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' => 'HOM05D001028', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '590', 'num_species' => '12' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'Aqoxy1G01649' => 'aox', 'Aqoxy1G02950' => 'aox', 'Aqoxy2G01005' => 'aox', 'Aqoxy2G01064' => 'aox', 'Aqoxy3G02267' => 'aox', 'Aqoxy3G02617' => 'aox', 'Aqoxy3G02693' => 'aox', 'Aqoxy5G03425' => 'aox', 'Aqoxy6G02164' => 'aox', 'Aqoxy6G02364' => 'aox', 'Aqoxy7G02284' => 'aox', 'Cc00_g09720' => 'ccan', 'Cc00_g21410' => 'ccan', 'Cc00_g31750' => 'ccan', 'Cc00_g34740' => 'ccan', 'Cc04_g16890' => 'ccan', 'Cc11_g03120' => 'ccan', 'CSS0000222' => 'camsi', 'CSS0000265' => 'camsi', 'CSS0000306' => 'camsi', 'CSS0000326' => 'camsi', 'CSS0000530' => 'camsi', 'CSS0000563' => 'camsi', 'CSS0000584' => 'camsi', 'CSS0000684' => 'camsi', 'CSS0001100' => 'camsi', 'CSS0001311' => 'camsi', 'CSS0001343' => 'camsi', 'CSS0001399' => 'camsi', 'CSS0001475' => 'camsi', 'CSS0001506' => 'camsi', 'CSS0001602' => 'camsi', 'CSS0001681' => 'camsi', 'CSS0001874' => 'camsi', 'CSS0001948' => 'camsi', 'CSS0002022' => 'camsi', 'CSS0002230' => 'camsi', 'CSS0002265' => 'camsi', 'CSS0002277' => 'camsi', 'CSS0002462' => 'camsi', 'CSS0002823' => 'camsi', 'CSS0003091' => 'camsi', 'CSS0003162' => 'camsi', 'CSS0003264' => 'camsi', 'CSS0003355' => 'camsi', 'CSS0003378' => 'camsi', 'CSS0003472' => 'camsi', 'CSS0003500' => 'camsi', 'CSS0003640' => 'camsi', 'CSS0003767' => 'camsi', 'CSS0003894' => 'camsi', 'CSS0003952' => 'camsi', 'CSS0003977' => 'camsi', 'CSS0004028' => 'camsi', 'CSS0004117' => 'camsi', 'CSS0004137' => 'camsi', 'CSS0004176' => 'camsi', 'CSS0004265' => 'camsi', 'CSS0004450' => 'camsi', 'CSS0004468' => 'camsi', 'CSS0004488' => 'camsi', 'CSS0004490' => 'camsi', 'CSS0004632' => 'camsi', 'CSS0004790' => 'camsi', 'CSS0004877' => 'camsi', 'CSS0004920' => 'camsi', 'CSS0004969' => 'camsi', 'CSS0005084' => 'camsi', 'CSS0005101' => 'camsi', 'CSS0005271' => 'camsi', 'CSS0005313' => 'camsi', 'CSS0005331' => 'camsi', 'CSS0005368' => 'camsi', 'CSS0005391' => 'camsi', 'CSS0005437' => 'camsi', 'CSS0005515' => 'camsi', 'CSS0005526' => 'camsi', 'CSS0005532' => 'camsi', 'CSS0005595' => 'camsi', 'CSS0005677' => 'camsi', 'CSS0005838' => 'camsi', 'CSS0005988' => 'camsi', 'CSS0006100' => 'camsi', 'CSS0006128' => 'camsi', 'CSS0006293' => 'camsi', 'CSS0006378' => 'camsi', 'CSS0006400' => 'camsi', 'CSS0006441' => 'camsi', 'CSS0006455' => 'camsi', 'CSS0006480' => 'camsi', 'CSS0006483' => 'camsi', 'CSS0006538' => 'camsi', 'CSS0006582' => 'camsi', 'CSS0006632' => 'camsi', 'CSS0006771' => 'camsi', 'CSS0006803' => 'camsi', 'CSS0006852' => 'camsi', 'CSS0006861' => 'camsi', 'CSS0006910' => 'camsi', 'CSS0007037' => 'camsi', 'CSS0007066' => 'camsi', 'CSS0007072' => 'camsi', 'CSS0007109' => 'camsi', 'CSS0007193' => 'camsi', 'CSS0007319' => 'camsi', 'CSS0007336' => 'camsi', 'CSS0007377' => 'camsi', 'CSS0007659' => 'camsi', 'CSS0007701' => 'camsi', 'CSS0007711' => 'camsi', 'CSS0007809' => 'camsi', 'CSS0008045' => 'camsi', 'CSS0008050' => 'camsi', 'CSS0008206' => 'camsi', 'CSS0008251' => 'camsi', 'CSS0008252' => 'camsi', 'CSS0008279' => 'camsi', 'CSS0008482' => 'camsi', 'CSS0008583' => 'camsi', 'CSS0008699' => 'camsi', 'CSS0008798' => 'camsi', 'CSS0008971' => 'camsi', 'CSS0009019' => 'camsi', 'CSS0009191' => 'camsi', 'CSS0009241' => 'camsi', 'CSS0009246' => 'camsi', 'CSS0009399' => 'camsi', 'CSS0009654' => 'camsi', 'CSS0009722' => 'camsi', 'CSS0009920' => 'camsi', 'CSS0009986' => 'camsi', 'CSS0010182' => 'camsi', 'CSS0010202' => 'camsi', 'CSS0010330' => 'camsi', 'CSS0010362' => 'camsi', 'CSS0010456' => 'camsi', 'CSS0010472' => 'camsi', 'CSS0010507' => 'camsi', 'CSS0010512' => 'camsi', 'CSS0010520' => 'camsi', 'CSS0010617' => 'camsi', 'CSS0010706' => 'camsi', 'CSS0010747' => 'camsi', 'CSS0010816' => 'camsi', 'CSS0011020' => 'camsi', 'CSS0011115' => 'camsi', 'CSS0011383' => 'camsi', 'CSS0011491' => 'camsi', 'CSS0011602' => 'camsi', 'CSS0011605' => 'camsi', 'CSS0011625' => 'camsi', 'CSS0011654' => 'camsi', 'CSS0011781' => 'camsi', 'CSS0011853' => 'camsi', 'CSS0011898' => 'camsi', 'CSS0011933' => 'camsi', 'CSS0011996' => 'camsi', 'CSS0012066' => 'camsi', 'CSS0012097' => 'camsi', 'CSS0012108' => 'camsi', 'CSS0012226' => 'camsi', 'CSS0012248' => 'camsi', 'CSS0012331' => 'camsi', 'CSS0012797' => 'camsi', 'CSS0012818' => 'camsi', 'CSS0012904' => 'camsi', 'CSS0013001' => 'camsi', 'CSS0013022' => 'camsi', 'CSS0013172' => 'camsi', 'CSS0013244' => 'camsi', 'CSS0013267' => 'camsi', 'CSS0013275' => 'camsi', 'CSS0013324' => 'camsi', 'CSS0013334' => 'camsi', 'CSS0013394' => 'camsi', 'CSS0013549' => 'camsi', 'CSS0013689' => 'camsi', 'CSS0014026' => 'camsi', 'CSS0014049' => 'camsi', 'CSS0014144' => 'camsi', 'CSS0014354' => 'camsi', 'CSS0014579' => 'camsi', 'CSS0014648' => 'camsi', 'CSS0014902' => 'camsi', 'CSS0014979' => 'camsi', 'CSS0015278' => 'camsi', 'CSS0015310' => 'camsi', 'CSS0015364' => 'camsi', 'CSS0015455' => 'camsi', 'CSS0015693' => 'camsi', 'CSS0015774' => 'camsi', 'CSS0015795' => 'camsi', 'CSS0015952' => 'camsi', 'CSS0016104' => 'camsi', 'CSS0016241' => 'camsi', 'CSS0016303' => 'camsi', 'CSS0016490' => 'camsi', 'CSS0016832' => 'camsi', 'CSS0016845' => 'camsi', 'CSS0016914' => 'camsi', 'CSS0016946' => 'camsi', 'CSS0017102' => 'camsi', 'CSS0017193' => 'camsi', 'CSS0017528' => 'camsi', 'CSS0017619' => 'camsi', 'CSS0017679' => 'camsi', 'CSS0017816' => 'camsi', 'CSS0017880' => 'camsi', 'CSS0018106' => 'camsi', 'CSS0018162' => 'camsi', 'CSS0018304' => 'camsi', 'CSS0018406' => 'camsi', 'CSS0018481' => 'camsi', 'CSS0018511' => 'camsi', 'CSS0018596' => 'camsi', 'CSS0018727' => 'camsi', 'CSS0018751' => 'camsi', 'CSS0018777' => 'camsi', 'CSS0018798' => 'camsi', 'CSS0019137' => 'camsi', 'CSS0019177' => 'camsi', 'CSS0019217' => 'camsi', 'CSS0019361' => 'camsi', 'CSS0019516' => 'camsi', 'CSS0019538' => 'camsi', 'CSS0019560' => 'camsi', 'CSS0019819' => 'camsi', 'CSS0019837' => 'camsi', 'CSS0019915' => 'camsi', 'CSS0019925' => 'camsi', 'CSS0020112' => 'camsi', 'CSS0020160' => 'camsi', 'CSS0020378' => 'camsi', 'CSS0020388' => 'camsi', 'CSS0020452' => 'camsi', 'CSS0020588' => 'camsi', 'CSS0020661' => 'camsi', 'CSS0020886' => 'camsi', 'CSS0020973' => 'camsi', 'CSS0021035' => 'camsi', 'CSS0021111' => 'camsi', 'CSS0021131' => 'camsi', 'CSS0021151' => 'camsi', 'CSS0021228' => 'camsi', 'CSS0021397' => 'camsi', 'CSS0021420' => 'camsi', 'CSS0021464' => 'camsi', 'CSS0021547' => 'camsi', 'CSS0021608' => 'camsi', 'CSS0021740' => 'camsi', 'CSS0021826' => 'camsi', 'CSS0021904' => 'camsi', 'CSS0021941' => 'camsi', 'CSS0022189' => 'camsi', 'CSS0022199' => 'camsi', 'CSS0022502' => 'camsi', 'CSS0022531' => 'camsi', 'CSS0022581' => 'camsi', 'CSS0022612' => 'camsi', 'CSS0022621' => 'camsi', 'CSS0022815' => 'camsi', 'CSS0022936' => 'camsi', 'CSS0022964' => 'camsi', 'CSS0022985' => 'camsi', 'CSS0023002' => 'camsi', 'CSS0023006' => 'camsi', 'CSS0023024' => 'camsi', 'CSS0023489' => 'camsi', 'CSS0023593' => 'camsi', 'CSS0023621' => 'camsi', 'CSS0023743' => 'camsi', 'CSS0023804' => 'camsi', 'CSS0023805' => 'camsi', 'CSS0023908' => 'camsi', 'CSS0023938' => 'camsi', 'CSS0023981' => 'camsi', 'CSS0024027' => 'camsi', 'CSS0024169' => 'camsi', 'CSS0024193' => 'camsi', 'CSS0024269' => 'camsi', 'CSS0024336' => 'camsi', 'CSS0024337' => 'camsi', 'CSS0024548' => 'camsi', 'CSS0024564' => 'camsi', 'CSS0024585' => 'camsi', 'CSS0024738' => 'camsi', 'CSS0024833' => 'camsi', 'CSS0024846' => 'camsi', 'CSS0024957' => 'camsi', 'CSS0024974' => 'camsi', 'CSS0025005' => 'camsi', 'CSS0025235' => 'camsi', 'CSS0025465' => 'camsi', 'CSS0025633' => 'camsi', 'CSS0025688' => 'camsi', 'CSS0025759' => 'camsi', 'CSS0025774' => 'camsi', 'CSS0025801' => 'camsi', 'CSS0025942' => 'camsi', 'CSS0026083' => 'camsi', 'CSS0026194' => 'camsi', 'CSS0026230' => 'camsi', 'CSS0026398' => 'camsi', 'CSS0026419' => 'camsi', 'CSS0026679' => 'camsi', 'CSS0026719' => 'camsi', 'CSS0026795' => 'camsi', 'CSS0026835' => 'camsi', 'CSS0026930' => 'camsi', 'CSS0027053' => 'camsi', 'CSS0027130' => 'camsi', 'CSS0027192' => 'camsi', 'CSS0027454' => 'camsi', 'CSS0027467' => 'camsi', 'CSS0027521' => 'camsi', 'CSS0027662' => 'camsi', 'CSS0027795' => 'camsi', 'CSS0027835' => 'camsi', 'CSS0027966' => 'camsi', 'CSS0028090' => 'camsi', 'CSS0028134' => 'camsi', 'CSS0028205' => 'camsi', 'CSS0028263' => 'camsi', 'CSS0028363' => 'camsi', 'CSS0028598' => 'camsi', 'CSS0029175' => 'camsi', 'CSS0029191' => 'camsi', 'CSS0029424' => 'camsi', 'CSS0029479' => 'camsi', 'CSS0029496' => 'camsi', 'CSS0029633' => 'camsi', 'CSS0029837' => 'camsi', 'CSS0029844' => 'camsi', 'CSS0029863' => 'camsi', 'CSS0029874' => 'camsi', 'CSS0029959' => 'camsi', 'CSS0030001' => 'camsi', 'CSS0030093' => 'camsi', 'CSS0030199' => 'camsi', 'CSS0030200' => 'camsi', 'CSS0030427' => 'camsi', 'CSS0030476' => 'camsi', 'CSS0030636' => 'camsi', 'CSS0030673' => 'camsi', 'CSS0030766' => 'camsi', 'CSS0030775' => 'camsi', 'CSS0030858' => 'camsi', 'CSS0030873' => 'camsi', 'CSS0030929' => 'camsi', 'CSS0031028' => 'camsi', 'CSS0031129' => 'camsi', 'CSS0031164' => 'camsi', 'CSS0031340' => 'camsi', 'CSS0031368' => 'camsi', 'CSS0031395' => 'camsi', 'CSS0031596' => 'camsi', 'CSS0031727' => 'camsi', 'CSS0032011' => 'camsi', 'CSS0032160' => 'camsi', 'CSS0032538' => 'camsi', 'CSS0032576' => 'camsi', 'CSS0032603' => 'camsi', 'CSS0032640' => 'camsi', 'CSS0032704' => 'camsi', 'CSS0032851' => 'camsi', 'CSS0032973' => 'camsi', 'CSS0033048' => 'camsi', 'CSS0033082' => 'camsi', 'CSS0033157' => 'camsi', 'CSS0033253' => 'camsi', 'CSS0033347' => 'camsi', 'CSS0033601' => 'camsi', 'CSS0033820' => 'camsi', 'CSS0033881' => 'camsi', 'CSS0033934' => 'camsi', 'CSS0034143' => 'camsi', 'CSS0034176' => 'camsi', 'CSS0034201' => 'camsi', 'CSS0034269' => 'camsi', 'CSS0034303' => 'camsi', 'CSS0034463' => 'camsi', 'CSS0034470' => 'camsi', 'CSS0034514' => 'camsi', 'CSS0034525' => 'camsi', 'CSS0034726' => 'camsi', 'CSS0034727' => 'camsi', 'CSS0034737' => 'camsi', 'CSS0034768' => 'camsi', 'CSS0034890' => 'camsi', 'CSS0034943' => 'camsi', 'CSS0034957' => 'camsi', 'CSS0034973' => 'camsi', 'CSS0035178' => 'camsi', 'CSS0035260' => 'camsi', 'CSS0035316' => 'camsi', 'CSS0035347' => 'camsi', 'CSS0035360' => 'camsi', 'CSS0035380' => 'camsi', 'CSS0035429' => 'camsi', 'CSS0035446' => 'camsi', 'CSS0035737' => 'camsi', 'CSS0035852' => 'camsi', 'CSS0035967' => 'camsi', 'CSS0036001' => 'camsi', 'CSS0036044' => 'camsi', 'CSS0036221' => 'camsi', 'CSS0036333' => 'camsi', 'CSS0036435' => 'camsi', 'CSS0036843' => 'camsi', 'CSS0036846' => 'camsi', 'CSS0037097' => 'camsi', 'CSS0037263' => 'camsi', 'CSS0037370' => 'camsi', 'CSS0037410' => 'camsi', 'CSS0037449' => 'camsi', 'CSS0037603' => 'camsi', 'CSS0037851' => 'camsi', 'CSS0037891' => 'camsi', 'CSS0037996' => 'camsi', 'CSS0038222' => 'camsi', 