL06p053821' => 'qlo', 'QL07p025287' => 'qlo', 'QL09p033218' => 'qlo', 'QL09p040841' => 'qlo', 'QL10p020337' => 'qlo', 'QL10p027209' => 'qlo', 'QL10p027969' => 'qlo', 'QL10p048988' => 'qlo', 'QL11p001241' => 'qlo', 'QL11p028487' => 'qlo', 'RcHm_v2.0_Chr2g0105031' => 'rch', 'RcHm_v2.0_Chr2g0117811' => 'rch', 'RcHm_v2.0_Chr6g0270241' => 'rch', 'RcHm_v2.0_Chr7g0215961' => 'rch', 'RcHm_v2.0_Chr7g0231991' => 'rch', 'Rhsim01G0041500' => 'rsi', 'Rhsim01G0115000' => 'rsi', 'Rhsim01G0115400' => 'rsi', 'Rhsim01G0133600' => 'rsi', 'Rhsim01G0159900' => 'rsi', 'Rhsim02G0189400' => 'rsi', 'Rhsim03G0135600' => 'rsi', 'Rhsim03G0149900' => 'rsi', 'Rhsim04G0125600' => 'rsi', 'Rhsim05G0091700' => 'rsi', 'Rhsim05G0092900' => 'rsi', 'Rhsim06G0075000' => 'rsi', 'Rhsim07G0066400' => 'rsi', 'Rhsim07G0156400' => 'rsi', 'Rhsim07G0182200' => 'rsi', 'Rhsim07G0182300' => 'rsi', 'Rhsim08G0180400' => 'rsi', 'Rhsim09G0056800' => 'rsi', 'Rhsim10G0153300' => 'rsi', 'Rhsim11G0012700' => 'rsi', 'Rhsim12G0031800' => 'rsi', 'Rhsim12G0055400' => 'rsi', 'Rhsim12G0091400' => 'rsi', 'Rhsim13G0070800' => 'rsi', 'Rhsim13G0193300' => 'rsi', 'RhsimUnG0111600' => 'rsi', 'RhsimUnG0137500' => 'rsi', 'RhsimUnG0172900' => 'rsi', 'SGA_v2.0_scaffold11G05878' => 'sas', 'SGA_v2.0_scaffold167G38458' => 'sas', 'SGA_v2.0_scaffold19G08588' => 'sas', 'SGA_v2.0_scaffold239G43990' => 'sas', 'SGA_v2.0_scaffold260G45865' => 'sas', 'SGA_v2.0_scaffold309G48177' => 'sas', 'SGA_v2.0_scaffold76G25122' => 'sas', 'SGA_v2.0_scaffold85G26708' => 'sas', 'SHI13914' => 'shi', 'SHI30402' => 'shi', 'TWI09G0020' => 'twi', 'TWI09G0456' => 'twi', 'TWI09G1572' => 'twi', 'TWI12G0266' => 'twi', 'TWI12G1451' => 'twi', 'TWI14G0851' => 'twi', 'TWI15G0796' => 'twi', 'TWI18G0820' => 'twi', 'TWI18G1152' => 'twi', 'TWI23G0007' => 'twi', 'TWI23G0314' => 'twi', 'TWI31G0674' => 'twi', 'TWI31G0938' => 'twi', 'TWI34G0641' => 'twi', 'TWI34G1527' => 'twi', 'TWI36G0193' => 'twi', 'TWI36G0405' => 'twi', 'TWI38G0892' => 'twi', 'TWI38G0936' => 'twi', 'TWI38G2218' => 'twi', 'TWI53G0679' => 'twi', 'TWI53G0863' => 'twi', 'TWI53G1133' => 'twi', 'TWI60G0823' => 'twi', 'TWI63G0919' => 'twi', 'TWI63G1436' => 'twi', 'TWI73G0140' => 'twi', 'TWI73G0419' => 'twi', 'TWI73G0420' => 'twi', 'TWI73G1276' => 'twi', 'TWI74G0405' => 'twi', 'TWI74G0837' => 'twi', 'TWI75G0594' => 'twi', 'TWI75G1615' => 'twi', 'TWI77G0816' => 'twi', 'vmacro03831' => 'vma', 'vmacro13746' => 'vma', 'vmacro16089' => 'vma', 'vmacro22863' => 'vma', 'Zm00001eb085790' => 'zma', 'Zm00001eb114250' => 'zma', 'Zm00001eb138070' => 'zma', 'Zm00001eb167560' => 'zma', 'Zm00001eb199990' => 'zma', 'Zm00001eb368180' => 'zma', 'Zm00001eb382470' => 'zma' ), 'gf_id' => 'HOM05D001576', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001576' ), 'data_identifier' => 'HOM05D001576', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001576', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '406', 'num_species' => '29' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'Aqoxy1G01456' => 'aox', 'Aqoxy1G02949' => 'aox', 'Aqoxy3G01274' => 'aox', 'Aqoxy3G02110' => 'aox', 'Aqoxy3G02268' => 'aox', 'Aqoxy5G02702' => 'aox', 'Aqoxy5G02988' => 'aox', 'Aqoxy5G03427' => 'aox', 'Aqoxy6G02363' => 'aox', 'Atru.chr1.3225' => 'acertr', 'Atru.chr8.1198' => 'acertr', 'Atru.chr9.790' => 'acertr', 'CANSAT01G3197' => 'cansat', 'Ciclev10003979m.g' => 'ccl', 'Ciclev10017471m.g' => 'ccl', 'Ciclev10018206m.g' => 'ccl', 'Ciclev10033751m.g' => 'ccl', 'CiPaw.01G000900' => 'cil', 'CiPaw.01G001000' => 'cil', 'CiPaw.01G033500' => 'cil', 'CiPaw.01G060300' => 'cil', 'CiPaw.01G070200' => 'cil', 'CiPaw.01G075100' => 'cil', 'CiPaw.01G084700' => 'cil', 'CiPaw.01G087900' => 'cil', 'CiPaw.01G092600' => 'cil', 'CiPaw.01G097200' => 'cil', 'CiPaw.01G098300' => 'cil', 'CiPaw.01G110200' => 'cil', 'CiPaw.01G118700' => 'cil', 'CiPaw.01G121200' => 'cil', 'CiPaw.01G132500' => 'cil', 'CiPaw.01G146900' => 'cil', 'CiPaw.01G174000' => 'cil', 'CiPaw.01G179900' => 'cil', 'CiPaw.01G183400' => 'cil', 'CiPaw.01G240000' => 'cil', 'CiPaw.01G283500' => 'cil', 'CiPaw.01G307400' => 'cil', 'CiPaw.02G030800' => 'cil', 'CiPaw.02G047200' => 'cil', 'CiPaw.02G050500' => 'cil', 'CiPaw.02G069900' => 'cil', 'CiPaw.02G091600' => 'cil', 'CiPaw.02G095000' => 'cil', 'CiPaw.02G131900' => 'cil', 'CiPaw.03G043000' => 'cil', 'CiPaw.03G069900' => 'cil', 'CiPaw.03G088100' => 'cil', 'CiPaw.03G089300' => 'cil', 'CiPaw.03G093100' => 'cil', 'CiPaw.03G129800' => 'cil', 'CiPaw.03G131200' => 'cil', 'CiPaw.03G134500' => 'cil', 'CiPaw.03G152100' => 'cil', 'CiPaw.03G162700' => 'cil', 'CiPaw.03G172800' => 'cil', 'CiPaw.03G175800' => 'cil', 'CiPaw.03G181800' => 'cil', 'CiPaw.03G191400' => 'cil', 'CiPaw.03G198300' => 'cil', 'CiPaw.03G201300' => 'cil', 'CiPaw.03G224700' => 'cil', 'CiPaw.03G225000' => 'cil', 'CiPaw.04G065100' => 'cil', 'CiPaw.04G080400' => 'cil', 'CiPaw.04G113500' => 'cil', 'CiPaw.04G121900' => 'cil', 'CiPaw.04G144100' => 'cil', 'CiPaw.04G176500' => 'cil', 'CiPaw.05G086200' => 'cil', 'CiPaw.05G100200' => 'cil', 'CiPaw.05G114200' => 'cil', 'CiPaw.05G126800' => 'cil', 'CiPaw.05G228800' => 'cil', 'CiPaw.05G230600' => 'cil', 'CiPaw.05G236500' => 'cil', 'CiPaw.05G244800' => 'cil', 'CiPaw.06G026600' => 'cil', 'CiPaw.06G027900' => 'cil', 'CiPaw.06G051800' => 'cil', 'CiPaw.06G128500' => 'cil', 'CiPaw.06G165900' => 'cil', 'CiPaw.07G045400' => 'cil', 'CiPaw.07G048000' => 'cil', 'CiPaw.07G052000' => 'cil', 'CiPaw.07G073800' => 'cil', 'CiPaw.07G099700' => 'cil', 'CiPaw.07G108700' => 'cil', 'CiPaw.07G120000' => 'cil', 'CiPaw.07G134100' => 'cil', 'CiPaw.07G147000' => 'cil', 'CiPaw.07G149700' => 'cil', 'CiPaw.07G178300' => 'cil', 'CiPaw.07G184900' => 'cil', 'CiPaw.08G044500' => 'cil', 'CiPaw.08G046900' => 'cil', 'CiPaw.08G047300' => 'cil', 'CiPaw.08G115400' => 'cil', 'CiPaw.08G134700' => 'cil', 'CiPaw.08G157400' => 'cil', 'CiPaw.09G014300' => 'cil', 'CiPaw.09G088900' => 'cil', 'CiPaw.09G130900' => 'cil', 'CiPaw.09G133100' => 'cil', 'CiPaw.09G151300' => 'cil', 'CiPaw.09G172800' => 'cil', 'CiPaw.09G174900' => 'cil', 'CiPaw.09G175000' => 'cil', 'CiPaw.10G012800' => 'cil', 'CiPaw.10G028800' => 'cil', 'CiPaw.10G044700' => 'cil', 'CiPaw.10G067400' => 'cil', 'CiPaw.10G115900' => 'cil', 'CiPaw.10G126200' => 'cil', 'CiPaw.10G139700' => 'cil', 'CiPaw.10G155100' => 'cil', 'CiPaw.11G011300' => 'cil', 'CiPaw.11G025900' => 'cil', 'CiPaw.11G104100' => 'cil', 'CiPaw.11G142700' => 'cil', 'CiPaw.11G164500' => 'cil', 'CiPaw.11G189100' => 'cil', 'CiPaw.11G197100' => 'cil', 'CiPaw.12G006100' => 'cil', 'CiPaw.12G038500' => 'cil', 'CiPaw.12G041400' => 'cil', 'CiPaw.12G041600' => 'cil', 'CiPaw.12G051300' => 'cil', 'CiPaw.12G101800' => 'cil', 'CiPaw.12G107800' => 'cil', 'CiPaw.13G033200' => 'cil', 'CiPaw.13G129900' => 'cil', 'CiPaw.13G160200' => 'cil', 'CiPaw.14G018900' => 'cil', 'CiPaw.14G029000' => 'cil', 'CiPaw.14G031000' => 'cil', 'CiPaw.14G032000' => 'cil', 'CiPaw.14G032300' => 'cil', 'CiPaw.14G040600' => 'cil', 'CiPaw.14G060500' => 'cil', 'CiPaw.14G061500' => 'cil', 'CiPaw.14G077500' => 'cil', 'CiPaw.14G088300' => 'cil', 'CiPaw.14G108500' => 'cil', 'CiPaw.14G121300' => 'cil', 'CiPaw.14G133000' => 'cil', 'CiPaw.14G134600' => 'cil', 'CiPaw.15G027200' => 'cil', 'CiPaw.15G037700' => 'cil', 'CiPaw.15G050900' => 'cil', 'CiPaw.15G067200' => 'cil', 'CiPaw.15G072000' => 'cil', 'CiPaw.15G112900' => 'cil', 'CiPaw.15G133200' => 'cil', 'CiPaw.15G139500' => 'cil', 'CiPaw.15G155400' => 'cil', 'CiPaw.16G006000' => 'cil', 'CiPaw.16G013100' => 'cil', 'CiPaw.16G047100' => 'cil', 'CiPaw.16G048900' => 'cil', 'CiPaw.16G070300' => 'cil', 'CSS0000195' => 'camsi', 'CSS0001664' => 'camsi', 'CSS0002566' => 'camsi', 'CSS0003077' => 'camsi', 'CSS0004257' => 'camsi', 'CSS0004495' => 'camsi', 'CSS0004599' => 'camsi', 'CSS0004943' => 'camsi', 'CSS0005302' => 'camsi', 'CSS0006274' => 'camsi', 'CSS0006547' => 'camsi', 'CSS0006860' => 'camsi', 'CSS0008814' => 'camsi', 'CSS0008946' => 'camsi', 'CSS0009093' => 'camsi', 'CSS0010221' => 'camsi', 'CSS0010296' => 'camsi', 'CSS0010386' => 'camsi', 'CSS0010831' => 'camsi', 'CSS0011061' => 'camsi', 'CSS0012008' => 'camsi', 'CSS0012194' => 'camsi', 'CSS0013580' => 'camsi', 'CSS0014176' => 'camsi', 'CSS0014280' => 'camsi', 'CSS0014799' => 'camsi', 'CSS0015368' => 'camsi', 'CSS0017473' => 'camsi', 'CSS0019281' => 'camsi', 'CSS0021320' => 'camsi', 'CSS0021750' => 'camsi', 'CSS0023642' => 'camsi', 'CSS0023792' => 'camsi', 'CSS0031528' => 'camsi', 'CSS0033894' => 'camsi', 'CSS0034959' => 'camsi', 'CSS0035632' => 'camsi', 'CSS0038450' => 'camsi', 'CSS0039293' => 'camsi', 'CSS0041053' => 'camsi', 'CSS0041981' => 'camsi', 'CSS0042573' => 'camsi', 'CSS0042927' => 'camsi', 'CSS0047725' => 'camsi', 'CSS0049636' => 'camsi', 'CSS0050513' => 'camsi', 'DCAR_030203' => 'dca', 'Dinv07939' => 'din', 'FAN01G0456' => 'fan', 'FAN02G3001' => 'fan', 'FAN04G2781' => 'fan', 'FAN05G1385' => 'fan', 'FAN05G3062' => 'fan', 'FAN08G2267' => 'fan', 'FAN10G0481' => 'fan', 'FAN10G1257' => 'fan', 'FAN14G0954' => 'fan', 'FAN14G2347' => 'fan', 'FAN15G0187' => 'fan', 'FAN25G2214' => 'fan', 'FvH4_1g21031' => 'fve', 'FvH4_3g16231' => 'fve', 'FvH4_3g26413' => 'fve', 'FvH4_3g29014' => 'fve', 'FvH4_3g31921' => 'fve', 'FvH4_4g19882' => 'fve', 'FvH4_5g21960' => 'fve', 'FvH4_5g29683' => 'fve', 'FvH4_7g13271' => 'fve', 'Glyma.01G062500' => 'gma', 'Glyma.07G140900' => 'gma', 'Glyma.09G140900' => 'gma', 'Glyma.12G112700' => 'gma', 'Glyma.17G168800' => 'gma', 'HanXRQChr01g0027001' => 'han', 'HanXRQChr04g0120511' => 'han', 'HanXRQChr08g0232381' => 'han', 'HanXRQChr09g0265661' => 'han', 'HanXRQChr13g0416031' => 'han', 'Haze_05835' => 'cav', 'Haze_06597' => 'cav', 'Haze_07921' => 'cav', 'Haze_08599' => 'cav', 'Haze_10686' => 'cav', 'Haze_12994' => 'cav', 'Haze_13466' => 'cav', 'Haze_16101' => 'cav', 'Haze_17766' => 'cav', 'Haze_18456' => 'cav', 'Haze_20229' => 'cav', 'Hma1.2p1_0324F.1_g125640' => 'hma', 'Hma1.2p1_0733F.1_g210230' => 'hma', 'Hma1.2p1_0921F.1_g236870' => 'hma', 'Hma1.2p1_1313F.1_g274940' => 'hma', 'Hma1.2p1_3059F.1_g332230' => 'hma', 'Hund15925' => 'sun', 'Hund19562' => 'sun', 'Hund21925' => 'sun', 'MD03G1177400' => 'mdo', 'MD07G1026100' => 'mdo', 'MD17G1218600' => 'mdo', 'Medtr0867s0010' => 'mtr', 'Medtr6g081150' => 'mtr', 'Os01g0527900' => 'osa', 'Os02g0463725' => 'osa', 'Os02g0785600' => 'osa', 'Os03g0433733' => 'osa', 'Os04g0286500' => 'osa', 'Os05g0227800' => 'osa', 'Os06g0521000' => 'osa', 'Os06g0635500' => 'osa', 'Os06g0660650' => 'osa', 'Os07g0554400' => 'osa', 'Os08g0225900' => 'osa', 'Os08g0561000' => 'osa', 'Os09g0241700' => 'osa', 'Os09g0351900' => 'osa', 'Os11g0220700' => 'osa', 'Os11g0282700' => 'osa', 'Os12g0169300' => 'osa', 'Os12g0228500' => 'osa', 'Os12g0543800' => 'osa', 'PGR044G1547' => 'pgr', 'Potri.005G239150' => 'ptr', 'Potri.010G014250' => 'ptr', 'Prupe.1G172500' => 'ppe', 'Prupe.1G196800' => 'ppe', 'Prupe.1G279700' => 'ppe', 'Prupe.2G026400' => 'ppe', 'Prupe.3G094000' => 'ppe', 'Prupe.4G287300' => 'ppe', 'QL01p022166' => 'qlo', 'QL01p051890' => 'qlo', 'QL02p009469' => 'qlo', 'QL02p046053' => 'qlo', 'QL02p057958' => 'qlo', 'QL02p093127' => 'qlo', 'QL03p006855' => 'qlo', 'QL03p071586' => 'qlo', 'QL04p000022' => 'qlo', 'QL04p000024' => 'qlo', 'QL04p003192' => 'qlo', 'QL05p011416' => 'qlo', 'QL06p039590' => 'qlo', 'QL06p052750' => 'qlo', 'QL06p053821' => 'qlo', 'QL07p025287' => 'qlo', 'QL09p033218' => 'qlo', 'QL09p040841' => 'qlo', 'QL10p020337' => 'qlo', 'QL10p027209' => 'qlo', 'QL10p027969' => 'qlo', 'QL10p048988' => 'qlo', 'QL11p001241' => 'qlo', 'QL11p028487' => 'qlo', 'RcHm_v2.0_Chr2g0105031' => 'rch', 'RcHm_v2.0_Chr2g0117811' => 'rch', 'RcHm_v2.0_Chr6g0270241' => 'rch', 'RcHm_v2.0_Chr7g0215961' => 'rch', 'RcHm_v2.0_Chr7g0231991' => 'rch', 'Rhsim01G0041500' => 'rsi', 'Rhsim01G0115000' => 'rsi', 'Rhsim01G0115400' => 'rsi', 'Rhsim01G0133600' => 'rsi', 'Rhsim01G0159900' => 'rsi', 'Rhsim02G0189400' => 'rsi', 'Rhsim03G0135600' => 'rsi', 'Rhsim03G0149900' => 'rsi', 'Rhsim04G0125600' => 'rsi', 'Rhsim05G0091700' => 'rsi', 'Rhsim05G0092900' => 'rsi', 'Rhsim06G0075000' => 'rsi', 'Rhsim07G0066400' => 'rsi', 'Rhsim07G0156400' => 'rsi', 'Rhsim07G0182200' => 'rsi', 'Rhsim07G0182300' => 'rsi', 'Rhsim08G0180400' => 'rsi', 'Rhsim09G0056800' => 'rsi', 'Rhsim10G0153300' => 'rsi', 'Rhsim11G0012700' => 'rsi', 'Rhsim12G0031800' => 'rsi', 'Rhsim12G0055400' => 'rsi', 'Rhsim12G0091400' => 'rsi', 'Rhsim13G0070800' => 'rsi', 'Rhsim13G0193300' => 'rsi', 'RhsimUnG0111600' => 'rsi', 'RhsimUnG0137500' => 'rsi', 'RhsimUnG0172900' => 'rsi', 'SGA_v2.0_scaffold11G05878' => 'sas', 'SGA_v2.0_scaffold167G38458' => 'sas', 'SGA_v2.0_scaffold19G08588' => 'sas', 'SGA_v2.0_scaffold239G43990' => 'sas', 'SGA_v2.0_scaffold260G45865' => 'sas', 'SGA_v2.0_scaffold309G48177' => 'sas', 'SGA_v2.0_scaffold76G25122' => 'sas', 'SGA_v2.0_scaffold85G26708' => 'sas', 'SHI13914' => 'shi', 'SHI30402' => 'shi', 'TWI09G0020' => 'twi', 'TWI09G0456' => 'twi', 'TWI09G1572' => 'twi', 'TWI12G0266' => 'twi', 'TWI12G1451' => 'twi', 'TWI14G0851' => 'twi', 'TWI15G0796' => 'twi', 'TWI18G0820' => 'twi', 'TWI18G1152' => 'twi', 'TWI23G0007' => 'twi', 'TWI23G0314' => 'twi', 'TWI31G0674' => 'twi', 'TWI31G0938' => 'twi', 'TWI34G0641' => 'twi', 'TWI34G1527' => 'twi', 'TWI36G0193' => 'twi', 'TWI36G0405' => 'twi', 'TWI38G0892' => 'twi', 'TWI38G0936' => 'twi', 'TWI38G2218' => 'twi', 'TWI53G0679' => 'twi', 'TWI53G0863' => 'twi', 'TWI53G1133' => 'twi', 'TWI60G0823' => 'twi', 'TWI63G0919' => 'twi', 'TWI63G1436' => 'twi', 'TWI73G0140' => 'twi', 'TWI73G0419' => 'twi', 'TWI73G0420' => 'twi', 'TWI73G1276' => 'twi', 'TWI74G0405' => 'twi', 'TWI74G0837' => 'twi', 'TWI75G0594' => 'twi', 'TWI75G1615' => 'twi', 'TWI77G0816' => 'twi', 'vmacro03831' => 'vma', 'vmacro13746' => 'vma', 'vmacro16089' => 'vma', 'vmacro22863' => 'vma', 'Zm00001eb085790' => 'zma', 'Zm00001eb114250' => 'zma', 'Zm00001eb138070' => 'zma', 'Zm00001eb167560' => 'zma', 'Zm00001eb199990' => 'zma', 'Zm00001eb368180' => 'zma', 'Zm00001eb382470' => 'zma' ) $gf_id = 'HOM05D001576' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001576' ) $data_identifier = 'HOM05D001576' $data_type = 'gf_id' $species_gene_counts = array( 'aox' => (int) 9, 'acertr' => (int) 3, 'cansat' => (int) 1, 'ccl' => (int) 4, 'cil' => (int) 145, 'camsi' => (int) 46, 'dca' => (int) 1, 'din' => (int) 1, 'fan' => (int) 12, 'fve' => (int) 9, 'gma' => (int) 5, 'han' => (int) 5, 'cav' => (int) 11, 'hma' => (int) 5, 'sun' => (int) 3, 'mdo' => (int) 3, 'mtr' => (int) 2, 'osa' => (int) 19, 'pgr' => (int) 1, 'ptr' => (int) 2, 'ppe' => (int) 6, 'qlo' => (int) 24, 'rch' => (int) 5, 'rsi' => (int) 28, 'sas' => (int) 8, 'shi' => (int) 2, 'twi' => (int) 35, 'vma' => (int) 4, 'zma' => (int) 7 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb382470' $species_info = array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ) $local_species = 'shi' $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' => 'HOM05D001576', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '406', 'num_species' => '29' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'Aqoxy1G01456' => 'aox', 'Aqoxy1G02949' => 'aox', 'Aqoxy3G01274' => 'aox', 'Aqoxy3G02110' => 'aox', 'Aqoxy3G02268' => 'aox', 'Aqoxy5G02702' => 'aox', 'Aqoxy5G02988' => 'aox', 'Aqoxy5G03427' => 'aox', 'Aqoxy6G02363' => 'aox', 'Atru.chr1.3225' => 'acertr', 'Atru.chr8.1198' => 'acertr', 'Atru.chr9.790' => 'acertr', 'CANSAT01G3197' => 'cansat', 'Ciclev10003979m.g' => 'ccl', 'Ciclev10017471m.g' => 'ccl', 'Ciclev10018206m.g' => 'ccl', 'Ciclev10033751m.g' => 'ccl', 'CiPaw.01G000900' => 'cil', 'CiPaw.01G001000' => 'cil', 'CiPaw.01G033500' => 'cil', 'CiPaw.01G060300' => 'cil', 'CiPaw.01G070200' => 'cil', 'CiPaw.01G075100' => 'cil', 'CiPaw.01G084700' => 'cil', 'CiPaw.01G087900' => 'cil', 'CiPaw.01G092600' => 'cil', 'CiPaw.01G097200' => 'cil', 'CiPaw.01G098300' => 'cil', 'CiPaw.01G110200' => 'cil', 'CiPaw.01G118700' => 'cil', 'CiPaw.01G121200' => 'cil', 'CiPaw.01G132500' => 'cil', 'CiPaw.01G146900' => 'cil', 'CiPaw.01G174000' => 'cil', 'CiPaw.01G179900' => 'cil', 'CiPaw.01G183400' => 'cil', 'CiPaw.01G240000' => 'cil', 'CiPaw.01G283500' => 'cil', 'CiPaw.01G307400' => 'cil', 'CiPaw.02G030800' => 'cil', 'CiPaw.02G047200' => 'cil', 'CiPaw.02G050500' => 'cil', 'CiPaw.02G069900' => 'cil', 'CiPaw.02G091600' => 'cil', 'CiPaw.02G095000' => 'cil', 'CiPaw.02G131900' => 'cil', 'CiPaw.03G043000' => 'cil', 'CiPaw.03G069900' => 'cil', 'CiPaw.03G088100' => 'cil', 'CiPaw.03G089300' => 'cil', 'CiPaw.03G093100' => 'cil', 'CiPaw.03G129800' => 'cil', 'CiPaw.03G131200' => 'cil', 'CiPaw.03G134500' => 'cil', 'CiPaw.03G152100' => 'cil', 'CiPaw.03G162700' => 'cil', 'CiPaw.03G172800' => 'cil', 'CiPaw.03G175800' => 'cil', 'CiPaw.03G181800' => 'cil', 'CiPaw.03G191400' => 'cil', 'CiPaw.03G198300' => 'cil', 'CiPaw.03G201300' => 'cil', 'CiPaw.03G224700' => 'cil', 'CiPaw.03G225000' => 'cil', 'CiPaw.04G065100' => 'cil', 'CiPaw.04G080400' => 'cil', 'CiPaw.04G113500' => 'cil', 'CiPaw.04G121900' => 'cil', 'CiPaw.04G144100' => 'cil', 'CiPaw.04G176500' => 'cil', 'CiPaw.05G086200' => 'cil', 'CiPaw.05G100200' => 'cil', 'CiPaw.05G114200' => 'cil', 'CiPaw.05G126800' => 'cil', 'CiPaw.05G228800' => 'cil', 'CiPaw.05G230600' => 'cil', 'CiPaw.05G236500' => 'cil', 'CiPaw.05G244800' => 'cil', 'CiPaw.06G026600' => 'cil', 'CiPaw.06G027900' => 'cil', 'CiPaw.06G051800' => 'cil', 'CiPaw.06G128500' => 'cil', 'CiPaw.06G165900' => 'cil', 'CiPaw.07G045400' => 'cil', 'CiPaw.07G048000' => 'cil', 'CiPaw.07G052000' => 'cil', 'CiPaw.07G073800' => 'cil', 'CiPaw.07G099700' => 'cil', 'CiPaw.07G108700' => 'cil', 'CiPaw.07G120000' => 'cil', 'CiPaw.07G134100' => 'cil', 'CiPaw.07G147000' => 'cil', 'CiPaw.07G149700' => 'cil', 'CiPaw.07G178300' => 'cil', 'CiPaw.07G184900' => 'cil', 'CiPaw.08G044500' => 'cil', 'CiPaw.08G046900' => 'cil', 'CiPaw.08G047300' => 'cil', 'CiPaw.08G115400' => 'cil', 'CiPaw.08G134700' => 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'TWI09G0020' => 'twi', 'TWI09G0456' => 'twi', 'TWI09G1572' => 'twi', 'TWI12G0266' => 'twi', 'TWI12G1451' => 'twi', 'TWI14G0851' => 'twi', 'TWI15G0796' => 'twi', 'TWI18G0820' => 'twi', 'TWI18G1152' => 'twi', 'TWI23G0007' => 'twi', 'TWI23G0314' => 'twi', 'TWI31G0674' => 'twi', 'TWI31G0938' => 'twi', 'TWI34G0641' => 'twi', 'TWI34G1527' => 'twi', 'TWI36G0193' => 'twi', 'TWI36G0405' => 'twi', 'TWI38G0892' => 'twi', 'TWI38G0936' => 'twi', 'TWI38G2218' => 'twi', 'TWI53G0679' => 'twi', 'TWI53G0863' => 'twi', 'TWI53G1133' => 'twi', 'TWI60G0823' => 'twi', 'TWI63G0919' => 'twi', 'TWI63G1436' => 'twi', 'TWI73G0140' => 'twi', 'TWI73G0419' => 'twi', 'TWI73G0420' => 'twi', 'TWI73G1276' => 'twi', 'TWI74G0405' => 'twi', 'TWI74G0837' => 'twi', 'TWI75G0594' => 'twi', 'TWI75G1615' => 'twi', 'TWI77G0816' => 'twi', 'vmacro03831' => 'vma', 'vmacro13746' => 'vma', 'vmacro16089' => 'vma', 'vmacro22863' => 'vma', 'Zm00001eb085790' => 'zma', 'Zm00001eb114250' => 'zma', 'Zm00001eb138070' => 'zma', 'Zm00001eb167560' => 'zma', 'Zm00001eb199990' => 'zma', 'Zm00001eb368180' => 'zma', 'Zm00001eb382470' => 'zma' ), 'gf_id' => 'HOM05D001576', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001576' ), 'data_identifier' => 'HOM05D001576', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001576', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '406', 'num_species' => '29' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'Aqoxy1G01456' => 'aox', 'Aqoxy1G02949' => 'aox', 'Aqoxy3G01274' => 'aox', 'Aqoxy3G02110' => 'aox', 'Aqoxy3G02268' => 'aox', 'Aqoxy5G02702' => 'aox', 'Aqoxy5G02988' => 'aox', 'Aqoxy5G03427' => 'aox', 'Aqoxy6G02363' => 'aox', 'Atru.chr1.3225' => 'acertr', 'Atru.chr8.1198' => 'acertr', 'Atru.chr9.790' => 'acertr', 'CANSAT01G3197' => 'cansat', 'Ciclev10003979m.g' => 'ccl', 'Ciclev10017471m.g' => 'ccl', 'Ciclev10018206m.g' => 'ccl', 'Ciclev10033751m.g' => 'ccl', 'CiPaw.01G000900' => 'cil', 'CiPaw.01G001000' => 'cil', 'CiPaw.01G033500' => 'cil', 'CiPaw.01G060300' => 'cil', 'CiPaw.01G070200' => 'cil', 'CiPaw.01G075100' => 'cil', 'CiPaw.01G084700' => 'cil', 'CiPaw.01G087900' => 'cil', 'CiPaw.01G092600' => 'cil', 'CiPaw.01G097200' => 'cil', 'CiPaw.01G098300' => 'cil', 'CiPaw.01G110200' => 'cil', 'CiPaw.01G118700' => 'cil', 'CiPaw.01G121200' => 'cil', 'CiPaw.01G132500' => 'cil', 'CiPaw.01G146900' => 'cil', 'CiPaw.01G174000' => 'cil', 'CiPaw.01G179900' => 'cil', 'CiPaw.01G183400' => 'cil', 'CiPaw.01G240000' => 'cil', 'CiPaw.01G283500' => 'cil', 'CiPaw.01G307400' => 'cil', 'CiPaw.02G030800' => 'cil', 'CiPaw.02G047200' => 'cil', 'CiPaw.02G050500' => 'cil', 'CiPaw.02G069900' => 'cil', 'CiPaw.02G091600' => 'cil', 'CiPaw.02G095000' => 'cil', 'CiPaw.02G131900' => 'cil', 'CiPaw.03G043000' => 'cil', 'CiPaw.03G069900' => 'cil', 'CiPaw.03G088100' => 'cil', 'CiPaw.03G089300' => 'cil', 'CiPaw.03G093100' => 'cil', 'CiPaw.03G129800' => 'cil', 'CiPaw.03G131200' => 'cil', 'CiPaw.03G134500' => 'cil', 'CiPaw.03G152100' => 'cil', 'CiPaw.03G162700' => 'cil', 'CiPaw.03G172800' => 'cil', 'CiPaw.03G175800' => 'cil', 'CiPaw.03G181800' => 'cil', 'CiPaw.03G191400' => 'cil', 'CiPaw.03G198300' => 'cil', 'CiPaw.03G201300' => 'cil', 'CiPaw.03G224700' => 'cil', 'CiPaw.03G225000' => 'cil', 'CiPaw.04G065100' => 'cil', 'CiPaw.04G080400' => 'cil', 'CiPaw.04G113500' => 'cil', 'CiPaw.04G121900' => 'cil', 'CiPaw.04G144100' => 'cil', 'CiPaw.04G176500' => 'cil', 'CiPaw.05G086200' => 'cil', 'CiPaw.05G100200' => 'cil', 'CiPaw.05G114200' => 'cil', 'CiPaw.05G126800' => 'cil', 'CiPaw.05G228800' => 'cil', 'CiPaw.05G230600' => 'cil', 'CiPaw.05G236500' => 'cil', 'CiPaw.05G244800' => 'cil', 'CiPaw.06G026600' => 'cil', 'CiPaw.06G027900' => 'cil', 'CiPaw.06G051800' => 'cil', 'CiPaw.06G128500' => 'cil', 'CiPaw.06G165900' => 'cil', 'CiPaw.07G045400' => 'cil', 'CiPaw.07G048000' => 'cil', 'CiPaw.07G052000' => 'cil', 'CiPaw.07G073800' => 'cil', 'CiPaw.07G099700' => 'cil', 'CiPaw.07G108700' => 'cil', 'CiPaw.07G120000' => 'cil', 'CiPaw.07G134100' => 'cil', 'CiPaw.07G147000' => 'cil', 'CiPaw.07G149700' => 'cil', 'CiPaw.07G178300' => 'cil', 'CiPaw.07G184900' => 'cil', 'CiPaw.08G044500' => 'cil', 'CiPaw.08G046900' => 'cil', 'CiPaw.08G047300' => 'cil', 'CiPaw.08G115400' => 'cil', 'CiPaw.08G134700' => 'cil', 'CiPaw.08G157400' => 'cil', 'CiPaw.09G014300' => 'cil', 'CiPaw.09G088900' => 'cil', 'CiPaw.09G130900' => 'cil', 'CiPaw.09G133100' => 'cil', 'CiPaw.09G151300' => 'cil', 'CiPaw.09G172800' => 'cil', 'CiPaw.09G174900' => 'cil', 'CiPaw.09G175000' => 'cil', 'CiPaw.10G012800' => 'cil', 'CiPaw.10G028800' => 'cil', 'CiPaw.10G044700' => 'cil', 'CiPaw.10G067400' => 'cil', 'CiPaw.10G115900' => 'cil', 'CiPaw.10G126200' => 'cil', 'CiPaw.10G139700' => 'cil', 'CiPaw.10G155100' => 'cil', 'CiPaw.11G011300' => 'cil', 'CiPaw.11G025900' => 'cil', 'CiPaw.11G104100' => 'cil', 'CiPaw.11G142700' => 'cil', 'CiPaw.11G164500' => 'cil', 'CiPaw.11G189100' => 'cil', 'CiPaw.11G197100' => 'cil', 'CiPaw.12G006100' => 'cil', 'CiPaw.12G038500' => 'cil', 'CiPaw.12G041400' => 'cil', 'CiPaw.12G041600' => 'cil', 'CiPaw.12G051300' => 'cil', 'CiPaw.12G101800' => 'cil', 'CiPaw.12G107800' => 'cil', 'CiPaw.13G033200' => 'cil', 'CiPaw.13G129900' => 'cil', 'CiPaw.13G160200' => 'cil', 'CiPaw.14G018900' => 'cil', 'CiPaw.14G029000' => 'cil', 'CiPaw.14G031000' => 'cil', 'CiPaw.14G032000' => 'cil', 'CiPaw.14G032300' => 'cil', 'CiPaw.14G040600' => 'cil', 'CiPaw.14G060500' => 'cil', 'CiPaw.14G061500' => 'cil', 'CiPaw.14G077500' => 'cil', 'CiPaw.14G088300' => 'cil', 'CiPaw.14G108500' => 'cil', 'CiPaw.14G121300' => 'cil', 'CiPaw.14G133000' => 'cil', 'CiPaw.14G134600' => 'cil', 'CiPaw.15G027200' => 'cil', 'CiPaw.15G037700' => 'cil', 'CiPaw.15G050900' => 'cil', 'CiPaw.15G067200' => 'cil', 'CiPaw.15G072000' => 'cil', 'CiPaw.15G112900' => 'cil', 'CiPaw.15G133200' => 'cil', 'CiPaw.15G139500' => 'cil', 'CiPaw.15G155400' => 'cil', 'CiPaw.16G006000' => 'cil', 'CiPaw.16G013100' => 'cil', 'CiPaw.16G047100' => 'cil', 'CiPaw.16G048900' => 'cil', 'CiPaw.16G070300' => 'cil', 'CSS0000195' => 'camsi', 'CSS0001664' => 'camsi', 'CSS0002566' => 'camsi', 'CSS0003077' => 'camsi', 'CSS0004257' => 'camsi', 'CSS0004495' => 'camsi', 'CSS0004599' => 'camsi', 'CSS0004943' => 'camsi', 'CSS0005302' => 'camsi', 'CSS0006274' => 'camsi', 'CSS0006547' => 'camsi', 'CSS0006860' => 'camsi', 'CSS0008814' => 'camsi', 'CSS0008946' => 'camsi', 'CSS0009093' => 'camsi', 'CSS0010221' => 'camsi', 'CSS0010296' => 'camsi', 'CSS0010386' => 'camsi', 'CSS0010831' => 'camsi', 'CSS0011061' => 'camsi', 'CSS0012008' => 'camsi', 'CSS0012194' => 'camsi', 'CSS0013580' => 'camsi', 'CSS0014176' => 'camsi', 'CSS0014280' => 'camsi', 'CSS0014799' => 'camsi', 'CSS0015368' => 'camsi', 'CSS0017473' => 'camsi', 'CSS0019281' => 'camsi', 'CSS0021320' => 'camsi', 'CSS0021750' => 'camsi', 'CSS0023642' => 'camsi', 'CSS0023792' => 'camsi', 'CSS0031528' => 'camsi', 'CSS0033894' => 'camsi', 'CSS0034959' => 'camsi', 'CSS0035632' => 'camsi', 'CSS0038450' => 'camsi', 'CSS0039293' => 'camsi', 'CSS0041053' => 'camsi', 'CSS0041981' => 'camsi', 'CSS0042573' => 'camsi', 'CSS0042927' => 'camsi', 'CSS0047725' => 'camsi', 'CSS0049636' => 'camsi', 'CSS0050513' => 'camsi', 'DCAR_030203' => 'dca', 'Dinv07939' => 'din', 'FAN01G0456' => 'fan', 'FAN02G3001' => 'fan', 'FAN04G2781' => 'fan', 'FAN05G1385' => 'fan', 'FAN05G3062' => 'fan', 'FAN08G2267' => 'fan', 'FAN10G0481' => 'fan', 'FAN10G1257' => 'fan', 'FAN14G0954' => 'fan', 'FAN14G2347' => 'fan', 'FAN15G0187' => 'fan', 'FAN25G2214' => 'fan', 'FvH4_1g21031' => 'fve', 'FvH4_3g16231' => 'fve', 'FvH4_3g26413' => 'fve', 'FvH4_3g29014' => 'fve', 'FvH4_3g31921' => 'fve', 'FvH4_4g19882' => 'fve', 'FvH4_5g21960' => 'fve', 'FvH4_5g29683' => 'fve', 'FvH4_7g13271' => 'fve', 'Glyma.01G062500' => 'gma', 'Glyma.07G140900' => 'gma', 'Glyma.09G140900' => 'gma', 'Glyma.12G112700' => 'gma', 'Glyma.17G168800' => 'gma', 'HanXRQChr01g0027001' => 'han', 'HanXRQChr04g0120511' => 'han', 'HanXRQChr08g0232381' => 'han', 'HanXRQChr09g0265661' => 'han', 'HanXRQChr13g0416031' => 'han', 'Haze_05835' => 'cav', 'Haze_06597' => 'cav', 'Haze_07921' => 'cav', 'Haze_08599' => 'cav', 'Haze_10686' => 'cav', 'Haze_12994' => 'cav', 'Haze_13466' => 'cav', 'Haze_16101' => 'cav', 'Haze_17766' => 'cav', 'Haze_18456' => 'cav', 'Haze_20229' => 'cav', 'Hma1.2p1_0324F.1_g125640' => 'hma', 'Hma1.2p1_0733F.1_g210230' => 'hma', 'Hma1.2p1_0921F.1_g236870' => 'hma', 'Hma1.2p1_1313F.1_g274940' => 'hma', 'Hma1.2p1_3059F.1_g332230' => 'hma', 'Hund15925' => 'sun', 'Hund19562' => 'sun', 'Hund21925' => 'sun', 'MD03G1177400' => 'mdo', 'MD07G1026100' => 'mdo', 'MD17G1218600' => 'mdo', 'Medtr0867s0010' => 'mtr', 'Medtr6g081150' => 'mtr', 'Os01g0527900' => 'osa', 'Os02g0463725' => 'osa', 'Os02g0785600' => 'osa', 'Os03g0433733' => 'osa', 'Os04g0286500' => 'osa', 'Os05g0227800' => 'osa', 'Os06g0521000' => 'osa', 'Os06g0635500' => 'osa', 'Os06g0660650' => 'osa', 'Os07g0554400' => 'osa', 'Os08g0225900' => 'osa', 'Os08g0561000' => 'osa', 'Os09g0241700' => 'osa', 'Os09g0351900' => 'osa', 'Os11g0220700' => 'osa', 'Os11g0282700' => 'osa', 'Os12g0169300' => 'osa', 'Os12g0228500' => 'osa', 'Os12g0543800' => 'osa', 'PGR044G1547' => 'pgr', 'Potri.005G239150' => 'ptr', 'Potri.010G014250' => 'ptr', 'Prupe.1G172500' => 'ppe', 'Prupe.1G196800' => 'ppe', 'Prupe.1G279700' => 'ppe', 'Prupe.2G026400' => 'ppe', 'Prupe.3G094000' => 'ppe', 'Prupe.4G287300' => 'ppe', 'QL01p022166' => 'qlo', 'QL01p051890' => 'qlo', 'QL02p009469' => 'qlo', 'QL02p046053' => 'qlo', 'QL02p057958' => 'qlo', 'QL02p093127' => 'qlo', 'QL03p006855' => 'qlo', 'QL03p071586' => 'qlo', 'QL04p000022' => 'qlo', 'QL04p000024' => 'qlo', 'QL04p003192' => 'qlo', 'QL05p011416' => 'qlo', 'QL06p039590' => 'qlo', 'QL06p052750' => 'qlo', 'QL06p053821' => 'qlo', 'QL07p025287' => 'qlo', 'QL09p033218' => 'qlo', 'QL09p040841' => 'qlo', 'QL10p020337' => 'qlo', 'QL10p027209' => 'qlo', 'QL10p027969' => 'qlo', 'QL10p048988' => 'qlo', 'QL11p001241' => 'qlo', 'QL11p028487' => 'qlo', 'RcHm_v2.0_Chr2g0105031' => 'rch', 'RcHm_v2.0_Chr2g0117811' => 'rch', 'RcHm_v2.0_Chr6g0270241' => 'rch', 'RcHm_v2.0_Chr7g0215961' => 'rch', 'RcHm_v2.0_Chr7g0231991' => 'rch', 'Rhsim01G0041500' => 'rsi', 'Rhsim01G0115000' => 'rsi', 'Rhsim01G0115400' => 'rsi', 'Rhsim01G0133600' => 'rsi', 'Rhsim01G0159900' => 'rsi', 'Rhsim02G0189400' => 'rsi', 'Rhsim03G0135600' => 'rsi', 'Rhsim03G0149900' => 'rsi', 'Rhsim04G0125600' => 'rsi', 'Rhsim05G0091700' => 'rsi', 'Rhsim05G0092900' => 'rsi', 'Rhsim06G0075000' => 'rsi', 'Rhsim07G0066400' => 'rsi', 'Rhsim07G0156400' => 'rsi', 'Rhsim07G0182200' => 'rsi', 'Rhsim07G0182300' => 'rsi', 'Rhsim08G0180400' => 'rsi', 'Rhsim09G0056800' => 'rsi', 'Rhsim10G0153300' => 'rsi', 'Rhsim11G0012700' => 'rsi', 'Rhsim12G0031800' => 'rsi', 'Rhsim12G0055400' => 'rsi', 'Rhsim12G0091400' => 'rsi', 'Rhsim13G0070800' => 'rsi', 'Rhsim13G0193300' => 'rsi', 'RhsimUnG0111600' => 'rsi', 'RhsimUnG0137500' => 'rsi', 'RhsimUnG0172900' => 'rsi', 'SGA_v2.0_scaffold11G05878' => 'sas', 'SGA_v2.0_scaffold167G38458' => 'sas', 'SGA_v2.0_scaffold19G08588' => 'sas', 'SGA_v2.0_scaffold239G43990' => 'sas', 'SGA_v2.0_scaffold260G45865' => 'sas', 'SGA_v2.0_scaffold309G48177' => 'sas', 'SGA_v2.0_scaffold76G25122' => 'sas', 'SGA_v2.0_scaffold85G26708' => 'sas', 'SHI13914' => 'shi', 'SHI30402' => 'shi', 'TWI09G0020' => 'twi', 'TWI09G0456' => 'twi', 'TWI09G1572' => 'twi', 'TWI12G0266' => 'twi', 'TWI12G1451' => 'twi', 'TWI14G0851' => 'twi', 'TWI15G0796' => 'twi', 'TWI18G0820' => 'twi', 'TWI18G1152' => 'twi', 'TWI23G0007' => 'twi', 'TWI23G0314' => 'twi', 'TWI31G0674' => 'twi', 'TWI31G0938' => 'twi', 'TWI34G0641' => 'twi', 'TWI34G1527' => 'twi', 'TWI36G0193' => 'twi', 'TWI36G0405' => 'twi', 'TWI38G0892' => 'twi', 'TWI38G0936' => 'twi', 'TWI38G2218' => 'twi', 'TWI53G0679' => 'twi', 'TWI53G0863' => 'twi', 'TWI53G1133' => 'twi', 'TWI60G0823' => 'twi', 'TWI63G0919' => 'twi', 'TWI63G1436' => 'twi', 'TWI73G0140' => 'twi', 'TWI73G0419' => 'twi', 'TWI73G0420' => 'twi', 'TWI73G1276' => 'twi', 'TWI74G0405' => 'twi', 'TWI74G0837' => 'twi', 'TWI75G0594' => 'twi', 'TWI75G1615' => 'twi', 'TWI77G0816' => 'twi', 'vmacro03831' => 'vma', 'vmacro13746' => 'vma', 'vmacro16089' => 'vma', 'vmacro22863' => 'vma', 'Zm00001eb085790' => 'zma', 'Zm00001eb114250' => 'zma', 'Zm00001eb138070' => 'zma', 'Zm00001eb167560' => 'zma', 'Zm00001eb199990' => 'zma', 'Zm00001eb368180' => 'zma', 'Zm00001eb382470' => 'zma' ) $gf_id = 'HOM05D001576' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001576' ) $data_identifier = 'HOM05D001576' $data_type = 'gf_id' $species_gene_counts = array( 'aox' => (int) 9, 'acertr' => (int) 3, 'cansat' => (int) 1, 'ccl' => (int) 4, 'cil' => (int) 145, 'camsi' => (int) 46, 'dca' => (int) 1, 'din' => (int) 1, 'fan' => (int) 12, 'fve' => (int) 9, 'gma' => (int) 5, 'han' => (int) 5, 'cav' => (int) 11, 'hma' => (int) 5, 'sun' => (int) 3, 'mdo' => (int) 3, 'mtr' => (int) 2, 'osa' => (int) 19, 'pgr' => (int) 1, 'ptr' => (int) 2, 'ppe' => (int) 6, 'qlo' => (int) 24, 'rch' => (int) 5, 'rsi' => (int) 28, 'sas' => (int) 8, 'shi' => (int) 2, 'twi' => (int) 35, 'vma' => (int) 4, 'zma' => (int) 7 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb382470' $species_info = array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ) $local_species = 'shi' $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' => 'HOM05D001576', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '406', 'num_species' => '29' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'Aqoxy1G01456' => 'aox', 'Aqoxy1G02949' => 'aox', 'Aqoxy3G01274' => 'aox', 'Aqoxy3G02110' => 'aox', 'Aqoxy3G02268' => 'aox', 'Aqoxy5G02702' => 'aox', 'Aqoxy5G02988' => 'aox', 'Aqoxy5G03427' => 'aox', 'Aqoxy6G02363' => 'aox', 'Atru.chr1.3225' => 'acertr', 'Atru.chr8.1198' => 'acertr', 'Atru.chr9.790' => 'acertr', 'CANSAT01G3197' => 'cansat', 'Ciclev10003979m.g' => 'ccl', 'Ciclev10017471m.g' => 'ccl', 'Ciclev10018206m.g' => 'ccl', 'Ciclev10033751m.g' => 'ccl', 'CiPaw.01G000900' => 'cil', 'CiPaw.01G001000' => 'cil', 'CiPaw.01G033500' => 'cil', 'CiPaw.01G060300' => 'cil', 'CiPaw.01G070200' => 'cil', 'CiPaw.01G075100' => 'cil', 'CiPaw.01G084700' => 'cil', 'CiPaw.01G087900' => 'cil', 'CiPaw.01G092600' => 'cil', 'CiPaw.01G097200' => 'cil', 'CiPaw.01G098300' => 'cil', 'CiPaw.01G110200' => 'cil', 'CiPaw.01G118700' => 'cil', 'CiPaw.01G121200' => 'cil', 'CiPaw.01G132500' => 'cil', 'CiPaw.01G146900' => 'cil', 'CiPaw.01G174000' => 'cil', 'CiPaw.01G179900' => 'cil', 'CiPaw.01G183400' => 'cil', 'CiPaw.01G240000' => 'cil', 'CiPaw.01G283500' => 'cil', 'CiPaw.01G307400' => 'cil', 'CiPaw.02G030800' => 'cil', 'CiPaw.02G047200' => 'cil', 'CiPaw.02G050500' => 'cil', 'CiPaw.02G069900' => 'cil', 'CiPaw.02G091600' => 'cil', 'CiPaw.02G095000' => 'cil', 'CiPaw.02G131900' => 'cil', 'CiPaw.03G043000' => 'cil', 'CiPaw.03G069900' => 'cil', 'CiPaw.03G088100' => 'cil', 'CiPaw.03G089300' => 'cil', 'CiPaw.03G093100' => 'cil', 'CiPaw.03G129800' => 'cil', 'CiPaw.03G131200' => 'cil', 'CiPaw.03G134500' => 'cil', 'CiPaw.03G152100' => 'cil', 'CiPaw.03G162700' => 'cil', 'CiPaw.03G172800' => 'cil', 'CiPaw.03G175800' => 'cil', 'CiPaw.03G181800' => 'cil', 'CiPaw.03G191400' => 'cil', 'CiPaw.03G198300' => 'cil', 'CiPaw.03G201300' => 'cil', 'CiPaw.03G224700' => 'cil', 'CiPaw.03G225000' => 'cil', 'CiPaw.04G065100' => 'cil', 'CiPaw.04G080400' => 'cil', 'CiPaw.04G113500' => 'cil', 'CiPaw.04G121900' => 'cil', 'CiPaw.04G144100' => 'cil', 'CiPaw.04G176500' => 'cil', 'CiPaw.05G086200' => 'cil', 'CiPaw.05G100200' => 'cil', 'CiPaw.05G114200' => 'cil', 'CiPaw.05G126800' => 'cil', 'CiPaw.05G228800' => 'cil', 'CiPaw.05G230600' => 'cil', 'CiPaw.05G236500' => 'cil', 'CiPaw.05G244800' => 'cil', 'CiPaw.06G026600' => 'cil', 'CiPaw.06G027900' => 'cil', 'CiPaw.06G051800' => 'cil', 'CiPaw.06G128500' => 'cil', 'CiPaw.06G165900' => 'cil', 'CiPaw.07G045400' => 'cil', 'CiPaw.07G048000' => 'cil', 'CiPaw.07G052000' => 'cil', 'CiPaw.07G073800' => 'cil', 'CiPaw.07G099700' => 'cil', 'CiPaw.07G108700' => 'cil', 'CiPaw.07G120000' => 'cil', 'CiPaw.07G134100' => 'cil', 'CiPaw.07G147000' => 'cil', 'CiPaw.07G149700' => 'cil', 'CiPaw.07G178300' => 'cil', 'CiPaw.07G184900' => 'cil', 'CiPaw.08G044500' => 'cil', 'CiPaw.08G046900' => 'cil', 'CiPaw.08G047300' => 'cil', 'CiPaw.08G115400' => 'cil', 'CiPaw.08G134700' => 'cil', 'CiPaw.08G157400' => 'cil', 'CiPaw.09G014300' => 'cil', 'CiPaw.09G088900' => 'cil', 'CiPaw.09G130900' => 'cil', 'CiPaw.09G133100' => 'cil', 'CiPaw.09G151300' => 'cil', 'CiPaw.09G172800' => 'cil', 'CiPaw.09G174900' => 'cil', 'CiPaw.09G175000' => 'cil', 'CiPaw.10G012800' => 'cil', 'CiPaw.10G028800' => 'cil', 'CiPaw.10G044700' => 'cil', 'CiPaw.10G067400' => 'cil', 'CiPaw.10G115900' => 'cil', 'CiPaw.10G126200' => 'cil', 'CiPaw.10G139700' => 'cil', 'CiPaw.10G155100' => 'cil', 'CiPaw.11G011300' => 'cil', 'CiPaw.11G025900' => 'cil', 'CiPaw.11G104100' => 'cil', 'CiPaw.11G142700' => 'cil', 'CiPaw.11G164500' => 'cil', 'CiPaw.11G189100' => 'cil', 'CiPaw.11G197100' => 'cil', 'CiPaw.12G006100' => 'cil', 'CiPaw.12G038500' => 'cil', 'CiPaw.12G041400' => 'cil', 'CiPaw.12G041600' => 'cil', 'CiPaw.12G051300' => 'cil', 'CiPaw.12G101800' => 'cil', 'CiPaw.12G107800' => 'cil', 'CiPaw.13G033200' => 'cil', 'CiPaw.13G129900' => 'cil', 'CiPaw.13G160200' => 'cil', 'CiPaw.14G018900' => 'cil', 'CiPaw.14G029000' => 'cil', 'CiPaw.14G031000' => 'cil', 'CiPaw.14G032000' => 'cil', 'CiPaw.14G032300' => 'cil', 'CiPaw.14G040600' => 'cil', 'CiPaw.14G060500' => 'cil', 'CiPaw.14G061500' => 'cil', 'CiPaw.14G077500' => 'cil', 'CiPaw.14G088300' => 'cil', 'CiPaw.14G108500' => 'cil', 'CiPaw.14G121300' => 'cil', 'CiPaw.14G133000' => 'cil', 'CiPaw.14G134600' => 'cil', 'CiPaw.15G027200' => 'cil', 'CiPaw.15G037700' => 'cil', 'CiPaw.15G050900' => 'cil', 'CiPaw.15G067200' => 'cil', 'CiPaw.15G072000' => 'cil', 'CiPaw.15G112900' => 'cil', 'CiPaw.15G133200' => 'cil', 'CiPaw.15G139500' => 'cil', 'CiPaw.15G155400' => 'cil', 'CiPaw.16G006000' => 'cil', 'CiPaw.16G013100' => 'cil', 'CiPaw.16G047100' => 'cil', 'CiPaw.16G048900' => 'cil', 'CiPaw.16G070300' => 'cil', 'CSS0000195' => 'camsi', 'CSS0001664' => 'camsi', 'CSS0002566' => 'camsi', 'CSS0003077' => 'camsi', 'CSS0004257' => 'camsi', 'CSS0004495' => 'camsi', 'CSS0004599' => 'camsi', 'CSS0004943' => 'camsi', 'CSS0005302' => 'camsi', 'CSS0006274' => 'camsi', 'CSS0006547' => 'camsi', 'CSS0006860' => 'camsi', 'CSS0008814' => 'camsi', 'CSS0008946' => 'camsi', 'CSS0009093' => 'camsi', 'CSS0010221' => 'camsi', 'CSS0010296' => 'camsi', 'CSS0010386' => 'camsi', 'CSS0010831' => 'camsi', 'CSS0011061' => 'camsi', 'CSS0012008' => 'camsi', 'CSS0012194' => 'camsi', 'CSS0013580' => 'camsi', 'CSS0014176' => 'camsi', 'CSS0014280' => 'camsi', 'CSS0014799' => 'camsi', 'CSS0015368' => 'camsi', 'CSS0017473' => 'camsi', 'CSS0019281' => 'camsi', 'CSS0021320' => 'camsi', 'CSS0021750' => 'camsi', 'CSS0023642' => 'camsi', 'CSS0023792' => 'camsi', 'CSS0031528' => 'camsi', 'CSS0033894' => 'camsi', 'CSS0034959' => 'camsi', 'CSS0035632' => 'camsi', 'CSS0038450' => 'camsi', 'CSS0039293' => 'camsi', 'CSS0041053' => 'camsi', 'CSS0041981' => 'camsi', 'CSS0042573' => 'camsi', 'CSS0042927' => 'camsi', 'CSS0047725' => 'camsi', 'CSS0049636' => 'camsi', 'CSS0050513' => 'camsi', 'DCAR_030203' => 'dca', 'Dinv07939' => 'din', 'FAN01G0456' => 'fan', 'FAN02G3001' => 'fan', 'FAN04G2781' => 'fan', 'FAN05G1385' => 'fan', 'FAN05G3062' => 'fan', 'FAN08G2267' => 'fan', 'FAN10G0481' => 'fan', 'FAN10G1257' => 'fan', 'FAN14G0954' => 'fan', 'FAN14G2347' => 'fan', 'FAN15G0187' => 'fan', 'FAN25G2214' => 'fan', 'FvH4_1g21031' => 'fve', 'FvH4_3g16231' => 'fve', 'FvH4_3g26413' => 'fve', 'FvH4_3g29014' => 'fve', 'FvH4_3g31921' => 'fve', 'FvH4_4g19882' => 'fve', 'FvH4_5g21960' => 'fve', 'FvH4_5g29683' => 'fve', 'FvH4_7g13271' => 'fve', 'Glyma.01G062500' => 'gma', 'Glyma.07G140900' => 'gma', 'Glyma.09G140900' => 'gma', 'Glyma.12G112700' => 'gma', 'Glyma.17G168800' => 'gma', 'HanXRQChr01g0027001' => 'han', 'HanXRQChr04g0120511' => 'han', 'HanXRQChr08g0232381' => 'han', 'HanXRQChr09g0265661' => 'han', 'HanXRQChr13g0416031' => 'han', 'Haze_05835' => 'cav', 'Haze_06597' => 'cav', 'Haze_07921' => 'cav', 'Haze_08599' => 'cav', 'Haze_10686' => 'cav', 'Haze_12994' => 'cav', 'Haze_13466' => 'cav', 'Haze_16101' => 'cav', 'Haze_17766' => 'cav', 'Haze_18456' => 'cav', 'Haze_20229' => 'cav', 'Hma1.2p1_0324F.1_g125640' => 'hma', 'Hma1.2p1_0733F.1_g210230' => 'hma', 'Hma1.2p1_0921F.1_g236870' => 'hma', 'Hma1.2p1_1313F.1_g274940' => 'hma', 'Hma1.2p1_3059F.1_g332230' => 'hma', 'Hund15925' => 'sun', 'Hund19562' => 'sun', 'Hund21925' => 'sun', 'MD03G1177400' => 'mdo', 'MD07G1026100' => 'mdo', 'MD17G1218600' => 'mdo', 'Medtr0867s0010' => 'mtr', 'Medtr6g081150' => 'mtr', 'Os01g0527900' => 'osa', 'Os02g0463725' => 'osa', 'Os02g0785600' => 'osa', 'Os03g0433733' => 'osa', 'Os04g0286500' => 'osa', 'Os05g0227800' => 'osa', 'Os06g0521000' => 'osa', 'Os06g0635500' => 'osa', 'Os06g0660650' => 'osa', 'Os07g0554400' => 'osa', 'Os08g0225900' => 'osa', 'Os08g0561000' => 'osa', 'Os09g0241700' => 'osa', 'Os09g0351900' => 'osa', 'Os11g0220700' => 'osa', 'Os11g0282700' => 'osa', 'Os12g0169300' => 'osa', 'Os12g0228500' => 'osa', 'Os12g0543800' => 'osa', 'PGR044G1547' => 'pgr', 'Potri.005G239150' => 'ptr', 'Potri.010G014250' => 'ptr', 'Prupe.1G172500' => 'ppe', 'Prupe.1G196800' => 'ppe', 'Prupe.1G279700' => 'ppe', 'Prupe.2G026400' => 'ppe', 'Prupe.3G094000' => 'ppe', 'Prupe.4G287300' => 'ppe', 'QL01p022166' => 'qlo', 'QL01p051890' => 'qlo', 'QL02p009469' => 'qlo', 'QL02p046053' => 'qlo', 'QL02p057958' => 'qlo', 'QL02p093127' => 'qlo', 'QL03p006855' => 'qlo', 'QL03p071586' => 'qlo', 'QL04p000022' => 'qlo', 'QL04p000024' => 'qlo', 'QL04p003192' => 'qlo', 'QL05p011416' => 'qlo', 'QL06p039590' => 'qlo', 'QL06p052750' => 'qlo', 'QL06p053821' => 'qlo', 'QL07p025287' => 'qlo', 'QL09p033218' => 'qlo', 'QL09p040841' => 'qlo', 'QL10p020337' => 'qlo', 'QL10p027209' => 'qlo', 'QL10p027969' => 'qlo', 'QL10p048988' => 'qlo', 'QL11p001241' => 'qlo', 'QL11p028487' => 'qlo', 'RcHm_v2.0_Chr2g0105031' => 'rch', 'RcHm_v2.0_Chr2g0117811' => 'rch', 'RcHm_v2.0_Chr6g0270241' => 'rch', 'RcHm_v2.0_Chr7g0215961' => 'rch', 'RcHm_v2.0_Chr7g0231991' => 'rch', 'Rhsim01G0041500' => 'rsi', 'Rhsim01G0115000' => 'rsi', 'Rhsim01G0115400' => 'rsi', 'Rhsim01G0133600' => 'rsi', 'Rhsim01G0159900' => 'rsi', 'Rhsim02G0189400' => 'rsi', 'Rhsim03G0135600' => 'rsi', 'Rhsim03G0149900' => 'rsi', 'Rhsim04G0125600' => 'rsi', 'Rhsim05G0091700' => 'rsi', 'Rhsim05G0092900' => 'rsi', 'Rhsim06G0075000' => 'rsi', 'Rhsim07G0066400' => 'rsi', 'Rhsim07G0156400' => 'rsi', 'Rhsim07G0182200' => 'rsi', 'Rhsim07G0182300' => 'rsi', 'Rhsim08G0180400' => 'rsi', 'Rhsim09G0056800' => 'rsi', 'Rhsim10G0153300' => 'rsi', 'Rhsim11G0012700' => 'rsi', 'Rhsim12G0031800' => 'rsi', 'Rhsim12G0055400' => 'rsi', 'Rhsim12G0091400' => 'rsi', 'Rhsim13G0070800' => 'rsi', 'Rhsim13G0193300' => 'rsi', 'RhsimUnG0111600' => 'rsi', 'RhsimUnG0137500' => 'rsi', 'RhsimUnG0172900' => 'rsi', 'SGA_v2.0_scaffold11G05878' => 'sas', 'SGA_v2.0_scaffold167G38458' => 'sas', 'SGA_v2.0_scaffold19G08588' => 'sas', 'SGA_v2.0_scaffold239G43990' => 'sas', 'SGA_v2.0_scaffold260G45865' => 'sas', 'SGA_v2.0_scaffold309G48177' => 'sas', 'SGA_v2.0_scaffold76G25122' => 'sas', 'SGA_v2.0_scaffold85G26708' => 'sas', 'SHI13914' => 'shi', 'SHI30402' => 'shi', 'TWI09G0020' => 'twi', 'TWI09G0456' => 'twi', 'TWI09G1572' => 'twi', 'TWI12G0266' => 'twi', 'TWI12G1451' => 'twi', 'TWI14G0851' => 'twi', 'TWI15G0796' => 'twi', 'TWI18G0820' => 'twi', 'TWI18G1152' => 'twi', 'TWI23G0007' => 'twi', 'TWI23G0314' => 'twi', 'TWI31G0674' => 'twi', 'TWI31G0938' => 'twi', 'TWI34G0641' => 'twi', 'TWI34G1527' => 'twi', 'TWI36G0193' => 'twi', 'TWI36G0405' => 'twi', 'TWI38G0892' => 'twi', 'TWI38G0936' => 'twi', 'TWI38G2218' => 'twi', 'TWI53G0679' => 'twi', 'TWI53G0863' => 'twi', 'TWI53G1133' => 'twi', 'TWI60G0823' => 'twi', 'TWI63G0919' => 'twi', 'TWI63G1436' => 'twi', 'TWI73G0140' => 'twi', 'TWI73G0419' => 'twi', 'TWI73G0420' => 'twi', 'TWI73G1276' => 'twi', 'TWI74G0405' => 'twi', 'TWI74G0837' => 'twi', 'TWI75G0594' => 'twi', 'TWI75G1615' => 'twi', 'TWI77G0816' => 'twi', 'vmacro03831' => 'vma', 'vmacro13746' => 'vma', 'vmacro16089' => 'vma', 'vmacro22863' => 'vma', 'Zm00001eb085790' => 'zma', 'Zm00001eb114250' => 'zma', 'Zm00001eb138070' => 'zma', 'Zm00001eb167560' => 'zma', 'Zm00001eb199990' => 'zma', 'Zm00001eb368180' => 'zma', 'Zm00001eb382470' => 'zma' ), 'gf_id' => 'HOM05D001576', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001576' ), 'data_identifier' => 'HOM05D001576', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001576', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '406', 'num_species' => '29' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'Aqoxy1G01456' => 'aox', 'Aqoxy1G02949' => 'aox', 'Aqoxy3G01274' => 'aox', 'Aqoxy3G02110' => 'aox', 'Aqoxy3G02268' => 'aox', 'Aqoxy5G02702' => 'aox', 'Aqoxy5G02988' => 'aox', 'Aqoxy5G03427' => 'aox', 'Aqoxy6G02363' => 'aox', 'Atru.chr1.3225' => 'acertr', 'Atru.chr8.1198' => 'acertr', 'Atru.chr9.790' => 'acertr', 'CANSAT01G3197' => 'cansat', 'Ciclev10003979m.g' => 'ccl', 'Ciclev10017471m.g' => 'ccl', 'Ciclev10018206m.g' => 'ccl', 'Ciclev10033751m.g' => 'ccl', 'CiPaw.01G000900' => 'cil', 'CiPaw.01G001000' => 'cil', 'CiPaw.01G033500' => 'cil', 'CiPaw.01G060300' => 'cil', 'CiPaw.01G070200' => 'cil', 'CiPaw.01G075100' => 'cil', 'CiPaw.01G084700' => 'cil', 'CiPaw.01G087900' => 'cil', 'CiPaw.01G092600' => 'cil', 'CiPaw.01G097200' => 'cil', 'CiPaw.01G098300' => 'cil', 'CiPaw.01G110200' => 'cil', 'CiPaw.01G118700' => 'cil', 'CiPaw.01G121200' => 'cil', 'CiPaw.01G132500' => 'cil', 'CiPaw.01G146900' => 'cil', 'CiPaw.01G174000' => 'cil', 'CiPaw.01G179900' => 'cil', 'CiPaw.01G183400' => 'cil', 'CiPaw.01G240000' => 'cil', 'CiPaw.01G283500' => 'cil', 'CiPaw.01G307400' => 'cil', 'CiPaw.02G030800' => 'cil', 'CiPaw.02G047200' => 'cil', 'CiPaw.02G050500' => 'cil', 'CiPaw.02G069900' => 'cil', 'CiPaw.02G091600' => 'cil', 'CiPaw.02G095000' => 'cil', 'CiPaw.02G131900' => 'cil', 'CiPaw.03G043000' => 'cil', 'CiPaw.03G069900' => 'cil', 'CiPaw.03G088100' => 'cil', 'CiPaw.03G089300' => 'cil', 'CiPaw.03G093100' => 'cil', 'CiPaw.03G129800' => 'cil', 'CiPaw.03G131200' => 'cil', 'CiPaw.03G134500' => 'cil', 'CiPaw.03G152100' => 'cil', 'CiPaw.03G162700' => 'cil', 'CiPaw.03G172800' => 'cil', 'CiPaw.03G175800' => 'cil', 'CiPaw.03G181800' => 'cil', 'CiPaw.03G191400' => 'cil', 'CiPaw.03G198300' => 'cil', 'CiPaw.03G201300' => 'cil', 'CiPaw.03G224700' => 'cil', 'CiPaw.03G225000' => 'cil', 'CiPaw.04G065100' => 'cil', 'CiPaw.04G080400' => 'cil', 'CiPaw.04G113500' => 'cil', 'CiPaw.04G121900' => 'cil', 'CiPaw.04G144100' => 'cil', 'CiPaw.04G176500' => 'cil', 'CiPaw.05G086200' => 'cil', 'CiPaw.05G100200' => 'cil', 'CiPaw.05G114200' => 'cil', 'CiPaw.05G126800' => 'cil', 'CiPaw.05G228800' => 'cil', 'CiPaw.05G230600' => 'cil', 'CiPaw.05G236500' => 'cil', 'CiPaw.05G244800' => 'cil', 'CiPaw.06G026600' => 'cil', 'CiPaw.06G027900' => 'cil', 'CiPaw.06G051800' => 'cil', 'CiPaw.06G128500' => 'cil', 'CiPaw.06G165900' => 'cil', 'CiPaw.07G045400' => 'cil', 'CiPaw.07G048000' => 'cil', 'CiPaw.07G052000' => 'cil', 'CiPaw.07G073800' => 'cil', 'CiPaw.07G099700' => 'cil', 'CiPaw.07G108700' => 'cil', 'CiPaw.07G120000' => 'cil', 'CiPaw.07G134100' => 'cil', 'CiPaw.07G147000' => 'cil', 'CiPaw.07G149700' => 'cil', 'CiPaw.07G178300' => 'cil', 'CiPaw.07G184900' => 'cil', 'CiPaw.08G044500' => 'cil', 'CiPaw.08G046900' => 'cil', 'CiPaw.08G047300' => 'cil', 'CiPaw.08G115400' => 'cil', 'CiPaw.08G134700' => 'cil', 'CiPaw.08G157400' => 'cil', 'CiPaw.09G014300' => 'cil', 'CiPaw.09G088900' => 'cil', 'CiPaw.09G130900' => 'cil', 'CiPaw.09G133100' => 'cil', 'CiPaw.09G151300' => 'cil', 'CiPaw.09G172800' => 'cil', 'CiPaw.09G174900' => 'cil', 'CiPaw.09G175000' => 'cil', 'CiPaw.10G012800' => 'cil', 'CiPaw.10G028800' => 'cil', 'CiPaw.10G044700' => 'cil', 'CiPaw.10G067400' => 'cil', 'CiPaw.10G115900' => 'cil', 'CiPaw.10G126200' => 'cil', 'CiPaw.10G139700' => 'cil', 'CiPaw.10G155100' => 'cil', 'CiPaw.11G011300' => 'cil', 'CiPaw.11G025900' => 'cil', 'CiPaw.11G104100' => 'cil', 'CiPaw.11G142700' => 'cil', 'CiPaw.11G164500' => 'cil', 'CiPaw.11G189100' => 'cil', 'CiPaw.11G197100' => 'cil', 'CiPaw.12G006100' => 'cil', 'CiPaw.12G038500' => 'cil', 'CiPaw.12G041400' => 'cil', 'CiPaw.12G041600' => 'cil', 'CiPaw.12G051300' => 'cil', 'CiPaw.12G101800' => 'cil', 'CiPaw.12G107800' => 'cil', 'CiPaw.13G033200' => 'cil', 'CiPaw.13G129900' => 'cil', 'CiPaw.13G160200' => 'cil', 'CiPaw.14G018900' => 'cil', 'CiPaw.14G029000' => 'cil', 'CiPaw.14G031000' => 'cil', 'CiPaw.14G032000' => 'cil', 'CiPaw.14G032300' => 'cil', 'CiPaw.14G040600' => 'cil', 'CiPaw.14G060500' => 'cil', 'CiPaw.14G061500' => 'cil', 'CiPaw.14G077500' => 'cil', 'CiPaw.14G088300' => 'cil', 'CiPaw.14G108500' => 'cil', 'CiPaw.14G121300' => 'cil', 'CiPaw.14G133000' => 'cil', 'CiPaw.14G134600' => 'cil', 'CiPaw.15G027200' => 'cil', 'CiPaw.15G037700' => 'cil', 'CiPaw.15G050900' => 'cil', 'CiPaw.15G067200' => 'cil', 'CiPaw.15G072000' => 'cil', 'CiPaw.15G112900' => 'cil', 'CiPaw.15G133200' => 'cil', 'CiPaw.15G139500' => 'cil', 'CiPaw.15G155400' => 'cil', 'CiPaw.16G006000' => 'cil', 'CiPaw.16G013100' => 'cil', 'CiPaw.16G047100' => 'cil', 'CiPaw.16G048900' => 'cil', 'CiPaw.16G070300' => 'cil', 'CSS0000195' => 'camsi', 'CSS0001664' => 'camsi', 'CSS0002566' => 'camsi', 'CSS0003077' => 'camsi', 'CSS0004257' => 'camsi', 'CSS0004495' => 'camsi', 'CSS0004599' => 'camsi', 'CSS0004943' => 'camsi', 'CSS0005302' => 'camsi', 'CSS0006274' => 'camsi', 'CSS0006547' => 'camsi', 'CSS0006860' => 'camsi', 'CSS0008814' => 'camsi', 'CSS0008946' => 'camsi', 'CSS0009093' => 'camsi', 'CSS0010221' => 'camsi', 'CSS0010296' => 'camsi', 'CSS0010386' => 'camsi', 'CSS0010831' => 'camsi', 'CSS0011061' => 'camsi', 'CSS0012008' => 'camsi', 'CSS0012194' => 'camsi', 'CSS0013580' => 'camsi', 'CSS0014176' => 'camsi', 'CSS0014280' => 'camsi', 'CSS0014799' => 'camsi', 'CSS0015368' => 'camsi', 'CSS0017473' => 'camsi', 'CSS0019281' => 'camsi', 'CSS0021320' => 'camsi', 'CSS0021750' => 'camsi', 'CSS0023642' => 'camsi', 'CSS0023792' => 'camsi', 'CSS0031528' => 'camsi', 'CSS0033894' => 'camsi', 'CSS0034959' => 'camsi', 'CSS0035632' => 'camsi', 'CSS0038450' => 'camsi', 'CSS0039293' => 'camsi', 'CSS0041053' => 'camsi', 'CSS0041981' => 'camsi', 'CSS0042573' => 'camsi', 'CSS0042927' => 'camsi', 'CSS0047725' => 'camsi', 'CSS0049636' => 'camsi', 'CSS0050513' => 'camsi', 'DCAR_030203' => 'dca', 'Dinv07939' => 'din', 'FAN01G0456' => 'fan', 'FAN02G3001' => 'fan', 'FAN04G2781' => 'fan', 'FAN05G1385' => 'fan', 'FAN05G3062' => 'fan', 'FAN08G2267' => 'fan', 'FAN10G0481' => 'fan', 'FAN10G1257' => 'fan', 'FAN14G0954' => 'fan', 'FAN14G2347' => 'fan', 'FAN15G0187' => 'fan', 'FAN25G2214' => 'fan', 'FvH4_1g21031' => 'fve', 'FvH4_3g16231' => 'fve', 'FvH4_3g26413' => 'fve', 'FvH4_3g29014' => 'fve', 'FvH4_3g31921' => 'fve', 'FvH4_4g19882' => 'fve', 'FvH4_5g21960' => 'fve', 'FvH4_5g29683' => 'fve', 'FvH4_7g13271' => 'fve', 'Glyma.01G062500' => 'gma', 'Glyma.07G140900' => 'gma', 'Glyma.09G140900' => 'gma', 'Glyma.12G112700' => 'gma', 'Glyma.17G168800' => 'gma', 'HanXRQChr01g0027001' => 'han', 'HanXRQChr04g0120511' => 'han', 'HanXRQChr08g0232381' => 'han', 'HanXRQChr09g0265661' => 'han', 'HanXRQChr13g0416031' => 'han', 'Haze_05835' => 'cav', 'Haze_06597' => 'cav', 'Haze_07921' => 'cav', 'Haze_08599' => 'cav', 'Haze_10686' => 'cav', 'Haze_12994' => 'cav', 'Haze_13466' => 'cav', 'Haze_16101' => 'cav', 'Haze_17766' => 'cav', 'Haze_18456' => 'cav', 'Haze_20229' => 'cav', 'Hma1.2p1_0324F.1_g125640' => 'hma', 'Hma1.2p1_0733F.1_g210230' => 'hma', 'Hma1.2p1_0921F.1_g236870' => 'hma', 'Hma1.2p1_1313F.1_g274940' => 'hma', 'Hma1.2p1_3059F.1_g332230' => 'hma', 'Hund15925' => 'sun', 'Hund19562' => 'sun', 'Hund21925' => 'sun', 'MD03G1177400' => 'mdo', 'MD07G1026100' => 'mdo', 'MD17G1218600' => 'mdo', 'Medtr0867s0010' => 'mtr', 'Medtr6g081150' => 'mtr', 'Os01g0527900' => 'osa', 'Os02g0463725' => 'osa', 'Os02g0785600' => 'osa', 'Os03g0433733' => 'osa', 'Os04g0286500' => 'osa', 'Os05g0227800' => 'osa', 'Os06g0521000' => 'osa', 'Os06g0635500' => 'osa', 'Os06g0660650' => 'osa', 'Os07g0554400' => 'osa', 'Os08g0225900' => 'osa', 'Os08g0561000' => 'osa', 'Os09g0241700' => 'osa', 'Os09g0351900' => 'osa', 'Os11g0220700' => 'osa', 'Os11g0282700' => 'osa', 'Os12g0169300' => 'osa', 'Os12g0228500' => 'osa', 'Os12g0543800' => 'osa', 'PGR044G1547' => 'pgr', 'Potri.005G239150' => 'ptr', 'Potri.010G014250' => 'ptr', 'Prupe.1G172500' => 'ppe', 'Prupe.1G196800' => 'ppe', 'Prupe.1G279700' => 'ppe', 'Prupe.2G026400' => 'ppe', 'Prupe.3G094000' => 'ppe', 'Prupe.4G287300' => 'ppe', 'QL01p022166' => 'qlo', 'QL01p051890' => 'qlo', 'QL02p009469' => 'qlo', 'QL02p046053' => 'qlo', 'QL02p057958' => 'qlo', 'QL02p093127' => 'qlo', 'QL03p006855' => 'qlo', 'QL03p071586' => 'qlo', 'QL04p000022' => 'qlo', 'QL04p000024' => 'qlo', 'QL04p003192' => 'qlo', 'QL05p011416' => 'qlo', 'QL06p039590' => 'qlo', 'QL06p052750' => 'qlo', 'QL06p053821' => 'qlo', 'QL07p025287' => 'qlo', 'QL09p033218' => 'qlo', 'QL09p040841' => 'qlo', 'QL10p020337' => 'qlo', 'QL10p027209' => 'qlo', 'QL10p027969' => 'qlo', 'QL10p048988' => 'qlo', 'QL11p001241' => 'qlo', 'QL11p028487' => 'qlo', 'RcHm_v2.0_Chr2g0105031' => 'rch', 'RcHm_v2.0_Chr2g0117811' => 'rch', 'RcHm_v2.0_Chr6g0270241' => 'rch', 'RcHm_v2.0_Chr7g0215961' => 'rch', 'RcHm_v2.0_Chr7g0231991' => 'rch', 'Rhsim01G0041500' => 'rsi', 'Rhsim01G0115000' => 'rsi', 'Rhsim01G0115400' => 'rsi', 'Rhsim01G0133600' => 'rsi', 'Rhsim01G0159900' => 'rsi', 'Rhsim02G0189400' => 'rsi', 'Rhsim03G0135600' => 'rsi', 'Rhsim03G0149900' => 'rsi', 'Rhsim04G0125600' => 'rsi', 'Rhsim05G0091700' => 'rsi', 'Rhsim05G0092900' => 'rsi', 'Rhsim06G0075000' => 'rsi', 'Rhsim07G0066400' => 'rsi', 'Rhsim07G0156400' => 'rsi', 'Rhsim07G0182200' => 'rsi', 'Rhsim07G0182300' => 'rsi', 'Rhsim08G0180400' => 'rsi', 'Rhsim09G0056800' => 'rsi', 'Rhsim10G0153300' => 'rsi', 'Rhsim11G0012700' => 'rsi', 'Rhsim12G0031800' => 'rsi', 'Rhsim12G0055400' => 'rsi', 'Rhsim12G0091400' => 'rsi', 'Rhsim13G0070800' => 'rsi', 'Rhsim13G0193300' => 'rsi', 'RhsimUnG0111600' => 'rsi', 'RhsimUnG0137500' => 'rsi', 'RhsimUnG0172900' => 'rsi', 'SGA_v2.0_scaffold11G05878' => 'sas', 'SGA_v2.0_scaffold167G38458' => 'sas', 'SGA_v2.0_scaffold19G08588' => 'sas', 'SGA_v2.0_scaffold239G43990' => 'sas', 'SGA_v2.0_scaffold260G45865' => 'sas', 'SGA_v2.0_scaffold309G48177' => 'sas', 'SGA_v2.0_scaffold76G25122' => 'sas', 'SGA_v2.0_scaffold85G26708' => 'sas', 'SHI13914' => 'shi', 'SHI30402' => 'shi', 'TWI09G0020' => 'twi', 'TWI09G0456' => 'twi', 'TWI09G1572' => 'twi', 'TWI12G0266' => 'twi', 'TWI12G1451' => 'twi', 'TWI14G0851' => 'twi', 'TWI15G0796' => 'twi', 'TWI18G0820' => 'twi', 'TWI18G1152' => 'twi', 'TWI23G0007' => 'twi', 'TWI23G0314' => 'twi', 'TWI31G0674' => 'twi', 'TWI31G0938' => 'twi', 'TWI34G0641' => 'twi', 'TWI34G1527' => 'twi', 'TWI36G0193' => 'twi', 'TWI36G0405' => 'twi', 'TWI38G0892' => 'twi', 'TWI38G0936' => 'twi', 'TWI38G2218' => 'twi', 'TWI53G0679' => 'twi', 'TWI53G0863' => 'twi', 'TWI53G1133' => 'twi', 'TWI60G0823' => 'twi', 'TWI63G0919' => 'twi', 'TWI63G1436' => 'twi', 'TWI73G0140' => 'twi', 'TWI73G0419' => 'twi', 'TWI73G0420' => 'twi', 'TWI73G1276' => 'twi', 'TWI74G0405' => 'twi', 'TWI74G0837' => 'twi', 'TWI75G0594' => 'twi', 'TWI75G1615' => 'twi', 'TWI77G0816' => 'twi', 'vmacro03831' => 'vma', 'vmacro13746' => 'vma', 'vmacro16089' => 'vma', 'vmacro22863' => 'vma', 'Zm00001eb085790' => 'zma', 'Zm00001eb114250' => 'zma', 'Zm00001eb138070' => 'zma', 'Zm00001eb167560' => 'zma', 'Zm00001eb199990' => 'zma', 'Zm00001eb368180' => 'zma', 'Zm00001eb382470' => 'zma' ) $gf_id = 'HOM05D001576' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001576' ) $data_identifier = 'HOM05D001576' $data_type = 'gf_id' $species_gene_counts = array( 'aox' => (int) 9, 'acertr' => (int) 3, 'cansat' => (int) 1, 'ccl' => (int) 4, 'cil' => (int) 145, 'camsi' => (int) 46, 'dca' => (int) 1, 'din' => (int) 1, 'fan' => (int) 12, 'fve' => (int) 9, 'gma' => (int) 5, 'han' => (int) 5, 'cav' => (int) 11, 'hma' => (int) 5, 'sun' => (int) 3, 'mdo' => (int) 3, 'mtr' => (int) 2, 'osa' => (int) 19, 'pgr' => (int) 1, 'ptr' => (int) 2, 'ppe' => (int) 6, 'qlo' => (int) 24, 'rch' => (int) 5, 'rsi' => (int) 28, 'sas' => (int) 8, 'shi' => (int) 2, 'twi' => (int) 35, 'vma' => (int) 4, 'zma' => (int) 7 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb382470' $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' => 'HOM05D001576', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '406', 'num_species' => '29' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'Aqoxy1G01456' => 'aox', 'Aqoxy1G02949' => 'aox', 'Aqoxy3G01274' => 'aox', 'Aqoxy3G02110' => 'aox', 'Aqoxy3G02268' => 'aox', 'Aqoxy5G02702' => 'aox', 'Aqoxy5G02988' => 'aox', 'Aqoxy5G03427' => 'aox', 'Aqoxy6G02363' => 'aox', 'Atru.chr1.3225' => 'acertr', 'Atru.chr8.1198' => 'acertr', 'Atru.chr9.790' => 'acertr', 'CANSAT01G3197' => 'cansat', 'Ciclev10003979m.g' => 'ccl', 'Ciclev10017471m.g' => 'ccl', 'Ciclev10018206m.g' => 'ccl', 'Ciclev10033751m.g' => 'ccl', 'CiPaw.01G000900' => 'cil', 'CiPaw.01G001000' => 'cil', 'CiPaw.01G033500' => 'cil', 'CiPaw.01G060300' => 'cil', 'CiPaw.01G070200' => 'cil', 'CiPaw.01G075100' => 'cil', 'CiPaw.01G084700' => 'cil', 'CiPaw.01G087900' => 'cil', 'CiPaw.01G092600' => 'cil', 'CiPaw.01G097200' => 'cil', 'CiPaw.01G098300' => 'cil', 'CiPaw.01G110200' => 'cil', 'CiPaw.01G118700' => 'cil', 'CiPaw.01G121200' => 'cil', 'CiPaw.01G132500' => 'cil', 'CiPaw.01G146900' => 'cil', 'CiPaw.01G174000' => 'cil', 'CiPaw.01G179900' => 'cil', 'CiPaw.01G183400' => 'cil', 'CiPaw.01G240000' => 'cil', 'CiPaw.01G283500' => 'cil', 'CiPaw.01G307400' => 'cil', 'CiPaw.02G030800' => 'cil', 'CiPaw.02G047200' => 'cil', 'CiPaw.02G050500' => 'cil', 'CiPaw.02G069900' => 'cil', 'CiPaw.02G091600' => 'cil', 'CiPaw.02G095000' => 'cil', 'CiPaw.02G131900' => 'cil', 'CiPaw.03G043000' => 'cil', 'CiPaw.03G069900' => 'cil', 'CiPaw.03G088100' => 'cil', 'CiPaw.03G089300' => 'cil', 'CiPaw.03G093100' => 'cil', 'CiPaw.03G129800' => 'cil', 'CiPaw.03G131200' => 'cil', 'CiPaw.03G134500' => 'cil', 'CiPaw.03G152100' => 'cil', 'CiPaw.03G162700' => 'cil', 'CiPaw.03G172800' => 'cil', 'CiPaw.03G175800' => 'cil', 'CiPaw.03G181800' => 'cil', 'CiPaw.03G191400' => 'cil', 'CiPaw.03G198300' => 'cil', 'CiPaw.03G201300' => 'cil', 'CiPaw.03G224700' => 'cil', 'CiPaw.03G225000' => 'cil', 'CiPaw.04G065100' => 'cil', 'CiPaw.04G080400' => 'cil', 'CiPaw.04G113500' => 'cil', 'CiPaw.04G121900' => 'cil', 'CiPaw.04G144100' => 'cil', 'CiPaw.04G176500' => 'cil', 'CiPaw.05G086200' => 'cil', 'CiPaw.05G100200' => 'cil', 'CiPaw.05G114200' => 'cil', 'CiPaw.05G126800' => 'cil', 'CiPaw.05G228800' => 'cil', 'CiPaw.05G230600' => 'cil', 'CiPaw.05G236500' => 'cil', 'CiPaw.05G244800' => 'cil', 'CiPaw.06G026600' => 'cil', 'CiPaw.06G027900' => 'cil', 'CiPaw.06G051800' => 'cil', 'CiPaw.06G128500' => 'cil', 'CiPaw.06G165900' => 'cil', 'CiPaw.07G045400' => 'cil', 'CiPaw.07G048000' => 'cil', 'CiPaw.07G052000' => 'cil', 'CiPaw.07G073800' => 'cil', 'CiPaw.07G099700' => 'cil', 'CiPaw.07G108700' => 'cil', 'CiPaw.07G120000' => 'cil', 'CiPaw.07G134100' => 'cil', 'CiPaw.07G147000' => 'cil', 'CiPaw.07G149700' => 'cil', 'CiPaw.07G178300' => 'cil', 'CiPaw.07G184900' => 'cil', 'CiPaw.08G044500' => 'cil', 'CiPaw.08G046900' => 'cil', 'CiPaw.08G047300' => 'cil', 'CiPaw.08G115400' => 'cil', 'CiPaw.08G134700' => 'cil', 'CiPaw.08G157400' => 'cil', 'CiPaw.09G014300' => 'cil', 'CiPaw.09G088900' => 'cil', 'CiPaw.09G130900' => 'cil', 'CiPaw.09G133100' => 'cil', 'CiPaw.09G151300' => 'cil', 'CiPaw.09G172800' => 'cil', 'CiPaw.09G174900' => 'cil', 'CiPaw.09G175000' => 'cil', 'CiPaw.10G012800' => 'cil', 'CiPaw.10G028800' => 'cil', 'CiPaw.10G044700' => 'cil', 'CiPaw.10G067400' => 'cil', 'CiPaw.10G115900' => 'cil', 'CiPaw.10G126200' => 'cil', 'CiPaw.10G139700' => 'cil', 'CiPaw.10G155100' => 'cil', 'CiPaw.11G011300' => 'cil', 'CiPaw.11G025900' => 'cil', 'CiPaw.11G104100' => 'cil', 'CiPaw.11G142700' => 'cil', 'CiPaw.11G164500' => 'cil', 'CiPaw.11G189100' => 'cil', 'CiPaw.11G197100' => 'cil', 'CiPaw.12G006100' => 'cil', 'CiPaw.12G038500' => 'cil', 'CiPaw.12G041400' => 'cil', 'CiPaw.12G041600' => 'cil', 'CiPaw.12G051300' => 'cil', 'CiPaw.12G101800' => 'cil', 'CiPaw.12G107800' => 'cil', 'CiPaw.13G033200' => 'cil', 'CiPaw.13G129900' => 'cil', 'CiPaw.13G160200' => 'cil', 'CiPaw.14G018900' => 'cil', 'CiPaw.14G029000' => 'cil', 'CiPaw.14G031000' => 'cil', 'CiPaw.14G032000' => 'cil', 'CiPaw.14G032300' => 'cil', 'CiPaw.14G040600' => 'cil', 'CiPaw.14G060500' => 'cil', 'CiPaw.14G061500' => 'cil', 'CiPaw.14G077500' => 'cil', 'CiPaw.14G088300' => 'cil', 'CiPaw.14G108500' => 'cil', 'CiPaw.14G121300' => 'cil', 'CiPaw.14G133000' => 'cil', 'CiPaw.14G134600' => 'cil', 'CiPaw.15G027200' => 'cil', 'CiPaw.15G037700' => 'cil', 'CiPaw.15G050900' => 'cil', 'CiPaw.15G067200' => 'cil', 'CiPaw.15G072000' => 'cil', 'CiPaw.15G112900' => 'cil', 'CiPaw.15G133200' => 'cil', 'CiPaw.15G139500' => 'cil', 'CiPaw.15G155400' => 'cil', 'CiPaw.16G006000' => 'cil', 'CiPaw.16G013100' => 'cil', 'CiPaw.16G047100' => 'cil', 'CiPaw.16G048900' => 'cil', 'CiPaw.16G070300' => 'cil', 'CSS0000195' => 'camsi', 'CSS0001664' => 'camsi', 'CSS0002566' => 'camsi', 'CSS0003077' => 'camsi', 'CSS0004257' => 'camsi', 'CSS0004495' => 'camsi', 'CSS0004599' => 'camsi', 'CSS0004943' => 'camsi', 'CSS0005302' => 'camsi', 'CSS0006274' => 'camsi', 'CSS0006547' => 'camsi', 'CSS0006860' => 'camsi', 'CSS0008814' => 'camsi', 'CSS0008946' => 'camsi', 'CSS0009093' => 'camsi', 'CSS0010221' => 'camsi', 'CSS0010296' => 'camsi', 'CSS0010386' => 'camsi', 'CSS0010831' => 'camsi', 'CSS0011061' => 'camsi', 'CSS0012008' => 'camsi', 'CSS0012194' => 'camsi', 'CSS0013580' => 'camsi', 'CSS0014176' => 'camsi', 'CSS0014280' => 'camsi', 'CSS0014799' => 'camsi', 'CSS0015368' => 'camsi', 'CSS0017473' => 'camsi', 'CSS0019281' => 'camsi', 'CSS0021320' => 'camsi', 'CSS0021750' => 'camsi', 'CSS0023642' => 'camsi', 'CSS0023792' => 'camsi', 'CSS0031528' => 'camsi', 'CSS0033894' => 'camsi', 'CSS0034959' => 'camsi', 'CSS0035632' => 'camsi', 'CSS0038450' => 'camsi', 'CSS0039293' => 'camsi', 'CSS0041053' => 'camsi', 'CSS0041981' => 'camsi', 'CSS0042573' => 'camsi', 'CSS0042927' => 'camsi', 'CSS0047725' => 'camsi', 'CSS0049636' => 'camsi', 'CSS0050513' => 'camsi', 'DCAR_030203' => 'dca', 'Dinv07939' => 'din', 'FAN01G0456' => 'fan', 'FAN02G3001' => 'fan', 'FAN04G2781' => 'fan', 'FAN05G1385' => 'fan', 'FAN05G3062' => 'fan', 'FAN08G2267' => 'fan', 'FAN10G0481' => 'fan', 'FAN10G1257' => 'fan', 'FAN14G0954' => 'fan', 'FAN14G2347' => 'fan', 'FAN15G0187' => 'fan', 'FAN25G2214' => 'fan', 'FvH4_1g21031' => 'fve', 'FvH4_3g16231' => 'fve', 'FvH4_3g26413' => 'fve', 'FvH4_3g29014' => 'fve', 'FvH4_3g31921' => 'fve', 'FvH4_4g19882' => 'fve', 'FvH4_5g21960' => 'fve', 'FvH4_5g29683' => 'fve', 'FvH4_7g13271' => 'fve', 'Glyma.01G062500' => 'gma', 'Glyma.07G140900' => 'gma', 'Glyma.09G140900' => 'gma', 'Glyma.12G112700' => 'gma', 'Glyma.17G168800' => 'gma', 'HanXRQChr01g0027001' => 'han', 'HanXRQChr04g0120511' => 'han', 'HanXRQChr08g0232381' => 'han', 'HanXRQChr09g0265661' => 'han', 'HanXRQChr13g0416031' => 'han', 'Haze_05835' => 'cav', 'Haze_06597' => 'cav', 'Haze_07921' => 'cav', 'Haze_08599' => 'cav', 'Haze_10686' => 'cav', 'Haze_12994' => 'cav', 'Haze_13466' => 'cav', 'Haze_16101' => 'cav', 'Haze_17766' => 'cav', 'Haze_18456' => 'cav', 'Haze_20229' => 'cav', 'Hma1.2p1_0324F.1_g125640' => 'hma', 'Hma1.2p1_0733F.1_g210230' => 'hma', 'Hma1.2p1_0921F.1_g236870' => 'hma', 'Hma1.2p1_1313F.1_g274940' => 'hma', 'Hma1.2p1_3059F.1_g332230' => 'hma', 'Hund15925' => 'sun', 'Hund19562' => 'sun', 'Hund21925' => 'sun', 'MD03G1177400' => 'mdo', 'MD07G1026100' => 'mdo', 'MD17G1218600' => 'mdo', 'Medtr0867s0010' => 'mtr', 'Medtr6g081150' => 'mtr', 'Os01g0527900' => 'osa', 'Os02g0463725' => 'osa', 'Os02g0785600' => 'osa', 'Os03g0433733' => 'osa', 'Os04g0286500' => 'osa', 'Os05g0227800' => 'osa', 'Os06g0521000' => 'osa', 'Os06g0635500' => 'osa', 'Os06g0660650' => 'osa', 'Os07g0554400' => 