'CSS0038433' => 'camsi', 'CSS0038441' => 'camsi', 'CSS0038718' => 'camsi', 'CSS0038890' => 'camsi', 'CSS0039049' => 'camsi', 'CSS0039145' => 'camsi', 'CSS0039243' => 'camsi', 'CSS0039294' => 'camsi', 'CSS0039324' => 'camsi', 'CSS0039376' => 'camsi', 'CSS0039475' => 'camsi', 'CSS0039539' => 'camsi', 'CSS0039546' => 'camsi', 'CSS0039567' => 'camsi', 'CSS0039599' => 'camsi', 'CSS0039763' => 'camsi', 'CSS0039863' => 'camsi', 'CSS0040107' => 'camsi', 'CSS0040124' => 'camsi', 'CSS0040151' => 'camsi', 'CSS0040165' => 'camsi', 'CSS0040309' => 'camsi', 'CSS0040318' => 'camsi', 'CSS0040347' => 'camsi', 'CSS0040371' => 'camsi', 'CSS0040456' => 'camsi', 'CSS0040551' => 'camsi', 'CSS0040975' => 'camsi', 'CSS0040981' => 'camsi', 'CSS0041299' => 'camsi', 'CSS0041493' => 'camsi', 'CSS0041658' => 'camsi', 'CSS0041899' => 'camsi', 'CSS0041927' => 'camsi', 'CSS0042016' => 'camsi', 'CSS0042034' => 'camsi', 'CSS0042103' => 'camsi', 'CSS0042172' => 'camsi', 'CSS0042198' => 'camsi', 'CSS0042201' => 'camsi', 'CSS0042308' => 'camsi', 'CSS0042329' => 'camsi', 'CSS0042348' => 'camsi', 'CSS0042349' => 'camsi', 'CSS0042489' => 'camsi', 'CSS0042575' => 'camsi', 'CSS0042624' => 'camsi', 'CSS0042660' => 'camsi', 'CSS0042694' => 'camsi', 'CSS0042995' => 'camsi', 'CSS0043079' => 'camsi', 'CSS0043165' => 'camsi', 'CSS0043171' => 'camsi', 'CSS0043314' => 'camsi', 'CSS0043361' => 'camsi', 'CSS0043375' => 'camsi', 'CSS0043518' => 'camsi', 'CSS0043536' => 'camsi', 'CSS0043678' => 'camsi', 'CSS0043765' => 'camsi', 'CSS0043897' => 'camsi', 'CSS0043944' => 'camsi', 'CSS0044126' => 'camsi', 'CSS0044136' => 'camsi', 'CSS0044179' => 'camsi', 'CSS0044290' => 'camsi', 'CSS0044437' => 'camsi', 'CSS0044502' => 'camsi', 'CSS0044603' => 'camsi', 'CSS0044680' => 'camsi', 'CSS0044685' => 'camsi', 'CSS0044700' => 'camsi', 'CSS0044888' => 'camsi', 'CSS0044923' => 'camsi', 'CSS0044926' => 'camsi', 'CSS0044979' => 'camsi', 'CSS0045049' => 'camsi', 'CSS0045132' => 'camsi', 'CSS0045161' => 'camsi', 'CSS0045219' => 'camsi', 'CSS0045230' => 'camsi', 'CSS0045259' => 'camsi', 'CSS0045324' => 'camsi', 'CSS0045368' => 'camsi', 'CSS0045435' => 'camsi', 'CSS0045856' => 'camsi', 'CSS0045955' => 'camsi', 'CSS0046158' => 'camsi', 'CSS0046334' => 'camsi', 'CSS0046365' => 'camsi', 'CSS0046396' => 'camsi', 'CSS0046400' => 'camsi', 'CSS0046445' => 'camsi', 'CSS0046493' => 'camsi', 'CSS0046640' => 'camsi', 'CSS0046657' => 'camsi', 'CSS0046702' => 'camsi', 'CSS0047208' => 'camsi', 'CSS0047368' => 'camsi', 'CSS0047403' => 'camsi', 'CSS0047417' => 'camsi', 'CSS0047469' => 'camsi', 'CSS0047480' => 'camsi', 'CSS0047482' => 'camsi', 'CSS0047693' => 'camsi', 'CSS0047766' => 'camsi', 'CSS0047866' => 'camsi', 'CSS0047884' => 'camsi', 'CSS0048235' => 'camsi', 'CSS0048383' => 'camsi', 'CSS0048438' => 'camsi', 'CSS0048502' => 'camsi', 'CSS0048546' => 'camsi', 'CSS0048653' => 'camsi', 'CSS0048658' => 'camsi', 'CSS0048729' => 'camsi', 'CSS0048867' => 'camsi', 'CSS0048988' => 'camsi', 'CSS0049053' => 'camsi', 'CSS0049099' => 'camsi', 'CSS0049166' => 'camsi', 'CSS0049174' => 'camsi', 'CSS0049212' => 'camsi', 'CSS0049280' => 'camsi', 'CSS0049391' => 'camsi', 'CSS0049546' => 'camsi', 'CSS0049634' => 'camsi', 'CSS0049655' => 'camsi', 'CSS0049813' => 'camsi', 'CSS0049949' => 'camsi', 'CSS0050009' => 'camsi', 'CSS0050118' => 'camsi', 'CSS0050205' => 'camsi', 'CSS0050275' => 'camsi', 'CSS0050480' => 'camsi', 'CSS0050488' => 'camsi', 'CSS0050497' => 'camsi', 'Dinv03126' => 'din', 'Dinv13140' => 'din', 'Dinv13247' => 'din', 'Dinv14217' => 'din', 'EL10Ac9g22435' => 'bvu', 'FAN20G1200' => 'fan', 'PGR142G2516' => 'pgr', 'Prupe.3G160200' => 'ppe', 'Prupe.5G238200' => 'ppe', 'Prupe.7G047500' => 'ppe', 'QL03p045360' => 'qlo', 'QL05p034369' => 'qlo', 'QL05p034412' => 'qlo', 'QL08p017802' => 'qlo', 'QL08p024762' => 'qlo', 'QL10p026237' => 'qlo', 'QL10p032070' => 'qlo', 'QL11p003821' => 'qlo', 'Rhsim04G0057300' => 'rsi', 'Rhsim05G0049200' => 'rsi', 'Rhsim12G0010400' => 'rsi', 'Rhsim12G0012800' => 'rsi', 'TAR624G0483' => 'tar', 'TAR703G0001' => 'tar', 'vmacro05414' => 'vma', 'vmacro07091' => 'vma', 'vmacro07116' => 'vma', 'vmacro08423' => 'vma', 'vmacro09046' => 'vma', 'vmacro14269' => 'vma', 'vmacro16092' => 'vma', 'vmacro17280' => 'vma', 'vmacro19601' => 'vma' ), 'gf_id' => 'HOM05D001028', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001028' ), 'data_identifier' => 'HOM05D001028', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001028', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '590', 'num_species' => '12' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'Aqoxy1G01649' => 'aox', 'Aqoxy1G02950' => 'aox', 'Aqoxy2G01005' => 'aox', 'Aqoxy2G01064' => 'aox', 'Aqoxy3G02267' => 'aox', 'Aqoxy3G02617' => 'aox', 'Aqoxy3G02693' => 'aox', 'Aqoxy5G03425' => 'aox', 'Aqoxy6G02164' => 'aox', 'Aqoxy6G02364' => 'aox', 'Aqoxy7G02284' => 'aox', 'Cc00_g09720' => 'ccan', 'Cc00_g21410' => 'ccan', 'Cc00_g31750' => 'ccan', 'Cc00_g34740' => 'ccan', 'Cc04_g16890' => 'ccan', 'Cc11_g03120' => 'ccan', 'CSS0000222' => 'camsi', 'CSS0000265' => 'camsi', 'CSS0000306' => 'camsi', 'CSS0000326' => 'camsi', 'CSS0000530' => 'camsi', 'CSS0000563' => 'camsi', 'CSS0000584' => 'camsi', 'CSS0000684' => 'camsi', 'CSS0001100' => 'camsi', 'CSS0001311' => 'camsi', 'CSS0001343' => 'camsi', 'CSS0001399' => 'camsi', 'CSS0001475' => 'camsi', 'CSS0001506' => 'camsi', 'CSS0001602' => 'camsi', 'CSS0001681' => 'camsi', 'CSS0001874' => 'camsi', 'CSS0001948' => 'camsi', 'CSS0002022' => 'camsi', 'CSS0002230' => 'camsi', 'CSS0002265' => 'camsi', 'CSS0002277' => 'camsi', 'CSS0002462' => 'camsi', 'CSS0002823' => 'camsi', 'CSS0003091' => 'camsi', 'CSS0003162' => 'camsi', 'CSS0003264' => 'camsi', 'CSS0003355' => 'camsi', 'CSS0003378' => 'camsi', 'CSS0003472' => 'camsi', 'CSS0003500' => 'camsi', 'CSS0003640' => 'camsi', 'CSS0003767' => 'camsi', 'CSS0003894' => 'camsi', 'CSS0003952' => 'camsi', 'CSS0003977' => 'camsi', 'CSS0004028' => 'camsi', 'CSS0004117' => 'camsi', 'CSS0004137' => 'camsi', 'CSS0004176' => 'camsi', 'CSS0004265' => 'camsi', 'CSS0004450' => 'camsi', 'CSS0004468' => 'camsi', 'CSS0004488' => 'camsi', 'CSS0004490' => 'camsi', 'CSS0004632' => 'camsi', 'CSS0004790' => 'camsi', 'CSS0004877' => 'camsi', 'CSS0004920' => 'camsi', 'CSS0004969' => 'camsi', 'CSS0005084' => 'camsi', 'CSS0005101' => 'camsi', 'CSS0005271' => 'camsi', 'CSS0005313' => 'camsi', 'CSS0005331' => 'camsi', 'CSS0005368' => 'camsi', 'CSS0005391' => 'camsi', 'CSS0005437' => 'camsi', 'CSS0005515' => 'camsi', 'CSS0005526' => 'camsi', 'CSS0005532' => 'camsi', 'CSS0005595' => 'camsi', 'CSS0005677' => 'camsi', 'CSS0005838' => 'camsi', 'CSS0005988' => 'camsi', 'CSS0006100' => 'camsi', 'CSS0006128' => 'camsi', 'CSS0006293' => 'camsi', 'CSS0006378' => 'camsi', 'CSS0006400' => 'camsi', 'CSS0006441' => 'camsi', 'CSS0006455' => 'camsi', 'CSS0006480' => 'camsi', 'CSS0006483' => 'camsi', 'CSS0006538' => 'camsi', 'CSS0006582' => 'camsi', 'CSS0006632' => 'camsi', 'CSS0006771' => 'camsi', 'CSS0006803' => 'camsi', 'CSS0006852' => 'camsi', 'CSS0006861' => 'camsi', 'CSS0006910' => 'camsi', 'CSS0007037' => 'camsi', 'CSS0007066' => 'camsi', 'CSS0007072' => 'camsi', 'CSS0007109' => 'camsi', 'CSS0007193' => 'camsi', 'CSS0007319' => 'camsi', 'CSS0007336' => 'camsi', 'CSS0007377' => 'camsi', 'CSS0007659' => 'camsi', 'CSS0007701' => 'camsi', 'CSS0007711' => 'camsi', 'CSS0007809' => 'camsi', 'CSS0008045' => 'camsi', 'CSS0008050' => 'camsi', 'CSS0008206' => 'camsi', 'CSS0008251' => 'camsi', 'CSS0008252' => 'camsi', 'CSS0008279' => 'camsi', 'CSS0008482' => 'camsi', 'CSS0008583' => 'camsi', 'CSS0008699' => 'camsi', 'CSS0008798' => 'camsi', 'CSS0008971' => 'camsi', 'CSS0009019' => 'camsi', 'CSS0009191' => 'camsi', 'CSS0009241' => 'camsi', 'CSS0009246' => 'camsi', 'CSS0009399' => 'camsi', 'CSS0009654' => 'camsi', 'CSS0009722' => 'camsi', 'CSS0009920' => 'camsi', 'CSS0009986' => 'camsi', 'CSS0010182' => 'camsi', 'CSS0010202' => 'camsi', 'CSS0010330' => 'camsi', 'CSS0010362' => 'camsi', 'CSS0010456' => 'camsi', 'CSS0010472' => 'camsi', 'CSS0010507' => 'camsi', 'CSS0010512' => 'camsi', 'CSS0010520' => 'camsi', 'CSS0010617' => 'camsi', 'CSS0010706' => 'camsi', 'CSS0010747' => 'camsi', 'CSS0010816' => 'camsi', 'CSS0011020' => 'camsi', 'CSS0011115' => 'camsi', 'CSS0011383' => 'camsi', 'CSS0011491' => 'camsi', 'CSS0011602' => 'camsi', 'CSS0011605' => 'camsi', 'CSS0011625' => 'camsi', 'CSS0011654' => 'camsi', 'CSS0011781' => 'camsi', 'CSS0011853' => 'camsi', 'CSS0011898' => 'camsi', 'CSS0011933' => 'camsi', 'CSS0011996' => 'camsi', 'CSS0012066' => 'camsi', 'CSS0012097' => 'camsi', 'CSS0012108' => 'camsi', 'CSS0012226' => 'camsi', 'CSS0012248' => 'camsi', 'CSS0012331' => 'camsi', 'CSS0012797' => 'camsi', 'CSS0012818' => 'camsi', 'CSS0012904' => 'camsi', 'CSS0013001' => 'camsi', 'CSS0013022' => 'camsi', 'CSS0013172' => 'camsi', 'CSS0013244' => 'camsi', 'CSS0013267' => 'camsi', 'CSS0013275' => 'camsi', 'CSS0013324' => 'camsi', 'CSS0013334' => 'camsi', 'CSS0013394' => 'camsi', 'CSS0013549' => 'camsi', 'CSS0013689' => 'camsi', 'CSS0014026' => 'camsi', 'CSS0014049' => 'camsi', 'CSS0014144' => 'camsi', 'CSS0014354' => 'camsi', 'CSS0014579' => 'camsi', 'CSS0014648' => 'camsi', 'CSS0014902' => 'camsi', 'CSS0014979' => 'camsi', 'CSS0015278' => 'camsi', 'CSS0015310' => 'camsi', 'CSS0015364' => 'camsi', 'CSS0015455' => 'camsi', 'CSS0015693' => 'camsi', 'CSS0015774' => 'camsi', 'CSS0015795' => 'camsi', 'CSS0015952' => 'camsi', 'CSS0016104' => 'camsi', 'CSS0016241' => 'camsi', 'CSS0016303' => 'camsi', 'CSS0016490' => 'camsi', 'CSS0016832' => 'camsi', 'CSS0016845' => 'camsi', 'CSS0016914' => 'camsi', 'CSS0016946' => 'camsi', 'CSS0017102' => 'camsi', 'CSS0017193' => 'camsi', 'CSS0017528' => 'camsi', 'CSS0017619' => 'camsi', 'CSS0017679' => 'camsi', 'CSS0017816' => 'camsi', 'CSS0017880' => 'camsi', 'CSS0018106' => 'camsi', 'CSS0018162' => 'camsi', 'CSS0018304' => 'camsi', 'CSS0018406' => 'camsi', 'CSS0018481' => 'camsi', 'CSS0018511' => 'camsi', 'CSS0018596' => 'camsi', 'CSS0018727' => 'camsi', 'CSS0018751' => 'camsi', 'CSS0018777' => 'camsi', 'CSS0018798' => 'camsi', 'CSS0019137' => 'camsi', 'CSS0019177' => 'camsi', 'CSS0019217' => 'camsi', 'CSS0019361' => 'camsi', 'CSS0019516' => 'camsi', 'CSS0019538' => 'camsi', 'CSS0019560' => 'camsi', 'CSS0019819' => 'camsi', 'CSS0019837' => 'camsi', 'CSS0019915' => 'camsi', 'CSS0019925' => 'camsi', 'CSS0020112' => 'camsi', 'CSS0020160' => 'camsi', 'CSS0020378' => 'camsi', 'CSS0020388' => 'camsi', 'CSS0020452' => 'camsi', 'CSS0020588' => 'camsi', 'CSS0020661' => 'camsi', 'CSS0020886' => 'camsi', 'CSS0020973' => 'camsi', 'CSS0021035' => 'camsi', 'CSS0021111' => 'camsi', 'CSS0021131' => 'camsi', 'CSS0021151' => 'camsi', 'CSS0021228' => 'camsi', 'CSS0021397' => 'camsi', 'CSS0021420' => 'camsi', 'CSS0021464' => 'camsi', 'CSS0021547' => 'camsi', 'CSS0021608' => 'camsi', 'CSS0021740' => 'camsi', 'CSS0021826' => 'camsi', 'CSS0021904' => 'camsi', 'CSS0021941' => 'camsi', 'CSS0022189' => 'camsi', 'CSS0022199' => 'camsi', 'CSS0022502' => 'camsi', 'CSS0022531' => 'camsi', 'CSS0022581' => 'camsi', 'CSS0022612' => 'camsi', 'CSS0022621' => 'camsi', 'CSS0022815' => 'camsi', 'CSS0022936' => 'camsi', 'CSS0022964' => 'camsi', 'CSS0022985' => 'camsi', 'CSS0023002' => 'camsi', 'CSS0023006' => 'camsi', 'CSS0023024' => 'camsi', 'CSS0023489' => 'camsi', 'CSS0023593' => 'camsi', 'CSS0023621' => 'camsi', 'CSS0023743' => 'camsi', 'CSS0023804' => 'camsi', 'CSS0023805' => 'camsi', 'CSS0023908' => 'camsi', 'CSS0023938' => 'camsi', 'CSS0023981' => 'camsi', 'CSS0024027' => 'camsi', 'CSS0024169' => 'camsi', 'CSS0024193' => 'camsi', 'CSS0024269' => 'camsi', 'CSS0024336' => 'camsi', 'CSS0024337' => 'camsi', 'CSS0024548' => 'camsi', 'CSS0024564' => 'camsi', 'CSS0024585' => 'camsi', 'CSS0024738' => 'camsi', 'CSS0024833' => 'camsi', 'CSS0024846' => 'camsi', 'CSS0024957' => 'camsi', 'CSS0024974' => 'camsi', 'CSS0025005' => 'camsi', 'CSS0025235' => 'camsi', 'CSS0025465' => 'camsi', 'CSS0025633' => 'camsi', 'CSS0025688' => 'camsi', 'CSS0025759' => 'camsi', 'CSS0025774' => 'camsi', 'CSS0025801' => 'camsi', 'CSS0025942' => 'camsi', 'CSS0026083' => 'camsi', 'CSS0026194' => 'camsi', 'CSS0026230' => 'camsi', 'CSS0026398' => 'camsi', 'CSS0026419' => 'camsi', 'CSS0026679' => 'camsi', 'CSS0026719' => 'camsi', 'CSS0026795' => 'camsi', 'CSS0026835' => 'camsi', 'CSS0026930' => 'camsi', 'CSS0027053' => 'camsi', 'CSS0027130' => 'camsi', 'CSS0027192' => 'camsi', 'CSS0027454' => 'camsi', 'CSS0027467' => 'camsi', 'CSS0027521' => 'camsi', 'CSS0027662' => 'camsi', 'CSS0027795' => 'camsi', 'CSS0027835' => 'camsi', 'CSS0027966' => 'camsi', 'CSS0028090' => 'camsi', 'CSS0028134' => 'camsi', 'CSS0028205' => 'camsi', 'CSS0028263' => 'camsi', 'CSS0028363' => 'camsi', 'CSS0028598' => 'camsi', 'CSS0029175' => 'camsi', 'CSS0029191' => 'camsi', 'CSS0029424' => 'camsi', 'CSS0029479' => 'camsi', 'CSS0029496' => 'camsi', 'CSS0029633' => 'camsi', 'CSS0029837' => 'camsi', 'CSS0029844' => 'camsi', 'CSS0029863' => 'camsi', 'CSS0029874' => 'camsi', 'CSS0029959' => 'camsi', 'CSS0030001' => 'camsi', 'CSS0030093' => 'camsi', 'CSS0030199' => 'camsi', 'CSS0030200' => 'camsi', 'CSS0030427' => 'camsi', 'CSS0030476' => 'camsi', 'CSS0030636' => 'camsi', 'CSS0030673' => 'camsi', 'CSS0030766' => 'camsi', 'CSS0030775' => 'camsi', 'CSS0030858' => 'camsi', 'CSS0030873' => 'camsi', 'CSS0030929' => 'camsi', 'CSS0031028' => 'camsi', 'CSS0031129' => 'camsi', 'CSS0031164' => 'camsi', 'CSS0031340' => 'camsi', 'CSS0031368' => 'camsi', 'CSS0031395' => 'camsi', 'CSS0031596' => 'camsi', 'CSS0031727' => 'camsi', 'CSS0032011' => 'camsi', 'CSS0032160' => 'camsi', 'CSS0032538' => 'camsi', 'CSS0032576' => 'camsi', 'CSS0032603' => 'camsi', 'CSS0032640' => 'camsi', 'CSS0032704' => 'camsi', 'CSS0032851' => 'camsi', 'CSS0032973' => 'camsi', 'CSS0033048' => 'camsi', 'CSS0033082' => 'camsi', 'CSS0033157' => 'camsi', 'CSS0033253' => 'camsi', 'CSS0033347' => 'camsi', 'CSS0033601' => 'camsi', 'CSS0033820' => 'camsi', 'CSS0033881' => 'camsi', 'CSS0033934' => 'camsi', 'CSS0034143' => 'camsi', 'CSS0034176' => 'camsi', 'CSS0034201' => 'camsi', 'CSS0034269' => 'camsi', 'CSS0034303' => 'camsi', 'CSS0034463' => 'camsi', 'CSS0034470' => 'camsi', 'CSS0034514' => 'camsi', 'CSS0034525' => 'camsi', 'CSS0034726' => 'camsi', 'CSS0034727' => 'camsi', 'CSS0034737' => 'camsi', 'CSS0034768' => 'camsi', 'CSS0034890' => 'camsi', 'CSS0034943' => 'camsi', 'CSS0034957' => 'camsi', 'CSS0034973' => 'camsi', 'CSS0035178' => 'camsi', 'CSS0035260' => 'camsi', 'CSS0035316' => 'camsi', 'CSS0035347' => 'camsi', 'CSS0035360' => 'camsi', 'CSS0035380' => 'camsi', 'CSS0035429' => 'camsi', 'CSS0035446' => 'camsi', 'CSS0035737' => 'camsi', 'CSS0035852' => 'camsi', 'CSS0035967' => 'camsi', 'CSS0036001' => 'camsi', 'CSS0036044' => 'camsi', 'CSS0036221' => 'camsi', 'CSS0036333' => 'camsi', 'CSS0036435' => 'camsi', 'CSS0036843' => 'camsi', 'CSS0036846' => 'camsi', 'CSS0037097' => 'camsi', 'CSS0037263' => 'camsi', 'CSS0037370' => 'camsi', 'CSS0037410' => 'camsi', 'CSS0037449' => 'camsi', 'CSS0037603' => 'camsi', 'CSS0037851' => 'camsi', 'CSS0037891' => 'camsi', 'CSS0037996' => 'camsi', 'CSS0038222' => 'camsi', 'CSS0038433' => 'camsi', 'CSS0038441' => 'camsi', 'CSS0038718' => 'camsi', 'CSS0038890' => 'camsi', 'CSS0039049' => 'camsi', 'CSS0039145' => 'camsi', 'CSS0039243' => 'camsi', 'CSS0039294' => 'camsi', 'CSS0039324' => 'camsi', 'CSS0039376' => 'camsi', 'CSS0039475' => 'camsi', 'CSS0039539' => 'camsi', 'CSS0039546' => 'camsi', 'CSS0039567' => 'camsi', 'CSS0039599' => 'camsi', 'CSS0039763' => 'camsi', 'CSS0039863' => 'camsi', 'CSS0040107' => 'camsi', 'CSS0040124' => 'camsi', 'CSS0040151' => 'camsi', 'CSS0040165' => 'camsi', 'CSS0040309' => 'camsi', 'CSS0040318' => 'camsi', 'CSS0040347' => 'camsi', 'CSS0040371' => 'camsi', 'CSS0040456' => 'camsi', 'CSS0040551' => 'camsi', 'CSS0040975' => 'camsi', 'CSS0040981' => 'camsi', 'CSS0041299' => 'camsi', 'CSS0041493' => 'camsi', 'CSS0041658' => 'camsi', 'CSS0041899' => 'camsi', 'CSS0041927' => 'camsi', 'CSS0042016' => 'camsi', 'CSS0042034' => 'camsi', 'CSS0042103' => 'camsi', 'CSS0042172' => 'camsi', 'CSS0042198' => 'camsi', 'CSS0042201' => 'camsi', 'CSS0042308' => 'camsi', 'CSS0042329' => 'camsi', 'CSS0042348' => 'camsi', 'CSS0042349' => 'camsi', 'CSS0042489' => 'camsi', 'CSS0042575' => 'camsi', 'CSS0042624' => 'camsi', 'CSS0042660' => 'camsi', 'CSS0042694' => 'camsi', 'CSS0042995' => 'camsi', 'CSS0043079' => 'camsi', 'CSS0043165' => 'camsi', 'CSS0043171' => 'camsi', 'CSS0043314' => 'camsi', 'CSS0043361' => 'camsi', 'CSS0043375' => 'camsi', 'CSS0043518' => 'camsi', 'CSS0043536' => 'camsi', 'CSS0043678' => 'camsi', 'CSS0043765' => 'camsi', 'CSS0043897' => 'camsi', 'CSS0043944' => 'camsi', 'CSS0044126' => 'camsi', 'CSS0044136' => 'camsi', 'CSS0044179' => 'camsi', 'CSS0044290' => 'camsi', 'CSS0044437' => 'camsi', 'CSS0044502' => 'camsi', 'CSS0044603' => 'camsi', 'CSS0044680' => 'camsi', 'CSS0044685' => 'camsi', 'CSS0044700' => 'camsi', 'CSS0044888' => 'camsi', 'CSS0044923' => 'camsi', 'CSS0044926' => 'camsi', 'CSS0044979' => 'camsi', 'CSS0045049' => 'camsi', 'CSS0045132' => 'camsi', 'CSS0045161' => 'camsi', 'CSS0045219' => 'camsi', 'CSS0045230' => 'camsi', 'CSS0045259' => 'camsi', 'CSS0045324' => 'camsi', 'CSS0045368' => 'camsi', 'CSS0045435' => 'camsi', 'CSS0045856' => 'camsi', 'CSS0045955' => 'camsi', 'CSS0046158' => 'camsi', 'CSS0046334' => 'camsi', 'CSS0046365' => 'camsi', 'CSS0046396' => 'camsi', 'CSS0046400' => 'camsi', 'CSS0046445' => 'camsi', 'CSS0046493' => 'camsi', 'CSS0046640' => 'camsi', 'CSS0046657' => 'camsi', 'CSS0046702' => 'camsi', 'CSS0047208' => 'camsi', 'CSS0047368' => 'camsi', 'CSS0047403' => 'camsi', 'CSS0047417' => 'camsi', 'CSS0047469' => 'camsi', 'CSS0047480' => 'camsi', 'CSS0047482' => 'camsi', 'CSS0047693' => 'camsi', 'CSS0047766' => 'camsi', 'CSS0047866' => 'camsi', 'CSS0047884' => 'camsi', 'CSS0048235' => 'camsi', 'CSS0048383' => 'camsi', 'CSS0048438' => 'camsi', 'CSS0048502' => 'camsi', 'CSS0048546' => 'camsi', 'CSS0048653' => 'camsi', 'CSS0048658' => 'camsi', 'CSS0048729' => 'camsi', 'CSS0048867' => 'camsi', 'CSS0048988' => 'camsi', 'CSS0049053' => 'camsi', 'CSS0049099' => 'camsi', 'CSS0049166' => 'camsi', 'CSS0049174' => 'camsi', 'CSS0049212' => 'camsi', 'CSS0049280' => 'camsi', 'CSS0049391' => 'camsi', 'CSS0049546' => 'camsi', 'CSS0049634' => 'camsi', 'CSS0049655' => 'camsi', 'CSS0049813' => 'camsi', 'CSS0049949' => 'camsi', 'CSS0050009' => 'camsi', 'CSS0050118' => 'camsi', 'CSS0050205' => 'camsi', 'CSS0050275' => 'camsi', 'CSS0050480' => 'camsi', 'CSS0050488' => 'camsi', 'CSS0050497' => 'camsi', 'Dinv03126' => 'din', 'Dinv13140' => 'din', 'Dinv13247' => 'din', 'Dinv14217' => 'din', 'EL10Ac9g22435' => 'bvu', 'FAN20G1200' => 'fan', 'PGR142G2516' => 'pgr', 'Prupe.3G160200' => 'ppe', 'Prupe.5G238200' => 'ppe', 'Prupe.7G047500' => 'ppe', 'QL03p045360' => 'qlo', 'QL05p034369' => 'qlo', 'QL05p034412' => 'qlo', 'QL08p017802' => 'qlo', 'QL08p024762' => 'qlo', 'QL10p026237' => 'qlo', 'QL10p032070' => 'qlo', 'QL11p003821' => 'qlo', 'Rhsim04G0057300' => 'rsi', 'Rhsim05G0049200' => 'rsi', 'Rhsim12G0010400' => 'rsi', 'Rhsim12G0012800' => 'rsi', 'TAR624G0483' => 'tar', 'TAR703G0001' => 'tar', 'vmacro05414' => 'vma', 'vmacro07091' => 'vma', 'vmacro07116' => 'vma', 'vmacro08423' => 'vma', 'vmacro09046' => 'vma', 'vmacro14269' => 'vma', 'vmacro16092' => 'vma', 'vmacro17280' => 'vma', 'vmacro19601' => 'vma' ) $gf_id = 'HOM05D001028' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001028' ) $data_identifier = 'HOM05D001028' $data_type = 'gf_id' $species_gene_counts = array( 'aox' => (int) 11, 'ccan' => (int) 6, 'camsi' => (int) 540, 'din' => (int) 4, 'bvu' => (int) 1, 'fan' => (int) 1, 'pgr' => (int) 1, 'ppe' => (int) 3, 'qlo' => (int) 8, 'rsi' => (int) 4, 'tar' => (int) 2, 'vma' => (int) 9 ) $gf_gene_species = 'vma' $gf_gene_id = 'vmacro19601' $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
$disabled = (!array_key_exists($local_species,$species_gene_counts))?"disabled":""; $selected = (isset($selected_species) && array_key_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' => 'HOM05D001028', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '590', 'num_species' => '12' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'Aqoxy1G01649' => 'aox', 'Aqoxy1G02950' => 'aox', 'Aqoxy2G01005' => 'aox', 'Aqoxy2G01064' => 'aox', 'Aqoxy3G02267' => 'aox', 'Aqoxy3G02617' => 'aox', 'Aqoxy3G02693' => 'aox', 'Aqoxy5G03425' => 'aox', 'Aqoxy6G02164' => 'aox', 'Aqoxy6G02364' => 'aox', 'Aqoxy7G02284' => 'aox', 'Cc00_g09720' => 'ccan', 'Cc00_g21410' => 'ccan', 'Cc00_g31750' => 'ccan', 'Cc00_g34740' => 'ccan', 'Cc04_g16890' => 'ccan', 'Cc11_g03120' => 'ccan', 'CSS0000222' => 'camsi', 'CSS0000265' => 'camsi', 'CSS0000306' => 'camsi', 'CSS0000326' => 'camsi', 'CSS0000530' => 'camsi', 'CSS0000563' => 'camsi', 'CSS0000584' => 'camsi', 'CSS0000684' => 'camsi', 'CSS0001100' => 'camsi', 'CSS0001311' => 'camsi', 'CSS0001343' => 'camsi', 'CSS0001399' => 'camsi', 'CSS0001475' => 'camsi', 'CSS0001506' => 'camsi', 'CSS0001602' => 'camsi', 'CSS0001681' => 'camsi', 'CSS0001874' => 'camsi', 'CSS0001948' => 'camsi', 'CSS0002022' => 'camsi', 'CSS0002230' => 'camsi', 'CSS0002265' => 'camsi', 'CSS0002277' => 'camsi', 'CSS0002462' => 'camsi', 'CSS0002823' => 'camsi', 'CSS0003091' => 'camsi', 'CSS0003162' => 'camsi', 'CSS0003264' => 'camsi', 'CSS0003355' => 'camsi', 'CSS0003378' => 'camsi', 'CSS0003472' => 'camsi', 'CSS0003500' => 'camsi', 'CSS0003640' => 'camsi', 'CSS0003767' => 'camsi', 'CSS0003894' => 'camsi', 