'osa', 'Os08g0225900' => 'osa', 'Os08g0561000' => 'osa', 'Os09g0241700' => 'osa', 'Os09g0351900' => 'osa', 'Os11g0220700' => 'osa', 'Os11g0282700' => 'osa', 'Os12g0169300' => 'osa', 'Os12g0228500' => 'osa', 'Os12g0543800' => 'osa', 'PGR044G1547' => 'pgr', 'Potri.005G239150' => 'ptr', 'Potri.010G014250' => 'ptr', 'Prupe.1G172500' => 'ppe', 'Prupe.1G196800' => 'ppe', 'Prupe.1G279700' => 'ppe', 'Prupe.2G026400' => 'ppe', 'Prupe.3G094000' => 'ppe', 'Prupe.4G287300' => 'ppe', 'QL01p022166' => 'qlo', 'QL01p051890' => 'qlo', 'QL02p009469' => 'qlo', 'QL02p046053' => 'qlo', 'QL02p057958' => 'qlo', 'QL02p093127' => 'qlo', 'QL03p006855' => 'qlo', 'QL03p071586' => 'qlo', 'QL04p000022' => 'qlo', 'QL04p000024' => 'qlo', 'QL04p003192' => 'qlo', 'QL05p011416' => 'qlo', 'QL06p039590' => 'qlo', 'QL06p052750' => 'qlo', 'QL06p053821' => 'qlo', 'QL07p025287' => 'qlo', 'QL09p033218' => 'qlo', 'QL09p040841' => 'qlo', 'QL10p020337' => 'qlo', 'QL10p027209' => 'qlo', 'QL10p027969' => 'qlo', 'QL10p048988' => 'qlo', 'QL11p001241' => 'qlo', 'QL11p028487' => 'qlo', 'RcHm_v2.0_Chr2g0105031' => 'rch', 'RcHm_v2.0_Chr2g0117811' => 'rch', 'RcHm_v2.0_Chr6g0270241' => 'rch', 'RcHm_v2.0_Chr7g0215961' => 'rch', 'RcHm_v2.0_Chr7g0231991' => 'rch', 'Rhsim01G0041500' => 'rsi', 'Rhsim01G0115000' => 'rsi', 'Rhsim01G0115400' => 'rsi', 'Rhsim01G0133600' => 'rsi', 'Rhsim01G0159900' => 'rsi', 'Rhsim02G0189400' => 'rsi', 'Rhsim03G0135600' => 'rsi', 'Rhsim03G0149900' => 'rsi', 'Rhsim04G0125600' => 'rsi', 'Rhsim05G0091700' => 'rsi', 'Rhsim05G0092900' => 'rsi', 'Rhsim06G0075000' => 'rsi', 'Rhsim07G0066400' => 'rsi', 'Rhsim07G0156400' => 'rsi', 'Rhsim07G0182200' => 'rsi', 'Rhsim07G0182300' => 'rsi', 'Rhsim08G0180400' => 'rsi', 'Rhsim09G0056800' => 'rsi', 'Rhsim10G0153300' => 'rsi', 'Rhsim11G0012700' => 'rsi', 'Rhsim12G0031800' => 'rsi', 'Rhsim12G0055400' => 'rsi', 'Rhsim12G0091400' => 'rsi', 'Rhsim13G0070800' => 'rsi', 'Rhsim13G0193300' => 'rsi', 'RhsimUnG0111600' => 'rsi', 'RhsimUnG0137500' => 'rsi', 'RhsimUnG0172900' => 'rsi', 'SGA_v2.0_scaffold11G05878' => 'sas', 'SGA_v2.0_scaffold167G38458' => 'sas', 'SGA_v2.0_scaffold19G08588' => 'sas', 'SGA_v2.0_scaffold239G43990' => 'sas', 'SGA_v2.0_scaffold260G45865' => 'sas', 'SGA_v2.0_scaffold309G48177' => 'sas', 'SGA_v2.0_scaffold76G25122' => 'sas', 'SGA_v2.0_scaffold85G26708' => 'sas', 'SHI13914' => 'shi', 'SHI30402' => 'shi', 'TWI09G0020' => 'twi', 'TWI09G0456' => 'twi', 'TWI09G1572' => 'twi', 'TWI12G0266' => 'twi', 'TWI12G1451' => 'twi', 'TWI14G0851' => 'twi', 'TWI15G0796' => 'twi', 'TWI18G0820' => 'twi', 'TWI18G1152' => 'twi', 'TWI23G0007' => 'twi', 'TWI23G0314' => 'twi', 'TWI31G0674' => 'twi', 'TWI31G0938' => 'twi', 'TWI34G0641' => 'twi', 'TWI34G1527' => 'twi', 'TWI36G0193' => 'twi', 'TWI36G0405' => 'twi', 'TWI38G0892' => 'twi', 'TWI38G0936' => 'twi', 'TWI38G2218' => 'twi', 'TWI53G0679' => 'twi', 'TWI53G0863' => 'twi', 'TWI53G1133' => 'twi', 'TWI60G0823' => 'twi', 'TWI63G0919' => 'twi', 'TWI63G1436' => 'twi', 'TWI73G0140' => 'twi', 'TWI73G0419' => 'twi', 'TWI73G0420' => 'twi', 'TWI73G1276' => 'twi', 'TWI74G0405' => 'twi', 'TWI74G0837' => 'twi', 'TWI75G0594' => 'twi', 'TWI75G1615' => 'twi', 'TWI77G0816' => 'twi', 'vmacro03831' => 'vma', 'vmacro13746' => 'vma', 'vmacro16089' => 'vma', 'vmacro22863' => 'vma', 'Zm00001eb085790' => 'zma', 'Zm00001eb114250' => 'zma', 'Zm00001eb138070' => 'zma', 'Zm00001eb167560' => 'zma', 'Zm00001eb199990' => 'zma', 'Zm00001eb368180' => 'zma', 'Zm00001eb382470' => 'zma' ), 'gf_id' => 'HOM05D001576', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001576' ), 'data_identifier' => 'HOM05D001576', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001576', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '406', 'num_species' => '29' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'Aqoxy1G01456' => 'aox', 'Aqoxy1G02949' => 'aox', 'Aqoxy3G01274' => 'aox', 'Aqoxy3G02110' => 'aox', 'Aqoxy3G02268' => 'aox', 'Aqoxy5G02702' => 'aox', 'Aqoxy5G02988' => 'aox', 'Aqoxy5G03427' => 'aox', 'Aqoxy6G02363' => 'aox', 'Atru.chr1.3225' => 'acertr', 'Atru.chr8.1198' => 'acertr', 'Atru.chr9.790' => 'acertr', 'CANSAT01G3197' => 'cansat', 'Ciclev10003979m.g' => 'ccl', 'Ciclev10017471m.g' => 'ccl', 'Ciclev10018206m.g' => 'ccl', 'Ciclev10033751m.g' => 'ccl', 'CiPaw.01G000900' => 'cil', 'CiPaw.01G001000' => 'cil', 'CiPaw.01G033500' => 'cil', 'CiPaw.01G060300' => 'cil', 'CiPaw.01G070200' => 'cil', 'CiPaw.01G075100' => 'cil', 'CiPaw.01G084700' => 'cil', 'CiPaw.01G087900' => 'cil', 'CiPaw.01G092600' => 'cil', 'CiPaw.01G097200' => 'cil', 'CiPaw.01G098300' => 'cil', 'CiPaw.01G110200' => 'cil', 'CiPaw.01G118700' => 'cil', 'CiPaw.01G121200' => 'cil', 'CiPaw.01G132500' => 'cil', 'CiPaw.01G146900' => 'cil', 'CiPaw.01G174000' => 'cil', 'CiPaw.01G179900' => 'cil', 'CiPaw.01G183400' => 'cil', 'CiPaw.01G240000' => 'cil', 'CiPaw.01G283500' => 'cil', 'CiPaw.01G307400' => 'cil', 'CiPaw.02G030800' => 'cil', 'CiPaw.02G047200' => 'cil', 'CiPaw.02G050500' => 'cil', 'CiPaw.02G069900' => 'cil', 'CiPaw.02G091600' => 'cil', 'CiPaw.02G095000' => 'cil', 'CiPaw.02G131900' => 'cil', 'CiPaw.03G043000' => 'cil', 'CiPaw.03G069900' => 'cil', 'CiPaw.03G088100' => 'cil', 'CiPaw.03G089300' => 'cil', 'CiPaw.03G093100' => 'cil', 'CiPaw.03G129800' => 'cil', 'CiPaw.03G131200' => 'cil', 'CiPaw.03G134500' => 'cil', 'CiPaw.03G152100' => 'cil', 'CiPaw.03G162700' => 'cil', 'CiPaw.03G172800' => 'cil', 'CiPaw.03G175800' => 'cil', 'CiPaw.03G181800' => 'cil', 'CiPaw.03G191400' => 'cil', 'CiPaw.03G198300' => 'cil', 'CiPaw.03G201300' => 'cil', 'CiPaw.03G224700' => 'cil', 'CiPaw.03G225000' => 'cil', 'CiPaw.04G065100' => 'cil', 'CiPaw.04G080400' => 'cil', 'CiPaw.04G113500' => 'cil', 'CiPaw.04G121900' => 'cil', 'CiPaw.04G144100' => 'cil', 'CiPaw.04G176500' => 'cil', 'CiPaw.05G086200' => 'cil', 'CiPaw.05G100200' => 'cil', 'CiPaw.05G114200' => 'cil', 'CiPaw.05G126800' => 'cil', 'CiPaw.05G228800' => 'cil', 'CiPaw.05G230600' => 'cil', 'CiPaw.05G236500' => 'cil', 'CiPaw.05G244800' => 'cil', 'CiPaw.06G026600' => 'cil', 'CiPaw.06G027900' => 'cil', 'CiPaw.06G051800' => 'cil', 'CiPaw.06G128500' => 'cil', 'CiPaw.06G165900' => 'cil', 'CiPaw.07G045400' => 'cil', 'CiPaw.07G048000' => 'cil', 'CiPaw.07G052000' => 'cil', 'CiPaw.07G073800' => 'cil', 'CiPaw.07G099700' => 'cil', 'CiPaw.07G108700' => 'cil', 'CiPaw.07G120000' => 'cil', 'CiPaw.07G134100' => 'cil', 'CiPaw.07G147000' => 'cil', 'CiPaw.07G149700' => 'cil', 'CiPaw.07G178300' => 'cil', 'CiPaw.07G184900' => 'cil', 'CiPaw.08G044500' => 'cil', 'CiPaw.08G046900' => 'cil', 'CiPaw.08G047300' => 'cil', 'CiPaw.08G115400' => 'cil', 'CiPaw.08G134700' => 'cil', 'CiPaw.08G157400' => 'cil', 'CiPaw.09G014300' => 'cil', 'CiPaw.09G088900' => 'cil', 'CiPaw.09G130900' => 'cil', 'CiPaw.09G133100' => 'cil', 'CiPaw.09G151300' => 'cil', 'CiPaw.09G172800' => 'cil', 'CiPaw.09G174900' => 'cil', 'CiPaw.09G175000' => 'cil', 'CiPaw.10G012800' => 'cil', 'CiPaw.10G028800' => 'cil', 'CiPaw.10G044700' => 'cil', 'CiPaw.10G067400' => 'cil', 'CiPaw.10G115900' => 'cil', 'CiPaw.10G126200' => 'cil', 'CiPaw.10G139700' => 'cil', 'CiPaw.10G155100' => 'cil', 'CiPaw.11G011300' => 'cil', 'CiPaw.11G025900' => 'cil', 'CiPaw.11G104100' => 'cil', 'CiPaw.11G142700' => 'cil', 'CiPaw.11G164500' => 'cil', 'CiPaw.11G189100' => 'cil', 'CiPaw.11G197100' => 'cil', 'CiPaw.12G006100' => 'cil', 'CiPaw.12G038500' => 'cil', 'CiPaw.12G041400' => 'cil', 'CiPaw.12G041600' => 'cil', 'CiPaw.12G051300' => 'cil', 'CiPaw.12G101800' => 'cil', 'CiPaw.12G107800' => 'cil', 'CiPaw.13G033200' => 'cil', 'CiPaw.13G129900' => 'cil', 'CiPaw.13G160200' => 'cil', 'CiPaw.14G018900' => 'cil', 'CiPaw.14G029000' => 'cil', 'CiPaw.14G031000' => 'cil', 'CiPaw.14G032000' => 'cil', 'CiPaw.14G032300' => 'cil', 'CiPaw.14G040600' => 'cil', 'CiPaw.14G060500' => 'cil', 'CiPaw.14G061500' => 'cil', 'CiPaw.14G077500' => 'cil', 'CiPaw.14G088300' => 'cil', 'CiPaw.14G108500' => 'cil', 'CiPaw.14G121300' => 'cil', 'CiPaw.14G133000' => 'cil', 'CiPaw.14G134600' => 'cil', 'CiPaw.15G027200' => 'cil', 'CiPaw.15G037700' => 'cil', 'CiPaw.15G050900' => 'cil', 'CiPaw.15G067200' => 'cil', 'CiPaw.15G072000' => 'cil', 'CiPaw.15G112900' => 'cil', 'CiPaw.15G133200' => 'cil', 'CiPaw.15G139500' => 'cil', 'CiPaw.15G155400' => 'cil', 'CiPaw.16G006000' => 'cil', 'CiPaw.16G013100' => 'cil', 'CiPaw.16G047100' => 'cil', 'CiPaw.16G048900' => 'cil', 'CiPaw.16G070300' => 'cil', 'CSS0000195' => 'camsi', 'CSS0001664' => 'camsi', 'CSS0002566' => 'camsi', 'CSS0003077' => 'camsi', 'CSS0004257' => 'camsi', 'CSS0004495' => 'camsi', 'CSS0004599' => 'camsi', 'CSS0004943' => 'camsi', 'CSS0005302' => 'camsi', 'CSS0006274' => 'camsi', 'CSS0006547' => 'camsi', 'CSS0006860' => 'camsi', 'CSS0008814' => 'camsi', 'CSS0008946' => 'camsi', 'CSS0009093' => 'camsi', 'CSS0010221' => 'camsi', 'CSS0010296' => 'camsi', 'CSS0010386' => 'camsi', 'CSS0010831' => 'camsi', 'CSS0011061' => 'camsi', 'CSS0012008' => 'camsi', 'CSS0012194' => 'camsi', 'CSS0013580' => 'camsi', 'CSS0014176' => 'camsi', 'CSS0014280' => 'camsi', 'CSS0014799' => 'camsi', 'CSS0015368' => 'camsi', 'CSS0017473' => 'camsi', 'CSS0019281' => 'camsi', 'CSS0021320' => 'camsi', 'CSS0021750' => 'camsi', 'CSS0023642' => 'camsi', 'CSS0023792' => 'camsi', 'CSS0031528' => 'camsi', 'CSS0033894' => 'camsi', 'CSS0034959' => 'camsi', 'CSS0035632' => 'camsi', 'CSS0038450' => 'camsi', 'CSS0039293' => 'camsi', 'CSS0041053' => 'camsi', 'CSS0041981' => 'camsi', 'CSS0042573' => 'camsi', 'CSS0042927' => 'camsi', 'CSS0047725' => 'camsi', 'CSS0049636' => 'camsi', 'CSS0050513' => 'camsi', 'DCAR_030203' => 'dca', 'Dinv07939' => 'din', 'FAN01G0456' => 'fan', 'FAN02G3001' => 'fan', 'FAN04G2781' => 'fan', 'FAN05G1385' => 'fan', 'FAN05G3062' => 'fan', 'FAN08G2267' => 'fan', 'FAN10G0481' => 'fan', 'FAN10G1257' => 'fan', 'FAN14G0954' => 'fan', 'FAN14G2347' => 'fan', 'FAN15G0187' => 'fan', 'FAN25G2214' => 'fan', 'FvH4_1g21031' => 'fve', 'FvH4_3g16231' => 'fve', 'FvH4_3g26413' => 'fve', 'FvH4_3g29014' => 'fve', 'FvH4_3g31921' => 'fve', 'FvH4_4g19882' => 'fve', 'FvH4_5g21960' => 'fve', 'FvH4_5g29683' => 'fve', 'FvH4_7g13271' => 'fve', 'Glyma.01G062500' => 'gma', 'Glyma.07G140900' => 'gma', 'Glyma.09G140900' => 'gma', 'Glyma.12G112700' => 'gma', 'Glyma.17G168800' => 'gma', 'HanXRQChr01g0027001' => 'han', 'HanXRQChr04g0120511' => 'han', 'HanXRQChr08g0232381' => 'han', 'HanXRQChr09g0265661' => 'han', 'HanXRQChr13g0416031' => 'han', 'Haze_05835' => 'cav', 'Haze_06597' => 'cav', 'Haze_07921' => 'cav', 'Haze_08599' => 'cav', 'Haze_10686' => 'cav', 'Haze_12994' => 'cav', 'Haze_13466' => 'cav', 'Haze_16101' => 'cav', 'Haze_17766' => 'cav', 'Haze_18456' => 'cav', 'Haze_20229' => 'cav', 'Hma1.2p1_0324F.1_g125640' => 'hma', 'Hma1.2p1_0733F.1_g210230' => 'hma', 'Hma1.2p1_0921F.1_g236870' => 'hma', 'Hma1.2p1_1313F.1_g274940' => 'hma', 'Hma1.2p1_3059F.1_g332230' => 'hma', 'Hund15925' => 'sun', 'Hund19562' => 'sun', 'Hund21925' => 'sun', 'MD03G1177400' => 'mdo', 'MD07G1026100' => 'mdo', 'MD17G1218600' => 'mdo', 'Medtr0867s0010' => 'mtr', 'Medtr6g081150' => 'mtr', 'Os01g0527900' => 'osa', 'Os02g0463725' => 'osa', 'Os02g0785600' => 'osa', 'Os03g0433733' => 'osa', 'Os04g0286500' => 'osa', 'Os05g0227800' => 'osa', 'Os06g0521000' => 'osa', 'Os06g0635500' => 'osa', 'Os06g0660650' => 'osa', 'Os07g0554400' => 'osa', 'Os08g0225900' => 'osa', 'Os08g0561000' => 'osa', 'Os09g0241700' => 'osa', 'Os09g0351900' => 'osa', 'Os11g0220700' => 'osa', 'Os11g0282700' => 'osa', 'Os12g0169300' => 'osa', 'Os12g0228500' => 'osa', 'Os12g0543800' => 'osa', 'PGR044G1547' => 'pgr', 'Potri.005G239150' => 'ptr', 'Potri.010G014250' => 'ptr', 'Prupe.1G172500' => 'ppe', 'Prupe.1G196800' => 'ppe', 'Prupe.1G279700' => 'ppe', 'Prupe.2G026400' => 'ppe', 'Prupe.3G094000' => 'ppe', 'Prupe.4G287300' => 'ppe', 'QL01p022166' => 'qlo', 'QL01p051890' => 'qlo', 'QL02p009469' => 'qlo', 'QL02p046053' => 'qlo', 'QL02p057958' => 'qlo', 'QL02p093127' => 'qlo', 'QL03p006855' => 'qlo', 'QL03p071586' => 'qlo', 'QL04p000022' => 'qlo', 'QL04p000024' => 'qlo', 'QL04p003192' => 'qlo', 'QL05p011416' => 'qlo', 'QL06p039590' => 'qlo', 'QL06p052750' => 'qlo', 'QL06p053821' => 'qlo', 'QL07p025287' => 'qlo', 'QL09p033218' => 'qlo', 'QL09p040841' => 'qlo', 'QL10p020337' => 'qlo', 'QL10p027209' => 'qlo', 'QL10p027969' => 'qlo', 'QL10p048988' => 'qlo', 'QL11p001241' => 'qlo', 'QL11p028487' => 'qlo', 'RcHm_v2.0_Chr2g0105031' => 'rch', 'RcHm_v2.0_Chr2g0117811' => 'rch', 'RcHm_v2.0_Chr6g0270241' => 'rch', 'RcHm_v2.0_Chr7g0215961' => 'rch', 'RcHm_v2.0_Chr7g0231991' => 'rch', 'Rhsim01G0041500' => 'rsi', 'Rhsim01G0115000' => 'rsi', 'Rhsim01G0115400' => 'rsi', 'Rhsim01G0133600' => 'rsi', 'Rhsim01G0159900' => 'rsi', 'Rhsim02G0189400' => 'rsi', 'Rhsim03G0135600' => 'rsi', 'Rhsim03G0149900' => 'rsi', 'Rhsim04G0125600' => 'rsi', 'Rhsim05G0091700' => 'rsi', 'Rhsim05G0092900' => 'rsi', 'Rhsim06G0075000' => 'rsi', 'Rhsim07G0066400' => 'rsi', 'Rhsim07G0156400' => 'rsi', 'Rhsim07G0182200' => 'rsi', 'Rhsim07G0182300' => 'rsi', 'Rhsim08G0180400' => 'rsi', 'Rhsim09G0056800' => 'rsi', 'Rhsim10G0153300' => 'rsi', 'Rhsim11G0012700' => 'rsi', 'Rhsim12G0031800' => 'rsi', 'Rhsim12G0055400' => 'rsi', 'Rhsim12G0091400' => 'rsi', 'Rhsim13G0070800' => 'rsi', 'Rhsim13G0193300' => 'rsi', 'RhsimUnG0111600' => 'rsi', 'RhsimUnG0137500' => 'rsi', 'RhsimUnG0172900' => 'rsi', 'SGA_v2.0_scaffold11G05878' => 'sas', 'SGA_v2.0_scaffold167G38458' => 'sas', 'SGA_v2.0_scaffold19G08588' => 'sas', 'SGA_v2.0_scaffold239G43990' => 'sas', 'SGA_v2.0_scaffold260G45865' => 'sas', 'SGA_v2.0_scaffold309G48177' => 'sas', 'SGA_v2.0_scaffold76G25122' => 'sas', 'SGA_v2.0_scaffold85G26708' => 'sas', 'SHI13914' => 'shi', 'SHI30402' => 'shi', 'TWI09G0020' => 'twi', 'TWI09G0456' => 'twi', 'TWI09G1572' => 'twi', 'TWI12G0266' => 'twi', 'TWI12G1451' => 'twi', 'TWI14G0851' => 'twi', 'TWI15G0796' => 'twi', 'TWI18G0820' => 'twi', 'TWI18G1152' => 'twi', 'TWI23G0007' => 'twi', 'TWI23G0314' => 'twi', 'TWI31G0674' => 'twi', 'TWI31G0938' => 'twi', 'TWI34G0641' => 'twi', 'TWI34G1527' => 'twi', 'TWI36G0193' => 'twi', 'TWI36G0405' => 'twi', 'TWI38G0892' => 'twi', 'TWI38G0936' => 'twi', 'TWI38G2218' => 'twi', 'TWI53G0679' => 'twi', 'TWI53G0863' => 'twi', 'TWI53G1133' => 'twi', 'TWI60G0823' => 'twi', 'TWI63G0919' => 'twi', 'TWI63G1436' => 'twi', 'TWI73G0140' => 'twi', 'TWI73G0419' => 'twi', 'TWI73G0420' => 'twi', 'TWI73G1276' => 'twi', 'TWI74G0405' => 'twi', 'TWI74G0837' => 'twi', 'TWI75G0594' => 'twi', 'TWI75G1615' => 'twi', 'TWI77G0816' => 'twi', 'vmacro03831' => 'vma', 'vmacro13746' => 'vma', 'vmacro16089' => 'vma', 'vmacro22863' => 'vma', 'Zm00001eb085790' => 'zma', 'Zm00001eb114250' => 'zma', 'Zm00001eb138070' => 'zma', 'Zm00001eb167560' => 'zma', 'Zm00001eb199990' => 'zma', 'Zm00001eb368180' => 'zma', 'Zm00001eb382470' => 'zma' ) $gf_id = 'HOM05D001576' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001576' ) $data_identifier = 'HOM05D001576' $data_type = 'gf_id' $species_gene_counts = array( 'aox' => (int) 9, 'acertr' => (int) 3, 'cansat' => (int) 1, 'ccl' => (int) 4, 'cil' => (int) 145, 'camsi' => (int) 46, 'dca' => (int) 1, 'din' => (int) 1, 'fan' => (int) 12, 'fve' => (int) 9, 'gma' => (int) 5, 'han' => (int) 5, 'cav' => (int) 11, 'hma' => (int) 5, 'sun' => (int) 3, 'mdo' => (int) 3, 'mtr' => (int) 2, 'osa' => (int) 19, 'pgr' => (int) 1, 'ptr' => (int) 2, 'ppe' => (int) 6, 'qlo' => (int) 24, 'rch' => (int) 5, 'rsi' => (int) 28, 'sas' => (int) 8, 'shi' => (int) 2, 'twi' => (int) 35, 'vma' => (int) 4, 'zma' => (int) 7 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb382470' $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' => 'HOM05D001576', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '406', 'num_species' => '29' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'Aqoxy1G01456' => 'aox', 'Aqoxy1G02949' => 'aox', 'Aqoxy3G01274' => 'aox', 'Aqoxy3G02110' => 'aox', 'Aqoxy3G02268' => 'aox', 'Aqoxy5G02702' => 'aox', 'Aqoxy5G02988' => 'aox', 'Aqoxy5G03427' => 'aox', 'Aqoxy6G02363' => 'aox', 'Atru.chr1.3225' => 'acertr', 'Atru.chr8.1198' => 'acertr', 'Atru.chr9.790' => 'acertr', 'CANSAT01G3197' => 'cansat', 'Ciclev10003979m.g' => 'ccl', 'Ciclev10017471m.g' => 'ccl', 'Ciclev10018206m.g' => 'ccl', 'Ciclev10033751m.g' => 'ccl', 'CiPaw.01G000900' => 'cil', 'CiPaw.01G001000' => 'cil', 'CiPaw.01G033500' => 'cil', 'CiPaw.01G060300' => 'cil', 'CiPaw.01G070200' => 'cil', 'CiPaw.01G075100' => 'cil', 'CiPaw.01G084700' => 'cil', 'CiPaw.01G087900' => 'cil', 'CiPaw.01G092600' => 'cil', 'CiPaw.01G097200' => 'cil', 'CiPaw.01G098300' => 'cil', 'CiPaw.01G110200' => 'cil', 'CiPaw.01G118700' => 'cil', 'CiPaw.01G121200' => 'cil', 'CiPaw.01G132500' => 'cil', 'CiPaw.01G146900' => 'cil', 'CiPaw.01G174000' => 'cil', 'CiPaw.01G179900' => 'cil', 'CiPaw.01G183400' => 'cil', 'CiPaw.01G240000' => 'cil', 'CiPaw.01G283500' => 'cil', 'CiPaw.01G307400' => 'cil', 'CiPaw.02G030800' => 'cil', 'CiPaw.02G047200' => 'cil', 'CiPaw.02G050500' => 'cil', 'CiPaw.02G069900' => 'cil', 'CiPaw.02G091600' => 'cil', 'CiPaw.02G095000' => 'cil', 'CiPaw.02G131900' => 'cil', 'CiPaw.03G043000' => 'cil', 'CiPaw.03G069900' => 'cil', 'CiPaw.03G088100' => 'cil', 'CiPaw.03G089300' => 'cil', 'CiPaw.03G093100' => 'cil', 'CiPaw.03G129800' => 'cil', 'CiPaw.03G131200' => 'cil', 'CiPaw.03G134500' => 'cil', 'CiPaw.03G152100' => 'cil', 'CiPaw.03G162700' => 'cil', 'CiPaw.03G172800' => 'cil', 'CiPaw.03G175800' => 'cil', 'CiPaw.03G181800' => 'cil', 'CiPaw.03G191400' => 'cil', 'CiPaw.03G198300' => 'cil', 'CiPaw.03G201300' => 'cil', 'CiPaw.03G224700' => 'cil', 'CiPaw.03G225000' => 'cil', 'CiPaw.04G065100' => 'cil', 'CiPaw.04G080400' => 'cil', 'CiPaw.04G113500' => 'cil', 'CiPaw.04G121900' => 'cil', 'CiPaw.04G144100' => 'cil', 'CiPaw.04G176500' => 'cil', 'CiPaw.05G086200' => 'cil', 'CiPaw.05G100200' => 'cil', 'CiPaw.05G114200' => 'cil', 'CiPaw.05G126800' => 'cil', 'CiPaw.05G228800' => 'cil', 'CiPaw.05G230600' => 'cil', 'CiPaw.05G236500' => 'cil', 'CiPaw.05G244800' => 'cil', 'CiPaw.06G026600' => 'cil', 'CiPaw.06G027900' => 'cil', 'CiPaw.06G051800' => 'cil', 'CiPaw.06G128500' => 'cil', 'CiPaw.06G165900' => 'cil', 'CiPaw.07G045400' => 'cil', 'CiPaw.07G048000' => 'cil', 'CiPaw.07G052000' => 'cil', 'CiPaw.07G073800' => 'cil', 'CiPaw.07G099700' => 'cil', 'CiPaw.07G108700' => 'cil', 'CiPaw.07G120000' => 'cil', 'CiPaw.07G134100' => 'cil', 'CiPaw.07G147000' => 'cil', 'CiPaw.07G149700' => 'cil', 'CiPaw.07G178300' => 'cil', 'CiPaw.07G184900' => 'cil', 'CiPaw.08G044500' => 'cil', 'CiPaw.08G046900' => 'cil', 'CiPaw.08G047300' => 'cil', 'CiPaw.08G115400' => 'cil', 'CiPaw.08G134700' => 'cil', 'CiPaw.08G157400' => 'cil', 'CiPaw.09G014300' => 'cil', 'CiPaw.09G088900' => 'cil', 'CiPaw.09G130900' => 'cil', 'CiPaw.09G133100' => 'cil', 'CiPaw.09G151300' => 'cil', 'CiPaw.09G172800' => 'cil', 'CiPaw.09G174900' => 'cil', 'CiPaw.09G175000' => 'cil', 'CiPaw.10G012800' => 'cil', 'CiPaw.10G028800' => 'cil', 'CiPaw.10G044700' => 'cil', 'CiPaw.10G067400' => 'cil', 'CiPaw.10G115900' => 'cil', 'CiPaw.10G126200' => 'cil', 'CiPaw.10G139700' => 'cil', 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=> 'qlo', 'QL07p025287' => 'qlo', 'QL09p033218' => 'qlo', 'QL09p040841' => 'qlo', 'QL10p020337' => 'qlo', 'QL10p027209' => 'qlo', 'QL10p027969' => 'qlo', 'QL10p048988' => 'qlo', 'QL11p001241' => 'qlo', 'QL11p028487' => 'qlo', 'RcHm_v2.0_Chr2g0105031' => 'rch', 'RcHm_v2.0_Chr2g0117811' => 'rch', 'RcHm_v2.0_Chr6g0270241' => 'rch', 'RcHm_v2.0_Chr7g0215961' => 'rch', 'RcHm_v2.0_Chr7g0231991' => 'rch', 'Rhsim01G0041500' => 'rsi', 'Rhsim01G0115000' => 'rsi', 'Rhsim01G0115400' => 'rsi', 'Rhsim01G0133600' => 'rsi', 'Rhsim01G0159900' => 'rsi', 'Rhsim02G0189400' => 'rsi', 'Rhsim03G0135600' => 'rsi', 'Rhsim03G0149900' => 'rsi', 'Rhsim04G0125600' => 'rsi', 'Rhsim05G0091700' => 'rsi', 'Rhsim05G0092900' => 'rsi', 'Rhsim06G0075000' => 'rsi', 'Rhsim07G0066400' => 'rsi', 'Rhsim07G0156400' => 'rsi', 'Rhsim07G0182200' => 'rsi', 'Rhsim07G0182300' => 'rsi', 'Rhsim08G0180400' => 'rsi', 'Rhsim09G0056800' => 'rsi', 'Rhsim10G0153300' => 'rsi', 'Rhsim11G0012700' => 'rsi', 'Rhsim12G0031800' => 'rsi', 'Rhsim12G0055400' => 'rsi', 'Rhsim12G0091400' => 'rsi', 'Rhsim13G0070800' => 'rsi', 'Rhsim13G0193300' => 'rsi', 'RhsimUnG0111600' => 'rsi', 'RhsimUnG0137500' => 'rsi', 'RhsimUnG0172900' => 'rsi', 'SGA_v2.0_scaffold11G05878' => 'sas', 'SGA_v2.0_scaffold167G38458' => 'sas', 'SGA_v2.0_scaffold19G08588' => 'sas', 'SGA_v2.0_scaffold239G43990' => 'sas', 'SGA_v2.0_scaffold260G45865' => 'sas', 'SGA_v2.0_scaffold309G48177' => 'sas', 'SGA_v2.0_scaffold76G25122' => 'sas', 'SGA_v2.0_scaffold85G26708' => 'sas', 'SHI13914' => 'shi', 'SHI30402' => 'shi', 'TWI09G0020' => 'twi', 'TWI09G0456' => 'twi', 'TWI09G1572' => 'twi', 'TWI12G0266' => 'twi', 'TWI12G1451' => 'twi', 'TWI14G0851' => 'twi', 'TWI15G0796' => 'twi', 'TWI18G0820' => 'twi', 'TWI18G1152' => 'twi', 'TWI23G0007' => 'twi', 'TWI23G0314' => 'twi', 'TWI31G0674' => 'twi', 'TWI31G0938' => 'twi', 'TWI34G0641' => 'twi', 'TWI34G1527' => 'twi', 'TWI36G0193' => 'twi', 'TWI36G0405' => 'twi', 'TWI38G0892' => 'twi', 'TWI38G0936' => 'twi', 'TWI38G2218' => 'twi', 'TWI53G0679' => 'twi', 'TWI53G0863' => 'twi', 'TWI53G1133' => 'twi', 'TWI60G0823' => 'twi', 'TWI63G0919' => 'twi', 'TWI63G1436' => 'twi', 'TWI73G0140' => 'twi', 'TWI73G0419' => 'twi', 'TWI73G0420' => 'twi', 'TWI73G1276' => 'twi', 'TWI74G0405' => 'twi', 'TWI74G0837' => 'twi', 'TWI75G0594' => 'twi', 'TWI75G1615' => 'twi', 'TWI77G0816' => 'twi', 'vmacro03831' => 'vma', 'vmacro13746' => 'vma', 'vmacro16089' => 'vma', 'vmacro22863' => 'vma', 'Zm00001eb085790' => 'zma', 'Zm00001eb114250' => 'zma', 'Zm00001eb138070' => 'zma', 'Zm00001eb167560' => 'zma', 'Zm00001eb199990' => 'zma', 'Zm00001eb368180' => 'zma', 'Zm00001eb382470' => 'zma' ), 'gf_id' => 'HOM05D001576', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001576' ), 'data_identifier' => 'HOM05D001576', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001576', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '406', 'num_species' => '29' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'Aqoxy1G01456' => 'aox', 'Aqoxy1G02949' => 'aox', 'Aqoxy3G01274' => 'aox', 'Aqoxy3G02110' => 'aox', 'Aqoxy3G02268' => 'aox', 'Aqoxy5G02702' => 'aox', 'Aqoxy5G02988' => 'aox', 'Aqoxy5G03427' => 'aox', 'Aqoxy6G02363' => 'aox', 'Atru.chr1.3225' => 'acertr', 'Atru.chr8.1198' => 'acertr', 'Atru.chr9.790' => 'acertr', 'CANSAT01G3197' => 'cansat', 'Ciclev10003979m.g' => 'ccl', 'Ciclev10017471m.g' => 'ccl', 'Ciclev10018206m.g' => 'ccl', 'Ciclev10033751m.g' => 'ccl', 'CiPaw.01G000900' => 'cil', 'CiPaw.01G001000' => 'cil', 'CiPaw.01G033500' => 'cil', 'CiPaw.01G060300' => 'cil', 'CiPaw.01G070200' => 'cil', 'CiPaw.01G075100' => 'cil', 'CiPaw.01G084700' => 'cil', 'CiPaw.01G087900' => 'cil', 'CiPaw.01G092600' => 'cil', 'CiPaw.01G097200' => 'cil', 'CiPaw.01G098300' => 'cil', 'CiPaw.01G110200' => 'cil', 'CiPaw.01G118700' => 'cil', 'CiPaw.01G121200' => 'cil', 'CiPaw.01G132500' => 'cil', 'CiPaw.01G146900' => 'cil', 'CiPaw.01G174000' => 'cil', 'CiPaw.01G179900' => 'cil', 'CiPaw.01G183400' => 'cil', 'CiPaw.01G240000' => 'cil', 'CiPaw.01G283500' => 'cil', 'CiPaw.01G307400' => 'cil', 'CiPaw.02G030800' => 'cil', 'CiPaw.02G047200' => 'cil', 'CiPaw.02G050500' => 'cil', 'CiPaw.02G069900' => 'cil', 'CiPaw.02G091600' => 'cil', 'CiPaw.02G095000' => 'cil', 'CiPaw.02G131900' => 'cil', 'CiPaw.03G043000' => 'cil', 'CiPaw.03G069900' => 'cil', 'CiPaw.03G088100' => 'cil', 'CiPaw.03G089300' => 'cil', 'CiPaw.03G093100' => 'cil', 'CiPaw.03G129800' => 'cil', 'CiPaw.03G131200' => 'cil', 'CiPaw.03G134500' => 'cil', 'CiPaw.03G152100' => 'cil', 'CiPaw.03G162700' => 'cil', 'CiPaw.03G172800' => 'cil', 'CiPaw.03G175800' => 'cil', 'CiPaw.03G181800' => 'cil', 'CiPaw.03G191400' => 'cil', 'CiPaw.03G198300' => 'cil', 'CiPaw.03G201300' => 'cil', 'CiPaw.03G224700' => 'cil', 'CiPaw.03G225000' => 'cil', 'CiPaw.04G065100' => 'cil', 'CiPaw.04G080400' => 'cil', 'CiPaw.04G113500' => 'cil', 'CiPaw.04G121900' => 'cil', 'CiPaw.04G144100' => 'cil', 'CiPaw.04G176500' => 'cil', 'CiPaw.05G086200' => 'cil', 'CiPaw.05G100200' => 'cil', 'CiPaw.05G114200' => 'cil', 'CiPaw.05G126800' => 'cil', 'CiPaw.05G228800' => 'cil', 'CiPaw.05G230600' => 'cil', 'CiPaw.05G236500' => 'cil', 'CiPaw.05G244800' => 'cil', 'CiPaw.06G026600' => 'cil', 'CiPaw.06G027900' => 'cil', 'CiPaw.06G051800' => 'cil', 'CiPaw.06G128500' => 'cil', 'CiPaw.06G165900' => 'cil', 'CiPaw.07G045400' => 'cil', 'CiPaw.07G048000' => 'cil', 'CiPaw.07G052000' => 'cil', 'CiPaw.07G073800' => 'cil', 'CiPaw.07G099700' => 'cil', 'CiPaw.07G108700' => 'cil', 'CiPaw.07G120000' => 'cil', 'CiPaw.07G134100' => 'cil', 'CiPaw.07G147000' => 'cil', 'CiPaw.07G149700' => 'cil', 'CiPaw.07G178300' => 'cil', 'CiPaw.07G184900' => 'cil', 'CiPaw.08G044500' => 'cil', 'CiPaw.08G046900' => 'cil', 'CiPaw.08G047300' => 'cil', 'CiPaw.08G115400' => 'cil', 'CiPaw.08G134700' => 'cil', 'CiPaw.08G157400' => 'cil', 'CiPaw.09G014300' => 'cil', 'CiPaw.09G088900' => 'cil', 'CiPaw.09G130900' => 'cil', 'CiPaw.09G133100' => 'cil', 'CiPaw.09G151300' => 'cil', 'CiPaw.09G172800' => 'cil', 'CiPaw.09G174900' => 'cil', 'CiPaw.09G175000' => 'cil', 'CiPaw.10G012800' => 'cil', 'CiPaw.10G028800' => 'cil', 'CiPaw.10G044700' => 'cil', 'CiPaw.10G067400' => 'cil', 'CiPaw.10G115900' => 'cil', 'CiPaw.10G126200' => 'cil', 'CiPaw.10G139700' => 'cil', 'CiPaw.10G155100' => 'cil', 'CiPaw.11G011300' => 'cil', 'CiPaw.11G025900' => 'cil', 'CiPaw.11G104100' => 'cil', 'CiPaw.11G142700' => 'cil', 'CiPaw.11G164500' => 'cil', 'CiPaw.11G189100' => 'cil', 'CiPaw.11G197100' => 'cil', 'CiPaw.12G006100' => 'cil', 'CiPaw.12G038500' => 'cil', 'CiPaw.12G041400' => 'cil', 'CiPaw.12G041600' => 'cil', 'CiPaw.12G051300' => 'cil', 'CiPaw.12G101800' => 'cil', 'CiPaw.12G107800' => 'cil', 'CiPaw.13G033200' => 'cil', 'CiPaw.13G129900' => 'cil', 'CiPaw.13G160200' => 'cil', 'CiPaw.14G018900' => 'cil', 'CiPaw.14G029000' => 'cil', 'CiPaw.14G031000' => 'cil', 'CiPaw.14G032000' => 'cil', 'CiPaw.14G032300' => 'cil', 'CiPaw.14G040600' => 'cil', 'CiPaw.14G060500' => 'cil', 'CiPaw.14G061500' => 'cil', 'CiPaw.14G077500' => 'cil', 'CiPaw.14G088300' => 'cil', 'CiPaw.14G108500' => 'cil', 'CiPaw.14G121300' => 'cil', 'CiPaw.14G133000' => 'cil', 'CiPaw.14G134600' => 'cil', 'CiPaw.15G027200' => 'cil', 'CiPaw.15G037700' => 'cil', 'CiPaw.15G050900' => 'cil', 'CiPaw.15G067200' => 'cil', 'CiPaw.15G072000' => 'cil', 'CiPaw.15G112900' => 'cil', 'CiPaw.15G133200' => 'cil', 'CiPaw.15G139500' => 'cil', 'CiPaw.15G155400' => 'cil', 'CiPaw.16G006000' => 'cil', 'CiPaw.16G013100' => 'cil', 'CiPaw.16G047100' => 'cil', 'CiPaw.16G048900' => 'cil', 'CiPaw.16G070300' => 'cil', 'CSS0000195' => 'camsi', 'CSS0001664' => 'camsi', 'CSS0002566' => 'camsi', 'CSS0003077' => 'camsi', 'CSS0004257' => 'camsi', 'CSS0004495' => 'camsi', 'CSS0004599' => 'camsi', 'CSS0004943' => 'camsi', 'CSS0005302' => 'camsi', 'CSS0006274' => 'camsi', 'CSS0006547' => 'camsi', 'CSS0006860' => 'camsi', 'CSS0008814' => 'camsi', 'CSS0008946' => 'camsi', 'CSS0009093' => 'camsi', 'CSS0010221' => 'camsi', 'CSS0010296' => 'camsi', 'CSS0010386' => 'camsi', 'CSS0010831' => 'camsi', 'CSS0011061' => 'camsi', 'CSS0012008' => 'camsi', 'CSS0012194' => 'camsi', 'CSS0013580' => 'camsi', 'CSS0014176' => 'camsi', 'CSS0014280' => 'camsi', 'CSS0014799' => 'camsi', 'CSS0015368' => 'camsi', 'CSS0017473' => 'camsi', 'CSS0019281' => 'camsi', 'CSS0021320' => 'camsi', 'CSS0021750' => 'camsi', 'CSS0023642' => 'camsi', 'CSS0023792' => 'camsi', 'CSS0031528' => 'camsi', 'CSS0033894' => 'camsi', 'CSS0034959' => 'camsi', 'CSS0035632' => 'camsi', 'CSS0038450' => 'camsi', 'CSS0039293' => 'camsi', 'CSS0041053' => 'camsi', 'CSS0041981' => 'camsi', 'CSS0042573' => 'camsi', 'CSS0042927' => 'camsi', 'CSS0047725' => 'camsi', 'CSS0049636' => 'camsi', 'CSS0050513' => 'camsi', 'DCAR_030203' => 'dca', 'Dinv07939' => 'din', 'FAN01G0456' => 'fan', 'FAN02G3001' => 'fan', 'FAN04G2781' => 'fan', 'FAN05G1385' => 'fan', 'FAN05G3062' => 'fan', 'FAN08G2267' => 'fan', 'FAN10G0481' => 'fan', 'FAN10G1257' => 'fan', 'FAN14G0954' => 'fan', 'FAN14G2347' => 'fan', 'FAN15G0187' => 'fan', 'FAN25G2214' => 'fan', 'FvH4_1g21031' => 'fve', 'FvH4_3g16231' => 'fve', 'FvH4_3g26413' => 'fve', 'FvH4_3g29014' => 'fve', 'FvH4_3g31921' => 'fve', 'FvH4_4g19882' => 'fve', 'FvH4_5g21960' => 'fve', 'FvH4_5g29683' => 'fve', 'FvH4_7g13271' => 'fve', 'Glyma.01G062500' => 'gma', 'Glyma.07G140900' => 'gma', 'Glyma.09G140900' => 'gma', 'Glyma.12G112700' => 'gma', 'Glyma.17G168800' => 'gma', 'HanXRQChr01g0027001' => 'han', 'HanXRQChr04g0120511' => 'han', 'HanXRQChr08g0232381' => 'han', 'HanXRQChr09g0265661' => 'han', 'HanXRQChr13g0416031' => 'han', 'Haze_05835' => 'cav', 'Haze_06597' => 'cav', 'Haze_07921' => 'cav', 'Haze_08599' => 'cav', 'Haze_10686' => 'cav', 'Haze_12994' => 'cav', 'Haze_13466' => 'cav', 'Haze_16101' => 'cav', 'Haze_17766' => 'cav', 'Haze_18456' => 'cav', 'Haze_20229' => 'cav', 'Hma1.2p1_0324F.1_g125640' => 'hma', 'Hma1.2p1_0733F.1_g210230' => 'hma', 'Hma1.2p1_0921F.1_g236870' => 'hma', 'Hma1.2p1_1313F.1_g274940' => 'hma', 'Hma1.2p1_3059F.1_g332230' => 'hma', 'Hund15925' => 'sun', 'Hund19562' => 'sun', 'Hund21925' => 'sun', 'MD03G1177400' => 'mdo', 'MD07G1026100' => 'mdo', 'MD17G1218600' => 'mdo', 'Medtr0867s0010' => 'mtr', 'Medtr6g081150' => 'mtr', 'Os01g0527900' => 'osa', 'Os02g0463725' => 'osa', 'Os02g0785600' => 'osa', 'Os03g0433733' => 'osa', 'Os04g0286500' => 'osa', 'Os05g0227800' => 'osa', 'Os06g0521000' => 'osa', 'Os06g0635500' => 'osa', 'Os06g0660650' => 'osa', 'Os07g0554400' => 'osa', 'Os08g0225900' => 'osa', 'Os08g0561000' => 'osa', 'Os09g0241700' => 'osa', 'Os09g0351900' => 'osa', 'Os11g0220700' => 'osa', 'Os11g0282700' => 'osa', 'Os12g0169300' => 'osa', 'Os12g0228500' => 'osa', 'Os12g0543800' => 'osa', 'PGR044G1547' => 'pgr', 'Potri.005G239150' => 'ptr', 'Potri.010G014250' => 'ptr', 'Prupe.1G172500' => 'ppe', 'Prupe.1G196800' => 'ppe', 'Prupe.1G279700' => 'ppe', 'Prupe.2G026400' => 'ppe', 'Prupe.3G094000' => 'ppe', 'Prupe.4G287300' => 'ppe', 'QL01p022166' => 'qlo', 'QL01p051890' => 'qlo', 'QL02p009469' => 'qlo', 'QL02p046053' => 'qlo', 'QL02p057958' => 'qlo', 'QL02p093127' => 'qlo', 'QL03p006855' => 'qlo', 'QL03p071586' => 'qlo', 'QL04p000022' => 'qlo', 'QL04p000024' => 'qlo', 'QL04p003192' => 'qlo', 'QL05p011416' => 'qlo', 'QL06p039590' => 'qlo', 'QL06p052750' => 'qlo', 'QL06p053821' => 'qlo', 'QL07p025287' => 'qlo', 'QL09p033218' => 'qlo', 'QL09p040841' => 'qlo', 'QL10p020337' => 'qlo', 'QL10p027209' => 'qlo', 'QL10p027969' => 'qlo', 'QL10p048988' => 'qlo', 'QL11p001241' => 'qlo', 'QL11p028487' => 'qlo', 'RcHm_v2.0_Chr2g0105031' => 'rch', 'RcHm_v2.0_Chr2g0117811' => 'rch', 'RcHm_v2.0_Chr6g0270241' => 'rch', 'RcHm_v2.0_Chr7g0215961' => 'rch', 'RcHm_v2.0_Chr7g0231991' => 'rch', 'Rhsim01G0041500' => 'rsi', 'Rhsim01G0115000' => 'rsi', 'Rhsim01G0115400' => 'rsi', 'Rhsim01G0133600' => 'rsi', 'Rhsim01G0159900' => 'rsi', 'Rhsim02G0189400' => 'rsi', 'Rhsim03G0135600' => 'rsi', 'Rhsim03G0149900' => 'rsi', 'Rhsim04G0125600' => 'rsi', 