'CSS0003952' => 'camsi', 'CSS0003977' => 'camsi', 'CSS0004028' => 'camsi', 'CSS0004117' => 'camsi', 'CSS0004137' => 'camsi', 'CSS0004176' => 'camsi', 'CSS0004265' => 'camsi', 'CSS0004450' => 'camsi', 'CSS0004468' => 'camsi', 'CSS0004488' => 'camsi', 'CSS0004490' => 'camsi', 'CSS0004632' => 'camsi', 'CSS0004790' => 'camsi', 'CSS0004877' => 'camsi', 'CSS0004920' => 'camsi', 'CSS0004969' => 'camsi', 'CSS0005084' => 'camsi', 'CSS0005101' => 'camsi', 'CSS0005271' => 'camsi', 'CSS0005313' => 'camsi', 'CSS0005331' => 'camsi', 'CSS0005368' => 'camsi', 'CSS0005391' => 'camsi', 'CSS0005437' => 'camsi', 'CSS0005515' => 'camsi', 'CSS0005526' => 'camsi', 'CSS0005532' => 'camsi', 'CSS0005595' => 'camsi', 'CSS0005677' => 'camsi', 'CSS0005838' => 'camsi', 'CSS0005988' => 'camsi', 'CSS0006100' => 'camsi', 'CSS0006128' => 'camsi', 'CSS0006293' => 'camsi', 'CSS0006378' => 'camsi', 'CSS0006400' => 'camsi', 'CSS0006441' => 'camsi', 'CSS0006455' => 'camsi', 'CSS0006480' => 'camsi', 'CSS0006483' => 'camsi', 'CSS0006538' => 'camsi', 'CSS0006582' => 'camsi', 'CSS0006632' => 'camsi', 'CSS0006771' => 'camsi', 'CSS0006803' => 'camsi', 'CSS0006852' => 'camsi', 'CSS0006861' => 'camsi', 'CSS0006910' => 'camsi', 'CSS0007037' => 'camsi', 'CSS0007066' => 'camsi', 'CSS0007072' => 'camsi', 'CSS0007109' => 'camsi', 'CSS0007193' => 'camsi', 'CSS0007319' => 'camsi', 'CSS0007336' => 'camsi', 'CSS0007377' => 'camsi', 'CSS0007659' => 'camsi', 'CSS0007701' => 'camsi', 'CSS0007711' => 'camsi', 'CSS0007809' => 'camsi', 'CSS0008045' => 'camsi', 'CSS0008050' => 'camsi', 'CSS0008206' => 'camsi', 'CSS0008251' => 'camsi', 'CSS0008252' => 'camsi', 'CSS0008279' => 'camsi', 'CSS0008482' => 'camsi', 'CSS0008583' => 'camsi', 'CSS0008699' => 'camsi', 'CSS0008798' => 'camsi', 'CSS0008971' => 'camsi', 'CSS0009019' => 'camsi', 'CSS0009191' => 'camsi', 'CSS0009241' => 'camsi', 'CSS0009246' => 'camsi', 'CSS0009399' => 'camsi', 'CSS0009654' => 'camsi', 'CSS0009722' => 'camsi', 'CSS0009920' => 'camsi', 'CSS0009986' => 'camsi', 'CSS0010182' => 'camsi', 'CSS0010202' => 'camsi', 'CSS0010330' => 'camsi', 'CSS0010362' => 'camsi', 'CSS0010456' => 'camsi', 'CSS0010472' => 'camsi', 'CSS0010507' => 'camsi', 'CSS0010512' => 'camsi', 'CSS0010520' => 'camsi', 'CSS0010617' => 'camsi', 'CSS0010706' => 'camsi', 'CSS0010747' => 'camsi', 'CSS0010816' => 'camsi', 'CSS0011020' => 'camsi', 'CSS0011115' => 'camsi', 'CSS0011383' => 'camsi', 'CSS0011491' => 'camsi', 'CSS0011602' => 'camsi', 'CSS0011605' => 'camsi', 'CSS0011625' => 'camsi', 'CSS0011654' => 'camsi', 'CSS0011781' => 'camsi', 'CSS0011853' => 'camsi', 'CSS0011898' => 'camsi', 'CSS0011933' => 'camsi', 'CSS0011996' => 'camsi', 'CSS0012066' => 'camsi', 'CSS0012097' => 'camsi', 'CSS0012108' => 'camsi', 'CSS0012226' => 'camsi', 'CSS0012248' => 'camsi', 'CSS0012331' => 'camsi', 'CSS0012797' => 'camsi', 'CSS0012818' => 'camsi', 'CSS0012904' => 'camsi', 'CSS0013001' => 'camsi', 'CSS0013022' => 'camsi', 'CSS0013172' => 'camsi', 'CSS0013244' => 'camsi', 'CSS0013267' => 'camsi', 'CSS0013275' => 'camsi', 'CSS0013324' => 'camsi', 'CSS0013334' => 'camsi', 'CSS0013394' => 'camsi', 'CSS0013549' => 'camsi', 'CSS0013689' => 'camsi', 'CSS0014026' => 'camsi', 'CSS0014049' => 'camsi', 'CSS0014144' => 'camsi', 'CSS0014354' => 'camsi', 'CSS0014579' => 'camsi', 'CSS0014648' => 'camsi', 'CSS0014902' => 'camsi', 'CSS0014979' => 'camsi', 'CSS0015278' => 'camsi', 'CSS0015310' => 'camsi', 'CSS0015364' => 'camsi', 'CSS0015455' => 'camsi', 'CSS0015693' => 'camsi', 'CSS0015774' => 'camsi', 'CSS0015795' => 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'camsi', 'CSS0050205' => 'camsi', 'CSS0050275' => 'camsi', 'CSS0050480' => 'camsi', 'CSS0050488' => 'camsi', 'CSS0050497' => 'camsi', 'Dinv03126' => 'din', 'Dinv13140' => 'din', 'Dinv13247' => 'din', 'Dinv14217' => 'din', 'EL10Ac9g22435' => 'bvu', 'FAN20G1200' => 'fan', 'PGR142G2516' => 'pgr', 'Prupe.3G160200' => 'ppe', 'Prupe.5G238200' => 'ppe', 'Prupe.7G047500' => 'ppe', 'QL03p045360' => 'qlo', 'QL05p034369' => 'qlo', 'QL05p034412' => 'qlo', 'QL08p017802' => 'qlo', 'QL08p024762' => 'qlo', 'QL10p026237' => 'qlo', 'QL10p032070' => 'qlo', 'QL11p003821' => 'qlo', 'Rhsim04G0057300' => 'rsi', 'Rhsim05G0049200' => 'rsi', 'Rhsim12G0010400' => 'rsi', 'Rhsim12G0012800' => 'rsi', 'TAR624G0483' => 'tar', 'TAR703G0001' => 'tar', 'vmacro05414' => 'vma', 'vmacro07091' => 'vma', 'vmacro07116' => 'vma', 'vmacro08423' => 'vma', 'vmacro09046' => 'vma', 'vmacro14269' => 'vma', 'vmacro16092' => 'vma', 'vmacro17280' => 'vma', 'vmacro19601' => 'vma' ), 'gf_id' => 'HOM05D001028', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001028' ), 'data_identifier' => 'HOM05D001028', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001028', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '590', 'num_species' => '12' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'Aqoxy1G01649' => 'aox', 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'CSS0021131' => 'camsi', 'CSS0021151' => 'camsi', 'CSS0021228' => 'camsi', 'CSS0021397' => 'camsi', 'CSS0021420' => 'camsi', 'CSS0021464' => 'camsi', 'CSS0021547' => 'camsi', 'CSS0021608' => 'camsi', 'CSS0021740' => 'camsi', 'CSS0021826' => 'camsi', 'CSS0021904' => 'camsi', 'CSS0021941' => 'camsi', 'CSS0022189' => 'camsi', 'CSS0022199' => 'camsi', 'CSS0022502' => 'camsi', 'CSS0022531' => 'camsi', 'CSS0022581' => 'camsi', 'CSS0022612' => 'camsi', 'CSS0022621' => 'camsi', 'CSS0022815' => 'camsi', 'CSS0022936' => 'camsi', 'CSS0022964' => 'camsi', 'CSS0022985' => 'camsi', 'CSS0023002' => 'camsi', 'CSS0023006' => 'camsi', 'CSS0023024' => 'camsi', 'CSS0023489' => 'camsi', 'CSS0023593' => 'camsi', 'CSS0023621' => 'camsi', 'CSS0023743' => 'camsi', 'CSS0023804' => 'camsi', 'CSS0023805' => 'camsi', 'CSS0023908' => 'camsi', 'CSS0023938' => 'camsi', 'CSS0023981' => 'camsi', 'CSS0024027' => 'camsi', 'CSS0024169' => 'camsi', 'CSS0024193' => 'camsi', 'CSS0024269' => 'camsi', 'CSS0024336' => 'camsi', 'CSS0024337' => 'camsi', 'CSS0024548' => 'camsi', 'CSS0024564' => 'camsi', 'CSS0024585' => 'camsi', 'CSS0024738' => 'camsi', 'CSS0024833' => 'camsi', 'CSS0024846' => 'camsi', 'CSS0024957' => 'camsi', 'CSS0024974' => 'camsi', 'CSS0025005' => 'camsi', 'CSS0025235' => 'camsi', 'CSS0025465' => 'camsi', 'CSS0025633' => 'camsi', 'CSS0025688' => 'camsi', 'CSS0025759' => 'camsi', 'CSS0025774' => 'camsi', 'CSS0025801' => 'camsi', 'CSS0025942' => 'camsi', 'CSS0026083' => 'camsi', 'CSS0026194' => 'camsi', 'CSS0026230' => 'camsi', 'CSS0026398' => 'camsi', 'CSS0026419' => 'camsi', 'CSS0026679' => 'camsi', 'CSS0026719' => 'camsi', 'CSS0026795' => 'camsi', 'CSS0026835' => 'camsi', 'CSS0026930' => 'camsi', 'CSS0027053' => 'camsi', 'CSS0027130' => 'camsi', 'CSS0027192' => 'camsi', 'CSS0027454' => 'camsi', 'CSS0027467' => 'camsi', 'CSS0027521' => 'camsi', 'CSS0027662' => 'camsi', 'CSS0027795' => 'camsi', 'CSS0027835' => 'camsi', 'CSS0027966' => 'camsi', 'CSS0028090' => 'camsi', 'CSS0028134' => 'camsi', 'CSS0028205' => 'camsi', 'CSS0028263' => 'camsi', 'CSS0028363' => 'camsi', 'CSS0028598' => 'camsi', 'CSS0029175' => 'camsi', 'CSS0029191' => 'camsi', 'CSS0029424' => 'camsi', 'CSS0029479' => 'camsi', 'CSS0029496' => 'camsi', 'CSS0029633' => 'camsi', 'CSS0029837' => 'camsi', 'CSS0029844' => 'camsi', 'CSS0029863' => 'camsi', 'CSS0029874' => 'camsi', 'CSS0029959' => 'camsi', 'CSS0030001' => 'camsi', 'CSS0030093' => 'camsi', 'CSS0030199' => 'camsi', 'CSS0030200' => 'camsi', 'CSS0030427' => 'camsi', 'CSS0030476' => 'camsi', 'CSS0030636' => 'camsi', 'CSS0030673' => 'camsi', 'CSS0030766' => 'camsi', 'CSS0030775' => 'camsi', 'CSS0030858' => 'camsi', 'CSS0030873' => 'camsi', 'CSS0030929' => 'camsi', 'CSS0031028' => 'camsi', 'CSS0031129' => 'camsi', 'CSS0031164' => 'camsi', 'CSS0031340' => 'camsi', 'CSS0031368' => 'camsi', 'CSS0031395' => 'camsi', 'CSS0031596' => 'camsi', 'CSS0031727' => 'camsi', 'CSS0032011' => 'camsi', 'CSS0032160' => 'camsi', 'CSS0032538' => 'camsi', 'CSS0032576' => 'camsi', 'CSS0032603' => 'camsi', 'CSS0032640' => 'camsi', 'CSS0032704' => 'camsi', 'CSS0032851' => 'camsi', 'CSS0032973' => 'camsi', 'CSS0033048' => 'camsi', 'CSS0033082' => 'camsi', 'CSS0033157' => 'camsi', 'CSS0033253' => 'camsi', 'CSS0033347' => 'camsi', 'CSS0033601' => 'camsi', 'CSS0033820' => 'camsi', 'CSS0033881' => 'camsi', 'CSS0033934' => 'camsi', 'CSS0034143' => 'camsi', 'CSS0034176' => 'camsi', 'CSS0034201' => 'camsi', 'CSS0034269' => 'camsi', 'CSS0034303' => 'camsi', 'CSS0034463' => 'camsi', 'CSS0034470' => 'camsi', 'CSS0034514' => 'camsi', 'CSS0034525' => 'camsi', 'CSS0034726' => 'camsi', 'CSS0034727' => 'camsi', 'CSS0034737' => 'camsi', 'CSS0034768' => 'camsi', 'CSS0034890' => 'camsi', 'CSS0034943' => 'camsi', 'CSS0034957' => 'camsi', 'CSS0034973' => 'camsi', 'CSS0035178' => 'camsi', 'CSS0035260' => 'camsi', 'CSS0035316' => 'camsi', 'CSS0035347' => 'camsi', 'CSS0035360' => 'camsi', 'CSS0035380' => 'camsi', 'CSS0035429' => 'camsi', 'CSS0035446' => 'camsi', 'CSS0035737' => 'camsi', 'CSS0035852' => 'camsi', 'CSS0035967' => 'camsi', 'CSS0036001' => 'camsi', 'CSS0036044' => 'camsi', 'CSS0036221' => 'camsi', 'CSS0036333' => 'camsi', 'CSS0036435' => 'camsi', 'CSS0036843' => 'camsi', 'CSS0036846' => 'camsi', 'CSS0037097' => 'camsi', 'CSS0037263' => 'camsi', 'CSS0037370' => 'camsi', 'CSS0037410' => 'camsi', 'CSS0037449' => 'camsi', 'CSS0037603' => 'camsi', 'CSS0037851' => 'camsi', 'CSS0037891' => 'camsi', 'CSS0037996' => 'camsi', 'CSS0038222' => 'camsi', 'CSS0038433' => 'camsi', 'CSS0038441' => 'camsi', 'CSS0038718' => 'camsi', 'CSS0038890' => 'camsi', 'CSS0039049' => 'camsi', 'CSS0039145' => 'camsi', 'CSS0039243' => 'camsi', 'CSS0039294' => 'camsi', 'CSS0039324' => 'camsi', 'CSS0039376' => 'camsi', 'CSS0039475' => 'camsi', 'CSS0039539' => 'camsi', 'CSS0039546' => 'camsi', 'CSS0039567' => 'camsi', 'CSS0039599' => 'camsi', 'CSS0039763' => 'camsi', 'CSS0039863' => 'camsi', 'CSS0040107' => 'camsi', 'CSS0040124' => 'camsi', 'CSS0040151' => 'camsi', 'CSS0040165' => 'camsi', 'CSS0040309' => 'camsi', 'CSS0040318' => 'camsi', 'CSS0040347' => 'camsi', 'CSS0040371' => 'camsi', 'CSS0040456' => 'camsi', 'CSS0040551' => 'camsi', 'CSS0040975' => 'camsi', 'CSS0040981' => 'camsi', 'CSS0041299' => 'camsi', 'CSS0041493' => 'camsi', 'CSS0041658' => 'camsi', 'CSS0041899' => 'camsi', 'CSS0041927' => 'camsi', 'CSS0042016' => 'camsi', 'CSS0042034' => 'camsi', 'CSS0042103' => 'camsi', 'CSS0042172' => 'camsi', 'CSS0042198' => 'camsi', 'CSS0042201' => 'camsi', 'CSS0042308' => 'camsi', 'CSS0042329' => 'camsi', 'CSS0042348' => 'camsi', 'CSS0042349' => 'camsi', 'CSS0042489' => 'camsi', 'CSS0042575' => 'camsi', 'CSS0042624' => 'camsi', 'CSS0042660' => 'camsi', 'CSS0042694' => 'camsi', 'CSS0042995' => 'camsi', 'CSS0043079' => 'camsi', 'CSS0043165' => 'camsi', 'CSS0043171' => 'camsi', 'CSS0043314' => 'camsi', 'CSS0043361' => 'camsi', 'CSS0043375' => 'camsi', 'CSS0043518' => 'camsi', 'CSS0043536' => 'camsi', 'CSS0043678' => 'camsi', 'CSS0043765' => 'camsi', 'CSS0043897' => 'camsi', 'CSS0043944' => 'camsi', 'CSS0044126' => 'camsi', 'CSS0044136' => 'camsi', 'CSS0044179' => 'camsi', 'CSS0044290' => 'camsi', 'CSS0044437' => 'camsi', 'CSS0044502' => 'camsi', 'CSS0044603' => 'camsi', 'CSS0044680' => 'camsi', 'CSS0044685' => 'camsi', 'CSS0044700' => 'camsi', 'CSS0044888' => 'camsi', 'CSS0044923' => 'camsi', 'CSS0044926' => 'camsi', 'CSS0044979' => 'camsi', 'CSS0045049' => 'camsi', 'CSS0045132' => 'camsi', 'CSS0045161' => 'camsi', 'CSS0045219' => 'camsi', 'CSS0045230' => 'camsi', 'CSS0045259' => 'camsi', 'CSS0045324' => 'camsi', 'CSS0045368' => 'camsi', 'CSS0045435' => 'camsi', 'CSS0045856' => 'camsi', 'CSS0045955' => 'camsi', 'CSS0046158' => 'camsi', 'CSS0046334' => 'camsi', 'CSS0046365' => 'camsi', 'CSS0046396' => 'camsi', 'CSS0046400' => 'camsi', 'CSS0046445' => 'camsi', 'CSS0046493' => 'camsi', 'CSS0046640' => 'camsi', 'CSS0046657' => 'camsi', 'CSS0046702' => 'camsi', 'CSS0047208' => 'camsi', 'CSS0047368' => 'camsi', 'CSS0047403' => 'camsi', 'CSS0047417' => 'camsi', 'CSS0047469' => 'camsi', 'CSS0047480' => 'camsi', 'CSS0047482' => 'camsi', 'CSS0047693' => 'camsi', 'CSS0047766' => 'camsi', 'CSS0047866' => 'camsi', 'CSS0047884' => 'camsi', 'CSS0048235' => 'camsi', 'CSS0048383' => 'camsi', 'CSS0048438' => 'camsi', 'CSS0048502' => 'camsi', 'CSS0048546' => 'camsi', 'CSS0048653' => 'camsi', 'CSS0048658' => 'camsi', 'CSS0048729' => 'camsi', 'CSS0048867' => 'camsi', 'CSS0048988' => 'camsi', 'CSS0049053' => 'camsi', 'CSS0049099' => 'camsi', 'CSS0049166' => 'camsi', 'CSS0049174' => 'camsi', 'CSS0049212' => 'camsi', 'CSS0049280' => 'camsi', 'CSS0049391' => 'camsi', 'CSS0049546' => 'camsi', 'CSS0049634' => 'camsi', 'CSS0049655' => 'camsi', 'CSS0049813' => 'camsi', 'CSS0049949' => 'camsi', 'CSS0050009' => 'camsi', 'CSS0050118' => 'camsi', 'CSS0050205' => 'camsi', 'CSS0050275' => 'camsi', 'CSS0050480' => 'camsi', 'CSS0050488' => 'camsi', 'CSS0050497' => 'camsi', 'Dinv03126' => 'din', 'Dinv13140' => 'din', 'Dinv13247' => 'din', 'Dinv14217' => 'din', 'EL10Ac9g22435' => 'bvu', 'FAN20G1200' => 'fan', 'PGR142G2516' => 'pgr', 'Prupe.3G160200' => 'ppe', 'Prupe.5G238200' => 'ppe', 'Prupe.7G047500' => 'ppe', 'QL03p045360' => 'qlo', 'QL05p034369' => 'qlo', 'QL05p034412' => 'qlo', 'QL08p017802' => 'qlo', 'QL08p024762' => 'qlo', 'QL10p026237' => 'qlo', 'QL10p032070' => 'qlo', 'QL11p003821' => 'qlo', 'Rhsim04G0057300' => 'rsi', 'Rhsim05G0049200' => 'rsi', 'Rhsim12G0010400' => 'rsi', 'Rhsim12G0012800' => 'rsi', 'TAR624G0483' => 'tar', 'TAR703G0001' => 'tar', 'vmacro05414' => 'vma', 'vmacro07091' => 'vma', 'vmacro07116' => 'vma', 'vmacro08423' => 'vma', 'vmacro09046' => 'vma', 'vmacro14269' => 'vma', 'vmacro16092' => 'vma', 'vmacro17280' => 'vma', 'vmacro19601' => 'vma' ) $gf_id = 'HOM05D001028' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001028' ) $data_identifier = 'HOM05D001028' $data_type = 'gf_id' $species_gene_counts = array( 'aox' => (int) 11, 'ccan' => (int) 6, 'camsi' => (int) 540, 'din' => (int) 4, 'bvu' => (int) 1, 'fan' => (int) 1, 'pgr' => (int) 1, 'ppe' => (int) 3, 'qlo' => (int) 8, 'rsi' => (int) 4, 'tar' => (int) 2, 'vma' => (int) 9 ) $gf_gene_species = 'vma' $gf_gene_id = 'vmacro19601' $species_info = array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ) $local_species = 'aox' $disabled = '' $selected = '' $num_hits = (int) 0
include - APP/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp, line 33 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933 View::_renderElement() - CORE/Cake/View/View.php, line 1224 View::element() - CORE/Cake/View/View.php, line 418 include - APP/View/Elements/analysis/phylogenetics_module/gf_data_settings.ctp, line 37 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933 View::_renderElement() - CORE/Cake/View/View.php, line 1224 View::element() - CORE/Cake/View/View.php, line 418 include - APP/View/Elements/analysis/phylogenetics_module/parameter_selection.ctp, line 64 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933 View::_renderElement() - CORE/Cake/View/View.php, line 1224 View::element() - CORE/Cake/View/View.php, line 418 include - APP/View/Analysis/custom_tree_creation.ctp, line 27 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933
Warning (2): count(): Parameter must be an array or an object that implements Countable [APP/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp, line 33]Code Context $disabled = (!array_key_exists($local_species,$species_gene_counts))?"disabled":""; $selected = (isset($selected_species) && array_key_exists($local_species,$selected_species))?"checked='checked'":""; $num_hits = (array_key_exists($local_species,$species_gene_counts))?count($species_gene_counts[$local_species]):0; $viewFile = '/www/bioinformatics01_ro/plaza/_dev_instances/feedback/app/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp' $dataForView = array( 'sidebar_info' => array( 'gf_id' => 'HOM05D001028', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '590', 'num_species' => '12' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'Aqoxy1G01649' => 'aox', 'Aqoxy1G02950' => 'aox', 'Aqoxy2G01005' => 'aox', 'Aqoxy2G01064' => 'aox', 'Aqoxy3G02267' => 'aox', 'Aqoxy3G02617' => 'aox', 'Aqoxy3G02693' => 'aox', 'Aqoxy5G03425' => 'aox', 'Aqoxy6G02164' => 'aox', 'Aqoxy6G02364' => 'aox', 'Aqoxy7G02284' => 'aox', 'Cc00_g09720' => 'ccan', 'Cc00_g21410' => 'ccan', 'Cc00_g31750' => 'ccan', 'Cc00_g34740' => 'ccan', 'Cc04_g16890' => 'ccan', 'Cc11_g03120' => 'ccan', 'CSS0000222' => 'camsi', 'CSS0000265' => 'camsi', 'CSS0000306' => 'camsi', 'CSS0000326' => 'camsi', 'CSS0000530' => 'camsi', 'CSS0000563' => 'camsi', 'CSS0000584' => 'camsi', 'CSS0000684' => 'camsi', 'CSS0001100' => 'camsi', 'CSS0001311' => 'camsi', 'CSS0001343' => 'camsi', 'CSS0001399' => 'camsi', 'CSS0001475' => 'camsi', 'CSS0001506' => 'camsi', 'CSS0001602' => 'camsi', 'CSS0001681' => 'camsi', 'CSS0001874' => 'camsi', 'CSS0001948' => 'camsi', 'CSS0002022' => 'camsi', 'CSS0002230' => 'camsi', 'CSS0002265' => 'camsi', 'CSS0002277' => 'camsi', 'CSS0002462' => 'camsi', 'CSS0002823' => 'camsi', 'CSS0003091' => 'camsi', 'CSS0003162' => 'camsi', 'CSS0003264' => 'camsi', 'CSS0003355' => 'camsi', 'CSS0003378' => 'camsi', 'CSS0003472' => 'camsi', 'CSS0003500' => 'camsi', 'CSS0003640' => 'camsi', 'CSS0003767' => 'camsi', 'CSS0003894' => 'camsi', 'CSS0003952' => 'camsi', 'CSS0003977' => 'camsi', 'CSS0004028' => 'camsi', 'CSS0004117' => 'camsi', 'CSS0004137' => 'camsi', 'CSS0004176' => 'camsi', 'CSS0004265' => 'camsi', 'CSS0004450' => 'camsi', 'CSS0004468' => 'camsi', 'CSS0004488' => 'camsi', 'CSS0004490' => 'camsi', 'CSS0004632' => 'camsi', 'CSS0004790' => 'camsi', 'CSS0004877' => 'camsi', 'CSS0004920' => 'camsi', 'CSS0004969' => 'camsi', 'CSS0005084' => 'camsi', 'CSS0005101' => 'camsi', 'CSS0005271' => 'camsi', 'CSS0005313' => 'camsi', 'CSS0005331' => 'camsi', 'CSS0005368' => 'camsi', 'CSS0005391' => 'camsi', 'CSS0005437' => 'camsi', 'CSS0005515' => 'camsi', 'CSS0005526' => 'camsi', 'CSS0005532' => 'camsi', 'CSS0005595' => 'camsi', 'CSS0005677' => 'camsi', 'CSS0005838' => 'camsi', 'CSS0005988' => 'camsi', 'CSS0006100' => 'camsi', 'CSS0006128' => 'camsi', 'CSS0006293' => 'camsi', 'CSS0006378' => 'camsi', 'CSS0006400' => 'camsi', 'CSS0006441' => 'camsi', 'CSS0006455' => 'camsi', 'CSS0006480' => 'camsi', 'CSS0006483' => 'camsi', 'CSS0006538' => 'camsi', 'CSS0006582' => 'camsi', 'CSS0006632' => 'camsi', 'CSS0006771' => 'camsi', 'CSS0006803' => 'camsi', 'CSS0006852' => 'camsi', 'CSS0006861' => 'camsi', 'CSS0006910' => 'camsi', 'CSS0007037' => 'camsi', 'CSS0007066' => 'camsi', 'CSS0007072' => 'camsi', 'CSS0007109' => 'camsi', 'CSS0007193' => 'camsi', 'CSS0007319' => 'camsi', 'CSS0007336' => 'camsi', 'CSS0007377' => 'camsi', 'CSS0007659' => 'camsi', 'CSS0007701' => 'camsi', 'CSS0007711' => 'camsi', 'CSS0007809' => 'camsi', 'CSS0008045' => 'camsi', 'CSS0008050' => 'camsi', 'CSS0008206' => 'camsi', 'CSS0008251' => 'camsi', 'CSS0008252' => 'camsi', 'CSS0008279' => 'camsi', 'CSS0008482' => 'camsi', 'CSS0008583' => 'camsi', 'CSS0008699' => 'camsi', 'CSS0008798' => 'camsi', 'CSS0008971' => 'camsi', 'CSS0009019' => 'camsi', 'CSS0009191' => 'camsi', 'CSS0009241' => 'camsi', 'CSS0009246' => 'camsi', 'CSS0009399' => 'camsi', 'CSS0009654' => 'camsi', 'CSS0009722' => 'camsi', 'CSS0009920' => 'camsi', 'CSS0009986' => 'camsi', 'CSS0010182' => 'camsi', 'CSS0010202' => 'camsi', 'CSS0010330' => 'camsi', 'CSS0010362' => 'camsi', 'CSS0010456' => 'camsi', 'CSS0010472' => 'camsi', 'CSS0010507' => 'camsi', 'CSS0010512' => 'camsi', 'CSS0010520' => 'camsi', 'CSS0010617' => 'camsi', 'CSS0010706' => 'camsi', 'CSS0010747' => 'camsi', 'CSS0010816' => 'camsi', 'CSS0011020' => 'camsi', 'CSS0011115' => 'camsi', 'CSS0011383' => 'camsi', 'CSS0011491' => 'camsi', 'CSS0011602' => 'camsi', 'CSS0011605' => 'camsi', 'CSS0011625' => 'camsi', 'CSS0011654' => 'camsi', 'CSS0011781' => 'camsi', 'CSS0011853' => 'camsi', 'CSS0011898' => 'camsi', 'CSS0011933' => 'camsi', 'CSS0011996' => 'camsi', 'CSS0012066' => 'camsi', 'CSS0012097' => 'camsi', 'CSS0012108' => 'camsi', 'CSS0012226' => 'camsi', 'CSS0012248' => 'camsi', 'CSS0012331' => 'camsi', 'CSS0012797' => 'camsi', 'CSS0012818' => 'camsi', 'CSS0012904' => 'camsi', 'CSS0013001' => 'camsi', 'CSS0013022' => 'camsi', 'CSS0013172' => 'camsi', 'CSS0013244' => 'camsi', 'CSS0013267' => 'camsi', 'CSS0013275' => 'camsi', 'CSS0013324' => 'camsi', 'CSS0013334' => 'camsi', 'CSS0013394' => 'camsi', 'CSS0013549' => 'camsi', 'CSS0013689' => 'camsi', 'CSS0014026' => 'camsi', 'CSS0014049' => 'camsi', 'CSS0014144' => 'camsi', 'CSS0014354' => 'camsi', 'CSS0014579' => 'camsi', 'CSS0014648' => 'camsi', 'CSS0014902' => 'camsi', 'CSS0014979' => 'camsi', 'CSS0015278' => 'camsi', 'CSS0015310' => 'camsi', 'CSS0015364' => 'camsi', 'CSS0015455' => 'camsi', 'CSS0015693' => 'camsi', 'CSS0015774' => 'camsi', 'CSS0015795' => 'camsi', 'CSS0015952' => 'camsi', 'CSS0016104' => 'camsi', 'CSS0016241' => 'camsi', 'CSS0016303' => 'camsi', 'CSS0016490' => 'camsi', 'CSS0016832' => 'camsi', 'CSS0016845' => 'camsi', 'CSS0016914' => 'camsi', 'CSS0016946' => 'camsi', 'CSS0017102' => 'camsi', 'CSS0017193' => 'camsi', 'CSS0017528' => 'camsi', 'CSS0017619' => 'camsi', 'CSS0017679' => 'camsi', 'CSS0017816' => 'camsi', 'CSS0017880' => 'camsi', 'CSS0018106' => 'camsi', 'CSS0018162' => 'camsi', 'CSS0018304' => 'camsi', 'CSS0018406' => 'camsi', 'CSS0018481' => 'camsi', 'CSS0018511' => 'camsi', 'CSS0018596' => 'camsi', 'CSS0018727' => 'camsi', 'CSS0018751' => 'camsi', 'CSS0018777' => 'camsi', 'CSS0018798' => 'camsi', 'CSS0019137' => 