'Rhsim05G0091700' => 'rsi', 'Rhsim05G0092900' => 'rsi', 'Rhsim06G0075000' => 'rsi', 'Rhsim07G0066400' => 'rsi', 'Rhsim07G0156400' => 'rsi', 'Rhsim07G0182200' => 'rsi', 'Rhsim07G0182300' => 'rsi', 'Rhsim08G0180400' => 'rsi', 'Rhsim09G0056800' => 'rsi', 'Rhsim10G0153300' => 'rsi', 'Rhsim11G0012700' => 'rsi', 'Rhsim12G0031800' => 'rsi', 'Rhsim12G0055400' => 'rsi', 'Rhsim12G0091400' => 'rsi', 'Rhsim13G0070800' => 'rsi', 'Rhsim13G0193300' => 'rsi', 'RhsimUnG0111600' => 'rsi', 'RhsimUnG0137500' => 'rsi', 'RhsimUnG0172900' => 'rsi', 'SGA_v2.0_scaffold11G05878' => 'sas', 'SGA_v2.0_scaffold167G38458' => 'sas', 'SGA_v2.0_scaffold19G08588' => 'sas', 'SGA_v2.0_scaffold239G43990' => 'sas', 'SGA_v2.0_scaffold260G45865' => 'sas', 'SGA_v2.0_scaffold309G48177' => 'sas', 'SGA_v2.0_scaffold76G25122' => 'sas', 'SGA_v2.0_scaffold85G26708' => 'sas', 'SHI13914' => 'shi', 'SHI30402' => 'shi', 'TWI09G0020' => 'twi', 'TWI09G0456' => 'twi', 'TWI09G1572' => 'twi', 'TWI12G0266' => 'twi', 'TWI12G1451' => 'twi', 'TWI14G0851' => 'twi', 'TWI15G0796' => 'twi', 'TWI18G0820' => 'twi', 'TWI18G1152' => 'twi', 'TWI23G0007' => 'twi', 'TWI23G0314' => 'twi', 'TWI31G0674' => 'twi', 'TWI31G0938' => 'twi', 'TWI34G0641' => 'twi', 'TWI34G1527' => 'twi', 'TWI36G0193' => 'twi', 'TWI36G0405' => 'twi', 'TWI38G0892' => 'twi', 'TWI38G0936' => 'twi', 'TWI38G2218' => 'twi', 'TWI53G0679' => 'twi', 'TWI53G0863' => 'twi', 'TWI53G1133' => 'twi', 'TWI60G0823' => 'twi', 'TWI63G0919' => 'twi', 'TWI63G1436' => 'twi', 'TWI73G0140' => 'twi', 'TWI73G0419' => 'twi', 'TWI73G0420' => 'twi', 'TWI73G1276' => 'twi', 'TWI74G0405' => 'twi', 'TWI74G0837' => 'twi', 'TWI75G0594' => 'twi', 'TWI75G1615' => 'twi', 'TWI77G0816' => 'twi', 'vmacro03831' => 'vma', 'vmacro13746' => 'vma', 'vmacro16089' => 'vma', 'vmacro22863' => 'vma', 'Zm00001eb085790' => 'zma', 'Zm00001eb114250' => 'zma', 'Zm00001eb138070' => 'zma', 'Zm00001eb167560' => 'zma', 'Zm00001eb199990' => 'zma', 'Zm00001eb368180' => 'zma', 'Zm00001eb382470' => 'zma' ) $gf_id = 'HOM05D001576' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001576' ) $data_identifier = 'HOM05D001576' $data_type = 'gf_id' $species_gene_counts = array( 'aox' => (int) 9, 'acertr' => (int) 3, 'cansat' => (int) 1, 'ccl' => (int) 4, 'cil' => (int) 145, 'camsi' => (int) 46, 'dca' => (int) 1, 'din' => (int) 1, 'fan' => (int) 12, 'fve' => (int) 9, 'gma' => (int) 5, 'han' => (int) 5, 'cav' => (int) 11, 'hma' => (int) 5, 'sun' => (int) 3, 'mdo' => (int) 3, 'mtr' => (int) 2, 'osa' => (int) 19, 'pgr' => (int) 1, 'ptr' => (int) 2, 'ppe' => (int) 6, 'qlo' => (int) 24, 'rch' => (int) 5, 'rsi' => (int) 28, 'sas' => (int) 8, 'shi' => (int) 2, 'twi' => (int) 35, 'vma' => (int) 4, 'zma' => (int) 7 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb382470' $species_info = array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ) $local_species = 'sas' $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' => 'HOM05D001576', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '406', 'num_species' => '29' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'Aqoxy1G01456' => 'aox', 'Aqoxy1G02949' => 'aox', 'Aqoxy3G01274' => 'aox', 'Aqoxy3G02110' => 'aox', 'Aqoxy3G02268' => 'aox', 'Aqoxy5G02702' => 'aox', 'Aqoxy5G02988' => 'aox', 'Aqoxy5G03427' => 'aox', 'Aqoxy6G02363' => 'aox', 'Atru.chr1.3225' => 'acertr', 'Atru.chr8.1198' => 'acertr', 'Atru.chr9.790' => 'acertr', 'CANSAT01G3197' => 'cansat', 'Ciclev10003979m.g' => 'ccl', 'Ciclev10017471m.g' => 'ccl', 'Ciclev10018206m.g' => 'ccl', 'Ciclev10033751m.g' => 'ccl', 'CiPaw.01G000900' => 'cil', 'CiPaw.01G001000' => 'cil', 'CiPaw.01G033500' => 'cil', 'CiPaw.01G060300' => 'cil', 'CiPaw.01G070200' => 'cil', 'CiPaw.01G075100' => 'cil', 'CiPaw.01G084700' => 'cil', 'CiPaw.01G087900' => 'cil', 'CiPaw.01G092600' => 'cil', 'CiPaw.01G097200' => 'cil', 'CiPaw.01G098300' => 'cil', 'CiPaw.01G110200' => 'cil', 'CiPaw.01G118700' => 'cil', 'CiPaw.01G121200' => 'cil', 'CiPaw.01G132500' => 'cil', 'CiPaw.01G146900' => 'cil', 'CiPaw.01G174000' => 'cil', 'CiPaw.01G179900' => 'cil', 'CiPaw.01G183400' => 'cil', 'CiPaw.01G240000' => 'cil', 'CiPaw.01G283500' => 'cil', 'CiPaw.01G307400' => 'cil', 'CiPaw.02G030800' => 'cil', 'CiPaw.02G047200' => 'cil', 'CiPaw.02G050500' => 'cil', 'CiPaw.02G069900' => 'cil', 'CiPaw.02G091600' => 'cil', 'CiPaw.02G095000' => 'cil', 'CiPaw.02G131900' => 'cil', 'CiPaw.03G043000' => 'cil', 'CiPaw.03G069900' => 'cil', 'CiPaw.03G088100' => 'cil', 'CiPaw.03G089300' => 'cil', 'CiPaw.03G093100' => 'cil', 'CiPaw.03G129800' => 'cil', 'CiPaw.03G131200' => 'cil', 'CiPaw.03G134500' => 'cil', 'CiPaw.03G152100' => 'cil', 'CiPaw.03G162700' => 'cil', 'CiPaw.03G172800' => 'cil', 'CiPaw.03G175800' => 'cil', 'CiPaw.03G181800' => 'cil', 'CiPaw.03G191400' => 'cil', 'CiPaw.03G198300' => 'cil', 'CiPaw.03G201300' => 'cil', 'CiPaw.03G224700' => 'cil', 'CiPaw.03G225000' => 'cil', 'CiPaw.04G065100' => 'cil', 'CiPaw.04G080400' => 'cil', 'CiPaw.04G113500' => 'cil', 'CiPaw.04G121900' => 'cil', 'CiPaw.04G144100' => 'cil', 'CiPaw.04G176500' => 'cil', 'CiPaw.05G086200' => 'cil', 'CiPaw.05G100200' => 'cil', 'CiPaw.05G114200' => 'cil', 'CiPaw.05G126800' => 'cil', 'CiPaw.05G228800' => 'cil', 'CiPaw.05G230600' => 'cil', 'CiPaw.05G236500' => 'cil', 'CiPaw.05G244800' => 'cil', 'CiPaw.06G026600' => 'cil', 'CiPaw.06G027900' => 'cil', 'CiPaw.06G051800' => 'cil', 'CiPaw.06G128500' => 'cil', 'CiPaw.06G165900' => 'cil', 'CiPaw.07G045400' => 'cil', 'CiPaw.07G048000' => 'cil', 'CiPaw.07G052000' => 'cil', 'CiPaw.07G073800' => 'cil', 'CiPaw.07G099700' => 'cil', 'CiPaw.07G108700' => 'cil', 'CiPaw.07G120000' => 'cil', 'CiPaw.07G134100' => 'cil', 'CiPaw.07G147000' => 'cil', 'CiPaw.07G149700' => 'cil', 'CiPaw.07G178300' => 'cil', 'CiPaw.07G184900' => 'cil', 'CiPaw.08G044500' => 'cil', 'CiPaw.08G046900' => 'cil', 'CiPaw.08G047300' => 'cil', 'CiPaw.08G115400' => 'cil', 'CiPaw.08G134700' => 'cil', 'CiPaw.08G157400' => 'cil', 'CiPaw.09G014300' => 'cil', 'CiPaw.09G088900' => 'cil', 'CiPaw.09G130900' => 'cil', 'CiPaw.09G133100' => 'cil', 'CiPaw.09G151300' => 'cil', 'CiPaw.09G172800' => 'cil', 'CiPaw.09G174900' => 'cil', 'CiPaw.09G175000' => 'cil', 'CiPaw.10G012800' => 'cil', 'CiPaw.10G028800' => 'cil', 'CiPaw.10G044700' => 'cil', 'CiPaw.10G067400' => 'cil', 'CiPaw.10G115900' => 'cil', 'CiPaw.10G126200' => 'cil', 'CiPaw.10G139700' => 'cil', 'CiPaw.10G155100' => 'cil', 'CiPaw.11G011300' => 'cil', 'CiPaw.11G025900' => 'cil', 'CiPaw.11G104100' => 'cil', 'CiPaw.11G142700' => 'cil', 'CiPaw.11G164500' => 'cil', 'CiPaw.11G189100' => 'cil', 'CiPaw.11G197100' => 'cil', 'CiPaw.12G006100' => 'cil', 'CiPaw.12G038500' => 'cil', 'CiPaw.12G041400' => 'cil', 'CiPaw.12G041600' => 'cil', 'CiPaw.12G051300' => 'cil', 'CiPaw.12G101800' => 'cil', 'CiPaw.12G107800' => 'cil', 'CiPaw.13G033200' => 'cil', 'CiPaw.13G129900' => 'cil', 'CiPaw.13G160200' => 'cil', 'CiPaw.14G018900' => 'cil', 'CiPaw.14G029000' => 'cil', 'CiPaw.14G031000' => 'cil', 'CiPaw.14G032000' => 'cil', 'CiPaw.14G032300' => 'cil', 'CiPaw.14G040600' => 'cil', 'CiPaw.14G060500' => 'cil', 'CiPaw.14G061500' => 'cil', 'CiPaw.14G077500' => 'cil', 'CiPaw.14G088300' => 'cil', 'CiPaw.14G108500' => 'cil', 'CiPaw.14G121300' => 'cil', 'CiPaw.14G133000' => 'cil', 'CiPaw.14G134600' => 'cil', 'CiPaw.15G027200' => 'cil', 'CiPaw.15G037700' => 'cil', 'CiPaw.15G050900' => 'cil', 'CiPaw.15G067200' => 'cil', 'CiPaw.15G072000' => 'cil', 'CiPaw.15G112900' => 'cil', 'CiPaw.15G133200' => 'cil', 'CiPaw.15G139500' => 'cil', 'CiPaw.15G155400' => 'cil', 'CiPaw.16G006000' => 'cil', 'CiPaw.16G013100' => 'cil', 'CiPaw.16G047100' => 'cil', 'CiPaw.16G048900' => 'cil', 'CiPaw.16G070300' => 'cil', 'CSS0000195' => 'camsi', 'CSS0001664' => 'camsi', 'CSS0002566' => 'camsi', 'CSS0003077' => 'camsi', 'CSS0004257' => 'camsi', 'CSS0004495' => 'camsi', 'CSS0004599' => 'camsi', 'CSS0004943' => 'camsi', 'CSS0005302' => 'camsi', 'CSS0006274' => 'camsi', 'CSS0006547' => 'camsi', 'CSS0006860' => 'camsi', 'CSS0008814' => 'camsi', 'CSS0008946' => 'camsi', 'CSS0009093' => 'camsi', 'CSS0010221' => 'camsi', 'CSS0010296' => 'camsi', 'CSS0010386' => 'camsi', 'CSS0010831' => 'camsi', 'CSS0011061' => 'camsi', 'CSS0012008' => 'camsi', 'CSS0012194' => 'camsi', 'CSS0013580' => 'camsi', 'CSS0014176' => 'camsi', 'CSS0014280' => 'camsi', 'CSS0014799' => 'camsi', 'CSS0015368' => 'camsi', 'CSS0017473' => 'camsi', 'CSS0019281' => 'camsi', 'CSS0021320' => 'camsi', 'CSS0021750' => 'camsi', 'CSS0023642' => 'camsi', 'CSS0023792' => 'camsi', 'CSS0031528' => 'camsi', 'CSS0033894' => 'camsi', 'CSS0034959' => 'camsi', 'CSS0035632' => 'camsi', 'CSS0038450' => 'camsi', 'CSS0039293' => 'camsi', 'CSS0041053' => 'camsi', 'CSS0041981' => 'camsi', 'CSS0042573' => 'camsi', 'CSS0042927' => 'camsi', 'CSS0047725' => 'camsi', 'CSS0049636' => 'camsi', 'CSS0050513' => 'camsi', 'DCAR_030203' => 'dca', 'Dinv07939' => 'din', 'FAN01G0456' => 'fan', 'FAN02G3001' => 'fan', 'FAN04G2781' => 'fan', 'FAN05G1385' => 'fan', 'FAN05G3062' => 'fan', 'FAN08G2267' => 'fan', 'FAN10G0481' => 'fan', 'FAN10G1257' => 'fan', 'FAN14G0954' => 'fan', 'FAN14G2347' => 'fan', 'FAN15G0187' => 'fan', 'FAN25G2214' => 'fan', 'FvH4_1g21031' => 'fve', 'FvH4_3g16231' => 'fve', 'FvH4_3g26413' => 'fve', 'FvH4_3g29014' => 'fve', 'FvH4_3g31921' => 'fve', 'FvH4_4g19882' => 'fve', 'FvH4_5g21960' => 'fve', 'FvH4_5g29683' => 'fve', 'FvH4_7g13271' => 'fve', 'Glyma.01G062500' => 'gma', 'Glyma.07G140900' => 'gma', 'Glyma.09G140900' => 'gma', 'Glyma.12G112700' => 'gma', 'Glyma.17G168800' => 'gma', 'HanXRQChr01g0027001' => 'han', 'HanXRQChr04g0120511' => 'han', 'HanXRQChr08g0232381' => 'han', 'HanXRQChr09g0265661' => 'han', 'HanXRQChr13g0416031' => 'han', 'Haze_05835' => 'cav', 'Haze_06597' => 'cav', 'Haze_07921' => 'cav', 'Haze_08599' => 'cav', 'Haze_10686' => 'cav', 'Haze_12994' => 'cav', 'Haze_13466' => 'cav', 'Haze_16101' => 'cav', 'Haze_17766' => 'cav', 'Haze_18456' => 'cav', 'Haze_20229' => 'cav', 'Hma1.2p1_0324F.1_g125640' => 'hma', 'Hma1.2p1_0733F.1_g210230' => 'hma', 'Hma1.2p1_0921F.1_g236870' => 'hma', 'Hma1.2p1_1313F.1_g274940' => 'hma', 'Hma1.2p1_3059F.1_g332230' => 'hma', 'Hund15925' => 'sun', 'Hund19562' => 'sun', 'Hund21925' => 'sun', 'MD03G1177400' => 'mdo', 'MD07G1026100' => 'mdo', 'MD17G1218600' => 'mdo', 'Medtr0867s0010' => 'mtr', 'Medtr6g081150' => 'mtr', 'Os01g0527900' => 'osa', 'Os02g0463725' => 'osa', 'Os02g0785600' => 'osa', 'Os03g0433733' => 'osa', 'Os04g0286500' => 'osa', 'Os05g0227800' => 'osa', 'Os06g0521000' => 'osa', 'Os06g0635500' => 'osa', 'Os06g0660650' => 'osa', 'Os07g0554400' => 'osa', 'Os08g0225900' => 'osa', 'Os08g0561000' => 'osa', 'Os09g0241700' => 'osa', 'Os09g0351900' => 'osa', 'Os11g0220700' => 'osa', 'Os11g0282700' => 'osa', 'Os12g0169300' => 'osa', 'Os12g0228500' => 'osa', 'Os12g0543800' => 'osa', 'PGR044G1547' => 'pgr', 'Potri.005G239150' => 'ptr', 'Potri.010G014250' => 'ptr', 'Prupe.1G172500' => 'ppe', 'Prupe.1G196800' => 'ppe', 'Prupe.1G279700' => 'ppe', 'Prupe.2G026400' => 'ppe', 'Prupe.3G094000' => 'ppe', 'Prupe.4G287300' => 'ppe', 'QL01p022166' => 'qlo', 'QL01p051890' => 'qlo', 'QL02p009469' => 'qlo', 'QL02p046053' => 'qlo', 'QL02p057958' => 'qlo', 'QL02p093127' => 'qlo', 'QL03p006855' => 'qlo', 'QL03p071586' => 'qlo', 'QL04p000022' => 'qlo', 'QL04p000024' => 'qlo', 'QL04p003192' => 'qlo', 'QL05p011416' => 'qlo', 'QL06p039590' => 'qlo', 'QL06p052750' => 'qlo', 'QL06p053821' => 'qlo', 'QL07p025287' => 'qlo', 'QL09p033218' => 'qlo', 'QL09p040841' => 'qlo', 'QL10p020337' => 'qlo', 'QL10p027209' => 'qlo', 'QL10p027969' => 'qlo', 'QL10p048988' => 'qlo', 'QL11p001241' => 'qlo', 'QL11p028487' => 'qlo', 'RcHm_v2.0_Chr2g0105031' => 'rch', 'RcHm_v2.0_Chr2g0117811' => 'rch', 'RcHm_v2.0_Chr6g0270241' => 'rch', 'RcHm_v2.0_Chr7g0215961' => 'rch', 'RcHm_v2.0_Chr7g0231991' => 'rch', 'Rhsim01G0041500' => 'rsi', 'Rhsim01G0115000' => 'rsi', 'Rhsim01G0115400' => 'rsi', 'Rhsim01G0133600' => 'rsi', 'Rhsim01G0159900' => 'rsi', 'Rhsim02G0189400' => 'rsi', 'Rhsim03G0135600' => 'rsi', 'Rhsim03G0149900' => 'rsi', 'Rhsim04G0125600' => 'rsi', 'Rhsim05G0091700' => 'rsi', 'Rhsim05G0092900' => 'rsi', 'Rhsim06G0075000' => 'rsi', 'Rhsim07G0066400' => 'rsi', 'Rhsim07G0156400' => 'rsi', 'Rhsim07G0182200' => 'rsi', 'Rhsim07G0182300' => 'rsi', 'Rhsim08G0180400' => 'rsi', 'Rhsim09G0056800' => 'rsi', 'Rhsim10G0153300' => 'rsi', 'Rhsim11G0012700' => 'rsi', 'Rhsim12G0031800' => 'rsi', 'Rhsim12G0055400' => 'rsi', 'Rhsim12G0091400' => 'rsi', 'Rhsim13G0070800' => 'rsi', 'Rhsim13G0193300' => 'rsi', 'RhsimUnG0111600' => 'rsi', 'RhsimUnG0137500' => 'rsi', 'RhsimUnG0172900' => 'rsi', 'SGA_v2.0_scaffold11G05878' => 'sas', 'SGA_v2.0_scaffold167G38458' => 'sas', 'SGA_v2.0_scaffold19G08588' => 'sas', 'SGA_v2.0_scaffold239G43990' => 'sas', 'SGA_v2.0_scaffold260G45865' => 'sas', 'SGA_v2.0_scaffold309G48177' => 'sas', 'SGA_v2.0_scaffold76G25122' => 'sas', 'SGA_v2.0_scaffold85G26708' => 'sas', 'SHI13914' => 'shi', 'SHI30402' => 'shi', 'TWI09G0020' => 'twi', 'TWI09G0456' => 'twi', 'TWI09G1572' => 'twi', 'TWI12G0266' => 'twi', 'TWI12G1451' => 'twi', 'TWI14G0851' => 'twi', 'TWI15G0796' => 'twi', 'TWI18G0820' => 'twi', 'TWI18G1152' => 'twi', 'TWI23G0007' => 'twi', 'TWI23G0314' => 'twi', 'TWI31G0674' => 'twi', 'TWI31G0938' => 'twi', 'TWI34G0641' => 'twi', 'TWI34G1527' => 'twi', 'TWI36G0193' => 'twi', 'TWI36G0405' => 'twi', 'TWI38G0892' => 'twi', 'TWI38G0936' => 'twi', 'TWI38G2218' => 'twi', 'TWI53G0679' => 'twi', 'TWI53G0863' => 'twi', 'TWI53G1133' => 'twi', 'TWI60G0823' => 'twi', 'TWI63G0919' => 'twi', 'TWI63G1436' => 'twi', 'TWI73G0140' => 'twi', 'TWI73G0419' => 'twi', 'TWI73G0420' => 'twi', 'TWI73G1276' => 'twi', 'TWI74G0405' => 'twi', 'TWI74G0837' => 'twi', 'TWI75G0594' => 'twi', 'TWI75G1615' => 'twi', 'TWI77G0816' => 'twi', 'vmacro03831' => 'vma', 'vmacro13746' => 'vma', 'vmacro16089' => 'vma', 'vmacro22863' => 'vma', 'Zm00001eb085790' => 'zma', 'Zm00001eb114250' => 'zma', 'Zm00001eb138070' => 'zma', 'Zm00001eb167560' => 'zma', 'Zm00001eb199990' => 'zma', 'Zm00001eb368180' => 'zma', 'Zm00001eb382470' => 'zma' ), 'gf_id' => 'HOM05D001576', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001576' ), 'data_identifier' => 'HOM05D001576', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001576', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '406', 'num_species' => '29' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'Aqoxy1G01456' => 'aox', 'Aqoxy1G02949' => 'aox', 'Aqoxy3G01274' => 'aox', 'Aqoxy3G02110' => 'aox', 'Aqoxy3G02268' => 'aox', 'Aqoxy5G02702' => 'aox', 'Aqoxy5G02988' => 'aox', 'Aqoxy5G03427' => 'aox', 'Aqoxy6G02363' => 'aox', 'Atru.chr1.3225' => 'acertr', 'Atru.chr8.1198' => 'acertr', 'Atru.chr9.790' => 'acertr', 'CANSAT01G3197' => 'cansat', 'Ciclev10003979m.g' => 'ccl', 'Ciclev10017471m.g' => 'ccl', 'Ciclev10018206m.g' => 'ccl', 'Ciclev10033751m.g' => 'ccl', 'CiPaw.01G000900' => 'cil', 'CiPaw.01G001000' => 'cil', 'CiPaw.01G033500' => 'cil', 'CiPaw.01G060300' => 'cil', 'CiPaw.01G070200' => 'cil', 'CiPaw.01G075100' => 'cil', 'CiPaw.01G084700' => 'cil', 'CiPaw.01G087900' => 'cil', 'CiPaw.01G092600' => 'cil', 'CiPaw.01G097200' => 'cil', 'CiPaw.01G098300' => 'cil', 'CiPaw.01G110200' => 'cil', 'CiPaw.01G118700' => 'cil', 'CiPaw.01G121200' => 'cil', 'CiPaw.01G132500' => 'cil', 'CiPaw.01G146900' => 'cil', 'CiPaw.01G174000' => 'cil', 'CiPaw.01G179900' => 'cil', 'CiPaw.01G183400' => 'cil', 'CiPaw.01G240000' => 'cil', 'CiPaw.01G283500' => 'cil', 'CiPaw.01G307400' => 'cil', 'CiPaw.02G030800' => 'cil', 'CiPaw.02G047200' => 'cil', 'CiPaw.02G050500' => 'cil', 'CiPaw.02G069900' => 'cil', 'CiPaw.02G091600' => 'cil', 'CiPaw.02G095000' => 'cil', 'CiPaw.02G131900' => 'cil', 'CiPaw.03G043000' => 'cil', 'CiPaw.03G069900' => 'cil', 'CiPaw.03G088100' => 'cil', 'CiPaw.03G089300' => 'cil', 'CiPaw.03G093100' => 'cil', 'CiPaw.03G129800' => 'cil', 'CiPaw.03G131200' => 'cil', 'CiPaw.03G134500' => 'cil', 'CiPaw.03G152100' => 'cil', 'CiPaw.03G162700' => 'cil', 'CiPaw.03G172800' => 'cil', 'CiPaw.03G175800' => 'cil', 'CiPaw.03G181800' => 'cil', 'CiPaw.03G191400' => 'cil', 'CiPaw.03G198300' => 'cil', 'CiPaw.03G201300' => 'cil', 'CiPaw.03G224700' => 'cil', 'CiPaw.03G225000' => 'cil', 'CiPaw.04G065100' => 'cil', 'CiPaw.04G080400' => 'cil', 'CiPaw.04G113500' => 'cil', 'CiPaw.04G121900' => 'cil', 'CiPaw.04G144100' => 'cil', 'CiPaw.04G176500' => 'cil', 'CiPaw.05G086200' => 'cil', 'CiPaw.05G100200' => 'cil', 'CiPaw.05G114200' => 'cil', 'CiPaw.05G126800' => 'cil', 'CiPaw.05G228800' => 'cil', 'CiPaw.05G230600' => 'cil', 'CiPaw.05G236500' => 'cil', 'CiPaw.05G244800' => 'cil', 'CiPaw.06G026600' => 'cil', 'CiPaw.06G027900' => 'cil', 'CiPaw.06G051800' => 'cil', 'CiPaw.06G128500' => 'cil', 'CiPaw.06G165900' => 'cil', 'CiPaw.07G045400' => 'cil', 'CiPaw.07G048000' => 'cil', 'CiPaw.07G052000' => 'cil', 'CiPaw.07G073800' => 'cil', 'CiPaw.07G099700' => 'cil', 'CiPaw.07G108700' => 'cil', 'CiPaw.07G120000' => 'cil', 'CiPaw.07G134100' => 'cil', 'CiPaw.07G147000' => 'cil', 'CiPaw.07G149700' => 'cil', 'CiPaw.07G178300' => 'cil', 'CiPaw.07G184900' => 'cil', 'CiPaw.08G044500' => 'cil', 'CiPaw.08G046900' => 'cil', 'CiPaw.08G047300' => 'cil', 'CiPaw.08G115400' => 'cil', 'CiPaw.08G134700' => 'cil', 'CiPaw.08G157400' => 'cil', 'CiPaw.09G014300' => 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'CiPaw.14G032000' => 'cil', 'CiPaw.14G032300' => 'cil', 'CiPaw.14G040600' => 'cil', 'CiPaw.14G060500' => 'cil', 'CiPaw.14G061500' => 'cil', 'CiPaw.14G077500' => 'cil', 'CiPaw.14G088300' => 'cil', 'CiPaw.14G108500' => 'cil', 'CiPaw.14G121300' => 'cil', 'CiPaw.14G133000' => 'cil', 'CiPaw.14G134600' => 'cil', 'CiPaw.15G027200' => 'cil', 'CiPaw.15G037700' => 'cil', 'CiPaw.15G050900' => 'cil', 'CiPaw.15G067200' => 'cil', 'CiPaw.15G072000' => 'cil', 'CiPaw.15G112900' => 'cil', 'CiPaw.15G133200' => 'cil', 'CiPaw.15G139500' => 'cil', 'CiPaw.15G155400' => 'cil', 'CiPaw.16G006000' => 'cil', 'CiPaw.16G013100' => 'cil', 'CiPaw.16G047100' => 'cil', 'CiPaw.16G048900' => 'cil', 'CiPaw.16G070300' => 'cil', 'CSS0000195' => 'camsi', 'CSS0001664' => 'camsi', 'CSS0002566' => 'camsi', 'CSS0003077' => 'camsi', 'CSS0004257' => 'camsi', 'CSS0004495' => 'camsi', 'CSS0004599' => 'camsi', 'CSS0004943' => 'camsi', 'CSS0005302' => 'camsi', 'CSS0006274' => 'camsi', 'CSS0006547' => 'camsi', 'CSS0006860' => 'camsi', 'CSS0008814' => 'camsi', 'CSS0008946' => 'camsi', 'CSS0009093' => 'camsi', 'CSS0010221' => 'camsi', 'CSS0010296' => 'camsi', 'CSS0010386' => 'camsi', 'CSS0010831' => 'camsi', 'CSS0011061' => 'camsi', 'CSS0012008' => 'camsi', 'CSS0012194' => 'camsi', 'CSS0013580' => 'camsi', 'CSS0014176' => 'camsi', 'CSS0014280' => 'camsi', 'CSS0014799' => 'camsi', 'CSS0015368' => 'camsi', 'CSS0017473' => 'camsi', 'CSS0019281' => 'camsi', 'CSS0021320' => 'camsi', 'CSS0021750' => 'camsi', 'CSS0023642' => 'camsi', 'CSS0023792' => 'camsi', 'CSS0031528' => 'camsi', 'CSS0033894' => 'camsi', 'CSS0034959' => 'camsi', 'CSS0035632' => 'camsi', 'CSS0038450' => 'camsi', 'CSS0039293' => 'camsi', 'CSS0041053' => 'camsi', 'CSS0041981' => 'camsi', 'CSS0042573' => 'camsi', 'CSS0042927' => 'camsi', 'CSS0047725' => 'camsi', 'CSS0049636' => 'camsi', 'CSS0050513' => 'camsi', 'DCAR_030203' => 'dca', 'Dinv07939' => 'din', 'FAN01G0456' => 'fan', 'FAN02G3001' => 'fan', 'FAN04G2781' => 'fan', 'FAN05G1385' => 'fan', 'FAN05G3062' => 'fan', 'FAN08G2267' => 'fan', 'FAN10G0481' => 'fan', 'FAN10G1257' => 'fan', 'FAN14G0954' => 'fan', 'FAN14G2347' => 'fan', 'FAN15G0187' => 'fan', 'FAN25G2214' => 'fan', 'FvH4_1g21031' => 'fve', 'FvH4_3g16231' => 'fve', 'FvH4_3g26413' => 'fve', 'FvH4_3g29014' => 'fve', 'FvH4_3g31921' => 'fve', 'FvH4_4g19882' => 'fve', 'FvH4_5g21960' => 'fve', 'FvH4_5g29683' => 'fve', 'FvH4_7g13271' => 'fve', 'Glyma.01G062500' => 'gma', 'Glyma.07G140900' => 'gma', 'Glyma.09G140900' => 'gma', 'Glyma.12G112700' => 'gma', 'Glyma.17G168800' => 'gma', 'HanXRQChr01g0027001' => 'han', 'HanXRQChr04g0120511' => 'han', 'HanXRQChr08g0232381' => 'han', 'HanXRQChr09g0265661' => 'han', 'HanXRQChr13g0416031' => 'han', 'Haze_05835' => 'cav', 'Haze_06597' => 'cav', 'Haze_07921' => 'cav', 'Haze_08599' => 'cav', 'Haze_10686' => 'cav', 'Haze_12994' => 'cav', 'Haze_13466' => 'cav', 'Haze_16101' => 'cav', 'Haze_17766' => 'cav', 'Haze_18456' => 'cav', 'Haze_20229' => 'cav', 'Hma1.2p1_0324F.1_g125640' => 'hma', 'Hma1.2p1_0733F.1_g210230' => 'hma', 'Hma1.2p1_0921F.1_g236870' => 'hma', 'Hma1.2p1_1313F.1_g274940' => 'hma', 'Hma1.2p1_3059F.1_g332230' => 'hma', 'Hund15925' => 'sun', 'Hund19562' => 'sun', 'Hund21925' => 'sun', 'MD03G1177400' => 'mdo', 'MD07G1026100' => 'mdo', 'MD17G1218600' => 'mdo', 'Medtr0867s0010' => 'mtr', 'Medtr6g081150' => 'mtr', 'Os01g0527900' => 'osa', 'Os02g0463725' => 'osa', 'Os02g0785600' => 'osa', 'Os03g0433733' => 'osa', 'Os04g0286500' => 'osa', 'Os05g0227800' => 'osa', 'Os06g0521000' => 'osa', 'Os06g0635500' => 'osa', 'Os06g0660650' => 'osa', 'Os07g0554400' => 'osa', 'Os08g0225900' => 'osa', 'Os08g0561000' => 'osa', 'Os09g0241700' => 'osa', 'Os09g0351900' => 'osa', 'Os11g0220700' => 'osa', 'Os11g0282700' => 'osa', 'Os12g0169300' => 'osa', 'Os12g0228500' => 'osa', 'Os12g0543800' => 'osa', 'PGR044G1547' => 'pgr', 'Potri.005G239150' => 'ptr', 'Potri.010G014250' => 'ptr', 'Prupe.1G172500' => 'ppe', 'Prupe.1G196800' => 'ppe', 'Prupe.1G279700' => 'ppe', 'Prupe.2G026400' => 'ppe', 'Prupe.3G094000' => 'ppe', 'Prupe.4G287300' => 'ppe', 'QL01p022166' => 'qlo', 'QL01p051890' => 'qlo', 'QL02p009469' => 'qlo', 'QL02p046053' => 'qlo', 'QL02p057958' => 'qlo', 'QL02p093127' => 'qlo', 'QL03p006855' => 'qlo', 'QL03p071586' => 'qlo', 'QL04p000022' => 'qlo', 'QL04p000024' => 'qlo', 'QL04p003192' => 'qlo', 'QL05p011416' => 'qlo', 'QL06p039590' => 'qlo', 'QL06p052750' => 'qlo', 'QL06p053821' => 'qlo', 'QL07p025287' => 'qlo', 'QL09p033218' => 'qlo', 'QL09p040841' => 'qlo', 'QL10p020337' => 'qlo', 'QL10p027209' => 'qlo', 'QL10p027969' => 'qlo', 'QL10p048988' => 'qlo', 'QL11p001241' => 'qlo', 'QL11p028487' => 'qlo', 'RcHm_v2.0_Chr2g0105031' => 'rch', 'RcHm_v2.0_Chr2g0117811' => 'rch', 'RcHm_v2.0_Chr6g0270241' => 'rch', 'RcHm_v2.0_Chr7g0215961' => 'rch', 'RcHm_v2.0_Chr7g0231991' => 'rch', 'Rhsim01G0041500' => 'rsi', 'Rhsim01G0115000' => 'rsi', 'Rhsim01G0115400' => 'rsi', 'Rhsim01G0133600' => 'rsi', 'Rhsim01G0159900' => 'rsi', 'Rhsim02G0189400' => 'rsi', 'Rhsim03G0135600' => 'rsi', 'Rhsim03G0149900' => 'rsi', 'Rhsim04G0125600' => 'rsi', 'Rhsim05G0091700' => 'rsi', 'Rhsim05G0092900' => 'rsi', 'Rhsim06G0075000' => 'rsi', 'Rhsim07G0066400' => 'rsi', 'Rhsim07G0156400' => 'rsi', 'Rhsim07G0182200' => 'rsi', 'Rhsim07G0182300' => 'rsi', 'Rhsim08G0180400' => 'rsi', 'Rhsim09G0056800' => 'rsi', 'Rhsim10G0153300' => 'rsi', 'Rhsim11G0012700' => 'rsi', 'Rhsim12G0031800' => 'rsi', 'Rhsim12G0055400' => 'rsi', 'Rhsim12G0091400' => 'rsi', 'Rhsim13G0070800' => 'rsi', 'Rhsim13G0193300' => 'rsi', 'RhsimUnG0111600' => 'rsi', 'RhsimUnG0137500' => 'rsi', 'RhsimUnG0172900' => 'rsi', 'SGA_v2.0_scaffold11G05878' => 'sas', 'SGA_v2.0_scaffold167G38458' => 'sas', 'SGA_v2.0_scaffold19G08588' => 'sas', 'SGA_v2.0_scaffold239G43990' => 'sas', 'SGA_v2.0_scaffold260G45865' => 'sas', 'SGA_v2.0_scaffold309G48177' => 'sas', 'SGA_v2.0_scaffold76G25122' => 'sas', 'SGA_v2.0_scaffold85G26708' => 'sas', 'SHI13914' => 'shi', 'SHI30402' => 'shi', 'TWI09G0020' => 'twi', 'TWI09G0456' => 'twi', 'TWI09G1572' => 'twi', 'TWI12G0266' => 'twi', 'TWI12G1451' => 'twi', 'TWI14G0851' => 'twi', 'TWI15G0796' => 'twi', 'TWI18G0820' => 'twi', 'TWI18G1152' => 'twi', 'TWI23G0007' => 'twi', 'TWI23G0314' => 'twi', 'TWI31G0674' => 'twi', 'TWI31G0938' => 'twi', 'TWI34G0641' => 'twi', 'TWI34G1527' => 'twi', 'TWI36G0193' => 'twi', 'TWI36G0405' => 'twi', 'TWI38G0892' => 'twi', 'TWI38G0936' => 'twi', 'TWI38G2218' => 'twi', 'TWI53G0679' => 'twi', 'TWI53G0863' => 'twi', 'TWI53G1133' => 'twi', 'TWI60G0823' => 'twi', 'TWI63G0919' => 'twi', 'TWI63G1436' => 'twi', 'TWI73G0140' => 'twi', 'TWI73G0419' => 'twi', 'TWI73G0420' => 'twi', 'TWI73G1276' => 'twi', 'TWI74G0405' => 'twi', 'TWI74G0837' => 'twi', 'TWI75G0594' => 'twi', 'TWI75G1615' => 'twi', 'TWI77G0816' => 'twi', 'vmacro03831' => 'vma', 'vmacro13746' => 'vma', 'vmacro16089' => 'vma', 'vmacro22863' => 'vma', 'Zm00001eb085790' => 'zma', 'Zm00001eb114250' => 'zma', 'Zm00001eb138070' => 'zma', 'Zm00001eb167560' => 'zma', 'Zm00001eb199990' => 'zma', 'Zm00001eb368180' => 'zma', 'Zm00001eb382470' => 'zma' ) $gf_id = 'HOM05D001576' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001576' ) $data_identifier = 'HOM05D001576' $data_type = 'gf_id' $species_gene_counts = array( 'aox' => (int) 9, 'acertr' => (int) 3, 'cansat' => (int) 1, 'ccl' => (int) 4, 'cil' => (int) 145, 'camsi' => (int) 46, 'dca' => (int) 1, 'din' => (int) 1, 'fan' => (int) 12, 'fve' => (int) 9, 'gma' => (int) 5, 'han' => (int) 5, 'cav' => (int) 11, 'hma' => (int) 5, 'sun' => (int) 3, 'mdo' => (int) 3, 'mtr' => (int) 2, 'osa' => (int) 19, 'pgr' => (int) 1, 'ptr' => (int) 2, 'ppe' => (int) 6, 'qlo' => (int) 24, 'rch' => (int) 5, 'rsi' => (int) 28, 'sas' => (int) 8, 'shi' => (int) 2, 'twi' => (int) 35, 'vma' => (int) 4, 'zma' => (int) 7 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb382470' $species_info = array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ) $local_species = 'sas' $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' => 'HOM05D001576', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '406', 'num_species' => '29' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'Aqoxy1G01456' => 'aox', 'Aqoxy1G02949' => 'aox', 'Aqoxy3G01274' => 'aox', 'Aqoxy3G02110' => 'aox', 'Aqoxy3G02268' => 'aox', 'Aqoxy5G02702' => 'aox', 'Aqoxy5G02988' => 'aox', 'Aqoxy5G03427' => 'aox', 'Aqoxy6G02363' => 'aox', 'Atru.chr1.3225' => 'acertr', 'Atru.chr8.1198' => 'acertr', 'Atru.chr9.790' => 'acertr', 'CANSAT01G3197' => 'cansat', 'Ciclev10003979m.g' => 'ccl', 'Ciclev10017471m.g' => 'ccl', 'Ciclev10018206m.g' => 'ccl', 'Ciclev10033751m.g' => 'ccl', 'CiPaw.01G000900' => 'cil', 'CiPaw.01G001000' => 'cil', 'CiPaw.01G033500' => 'cil', 'CiPaw.01G060300' => 'cil', 'CiPaw.01G070200' => 'cil', 'CiPaw.01G075100' => 'cil', 'CiPaw.01G084700' => 'cil', 'CiPaw.01G087900' => 'cil', 'CiPaw.01G092600' => 'cil', 'CiPaw.01G097200' => 'cil', 'CiPaw.01G098300' => 'cil', 'CiPaw.01G110200' => 'cil', 'CiPaw.01G118700' => 'cil', 'CiPaw.01G121200' => 'cil', 'CiPaw.01G132500' => 'cil', 'CiPaw.01G146900' => 'cil', 'CiPaw.01G174000' => 'cil', 'CiPaw.01G179900' => 'cil', 'CiPaw.01G183400' => 'cil', 'CiPaw.01G240000' => 'cil', 'CiPaw.01G283500' => 'cil', 'CiPaw.01G307400' => 'cil', 'CiPaw.02G030800' => 'cil', 'CiPaw.02G047200' => 'cil', 'CiPaw.02G050500' => 'cil', 'CiPaw.02G069900' => 'cil', 'CiPaw.02G091600' => 'cil', 'CiPaw.02G095000' => 'cil', 'CiPaw.02G131900' => 'cil', 'CiPaw.03G043000' => 'cil', 'CiPaw.03G069900' => 'cil', 'CiPaw.03G088100' => 'cil', 'CiPaw.03G089300' => 'cil', 'CiPaw.03G093100' => 'cil', 'CiPaw.03G129800' => 'cil', 'CiPaw.03G131200' => 'cil', 'CiPaw.03G134500' => 'cil', 'CiPaw.03G152100' => 'cil', 'CiPaw.03G162700' => 'cil', 'CiPaw.03G172800' => 'cil', 'CiPaw.03G175800' => 'cil', 'CiPaw.03G181800' => 'cil', 'CiPaw.03G191400' => 'cil', 'CiPaw.03G198300' => 'cil', 'CiPaw.03G201300' => 'cil', 'CiPaw.03G224700' => 'cil', 'CiPaw.03G225000' => 'cil', 'CiPaw.04G065100' => 'cil', 'CiPaw.04G080400' => 'cil', 'CiPaw.04G113500' => 'cil', 'CiPaw.04G121900' => 'cil', 'CiPaw.04G144100' => 'cil', 'CiPaw.04G176500' => 'cil', 'CiPaw.05G086200' => 'cil', 'CiPaw.05G100200' => 'cil', 'CiPaw.05G114200' => 'cil', 'CiPaw.05G126800' => 'cil', 'CiPaw.05G228800' => 'cil', 'CiPaw.05G230600' => 'cil', 'CiPaw.05G236500' => 'cil', 'CiPaw.05G244800' => 'cil', 'CiPaw.06G026600' => 'cil', 'CiPaw.06G027900' => 'cil', 'CiPaw.06G051800' => 'cil', 'CiPaw.06G128500' => 'cil', 'CiPaw.06G165900' => 'cil', 'CiPaw.07G045400' => 'cil', 'CiPaw.07G048000' => 'cil', 'CiPaw.07G052000' => 'cil', 'CiPaw.07G073800' => 'cil', 'CiPaw.07G099700' => 'cil', 'CiPaw.07G108700' => 'cil', 'CiPaw.07G120000' => 'cil', 'CiPaw.07G134100' => 'cil', 'CiPaw.07G147000' => 'cil', 'CiPaw.07G149700' => 'cil', 'CiPaw.07G178300' => 'cil', 'CiPaw.07G184900' => 'cil', 'CiPaw.08G044500' => 'cil', 'CiPaw.08G046900' => 'cil', 'CiPaw.08G047300' => 'cil', 'CiPaw.08G115400' => 'cil', 'CiPaw.08G134700' => 'cil', 'CiPaw.08G157400' => 'cil', 'CiPaw.09G014300' => 'cil', 'CiPaw.09G088900' => 'cil', 'CiPaw.09G130900' => 'cil', 'CiPaw.09G133100' => 'cil', 'CiPaw.09G151300' => 'cil', 'CiPaw.09G172800' => 'cil', 'CiPaw.09G174900' => 'cil', 'CiPaw.09G175000' => 'cil', 'CiPaw.10G012800' => 'cil', 'CiPaw.10G028800' => 'cil', 'CiPaw.10G044700' => 'cil', 'CiPaw.10G067400' => 'cil', 'CiPaw.10G115900' => 'cil', 'CiPaw.10G126200' => 'cil', 'CiPaw.10G139700' => 'cil', 'CiPaw.10G155100' => 'cil', 'CiPaw.11G011300' => 'cil', 'CiPaw.11G025900' => 'cil', 'CiPaw.11G104100' => 'cil', 'CiPaw.11G142700' => 'cil', 'CiPaw.11G164500' => 'cil', 'CiPaw.11G189100' => 'cil', 'CiPaw.11G197100' => 'cil', 'CiPaw.12G006100' => 'cil', 'CiPaw.12G038500' => 'cil', 'CiPaw.12G041400' => 'cil', 'CiPaw.12G041600' => 'cil', 'CiPaw.12G051300' => 'cil', 'CiPaw.12G101800' => 'cil', 'CiPaw.12G107800' => 'cil', 'CiPaw.13G033200' => 'cil', 'CiPaw.13G129900' => 'cil', 'CiPaw.13G160200' => 'cil', 'CiPaw.14G018900' => 'cil', 'CiPaw.14G029000' => 'cil', 'CiPaw.14G031000' => 'cil', 'CiPaw.14G032000' => 'cil', 'CiPaw.14G032300' => 'cil', 'CiPaw.14G040600' => 'cil', 'CiPaw.14G060500' => 'cil', 'CiPaw.14G061500' => 'cil', 'CiPaw.14G077500' => 'cil', 'CiPaw.14G088300' => 'cil', 'CiPaw.14G108500' => 'cil', 'CiPaw.14G121300' => 'cil', 'CiPaw.14G133000' => 'cil', 'CiPaw.14G134600' => 'cil', 'CiPaw.15G027200' => 'cil', 'CiPaw.15G037700' => 'cil', 'CiPaw.15G050900' => 'cil', 'CiPaw.15G067200' => 'cil', 'CiPaw.15G072000' => 'cil', 'CiPaw.15G112900' => 'cil', 'CiPaw.15G133200' => 'cil', 'CiPaw.15G139500' => 'cil', 'CiPaw.15G155400' => 'cil', 'CiPaw.16G006000' => 'cil', 'CiPaw.16G013100' => 'cil', 'CiPaw.16G047100' => 'cil', 'CiPaw.16G048900' => 'cil', 'CiPaw.16G070300' => 'cil', 'CSS0000195' => 'camsi', 'CSS0001664' => 'camsi', 'CSS0002566' => 'camsi', 'CSS0003077' => 'camsi', 'CSS0004257' => 'camsi', 'CSS0004495' => 'camsi', 'CSS0004599' => 'camsi', 'CSS0004943' => 'camsi', 'CSS0005302' => 'camsi', 'CSS0006274' => 'camsi', 'CSS0006547' => 'camsi', 'CSS0006860' => 'camsi', 'CSS0008814' => 'camsi', 'CSS0008946' => 'camsi', 'CSS0009093' => 'camsi', 'CSS0010221' => 'camsi', 'CSS0010296' => 'camsi', 'CSS0010386' => 'camsi', 'CSS0010831' => 'camsi', 'CSS0011061' => 'camsi', 'CSS0012008' => 'camsi', 'CSS0012194' => 'camsi', 'CSS0013580' => 'camsi', 'CSS0014176' => 'camsi', 'CSS0014280' => 'camsi', 'CSS0014799' => 'camsi', 'CSS0015368' => 'camsi', 'CSS0017473' => 'camsi', 'CSS0019281' => 'camsi', 'CSS0021320' => 'camsi', 'CSS0021750' => 'camsi', 'CSS0023642' => 'camsi', 'CSS0023792' => 'camsi', 'CSS0031528' => 'camsi', 'CSS0033894' => 'camsi', 'CSS0034959' => 'camsi', 'CSS0035632' => 'camsi', 'CSS0038450' => 'camsi', 'CSS0039293' => 'camsi', 'CSS0041053' => 