'camsi', 'CSS0019177' => 'camsi', 'CSS0019217' => 'camsi', 'CSS0019361' => 'camsi', 'CSS0019516' => 'camsi', 'CSS0019538' => 'camsi', 'CSS0019560' => 'camsi', 'CSS0019819' => 'camsi', 'CSS0019837' => 'camsi', 'CSS0019915' => 'camsi', 'CSS0019925' => 'camsi', 'CSS0020112' => 'camsi', 'CSS0020160' => 'camsi', 'CSS0020378' => 'camsi', 'CSS0020388' => 'camsi', 'CSS0020452' => 'camsi', 'CSS0020588' => 'camsi', 'CSS0020661' => 'camsi', 'CSS0020886' => 'camsi', 'CSS0020973' => 'camsi', 'CSS0021035' => 'camsi', 'CSS0021111' => 'camsi', 'CSS0021131' => 'camsi', 'CSS0021151' => 'camsi', 'CSS0021228' => 'camsi', 'CSS0021397' => 'camsi', 'CSS0021420' => 'camsi', 'CSS0021464' => 'camsi', 'CSS0021547' => 'camsi', 'CSS0021608' => 'camsi', 'CSS0021740' => 'camsi', 'CSS0021826' => 'camsi', 'CSS0021904' => 'camsi', 'CSS0021941' => 'camsi', 'CSS0022189' => 'camsi', 'CSS0022199' => 'camsi', 'CSS0022502' => 'camsi', 'CSS0022531' => 'camsi', 'CSS0022581' => 'camsi', 'CSS0022612' => 'camsi', 'CSS0022621' => 'camsi', 'CSS0022815' => 'camsi', 'CSS0022936' => 'camsi', 'CSS0022964' => 'camsi', 'CSS0022985' => 'camsi', 'CSS0023002' => 'camsi', 'CSS0023006' => 'camsi', 'CSS0023024' => 'camsi', 'CSS0023489' => 'camsi', 'CSS0023593' => 'camsi', 'CSS0023621' => 'camsi', 'CSS0023743' => 'camsi', 'CSS0023804' => 'camsi', 'CSS0023805' => 'camsi', 'CSS0023908' => 'camsi', 'CSS0023938' => 'camsi', 'CSS0023981' => 'camsi', 'CSS0024027' => 'camsi', 'CSS0024169' => 'camsi', 'CSS0024193' => 'camsi', 'CSS0024269' => 'camsi', 'CSS0024336' => 'camsi', 'CSS0024337' => 'camsi', 'CSS0024548' => 'camsi', 'CSS0024564' => 'camsi', 'CSS0024585' => 'camsi', 'CSS0024738' => 'camsi', 'CSS0024833' => 'camsi', 'CSS0024846' => 'camsi', 'CSS0024957' => 'camsi', 'CSS0024974' => 'camsi', 'CSS0025005' => 'camsi', 'CSS0025235' => 'camsi', 'CSS0025465' => 'camsi', 'CSS0025633' => 'camsi', 'CSS0025688' => 'camsi', 'CSS0025759' => 'camsi', 'CSS0025774' => 'camsi', 'CSS0025801' => 'camsi', 'CSS0025942' => 'camsi', 'CSS0026083' => 'camsi', 'CSS0026194' => 'camsi', 'CSS0026230' => 'camsi', 'CSS0026398' => 'camsi', 'CSS0026419' => 'camsi', 'CSS0026679' => 'camsi', 'CSS0026719' => 'camsi', 'CSS0026795' => 'camsi', 'CSS0026835' => 'camsi', 'CSS0026930' => 'camsi', 'CSS0027053' => 'camsi', 'CSS0027130' => 'camsi', 'CSS0027192' => 'camsi', 'CSS0027454' => 'camsi', 'CSS0027467' => 'camsi', 'CSS0027521' => 'camsi', 'CSS0027662' => 'camsi', 'CSS0027795' => 'camsi', 'CSS0027835' => 'camsi', 'CSS0027966' => 'camsi', 'CSS0028090' => 'camsi', 'CSS0028134' => 'camsi', 'CSS0028205' => 'camsi', 'CSS0028263' => 'camsi', 'CSS0028363' => 'camsi', 'CSS0028598' => 'camsi', 'CSS0029175' => 'camsi', 'CSS0029191' => 'camsi', 'CSS0029424' => 'camsi', 'CSS0029479' => 'camsi', 'CSS0029496' => 'camsi', 'CSS0029633' => 'camsi', 'CSS0029837' => 'camsi', 'CSS0029844' => 'camsi', 'CSS0029863' => 'camsi', 'CSS0029874' => 'camsi', 'CSS0029959' => 'camsi', 'CSS0030001' => 'camsi', 'CSS0030093' => 'camsi', 'CSS0030199' => 'camsi', 'CSS0030200' => 'camsi', 'CSS0030427' => 'camsi', 'CSS0030476' => 'camsi', 'CSS0030636' => 'camsi', 'CSS0030673' => 'camsi', 'CSS0030766' => 'camsi', 'CSS0030775' => 'camsi', 'CSS0030858' => 'camsi', 'CSS0030873' => 'camsi', 'CSS0030929' => 'camsi', 'CSS0031028' => 'camsi', 'CSS0031129' => 'camsi', 'CSS0031164' => 'camsi', 'CSS0031340' => 'camsi', 'CSS0031368' => 'camsi', 'CSS0031395' => 'camsi', 'CSS0031596' => 'camsi', 'CSS0031727' => 'camsi', 'CSS0032011' => 'camsi', 'CSS0032160' => 'camsi', 'CSS0032538' => 'camsi', 'CSS0032576' => 'camsi', 'CSS0032603' => 'camsi', 'CSS0032640' => 'camsi', 'CSS0032704' => 'camsi', 'CSS0032851' => 'camsi', 'CSS0032973' => 'camsi', 'CSS0033048' => 'camsi', 'CSS0033082' => 'camsi', 'CSS0033157' => 'camsi', 'CSS0033253' => 'camsi', 'CSS0033347' => 'camsi', 'CSS0033601' => 'camsi', 'CSS0033820' => 'camsi', 'CSS0033881' => 'camsi', 'CSS0033934' => 'camsi', 'CSS0034143' => 'camsi', 'CSS0034176' => 'camsi', 'CSS0034201' => 'camsi', 'CSS0034269' => 'camsi', 'CSS0034303' => 'camsi', 'CSS0034463' => 'camsi', 'CSS0034470' => 'camsi', 'CSS0034514' => 'camsi', 'CSS0034525' => 'camsi', 'CSS0034726' => 'camsi', 'CSS0034727' => 'camsi', 'CSS0034737' => 'camsi', 'CSS0034768' => 'camsi', 'CSS0034890' => 'camsi', 'CSS0034943' => 'camsi', 'CSS0034957' => 'camsi', 'CSS0034973' => 'camsi', 'CSS0035178' => 'camsi', 'CSS0035260' => 'camsi', 'CSS0035316' => 'camsi', 'CSS0035347' => 'camsi', 'CSS0035360' => 'camsi', 'CSS0035380' => 'camsi', 'CSS0035429' => 'camsi', 'CSS0035446' => 'camsi', 'CSS0035737' => 'camsi', 'CSS0035852' => 'camsi', 'CSS0035967' => 'camsi', 'CSS0036001' => 'camsi', 'CSS0036044' => 'camsi', 'CSS0036221' => 'camsi', 'CSS0036333' => 'camsi', 'CSS0036435' => 'camsi', 'CSS0036843' => 'camsi', 'CSS0036846' => 'camsi', 'CSS0037097' => 'camsi', 'CSS0037263' => 'camsi', 'CSS0037370' => 'camsi', 'CSS0037410' => 'camsi', 'CSS0037449' => 'camsi', 'CSS0037603' => 'camsi', 'CSS0037851' => 'camsi', 'CSS0037891' => 'camsi', 'CSS0037996' => 'camsi', 'CSS0038222' => 'camsi', 'CSS0038433' => 'camsi', 'CSS0038441' => 'camsi', 'CSS0038718' => 'camsi', 'CSS0038890' => 'camsi', 'CSS0039049' => 'camsi', 'CSS0039145' => 'camsi', 'CSS0039243' => 'camsi', 'CSS0039294' => 'camsi', 'CSS0039324' => 'camsi', 'CSS0039376' => 'camsi', 'CSS0039475' => 'camsi', 'CSS0039539' => 'camsi', 'CSS0039546' => 'camsi', 'CSS0039567' => 'camsi', 'CSS0039599' => 'camsi', 'CSS0039763' => 'camsi', 'CSS0039863' => 'camsi', 'CSS0040107' => 'camsi', 'CSS0040124' => 'camsi', 'CSS0040151' => 'camsi', 'CSS0040165' => 'camsi', 'CSS0040309' => 'camsi', 'CSS0040318' => 'camsi', 'CSS0040347' => 'camsi', 'CSS0040371' => 'camsi', 'CSS0040456' => 'camsi', 'CSS0040551' => 'camsi', 'CSS0040975' => 'camsi', 'CSS0040981' => 'camsi', 'CSS0041299' => 'camsi', 'CSS0041493' => 'camsi', 'CSS0041658' => 'camsi', 'CSS0041899' => 'camsi', 'CSS0041927' => 'camsi', 'CSS0042016' => 'camsi', 'CSS0042034' => 'camsi', 'CSS0042103' => 'camsi', 'CSS0042172' => 'camsi', 'CSS0042198' => 'camsi', 'CSS0042201' => 'camsi', 'CSS0042308' => 'camsi', 'CSS0042329' => 'camsi', 'CSS0042348' => 'camsi', 'CSS0042349' => 'camsi', 'CSS0042489' => 'camsi', 'CSS0042575' => 'camsi', 'CSS0042624' => 'camsi', 'CSS0042660' => 'camsi', 'CSS0042694' => 'camsi', 'CSS0042995' => 'camsi', 'CSS0043079' => 'camsi', 'CSS0043165' => 'camsi', 'CSS0043171' => 'camsi', 'CSS0043314' => 'camsi', 'CSS0043361' => 'camsi', 'CSS0043375' => 'camsi', 'CSS0043518' => 'camsi', 'CSS0043536' => 'camsi', 'CSS0043678' => 'camsi', 'CSS0043765' => 'camsi', 'CSS0043897' => 'camsi', 'CSS0043944' => 'camsi', 'CSS0044126' => 'camsi', 'CSS0044136' => 'camsi', 'CSS0044179' => 'camsi', 'CSS0044290' => 'camsi', 'CSS0044437' => 'camsi', 'CSS0044502' => 'camsi', 'CSS0044603' => 'camsi', 'CSS0044680' => 'camsi', 'CSS0044685' => 'camsi', 'CSS0044700' => 'camsi', 'CSS0044888' => 'camsi', 'CSS0044923' => 'camsi', 'CSS0044926' => 'camsi', 'CSS0044979' => 'camsi', 'CSS0045049' => 'camsi', 'CSS0045132' => 'camsi', 'CSS0045161' => 'camsi', 'CSS0045219' => 'camsi', 'CSS0045230' => 'camsi', 'CSS0045259' => 'camsi', 'CSS0045324' => 'camsi', 'CSS0045368' => 'camsi', 'CSS0045435' => 'camsi', 'CSS0045856' => 'camsi', 'CSS0045955' => 'camsi', 'CSS0046158' => 'camsi', 'CSS0046334' => 'camsi', 'CSS0046365' => 'camsi', 'CSS0046396' => 'camsi', 'CSS0046400' => 'camsi', 'CSS0046445' => 'camsi', 'CSS0046493' => 'camsi', 'CSS0046640' => 'camsi', 'CSS0046657' => 'camsi', 'CSS0046702' => 'camsi', 'CSS0047208' => 'camsi', 'CSS0047368' => 'camsi', 'CSS0047403' => 'camsi', 'CSS0047417' => 'camsi', 'CSS0047469' => 'camsi', 'CSS0047480' => 'camsi', 'CSS0047482' => 'camsi', 'CSS0047693' => 'camsi', 'CSS0047766' => 'camsi', 'CSS0047866' => 'camsi', 'CSS0047884' => 'camsi', 'CSS0048235' => 'camsi', 'CSS0048383' => 'camsi', 'CSS0048438' => 'camsi', 'CSS0048502' => 'camsi', 'CSS0048546' => 'camsi', 'CSS0048653' => 'camsi', 'CSS0048658' => 'camsi', 'CSS0048729' => 'camsi', 'CSS0048867' => 'camsi', 'CSS0048988' => 'camsi', 'CSS0049053' => 'camsi', 'CSS0049099' => 'camsi', 'CSS0049166' => 'camsi', 'CSS0049174' => 'camsi', 'CSS0049212' => 'camsi', 'CSS0049280' => 'camsi', 'CSS0049391' => 'camsi', 'CSS0049546' => 'camsi', 'CSS0049634' => 'camsi', 'CSS0049655' => 'camsi', 'CSS0049813' => 'camsi', 'CSS0049949' => 'camsi', 'CSS0050009' => 'camsi', 'CSS0050118' => 'camsi', 'CSS0050205' => 'camsi', 'CSS0050275' => 'camsi', 'CSS0050480' => 'camsi', 'CSS0050488' => 'camsi', 'CSS0050497' => 'camsi', 'Dinv03126' => 'din', 'Dinv13140' => 'din', 'Dinv13247' => 'din', 'Dinv14217' => 'din', 'EL10Ac9g22435' => 'bvu', 'FAN20G1200' => 'fan', 'PGR142G2516' => 'pgr', 'Prupe.3G160200' => 'ppe', 'Prupe.5G238200' => 'ppe', 'Prupe.7G047500' => 'ppe', 'QL03p045360' => 'qlo', 'QL05p034369' => 'qlo', 'QL05p034412' => 'qlo', 'QL08p017802' => 'qlo', 'QL08p024762' => 'qlo', 'QL10p026237' => 'qlo', 'QL10p032070' => 'qlo', 'QL11p003821' => 'qlo', 'Rhsim04G0057300' => 'rsi', 'Rhsim05G0049200' => 'rsi', 'Rhsim12G0010400' => 'rsi', 'Rhsim12G0012800' => 'rsi', 'TAR624G0483' => 'tar', 'TAR703G0001' => 'tar', 'vmacro05414' => 'vma', 'vmacro07091' => 'vma', 'vmacro07116' => 'vma', 'vmacro08423' => 'vma', 'vmacro09046' => 'vma', 'vmacro14269' => 'vma', 'vmacro16092' => 'vma', 'vmacro17280' => 'vma', 'vmacro19601' => 'vma' ), 'gf_id' => 'HOM05D001028', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001028' ), 'data_identifier' => 'HOM05D001028', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001028', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '590', 'num_species' => '12' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'Aqoxy1G01649' => 'aox', 'Aqoxy1G02950' => 'aox', 'Aqoxy2G01005' => 'aox', 'Aqoxy2G01064' => 'aox', 'Aqoxy3G02267' => 'aox', 'Aqoxy3G02617' => 'aox', 'Aqoxy3G02693' => 'aox', 'Aqoxy5G03425' => 'aox', 'Aqoxy6G02164' => 'aox', 'Aqoxy6G02364' => 'aox', 'Aqoxy7G02284' => 'aox', 'Cc00_g09720' => 'ccan', 'Cc00_g21410' => 'ccan', 'Cc00_g31750' => 'ccan', 'Cc00_g34740' => 'ccan', 'Cc04_g16890' => 'ccan', 'Cc11_g03120' => 'ccan', 'CSS0000222' => 'camsi', 'CSS0000265' => 'camsi', 'CSS0000306' => 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'camsi', 'CSS0038433' => 'camsi', 'CSS0038441' => 'camsi', 'CSS0038718' => 'camsi', 'CSS0038890' => 'camsi', 'CSS0039049' => 'camsi', 'CSS0039145' => 'camsi', 'CSS0039243' => 'camsi', 'CSS0039294' => 'camsi', 'CSS0039324' => 'camsi', 'CSS0039376' => 'camsi', 'CSS0039475' => 'camsi', 'CSS0039539' => 'camsi', 'CSS0039546' => 'camsi', 'CSS0039567' => 'camsi', 'CSS0039599' => 'camsi', 'CSS0039763' => 'camsi', 'CSS0039863' => 'camsi', 'CSS0040107' => 'camsi', 'CSS0040124' => 'camsi', 'CSS0040151' => 'camsi', 'CSS0040165' => 'camsi', 'CSS0040309' => 'camsi', 'CSS0040318' => 'camsi', 'CSS0040347' => 'camsi', 'CSS0040371' => 'camsi', 'CSS0040456' => 'camsi', 'CSS0040551' => 'camsi', 'CSS0040975' => 'camsi', 'CSS0040981' => 'camsi', 'CSS0041299' => 'camsi', 'CSS0041493' => 'camsi', 'CSS0041658' => 'camsi', 'CSS0041899' => 'camsi', 'CSS0041927' => 'camsi', 'CSS0042016' => 'camsi', 'CSS0042034' => 'camsi', 'CSS0042103' => 'camsi', 'CSS0042172' => 'camsi', 'CSS0042198' => 'camsi', 'CSS0042201' => 'camsi', 'CSS0042308' => 'camsi', 'CSS0042329' => 'camsi', 'CSS0042348' => 'camsi', 'CSS0042349' => 'camsi', 'CSS0042489' => 'camsi', 'CSS0042575' => 'camsi', 'CSS0042624' => 'camsi', 'CSS0042660' => 'camsi', 'CSS0042694' => 'camsi', 'CSS0042995' => 'camsi', 'CSS0043079' => 'camsi', 'CSS0043165' => 'camsi', 'CSS0043171' => 'camsi', 'CSS0043314' => 'camsi', 'CSS0043361' => 'camsi', 'CSS0043375' => 'camsi', 'CSS0043518' => 'camsi', 'CSS0043536' => 'camsi', 'CSS0043678' => 'camsi', 'CSS0043765' => 'camsi', 'CSS0043897' => 'camsi', 'CSS0043944' => 'camsi', 'CSS0044126' => 'camsi', 'CSS0044136' => 'camsi', 'CSS0044179' => 'camsi', 'CSS0044290' => 'camsi', 'CSS0044437' => 'camsi', 'CSS0044502' => 'camsi', 'CSS0044603' => 'camsi', 'CSS0044680' => 'camsi', 'CSS0044685' => 'camsi', 'CSS0044700' => 'camsi', 'CSS0044888' => 'camsi', 'CSS0044923' => 'camsi', 'CSS0044926' => 'camsi', 'CSS0044979' => 'camsi', 'CSS0045049' => 'camsi', 'CSS0045132' => 'camsi', 'CSS0045161' => 'camsi', 'CSS0045219' => 'camsi', 'CSS0045230' => 'camsi', 'CSS0045259' => 'camsi', 'CSS0045324' => 'camsi', 'CSS0045368' => 'camsi', 'CSS0045435' => 'camsi', 'CSS0045856' => 'camsi', 'CSS0045955' => 'camsi', 'CSS0046158' => 'camsi', 'CSS0046334' => 'camsi', 'CSS0046365' => 'camsi', 'CSS0046396' => 'camsi', 'CSS0046400' => 'camsi', 'CSS0046445' => 'camsi', 'CSS0046493' => 'camsi', 'CSS0046640' => 'camsi', 'CSS0046657' => 'camsi', 'CSS0046702' => 'camsi', 'CSS0047208' => 'camsi', 'CSS0047368' => 'camsi', 'CSS0047403' => 'camsi', 'CSS0047417' => 'camsi', 'CSS0047469' => 'camsi', 'CSS0047480' => 'camsi', 'CSS0047482' => 'camsi', 'CSS0047693' => 'camsi', 'CSS0047766' => 'camsi', 'CSS0047866' => 'camsi', 'CSS0047884' => 'camsi', 'CSS0048235' => 'camsi', 'CSS0048383' => 'camsi', 'CSS0048438' => 'camsi', 'CSS0048502' => 'camsi', 'CSS0048546' => 'camsi', 'CSS0048653' => 'camsi', 'CSS0048658' => 'camsi', 'CSS0048729' => 'camsi', 'CSS0048867' => 'camsi', 'CSS0048988' => 'camsi', 'CSS0049053' => 'camsi', 'CSS0049099' => 'camsi', 'CSS0049166' => 'camsi', 'CSS0049174' => 'camsi', 'CSS0049212' => 'camsi', 'CSS0049280' => 'camsi', 'CSS0049391' => 'camsi', 'CSS0049546' => 'camsi', 'CSS0049634' => 'camsi', 'CSS0049655' => 'camsi', 'CSS0049813' => 'camsi', 'CSS0049949' => 'camsi', 'CSS0050009' => 'camsi', 'CSS0050118' => 'camsi', 'CSS0050205' => 'camsi', 'CSS0050275' => 'camsi', 'CSS0050480' => 'camsi', 'CSS0050488' => 'camsi', 'CSS0050497' => 'camsi', 'Dinv03126' => 'din', 'Dinv13140' => 'din', 'Dinv13247' => 'din', 'Dinv14217' => 'din', 'EL10Ac9g22435' => 'bvu', 'FAN20G1200' => 'fan', 'PGR142G2516' => 'pgr', 'Prupe.3G160200' => 'ppe', 'Prupe.5G238200' => 'ppe', 'Prupe.7G047500' => 'ppe', 'QL03p045360' => 'qlo', 'QL05p034369' => 'qlo', 'QL05p034412' => 'qlo', 'QL08p017802' => 'qlo', 'QL08p024762' => 'qlo', 'QL10p026237' => 'qlo', 'QL10p032070' => 'qlo', 'QL11p003821' => 'qlo', 'Rhsim04G0057300' => 'rsi', 'Rhsim05G0049200' => 'rsi', 'Rhsim12G0010400' => 'rsi', 'Rhsim12G0012800' => 'rsi', 'TAR624G0483' => 'tar', 'TAR703G0001' => 'tar', 'vmacro05414' => 'vma', 'vmacro07091' => 'vma', 'vmacro07116' => 'vma', 'vmacro08423' => 'vma', 'vmacro09046' => 'vma', 'vmacro14269' => 'vma', 'vmacro16092' => 'vma', 'vmacro17280' => 'vma', 'vmacro19601' => 'vma' ) $gf_id = 'HOM05D001028' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001028' ) $data_identifier = 'HOM05D001028' $data_type = 'gf_id' $species_gene_counts = array( 'aox' => (int) 11, 'ccan' => (int) 6, 'camsi' => (int) 540, 'din' => (int) 4, 'bvu' => (int) 1, 'fan' => (int) 1, 'pgr' => (int) 1, 'ppe' => (int) 3, 'qlo' => (int) 8, 'rsi' => (int) 4, 'tar' => (int) 2, 'vma' => (int) 9 ) $gf_gene_species = 'vma' $gf_gene_id = 'vmacro19601' $species_info = array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ) $local_species = 'bvu' $disabled = '' $selected = '' $num_hits = (int) 0include - APP/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp, line 33 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933 View::_renderElement() - CORE/Cake/View/View.php, line 1224 View::element() - CORE/Cake/View/View.php, line 418 include - APP/View/Elements/analysis/phylogenetics_module/gf_data_settings.ctp, line 37 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933 View::_renderElement() - CORE/Cake/View/View.php, line 1224 View::element() - CORE/Cake/View/View.php, line 418 include - APP/View/Elements/analysis/phylogenetics_module/parameter_selection.ctp, line 64 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933 View::_renderElement() - CORE/Cake/View/View.php, line 1224 View::element() - CORE/Cake/View/View.php, line 418 include - APP/View/Analysis/custom_tree_creation.ctp, line 27 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933
$viewFile = '/www/bioinformatics01_ro/plaza/_dev_instances/feedback/app/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp' $dataForView = array( 'sidebar_info' => array( 'gf_id' => 'HOM05D001028', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '590', 'num_species' => '12' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'Aqoxy1G01649' => 'aox', 'Aqoxy1G02950' => 'aox', 'Aqoxy2G01005' => 'aox', 'Aqoxy2G01064' => 'aox', 'Aqoxy3G02267' => 'aox', 'Aqoxy3G02617' => 'aox', 'Aqoxy3G02693' => 'aox', 'Aqoxy5G03425' => 'aox', 'Aqoxy6G02164' => 'aox', 'Aqoxy6G02364' => 'aox', 'Aqoxy7G02284' => 'aox', 'Cc00_g09720' => 'ccan', 'Cc00_g21410' => 'ccan', 'Cc00_g31750' => 'ccan', 'Cc00_g34740' => 'ccan', 'Cc04_g16890' => 'ccan', 'Cc11_g03120' => 'ccan', 'CSS0000222' => 'camsi', 'CSS0000265' => 'camsi', 'CSS0000306' => 'camsi', 'CSS0000326' => 'camsi', 'CSS0000530' => 'camsi', 'CSS0000563' => 'camsi', 'CSS0000584' => 'camsi', 'CSS0000684' => 'camsi', 'CSS0001100' => 'camsi', 'CSS0001311' => 'camsi', 'CSS0001343' => 'camsi', 'CSS0001399' => 'camsi', 'CSS0001475' => 'camsi', 'CSS0001506' => 'camsi', 'CSS0001602' => 'camsi', 'CSS0001681' => 'camsi', 'CSS0001874' => 'camsi', 'CSS0001948' => 'camsi', 'CSS0002022' => 'camsi', 'CSS0002230' => 'camsi', 'CSS0002265' => 'camsi', 'CSS0002277' => 'camsi', 'CSS0002462' => 'camsi', 'CSS0002823' => 'camsi', 'CSS0003091' => 'camsi', 'CSS0003162' => 'camsi', 'CSS0003264' => 'camsi', 'CSS0003355' => 'camsi', 'CSS0003378' => 'camsi', 'CSS0003472' => 'camsi', 'CSS0003500' => 'camsi', 'CSS0003640' => 'camsi', 'CSS0003767' => 'camsi', 'CSS0003894' => 'camsi', 'CSS0003952' => 'camsi', 'CSS0003977' => 'camsi', 'CSS0004028' => 'camsi', 'CSS0004117' => 'camsi', 'CSS0004137' => 'camsi', 'CSS0004176' => 'camsi', 'CSS0004265' => 'camsi', 'CSS0004450' => 'camsi', 'CSS0004468' => 'camsi', 'CSS0004488' => 'camsi', 'CSS0004490' => 'camsi', 'CSS0004632' => 'camsi', 'CSS0004790' => 'camsi', 'CSS0004877' => 'camsi', 'CSS0004920' => 'camsi', 'CSS0004969' => 'camsi', 'CSS0005084' => 'camsi', 'CSS0005101' => 'camsi', 'CSS0005271' => 'camsi', 'CSS0005313' => 'camsi', 'CSS0005331' => 'camsi', 'CSS0005368' => 'camsi', 'CSS0005391' => 'camsi', 'CSS0005437' => 'camsi', 'CSS0005515' => 'camsi', 'CSS0005526' => 'camsi', 'CSS0005532' => 'camsi', 'CSS0005595' => 'camsi', 'CSS0005677' => 'camsi', 'CSS0005838' => 'camsi', 'CSS0005988' => 'camsi', 'CSS0006100' => 'camsi', 'CSS0006128' => 'camsi', 'CSS0006293' => 'camsi', 'CSS0006378' => 'camsi', 'CSS0006400' => 'camsi', 'CSS0006441' => 'camsi', 'CSS0006455' => 'camsi', 'CSS0006480' => 'camsi', 'CSS0006483' => 'camsi', 'CSS0006538' => 'camsi', 'CSS0006582' => 'camsi', 'CSS0006632' => 'camsi', 'CSS0006771' => 'camsi', 'CSS0006803' => 'camsi', 'CSS0006852' => 'camsi', 'CSS0006861' => 'camsi', 'CSS0006910' => 'camsi', 'CSS0007037' => 'camsi', 'CSS0007066' => 'camsi', 'CSS0007072' => 'camsi', 'CSS0007109' => 'camsi', 'CSS0007193' => 'camsi', 'CSS0007319' => 'camsi', 'CSS0007336' => 'camsi', 'CSS0007377' => 'camsi', 'CSS0007659' => 'camsi', 'CSS0007701' => 'camsi', 'CSS0007711' => 'camsi', 'CSS0007809' => 'camsi', 'CSS0008045' => 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'camsi', 'CSS0020378' => 'camsi', 'CSS0020388' => 'camsi', 'CSS0020452' => 'camsi', 'CSS0020588' => 'camsi', 'CSS0020661' => 'camsi', 'CSS0020886' => 'camsi', 'CSS0020973' => 'camsi', 'CSS0021035' => 'camsi', 'CSS0021111' => 'camsi', 'CSS0021131' => 'camsi', 'CSS0021151' => 'camsi', 'CSS0021228' => 'camsi', 'CSS0021397' => 'camsi', 'CSS0021420' => 'camsi', 'CSS0021464' => 'camsi', 'CSS0021547' => 'camsi', 'CSS0021608' => 'camsi', 'CSS0021740' => 'camsi', 'CSS0021826' => 'camsi', 'CSS0021904' => 'camsi', 'CSS0021941' => 'camsi', 'CSS0022189' => 'camsi', 'CSS0022199' => 'camsi', 'CSS0022502' => 'camsi', 'CSS0022531' => 'camsi', 'CSS0022581' => 'camsi', 'CSS0022612' => 'camsi', 'CSS0022621' => 'camsi', 'CSS0022815' => 'camsi', 'CSS0022936' => 'camsi', 'CSS0022964' => 'camsi', 'CSS0022985' => 'camsi', 'CSS0023002' => 'camsi', 'CSS0023006' => 'camsi', 'CSS0023024' => 'camsi', 'CSS0023489' => 'camsi', 'CSS0023593' => 'camsi', 'CSS0023621' => 'camsi', 'CSS0023743' => 'camsi', 'CSS0023804' => 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'camsi', 'CSS0046445' => 'camsi', 'CSS0046493' => 'camsi', 'CSS0046640' => 'camsi', 'CSS0046657' => 'camsi', 'CSS0046702' => 'camsi', 'CSS0047208' => 'camsi', 'CSS0047368' => 'camsi', 'CSS0047403' => 'camsi', 'CSS0047417' => 'camsi', 'CSS0047469' => 'camsi', 'CSS0047480' => 'camsi', 'CSS0047482' => 'camsi', 'CSS0047693' => 'camsi', 'CSS0047766' => 'camsi', 'CSS0047866' => 'camsi', 'CSS0047884' => 'camsi', 'CSS0048235' => 'camsi', 'CSS0048383' => 'camsi', 'CSS0048438' => 'camsi', 'CSS0048502' => 'camsi', 'CSS0048546' => 'camsi', 'CSS0048653' => 'camsi', 'CSS0048658' => 'camsi', 'CSS0048729' => 'camsi', 'CSS0048867' => 'camsi', 'CSS0048988' => 'camsi', 'CSS0049053' => 'camsi', 'CSS0049099' => 'camsi', 'CSS0049166' => 'camsi', 'CSS0049174' => 'camsi', 'CSS0049212' => 'camsi', 'CSS0049280' => 'camsi', 'CSS0049391' => 'camsi', 'CSS0049546' => 'camsi', 'CSS0049634' => 'camsi', 'CSS0049655' => 'camsi', 'CSS0049813' => 'camsi', 'CSS0049949' => 'camsi', 'CSS0050009' => 'camsi', 'CSS0050118' => 'camsi', 'CSS0050205' => 'camsi', 'CSS0050275' => 'camsi', 'CSS0050480' => 'camsi', 'CSS0050488' => 'camsi', 'CSS0050497' => 'camsi', 'Dinv03126' => 'din', 'Dinv13140' => 'din', 'Dinv13247' => 'din', 'Dinv14217' => 'din', 'EL10Ac9g22435' => 'bvu', 'FAN20G1200' => 'fan', 'PGR142G2516' => 'pgr', 'Prupe.3G160200' => 'ppe', 'Prupe.5G238200' => 'ppe', 