'camsi', 'CSS0041981' => 'camsi', 'CSS0042573' => 'camsi', 'CSS0042927' => 'camsi', 'CSS0047725' => 'camsi', 'CSS0049636' => 'camsi', 'CSS0050513' => 'camsi', 'DCAR_030203' => 'dca', 'Dinv07939' => 'din', 'FAN01G0456' => 'fan', 'FAN02G3001' => 'fan', 'FAN04G2781' => 'fan', 'FAN05G1385' => 'fan', 'FAN05G3062' => 'fan', 'FAN08G2267' => 'fan', 'FAN10G0481' => 'fan', 'FAN10G1257' => 'fan', 'FAN14G0954' => 'fan', 'FAN14G2347' => 'fan', 'FAN15G0187' => 'fan', 'FAN25G2214' => 'fan', 'FvH4_1g21031' => 'fve', 'FvH4_3g16231' => 'fve', 'FvH4_3g26413' => 'fve', 'FvH4_3g29014' => 'fve', 'FvH4_3g31921' => 'fve', 'FvH4_4g19882' => 'fve', 'FvH4_5g21960' => 'fve', 'FvH4_5g29683' => 'fve', 'FvH4_7g13271' => 'fve', 'Glyma.01G062500' => 'gma', 'Glyma.07G140900' => 'gma', 'Glyma.09G140900' => 'gma', 'Glyma.12G112700' => 'gma', 'Glyma.17G168800' => 'gma', 'HanXRQChr01g0027001' => 'han', 'HanXRQChr04g0120511' => 'han', 'HanXRQChr08g0232381' => 'han', 'HanXRQChr09g0265661' => 'han', 'HanXRQChr13g0416031' => 'han', 'Haze_05835' => 'cav', 'Haze_06597' => 'cav', 'Haze_07921' => 'cav', 'Haze_08599' => 'cav', 'Haze_10686' => 'cav', 'Haze_12994' => 'cav', 'Haze_13466' => 'cav', 'Haze_16101' => 'cav', 'Haze_17766' => 'cav', 'Haze_18456' => 'cav', 'Haze_20229' => 'cav', 'Hma1.2p1_0324F.1_g125640' => 'hma', 'Hma1.2p1_0733F.1_g210230' => 'hma', 'Hma1.2p1_0921F.1_g236870' => 'hma', 'Hma1.2p1_1313F.1_g274940' => 'hma', 'Hma1.2p1_3059F.1_g332230' => 'hma', 'Hund15925' => 'sun', 'Hund19562' => 'sun', 'Hund21925' => 'sun', 'MD03G1177400' => 'mdo', 'MD07G1026100' => 'mdo', 'MD17G1218600' => 'mdo', 'Medtr0867s0010' => 'mtr', 'Medtr6g081150' => 'mtr', 'Os01g0527900' => 'osa', 'Os02g0463725' => 'osa', 'Os02g0785600' => 'osa', 'Os03g0433733' => 'osa', 'Os04g0286500' => 'osa', 'Os05g0227800' => 'osa', 'Os06g0521000' => 'osa', 'Os06g0635500' => 'osa', 'Os06g0660650' => 'osa', 'Os07g0554400' => 'osa', 'Os08g0225900' => 'osa', 'Os08g0561000' => 'osa', 'Os09g0241700' => 'osa', 'Os09g0351900' => 'osa', 'Os11g0220700' => 'osa', 'Os11g0282700' => 'osa', 'Os12g0169300' => 'osa', 'Os12g0228500' => 'osa', 'Os12g0543800' => 'osa', 'PGR044G1547' => 'pgr', 'Potri.005G239150' => 'ptr', 'Potri.010G014250' => 'ptr', 'Prupe.1G172500' => 'ppe', 'Prupe.1G196800' => 'ppe', 'Prupe.1G279700' => 'ppe', 'Prupe.2G026400' => 'ppe', 'Prupe.3G094000' => 'ppe', 'Prupe.4G287300' => 'ppe', 'QL01p022166' => 'qlo', 'QL01p051890' => 'qlo', 'QL02p009469' => 'qlo', 'QL02p046053' => 'qlo', 'QL02p057958' => 'qlo', 'QL02p093127' => 'qlo', 'QL03p006855' => 'qlo', 'QL03p071586' => 'qlo', 'QL04p000022' => 'qlo', 'QL04p000024' => 'qlo', 'QL04p003192' => 'qlo', 'QL05p011416' => 'qlo', 'QL06p039590' => 'qlo', 'QL06p052750' => 'qlo', 'QL06p053821' => 'qlo', 'QL07p025287' => 'qlo', 'QL09p033218' => 'qlo', 'QL09p040841' => 'qlo', 'QL10p020337' => 'qlo', 'QL10p027209' => 'qlo', 'QL10p027969' => 'qlo', 'QL10p048988' => 'qlo', 'QL11p001241' => 'qlo', 'QL11p028487' => 'qlo', 'RcHm_v2.0_Chr2g0105031' => 'rch', 'RcHm_v2.0_Chr2g0117811' => 'rch', 'RcHm_v2.0_Chr6g0270241' => 'rch', 'RcHm_v2.0_Chr7g0215961' => 'rch', 'RcHm_v2.0_Chr7g0231991' => 'rch', 'Rhsim01G0041500' => 'rsi', 'Rhsim01G0115000' => 'rsi', 'Rhsim01G0115400' => 'rsi', 'Rhsim01G0133600' => 'rsi', 'Rhsim01G0159900' => 'rsi', 'Rhsim02G0189400' => 'rsi', 'Rhsim03G0135600' => 'rsi', 'Rhsim03G0149900' => 'rsi', 'Rhsim04G0125600' => 'rsi', 'Rhsim05G0091700' => 'rsi', 'Rhsim05G0092900' => 'rsi', 'Rhsim06G0075000' => 'rsi', 'Rhsim07G0066400' => 'rsi', 'Rhsim07G0156400' => 'rsi', 'Rhsim07G0182200' => 'rsi', 'Rhsim07G0182300' => 'rsi', 'Rhsim08G0180400' => 'rsi', 'Rhsim09G0056800' => 'rsi', 'Rhsim10G0153300' => 'rsi', 'Rhsim11G0012700' => 'rsi', 'Rhsim12G0031800' => 'rsi', 'Rhsim12G0055400' => 'rsi', 'Rhsim12G0091400' => 'rsi', 'Rhsim13G0070800' => 'rsi', 'Rhsim13G0193300' => 'rsi', 'RhsimUnG0111600' => 'rsi', 'RhsimUnG0137500' => 'rsi', 'RhsimUnG0172900' => 'rsi', 'SGA_v2.0_scaffold11G05878' => 'sas', 'SGA_v2.0_scaffold167G38458' => 'sas', 'SGA_v2.0_scaffold19G08588' => 'sas', 'SGA_v2.0_scaffold239G43990' => 'sas', 'SGA_v2.0_scaffold260G45865' => 'sas', 'SGA_v2.0_scaffold309G48177' => 'sas', 'SGA_v2.0_scaffold76G25122' => 'sas', 'SGA_v2.0_scaffold85G26708' => 'sas', 'SHI13914' => 'shi', 'SHI30402' => 'shi', 'TWI09G0020' => 'twi', 'TWI09G0456' => 'twi', 'TWI09G1572' => 'twi', 'TWI12G0266' => 'twi', 'TWI12G1451' => 'twi', 'TWI14G0851' => 'twi', 'TWI15G0796' => 'twi', 'TWI18G0820' => 'twi', 'TWI18G1152' => 'twi', 'TWI23G0007' => 'twi', 'TWI23G0314' => 'twi', 'TWI31G0674' => 'twi', 'TWI31G0938' => 'twi', 'TWI34G0641' => 'twi', 'TWI34G1527' => 'twi', 'TWI36G0193' => 'twi', 'TWI36G0405' => 'twi', 'TWI38G0892' => 'twi', 'TWI38G0936' => 'twi', 'TWI38G2218' => 'twi', 'TWI53G0679' => 'twi', 'TWI53G0863' => 'twi', 'TWI53G1133' => 'twi', 'TWI60G0823' => 'twi', 'TWI63G0919' => 'twi', 'TWI63G1436' => 'twi', 'TWI73G0140' => 'twi', 'TWI73G0419' => 'twi', 'TWI73G0420' => 'twi', 'TWI73G1276' => 'twi', 'TWI74G0405' => 'twi', 'TWI74G0837' => 'twi', 'TWI75G0594' => 'twi', 'TWI75G1615' => 'twi', 'TWI77G0816' => 'twi', 'vmacro03831' => 'vma', 'vmacro13746' => 'vma', 'vmacro16089' => 'vma', 'vmacro22863' => 'vma', 'Zm00001eb085790' => 'zma', 'Zm00001eb114250' => 'zma', 'Zm00001eb138070' => 'zma', 'Zm00001eb167560' => 'zma', 'Zm00001eb199990' => 'zma', 'Zm00001eb368180' => 'zma', 'Zm00001eb382470' => 'zma' ), 'gf_id' => 'HOM05D001576', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001576' ), 'data_identifier' => 'HOM05D001576', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001576', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '406', 'num_species' => '29' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'Aqoxy1G01456' => 'aox', 'Aqoxy1G02949' => 'aox', 'Aqoxy3G01274' => 'aox', 'Aqoxy3G02110' => 'aox', 'Aqoxy3G02268' => 'aox', 'Aqoxy5G02702' => 'aox', 'Aqoxy5G02988' => 'aox', 'Aqoxy5G03427' => 'aox', 'Aqoxy6G02363' => 'aox', 'Atru.chr1.3225' => 'acertr', 'Atru.chr8.1198' => 'acertr', 'Atru.chr9.790' => 'acertr', 'CANSAT01G3197' => 'cansat', 'Ciclev10003979m.g' => 'ccl', 'Ciclev10017471m.g' => 'ccl', 'Ciclev10018206m.g' => 'ccl', 'Ciclev10033751m.g' => 'ccl', 'CiPaw.01G000900' => 'cil', 'CiPaw.01G001000' => 'cil', 'CiPaw.01G033500' => 'cil', 'CiPaw.01G060300' => 'cil', 'CiPaw.01G070200' => 'cil', 'CiPaw.01G075100' => 'cil', 'CiPaw.01G084700' => 'cil', 'CiPaw.01G087900' => 'cil', 'CiPaw.01G092600' => 'cil', 'CiPaw.01G097200' => 'cil', 'CiPaw.01G098300' => 'cil', 'CiPaw.01G110200' => 'cil', 'CiPaw.01G118700' => 'cil', 'CiPaw.01G121200' => 'cil', 'CiPaw.01G132500' => 'cil', 'CiPaw.01G146900' => 'cil', 'CiPaw.01G174000' => 'cil', 'CiPaw.01G179900' => 'cil', 'CiPaw.01G183400' => 'cil', 'CiPaw.01G240000' => 'cil', 'CiPaw.01G283500' => 'cil', 'CiPaw.01G307400' => 'cil', 'CiPaw.02G030800' => 'cil', 'CiPaw.02G047200' => 'cil', 'CiPaw.02G050500' => 'cil', 'CiPaw.02G069900' => 'cil', 'CiPaw.02G091600' => 'cil', 'CiPaw.02G095000' => 'cil', 'CiPaw.02G131900' => 'cil', 'CiPaw.03G043000' => 'cil', 'CiPaw.03G069900' => 'cil', 'CiPaw.03G088100' => 'cil', 'CiPaw.03G089300' => 'cil', 'CiPaw.03G093100' => 'cil', 'CiPaw.03G129800' => 'cil', 'CiPaw.03G131200' => 'cil', 'CiPaw.03G134500' => 'cil', 'CiPaw.03G152100' => 'cil', 'CiPaw.03G162700' => 'cil', 'CiPaw.03G172800' => 'cil', 'CiPaw.03G175800' => 'cil', 'CiPaw.03G181800' => 'cil', 'CiPaw.03G191400' => 'cil', 'CiPaw.03G198300' => 'cil', 'CiPaw.03G201300' => 'cil', 'CiPaw.03G224700' => 'cil', 'CiPaw.03G225000' => 'cil', 'CiPaw.04G065100' => 'cil', 'CiPaw.04G080400' => 'cil', 'CiPaw.04G113500' => 'cil', 'CiPaw.04G121900' => 'cil', 'CiPaw.04G144100' => 'cil', 'CiPaw.04G176500' => 'cil', 'CiPaw.05G086200' => 'cil', 'CiPaw.05G100200' => 'cil', 'CiPaw.05G114200' => 'cil', 'CiPaw.05G126800' => 'cil', 'CiPaw.05G228800' => 'cil', 'CiPaw.05G230600' => 'cil', 'CiPaw.05G236500' => 'cil', 'CiPaw.05G244800' => 'cil', 'CiPaw.06G026600' => 'cil', 'CiPaw.06G027900' => 'cil', 'CiPaw.06G051800' => 'cil', 'CiPaw.06G128500' => 'cil', 'CiPaw.06G165900' => 'cil', 'CiPaw.07G045400' => 'cil', 'CiPaw.07G048000' => 'cil', 'CiPaw.07G052000' => 'cil', 'CiPaw.07G073800' => 'cil', 'CiPaw.07G099700' => 'cil', 'CiPaw.07G108700' => 'cil', 'CiPaw.07G120000' => 'cil', 'CiPaw.07G134100' => 'cil', 'CiPaw.07G147000' => 'cil', 'CiPaw.07G149700' => 'cil', 'CiPaw.07G178300' => 'cil', 'CiPaw.07G184900' => 'cil', 'CiPaw.08G044500' => 'cil', 'CiPaw.08G046900' => 'cil', 'CiPaw.08G047300' => 'cil', 'CiPaw.08G115400' => 'cil', 'CiPaw.08G134700' => 'cil', 'CiPaw.08G157400' => 'cil', 'CiPaw.09G014300' => 'cil', 'CiPaw.09G088900' => 'cil', 'CiPaw.09G130900' => 'cil', 'CiPaw.09G133100' => 'cil', 'CiPaw.09G151300' => 'cil', 'CiPaw.09G172800' => 'cil', 'CiPaw.09G174900' => 'cil', 'CiPaw.09G175000' => 'cil', 'CiPaw.10G012800' => 'cil', 'CiPaw.10G028800' => 'cil', 'CiPaw.10G044700' => 'cil', 'CiPaw.10G067400' => 'cil', 'CiPaw.10G115900' => 'cil', 'CiPaw.10G126200' => 'cil', 'CiPaw.10G139700' => 'cil', 'CiPaw.10G155100' => 'cil', 'CiPaw.11G011300' => 'cil', 'CiPaw.11G025900' => 'cil', 'CiPaw.11G104100' => 'cil', 'CiPaw.11G142700' => 'cil', 'CiPaw.11G164500' => 'cil', 'CiPaw.11G189100' => 'cil', 'CiPaw.11G197100' => 'cil', 'CiPaw.12G006100' => 'cil', 'CiPaw.12G038500' => 'cil', 'CiPaw.12G041400' => 'cil', 'CiPaw.12G041600' => 'cil', 'CiPaw.12G051300' => 'cil', 'CiPaw.12G101800' => 'cil', 'CiPaw.12G107800' => 'cil', 'CiPaw.13G033200' => 'cil', 'CiPaw.13G129900' => 'cil', 'CiPaw.13G160200' => 'cil', 'CiPaw.14G018900' => 'cil', 'CiPaw.14G029000' => 'cil', 'CiPaw.14G031000' => 'cil', 'CiPaw.14G032000' => 'cil', 'CiPaw.14G032300' => 'cil', 'CiPaw.14G040600' => 'cil', 'CiPaw.14G060500' => 'cil', 'CiPaw.14G061500' => 'cil', 'CiPaw.14G077500' => 'cil', 'CiPaw.14G088300' => 'cil', 'CiPaw.14G108500' => 'cil', 'CiPaw.14G121300' => 'cil', 'CiPaw.14G133000' => 'cil', 'CiPaw.14G134600' => 'cil', 'CiPaw.15G027200' => 'cil', 'CiPaw.15G037700' => 'cil', 'CiPaw.15G050900' => 'cil', 'CiPaw.15G067200' => 'cil', 'CiPaw.15G072000' => 'cil', 'CiPaw.15G112900' => 'cil', 'CiPaw.15G133200' => 'cil', 'CiPaw.15G139500' => 'cil', 'CiPaw.15G155400' => 'cil', 'CiPaw.16G006000' => 'cil', 'CiPaw.16G013100' => 'cil', 'CiPaw.16G047100' => 'cil', 'CiPaw.16G048900' => 'cil', 'CiPaw.16G070300' => 'cil', 'CSS0000195' => 'camsi', 'CSS0001664' => 'camsi', 'CSS0002566' => 'camsi', 'CSS0003077' => 'camsi', 'CSS0004257' => 'camsi', 'CSS0004495' => 'camsi', 'CSS0004599' => 'camsi', 'CSS0004943' => 'camsi', 'CSS0005302' => 'camsi', 'CSS0006274' => 'camsi', 'CSS0006547' => 'camsi', 'CSS0006860' => 'camsi', 'CSS0008814' => 'camsi', 'CSS0008946' => 'camsi', 'CSS0009093' => 'camsi', 'CSS0010221' => 'camsi', 'CSS0010296' => 'camsi', 'CSS0010386' => 'camsi', 'CSS0010831' => 'camsi', 'CSS0011061' => 'camsi', 'CSS0012008' => 'camsi', 'CSS0012194' => 'camsi', 'CSS0013580' => 'camsi', 'CSS0014176' => 'camsi', 'CSS0014280' => 'camsi', 'CSS0014799' => 'camsi', 'CSS0015368' => 'camsi', 'CSS0017473' => 'camsi', 'CSS0019281' => 'camsi', 'CSS0021320' => 'camsi', 'CSS0021750' => 'camsi', 'CSS0023642' => 'camsi', 'CSS0023792' => 'camsi', 'CSS0031528' => 'camsi', 'CSS0033894' => 'camsi', 'CSS0034959' => 'camsi', 'CSS0035632' => 'camsi', 'CSS0038450' => 'camsi', 'CSS0039293' => 'camsi', 'CSS0041053' => 'camsi', 'CSS0041981' => 'camsi', 'CSS0042573' => 'camsi', 'CSS0042927' => 'camsi', 'CSS0047725' => 'camsi', 'CSS0049636' => 'camsi', 'CSS0050513' => 'camsi', 'DCAR_030203' => 'dca', 'Dinv07939' => 'din', 'FAN01G0456' => 'fan', 'FAN02G3001' => 'fan', 'FAN04G2781' => 'fan', 'FAN05G1385' => 'fan', 'FAN05G3062' => 'fan', 'FAN08G2267' => 'fan', 'FAN10G0481' => 'fan', 'FAN10G1257' => 'fan', 'FAN14G0954' => 'fan', 'FAN14G2347' => 'fan', 'FAN15G0187' => 'fan', 'FAN25G2214' => 'fan', 'FvH4_1g21031' => 'fve', 'FvH4_3g16231' => 'fve', 'FvH4_3g26413' => 'fve', 'FvH4_3g29014' => 'fve', 'FvH4_3g31921' => 'fve', 'FvH4_4g19882' => 'fve', 'FvH4_5g21960' => 'fve', 'FvH4_5g29683' => 'fve', 'FvH4_7g13271' => 'fve', 'Glyma.01G062500' => 'gma', 'Glyma.07G140900' => 'gma', 'Glyma.09G140900' => 'gma', 'Glyma.12G112700' => 'gma', 'Glyma.17G168800' => 'gma', 'HanXRQChr01g0027001' => 'han', 'HanXRQChr04g0120511' => 'han', 'HanXRQChr08g0232381' => 'han', 'HanXRQChr09g0265661' => 'han', 'HanXRQChr13g0416031' => 'han', 'Haze_05835' => 'cav', 'Haze_06597' => 'cav', 'Haze_07921' => 'cav', 'Haze_08599' => 'cav', 'Haze_10686' => 'cav', 'Haze_12994' => 'cav', 'Haze_13466' => 'cav', 'Haze_16101' => 'cav', 'Haze_17766' => 'cav', 'Haze_18456' => 'cav', 'Haze_20229' => 'cav', 'Hma1.2p1_0324F.1_g125640' => 'hma', 'Hma1.2p1_0733F.1_g210230' => 'hma', 'Hma1.2p1_0921F.1_g236870' => 'hma', 'Hma1.2p1_1313F.1_g274940' => 'hma', 'Hma1.2p1_3059F.1_g332230' => 'hma', 'Hund15925' => 'sun', 'Hund19562' => 'sun', 'Hund21925' => 'sun', 'MD03G1177400' => 'mdo', 'MD07G1026100' => 'mdo', 'MD17G1218600' => 'mdo', 'Medtr0867s0010' => 'mtr', 'Medtr6g081150' => 'mtr', 'Os01g0527900' => 'osa', 'Os02g0463725' => 'osa', 'Os02g0785600' => 'osa', 'Os03g0433733' => 'osa', 'Os04g0286500' => 'osa', 'Os05g0227800' => 'osa', 'Os06g0521000' => 'osa', 'Os06g0635500' => 'osa', 'Os06g0660650' => 'osa', 'Os07g0554400' => 'osa', 'Os08g0225900' => 'osa', 'Os08g0561000' => 'osa', 'Os09g0241700' => 'osa', 'Os09g0351900' => 'osa', 'Os11g0220700' => 'osa', 'Os11g0282700' => 'osa', 'Os12g0169300' => 'osa', 'Os12g0228500' => 'osa', 'Os12g0543800' => 'osa', 'PGR044G1547' => 'pgr', 'Potri.005G239150' => 'ptr', 'Potri.010G014250' => 'ptr', 'Prupe.1G172500' => 'ppe', 'Prupe.1G196800' => 'ppe', 'Prupe.1G279700' => 'ppe', 'Prupe.2G026400' => 'ppe', 'Prupe.3G094000' => 'ppe', 'Prupe.4G287300' => 'ppe', 'QL01p022166' => 'qlo', 'QL01p051890' => 'qlo', 'QL02p009469' => 'qlo', 'QL02p046053' => 'qlo', 'QL02p057958' => 'qlo', 'QL02p093127' => 'qlo', 'QL03p006855' => 'qlo', 'QL03p071586' => 'qlo', 'QL04p000022' => 'qlo', 'QL04p000024' => 'qlo', 'QL04p003192' => 'qlo', 'QL05p011416' => 'qlo', 'QL06p039590' => 'qlo', 'QL06p052750' => 'qlo', 'QL06p053821' => 'qlo', 'QL07p025287' => 'qlo', 'QL09p033218' => 'qlo', 'QL09p040841' => 'qlo', 'QL10p020337' => 'qlo', 'QL10p027209' => 'qlo', 'QL10p027969' => 'qlo', 'QL10p048988' => 'qlo', 'QL11p001241' => 'qlo', 'QL11p028487' => 'qlo', 'RcHm_v2.0_Chr2g0105031' => 'rch', 'RcHm_v2.0_Chr2g0117811' => 'rch', 'RcHm_v2.0_Chr6g0270241' => 'rch', 'RcHm_v2.0_Chr7g0215961' => 'rch', 'RcHm_v2.0_Chr7g0231991' => 'rch', 'Rhsim01G0041500' => 'rsi', 'Rhsim01G0115000' => 'rsi', 'Rhsim01G0115400' => 'rsi', 'Rhsim01G0133600' => 'rsi', 'Rhsim01G0159900' => 'rsi', 'Rhsim02G0189400' => 'rsi', 'Rhsim03G0135600' => 'rsi', 'Rhsim03G0149900' => 'rsi', 'Rhsim04G0125600' => 'rsi', 'Rhsim05G0091700' => 'rsi', 'Rhsim05G0092900' => 'rsi', 'Rhsim06G0075000' => 'rsi', 'Rhsim07G0066400' => 'rsi', 'Rhsim07G0156400' => 'rsi', 'Rhsim07G0182200' => 'rsi', 'Rhsim07G0182300' => 'rsi', 'Rhsim08G0180400' => 'rsi', 'Rhsim09G0056800' => 'rsi', 'Rhsim10G0153300' => 'rsi', 'Rhsim11G0012700' => 'rsi', 'Rhsim12G0031800' => 'rsi', 'Rhsim12G0055400' => 'rsi', 'Rhsim12G0091400' => 'rsi', 'Rhsim13G0070800' => 'rsi', 'Rhsim13G0193300' => 'rsi', 'RhsimUnG0111600' => 'rsi', 'RhsimUnG0137500' => 'rsi', 'RhsimUnG0172900' => 'rsi', 'SGA_v2.0_scaffold11G05878' => 'sas', 'SGA_v2.0_scaffold167G38458' => 'sas', 'SGA_v2.0_scaffold19G08588' => 'sas', 'SGA_v2.0_scaffold239G43990' => 'sas', 'SGA_v2.0_scaffold260G45865' => 'sas', 'SGA_v2.0_scaffold309G48177' => 'sas', 'SGA_v2.0_scaffold76G25122' => 'sas', 'SGA_v2.0_scaffold85G26708' => 'sas', 'SHI13914' => 'shi', 'SHI30402' => 'shi', 'TWI09G0020' => 'twi', 'TWI09G0456' => 'twi', 'TWI09G1572' => 'twi', 'TWI12G0266' => 'twi', 'TWI12G1451' => 'twi', 'TWI14G0851' => 'twi', 'TWI15G0796' => 'twi', 'TWI18G0820' => 'twi', 'TWI18G1152' => 'twi', 'TWI23G0007' => 'twi', 'TWI23G0314' => 'twi', 'TWI31G0674' => 'twi', 'TWI31G0938' => 'twi', 'TWI34G0641' => 'twi', 'TWI34G1527' => 'twi', 'TWI36G0193' => 'twi', 'TWI36G0405' => 'twi', 'TWI38G0892' => 'twi', 'TWI38G0936' => 'twi', 'TWI38G2218' => 'twi', 'TWI53G0679' => 'twi', 'TWI53G0863' => 'twi', 'TWI53G1133' => 'twi', 'TWI60G0823' => 'twi', 'TWI63G0919' => 'twi', 'TWI63G1436' => 'twi', 'TWI73G0140' => 'twi', 'TWI73G0419' => 'twi', 'TWI73G0420' => 'twi', 'TWI73G1276' => 'twi', 'TWI74G0405' => 'twi', 'TWI74G0837' => 'twi', 'TWI75G0594' => 'twi', 'TWI75G1615' => 'twi', 'TWI77G0816' => 'twi', 'vmacro03831' => 'vma', 'vmacro13746' => 'vma', 'vmacro16089' => 'vma', 'vmacro22863' => 'vma', 'Zm00001eb085790' => 'zma', 'Zm00001eb114250' => 'zma', 'Zm00001eb138070' => 'zma', 'Zm00001eb167560' => 'zma', 'Zm00001eb199990' => 'zma', 'Zm00001eb368180' => 'zma', 'Zm00001eb382470' => 'zma' ) $gf_id = 'HOM05D001576' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001576' ) $data_identifier = 'HOM05D001576' $data_type = 'gf_id' $species_gene_counts = array( 'aox' => (int) 9, 'acertr' => (int) 3, 'cansat' => (int) 1, 'ccl' => (int) 4, 'cil' => (int) 145, 'camsi' => (int) 46, 'dca' => (int) 1, 'din' => (int) 1, 'fan' => (int) 12, 'fve' => (int) 9, 'gma' => (int) 5, 'han' => (int) 5, 'cav' => (int) 11, 'hma' => (int) 5, 'sun' => (int) 3, 'mdo' => (int) 3, 'mtr' => (int) 2, 'osa' => (int) 19, 'pgr' => (int) 1, 'ptr' => (int) 2, 'ppe' => (int) 6, 'qlo' => (int) 24, 'rch' => (int) 5, 'rsi' => (int) 28, 'sas' => (int) 8, 'shi' => (int) 2, 'twi' => (int) 35, 'vma' => (int) 4, 'zma' => (int) 7 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb382470' $species_info = array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ) $local_species = 'twi' $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' => 'HOM05D001576', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '406', 'num_species' => '29' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'Aqoxy1G01456' => 'aox', 'Aqoxy1G02949' => 'aox', 'Aqoxy3G01274' => 'aox', 'Aqoxy3G02110' => 'aox', 'Aqoxy3G02268' => 'aox', 'Aqoxy5G02702' => 'aox', 'Aqoxy5G02988' => 'aox', 'Aqoxy5G03427' => 'aox', 'Aqoxy6G02363' => 'aox', 'Atru.chr1.3225' => 'acertr', 'Atru.chr8.1198' => 'acertr', 'Atru.chr9.790' => 'acertr', 'CANSAT01G3197' => 'cansat', 'Ciclev10003979m.g' => 'ccl', 'Ciclev10017471m.g' => 'ccl', 'Ciclev10018206m.g' => 'ccl', 'Ciclev10033751m.g' => 'ccl', 'CiPaw.01G000900' => 'cil', 'CiPaw.01G001000' => 'cil', 'CiPaw.01G033500' => 'cil', 'CiPaw.01G060300' => 'cil', 'CiPaw.01G070200' => 'cil', 'CiPaw.01G075100' => 'cil', 'CiPaw.01G084700' => 'cil', 'CiPaw.01G087900' => 'cil', 'CiPaw.01G092600' => 'cil', 'CiPaw.01G097200' => 'cil', 'CiPaw.01G098300' => 'cil', 'CiPaw.01G110200' => 'cil', 'CiPaw.01G118700' => 'cil', 'CiPaw.01G121200' => 'cil', 'CiPaw.01G132500' => 'cil', 'CiPaw.01G146900' => 'cil', 'CiPaw.01G174000' => 'cil', 'CiPaw.01G179900' => 'cil', 'CiPaw.01G183400' => 'cil', 'CiPaw.01G240000' => 'cil', 'CiPaw.01G283500' => 'cil', 'CiPaw.01G307400' => 'cil', 'CiPaw.02G030800' => 'cil', 'CiPaw.02G047200' => 'cil', 'CiPaw.02G050500' => 'cil', 'CiPaw.02G069900' => 'cil', 'CiPaw.02G091600' => 'cil', 'CiPaw.02G095000' => 'cil', 'CiPaw.02G131900' => 'cil', 'CiPaw.03G043000' => 'cil', 'CiPaw.03G069900' => 'cil', 'CiPaw.03G088100' => 'cil', 'CiPaw.03G089300' => 'cil', 'CiPaw.03G093100' => 'cil', 'CiPaw.03G129800' => 'cil', 'CiPaw.03G131200' => 'cil', 'CiPaw.03G134500' => 'cil', 'CiPaw.03G152100' => 'cil', 'CiPaw.03G162700' => 'cil', 'CiPaw.03G172800' => 'cil', 'CiPaw.03G175800' => 'cil', 'CiPaw.03G181800' => 'cil', 'CiPaw.03G191400' => 'cil', 'CiPaw.03G198300' => 'cil', 'CiPaw.03G201300' => 'cil', 'CiPaw.03G224700' => 'cil', 'CiPaw.03G225000' => 'cil', 'CiPaw.04G065100' => 'cil', 'CiPaw.04G080400' => 'cil', 'CiPaw.04G113500' => 'cil', 'CiPaw.04G121900' => 'cil', 'CiPaw.04G144100' => 'cil', 'CiPaw.04G176500' => 'cil', 'CiPaw.05G086200' => 'cil', 'CiPaw.05G100200' => 'cil', 'CiPaw.05G114200' => 'cil', 'CiPaw.05G126800' => 'cil', 'CiPaw.05G228800' => 'cil', 'CiPaw.05G230600' => 'cil', 'CiPaw.05G236500' => 'cil', 'CiPaw.05G244800' => 'cil', 'CiPaw.06G026600' => 'cil', 'CiPaw.06G027900' => 'cil', 'CiPaw.06G051800' => 'cil', 'CiPaw.06G128500' => 'cil', 'CiPaw.06G165900' => 'cil', 'CiPaw.07G045400' => 'cil', 'CiPaw.07G048000' => 'cil', 'CiPaw.07G052000' => 'cil', 'CiPaw.07G073800' => 'cil', 'CiPaw.07G099700' => 'cil', 'CiPaw.07G108700' => 'cil', 'CiPaw.07G120000' => 'cil', 'CiPaw.07G134100' => 'cil', 'CiPaw.07G147000' => 'cil', 'CiPaw.07G149700' => 'cil', 'CiPaw.07G178300' => 'cil', 'CiPaw.07G184900' => 'cil', 'CiPaw.08G044500' => 'cil', 'CiPaw.08G046900' => 'cil', 'CiPaw.08G047300' => 'cil', 'CiPaw.08G115400' => 'cil', 'CiPaw.08G134700' => 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'TWI09G0020' => 'twi', 'TWI09G0456' => 'twi', 'TWI09G1572' => 'twi', 'TWI12G0266' => 'twi', 'TWI12G1451' => 'twi', 'TWI14G0851' => 'twi', 'TWI15G0796' => 'twi', 'TWI18G0820' => 'twi', 'TWI18G1152' => 'twi', 'TWI23G0007' => 'twi', 'TWI23G0314' => 'twi', 'TWI31G0674' => 'twi', 'TWI31G0938' => 'twi', 'TWI34G0641' => 'twi', 'TWI34G1527' => 'twi', 'TWI36G0193' => 'twi', 'TWI36G0405' => 'twi', 'TWI38G0892' => 'twi', 'TWI38G0936' => 'twi', 'TWI38G2218' => 'twi', 'TWI53G0679' => 'twi', 'TWI53G0863' => 'twi', 'TWI53G1133' => 'twi', 'TWI60G0823' => 'twi', 'TWI63G0919' => 'twi', 'TWI63G1436' => 'twi', 'TWI73G0140' => 'twi', 'TWI73G0419' => 'twi', 'TWI73G0420' => 'twi', 'TWI73G1276' => 'twi', 'TWI74G0405' => 'twi', 'TWI74G0837' => 'twi', 'TWI75G0594' => 'twi', 'TWI75G1615' => 'twi', 'TWI77G0816' => 'twi', 'vmacro03831' => 'vma', 'vmacro13746' => 'vma', 'vmacro16089' => 'vma', 'vmacro22863' => 'vma', 'Zm00001eb085790' => 'zma', 'Zm00001eb114250' => 'zma', 'Zm00001eb138070' => 'zma', 'Zm00001eb167560' => 'zma', 'Zm00001eb199990' => 'zma', 'Zm00001eb368180' => 'zma', 'Zm00001eb382470' => 'zma' ), 'gf_id' => 'HOM05D001576', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001576' ), 'data_identifier' => 'HOM05D001576', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001576', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '406', 'num_species' => '29' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'Aqoxy1G01456' => 'aox', 'Aqoxy1G02949' => 'aox', 'Aqoxy3G01274' => 'aox', 'Aqoxy3G02110' => 'aox', 'Aqoxy3G02268' => 'aox', 'Aqoxy5G02702' => 'aox', 'Aqoxy5G02988' => 'aox', 'Aqoxy5G03427' => 'aox', 'Aqoxy6G02363' => 'aox', 'Atru.chr1.3225' => 'acertr', 'Atru.chr8.1198' => 'acertr', 'Atru.chr9.790' => 'acertr', 'CANSAT01G3197' => 'cansat', 'Ciclev10003979m.g' => 'ccl', 'Ciclev10017471m.g' => 'ccl', 'Ciclev10018206m.g' => 'ccl', 'Ciclev10033751m.g' => 'ccl', 'CiPaw.01G000900' => 'cil', 'CiPaw.01G001000' => 'cil', 'CiPaw.01G033500' => 'cil', 'CiPaw.01G060300' => 'cil', 'CiPaw.01G070200' => 'cil', 'CiPaw.01G075100' => 'cil', 'CiPaw.01G084700' => 'cil', 'CiPaw.01G087900' => 'cil', 'CiPaw.01G092600' => 'cil', 'CiPaw.01G097200' => 'cil', 'CiPaw.01G098300' => 'cil', 'CiPaw.01G110200' => 'cil', 'CiPaw.01G118700' => 'cil', 'CiPaw.01G121200' => 'cil', 'CiPaw.01G132500' => 'cil', 'CiPaw.01G146900' => 'cil', 'CiPaw.01G174000' => 'cil', 'CiPaw.01G179900' => 'cil', 'CiPaw.01G183400' => 'cil', 'CiPaw.01G240000' => 'cil', 'CiPaw.01G283500' => 'cil', 'CiPaw.01G307400' => 'cil', 'CiPaw.02G030800' => 'cil', 'CiPaw.02G047200' => 'cil', 'CiPaw.02G050500' => 'cil', 'CiPaw.02G069900' => 'cil', 'CiPaw.02G091600' => 'cil', 'CiPaw.02G095000' => 'cil', 'CiPaw.02G131900' => 'cil', 'CiPaw.03G043000' => 'cil', 'CiPaw.03G069900' => 'cil', 'CiPaw.03G088100' => 'cil', 'CiPaw.03G089300' => 'cil', 'CiPaw.03G093100' => 'cil', 'CiPaw.03G129800' => 'cil', 'CiPaw.03G131200' => 'cil', 'CiPaw.03G134500' => 'cil', 'CiPaw.03G152100' => 'cil', 'CiPaw.03G162700' => 'cil', 'CiPaw.03G172800' => 'cil', 'CiPaw.03G175800' => 'cil', 'CiPaw.03G181800' => 'cil', 'CiPaw.03G191400' => 'cil', 'CiPaw.03G198300' => 'cil', 'CiPaw.03G201300' => 'cil', 'CiPaw.03G224700' => 'cil', 'CiPaw.03G225000' => 'cil', 'CiPaw.04G065100' => 'cil', 'CiPaw.04G080400' => 'cil', 'CiPaw.04G113500' => 'cil', 'CiPaw.04G121900' => 'cil', 'CiPaw.04G144100' => 'cil', 'CiPaw.04G176500' => 'cil', 'CiPaw.05G086200' => 'cil', 'CiPaw.05G100200' => 'cil', 'CiPaw.05G114200' => 'cil', 'CiPaw.05G126800' => 'cil', 'CiPaw.05G228800' => 'cil', 'CiPaw.05G230600' => 'cil', 'CiPaw.05G236500' => 'cil', 'CiPaw.05G244800' => 'cil', 'CiPaw.06G026600' => 'cil', 'CiPaw.06G027900' => 'cil', 'CiPaw.06G051800' => 'cil', 'CiPaw.06G128500' => 'cil', 'CiPaw.06G165900' => 'cil', 'CiPaw.07G045400' => 'cil', 'CiPaw.07G048000' => 'cil', 'CiPaw.07G052000' => 'cil', 'CiPaw.07G073800' => 'cil', 'CiPaw.07G099700' => 'cil', 'CiPaw.07G108700' => 'cil', 'CiPaw.07G120000' => 'cil', 'CiPaw.07G134100' => 'cil', 'CiPaw.07G147000' => 'cil', 'CiPaw.07G149700' => 'cil', 'CiPaw.07G178300' => 'cil', 'CiPaw.07G184900' => 'cil', 'CiPaw.08G044500' => 'cil', 'CiPaw.08G046900' => 'cil', 'CiPaw.08G047300' => 'cil', 'CiPaw.08G115400' => 'cil', 'CiPaw.08G134700' => 'cil', 'CiPaw.08G157400' => 'cil', 'CiPaw.09G014300' => 'cil', 'CiPaw.09G088900' => 'cil', 'CiPaw.09G130900' => 'cil', 'CiPaw.09G133100' => 'cil', 'CiPaw.09G151300' => 'cil', 'CiPaw.09G172800' => 'cil', 'CiPaw.09G174900' => 'cil', 'CiPaw.09G175000' => 'cil', 'CiPaw.10G012800' => 'cil', 'CiPaw.10G028800' => 'cil', 'CiPaw.10G044700' => 'cil', 'CiPaw.10G067400' => 'cil', 'CiPaw.10G115900' => 'cil', 'CiPaw.10G126200' => 'cil', 'CiPaw.10G139700' => 'cil', 'CiPaw.10G155100' => 'cil', 'CiPaw.11G011300' => 'cil', 'CiPaw.11G025900' => 'cil', 'CiPaw.11G104100' => 'cil', 'CiPaw.11G142700' => 'cil', 'CiPaw.11G164500' => 'cil', 'CiPaw.11G189100' => 'cil', 'CiPaw.11G197100' => 'cil', 'CiPaw.12G006100' => 'cil', 'CiPaw.12G038500' => 'cil', 'CiPaw.12G041400' => 'cil', 'CiPaw.12G041600' => 'cil', 'CiPaw.12G051300' => 'cil', 'CiPaw.12G101800' => 'cil', 'CiPaw.12G107800' => 'cil', 'CiPaw.13G033200' => 'cil', 'CiPaw.13G129900' => 'cil', 'CiPaw.13G160200' => 'cil', 'CiPaw.14G018900' => 'cil', 'CiPaw.14G029000' => 'cil', 'CiPaw.14G031000' => 'cil', 'CiPaw.14G032000' => 'cil', 'CiPaw.14G032300' => 'cil', 'CiPaw.14G040600' => 'cil', 'CiPaw.14G060500' => 'cil', 'CiPaw.14G061500' => 'cil', 'CiPaw.14G077500' => 'cil', 'CiPaw.14G088300' => 'cil', 'CiPaw.14G108500' => 'cil', 'CiPaw.14G121300' => 'cil', 'CiPaw.14G133000' => 'cil', 'CiPaw.14G134600' => 'cil', 'CiPaw.15G027200' => 'cil', 'CiPaw.15G037700' => 'cil', 'CiPaw.15G050900' => 'cil', 'CiPaw.15G067200' => 'cil', 'CiPaw.15G072000' => 'cil', 'CiPaw.15G112900' => 'cil', 'CiPaw.15G133200' => 'cil', 'CiPaw.15G139500' => 'cil', 'CiPaw.15G155400' => 'cil', 'CiPaw.16G006000' => 'cil', 'CiPaw.16G013100' => 'cil', 'CiPaw.16G047100' => 'cil', 'CiPaw.16G048900' => 'cil', 'CiPaw.16G070300' => 'cil', 'CSS0000195' => 'camsi', 'CSS0001664' => 'camsi', 'CSS0002566' => 'camsi', 'CSS0003077' => 'camsi', 'CSS0004257' => 'camsi', 'CSS0004495' => 'camsi', 'CSS0004599' => 'camsi', 'CSS0004943' => 'camsi', 'CSS0005302' => 'camsi', 'CSS0006274' => 'camsi', 'CSS0006547' => 'camsi', 'CSS0006860' => 'camsi', 'CSS0008814' => 'camsi', 'CSS0008946' => 'camsi', 'CSS0009093' => 'camsi', 'CSS0010221' => 'camsi', 'CSS0010296' => 'camsi', 'CSS0010386' => 'camsi', 'CSS0010831' => 'camsi', 'CSS0011061' => 'camsi', 'CSS0012008' => 'camsi', 'CSS0012194' => 'camsi', 'CSS0013580' => 'camsi', 'CSS0014176' => 'camsi', 'CSS0014280' => 'camsi', 'CSS0014799' => 'camsi', 'CSS0015368' => 'camsi', 'CSS0017473' => 'camsi', 'CSS0019281' => 'camsi', 'CSS0021320' => 'camsi', 'CSS0021750' => 'camsi', 'CSS0023642' => 'camsi', 'CSS0023792' => 'camsi', 'CSS0031528' => 'camsi', 'CSS0033894' => 'camsi', 'CSS0034959' => 'camsi', 'CSS0035632' => 'camsi', 'CSS0038450' => 'camsi', 'CSS0039293' => 'camsi', 'CSS0041053' => 'camsi', 'CSS0041981' => 'camsi', 'CSS0042573' => 'camsi', 'CSS0042927' => 'camsi', 'CSS0047725' => 'camsi', 'CSS0049636' => 'camsi', 'CSS0050513' => 'camsi', 'DCAR_030203' => 'dca', 'Dinv07939' => 'din', 'FAN01G0456' => 'fan', 'FAN02G3001' => 'fan', 'FAN04G2781' => 'fan', 'FAN05G1385' => 'fan', 'FAN05G3062' => 'fan', 'FAN08G2267' => 'fan', 'FAN10G0481' => 'fan', 'FAN10G1257' => 'fan', 'FAN14G0954' => 'fan', 'FAN14G2347' => 'fan', 'FAN15G0187' => 'fan', 'FAN25G2214' => 'fan', 'FvH4_1g21031' => 'fve', 'FvH4_3g16231' => 'fve', 'FvH4_3g26413' => 'fve', 'FvH4_3g29014' => 'fve', 'FvH4_3g31921' => 'fve', 'FvH4_4g19882' => 'fve', 'FvH4_5g21960' => 'fve', 'FvH4_5g29683' => 'fve', 'FvH4_7g13271' => 'fve', 'Glyma.01G062500' => 'gma', 'Glyma.07G140900' => 'gma', 'Glyma.09G140900' => 'gma', 'Glyma.12G112700' => 'gma', 'Glyma.17G168800' => 'gma', 'HanXRQChr01g0027001' => 'han', 'HanXRQChr04g0120511' => 'han', 'HanXRQChr08g0232381' => 'han', 'HanXRQChr09g0265661' => 'han', 'HanXRQChr13g0416031' => 'han', 'Haze_05835' => 'cav', 'Haze_06597' => 'cav', 'Haze_07921' => 'cav', 'Haze_08599' => 'cav', 'Haze_10686' => 'cav', 'Haze_12994' => 'cav', 'Haze_13466' => 'cav', 'Haze_16101' => 'cav', 'Haze_17766' => 'cav', 'Haze_18456' => 'cav', 'Haze_20229' => 'cav', 'Hma1.2p1_0324F.1_g125640' => 'hma', 'Hma1.2p1_0733F.1_g210230' => 'hma', 'Hma1.2p1_0921F.1_g236870' => 'hma', 'Hma1.2p1_1313F.1_g274940' => 'hma', 'Hma1.2p1_3059F.1_g332230' => 'hma', 'Hund15925' => 'sun', 'Hund19562' => 'sun', 'Hund21925' => 'sun', 'MD03G1177400' => 'mdo', 'MD07G1026100' => 'mdo', 'MD17G1218600' => 'mdo', 'Medtr0867s0010' => 'mtr', 'Medtr6g081150' => 'mtr', 'Os01g0527900' => 'osa', 'Os02g0463725' => 'osa', 'Os02g0785600' => 'osa', 'Os03g0433733' => 'osa', 'Os04g0286500' => 'osa', 'Os05g0227800' => 'osa', 'Os06g0521000' => 'osa', 'Os06g0635500' => 'osa', 'Os06g0660650' => 'osa', 'Os07g0554400' => 'osa', 'Os08g0225900' => 'osa', 'Os08g0561000' => 'osa', 'Os09g0241700' => 'osa', 'Os09g0351900' => 'osa', 'Os11g0220700' => 'osa', 'Os11g0282700' => 'osa', 'Os12g0169300' => 'osa', 'Os12g0228500' => 'osa', 'Os12g0543800' => 'osa', 'PGR044G1547' => 'pgr', 'Potri.005G239150' => 'ptr', 'Potri.010G014250' => 'ptr', 'Prupe.1G172500' => 'ppe', 'Prupe.1G196800' => 'ppe', 'Prupe.1G279700' => 'ppe', 'Prupe.2G026400' => 'ppe', 'Prupe.3G094000' => 'ppe', 'Prupe.4G287300' => 'ppe', 'QL01p022166' => 'qlo', 'QL01p051890' => 'qlo', 'QL02p009469' => 'qlo', 'QL02p046053' => 'qlo', 'QL02p057958' => 'qlo', 'QL02p093127' => 'qlo', 'QL03p006855' => 'qlo', 'QL03p071586' => 'qlo', 'QL04p000022' => 'qlo', 'QL04p000024' => 'qlo', 'QL04p003192' => 'qlo', 'QL05p011416' => 'qlo', 'QL06p039590' => 'qlo', 'QL06p052750' => 'qlo', 'QL06p053821' => 'qlo', 'QL07p025287' => 'qlo', 'QL09p033218' => 'qlo', 'QL09p040841' => 'qlo', 'QL10p020337' => 'qlo', 'QL10p027209' => 'qlo', 'QL10p027969' => 'qlo', 'QL10p048988' => 'qlo', 'QL11p001241' => 'qlo', 'QL11p028487' => 'qlo', 'RcHm_v2.0_Chr2g0105031' => 'rch', 'RcHm_v2.0_Chr2g0117811' => 'rch', 'RcHm_v2.0_Chr6g0270241' => 'rch', 'RcHm_v2.0_Chr7g0215961' => 'rch', 'RcHm_v2.0_Chr7g0231991' => 'rch', 'Rhsim01G0041500' => 'rsi', 'Rhsim01G0115000' => 'rsi', 'Rhsim01G0115400' => 'rsi', 'Rhsim01G0133600' => 'rsi', 'Rhsim01G0159900' => 'rsi', 'Rhsim02G0189400' => 'rsi', 'Rhsim03G0135600' => 'rsi', 'Rhsim03G0149900' => 'rsi', 'Rhsim04G0125600' => 'rsi', 'Rhsim05G0091700' => 'rsi', 'Rhsim05G0092900' => 'rsi', 'Rhsim06G0075000' => 'rsi', 'Rhsim07G0066400' => 'rsi', 'Rhsim07G0156400' => 'rsi', 'Rhsim07G0182200' => 'rsi', 'Rhsim07G0182300' => 'rsi', 'Rhsim08G0180400' => 'rsi', 'Rhsim09G0056800' => 'rsi', 'Rhsim10G0153300' => 'rsi', 'Rhsim11G0012700' => 'rsi', 'Rhsim12G0031800' => 'rsi', 'Rhsim12G0055400' => 'rsi', 'Rhsim12G0091400' => 'rsi', 'Rhsim13G0070800' => 'rsi', 'Rhsim13G0193300' => 'rsi', 'RhsimUnG0111600' => 'rsi', 'RhsimUnG0137500' => 'rsi', 'RhsimUnG0172900' => 'rsi', 'SGA_v2.0_scaffold11G05878' => 'sas', 'SGA_v2.0_scaffold167G38458' => 'sas', 'SGA_v2.0_scaffold19G08588' => 'sas', 'SGA_v2.0_scaffold239G43990' => 'sas', 'SGA_v2.0_scaffold260G45865' => 'sas', 'SGA_v2.0_scaffold309G48177' => 'sas', 'SGA_v2.0_scaffold76G25122' => 'sas', 'SGA_v2.0_scaffold85G26708' => 'sas', 'SHI13914' => 'shi', 'SHI30402' => 'shi', 'TWI09G0020' => 'twi', 'TWI09G0456' => 'twi', 'TWI09G1572' => 'twi', 'TWI12G0266' => 'twi', 'TWI12G1451' => 'twi', 'TWI14G0851' => 'twi', 'TWI15G0796' => 'twi', 'TWI18G0820' => 'twi', 'TWI18G1152' => 'twi', 'TWI23G0007' => 'twi', 'TWI23G0314' => 'twi', 'TWI31G0674' => 'twi', 'TWI31G0938' => 'twi', 'TWI34G0641' => 'twi', 'TWI34G1527' => 'twi', 'TWI36G0193' => 'twi', 'TWI36G0405' => 'twi', 'TWI38G0892' => 'twi', 'TWI38G0936' => 'twi', 'TWI38G2218' => 'twi', 'TWI53G0679' => 'twi', 'TWI53G0863' => 'twi', 'TWI53G1133' => 'twi', 'TWI60G0823' => 'twi', 'TWI63G0919' => 'twi', 'TWI63G1436' => 'twi', 'TWI73G0140' => 'twi', 'TWI73G0419' => 'twi', 'TWI73G0420' => 'twi', 'TWI73G1276' => 'twi', 'TWI74G0405' => 'twi', 'TWI74G0837' => 'twi', 'TWI75G0594' => 'twi', 'TWI75G1615' => 'twi', 'TWI77G0816' => 'twi', 'vmacro03831' => 'vma', 'vmacro13746' => 'vma', 'vmacro16089' => 'vma', 'vmacro22863' => 'vma', 'Zm00001eb085790' => 'zma', 'Zm00001eb114250' => 'zma', 'Zm00001eb138070' => 'zma', 'Zm00001eb167560' => 'zma', 'Zm00001eb199990' => 'zma', 'Zm00001eb368180' => 'zma', 'Zm00001eb382470' => 'zma' ) $gf_id = 'HOM05D001576' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001576' ) $data_identifier = 'HOM05D001576' $data_type = 'gf_id' $species_gene_counts = array( 'aox' => (int) 9, 'acertr' => (int) 3, 'cansat' => (int) 1, 'ccl' => (int) 4, 'cil' => (int) 145, 'camsi' => (int) 46, 'dca' => (int) 1, 'din' => (int) 1, 'fan' => (int) 12, 'fve' => (int) 9, 'gma' => (int) 5, 'han' => (int) 5, 'cav' => (int) 11, 'hma' => (int) 5, 'sun' => (int) 3, 'mdo' => (int) 3, 'mtr' => (int) 2, 'osa' => (int) 19, 'pgr' => (int) 1, 'ptr' => (int) 2, 'ppe' => (int) 6, 'qlo' => (int) 24, 'rch' => (int) 5, 'rsi' => (int) 28, 'sas' => (int) 8, 'shi' => (int) 2, 'twi' => (int) 35, 'vma' => (int) 4, 'zma' => (int) 7 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb382470' $species_info = array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ) $local_species = 'twi' $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' => 'HOM05D001576', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '406', 'num_species' => '29' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'Aqoxy1G01456' => 'aox', 'Aqoxy1G02949' => 'aox', 'Aqoxy3G01274' => 'aox', 'Aqoxy3G02110' => 'aox', 'Aqoxy3G02268' => 'aox', 'Aqoxy5G02702' => 'aox', 'Aqoxy5G02988' => 'aox', 'Aqoxy5G03427' => 'aox', 'Aqoxy6G02363' => 'aox', 'Atru.chr1.3225' => 'acertr', 'Atru.chr8.1198' => 'acertr', 'Atru.chr9.790' => 'acertr', 'CANSAT01G3197' => 'cansat', 'Ciclev10003979m.g' => 'ccl', 'Ciclev10017471m.g' => 'ccl', 'Ciclev10018206m.g' => 'ccl', 'Ciclev10033751m.g' => 'ccl', 'CiPaw.01G000900' => 'cil', 'CiPaw.01G001000' => 'cil', 'CiPaw.01G033500' => 'cil', 'CiPaw.01G060300' => 'cil', 'CiPaw.01G070200' => 'cil', 'CiPaw.01G075100' => 'cil', 'CiPaw.01G084700' => 'cil', 'CiPaw.01G087900' => 'cil', 'CiPaw.01G092600' => 'cil', 'CiPaw.01G097200' => 'cil', 'CiPaw.01G098300' => 'cil', 'CiPaw.01G110200' => 'cil', 'CiPaw.01G118700' => 'cil', 'CiPaw.01G121200' => 'cil', 'CiPaw.01G132500' => 'cil', 'CiPaw.01G146900' => 'cil', 'CiPaw.01G174000' => 'cil', 'CiPaw.01G179900' => 'cil', 'CiPaw.01G183400' => 'cil', 'CiPaw.01G240000' => 'cil', 'CiPaw.01G283500' => 'cil', 'CiPaw.01G307400' => 'cil', 'CiPaw.02G030800' => 'cil', 'CiPaw.02G047200' => 'cil', 'CiPaw.02G050500' => 'cil', 'CiPaw.02G069900' => 'cil', 'CiPaw.02G091600' => 'cil', 'CiPaw.02G095000' => 'cil', 'CiPaw.02G131900' => 'cil', 'CiPaw.03G043000' => 'cil', 'CiPaw.03G069900' => 'cil', 'CiPaw.03G088100' => 'cil', 'CiPaw.03G089300' => 'cil', 'CiPaw.03G093100' => 'cil', 'CiPaw.03G129800' => 'cil', 'CiPaw.03G131200' => 'cil', 'CiPaw.03G134500' => 'cil', 'CiPaw.03G152100' => 'cil', 'CiPaw.03G162700' => 'cil', 'CiPaw.03G172800' => 'cil', 'CiPaw.03G175800' => 'cil', 'CiPaw.03G181800' => 'cil', 'CiPaw.03G191400' => 'cil', 'CiPaw.03G198300' => 'cil', 'CiPaw.03G201300' => 'cil', 'CiPaw.03G224700' => 'cil', 'CiPaw.03G225000' => 'cil', 'CiPaw.04G065100' => 'cil', 'CiPaw.04G080400' => 'cil', 'CiPaw.04G113500' => 'cil', 'CiPaw.04G121900' => 'cil', 'CiPaw.04G144100' => 'cil', 'CiPaw.04G176500' => 'cil', 'CiPaw.05G086200' => 'cil', 'CiPaw.05G100200' => 'cil', 'CiPaw.05G114200' => 'cil', 'CiPaw.05G126800' => 'cil', 'CiPaw.05G228800' => 'cil', 'CiPaw.05G230600' => 'cil', 'CiPaw.05G236500' => 'cil', 'CiPaw.05G244800' => 'cil', 'CiPaw.06G026600' => 'cil', 'CiPaw.06G027900' => 'cil', 'CiPaw.06G051800' => 'cil', 'CiPaw.06G128500' => 'cil', 'CiPaw.06G165900' => 'cil', 'CiPaw.07G045400' => 'cil', 'CiPaw.07G048000' => 'cil', 'CiPaw.07G052000' => 'cil', 'CiPaw.07G073800' => 'cil', 'CiPaw.07G099700' => 'cil', 'CiPaw.07G108700' => 'cil', 'CiPaw.07G120000' => 'cil', 'CiPaw.07G134100' => 'cil', 'CiPaw.07G147000' => 'cil', 'CiPaw.07G149700' => 'cil', 'CiPaw.07G178300' => 'cil', 'CiPaw.07G184900' => 'cil', 'CiPaw.08G044500' => 'cil', 'CiPaw.08G046900' => 'cil', 'CiPaw.08G047300' => 'cil', 'CiPaw.08G115400' => 'cil', 'CiPaw.08G134700' => 'cil', 'CiPaw.08G157400' => 'cil', 'CiPaw.09G014300' => 'cil', 'CiPaw.09G088900' => 'cil', 'CiPaw.09G130900' => 'cil', 'CiPaw.09G133100' => 'cil', 'CiPaw.09G151300' => 'cil', 'CiPaw.09G172800' => 'cil', 'CiPaw.09G174900' => 'cil', 'CiPaw.09G175000' => 'cil', 'CiPaw.10G012800' => 'cil', 'CiPaw.10G028800' => 'cil', 'CiPaw.10G044700' => 'cil', 'CiPaw.10G067400' => 'cil', 'CiPaw.10G115900' => 'cil', 'CiPaw.10G126200' => 'cil', 'CiPaw.10G139700' => 'cil', 'CiPaw.10G155100' => 'cil', 'CiPaw.11G011300' => 'cil', 'CiPaw.11G025900' => 'cil', 'CiPaw.11G104100' => 'cil', 'CiPaw.11G142700' => 'cil', 'CiPaw.11G164500' => 'cil', 'CiPaw.11G189100' => 'cil', 'CiPaw.11G197100' => 'cil', 'CiPaw.12G006100' => 'cil', 'CiPaw.12G038500' => 'cil', 'CiPaw.12G041400' => 'cil', 'CiPaw.12G041600' => 'cil', 'CiPaw.12G051300' => 'cil', 'CiPaw.12G101800' => 'cil', 'CiPaw.12G107800' => 'cil', 'CiPaw.13G033200' => 'cil', 'CiPaw.13G129900' => 'cil', 'CiPaw.13G160200' => 'cil', 'CiPaw.14G018900' => 'cil', 'CiPaw.14G029000' => 'cil', 'CiPaw.14G031000' => 'cil', 'CiPaw.14G032000' => 'cil', 'CiPaw.14G032300' => 'cil', 'CiPaw.14G040600' => 'cil', 'CiPaw.14G060500' => 'cil', 'CiPaw.14G061500' => 'cil', 'CiPaw.14G077500' => 'cil', 'CiPaw.14G088300' => 'cil', 'CiPaw.14G108500' => 'cil', 'CiPaw.14G121300' => 'cil', 'CiPaw.14G133000' => 'cil', 'CiPaw.14G134600' => 'cil', 'CiPaw.15G027200' => 'cil', 'CiPaw.15G037700' => 'cil', 'CiPaw.15G050900' => 'cil', 'CiPaw.15G067200' => 'cil', 'CiPaw.15G072000' => 'cil', 'CiPaw.15G112900' => 'cil', 'CiPaw.15G133200' => 'cil', 'CiPaw.15G139500' => 'cil', 'CiPaw.15G155400' => 'cil', 'CiPaw.16G006000' => 'cil', 'CiPaw.16G013100' => 'cil', 'CiPaw.16G047100' => 'cil', 'CiPaw.16G048900' => 'cil', 'CiPaw.16G070300' => 'cil', 'CSS0000195' => 'camsi', 'CSS0001664' => 'camsi', 'CSS0002566' => 'camsi', 'CSS0003077' => 'camsi', 'CSS0004257' => 'camsi', 'CSS0004495' => 'camsi', 'CSS0004599' => 'camsi', 'CSS0004943' => 'camsi', 'CSS0005302' => 'camsi', 'CSS0006274' => 'camsi', 'CSS0006547' => 'camsi', 'CSS0006860' => 'camsi', 'CSS0008814' => 'camsi', 'CSS0008946' => 'camsi', 'CSS0009093' => 'camsi', 'CSS0010221' => 'camsi', 'CSS0010296' => 'camsi', 'CSS0010386' => 'camsi', 'CSS0010831' => 'camsi', 'CSS0011061' => 'camsi', 'CSS0012008' => 'camsi', 'CSS0012194' => 'camsi', 'CSS0013580' => 'camsi', 'CSS0014176' => 'camsi', 'CSS0014280' => 'camsi', 'CSS0014799' => 'camsi', 'CSS0015368' => 'camsi', 'CSS0017473' => 'camsi', 'CSS0019281' => 'camsi', 'CSS0021320' => 'camsi', 'CSS0021750' => 'camsi', 'CSS0023642' => 'camsi', 'CSS0023792' => 'camsi', 'CSS0031528' => 'camsi', 'CSS0033894' => 'camsi', 'CSS0034959' => 'camsi', 'CSS0035632' => 'camsi', 'CSS0038450' => 'camsi', 'CSS0039293' => 'camsi', 'CSS0041053' => 'camsi', 'CSS0041981' => 'camsi', 'CSS0042573' => 'camsi', 'CSS0042927' => 'camsi', 'CSS0047725' => 'camsi', 'CSS0049636' => 'camsi', 'CSS0050513' => 'camsi', 'DCAR_030203' => 'dca', 'Dinv07939' => 'din', 'FAN01G0456' => 'fan', 'FAN02G3001' => 'fan', 'FAN04G2781' => 'fan', 'FAN05G1385' => 'fan', 'FAN05G3062' => 'fan', 'FAN08G2267' => 'fan', 'FAN10G0481' => 'fan', 'FAN10G1257' => 'fan', 'FAN14G0954' => 'fan', 'FAN14G2347' => 'fan', 'FAN15G0187' => 'fan', 'FAN25G2214' => 'fan', 'FvH4_1g21031' => 'fve', 'FvH4_3g16231' => 'fve', 'FvH4_3g26413' => 'fve', 'FvH4_3g29014' => 'fve', 'FvH4_3g31921' => 'fve', 'FvH4_4g19882' => 'fve', 'FvH4_5g21960' => 'fve', 'FvH4_5g29683' => 'fve', 'FvH4_7g13271' => 'fve', 'Glyma.01G062500' => 'gma', 'Glyma.07G140900' => 'gma', 'Glyma.09G140900' => 'gma', 'Glyma.12G112700' => 'gma', 'Glyma.17G168800' => 'gma', 'HanXRQChr01g0027001' => 'han', 'HanXRQChr04g0120511' => 'han', 'HanXRQChr08g0232381' => 'han', 'HanXRQChr09g0265661' => 'han', 'HanXRQChr13g0416031' => 'han', 'Haze_05835' => 'cav', 'Haze_06597' => 'cav', 'Haze_07921' => 'cav', 'Haze_08599' => 'cav', 'Haze_10686' => 'cav', 'Haze_12994' => 'cav', 'Haze_13466' => 'cav', 'Haze_16101' => 'cav', 'Haze_17766' => 'cav', 'Haze_18456' => 'cav', 'Haze_20229' => 'cav', 'Hma1.2p1_0324F.1_g125640' => 'hma', 'Hma1.2p1_0733F.1_g210230' => 'hma', 'Hma1.2p1_0921F.1_g236870' => 'hma', 'Hma1.2p1_1313F.1_g274940' => 'hma', 'Hma1.2p1_3059F.1_g332230' => 'hma', 'Hund15925' => 'sun', 'Hund19562' => 'sun', 'Hund21925' => 'sun', 'MD03G1177400' => 'mdo', 'MD07G1026100' => 'mdo', 'MD17G1218600' => 'mdo', 'Medtr0867s0010' => 'mtr', 'Medtr6g081150' => 'mtr', 'Os01g0527900' => 'osa', 'Os02g0463725' => 'osa', 'Os02g0785600' => 'osa', 'Os03g0433733' => 'osa', 'Os04g0286500' => 'osa', 'Os05g0227800' => 'osa', 'Os06g0521000' => 'osa', 'Os06g0635500' => 'osa', 'Os06g0660650' => 'osa', 'Os07g0554400' => 'osa', 'Os08g0225900' => 'osa', 'Os08g0561000' => 'osa', 'Os09g0241700' => 'osa', 'Os09g0351900' => 'osa', 'Os11g0220700' => 'osa', 'Os11g0282700' => 'osa', 'Os12g0169300' => 'osa', 'Os12g0228500' => 'osa', 'Os12g0543800' => 'osa', 'PGR044G1547' => 'pgr', 'Potri.005G239150' => 'ptr', 'Potri.010G014250' => 'ptr', 'Prupe.1G172500' => 'ppe', 'Prupe.1G196800' => 'ppe', 'Prupe.1G279700' => 'ppe', 'Prupe.2G026400' => 'ppe', 'Prupe.3G094000' => 'ppe', 'Prupe.4G287300' => 'ppe', 'QL01p022166' => 'qlo', 'QL01p051890' => 'qlo', 'QL02p009469' => 'qlo', 'QL02p046053' => 'qlo', 'QL02p057958' => 'qlo', 'QL02p093127' => 'qlo', 'QL03p006855' => 'qlo', 'QL03p071586' => 'qlo', 'QL04p000022' => 'qlo', 'QL04p000024' => 'qlo', 'QL04p003192' => 'qlo', 'QL05p011416' => 'qlo', 'QL06p039590' => 'qlo', 'QL06p052750' => 'qlo', 'QL06p053821' => 'qlo', 'QL07p025287' => 'qlo', 'QL09p033218' => 'qlo', 'QL09p040841' => 'qlo', 'QL10p020337' => 'qlo', 'QL10p027209' => 'qlo', 'QL10p027969' => 'qlo', 'QL10p048988' => 'qlo', 'QL11p001241' => 'qlo', 'QL11p028487' => 'qlo', 'RcHm_v2.0_Chr2g0105031' => 'rch', 'RcHm_v2.0_Chr2g0117811' => 'rch', 'RcHm_v2.0_Chr6g0270241' => 'rch', 'RcHm_v2.0_Chr7g0215961' => 'rch', 'RcHm_v2.0_Chr7g0231991' => 'rch', 'Rhsim01G0041500' => 'rsi', 'Rhsim01G0115000' => 'rsi', 'Rhsim01G0115400' => 'rsi', 'Rhsim01G0133600' => 'rsi', 'Rhsim01G0159900' => 'rsi', 'Rhsim02G0189400' => 'rsi', 'Rhsim03G0135600' => 'rsi', 'Rhsim03G0149900' => 'rsi', 'Rhsim04G0125600' => 'rsi', 'Rhsim05G0091700' => 'rsi', 'Rhsim05G0092900' => 'rsi', 'Rhsim06G0075000' => 'rsi', 'Rhsim07G0066400' => 'rsi', 'Rhsim07G0156400' => 'rsi', 'Rhsim07G0182200' => 'rsi', 'Rhsim07G0182300' => 'rsi', 'Rhsim08G0180400' => 'rsi', 'Rhsim09G0056800' => 'rsi', 'Rhsim10G0153300' => 'rsi', 'Rhsim11G0012700' => 'rsi', 'Rhsim12G0031800' => 'rsi', 'Rhsim12G0055400' => 'rsi', 'Rhsim12G0091400' => 'rsi', 'Rhsim13G0070800' => 'rsi', 'Rhsim13G0193300' => 'rsi', 'RhsimUnG0111600' => 'rsi', 'RhsimUnG0137500' => 'rsi', 'RhsimUnG0172900' => 'rsi', 'SGA_v2.0_scaffold11G05878' => 'sas', 'SGA_v2.0_scaffold167G38458' => 'sas', 'SGA_v2.0_scaffold19G08588' => 'sas', 'SGA_v2.0_scaffold239G43990' => 'sas', 'SGA_v2.0_scaffold260G45865' => 'sas', 'SGA_v2.0_scaffold309G48177' => 'sas', 'SGA_v2.0_scaffold76G25122' => 'sas', 'SGA_v2.0_scaffold85G26708' => 'sas', 'SHI13914' => 'shi', 'SHI30402' => 'shi', 'TWI09G0020' => 'twi', 'TWI09G0456' => 'twi', 'TWI09G1572' => 'twi', 'TWI12G0266' => 'twi', 'TWI12G1451' => 'twi', 'TWI14G0851' => 'twi', 'TWI15G0796' => 'twi', 'TWI18G0820' => 'twi', 'TWI18G1152' => 'twi', 'TWI23G0007' => 'twi', 'TWI23G0314' => 'twi', 'TWI31G0674' => 'twi', 'TWI31G0938' => 'twi', 'TWI34G0641' => 'twi', 'TWI34G1527' => 'twi', 'TWI36G0193' => 'twi', 'TWI36G0405' => 'twi', 'TWI38G0892' => 'twi', 'TWI38G0936' => 'twi', 'TWI38G2218' => 'twi', 'TWI53G0679' => 'twi', 'TWI53G0863' => 'twi', 'TWI53G1133' => 'twi', 'TWI60G0823' => 'twi', 'TWI63G0919' => 'twi', 'TWI63G1436' => 'twi', 'TWI73G0140' => 'twi', 'TWI73G0419' => 'twi', 'TWI73G0420' => 'twi', 'TWI73G1276' => 'twi', 'TWI74G0405' => 'twi', 'TWI74G0837' => 'twi', 'TWI75G0594' => 'twi', 'TWI75G1615' => 'twi', 'TWI77G0816' => 'twi', 'vmacro03831' => 'vma', 'vmacro13746' => 'vma', 'vmacro16089' => 'vma', 'vmacro22863' => 'vma', 'Zm00001eb085790' => 'zma', 'Zm00001eb114250' => 'zma', 'Zm00001eb138070' => 'zma', 'Zm00001eb167560' => 'zma', 'Zm00001eb199990' => 'zma', 'Zm00001eb368180' => 'zma', 'Zm00001eb382470' => 'zma' ), 'gf_id' => 'HOM05D001576', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001576' ), 'data_identifier' => 'HOM05D001576', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001576', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '406', 'num_species' => '29' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'Aqoxy1G01456' => 'aox', 'Aqoxy1G02949' => 'aox', 'Aqoxy3G01274' => 'aox', 'Aqoxy3G02110' => 'aox', 'Aqoxy3G02268' => 'aox', 'Aqoxy5G02702' => 'aox', 'Aqoxy5G02988' => 'aox', 'Aqoxy5G03427' => 'aox', 'Aqoxy6G02363' => 'aox', 'Atru.chr1.3225' => 'acertr', 'Atru.chr8.1198' => 'acertr', 'Atru.chr9.790' => 'acertr', 'CANSAT01G3197' => 'cansat', 'Ciclev10003979m.g' => 'ccl', 'Ciclev10017471m.g' => 'ccl', 'Ciclev10018206m.g' => 'ccl', 'Ciclev10033751m.g' => 'ccl', 'CiPaw.01G000900' => 'cil', 'CiPaw.01G001000' => 'cil', 'CiPaw.01G033500' => 'cil', 'CiPaw.01G060300' => 'cil', 'CiPaw.01G070200' => 'cil', 'CiPaw.01G075100' => 'cil', 'CiPaw.01G084700' => 'cil', 'CiPaw.01G087900' => 'cil', 'CiPaw.01G092600' => 'cil', 'CiPaw.01G097200' => 'cil', 'CiPaw.01G098300' => 'cil', 'CiPaw.01G110200' => 'cil', 'CiPaw.01G118700' => 'cil', 'CiPaw.01G121200' => 'cil', 'CiPaw.01G132500' => 'cil', 'CiPaw.01G146900' => 'cil', 'CiPaw.01G174000' => 'cil', 'CiPaw.01G179900' => 'cil', 'CiPaw.01G183400' => 'cil', 'CiPaw.01G240000' => 'cil', 'CiPaw.01G283500' => 'cil', 'CiPaw.01G307400' => 'cil', 'CiPaw.02G030800' => 'cil', 'CiPaw.02G047200' => 'cil', 'CiPaw.02G050500' => 'cil', 'CiPaw.02G069900' => 'cil', 'CiPaw.02G091600' => 'cil', 'CiPaw.02G095000' => 'cil', 'CiPaw.02G131900' => 'cil', 'CiPaw.03G043000' => 'cil', 'CiPaw.03G069900' => 'cil', 'CiPaw.03G088100' => 'cil', 'CiPaw.03G089300' => 'cil', 'CiPaw.03G093100' => 'cil', 'CiPaw.03G129800' => 'cil', 'CiPaw.03G131200' => 'cil', 'CiPaw.03G134500' => 'cil', 'CiPaw.03G152100' => 'cil', 'CiPaw.03G162700' => 'cil', 'CiPaw.03G172800' => 'cil', 'CiPaw.03G175800' => 'cil', 'CiPaw.03G181800' => 'cil', 'CiPaw.03G191400' => 'cil', 'CiPaw.03G198300' => 'cil', 'CiPaw.03G201300' => 'cil', 'CiPaw.03G224700' => 'cil', 'CiPaw.03G225000' => 'cil', 'CiPaw.04G065100' => 'cil', 'CiPaw.04G080400' => 'cil', 'CiPaw.04G113500' => 'cil', 'CiPaw.04G121900' => 'cil', 'CiPaw.04G144100' => 'cil', 'CiPaw.04G176500' => 'cil', 'CiPaw.05G086200' => 'cil', 'CiPaw.05G100200' => 'cil', 'CiPaw.05G114200' => 'cil', 'CiPaw.05G126800' => 'cil', 'CiPaw.05G228800' => 'cil', 'CiPaw.05G230600' => 'cil', 'CiPaw.05G236500' => 'cil', 'CiPaw.05G244800' => 'cil', 'CiPaw.06G026600' => 'cil', 'CiPaw.06G027900' => 'cil', 'CiPaw.06G051800' => 'cil', 'CiPaw.06G128500' => 'cil', 'CiPaw.06G165900' => 'cil', 'CiPaw.07G045400' => 'cil', 'CiPaw.07G048000' => 'cil', 'CiPaw.07G052000' => 'cil', 'CiPaw.07G073800' => 'cil', 'CiPaw.07G099700' => 'cil', 'CiPaw.07G108700' => 'cil', 'CiPaw.07G120000' => 'cil', 'CiPaw.07G134100' => 'cil', 'CiPaw.07G147000' => 'cil', 'CiPaw.07G149700' => 'cil', 'CiPaw.07G178300' => 'cil', 'CiPaw.07G184900' => 'cil', 'CiPaw.08G044500' => 'cil', 'CiPaw.08G046900' => 'cil', 'CiPaw.08G047300' => 'cil', 'CiPaw.08G115400' => 'cil', 'CiPaw.08G134700' => 'cil', 'CiPaw.08G157400' => 'cil', 'CiPaw.09G014300' => 'cil', 'CiPaw.09G088900' => 'cil', 'CiPaw.09G130900' => 'cil', 'CiPaw.09G133100' => 'cil', 'CiPaw.09G151300' => 'cil', 'CiPaw.09G172800' => 'cil', 'CiPaw.09G174900' => 'cil', 'CiPaw.09G175000' => 'cil', 'CiPaw.10G012800' => 'cil', 'CiPaw.10G028800' => 'cil', 'CiPaw.10G044700' => 'cil', 'CiPaw.10G067400' => 'cil', 'CiPaw.10G115900' => 'cil', 'CiPaw.10G126200' => 'cil', 'CiPaw.10G139700' => 'cil', 'CiPaw.10G155100' => 'cil', 'CiPaw.11G011300' => 'cil', 'CiPaw.11G025900' => 'cil', 'CiPaw.11G104100' => 'cil', 'CiPaw.11G142700' => 'cil', 'CiPaw.11G164500' => 'cil', 'CiPaw.11G189100' => 'cil', 'CiPaw.11G197100' => 'cil', 'CiPaw.12G006100' => 'cil', 'CiPaw.12G038500' => 'cil', 'CiPaw.12G041400' => 'cil', 'CiPaw.12G041600' => 'cil', 'CiPaw.12G051300' => 'cil', 'CiPaw.12G101800' => 'cil', 'CiPaw.12G107800' => 'cil', 'CiPaw.13G033200' => 'cil', 'CiPaw.13G129900' => 'cil', 'CiPaw.13G160200' => 'cil', 'CiPaw.14G018900' => 'cil', 'CiPaw.14G029000' => 'cil', 'CiPaw.14G031000' => 'cil', 'CiPaw.14G032000' => 'cil', 'CiPaw.14G032300' => 'cil', 'CiPaw.14G040600' => 'cil', 'CiPaw.14G060500' => 'cil', 'CiPaw.14G061500' => 'cil', 'CiPaw.14G077500' => 'cil', 'CiPaw.14G088300' => 'cil', 'CiPaw.14G108500' => 'cil', 'CiPaw.14G121300' => 'cil', 'CiPaw.14G133000' => 'cil', 'CiPaw.14G134600' => 'cil', 'CiPaw.15G027200' => 'cil', 'CiPaw.15G037700' => 'cil', 'CiPaw.15G050900' => 'cil', 'CiPaw.15G067200' => 'cil', 'CiPaw.15G072000' => 'cil', 'CiPaw.15G112900' => 'cil', 'CiPaw.15G133200' => 'cil', 'CiPaw.15G139500' => 'cil', 'CiPaw.15G155400' => 'cil', 'CiPaw.16G006000' => 'cil', 'CiPaw.16G013100' => 'cil', 'CiPaw.16G047100' => 'cil', 'CiPaw.16G048900' => 'cil', 'CiPaw.16G070300' => 'cil', 'CSS0000195' => 'camsi', 'CSS0001664' => 'camsi', 'CSS0002566' => 'camsi', 'CSS0003077' => 'camsi', 'CSS0004257' => 'camsi', 'CSS0004495' => 'camsi', 'CSS0004599' => 'camsi', 'CSS0004943' => 'camsi', 'CSS0005302' => 'camsi', 'CSS0006274' => 'camsi', 'CSS0006547' => 'camsi', 'CSS0006860' => 'camsi', 'CSS0008814' => 'camsi', 'CSS0008946' => 'camsi', 'CSS0009093' => 'camsi', 'CSS0010221' => 'camsi', 'CSS0010296' => 'camsi', 'CSS0010386' => 'camsi', 'CSS0010831' => 'camsi', 'CSS0011061' => 'camsi', 'CSS0012008' => 'camsi', 'CSS0012194' => 'camsi', 'CSS0013580' => 'camsi', 'CSS0014176' => 'camsi', 'CSS0014280' => 'camsi', 'CSS0014799' => 'camsi', 'CSS0015368' => 'camsi', 'CSS0017473' => 'camsi', 'CSS0019281' => 'camsi', 'CSS0021320' => 'camsi', 'CSS0021750' => 'camsi', 'CSS0023642' => 'camsi', 'CSS0023792' => 'camsi', 'CSS0031528' => 'camsi', 'CSS0033894' => 'camsi', 'CSS0034959' => 'camsi', 'CSS0035632' => 'camsi', 'CSS0038450' => 'camsi', 'CSS0039293' => 'camsi', 'CSS0041053' => 'camsi', 'CSS0041981' => 'camsi', 'CSS0042573' => 'camsi', 'CSS0042927' => 'camsi', 'CSS0047725' => 'camsi', 'CSS0049636' => 'camsi', 'CSS0050513' => 'camsi', 'DCAR_030203' => 'dca', 'Dinv07939' => 'din', 'FAN01G0456' => 'fan', 'FAN02G3001' => 'fan', 'FAN04G2781' => 'fan', 'FAN05G1385' => 'fan', 'FAN05G3062' => 'fan', 'FAN08G2267' => 'fan', 'FAN10G0481' => 'fan', 'FAN10G1257' => 'fan', 'FAN14G0954' => 'fan', 'FAN14G2347' => 'fan', 'FAN15G0187' => 'fan', 'FAN25G2214' => 'fan', 'FvH4_1g21031' => 'fve', 'FvH4_3g16231' => 'fve', 'FvH4_3g26413' => 'fve', 'FvH4_3g29014' => 'fve', 'FvH4_3g31921' => 'fve', 'FvH4_4g19882' => 'fve', 'FvH4_5g21960' => 'fve', 'FvH4_5g29683' => 'fve', 'FvH4_7g13271' => 'fve', 'Glyma.01G062500' => 'gma', 'Glyma.07G140900' => 'gma', 'Glyma.09G140900' => 'gma', 'Glyma.12G112700' => 'gma', 'Glyma.17G168800' => 'gma', 'HanXRQChr01g0027001' => 'han', 'HanXRQChr04g0120511' => 'han', 'HanXRQChr08g0232381' => 'han', 'HanXRQChr09g0265661' => 'han', 'HanXRQChr13g0416031' => 'han', 'Haze_05835' => 'cav', 'Haze_06597' => 'cav', 'Haze_07921' => 'cav', 'Haze_08599' => 'cav', 'Haze_10686' => 'cav', 'Haze_12994' => 'cav', 'Haze_13466' => 'cav', 'Haze_16101' => 'cav', 'Haze_17766' => 'cav', 'Haze_18456' => 'cav', 'Haze_20229' => 'cav', 'Hma1.2p1_0324F.1_g125640' => 'hma', 'Hma1.2p1_0733F.1_g210230' => 'hma', 'Hma1.2p1_0921F.1_g236870' => 'hma', 'Hma1.2p1_1313F.1_g274940' => 'hma', 'Hma1.2p1_3059F.1_g332230' => 'hma', 'Hund15925' => 'sun', 'Hund19562' => 'sun', 'Hund21925' => 'sun', 'MD03G1177400' => 'mdo', 'MD07G1026100' => 'mdo', 'MD17G1218600' => 'mdo', 'Medtr0867s0010' => 'mtr', 'Medtr6g081150' => 'mtr', 'Os01g0527900' => 'osa', 'Os02g0463725' => 'osa', 'Os02g0785600' => 'osa', 'Os03g0433733' => 'osa', 'Os04g0286500' => 'osa', 'Os05g0227800' => 'osa', 'Os06g0521000' => 'osa', 'Os06g0635500' => 'osa', 'Os06g0660650' => 'osa', 'Os07g0554400' => 'osa', 'Os08g0225900' => 'osa', 'Os08g0561000' => 'osa', 'Os09g0241700' => 'osa', 'Os09g0351900' => 'osa', 'Os11g0220700' => 'osa', 'Os11g0282700' => 'osa', 'Os12g0169300' => 'osa', 'Os12g0228500' => 'osa', 'Os12g0543800' => 'osa', 'PGR044G1547' => 'pgr', 'Potri.005G239150' => 'ptr', 'Potri.010G014250' => 'ptr', 'Prupe.1G172500' => 'ppe', 'Prupe.1G196800' => 'ppe', 'Prupe.1G279700' => 'ppe', 'Prupe.2G026400' => 'ppe', 'Prupe.3G094000' => 'ppe', 'Prupe.4G287300' => 'ppe', 'QL01p022166' => 'qlo', 'QL01p051890' => 'qlo', 'QL02p009469' => 'qlo', 'QL02p046053' => 'qlo', 'QL02p057958' => 'qlo', 'QL02p093127' => 'qlo', 'QL03p006855' => 'qlo', 'QL03p071586' => 'qlo', 'QL04p000022' => 'qlo', 'QL04p000024' => 'qlo', 'QL04p003192' => 'qlo', 'QL05p011416' => 'qlo', 'QL06p039590' => 'qlo', 'QL06p052750' => 'qlo', 'QL06p053821' => 'qlo', 'QL07p025287' => 'qlo', 'QL09p033218' => 'qlo', 'QL09p040841' => 'qlo', 'QL10p020337' => 'qlo', 'QL10p027209' => 'qlo', 'QL10p027969' => 'qlo', 'QL10p048988' => 'qlo', 'QL11p001241' => 'qlo', 'QL11p028487' => 'qlo', 'RcHm_v2.0_Chr2g0105031' => 'rch', 'RcHm_v2.0_Chr2g0117811' => 'rch', 'RcHm_v2.0_Chr6g0270241' => 'rch', 'RcHm_v2.0_Chr7g0215961' => 'rch', 'RcHm_v2.0_Chr7g0231991' => 'rch', 'Rhsim01G0041500' => 'rsi', 'Rhsim01G0115000' => 'rsi', 'Rhsim01G0115400' => 'rsi', 'Rhsim01G0133600' => 'rsi', 'Rhsim01G0159900' => 'rsi', 'Rhsim02G0189400' => 'rsi', 'Rhsim03G0135600' => 'rsi', 'Rhsim03G0149900' => 'rsi', 'Rhsim04G0125600' => 'rsi', 'Rhsim05G0091700' => 'rsi', 'Rhsim05G0092900' => 'rsi', 'Rhsim06G0075000' => 'rsi', 'Rhsim07G0066400' => 'rsi', 'Rhsim07G0156400' => 'rsi', 'Rhsim07G0182200' => 'rsi', 'Rhsim07G0182300' => 'rsi', 'Rhsim08G0180400' => 'rsi', 'Rhsim09G0056800' => 'rsi', 'Rhsim10G0153300' => 'rsi', 'Rhsim11G0012700' => 'rsi', 'Rhsim12G0031800' => 'rsi', 'Rhsim12G0055400' => 'rsi', 'Rhsim12G0091400' => 'rsi', 'Rhsim13G0070800' => 'rsi', 'Rhsim13G0193300' => 'rsi', 'RhsimUnG0111600' => 'rsi', 'RhsimUnG0137500' => 'rsi', 'RhsimUnG0172900' => 'rsi', 'SGA_v2.0_scaffold11G05878' => 'sas', 'SGA_v2.0_scaffold167G38458' => 'sas', 'SGA_v2.0_scaffold19G08588' => 'sas', 'SGA_v2.0_scaffold239G43990' => 'sas', 'SGA_v2.0_scaffold260G45865' => 'sas', 'SGA_v2.0_scaffold309G48177' => 'sas', 'SGA_v2.0_scaffold76G25122' => 'sas', 'SGA_v2.0_scaffold85G26708' => 'sas', 'SHI13914' => 'shi', 'SHI30402' => 'shi', 'TWI09G0020' => 'twi', 'TWI09G0456' => 'twi', 'TWI09G1572' => 'twi', 'TWI12G0266' => 'twi', 'TWI12G1451' => 'twi', 'TWI14G0851' => 'twi', 'TWI15G0796' => 'twi', 'TWI18G0820' => 'twi', 'TWI18G1152' => 'twi', 'TWI23G0007' => 'twi', 'TWI23G0314' => 'twi', 'TWI31G0674' => 'twi', 'TWI31G0938' => 'twi', 'TWI34G0641' => 'twi', 'TWI34G1527' => 'twi', 'TWI36G0193' => 'twi', 'TWI36G0405' => 'twi', 'TWI38G0892' => 'twi', 'TWI38G0936' => 'twi', 'TWI38G2218' => 'twi', 'TWI53G0679' => 'twi', 'TWI53G0863' => 'twi', 'TWI53G1133' => 'twi', 'TWI60G0823' => 'twi', 'TWI63G0919' => 'twi', 'TWI63G1436' => 'twi', 'TWI73G0140' => 'twi', 'TWI73G0419' => 'twi', 'TWI73G0420' => 'twi', 'TWI73G1276' => 'twi', 'TWI74G0405' => 'twi', 'TWI74G0837' => 'twi', 'TWI75G0594' => 'twi', 'TWI75G1615' => 'twi', 'TWI77G0816' => 'twi', 'vmacro03831' => 'vma', 'vmacro13746' => 'vma', 'vmacro16089' => 'vma', 'vmacro22863' => 'vma', 'Zm00001eb085790' => 'zma', 'Zm00001eb114250' => 'zma', 'Zm00001eb138070' => 'zma', 'Zm00001eb167560' => 'zma', 'Zm00001eb199990' => 'zma', 'Zm00001eb368180' => 'zma', 'Zm00001eb382470' => 'zma' ) $gf_id = 'HOM05D001576' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001576' ) $data_identifier = 'HOM05D001576' $data_type = 'gf_id' $species_gene_counts = array( 'aox' => (int) 9, 'acertr' => (int) 3, 'cansat' => (int) 1, 'ccl' => (int) 4, 'cil' => (int) 145, 'camsi' => (int) 46, 'dca' => (int) 1, 'din' => (int) 1, 'fan' => (int) 12, 'fve' => (int) 9, 'gma' => (int) 5, 'han' => (int) 5, 'cav' => (int) 11, 'hma' => (int) 5, 'sun' => (int) 3, 'mdo' => (int) 3, 'mtr' => (int) 2, 'osa' => (int) 19, 'pgr' => (int) 1, 'ptr' => (int) 2, 'ppe' => (int) 6, 'qlo' => (int) 24, 'rch' => (int) 5, 'rsi' => (int) 28, 'sas' => (int) 8, 'shi' => (int) 2, 'twi' => (int) 35, 'vma' => (int) 4, 'zma' => (int) 7 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb382470' $species_info = array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ) $local_species = 'vma' $disabled = '' $selected = '' $num_hits = (int) 0include - APP/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp, line 33 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933 View::_renderElement() - CORE/Cake/View/View.php, line 1224 View::element() - CORE/Cake/View/View.php, line 418 include - APP/View/Elements/analysis/phylogenetics_module/gf_data_settings.ctp, line 37 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933 View::_renderElement() - CORE/Cake/View/View.php, line 1224 View::element() - CORE/Cake/View/View.php, line 418 include - APP/View/Elements/analysis/phylogenetics_module/parameter_selection.ctp, line 64 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933 View::_renderElement() - CORE/Cake/View/View.php, line 1224 View::element() - CORE/Cake/View/View.php, line 418 include - APP/View/Analysis/custom_tree_creation.ctp, line 27 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933
$viewFile = '/www/bioinformatics01_ro/plaza/_dev_instances/feedback/app/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp' $dataForView = array( 'sidebar_info' => array( 'gf_id' => 'HOM05D001576', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '406', 'num_species' => '29' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'Aqoxy1G01456' => 'aox', 'Aqoxy1G02949' => 'aox', 'Aqoxy3G01274' => 'aox', 'Aqoxy3G02110' => 'aox', 'Aqoxy3G02268' => 'aox', 'Aqoxy5G02702' => 'aox', 'Aqoxy5G02988' => 'aox', 'Aqoxy5G03427' => 'aox', 'Aqoxy6G02363' => 'aox', 'Atru.chr1.3225' => 'acertr', 'Atru.chr8.1198' => 'acertr', 'Atru.chr9.790' => 'acertr', 'CANSAT01G3197' => 'cansat', 'Ciclev10003979m.g' => 'ccl', 'Ciclev10017471m.g' => 'ccl', 'Ciclev10018206m.g' => 'ccl', 'Ciclev10033751m.g' => 'ccl', 'CiPaw.01G000900' => 'cil', 'CiPaw.01G001000' => 'cil', 'CiPaw.01G033500' => 'cil', 'CiPaw.01G060300' => 'cil', 'CiPaw.01G070200' => 'cil', 'CiPaw.01G075100' => 'cil', 'CiPaw.01G084700' => 'cil', 'CiPaw.01G087900' => 'cil', 'CiPaw.01G092600' => 'cil', 'CiPaw.01G097200' => 'cil', 'CiPaw.01G098300' => 'cil', 'CiPaw.01G110200' => 'cil', 'CiPaw.01G118700' => 'cil', 'CiPaw.01G121200' => 'cil', 'CiPaw.01G132500' => 'cil', 'CiPaw.01G146900' => 'cil', 'CiPaw.01G174000' => 'cil', 'CiPaw.01G179900' => 'cil', 'CiPaw.01G183400' => 'cil', 'CiPaw.01G240000' => 'cil', 'CiPaw.01G283500' => 'cil', 'CiPaw.01G307400' => 'cil', 'CiPaw.02G030800' => 'cil', 'CiPaw.02G047200' => 'cil', 'CiPaw.02G050500' => 'cil', 'CiPaw.02G069900' => 'cil', 'CiPaw.02G091600' => 'cil', 'CiPaw.02G095000' => 'cil', 'CiPaw.02G131900' => 'cil', 'CiPaw.03G043000' => 'cil', 'CiPaw.03G069900' => 'cil', 'CiPaw.03G088100' => 'cil', 'CiPaw.03G089300' => 'cil', 'CiPaw.03G093100' => 'cil', 'CiPaw.03G129800' => 'cil', 'CiPaw.03G131200' => 'cil', 'CiPaw.03G134500' => 'cil', 'CiPaw.03G152100' => 'cil', 'CiPaw.03G162700' => 'cil', 'CiPaw.03G172800' => 'cil', 'CiPaw.03G175800' => 'cil', 'CiPaw.03G181800' => 'cil', 'CiPaw.03G191400' => 'cil', 'CiPaw.03G198300' => 'cil', 'CiPaw.03G201300' => 'cil', 'CiPaw.03G224700' => 'cil', 'CiPaw.03G225000' => 'cil', 'CiPaw.04G065100' => 'cil', 'CiPaw.04G080400' => 'cil', 'CiPaw.04G113500' => 'cil', 'CiPaw.04G121900' => 'cil', 'CiPaw.04G144100' => 'cil', 'CiPaw.04G176500' => 'cil', 'CiPaw.05G086200' => 'cil', 'CiPaw.05G100200' => 'cil', 'CiPaw.05G114200' => 'cil', 'CiPaw.05G126800' => 'cil', 'CiPaw.05G228800' => 'cil', 'CiPaw.05G230600' => 'cil', 'CiPaw.05G236500' => 'cil', 'CiPaw.05G244800' => 'cil', 'CiPaw.06G026600' => 'cil', 'CiPaw.06G027900' => 'cil', 'CiPaw.06G051800' => 'cil', 'CiPaw.06G128500' => 'cil', 'CiPaw.06G165900' => 'cil', 'CiPaw.07G045400' => 'cil', 'CiPaw.07G048000' => 'cil', 'CiPaw.07G052000' => 'cil', 'CiPaw.07G073800' => 'cil', 'CiPaw.07G099700' => 'cil', 'CiPaw.07G108700' => 'cil', 'CiPaw.07G120000' => 'cil', 'CiPaw.07G134100' => 'cil', 'CiPaw.07G147000' => 'cil', 'CiPaw.07G149700' => 'cil', 'CiPaw.07G178300' => 'cil', 'CiPaw.07G184900' => 'cil', 'CiPaw.08G044500' => 'cil', 'CiPaw.08G046900' => 'cil', 'CiPaw.08G047300' => 'cil', 'CiPaw.08G115400' => 'cil', 'CiPaw.08G134700' => 'cil', 'CiPaw.08G157400' => 'cil', 'CiPaw.09G014300' => 'cil', 'CiPaw.09G088900' => 'cil', 'CiPaw.09G130900' => 'cil', 'CiPaw.09G133100' => 'cil', 'CiPaw.09G151300' => 'cil', 'CiPaw.09G172800' => 'cil', 'CiPaw.09G174900' => 'cil', 'CiPaw.09G175000' => 'cil', 'CiPaw.10G012800' => 'cil', 'CiPaw.10G028800' => 'cil', 'CiPaw.10G044700' => 'cil', 'CiPaw.10G067400' => 'cil', 'CiPaw.10G115900' => 'cil', 'CiPaw.10G126200' => 'cil', 'CiPaw.10G139700' => 'cil', 'CiPaw.10G155100' => 'cil', 'CiPaw.11G011300' => 'cil', 'CiPaw.11G025900' => 'cil', 'CiPaw.11G104100' => 'cil', 'CiPaw.11G142700' => 'cil', 'CiPaw.11G164500' => 'cil', 'CiPaw.11G189100' => 'cil', 'CiPaw.11G197100' => 'cil', 'CiPaw.12G006100' => 'cil', 'CiPaw.12G038500' => 'cil', 'CiPaw.12G041400' => 'cil', 'CiPaw.12G041600' => 'cil', 'CiPaw.12G051300' => 'cil', 'CiPaw.12G101800' => 'cil', 'CiPaw.12G107800' => 'cil', 'CiPaw.13G033200' => 'cil', 'CiPaw.13G129900' => 'cil', 'CiPaw.13G160200' => 'cil', 'CiPaw.14G018900' => 'cil', 'CiPaw.14G029000' => 'cil', 'CiPaw.14G031000' => 'cil', 'CiPaw.14G032000' => 'cil', 'CiPaw.14G032300' => 'cil', 'CiPaw.14G040600' => 'cil', 'CiPaw.14G060500' => 'cil', 'CiPaw.14G061500' => 'cil', 'CiPaw.14G077500' => 'cil', 'CiPaw.14G088300' => 'cil', 'CiPaw.14G108500' => 'cil', 'CiPaw.14G121300' => 'cil', 'CiPaw.14G133000' => 'cil', 'CiPaw.14G134600' => 'cil', 'CiPaw.15G027200' => 'cil', 'CiPaw.15G037700' => 'cil', 'CiPaw.15G050900' => 'cil', 'CiPaw.15G067200' => 'cil', 'CiPaw.15G072000' => 'cil', 'CiPaw.15G112900' => 'cil', 'CiPaw.15G133200' => 'cil', 'CiPaw.15G139500' => 'cil', 'CiPaw.15G155400' => 'cil', 'CiPaw.16G006000' => 'cil', 'CiPaw.16G013100' => 'cil', 'CiPaw.16G047100' => 'cil', 'CiPaw.16G048900' => 'cil', 'CiPaw.16G070300' => 'cil', 'CSS0000195' => 'camsi', 'CSS0001664' => 'camsi', 'CSS0002566' => 'camsi', 'CSS0003077' => 'camsi', 'CSS0004257' => 'camsi', 'CSS0004495' => 'camsi', 'CSS0004599' => 'camsi', 'CSS0004943' => 'camsi', 'CSS0005302' => 'camsi', 'CSS0006274' => 'camsi', 'CSS0006547' => 'camsi', 'CSS0006860' => 'camsi', 'CSS0008814' => 'camsi', 'CSS0008946' => 'camsi', 'CSS0009093' => 'camsi', 'CSS0010221' => 'camsi', 'CSS0010296' => 'camsi', 'CSS0010386' => 'camsi', 'CSS0010831' => 'camsi', 'CSS0011061' => 'camsi', 'CSS0012008' => 'camsi', 'CSS0012194' => 'camsi', 'CSS0013580' => 'camsi', 'CSS0014176' => 'camsi', 'CSS0014280' => 'camsi', 'CSS0014799' => 'camsi', 'CSS0015368' => 'camsi', 'CSS0017473' => 'camsi', 'CSS0019281' => 'camsi', 'CSS0021320' => 'camsi', 'CSS0021750' => 'camsi', 'CSS0023642' => 'camsi', 'CSS0023792' => 'camsi', 'CSS0031528' => 'camsi', 'CSS0033894' => 'camsi', 'CSS0034959' => 'camsi', 'CSS0035632' => 'camsi', 'CSS0038450' => 'camsi', 'CSS0039293' => 'camsi', 'CSS0041053' => 'camsi', 'CSS0041981' => 'camsi', 'CSS0042573' => 'camsi', 'CSS0042927' => 'camsi', 'CSS0047725' => 'camsi', 'CSS0049636' => 'camsi', 'CSS0050513' => 'camsi', 'DCAR_030203' => 'dca', 'Dinv07939' => 'din', 'FAN01G0456' => 'fan', 'FAN02G3001' => 'fan', 'FAN04G2781' => 'fan', 'FAN05G1385' => 'fan', 'FAN05G3062' => 'fan', 'FAN08G2267' => 'fan', 'FAN10G0481' => 'fan', 'FAN10G1257' => 'fan', 'FAN14G0954' => 'fan', 'FAN14G2347' => 'fan', 'FAN15G0187' => 'fan', 'FAN25G2214' => 'fan', 'FvH4_1g21031' => 'fve', 'FvH4_3g16231' => 'fve', 'FvH4_3g26413' => 'fve', 'FvH4_3g29014' => 'fve', 'FvH4_3g31921' => 'fve', 'FvH4_4g19882' => 'fve', 'FvH4_5g21960' => 'fve', 'FvH4_5g29683' => 'fve', 'FvH4_7g13271' => 'fve', 'Glyma.01G062500' => 'gma', 'Glyma.07G140900' => 'gma', 'Glyma.09G140900' => 'gma', 'Glyma.12G112700' => 'gma', 'Glyma.17G168800' => 'gma', 'HanXRQChr01g0027001' => 'han', 'HanXRQChr04g0120511' => 'han', 'HanXRQChr08g0232381' => 'han', 'HanXRQChr09g0265661' => 'han', 'HanXRQChr13g0416031' => 'han', 'Haze_05835' => 'cav', 'Haze_06597' => 'cav', 'Haze_07921' => 'cav', 'Haze_08599' => 'cav', 'Haze_10686' => 'cav', 'Haze_12994' => 'cav', 'Haze_13466' => 'cav', 'Haze_16101' => 'cav', 'Haze_17766' => 'cav', 'Haze_18456' => 'cav', 'Haze_20229' => 'cav', 'Hma1.2p1_0324F.1_g125640' => 'hma', 'Hma1.2p1_0733F.1_g210230' => 'hma', 'Hma1.2p1_0921F.1_g236870' => 'hma', 'Hma1.2p1_1313F.1_g274940' => 'hma', 'Hma1.2p1_3059F.1_g332230' => 'hma', 'Hund15925' => 'sun', 'Hund19562' => 'sun', 'Hund21925' => 'sun', 'MD03G1177400' => 'mdo', 'MD07G1026100' => 'mdo', 'MD17G1218600' => 'mdo', 'Medtr0867s0010' => 'mtr', 'Medtr6g081150' => 'mtr', 'Os01g0527900' => 'osa', 'Os02g0463725' => 'osa', 'Os02g0785600' => 'osa', 'Os03g0433733' => 'osa', 'Os04g0286500' => 'osa', 'Os05g0227800' => 'osa', 'Os06g0521000' => 'osa', 'Os06g0635500' => 'osa', 'Os06g0660650' => 'osa', 'Os07g0554400' => 'osa', 'Os08g0225900' => 'osa', 'Os08g0561000' => 'osa', 'Os09g0241700' => 'osa', 'Os09g0351900' => 'osa', 'Os11g0220700' => 'osa', 'Os11g0282700' => 'osa', 'Os12g0169300' => 'osa', 'Os12g0228500' => 'osa', 'Os12g0543800' => 'osa', 'PGR044G1547' => 'pgr', 'Potri.005G239150' => 'ptr', 'Potri.010G014250' => 'ptr', 'Prupe.1G172500' => 'ppe', 'Prupe.1G196800' => 'ppe', 'Prupe.1G279700' => 'ppe', 'Prupe.2G026400' => 'ppe', 'Prupe.3G094000' => 'ppe', 'Prupe.4G287300' => 'ppe', 'QL01p022166' => 'qlo', 'QL01p051890' => 'qlo', 'QL02p009469' => 'qlo', 'QL02p046053' => 'qlo', 'QL02p057958' => 'qlo', 'QL02p093127' => 'qlo', 'QL03p006855' => 'qlo', 'QL03p071586' => 'qlo', 'QL04p000022' => 'qlo', 'QL04p000024' => 'qlo', 'QL04p003192' => 'qlo', 'QL05p011416' => 'qlo', 'QL06p039590' => 'qlo', 'QL06p052750' => 'qlo', 'QL06p053821' => 'qlo', 'QL07p025287' => 'qlo', 'QL09p033218' => 'qlo', 'QL09p040841' => 'qlo', 'QL10p020337' => 'qlo', 'QL10p027209' => 'qlo', 'QL10p027969' => 'qlo', 'QL10p048988' => 'qlo', 'QL11p001241' => 'qlo', 'QL11p028487' => 'qlo', 'RcHm_v2.0_Chr2g0105031' => 'rch', 'RcHm_v2.0_Chr2g0117811' => 'rch', 'RcHm_v2.0_Chr6g0270241' => 'rch', 'RcHm_v2.0_Chr7g0215961' => 'rch', 'RcHm_v2.0_Chr7g0231991' => 'rch', 'Rhsim01G0041500' => 'rsi', 'Rhsim01G0115000' => 'rsi', 'Rhsim01G0115400' => 'rsi', 'Rhsim01G0133600' => 'rsi', 'Rhsim01G0159900' => 'rsi', 'Rhsim02G0189400' => 'rsi', 'Rhsim03G0135600' => 'rsi', 'Rhsim03G0149900' => 'rsi', 'Rhsim04G0125600' => 'rsi', 'Rhsim05G0091700' => 'rsi', 'Rhsim05G0092900' => 'rsi', 'Rhsim06G0075000' => 'rsi', 'Rhsim07G0066400' => 'rsi', 'Rhsim07G0156400' => 'rsi', 'Rhsim07G0182200' => 'rsi', 'Rhsim07G0182300' => 'rsi', 'Rhsim08G0180400' => 'rsi', 'Rhsim09G0056800' => 'rsi', 'Rhsim10G0153300' => 'rsi', 'Rhsim11G0012700' => 'rsi', 'Rhsim12G0031800' => 'rsi', 'Rhsim12G0055400' => 'rsi', 'Rhsim12G0091400' => 'rsi', 'Rhsim13G0070800' => 'rsi', 'Rhsim13G0193300' => 'rsi', 'RhsimUnG0111600' => 'rsi', 'RhsimUnG0137500' => 'rsi', 'RhsimUnG0172900' => 'rsi', 'SGA_v2.0_scaffold11G05878' => 'sas', 'SGA_v2.0_scaffold167G38458' => 'sas', 'SGA_v2.0_scaffold19G08588' => 'sas', 'SGA_v2.0_scaffold239G43990' => 'sas', 'SGA_v2.0_scaffold260G45865' => 'sas', 'SGA_v2.0_scaffold309G48177' => 'sas', 'SGA_v2.0_scaffold76G25122' => 'sas', 'SGA_v2.0_scaffold85G26708' => 'sas', 'SHI13914' => 'shi', 'SHI30402' => 'shi', 'TWI09G0020' => 'twi', 'TWI09G0456' => 'twi', 'TWI09G1572' => 'twi', 'TWI12G0266' => 'twi', 'TWI12G1451' => 'twi', 'TWI14G0851' => 'twi', 'TWI15G0796' => 'twi', 'TWI18G0820' => 'twi', 'TWI18G1152' => 'twi', 'TWI23G0007' => 'twi', 'TWI23G0314' => 'twi', 'TWI31G0674' => 'twi', 'TWI31G0938' => 'twi', 'TWI34G0641' => 'twi', 'TWI34G1527' => 'twi', 'TWI36G0193' => 'twi', 'TWI36G0405' => 'twi', 'TWI38G0892' => 'twi', 'TWI38G0936' => 'twi', 'TWI38G2218' => 'twi', 'TWI53G0679' => 'twi', 'TWI53G0863' => 'twi', 'TWI53G1133' => 'twi', 'TWI60G0823' => 'twi', 'TWI63G0919' => 'twi', 'TWI63G1436' => 'twi', 'TWI73G0140' => 'twi', 'TWI73G0419' => 'twi', 'TWI73G0420' => 'twi', 'TWI73G1276' => 'twi', 'TWI74G0405' => 'twi', 'TWI74G0837' => 'twi', 'TWI75G0594' => 'twi', 'TWI75G1615' => 'twi', 'TWI77G0816' => 'twi', 'vmacro03831' => 'vma', 'vmacro13746' => 'vma', 'vmacro16089' => 'vma', 'vmacro22863' => 'vma', 'Zm00001eb085790' => 'zma', 'Zm00001eb114250' => 'zma', 'Zm00001eb138070' => 'zma', 'Zm00001eb167560' => 'zma', 'Zm00001eb199990' => 'zma', 'Zm00001eb368180' => 'zma', 'Zm00001eb382470' => 'zma' ), 'gf_id' => 'HOM05D001576', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001576' ), 'data_identifier' => 'HOM05D001576', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001576', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '406', 'num_species' => '29' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'Aqoxy1G01456' => 'aox', 'Aqoxy1G02949' => 'aox', 'Aqoxy3G01274' => 'aox', 'Aqoxy3G02110' => 'aox', 'Aqoxy3G02268' => 'aox', 'Aqoxy5G02702' => 'aox', 'Aqoxy5G02988' => 'aox', 'Aqoxy5G03427' => 'aox', 'Aqoxy6G02363' => 'aox', 'Atru.chr1.3225' => 'acertr', 'Atru.chr8.1198' => 'acertr', 'Atru.chr9.790' => 'acertr', 'CANSAT01G3197' => 'cansat', 'Ciclev10003979m.g' => 'ccl', 'Ciclev10017471m.g' => 'ccl', 'Ciclev10018206m.g' => 'ccl', 'Ciclev10033751m.g' => 'ccl', 'CiPaw.01G000900' => 'cil', 'CiPaw.01G001000' => 'cil', 'CiPaw.01G033500' => 'cil', 'CiPaw.01G060300' => 'cil', 'CiPaw.01G070200' => 'cil', 'CiPaw.01G075100' => 'cil', 'CiPaw.01G084700' => 'cil', 'CiPaw.01G087900' => 'cil', 'CiPaw.01G092600' => 'cil', 'CiPaw.01G097200' => 'cil', 'CiPaw.01G098300' => 'cil', 'CiPaw.01G110200' => 'cil', 'CiPaw.01G118700' => 'cil', 'CiPaw.01G121200' => 'cil', 'CiPaw.01G132500' => 'cil', 'CiPaw.01G146900' => 'cil', 'CiPaw.01G174000' => 'cil', 'CiPaw.01G179900' => 'cil', 'CiPaw.01G183400' => 'cil', 'CiPaw.01G240000' => 'cil', 'CiPaw.01G283500' => 'cil', 'CiPaw.01G307400' => 'cil', 'CiPaw.02G030800' => 'cil', 'CiPaw.02G047200' => 'cil', 'CiPaw.02G050500' => 'cil', 'CiPaw.02G069900' => 'cil', 'CiPaw.02G091600' => 'cil', 'CiPaw.02G095000' => 'cil', 'CiPaw.02G131900' => 'cil', 'CiPaw.03G043000' => 'cil', 'CiPaw.03G069900' => 'cil', 'CiPaw.03G088100' => 'cil', 'CiPaw.03G089300' => 'cil', 'CiPaw.03G093100' => 'cil', 'CiPaw.03G129800' => 'cil', 'CiPaw.03G131200' => 'cil', 'CiPaw.03G134500' => 'cil', 'CiPaw.03G152100' => 'cil', 'CiPaw.03G162700' => 'cil', 'CiPaw.03G172800' => 'cil', 'CiPaw.03G175800' => 'cil', 'CiPaw.03G181800' => 'cil', 'CiPaw.03G191400' => 'cil', 'CiPaw.03G198300' => 'cil', 'CiPaw.03G201300' => 'cil', 'CiPaw.03G224700' => 'cil', 'CiPaw.03G225000' => 'cil', 'CiPaw.04G065100' => 'cil', 'CiPaw.04G080400' => 'cil', 'CiPaw.04G113500' => 'cil', 'CiPaw.04G121900' => 'cil', 'CiPaw.04G144100' => 'cil', 'CiPaw.04G176500' => 'cil', 'CiPaw.05G086200' => 'cil', 'CiPaw.05G100200' => 'cil', 'CiPaw.05G114200' => 'cil', 'CiPaw.05G126800' => 'cil', 'CiPaw.05G228800' => 'cil', 'CiPaw.05G230600' => 'cil', 'CiPaw.05G236500' => 'cil', 'CiPaw.05G244800' => 'cil', 'CiPaw.06G026600' => 'cil', 'CiPaw.06G027900' => 'cil', 'CiPaw.06G051800' => 'cil', 'CiPaw.06G128500' => 'cil', 'CiPaw.06G165900' => 'cil', 'CiPaw.07G045400' => 'cil', 'CiPaw.07G048000' => 'cil', 'CiPaw.07G052000' => 'cil', 'CiPaw.07G073800' => 'cil', 'CiPaw.07G099700' => 'cil', 'CiPaw.07G108700' => 'cil', 'CiPaw.07G120000' => 'cil', 'CiPaw.07G134100' => 'cil', 'CiPaw.07G147000' => 'cil', 'CiPaw.07G149700' => 'cil', 'CiPaw.07G178300' => 'cil', 'CiPaw.07G184900' => 'cil', 'CiPaw.08G044500' => 'cil', 'CiPaw.08G046900' => 'cil', 'CiPaw.08G047300' => 'cil', 'CiPaw.08G115400' => 'cil', 'CiPaw.08G134700' => 'cil', 'CiPaw.08G157400' => 'cil', 'CiPaw.09G014300' => 'cil', 'CiPaw.09G088900' => 'cil', 'CiPaw.09G130900' => 'cil', 'CiPaw.09G133100' => 'cil', 'CiPaw.09G151300' => 'cil', 'CiPaw.09G172800' => 'cil', 'CiPaw.09G174900' => 'cil', 'CiPaw.09G175000' => 'cil', 'CiPaw.10G012800' => 'cil', 'CiPaw.10G028800' => 'cil', 'CiPaw.10G044700' => 'cil', 'CiPaw.10G067400' => 'cil', 'CiPaw.10G115900' => 'cil', 'CiPaw.10G126200' => 'cil', 'CiPaw.10G139700' => 'cil', 'CiPaw.10G155100' => 'cil', 'CiPaw.11G011300' => 'cil', 'CiPaw.11G025900' => 'cil', 'CiPaw.11G104100' => 'cil', 'CiPaw.11G142700' => 'cil', 'CiPaw.11G164500' => 'cil', 'CiPaw.11G189100' => 'cil', 'CiPaw.11G197100' => 'cil', 'CiPaw.12G006100' => 'cil', 'CiPaw.12G038500' => 'cil', 'CiPaw.12G041400' => 'cil', 'CiPaw.12G041600' => 'cil', 'CiPaw.12G051300' => 'cil', 'CiPaw.12G101800' => 'cil', 'CiPaw.12G107800' => 'cil', 'CiPaw.13G033200' => 'cil', 'CiPaw.13G129900' => 'cil', 'CiPaw.13G160200' => 'cil', 'CiPaw.14G018900' => 'cil', 'CiPaw.14G029000' => 'cil', 'CiPaw.14G031000' => 'cil', 'CiPaw.14G032000' => 'cil', 'CiPaw.14G032300' => 'cil', 'CiPaw.14G040600' => 'cil', 'CiPaw.14G060500' => 'cil', 'CiPaw.14G061500' => 'cil', 'CiPaw.14G077500' => 'cil', 'CiPaw.14G088300' => 'cil', 'CiPaw.14G108500' => 'cil', 'CiPaw.14G121300' => 'cil', 'CiPaw.14G133000' => 'cil', 'CiPaw.14G134600' => 'cil', 'CiPaw.15G027200' => 'cil', 'CiPaw.15G037700' => 'cil', 'CiPaw.15G050900' => 'cil', 'CiPaw.15G067200' => 'cil', 'CiPaw.15G072000' => 'cil', 'CiPaw.15G112900' => 'cil', 'CiPaw.15G133200' => 'cil', 'CiPaw.15G139500' => 'cil', 'CiPaw.15G155400' => 'cil', 'CiPaw.16G006000' => 'cil', 'CiPaw.16G013100' => 'cil', 'CiPaw.16G047100' => 'cil', 'CiPaw.16G048900' => 'cil', 'CiPaw.16G070300' => 'cil', 'CSS0000195' => 'camsi', 'CSS0001664' => 'camsi', 'CSS0002566' => 'camsi', 'CSS0003077' => 'camsi', 'CSS0004257' => 'camsi', 'CSS0004495' => 'camsi', 'CSS0004599' => 'camsi', 'CSS0004943' => 'camsi', 'CSS0005302' => 'camsi', 'CSS0006274' => 'camsi', 'CSS0006547' => 'camsi', 'CSS0006860' => 'camsi', 'CSS0008814' => 'camsi', 'CSS0008946' => 'camsi', 'CSS0009093' => 'camsi', 'CSS0010221' => 'camsi', 'CSS0010296' => 'camsi', 'CSS0010386' => 'camsi', 'CSS0010831' => 'camsi', 'CSS0011061' => 'camsi', 'CSS0012008' => 'camsi', 'CSS0012194' => 'camsi', 'CSS0013580' => 'camsi', 'CSS0014176' => 'camsi', 'CSS0014280' => 'camsi', 'CSS0014799' => 'camsi', 'CSS0015368' => 'camsi', 'CSS0017473' => 'camsi', 'CSS0019281' => 'camsi', 'CSS0021320' => 'camsi', 'CSS0021750' => 'camsi', 'CSS0023642' => 'camsi', 'CSS0023792' => 'camsi', 'CSS0031528' => 'camsi', 'CSS0033894' => 'camsi', 'CSS0034959' => 'camsi', 'CSS0035632' => 'camsi', 'CSS0038450' => 'camsi', 'CSS0039293' => 'camsi', 'CSS0041053' => 'camsi', 'CSS0041981' => 'camsi', 'CSS0042573' => 'camsi', 'CSS0042927' => 'camsi', 'CSS0047725' => 'camsi', 'CSS0049636' => 'camsi', 'CSS0050513' => 'camsi', 'DCAR_030203' => 'dca', 'Dinv07939' => 'din', 'FAN01G0456' => 'fan', 'FAN02G3001' => 'fan', 'FAN04G2781' => 'fan', 'FAN05G1385' => 'fan', 'FAN05G3062' => 'fan', 'FAN08G2267' => 'fan', 'FAN10G0481' => 'fan', 'FAN10G1257' => 'fan', 'FAN14G0954' => 'fan', 'FAN14G2347' => 'fan', 'FAN15G0187' => 'fan', 'FAN25G2214' => 'fan', 'FvH4_1g21031' => 'fve', 'FvH4_3g16231' => 'fve', 'FvH4_3g26413' => 'fve', 'FvH4_3g29014' => 'fve', 'FvH4_3g31921' => 'fve', 'FvH4_4g19882' => 'fve', 'FvH4_5g21960' => 'fve', 'FvH4_5g29683' => 'fve', 'FvH4_7g13271' => 'fve', 'Glyma.01G062500' => 'gma', 'Glyma.07G140900' => 'gma', 'Glyma.09G140900' => 'gma', 'Glyma.12G112700' => 'gma', 'Glyma.17G168800' => 'gma', 'HanXRQChr01g0027001' => 'han', 'HanXRQChr04g0120511' => 'han', 'HanXRQChr08g0232381' => 'han', 'HanXRQChr09g0265661' => 'han', 'HanXRQChr13g0416031' => 'han', 'Haze_05835' => 'cav', 'Haze_06597' => 'cav', 'Haze_07921' => 'cav', 'Haze_08599' => 'cav', 'Haze_10686' => 'cav', 'Haze_12994' => 'cav', 'Haze_13466' => 'cav', 'Haze_16101' => 'cav', 'Haze_17766' => 'cav', 'Haze_18456' => 'cav', 'Haze_20229' => 'cav', 'Hma1.2p1_0324F.1_g125640' => 'hma', 'Hma1.2p1_0733F.1_g210230' => 'hma', 'Hma1.2p1_0921F.1_g236870' => 'hma', 'Hma1.2p1_1313F.1_g274940' => 'hma', 'Hma1.2p1_3059F.1_g332230' => 'hma', 'Hund15925' => 'sun', 'Hund19562' => 'sun', 'Hund21925' => 'sun', 'MD03G1177400' => 'mdo', 'MD07G1026100' => 'mdo', 'MD17G1218600' => 'mdo', 'Medtr0867s0010' => 'mtr', 'Medtr6g081150' => 'mtr', 'Os01g0527900' => 'osa', 'Os02g0463725' => 'osa', 'Os02g0785600' => 'osa', 'Os03g0433733' => 'osa', 'Os04g0286500' => 'osa', 'Os05g0227800' => 'osa', 'Os06g0521000' => 'osa', 'Os06g0635500' => 'osa', 'Os06g0660650' => 'osa', 'Os07g0554400' => 'osa', 'Os08g0225900' => 'osa', 'Os08g0561000' => 'osa', 'Os09g0241700' => 'osa', 'Os09g0351900' => 'osa', 'Os11g0220700' => 'osa', 'Os11g0282700' => 'osa', 'Os12g0169300' => 'osa', 'Os12g0228500' => 'osa', 'Os12g0543800' => 'osa', 'PGR044G1547' => 'pgr', 'Potri.005G239150' => 'ptr', 'Potri.010G014250' => 'ptr', 'Prupe.1G172500' => 'ppe', 'Prupe.1G196800' => 'ppe', 'Prupe.1G279700' => 'ppe', 'Prupe.2G026400' => 'ppe', 'Prupe.3G094000' => 'ppe', 'Prupe.4G287300' => 'ppe', 'QL01p022166' => 'qlo', 'QL01p051890' => 'qlo', 'QL02p009469' => 'qlo', 'QL02p046053' => 'qlo', 'QL02p057958' => 'qlo', 'QL02p093127' => 'qlo', 'QL03p006855' => 'qlo', 'QL03p071586' => 'qlo', 'QL04p000022' => 'qlo', 'QL04p000024' => 'qlo', 'QL04p003192' => 'qlo', 'QL05p011416' => 'qlo', 'QL06p039590' => 'qlo', 'QL06p052750' => 'qlo', 'QL06p053821' => 'qlo', 'QL07p025287' => 'qlo', 'QL09p033218' => 'qlo', 'QL09p040841' => 'qlo', 'QL10p020337' => 'qlo', 'QL10p027209' => 'qlo', 'QL10p027969' => 'qlo', 'QL10p048988' => 'qlo', 'QL11p001241' => 'qlo', 'QL11p028487' => 'qlo', 'RcHm_v2.0_Chr2g0105031' => 'rch', 'RcHm_v2.0_Chr2g0117811' => 'rch', 'RcHm_v2.0_Chr6g0270241' => 'rch', 'RcHm_v2.0_Chr7g0215961' => 'rch', 'RcHm_v2.0_Chr7g0231991' => 'rch', 'Rhsim01G0041500' => 'rsi', 'Rhsim01G0115000' => 'rsi', 'Rhsim01G0115400' => 'rsi', 'Rhsim01G0133600' => 'rsi', 'Rhsim01G0159900' => 'rsi', 'Rhsim02G0189400' => 'rsi', 'Rhsim03G0135600' => 'rsi', 'Rhsim03G0149900' => 'rsi', 'Rhsim04G0125600' => 'rsi', 'Rhsim05G0091700' => 'rsi', 'Rhsim05G0092900' => 'rsi', 'Rhsim06G0075000' => 'rsi', 'Rhsim07G0066400' => 'rsi', 'Rhsim07G0156400' => 'rsi', 'Rhsim07G0182200' => 'rsi', 'Rhsim07G0182300' => 'rsi', 'Rhsim08G0180400' => 'rsi', 'Rhsim09G0056800' => 'rsi', 'Rhsim10G0153300' => 'rsi', 'Rhsim11G0012700' => 'rsi', 'Rhsim12G0031800' => 'rsi', 'Rhsim12G0055400' => 'rsi', 'Rhsim12G0091400' => 'rsi', 'Rhsim13G0070800' => 'rsi', 'Rhsim13G0193300' => 'rsi', 'RhsimUnG0111600' => 'rsi', 'RhsimUnG0137500' => 'rsi', 'RhsimUnG0172900' => 'rsi', 'SGA_v2.0_scaffold11G05878' => 'sas', 'SGA_v2.0_scaffold167G38458' => 'sas', 'SGA_v2.0_scaffold19G08588' => 'sas', 'SGA_v2.0_scaffold239G43990' => 'sas', 'SGA_v2.0_scaffold260G45865' => 'sas', 'SGA_v2.0_scaffold309G48177' => 'sas', 'SGA_v2.0_scaffold76G25122' => 'sas', 'SGA_v2.0_scaffold85G26708' => 'sas', 'SHI13914' => 'shi', 'SHI30402' => 'shi', 'TWI09G0020' => 'twi', 'TWI09G0456' => 'twi', 'TWI09G1572' => 'twi', 'TWI12G0266' => 'twi', 'TWI12G1451' => 'twi', 'TWI14G0851' => 'twi', 'TWI15G0796' => 'twi', 'TWI18G0820' => 'twi', 'TWI18G1152' => 'twi', 'TWI23G0007' => 'twi', 'TWI23G0314' => 'twi', 'TWI31G0674' => 'twi', 'TWI31G0938' => 'twi', 'TWI34G0641' => 'twi', 'TWI34G1527' => 'twi', 'TWI36G0193' => 'twi', 'TWI36G0405' => 'twi', 'TWI38G0892' => 'twi', 'TWI38G0936' => 'twi', 'TWI38G2218' => 'twi', 'TWI53G0679' => 'twi', 'TWI53G0863' => 'twi', 'TWI53G1133' => 'twi', 'TWI60G0823' => 'twi', 'TWI63G0919' => 'twi', 'TWI63G1436' => 'twi', 'TWI73G0140' => 'twi', 'TWI73G0419' => 'twi', 'TWI73G0420' => 'twi', 'TWI73G1276' => 'twi', 'TWI74G0405' => 'twi', 'TWI74G0837' => 'twi', 'TWI75G0594' => 'twi', 'TWI75G1615' => 'twi', 'TWI77G0816' => 'twi', 'vmacro03831' => 'vma', 'vmacro13746' => 'vma', 'vmacro16089' => 'vma', 'vmacro22863' => 'vma', 'Zm00001eb085790' => 'zma', 'Zm00001eb114250' => 'zma', 'Zm00001eb138070' => 'zma', 'Zm00001eb167560' => 'zma', 'Zm00001eb199990' => 'zma', 'Zm00001eb368180' => 'zma', 'Zm00001eb382470' => 'zma' ) $gf_id = 'HOM05D001576' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001576' ) $data_identifier = 'HOM05D001576' $data_type = 'gf_id' $species_gene_counts = array( 'aox' => (int) 9, 'acertr' => (int) 3, 'cansat' => (int) 1, 'ccl' => (int) 4, 'cil' => (int) 145, 'camsi' => (int) 46, 'dca' => (int) 1, 'din' => (int) 1, 'fan' => (int) 12, 'fve' => (int) 9, 'gma' => (int) 5, 'han' => (int) 5, 'cav' => (int) 11, 'hma' => (int) 5, 'sun' => (int) 3, 'mdo' => (int) 3, 'mtr' => (int) 2, 'osa' => (int) 19, 'pgr' => (int) 1, 'ptr' => (int) 2, 'ppe' => (int) 6, 'qlo' => (int) 24, 'rch' => (int) 5, 'rsi' => (int) 28, 'sas' => (int) 8, 'shi' => (int) 2, 'twi' => (int) 35, 'vma' => (int) 4, 'zma' => (int) 7 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb382470' $species_info = array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ) $local_species = 'vma' $disabled = '' $selected = '' $num_hits = (int) 0
Warning (2): count(): Parameter must be an array or an object that implements Countable [APP/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp, line 33]Code Context $disabled = (!array_key_exists($local_species,$species_gene_counts))?"disabled":""; $selected = (isset($selected_species) && array_key_exists($local_species,$selected_species))?"checked='checked'":""; $num_hits = (array_key_exists($local_species,$species_gene_counts))?count($species_gene_counts[$local_species]):0; $viewFile = '/www/bioinformatics01_ro/plaza/_dev_instances/feedback/app/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp' $dataForView = array( 'sidebar_info' => array( 'gf_id' => 'HOM05D001576', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '406', 'num_species' => '29' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'Aqoxy1G01456' => 'aox', 'Aqoxy1G02949' => 'aox', 'Aqoxy3G01274' => 'aox', 'Aqoxy3G02110' => 'aox', 'Aqoxy3G02268' => 'aox', 'Aqoxy5G02702' => 'aox', 'Aqoxy5G02988' => 'aox', 'Aqoxy5G03427' => 'aox', 'Aqoxy6G02363' => 'aox', 'Atru.chr1.3225' => 'acertr', 'Atru.chr8.1198' => 'acertr', 'Atru.chr9.790' => 'acertr', 'CANSAT01G3197' => 'cansat', 'Ciclev10003979m.g' => 'ccl', 'Ciclev10017471m.g' => 'ccl', 'Ciclev10018206m.g' => 'ccl', 'Ciclev10033751m.g' => 'ccl', 'CiPaw.01G000900' => 'cil', 'CiPaw.01G001000' => 'cil', 'CiPaw.01G033500' => 'cil', 'CiPaw.01G060300' => 'cil', 'CiPaw.01G070200' => 'cil', 'CiPaw.01G075100' => 'cil', 'CiPaw.01G084700' => 'cil', 'CiPaw.01G087900' => 'cil', 'CiPaw.01G092600' => 'cil', 'CiPaw.01G097200' => 'cil', 'CiPaw.01G098300' => 'cil', 'CiPaw.01G110200' => 'cil', 'CiPaw.01G118700' => 'cil', 'CiPaw.01G121200' => 'cil', 'CiPaw.01G132500' => 'cil', 'CiPaw.01G146900' => 'cil', 'CiPaw.01G174000' => 'cil', 'CiPaw.01G179900' => 'cil', 'CiPaw.01G183400' => 'cil', 'CiPaw.01G240000' => 'cil', 'CiPaw.01G283500' => 'cil', 'CiPaw.01G307400' => 'cil', 'CiPaw.02G030800' => 'cil', 'CiPaw.02G047200' => 'cil', 'CiPaw.02G050500' => 'cil', 'CiPaw.02G069900' => 'cil', 'CiPaw.02G091600' => 'cil', 'CiPaw.02G095000' => 'cil', 'CiPaw.02G131900' => 'cil', 'CiPaw.03G043000' => 'cil', 'CiPaw.03G069900' => 'cil', 'CiPaw.03G088100' => 'cil', 'CiPaw.03G089300' => 'cil', 'CiPaw.03G093100' => 'cil', 'CiPaw.03G129800' => 'cil', 'CiPaw.03G131200' => 'cil', 'CiPaw.03G134500' => 'cil', 'CiPaw.03G152100' => 'cil', 'CiPaw.03G162700' => 'cil', 'CiPaw.03G172800' => 'cil', 'CiPaw.03G175800' => 'cil', 'CiPaw.03G181800' => 'cil', 'CiPaw.03G191400' => 'cil', 'CiPaw.03G198300' => 'cil', 'CiPaw.03G201300' => 'cil', 'CiPaw.03G224700' => 'cil', 'CiPaw.03G225000' => 'cil', 'CiPaw.04G065100' => 'cil', 'CiPaw.04G080400' => 'cil', 'CiPaw.04G113500' => 'cil', 'CiPaw.04G121900' => 'cil', 'CiPaw.04G144100' => 'cil', 'CiPaw.04G176500' => 'cil', 'CiPaw.05G086200' => 'cil', 'CiPaw.05G100200' => 'cil', 'CiPaw.05G114200' => 'cil', 'CiPaw.05G126800' => 'cil', 'CiPaw.05G228800' => 'cil', 'CiPaw.05G230600' => 'cil', 'CiPaw.05G236500' => 'cil', 'CiPaw.05G244800' => 'cil', 'CiPaw.06G026600' => 'cil', 'CiPaw.06G027900' => 'cil', 'CiPaw.06G051800' => 'cil', 'CiPaw.06G128500' => 'cil', 'CiPaw.06G165900' => 'cil', 'CiPaw.07G045400' => 'cil', 'CiPaw.07G048000' => 'cil', 'CiPaw.07G052000' => 'cil', 'CiPaw.07G073800' => 'cil', 'CiPaw.07G099700' => 'cil', 'CiPaw.07G108700' => 'cil', 'CiPaw.07G120000' => 'cil', 'CiPaw.07G134100' => 'cil', 'CiPaw.07G147000' => 'cil', 'CiPaw.07G149700' => 'cil', 'CiPaw.07G178300' => 'cil', 'CiPaw.07G184900' => 'cil', 'CiPaw.08G044500' => 'cil', 'CiPaw.08G046900' => 'cil', 'CiPaw.08G047300' => 'cil', 'CiPaw.08G115400' => 'cil', 'CiPaw.08G134700' => 'cil', 'CiPaw.08G157400' => 'cil', 'CiPaw.09G014300' => 'cil', 'CiPaw.09G088900' => 'cil', 'CiPaw.09G130900' => 'cil', 'CiPaw.09G133100' => 'cil', 'CiPaw.09G151300' => 'cil', 'CiPaw.09G172800' => 'cil', 'CiPaw.09G174900' => 'cil', 'CiPaw.09G175000' => 'cil', 'CiPaw.10G012800' => 'cil', 'CiPaw.10G028800' => 'cil', 'CiPaw.10G044700' => 'cil', 'CiPaw.10G067400' => 'cil', 'CiPaw.10G115900' => 'cil', 'CiPaw.10G126200' => 'cil', 'CiPaw.10G139700' => 'cil', 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=> 'qlo', 'QL07p025287' => 'qlo', 'QL09p033218' => 'qlo', 'QL09p040841' => 'qlo', 'QL10p020337' => 'qlo', 'QL10p027209' => 'qlo', 'QL10p027969' => 'qlo', 'QL10p048988' => 'qlo', 'QL11p001241' => 'qlo', 'QL11p028487' => 'qlo', 'RcHm_v2.0_Chr2g0105031' => 'rch', 'RcHm_v2.0_Chr2g0117811' => 'rch', 'RcHm_v2.0_Chr6g0270241' => 'rch', 'RcHm_v2.0_Chr7g0215961' => 'rch', 'RcHm_v2.0_Chr7g0231991' => 'rch', 'Rhsim01G0041500' => 'rsi', 'Rhsim01G0115000' => 'rsi', 'Rhsim01G0115400' => 'rsi', 'Rhsim01G0133600' => 'rsi', 'Rhsim01G0159900' => 'rsi', 'Rhsim02G0189400' => 'rsi', 'Rhsim03G0135600' => 'rsi', 'Rhsim03G0149900' => 'rsi', 'Rhsim04G0125600' => 'rsi', 'Rhsim05G0091700' => 'rsi', 'Rhsim05G0092900' => 'rsi', 'Rhsim06G0075000' => 'rsi', 'Rhsim07G0066400' => 'rsi', 'Rhsim07G0156400' => 'rsi', 'Rhsim07G0182200' => 'rsi', 'Rhsim07G0182300' => 'rsi', 'Rhsim08G0180400' => 'rsi', 'Rhsim09G0056800' => 'rsi', 'Rhsim10G0153300' => 'rsi', 'Rhsim11G0012700' => 'rsi', 'Rhsim12G0031800' => 'rsi', 'Rhsim12G0055400' => 'rsi', 'Rhsim12G0091400' => 'rsi', 'Rhsim13G0070800' => 'rsi', 'Rhsim13G0193300' => 'rsi', 'RhsimUnG0111600' => 'rsi', 'RhsimUnG0137500' => 'rsi', 'RhsimUnG0172900' => 'rsi', 'SGA_v2.0_scaffold11G05878' => 'sas', 'SGA_v2.0_scaffold167G38458' => 'sas', 'SGA_v2.0_scaffold19G08588' => 'sas', 'SGA_v2.0_scaffold239G43990' => 'sas', 'SGA_v2.0_scaffold260G45865' => 'sas', 'SGA_v2.0_scaffold309G48177' => 'sas', 'SGA_v2.0_scaffold76G25122' => 'sas', 'SGA_v2.0_scaffold85G26708' => 'sas', 'SHI13914' => 'shi', 'SHI30402' => 'shi', 'TWI09G0020' => 'twi', 'TWI09G0456' => 'twi', 'TWI09G1572' => 'twi', 'TWI12G0266' => 'twi', 'TWI12G1451' => 'twi', 'TWI14G0851' => 'twi', 'TWI15G0796' => 'twi', 'TWI18G0820' => 'twi', 'TWI18G1152' => 'twi', 'TWI23G0007' => 'twi', 'TWI23G0314' => 'twi', 'TWI31G0674' => 'twi', 'TWI31G0938' => 'twi', 'TWI34G0641' => 'twi', 'TWI34G1527' => 'twi', 'TWI36G0193' => 'twi', 'TWI36G0405' => 'twi', 'TWI38G0892' => 'twi', 'TWI38G0936' => 'twi', 'TWI38G2218' => 'twi', 'TWI53G0679' => 'twi', 'TWI53G0863' => 'twi', 'TWI53G1133' => 'twi', 'TWI60G0823' => 'twi', 'TWI63G0919' => 'twi', 'TWI63G1436' => 'twi', 'TWI73G0140' => 'twi', 'TWI73G0419' => 'twi', 'TWI73G0420' => 'twi', 'TWI73G1276' => 'twi', 'TWI74G0405' => 'twi', 'TWI74G0837' => 'twi', 'TWI75G0594' => 'twi', 'TWI75G1615' => 'twi', 'TWI77G0816' => 'twi', 'vmacro03831' => 'vma', 'vmacro13746' => 'vma', 'vmacro16089' => 'vma', 'vmacro22863' => 'vma', 'Zm00001eb085790' => 'zma', 'Zm00001eb114250' => 'zma', 'Zm00001eb138070' => 'zma', 'Zm00001eb167560' => 'zma', 'Zm00001eb199990' => 'zma', 'Zm00001eb368180' => 'zma', 'Zm00001eb382470' => 'zma' ), 'gf_id' => 'HOM05D001576', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001576' ), 'data_identifier' => 'HOM05D001576', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001576', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '406', 'num_species' => '29' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'Aqoxy1G01456' => 'aox', 'Aqoxy1G02949' => 'aox', 'Aqoxy3G01274' => 'aox', 'Aqoxy3G02110' => 'aox', 'Aqoxy3G02268' => 'aox', 'Aqoxy5G02702' => 'aox', 'Aqoxy5G02988' => 'aox', 'Aqoxy5G03427' => 'aox', 'Aqoxy6G02363' => 'aox', 'Atru.chr1.3225' => 'acertr', 'Atru.chr8.1198' => 'acertr', 'Atru.chr9.790' => 'acertr', 'CANSAT01G3197' => 'cansat', 'Ciclev10003979m.g' => 'ccl', 'Ciclev10017471m.g' => 'ccl', 'Ciclev10018206m.g' => 'ccl', 'Ciclev10033751m.g' => 'ccl', 'CiPaw.01G000900' => 'cil', 'CiPaw.01G001000' => 'cil', 'CiPaw.01G033500' => 'cil', 'CiPaw.01G060300' => 'cil', 'CiPaw.01G070200' => 'cil', 'CiPaw.01G075100' => 'cil', 'CiPaw.01G084700' => 'cil', 'CiPaw.01G087900' => 'cil', 'CiPaw.01G092600' => 'cil', 'CiPaw.01G097200' => 'cil', 'CiPaw.01G098300' => 'cil', 'CiPaw.01G110200' => 'cil', 'CiPaw.01G118700' => 'cil', 'CiPaw.01G121200' => 'cil', 'CiPaw.01G132500' => 'cil', 'CiPaw.01G146900' => 'cil', 'CiPaw.01G174000' => 'cil', 'CiPaw.01G179900' => 'cil', 'CiPaw.01G183400' => 'cil', 'CiPaw.01G240000' => 'cil', 'CiPaw.01G283500' => 'cil', 'CiPaw.01G307400' => 'cil', 'CiPaw.02G030800' => 'cil', 'CiPaw.02G047200' => 'cil', 'CiPaw.02G050500' => 'cil', 'CiPaw.02G069900' => 'cil', 'CiPaw.02G091600' => 'cil', 'CiPaw.02G095000' => 'cil', 'CiPaw.02G131900' => 'cil', 'CiPaw.03G043000' => 'cil', 'CiPaw.03G069900' => 'cil', 'CiPaw.03G088100' => 'cil', 'CiPaw.03G089300' => 'cil', 'CiPaw.03G093100' => 'cil', 'CiPaw.03G129800' => 'cil', 'CiPaw.03G131200' => 'cil', 'CiPaw.03G134500' => 'cil', 'CiPaw.03G152100' => 'cil', 'CiPaw.03G162700' => 'cil', 'CiPaw.03G172800' => 'cil', 'CiPaw.03G175800' => 'cil', 'CiPaw.03G181800' => 'cil', 'CiPaw.03G191400' => 'cil', 'CiPaw.03G198300' => 'cil', 'CiPaw.03G201300' => 'cil', 'CiPaw.03G224700' => 'cil', 'CiPaw.03G225000' => 'cil', 'CiPaw.04G065100' => 'cil', 'CiPaw.04G080400' => 'cil', 'CiPaw.04G113500' => 'cil', 'CiPaw.04G121900' => 'cil', 'CiPaw.04G144100' => 'cil', 'CiPaw.04G176500' => 'cil', 'CiPaw.05G086200' => 'cil', 'CiPaw.05G100200' => 'cil', 'CiPaw.05G114200' => 'cil', 'CiPaw.05G126800' => 'cil', 'CiPaw.05G228800' => 'cil', 'CiPaw.05G230600' => 'cil', 'CiPaw.05G236500' => 'cil', 'CiPaw.05G244800' => 'cil', 'CiPaw.06G026600' => 'cil', 'CiPaw.06G027900' => 'cil', 'CiPaw.06G051800' => 'cil', 'CiPaw.06G128500' => 'cil', 'CiPaw.06G165900' => 'cil', 'CiPaw.07G045400' => 'cil', 'CiPaw.07G048000' => 'cil', 'CiPaw.07G052000' => 'cil', 'CiPaw.07G073800' => 'cil', 'CiPaw.07G099700' => 'cil', 'CiPaw.07G108700' => 'cil', 'CiPaw.07G120000' => 'cil', 'CiPaw.07G134100' => 'cil', 'CiPaw.07G147000' => 'cil', 'CiPaw.07G149700' => 'cil', 'CiPaw.07G178300' => 'cil', 'CiPaw.07G184900' => 'cil', 'CiPaw.08G044500' => 'cil', 'CiPaw.08G046900' => 'cil', 'CiPaw.08G047300' => 'cil', 'CiPaw.08G115400' => 'cil', 'CiPaw.08G134700' => 'cil', 'CiPaw.08G157400' => 'cil', 'CiPaw.09G014300' => 'cil', 'CiPaw.09G088900' => 'cil', 'CiPaw.09G130900' => 'cil', 'CiPaw.09G133100' => 'cil', 'CiPaw.09G151300' => 'cil', 'CiPaw.09G172800' => 'cil', 'CiPaw.09G174900' => 'cil', 'CiPaw.09G175000' => 'cil', 'CiPaw.10G012800' => 'cil', 'CiPaw.10G028800' => 'cil', 'CiPaw.10G044700' => 'cil', 'CiPaw.10G067400' => 'cil', 'CiPaw.10G115900' => 'cil', 'CiPaw.10G126200' => 'cil', 'CiPaw.10G139700' => 'cil', 'CiPaw.10G155100' => 'cil', 'CiPaw.11G011300' => 'cil', 'CiPaw.11G025900' => 'cil', 'CiPaw.11G104100' => 'cil', 'CiPaw.11G142700' => 'cil', 'CiPaw.11G164500' => 'cil', 'CiPaw.11G189100' => 'cil', 'CiPaw.11G197100' => 'cil', 'CiPaw.12G006100' => 'cil', 'CiPaw.12G038500' => 'cil', 'CiPaw.12G041400' => 'cil', 'CiPaw.12G041600' => 'cil', 'CiPaw.12G051300' => 'cil', 'CiPaw.12G101800' => 'cil', 'CiPaw.12G107800' => 'cil', 'CiPaw.13G033200' => 'cil', 'CiPaw.13G129900' => 'cil', 'CiPaw.13G160200' => 'cil', 'CiPaw.14G018900' => 'cil', 'CiPaw.14G029000' => 'cil', 'CiPaw.14G031000' => 'cil', 'CiPaw.14G032000' => 'cil', 'CiPaw.14G032300' => 'cil', 'CiPaw.14G040600' => 'cil', 'CiPaw.14G060500' => 'cil', 'CiPaw.14G061500' => 'cil', 'CiPaw.14G077500' => 'cil', 'CiPaw.14G088300' => 'cil', 'CiPaw.14G108500' => 'cil', 'CiPaw.14G121300' => 'cil', 'CiPaw.14G133000' => 'cil', 'CiPaw.14G134600' => 'cil', 'CiPaw.15G027200' => 'cil', 'CiPaw.15G037700' => 'cil', 'CiPaw.15G050900' => 'cil', 'CiPaw.15G067200' => 'cil', 'CiPaw.15G072000' => 'cil', 'CiPaw.15G112900' => 'cil', 'CiPaw.15G133200' => 'cil', 'CiPaw.15G139500' => 'cil', 'CiPaw.15G155400' => 'cil', 'CiPaw.16G006000' => 'cil', 'CiPaw.16G013100' => 'cil', 'CiPaw.16G047100' => 'cil', 'CiPaw.16G048900' => 'cil', 'CiPaw.16G070300' => 'cil', 'CSS0000195' => 'camsi', 'CSS0001664' => 'camsi', 'CSS0002566' => 'camsi', 'CSS0003077' => 'camsi', 'CSS0004257' => 'camsi', 'CSS0004495' => 'camsi', 'CSS0004599' => 'camsi', 'CSS0004943' => 'camsi', 'CSS0005302' => 'camsi', 'CSS0006274' => 'camsi', 'CSS0006547' => 'camsi', 'CSS0006860' => 'camsi', 'CSS0008814' => 'camsi', 'CSS0008946' => 'camsi', 'CSS0009093' => 'camsi', 'CSS0010221' => 'camsi', 'CSS0010296' => 'camsi', 'CSS0010386' => 'camsi', 'CSS0010831' => 'camsi', 'CSS0011061' => 'camsi', 'CSS0012008' => 'camsi', 'CSS0012194' => 'camsi', 'CSS0013580' => 'camsi', 'CSS0014176' => 'camsi', 'CSS0014280' => 'camsi', 'CSS0014799' => 'camsi', 'CSS0015368' => 'camsi', 'CSS0017473' => 'camsi', 'CSS0019281' => 'camsi', 'CSS0021320' => 'camsi', 'CSS0021750' => 'camsi', 'CSS0023642' => 'camsi', 'CSS0023792' => 'camsi', 'CSS0031528' => 'camsi', 'CSS0033894' => 'camsi', 'CSS0034959' => 'camsi', 'CSS0035632' => 'camsi', 'CSS0038450' => 'camsi', 'CSS0039293' => 'camsi', 'CSS0041053' => 'camsi', 'CSS0041981' => 'camsi', 'CSS0042573' => 'camsi', 'CSS0042927' => 'camsi', 'CSS0047725' => 'camsi', 'CSS0049636' => 'camsi', 'CSS0050513' => 'camsi', 'DCAR_030203' => 'dca', 'Dinv07939' => 'din', 'FAN01G0456' => 'fan', 'FAN02G3001' => 'fan', 'FAN04G2781' => 'fan', 'FAN05G1385' => 'fan', 'FAN05G3062' => 'fan', 'FAN08G2267' => 'fan', 'FAN10G0481' => 'fan', 'FAN10G1257' => 'fan', 'FAN14G0954' => 'fan', 'FAN14G2347' => 'fan', 'FAN15G0187' => 'fan', 'FAN25G2214' => 'fan', 'FvH4_1g21031' => 'fve', 'FvH4_3g16231' => 'fve', 'FvH4_3g26413' => 'fve', 'FvH4_3g29014' => 'fve', 'FvH4_3g31921' => 'fve', 'FvH4_4g19882' => 'fve', 'FvH4_5g21960' => 'fve', 'FvH4_5g29683' => 'fve', 'FvH4_7g13271' => 'fve', 'Glyma.01G062500' => 'gma', 'Glyma.07G140900' => 'gma', 'Glyma.09G140900' => 'gma', 'Glyma.12G112700' => 'gma', 'Glyma.17G168800' => 'gma', 'HanXRQChr01g0027001' => 'han', 'HanXRQChr04g0120511' => 'han', 'HanXRQChr08g0232381' => 'han', 'HanXRQChr09g0265661' => 'han', 'HanXRQChr13g0416031' => 'han', 'Haze_05835' => 'cav', 'Haze_06597' => 'cav', 'Haze_07921' => 'cav', 'Haze_08599' => 'cav', 'Haze_10686' => 'cav', 'Haze_12994' => 'cav', 'Haze_13466' => 'cav', 'Haze_16101' => 'cav', 'Haze_17766' => 'cav', 'Haze_18456' => 'cav', 'Haze_20229' => 'cav', 'Hma1.2p1_0324F.1_g125640' => 'hma', 'Hma1.2p1_0733F.1_g210230' => 'hma', 'Hma1.2p1_0921F.1_g236870' => 'hma', 'Hma1.2p1_1313F.1_g274940' => 'hma', 'Hma1.2p1_3059F.1_g332230' => 'hma', 'Hund15925' => 'sun', 'Hund19562' => 'sun', 'Hund21925' => 'sun', 'MD03G1177400' => 'mdo', 'MD07G1026100' => 'mdo', 'MD17G1218600' => 'mdo', 'Medtr0867s0010' => 'mtr', 'Medtr6g081150' => 'mtr', 'Os01g0527900' => 'osa', 'Os02g0463725' => 'osa', 'Os02g0785600' => 'osa', 'Os03g0433733' => 'osa', 'Os04g0286500' => 'osa', 'Os05g0227800' => 'osa', 'Os06g0521000' => 'osa', 'Os06g0635500' => 'osa', 'Os06g0660650' => 'osa', 'Os07g0554400' => 'osa', 'Os08g0225900' => 'osa', 'Os08g0561000' => 'osa', 'Os09g0241700' => 'osa', 'Os09g0351900' => 'osa', 'Os11g0220700' => 'osa', 'Os11g0282700' => 'osa', 'Os12g0169300' => 'osa', 'Os12g0228500' => 'osa', 'Os12g0543800' => 'osa', 'PGR044G1547' => 'pgr', 'Potri.005G239150' => 'ptr', 'Potri.010G014250' => 'ptr', 'Prupe.1G172500' => 'ppe', 'Prupe.1G196800' => 'ppe', 'Prupe.1G279700' => 'ppe', 'Prupe.2G026400' => 'ppe', 'Prupe.3G094000' => 'ppe', 'Prupe.4G287300' => 'ppe', 'QL01p022166' => 'qlo', 'QL01p051890' => 'qlo', 'QL02p009469' => 'qlo', 'QL02p046053' => 'qlo', 'QL02p057958' => 'qlo', 'QL02p093127' => 'qlo', 'QL03p006855' => 'qlo', 'QL03p071586' => 'qlo', 'QL04p000022' => 'qlo', 'QL04p000024' => 'qlo', 'QL04p003192' => 'qlo', 'QL05p011416' => 'qlo', 'QL06p039590' => 'qlo', 'QL06p052750' => 'qlo', 'QL06p053821' => 'qlo', 'QL07p025287' => 'qlo', 'QL09p033218' => 'qlo', 'QL09p040841' => 'qlo', 'QL10p020337' => 'qlo', 'QL10p027209' => 'qlo', 'QL10p027969' => 'qlo', 'QL10p048988' => 'qlo', 'QL11p001241' => 'qlo', 'QL11p028487' => 'qlo', 'RcHm_v2.0_Chr2g0105031' => 'rch', 'RcHm_v2.0_Chr2g0117811' => 'rch', 'RcHm_v2.0_Chr6g0270241' => 'rch', 'RcHm_v2.0_Chr7g0215961' => 'rch', 'RcHm_v2.0_Chr7g0231991' => 'rch', 'Rhsim01G0041500' => 'rsi', 'Rhsim01G0115000' => 'rsi', 'Rhsim01G0115400' => 'rsi', 'Rhsim01G0133600' => 'rsi', 'Rhsim01G0159900' => 'rsi', 'Rhsim02G0189400' => 'rsi', 'Rhsim03G0135600' => 'rsi', 'Rhsim03G0149900' => 'rsi', 'Rhsim04G0125600' => 'rsi', 'Rhsim05G0091700' => 'rsi', 'Rhsim05G0092900' => 'rsi', 'Rhsim06G0075000' => 'rsi', 'Rhsim07G0066400' => 'rsi', 'Rhsim07G0156400' => 'rsi', 'Rhsim07G0182200' => 'rsi', 'Rhsim07G0182300' => 'rsi', 'Rhsim08G0180400' => 'rsi', 'Rhsim09G0056800' => 'rsi', 'Rhsim10G0153300' => 'rsi', 'Rhsim11G0012700' => 'rsi', 'Rhsim12G0031800' => 'rsi', 'Rhsim12G0055400' => 'rsi', 'Rhsim12G0091400' => 'rsi', 'Rhsim13G0070800' => 'rsi', 'Rhsim13G0193300' => 'rsi', 'RhsimUnG0111600' => 'rsi', 'RhsimUnG0137500' => 'rsi', 'RhsimUnG0172900' => 'rsi', 'SGA_v2.0_scaffold11G05878' => 'sas', 'SGA_v2.0_scaffold167G38458' => 'sas', 'SGA_v2.0_scaffold19G08588' => 'sas', 'SGA_v2.0_scaffold239G43990' => 'sas', 'SGA_v2.0_scaffold260G45865' => 'sas', 'SGA_v2.0_scaffold309G48177' => 'sas', 'SGA_v2.0_scaffold76G25122' => 'sas', 'SGA_v2.0_scaffold85G26708' => 'sas', 'SHI13914' => 'shi', 'SHI30402' => 'shi', 'TWI09G0020' => 'twi', 'TWI09G0456' => 'twi', 'TWI09G1572' => 'twi', 'TWI12G0266' => 'twi', 'TWI12G1451' => 'twi', 'TWI14G0851' => 'twi', 'TWI15G0796' => 'twi', 'TWI18G0820' => 'twi', 'TWI18G1152' => 'twi', 'TWI23G0007' => 'twi', 'TWI23G0314' => 'twi', 'TWI31G0674' => 'twi', 'TWI31G0938' => 'twi', 'TWI34G0641' => 'twi', 'TWI34G1527' => 'twi', 'TWI36G0193' => 'twi', 'TWI36G0405' => 'twi', 'TWI38G0892' => 'twi', 'TWI38G0936' => 'twi', 'TWI38G2218' => 'twi', 'TWI53G0679' => 'twi', 'TWI53G0863' => 'twi', 'TWI53G1133' => 'twi', 'TWI60G0823' => 'twi', 'TWI63G0919' => 'twi', 'TWI63G1436' => 'twi', 'TWI73G0140' => 'twi', 'TWI73G0419' => 'twi', 'TWI73G0420' => 'twi', 'TWI73G1276' => 'twi', 'TWI74G0405' => 'twi', 'TWI74G0837' => 'twi', 'TWI75G0594' => 'twi', 'TWI75G1615' => 'twi', 'TWI77G0816' => 'twi', 'vmacro03831' => 'vma', 'vmacro13746' => 'vma', 'vmacro16089' => 'vma', 'vmacro22863' => 'vma', 'Zm00001eb085790' => 'zma', 'Zm00001eb114250' => 'zma', 'Zm00001eb138070' => 'zma', 'Zm00001eb167560' => 'zma', 'Zm00001eb199990' => 'zma', 'Zm00001eb368180' => 'zma', 'Zm00001eb382470' => 'zma' ) $gf_id = 'HOM05D001576' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001576' ) $data_identifier = 'HOM05D001576' $data_type = 'gf_id' $species_gene_counts = array( 'aox' => (int) 9, 'acertr' => (int) 3, 'cansat' => (int) 1, 'ccl' => (int) 4, 'cil' => (int) 145, 'camsi' => (int) 46, 'dca' => (int) 1, 'din' => (int) 1, 'fan' => (int) 12, 'fve' => (int) 9, 'gma' => (int) 5, 'han' => (int) 5, 'cav' => (int) 11, 'hma' => (int) 5, 'sun' => (int) 3, 'mdo' => (int) 3, 'mtr' => (int) 2, 'osa' => (int) 19, 'pgr' => (int) 1, 'ptr' => (int) 2, 'ppe' => (int) 6, 'qlo' => (int) 24, 'rch' => (int) 5, 'rsi' => (int) 28, 'sas' => (int) 8, 'shi' => (int) 2, 'twi' => (int) 35, 'vma' => (int) 4, 'zma' => (int) 7 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb382470' $species_info = array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) $local_species = 'zma' $disabled = '' $selected = '' $num_hits = (int) 0include - APP/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp, line 33 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933 View::_renderElement() - CORE/Cake/View/View.php, line 1224 View::element() - CORE/Cake/View/View.php, line 418 include - APP/View/Elements/analysis/phylogenetics_module/gf_data_settings.ctp, line 37 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933 View::_renderElement() - CORE/Cake/View/View.php, line 1224 View::element() - CORE/Cake/View/View.php, line 418 include - APP/View/Elements/analysis/phylogenetics_module/parameter_selection.ctp, line 64 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933 View::_renderElement() - CORE/Cake/View/View.php, line 1224 View::element() - CORE/Cake/View/View.php, line 418 include - APP/View/Analysis/custom_tree_creation.ctp, line 27 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933
$viewFile = '/www/bioinformatics01_ro/plaza/_dev_instances/feedback/app/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp' $dataForView = array( 'sidebar_info' => array( 'gf_id' => 'HOM05D001576', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '406', 'num_species' => '29' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'Aqoxy1G01456' => 'aox', 'Aqoxy1G02949' => 'aox', 'Aqoxy3G01274' => 'aox', 'Aqoxy3G02110' => 'aox', 'Aqoxy3G02268' => 'aox', 'Aqoxy5G02702' => 'aox', 'Aqoxy5G02988' => 'aox', 'Aqoxy5G03427' => 'aox', 'Aqoxy6G02363' => 'aox', 'Atru.chr1.3225' => 'acertr', 'Atru.chr8.1198' => 'acertr', 'Atru.chr9.790' => 'acertr', 'CANSAT01G3197' => 'cansat', 'Ciclev10003979m.g' => 'ccl', 'Ciclev10017471m.g' => 'ccl', 'Ciclev10018206m.g' => 'ccl', 'Ciclev10033751m.g' => 'ccl', 'CiPaw.01G000900' => 'cil', 'CiPaw.01G001000' => 'cil', 'CiPaw.01G033500' => 'cil', 'CiPaw.01G060300' => 'cil', 'CiPaw.01G070200' => 'cil', 'CiPaw.01G075100' => 'cil', 'CiPaw.01G084700' => 'cil', 'CiPaw.01G087900' => 'cil', 'CiPaw.01G092600' => 'cil', 'CiPaw.01G097200' => 'cil', 'CiPaw.01G098300' => 'cil', 'CiPaw.01G110200' => 'cil', 'CiPaw.01G118700' => 'cil', 'CiPaw.01G121200' => 'cil', 'CiPaw.01G132500' => 'cil', 'CiPaw.01G146900' => 'cil', 'CiPaw.01G174000' => 'cil', 'CiPaw.01G179900' => 'cil', 'CiPaw.01G183400' => 'cil', 'CiPaw.01G240000' => 'cil', 'CiPaw.01G283500' => 'cil', 'CiPaw.01G307400' => 'cil', 'CiPaw.02G030800' => 'cil', 'CiPaw.02G047200' => 'cil', 'CiPaw.02G050500' => 'cil', 'CiPaw.02G069900' => 'cil', 'CiPaw.02G091600' => 'cil', 'CiPaw.02G095000' => 'cil', 'CiPaw.02G131900' => 'cil', 'CiPaw.03G043000' => 'cil', 'CiPaw.03G069900' => 'cil', 'CiPaw.03G088100' => 'cil', 'CiPaw.03G089300' => 'cil', 'CiPaw.03G093100' => 'cil', 'CiPaw.03G129800' => 'cil', 'CiPaw.03G131200' => 'cil', 'CiPaw.03G134500' => 'cil', 'CiPaw.03G152100' => 'cil', 'CiPaw.03G162700' => 'cil', 'CiPaw.03G172800' => 'cil', 'CiPaw.03G175800' => 'cil', 'CiPaw.03G181800' => 'cil', 'CiPaw.03G191400' => 'cil', 'CiPaw.03G198300' => 'cil', 'CiPaw.03G201300' => 'cil', 'CiPaw.03G224700' => 'cil', 'CiPaw.03G225000' => 'cil', 'CiPaw.04G065100' => 'cil', 'CiPaw.04G080400' => 'cil', 'CiPaw.04G113500' => 'cil', 'CiPaw.04G121900' => 'cil', 'CiPaw.04G144100' => 'cil', 'CiPaw.04G176500' => 'cil', 'CiPaw.05G086200' => 'cil', 'CiPaw.05G100200' => 'cil', 'CiPaw.05G114200' => 'cil', 'CiPaw.05G126800' => 'cil', 'CiPaw.05G228800' => 'cil', 'CiPaw.05G230600' => 'cil', 'CiPaw.05G236500' => 'cil', 'CiPaw.05G244800' => 'cil', 'CiPaw.06G026600' => 'cil', 'CiPaw.06G027900' => 'cil', 'CiPaw.06G051800' => 'cil', 'CiPaw.06G128500' => 'cil', 'CiPaw.06G165900' => 'cil', 'CiPaw.07G045400' => 'cil', 'CiPaw.07G048000' => 'cil', 'CiPaw.07G052000' => 'cil', 'CiPaw.07G073800' => 'cil', 'CiPaw.07G099700' => 'cil', 'CiPaw.07G108700' => 'cil', 'CiPaw.07G120000' => 'cil', 'CiPaw.07G134100' => 'cil', 'CiPaw.07G147000' => 'cil', 'CiPaw.07G149700' => 'cil', 'CiPaw.07G178300' => 'cil', 'CiPaw.07G184900' => 'cil', 'CiPaw.08G044500' => 'cil', 'CiPaw.08G046900' => 'cil', 'CiPaw.08G047300' => 'cil', 'CiPaw.08G115400' => 'cil', 'CiPaw.08G134700' => 'cil', 'CiPaw.08G157400' => 'cil', 'CiPaw.09G014300' => 'cil', 'CiPaw.09G088900' => 'cil', 'CiPaw.09G130900' => 'cil', 'CiPaw.09G133100' => 'cil', 'CiPaw.09G151300' => 'cil', 'CiPaw.09G172800' => 'cil', 'CiPaw.09G174900' => 'cil', 'CiPaw.09G175000' => 'cil', 'CiPaw.10G012800' => 'cil', 'CiPaw.10G028800' => 'cil', 'CiPaw.10G044700' => 'cil', 'CiPaw.10G067400' => 'cil', 'CiPaw.10G115900' => 'cil', 'CiPaw.10G126200' => 'cil', 'CiPaw.10G139700' => 'cil', 'CiPaw.10G155100' => 'cil', 'CiPaw.11G011300' => 'cil', 'CiPaw.11G025900' => 'cil', 'CiPaw.11G104100' => 'cil', 'CiPaw.11G142700' => 'cil', 'CiPaw.11G164500' => 'cil', 'CiPaw.11G189100' => 'cil', 'CiPaw.11G197100' => 'cil', 'CiPaw.12G006100' => 'cil', 'CiPaw.12G038500' => 'cil', 'CiPaw.12G041400' => 'cil', 'CiPaw.12G041600' => 'cil', 'CiPaw.12G051300' => 'cil', 'CiPaw.12G101800' => 'cil', 'CiPaw.12G107800' => 'cil', 'CiPaw.13G033200' => 'cil', 'CiPaw.13G129900' => 'cil', 'CiPaw.13G160200' => 'cil', 'CiPaw.14G018900' => 'cil', 'CiPaw.14G029000' => 'cil', 'CiPaw.14G031000' => 'cil', 'CiPaw.14G032000' => 'cil', 'CiPaw.14G032300' => 'cil', 'CiPaw.14G040600' => 'cil', 'CiPaw.14G060500' => 'cil', 'CiPaw.14G061500' => 'cil', 'CiPaw.14G077500' => 'cil', 'CiPaw.14G088300' => 'cil', 'CiPaw.14G108500' => 'cil', 'CiPaw.14G121300' => 'cil', 'CiPaw.14G133000' => 'cil', 'CiPaw.14G134600' => 'cil', 'CiPaw.15G027200' => 'cil', 'CiPaw.15G037700' => 'cil', 'CiPaw.15G050900' => 'cil', 'CiPaw.15G067200' => 'cil', 'CiPaw.15G072000' => 'cil', 'CiPaw.15G112900' => 'cil', 'CiPaw.15G133200' => 'cil', 'CiPaw.15G139500' => 'cil', 'CiPaw.15G155400' => 'cil', 'CiPaw.16G006000' => 'cil', 'CiPaw.16G013100' => 'cil', 'CiPaw.16G047100' => 'cil', 'CiPaw.16G048900' => 'cil', 'CiPaw.16G070300' => 'cil', 'CSS0000195' => 'camsi', 'CSS0001664' => 'camsi', 'CSS0002566' => 'camsi', 'CSS0003077' => 'camsi', 'CSS0004257' => 'camsi', 'CSS0004495' => 'camsi', 'CSS0004599' => 'camsi', 'CSS0004943' => 'camsi', 'CSS0005302' => 'camsi', 'CSS0006274' => 'camsi', 'CSS0006547' => 'camsi', 'CSS0006860' => 'camsi', 'CSS0008814' => 'camsi', 'CSS0008946' => 'camsi', 'CSS0009093' => 'camsi', 'CSS0010221' => 'camsi', 'CSS0010296' => 'camsi', 'CSS0010386' => 'camsi', 'CSS0010831' => 'camsi', 'CSS0011061' => 'camsi', 'CSS0012008' => 'camsi', 'CSS0012194' => 'camsi', 'CSS0013580' => 'camsi', 'CSS0014176' => 'camsi', 'CSS0014280' => 'camsi', 'CSS0014799' => 'camsi', 'CSS0015368' => 'camsi', 'CSS0017473' => 'camsi', 'CSS0019281' => 'camsi', 'CSS0021320' => 'camsi', 'CSS0021750' => 'camsi', 'CSS0023642' => 'camsi', 'CSS0023792' => 'camsi', 'CSS0031528' => 'camsi', 'CSS0033894' => 'camsi', 'CSS0034959' => 'camsi', 'CSS0035632' => 'camsi', 'CSS0038450' => 'camsi', 'CSS0039293' => 'camsi', 'CSS0041053' => 'camsi', 'CSS0041981' => 'camsi', 'CSS0042573' => 'camsi', 'CSS0042927' => 'camsi', 'CSS0047725' => 'camsi', 'CSS0049636' => 'camsi', 'CSS0050513' => 'camsi', 'DCAR_030203' => 'dca', 'Dinv07939' => 'din', 'FAN01G0456' => 'fan', 'FAN02G3001' => 'fan', 'FAN04G2781' => 'fan', 'FAN05G1385' => 'fan', 'FAN05G3062' => 'fan', 'FAN08G2267' => 'fan', 'FAN10G0481' => 'fan', 'FAN10G1257' => 'fan', 'FAN14G0954' => 'fan', 'FAN14G2347' => 'fan', 'FAN15G0187' => 'fan', 'FAN25G2214' => 'fan', 'FvH4_1g21031' => 'fve', 'FvH4_3g16231' => 'fve', 'FvH4_3g26413' => 'fve', 'FvH4_3g29014' => 'fve', 'FvH4_3g31921' => 'fve', 'FvH4_4g19882' => 'fve', 'FvH4_5g21960' => 'fve', 'FvH4_5g29683' => 'fve', 'FvH4_7g13271' => 'fve', 'Glyma.01G062500' => 'gma', 'Glyma.07G140900' => 'gma', 'Glyma.09G140900' => 'gma', 'Glyma.12G112700' => 'gma', 'Glyma.17G168800' => 'gma', 'HanXRQChr01g0027001' => 'han', 'HanXRQChr04g0120511' => 'han', 'HanXRQChr08g0232381' => 'han', 'HanXRQChr09g0265661' => 'han', 'HanXRQChr13g0416031' => 'han', 'Haze_05835' => 'cav', 'Haze_06597' => 'cav', 'Haze_07921' => 'cav', 'Haze_08599' => 'cav', 'Haze_10686' => 'cav', 'Haze_12994' => 'cav', 'Haze_13466' => 'cav', 'Haze_16101' => 'cav', 'Haze_17766' => 'cav', 'Haze_18456' => 'cav', 'Haze_20229' => 'cav', 'Hma1.2p1_0324F.1_g125640' => 'hma', 'Hma1.2p1_0733F.1_g210230' => 'hma', 'Hma1.2p1_0921F.1_g236870' => 'hma', 'Hma1.2p1_1313F.1_g274940' => 'hma', 'Hma1.2p1_3059F.1_g332230' => 'hma', 'Hund15925' => 'sun', 'Hund19562' => 'sun', 'Hund21925' => 'sun', 'MD03G1177400' => 'mdo', 'MD07G1026100' => 'mdo', 'MD17G1218600' => 'mdo', 'Medtr0867s0010' => 'mtr', 'Medtr6g081150' => 'mtr', 'Os01g0527900' => 'osa', 'Os02g0463725' => 'osa', 'Os02g0785600' => 'osa', 'Os03g0433733' => 'osa', 'Os04g0286500' => 'osa', 'Os05g0227800' => 'osa', 'Os06g0521000' => 'osa', 'Os06g0635500' => 'osa', 'Os06g0660650' => 'osa', 'Os07g0554400' => 'osa', 'Os08g0225900' => 'osa', 'Os08g0561000' => 'osa', 'Os09g0241700' => 'osa', 'Os09g0351900' => 'osa', 'Os11g0220700' => 'osa', 'Os11g0282700' => 'osa', 'Os12g0169300' => 'osa', 'Os12g0228500' => 'osa', 'Os12g0543800' => 'osa', 'PGR044G1547' => 'pgr', 'Potri.005G239150' => 'ptr', 'Potri.010G014250' => 'ptr', 'Prupe.1G172500' => 'ppe', 'Prupe.1G196800' => 'ppe', 'Prupe.1G279700' => 'ppe', 'Prupe.2G026400' => 'ppe', 'Prupe.3G094000' => 'ppe', 'Prupe.4G287300' => 'ppe', 'QL01p022166' => 'qlo', 'QL01p051890' => 'qlo', 'QL02p009469' => 'qlo', 'QL02p046053' => 'qlo', 'QL02p057958' => 'qlo', 'QL02p093127' => 'qlo', 'QL03p006855' => 'qlo', 'QL03p071586' => 'qlo', 'QL04p000022' => 'qlo', 'QL04p000024' => 'qlo', 'QL04p003192' => 'qlo', 'QL05p011416' => 'qlo', 'QL06p039590' => 'qlo', 'QL06p052750' => 'qlo', 'QL06p053821' => 'qlo', 'QL07p025287' => 'qlo', 'QL09p033218' => 'qlo', 'QL09p040841' => 'qlo', 'QL10p020337' => 'qlo', 'QL10p027209' => 'qlo', 'QL10p027969' => 'qlo', 'QL10p048988' => 'qlo', 'QL11p001241' => 'qlo', 'QL11p028487' => 'qlo', 'RcHm_v2.0_Chr2g0105031' => 'rch', 'RcHm_v2.0_Chr2g0117811' => 'rch', 'RcHm_v2.0_Chr6g0270241' => 'rch', 'RcHm_v2.0_Chr7g0215961' => 'rch', 'RcHm_v2.0_Chr7g0231991' => 'rch', 'Rhsim01G0041500' => 'rsi', 'Rhsim01G0115000' => 'rsi', 'Rhsim01G0115400' => 'rsi', 'Rhsim01G0133600' => 'rsi', 'Rhsim01G0159900' => 'rsi', 'Rhsim02G0189400' => 'rsi', 'Rhsim03G0135600' => 'rsi', 'Rhsim03G0149900' => 'rsi', 'Rhsim04G0125600' => 'rsi', 'Rhsim05G0091700' => 'rsi', 'Rhsim05G0092900' => 'rsi', 'Rhsim06G0075000' => 'rsi', 'Rhsim07G0066400' => 'rsi', 'Rhsim07G0156400' => 'rsi', 'Rhsim07G0182200' => 'rsi', 'Rhsim07G0182300' => 'rsi', 'Rhsim08G0180400' => 'rsi', 'Rhsim09G0056800' => 'rsi', 'Rhsim10G0153300' => 'rsi', 'Rhsim11G0012700' => 'rsi', 'Rhsim12G0031800' => 'rsi', 'Rhsim12G0055400' => 'rsi', 'Rhsim12G0091400' => 'rsi', 'Rhsim13G0070800' => 'rsi', 'Rhsim13G0193300' => 'rsi', 'RhsimUnG0111600' => 'rsi', 'RhsimUnG0137500' => 'rsi', 'RhsimUnG0172900' => 'rsi', 'SGA_v2.0_scaffold11G05878' => 'sas', 'SGA_v2.0_scaffold167G38458' => 'sas', 'SGA_v2.0_scaffold19G08588' => 'sas', 'SGA_v2.0_scaffold239G43990' => 'sas', 'SGA_v2.0_scaffold260G45865' => 'sas', 'SGA_v2.0_scaffold309G48177' => 'sas', 'SGA_v2.0_scaffold76G25122' => 'sas', 'SGA_v2.0_scaffold85G26708' => 'sas', 'SHI13914' => 'shi', 'SHI30402' => 'shi', 'TWI09G0020' => 'twi', 'TWI09G0456' => 'twi', 'TWI09G1572' => 'twi', 'TWI12G0266' => 'twi', 'TWI12G1451' => 'twi', 'TWI14G0851' => 'twi', 'TWI15G0796' => 'twi', 'TWI18G0820' => 'twi', 'TWI18G1152' => 'twi', 'TWI23G0007' => 'twi', 'TWI23G0314' => 'twi', 'TWI31G0674' => 'twi', 'TWI31G0938' => 'twi', 'TWI34G0641' => 'twi', 'TWI34G1527' => 'twi', 'TWI36G0193' => 'twi', 'TWI36G0405' => 'twi', 'TWI38G0892' => 'twi', 'TWI38G0936' => 'twi', 'TWI38G2218' => 'twi', 'TWI53G0679' => 'twi', 'TWI53G0863' => 'twi', 'TWI53G1133' => 'twi', 'TWI60G0823' => 'twi', 'TWI63G0919' => 'twi', 'TWI63G1436' => 'twi', 'TWI73G0140' => 'twi', 'TWI73G0419' => 'twi', 'TWI73G0420' => 'twi', 'TWI73G1276' => 'twi', 'TWI74G0405' => 'twi', 'TWI74G0837' => 'twi', 'TWI75G0594' => 'twi', 'TWI75G1615' => 'twi', 'TWI77G0816' => 'twi', 'vmacro03831' => 'vma', 'vmacro13746' => 'vma', 'vmacro16089' => 'vma', 'vmacro22863' => 'vma', 'Zm00001eb085790' => 'zma', 'Zm00001eb114250' => 'zma', 'Zm00001eb138070' => 'zma', 'Zm00001eb167560' => 'zma', 'Zm00001eb199990' => 'zma', 'Zm00001eb368180' => 'zma', 'Zm00001eb382470' => 'zma' ), 'gf_id' => 'HOM05D001576', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001576' ), 'data_identifier' => 'HOM05D001576', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001576', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '406', 'num_species' => '29' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'Aqoxy1G01456' => 'aox', 'Aqoxy1G02949' => 'aox', 'Aqoxy3G01274' => 'aox', 'Aqoxy3G02110' => 'aox', 'Aqoxy3G02268' => 'aox', 'Aqoxy5G02702' => 'aox', 'Aqoxy5G02988' => 'aox', 'Aqoxy5G03427' => 'aox', 'Aqoxy6G02363' => 'aox', 'Atru.chr1.3225' => 'acertr', 'Atru.chr8.1198' => 'acertr', 'Atru.chr9.790' => 'acertr', 'CANSAT01G3197' => 'cansat', 'Ciclev10003979m.g' => 'ccl', 'Ciclev10017471m.g' => 'ccl', 'Ciclev10018206m.g' => 'ccl', 'Ciclev10033751m.g' => 'ccl', 'CiPaw.01G000900' => 'cil', 'CiPaw.01G001000' => 'cil', 'CiPaw.01G033500' => 'cil', 'CiPaw.01G060300' => 'cil', 'CiPaw.01G070200' => 'cil', 'CiPaw.01G075100' => 'cil', 'CiPaw.01G084700' => 'cil', 'CiPaw.01G087900' => 'cil', 'CiPaw.01G092600' => 'cil', 'CiPaw.01G097200' => 'cil', 'CiPaw.01G098300' => 'cil', 'CiPaw.01G110200' => 'cil', 'CiPaw.01G118700' => 'cil', 'CiPaw.01G121200' => 'cil', 'CiPaw.01G132500' => 'cil', 'CiPaw.01G146900' => 'cil', 'CiPaw.01G174000' => 'cil', 'CiPaw.01G179900' => 'cil', 'CiPaw.01G183400' => 'cil', 'CiPaw.01G240000' => 'cil', 'CiPaw.01G283500' => 'cil', 'CiPaw.01G307400' => 'cil', 'CiPaw.02G030800' => 'cil', 'CiPaw.02G047200' => 'cil', 'CiPaw.02G050500' => 'cil', 'CiPaw.02G069900' => 'cil', 'CiPaw.02G091600' => 'cil', 'CiPaw.02G095000' => 'cil', 'CiPaw.02G131900' => 'cil', 'CiPaw.03G043000' => 'cil', 'CiPaw.03G069900' => 'cil', 'CiPaw.03G088100' => 'cil', 'CiPaw.03G089300' => 'cil', 'CiPaw.03G093100' => 'cil', 'CiPaw.03G129800' => 'cil', 'CiPaw.03G131200' => 'cil', 'CiPaw.03G134500' => 'cil', 'CiPaw.03G152100' => 'cil', 'CiPaw.03G162700' => 'cil', 'CiPaw.03G172800' => 'cil', 'CiPaw.03G175800' => 'cil', 'CiPaw.03G181800' => 'cil', 'CiPaw.03G191400' => 'cil', 'CiPaw.03G198300' => 'cil', 'CiPaw.03G201300' => 'cil', 'CiPaw.03G224700' => 'cil', 'CiPaw.03G225000' => 'cil', 'CiPaw.04G065100' => 'cil', 'CiPaw.04G080400' => 'cil', 'CiPaw.04G113500' => 'cil', 'CiPaw.04G121900' => 'cil', 'CiPaw.04G144100' => 'cil', 'CiPaw.04G176500' => 'cil', 'CiPaw.05G086200' => 'cil', 'CiPaw.05G100200' => 'cil', 'CiPaw.05G114200' => 'cil', 'CiPaw.05G126800' => 'cil', 'CiPaw.05G228800' => 'cil', 'CiPaw.05G230600' => 'cil', 'CiPaw.05G236500' => 'cil', 'CiPaw.05G244800' => 'cil', 'CiPaw.06G026600' => 'cil', 'CiPaw.06G027900' => 'cil', 'CiPaw.06G051800' => 'cil', 'CiPaw.06G128500' => 'cil', 'CiPaw.06G165900' => 'cil', 'CiPaw.07G045400' => 'cil', 'CiPaw.07G048000' => 'cil', 'CiPaw.07G052000' => 'cil', 'CiPaw.07G073800' => 'cil', 'CiPaw.07G099700' => 'cil', 'CiPaw.07G108700' => 'cil', 'CiPaw.07G120000' => 'cil', 'CiPaw.07G134100' => 'cil', 'CiPaw.07G147000' => 'cil', 'CiPaw.07G149700' => 'cil', 'CiPaw.07G178300' => 'cil', 'CiPaw.07G184900' => 'cil', 'CiPaw.08G044500' => 'cil', 'CiPaw.08G046900' => 'cil', 'CiPaw.08G047300' => 'cil', 'CiPaw.08G115400' => 'cil', 'CiPaw.08G134700' => 'cil', 'CiPaw.08G157400' => 'cil', 'CiPaw.09G014300' => 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'CiPaw.14G032000' => 'cil', 'CiPaw.14G032300' => 'cil', 'CiPaw.14G040600' => 'cil', 'CiPaw.14G060500' => 'cil', 'CiPaw.14G061500' => 'cil', 'CiPaw.14G077500' => 'cil', 'CiPaw.14G088300' => 'cil', 'CiPaw.14G108500' => 'cil', 'CiPaw.14G121300' => 'cil', 'CiPaw.14G133000' => 'cil', 'CiPaw.14G134600' => 'cil', 'CiPaw.15G027200' => 'cil', 'CiPaw.15G037700' => 'cil', 'CiPaw.15G050900' => 'cil', 'CiPaw.15G067200' => 'cil', 'CiPaw.15G072000' => 'cil', 'CiPaw.15G112900' => 'cil', 'CiPaw.15G133200' => 'cil', 'CiPaw.15G139500' => 'cil', 'CiPaw.15G155400' => 'cil', 'CiPaw.16G006000' => 'cil', 'CiPaw.16G013100' => 'cil', 'CiPaw.16G047100' => 'cil', 'CiPaw.16G048900' => 'cil', 'CiPaw.16G070300' => 'cil', 'CSS0000195' => 'camsi', 'CSS0001664' => 'camsi', 'CSS0002566' => 'camsi', 'CSS0003077' => 'camsi', 'CSS0004257' => 'camsi', 'CSS0004495' => 'camsi', 'CSS0004599' => 'camsi', 'CSS0004943' => 'camsi', 'CSS0005302' => 'camsi', 'CSS0006274' => 'camsi', 'CSS0006547' => 'camsi', 'CSS0006860' => 'camsi', 'CSS0008814' => 'camsi', 'CSS0008946' => 'camsi', 'CSS0009093' => 'camsi', 'CSS0010221' => 'camsi', 'CSS0010296' => 'camsi', 'CSS0010386' => 'camsi', 'CSS0010831' => 'camsi', 'CSS0011061' => 'camsi', 'CSS0012008' => 'camsi', 'CSS0012194' => 'camsi', 'CSS0013580' => 'camsi', 'CSS0014176' => 'camsi', 'CSS0014280' => 'camsi', 'CSS0014799' => 'camsi', 'CSS0015368' => 'camsi', 'CSS0017473' => 'camsi', 'CSS0019281' => 'camsi', 'CSS0021320' => 'camsi', 'CSS0021750' => 'camsi', 'CSS0023642' => 'camsi', 'CSS0023792' => 'camsi', 'CSS0031528' => 'camsi', 'CSS0033894' => 'camsi', 'CSS0034959' => 'camsi', 'CSS0035632' => 'camsi', 'CSS0038450' => 'camsi', 'CSS0039293' => 'camsi', 'CSS0041053' => 'camsi', 'CSS0041981' => 'camsi', 'CSS0042573' => 'camsi', 'CSS0042927' => 'camsi', 'CSS0047725' => 'camsi', 'CSS0049636' => 'camsi', 'CSS0050513' => 'camsi', 'DCAR_030203' => 'dca', 'Dinv07939' => 'din', 'FAN01G0456' => 'fan', 'FAN02G3001' => 'fan', 'FAN04G2781' => 'fan', 'FAN05G1385' => 'fan', 'FAN05G3062' => 'fan', 'FAN08G2267' => 'fan', 'FAN10G0481' => 'fan', 'FAN10G1257' => 'fan', 'FAN14G0954' => 'fan', 'FAN14G2347' => 'fan', 'FAN15G0187' => 'fan', 'FAN25G2214' => 'fan', 'FvH4_1g21031' => 'fve', 'FvH4_3g16231' => 'fve', 'FvH4_3g26413' => 'fve', 'FvH4_3g29014' => 'fve', 'FvH4_3g31921' => 'fve', 'FvH4_4g19882' => 'fve', 'FvH4_5g21960' => 'fve', 'FvH4_5g29683' => 'fve', 'FvH4_7g13271' => 'fve', 'Glyma.01G062500' => 'gma', 'Glyma.07G140900' => 'gma', 'Glyma.09G140900' => 'gma', 'Glyma.12G112700' => 'gma', 'Glyma.17G168800' => 'gma', 'HanXRQChr01g0027001' => 'han', 'HanXRQChr04g0120511' => 'han', 'HanXRQChr08g0232381' => 'han', 'HanXRQChr09g0265661' => 'han', 'HanXRQChr13g0416031' => 'han', 'Haze_05835' => 'cav', 'Haze_06597' => 'cav', 'Haze_07921' => 'cav', 'Haze_08599' => 'cav', 'Haze_10686' => 'cav', 'Haze_12994' => 'cav', 'Haze_13466' => 'cav', 'Haze_16101' => 'cav', 'Haze_17766' => 'cav', 'Haze_18456' => 'cav', 'Haze_20229' => 'cav', 'Hma1.2p1_0324F.1_g125640' => 'hma', 'Hma1.2p1_0733F.1_g210230' => 'hma', 'Hma1.2p1_0921F.1_g236870' => 'hma', 'Hma1.2p1_1313F.1_g274940' => 'hma', 'Hma1.2p1_3059F.1_g332230' => 'hma', 'Hund15925' => 'sun', 'Hund19562' => 'sun', 'Hund21925' => 'sun', 'MD03G1177400' => 'mdo', 'MD07G1026100' => 'mdo', 'MD17G1218600' => 'mdo', 'Medtr0867s0010' => 'mtr', 'Medtr6g081150' => 'mtr', 'Os01g0527900' => 'osa', 'Os02g0463725' => 'osa', 'Os02g0785600' => 'osa', 'Os03g0433733' => 'osa', 'Os04g0286500' => 'osa', 'Os05g0227800' => 'osa', 'Os06g0521000' => 'osa', 'Os06g0635500' => 'osa', 'Os06g0660650' => 'osa', 'Os07g0554400' => 'osa', 'Os08g0225900' => 'osa', 'Os08g0561000' => 'osa', 'Os09g0241700' => 'osa', 'Os09g0351900' => 'osa', 'Os11g0220700' => 'osa', 'Os11g0282700' => 'osa', 'Os12g0169300' => 'osa', 'Os12g0228500' => 'osa', 'Os12g0543800' => 'osa', 'PGR044G1547' => 'pgr', 'Potri.005G239150' => 'ptr', 'Potri.010G014250' => 'ptr', 'Prupe.1G172500' => 'ppe', 'Prupe.1G196800' => 'ppe', 'Prupe.1G279700' => 'ppe', 'Prupe.2G026400' => 'ppe', 'Prupe.3G094000' => 'ppe', 'Prupe.4G287300' => 'ppe', 'QL01p022166' => 'qlo', 'QL01p051890' => 'qlo', 'QL02p009469' => 'qlo', 'QL02p046053' => 'qlo', 'QL02p057958' => 'qlo', 'QL02p093127' => 'qlo', 'QL03p006855' => 'qlo', 'QL03p071586' => 'qlo', 'QL04p000022' => 'qlo', 'QL04p000024' => 'qlo', 'QL04p003192' => 'qlo', 'QL05p011416' => 'qlo', 'QL06p039590' => 'qlo', 'QL06p052750' => 'qlo', 'QL06p053821' => 'qlo', 'QL07p025287' => 'qlo', 'QL09p033218' => 'qlo', 'QL09p040841' => 'qlo', 'QL10p020337' => 'qlo', 'QL10p027209' => 'qlo', 'QL10p027969' => 'qlo', 'QL10p048988' => 'qlo', 'QL11p001241' => 'qlo', 'QL11p028487' => 'qlo', 'RcHm_v2.0_Chr2g0105031' => 'rch', 'RcHm_v2.0_Chr2g0117811' => 'rch', 'RcHm_v2.0_Chr6g0270241' => 'rch', 'RcHm_v2.0_Chr7g0215961' => 'rch', 'RcHm_v2.0_Chr7g0231991' => 'rch', 'Rhsim01G0041500' => 'rsi', 'Rhsim01G0115000' => 'rsi', 'Rhsim01G0115400' => 'rsi', 'Rhsim01G0133600' => 'rsi', 'Rhsim01G0159900' => 'rsi', 'Rhsim02G0189400' => 'rsi', 'Rhsim03G0135600' => 'rsi', 'Rhsim03G0149900' => 'rsi', 'Rhsim04G0125600' => 'rsi', 'Rhsim05G0091700' => 'rsi', 'Rhsim05G0092900' => 'rsi', 'Rhsim06G0075000' => 'rsi', 'Rhsim07G0066400' => 'rsi', 'Rhsim07G0156400' => 'rsi', 'Rhsim07G0182200' => 'rsi', 'Rhsim07G0182300' => 'rsi', 'Rhsim08G0180400' => 'rsi', 'Rhsim09G0056800' => 'rsi', 'Rhsim10G0153300' => 'rsi', 'Rhsim11G0012700' => 'rsi', 'Rhsim12G0031800' => 'rsi', 'Rhsim12G0055400' => 'rsi', 'Rhsim12G0091400' => 'rsi', 'Rhsim13G0070800' => 'rsi', 'Rhsim13G0193300' => 'rsi', 'RhsimUnG0111600' => 'rsi', 'RhsimUnG0137500' => 'rsi', 'RhsimUnG0172900' => 'rsi', 'SGA_v2.0_scaffold11G05878' => 'sas', 'SGA_v2.0_scaffold167G38458' => 'sas', 'SGA_v2.0_scaffold19G08588' => 'sas', 'SGA_v2.0_scaffold239G43990' => 'sas', 'SGA_v2.0_scaffold260G45865' => 'sas', 'SGA_v2.0_scaffold309G48177' => 'sas', 'SGA_v2.0_scaffold76G25122' => 'sas', 'SGA_v2.0_scaffold85G26708' => 'sas', 'SHI13914' => 'shi', 'SHI30402' => 'shi', 'TWI09G0020' => 'twi', 'TWI09G0456' => 'twi', 'TWI09G1572' => 'twi', 'TWI12G0266' => 'twi', 'TWI12G1451' => 'twi', 'TWI14G0851' => 'twi', 'TWI15G0796' => 'twi', 'TWI18G0820' => 'twi', 'TWI18G1152' => 'twi', 'TWI23G0007' => 'twi', 'TWI23G0314' => 'twi', 'TWI31G0674' => 'twi', 'TWI31G0938' => 'twi', 'TWI34G0641' => 'twi', 'TWI34G1527' => 'twi', 'TWI36G0193' => 'twi', 'TWI36G0405' => 'twi', 'TWI38G0892' => 'twi', 'TWI38G0936' => 'twi', 'TWI38G2218' => 'twi', 'TWI53G0679' => 'twi', 'TWI53G0863' => 'twi', 'TWI53G1133' => 'twi', 'TWI60G0823' => 'twi', 'TWI63G0919' => 'twi', 'TWI63G1436' => 'twi', 'TWI73G0140' => 'twi', 'TWI73G0419' => 'twi', 'TWI73G0420' => 'twi', 'TWI73G1276' => 'twi', 'TWI74G0405' => 'twi', 'TWI74G0837' => 'twi', 'TWI75G0594' => 'twi', 'TWI75G1615' => 'twi', 'TWI77G0816' => 'twi', 'vmacro03831' => 'vma', 'vmacro13746' => 'vma', 'vmacro16089' => 'vma', 'vmacro22863' => 'vma', 'Zm00001eb085790' => 'zma', 'Zm00001eb114250' => 'zma', 'Zm00001eb138070' => 'zma', 'Zm00001eb167560' => 'zma', 'Zm00001eb199990' => 'zma', 'Zm00001eb368180' => 'zma', 'Zm00001eb382470' => 'zma' ) $gf_id = 'HOM05D001576' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001576' ) $data_identifier = 'HOM05D001576' $data_type = 'gf_id' $species_gene_counts = array( 'aox' => (int) 9, 'acertr' => (int) 3, 'cansat' => (int) 1, 'ccl' => (int) 4, 'cil' => (int) 145, 'camsi' => (int) 46, 'dca' => (int) 1, 'din' => (int) 1, 'fan' => (int) 12, 'fve' => (int) 9, 'gma' => (int) 5, 'han' => (int) 5, 'cav' => (int) 11, 'hma' => (int) 5, 'sun' => (int) 3, 'mdo' => (int) 3, 'mtr' => (int) 2, 'osa' => (int) 19, 'pgr' => (int) 1, 'ptr' => (int) 2, 'ppe' => (int) 6, 'qlo' => (int) 24, 'rch' => (int) 5, 'rsi' => (int) 28, 'sas' => (int) 8, 'shi' => (int) 2, 'twi' => (int) 35, 'vma' => (int) 4, 'zma' => (int) 7 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb382470' $species_info = array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) $local_species = 'zma' $disabled = '' $selected = '' $num_hits = (int) 0