'Prupe.7G047500' => 'ppe', 'QL03p045360' => 'qlo', 'QL05p034369' => 'qlo', 'QL05p034412' => 'qlo', 'QL08p017802' => 'qlo', 'QL08p024762' => 'qlo', 'QL10p026237' => 'qlo', 'QL10p032070' => 'qlo', 'QL11p003821' => 'qlo', 'Rhsim04G0057300' => 'rsi', 'Rhsim05G0049200' => 'rsi', 'Rhsim12G0010400' => 'rsi', 'Rhsim12G0012800' => 'rsi', 'TAR624G0483' => 'tar', 'TAR703G0001' => 'tar', 'vmacro05414' => 'vma', 'vmacro07091' => 'vma', 'vmacro07116' => 'vma', 'vmacro08423' => 'vma', 'vmacro09046' => 'vma', 'vmacro14269' => 'vma', 'vmacro16092' => 'vma', 'vmacro17280' => 'vma', 'vmacro19601' => 'vma' ), 'gf_id' => 'HOM05D001028', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001028' ), 'data_identifier' => 'HOM05D001028', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001028', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '590', 'num_species' => '12' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'Aqoxy1G01649' => 'aox', 'Aqoxy1G02950' => 'aox', 'Aqoxy2G01005' => 'aox', 'Aqoxy2G01064' => 'aox', 'Aqoxy3G02267' => 'aox', 'Aqoxy3G02617' => 'aox', 'Aqoxy3G02693' => 'aox', 'Aqoxy5G03425' => 'aox', 'Aqoxy6G02164' => 'aox', 'Aqoxy6G02364' => 'aox', 'Aqoxy7G02284' => 'aox', 'Cc00_g09720' => 'ccan', 'Cc00_g21410' => 'ccan', 'Cc00_g31750' => 'ccan', 'Cc00_g34740' => 'ccan', 'Cc04_g16890' => 'ccan', 'Cc11_g03120' => 'ccan', 'CSS0000222' => 'camsi', 'CSS0000265' => 'camsi', 'CSS0000306' => 'camsi', 'CSS0000326' => 'camsi', 'CSS0000530' => 'camsi', 'CSS0000563' => 'camsi', 'CSS0000584' => 'camsi', 'CSS0000684' => 'camsi', 'CSS0001100' => 'camsi', 'CSS0001311' => 'camsi', 'CSS0001343' => 'camsi', 'CSS0001399' => 'camsi', 'CSS0001475' => 'camsi', 'CSS0001506' => 'camsi', 'CSS0001602' => 'camsi', 'CSS0001681' => 'camsi', 'CSS0001874' => 'camsi', 'CSS0001948' => 'camsi', 'CSS0002022' => 'camsi', 'CSS0002230' => 'camsi', 'CSS0002265' => 'camsi', 'CSS0002277' => 'camsi', 'CSS0002462' => 'camsi', 'CSS0002823' => 'camsi', 'CSS0003091' => 'camsi', 'CSS0003162' => 'camsi', 'CSS0003264' => 'camsi', 'CSS0003355' => 'camsi', 'CSS0003378' => 'camsi', 'CSS0003472' => 'camsi', 'CSS0003500' => 'camsi', 'CSS0003640' => 'camsi', 'CSS0003767' => 'camsi', 'CSS0003894' => 'camsi', 'CSS0003952' => 'camsi', 'CSS0003977' => 'camsi', 'CSS0004028' => 'camsi', 'CSS0004117' => 'camsi', 'CSS0004137' => 'camsi', 'CSS0004176' => 'camsi', 'CSS0004265' => 'camsi', 'CSS0004450' => 'camsi', 'CSS0004468' => 'camsi', 'CSS0004488' => 'camsi', 'CSS0004490' => 'camsi', 'CSS0004632' => 'camsi', 'CSS0004790' => 'camsi', 'CSS0004877' => 'camsi', 'CSS0004920' => 'camsi', 'CSS0004969' => 'camsi', 'CSS0005084' => 'camsi', 'CSS0005101' => 'camsi', 'CSS0005271' => 'camsi', 'CSS0005313' => 'camsi', 'CSS0005331' => 'camsi', 'CSS0005368' => 'camsi', 'CSS0005391' => 'camsi', 'CSS0005437' => 'camsi', 'CSS0005515' => 'camsi', 'CSS0005526' => 'camsi', 'CSS0005532' => 'camsi', 'CSS0005595' => 'camsi', 'CSS0005677' => 'camsi', 'CSS0005838' => 'camsi', 'CSS0005988' => 'camsi', 'CSS0006100' => 'camsi', 'CSS0006128' => 'camsi', 'CSS0006293' => 'camsi', 'CSS0006378' => 'camsi', 'CSS0006400' => 'camsi', 'CSS0006441' => 'camsi', 'CSS0006455' => 'camsi', 'CSS0006480' => 'camsi', 'CSS0006483' => 'camsi', 'CSS0006538' => 'camsi', 'CSS0006582' => 'camsi', 'CSS0006632' => 'camsi', 'CSS0006771' => 'camsi', 'CSS0006803' => 'camsi', 'CSS0006852' => 'camsi', 'CSS0006861' => 'camsi', 'CSS0006910' => 'camsi', 'CSS0007037' => 'camsi', 'CSS0007066' => 'camsi', 'CSS0007072' => 'camsi', 'CSS0007109' => 'camsi', 'CSS0007193' => 'camsi', 'CSS0007319' => 'camsi', 'CSS0007336' => 'camsi', 'CSS0007377' => 'camsi', 'CSS0007659' => 'camsi', 'CSS0007701' => 'camsi', 'CSS0007711' => 'camsi', 'CSS0007809' => 'camsi', 'CSS0008045' => 'camsi', 'CSS0008050' => 'camsi', 'CSS0008206' => 'camsi', 'CSS0008251' => 'camsi', 'CSS0008252' => 'camsi', 'CSS0008279' => 'camsi', 'CSS0008482' => 'camsi', 'CSS0008583' => 'camsi', 'CSS0008699' => 'camsi', 'CSS0008798' => 'camsi', 'CSS0008971' => 'camsi', 'CSS0009019' => 'camsi', 'CSS0009191' => 'camsi', 'CSS0009241' => 'camsi', 'CSS0009246' => 'camsi', 'CSS0009399' => 'camsi', 'CSS0009654' => 'camsi', 'CSS0009722' => 'camsi', 'CSS0009920' => 'camsi', 'CSS0009986' => 'camsi', 'CSS0010182' => 'camsi', 'CSS0010202' => 'camsi', 'CSS0010330' => 'camsi', 'CSS0010362' => 'camsi', 'CSS0010456' => 'camsi', 'CSS0010472' => 'camsi', 'CSS0010507' => 'camsi', 'CSS0010512' => 'camsi', 'CSS0010520' => 'camsi', 'CSS0010617' => 'camsi', 'CSS0010706' => 'camsi', 'CSS0010747' => 'camsi', 'CSS0010816' => 'camsi', 'CSS0011020' => 'camsi', 'CSS0011115' => 'camsi', 'CSS0011383' => 'camsi', 'CSS0011491' => 'camsi', 'CSS0011602' => 'camsi', 'CSS0011605' => 'camsi', 'CSS0011625' => 'camsi', 'CSS0011654' => 'camsi', 'CSS0011781' => 'camsi', 'CSS0011853' => 'camsi', 'CSS0011898' => 'camsi', 'CSS0011933' => 'camsi', 'CSS0011996' => 'camsi', 'CSS0012066' => 'camsi', 'CSS0012097' => 'camsi', 'CSS0012108' => 'camsi', 'CSS0012226' => 'camsi', 'CSS0012248' => 'camsi', 'CSS0012331' => 'camsi', 'CSS0012797' => 'camsi', 'CSS0012818' => 'camsi', 'CSS0012904' => 'camsi', 'CSS0013001' => 'camsi', 'CSS0013022' => 'camsi', 'CSS0013172' => 'camsi', 'CSS0013244' => 'camsi', 'CSS0013267' => 'camsi', 'CSS0013275' => 'camsi', 'CSS0013324' => 'camsi', 'CSS0013334' => 'camsi', 'CSS0013394' => 'camsi', 'CSS0013549' => 'camsi', 'CSS0013689' => 'camsi', 'CSS0014026' => 'camsi', 'CSS0014049' => 'camsi', 'CSS0014144' => 'camsi', 'CSS0014354' => 'camsi', 'CSS0014579' => 'camsi', 'CSS0014648' => 'camsi', 'CSS0014902' => 'camsi', 'CSS0014979' => 'camsi', 'CSS0015278' => 'camsi', 'CSS0015310' => 'camsi', 'CSS0015364' => 'camsi', 'CSS0015455' => 'camsi', 'CSS0015693' => 'camsi', 'CSS0015774' => 'camsi', 'CSS0015795' => 'camsi', 'CSS0015952' => 'camsi', 'CSS0016104' => 'camsi', 'CSS0016241' => 'camsi', 'CSS0016303' => 'camsi', 'CSS0016490' => 'camsi', 'CSS0016832' => 'camsi', 'CSS0016845' => 'camsi', 'CSS0016914' => 'camsi', 'CSS0016946' => 'camsi', 'CSS0017102' => 'camsi', 'CSS0017193' => 'camsi', 'CSS0017528' => 'camsi', 'CSS0017619' => 'camsi', 'CSS0017679' => 'camsi', 'CSS0017816' => 'camsi', 'CSS0017880' => 'camsi', 'CSS0018106' => 'camsi', 'CSS0018162' => 'camsi', 'CSS0018304' => 'camsi', 'CSS0018406' => 'camsi', 'CSS0018481' => 'camsi', 'CSS0018511' => 'camsi', 'CSS0018596' => 'camsi', 'CSS0018727' => 'camsi', 'CSS0018751' => 'camsi', 'CSS0018777' => 'camsi', 'CSS0018798' => 'camsi', 'CSS0019137' => 'camsi', 'CSS0019177' => 'camsi', 'CSS0019217' => 'camsi', 'CSS0019361' => 'camsi', 'CSS0019516' => 'camsi', 'CSS0019538' => 'camsi', 'CSS0019560' => 'camsi', 'CSS0019819' => 'camsi', 'CSS0019837' => 'camsi', 'CSS0019915' => 'camsi', 'CSS0019925' => 'camsi', 'CSS0020112' => 'camsi', 'CSS0020160' => 'camsi', 'CSS0020378' => 'camsi', 'CSS0020388' => 'camsi', 'CSS0020452' => 'camsi', 'CSS0020588' => 'camsi', 'CSS0020661' => 'camsi', 'CSS0020886' => 'camsi', 'CSS0020973' => 'camsi', 'CSS0021035' => 'camsi', 'CSS0021111' => 'camsi', 'CSS0021131' => 'camsi', 'CSS0021151' => 'camsi', 'CSS0021228' => 'camsi', 'CSS0021397' => 'camsi', 'CSS0021420' => 'camsi', 'CSS0021464' => 'camsi', 'CSS0021547' => 'camsi', 'CSS0021608' => 'camsi', 'CSS0021740' => 'camsi', 'CSS0021826' => 'camsi', 'CSS0021904' => 'camsi', 'CSS0021941' => 'camsi', 'CSS0022189' => 'camsi', 'CSS0022199' => 'camsi', 'CSS0022502' => 'camsi', 'CSS0022531' => 'camsi', 'CSS0022581' => 'camsi', 'CSS0022612' => 'camsi', 'CSS0022621' => 'camsi', 'CSS0022815' => 'camsi', 'CSS0022936' => 'camsi', 'CSS0022964' => 'camsi', 'CSS0022985' => 'camsi', 'CSS0023002' => 'camsi', 'CSS0023006' => 'camsi', 'CSS0023024' => 'camsi', 'CSS0023489' => 'camsi', 'CSS0023593' => 'camsi', 'CSS0023621' => 'camsi', 'CSS0023743' => 'camsi', 'CSS0023804' => 'camsi', 'CSS0023805' => 'camsi', 'CSS0023908' => 'camsi', 'CSS0023938' => 'camsi', 'CSS0023981' => 'camsi', 'CSS0024027' => 'camsi', 'CSS0024169' => 'camsi', 'CSS0024193' => 'camsi', 'CSS0024269' => 'camsi', 'CSS0024336' => 'camsi', 'CSS0024337' => 'camsi', 'CSS0024548' => 'camsi', 'CSS0024564' => 'camsi', 'CSS0024585' => 'camsi', 'CSS0024738' => 'camsi', 'CSS0024833' => 'camsi', 'CSS0024846' => 'camsi', 'CSS0024957' => 'camsi', 'CSS0024974' => 'camsi', 'CSS0025005' => 'camsi', 'CSS0025235' => 'camsi', 'CSS0025465' => 'camsi', 'CSS0025633' => 'camsi', 'CSS0025688' => 'camsi', 'CSS0025759' => 'camsi', 'CSS0025774' => 'camsi', 'CSS0025801' => 'camsi', 'CSS0025942' => 'camsi', 'CSS0026083' => 'camsi', 'CSS0026194' => 'camsi', 'CSS0026230' => 'camsi', 'CSS0026398' => 'camsi', 'CSS0026419' => 'camsi', 'CSS0026679' => 'camsi', 'CSS0026719' => 'camsi', 'CSS0026795' => 'camsi', 'CSS0026835' => 'camsi', 'CSS0026930' => 'camsi', 'CSS0027053' => 'camsi', 'CSS0027130' => 'camsi', 'CSS0027192' => 'camsi', 'CSS0027454' => 'camsi', 'CSS0027467' => 'camsi', 'CSS0027521' => 'camsi', 'CSS0027662' => 'camsi', 'CSS0027795' => 'camsi', 'CSS0027835' => 'camsi', 'CSS0027966' => 'camsi', 'CSS0028090' => 'camsi', 'CSS0028134' => 'camsi', 'CSS0028205' => 'camsi', 'CSS0028263' => 'camsi', 'CSS0028363' => 'camsi', 'CSS0028598' => 'camsi', 'CSS0029175' => 'camsi', 'CSS0029191' => 'camsi', 'CSS0029424' => 'camsi', 'CSS0029479' => 'camsi', 'CSS0029496' => 'camsi', 'CSS0029633' => 'camsi', 'CSS0029837' => 'camsi', 'CSS0029844' => 'camsi', 'CSS0029863' => 'camsi', 'CSS0029874' => 'camsi', 'CSS0029959' => 'camsi', 'CSS0030001' => 'camsi', 'CSS0030093' => 'camsi', 'CSS0030199' => 'camsi', 'CSS0030200' => 'camsi', 'CSS0030427' => 'camsi', 'CSS0030476' => 'camsi', 'CSS0030636' => 'camsi', 'CSS0030673' => 'camsi', 'CSS0030766' => 'camsi', 'CSS0030775' => 'camsi', 'CSS0030858' => 'camsi', 'CSS0030873' => 'camsi', 'CSS0030929' => 'camsi', 'CSS0031028' => 'camsi', 'CSS0031129' => 'camsi', 'CSS0031164' => 'camsi', 'CSS0031340' => 'camsi', 'CSS0031368' => 'camsi', 'CSS0031395' => 'camsi', 'CSS0031596' => 'camsi', 'CSS0031727' => 'camsi', 'CSS0032011' => 'camsi', 'CSS0032160' => 'camsi', 'CSS0032538' => 'camsi', 'CSS0032576' => 'camsi', 'CSS0032603' => 'camsi', 'CSS0032640' => 'camsi', 'CSS0032704' => 'camsi', 'CSS0032851' => 'camsi', 'CSS0032973' => 'camsi', 'CSS0033048' => 'camsi', 'CSS0033082' => 'camsi', 'CSS0033157' => 'camsi', 'CSS0033253' => 'camsi', 'CSS0033347' => 'camsi', 'CSS0033601' => 'camsi', 'CSS0033820' => 'camsi', 'CSS0033881' => 'camsi', 'CSS0033934' => 'camsi', 'CSS0034143' => 'camsi', 'CSS0034176' => 'camsi', 'CSS0034201' => 'camsi', 'CSS0034269' => 'camsi', 'CSS0034303' => 'camsi', 'CSS0034463' => 'camsi', 'CSS0034470' => 'camsi', 'CSS0034514' => 'camsi', 'CSS0034525' => 'camsi', 'CSS0034726' => 'camsi', 'CSS0034727' => 'camsi', 'CSS0034737' => 'camsi', 'CSS0034768' => 'camsi', 'CSS0034890' => 'camsi', 'CSS0034943' => 'camsi', 'CSS0034957' => 'camsi', 'CSS0034973' => 'camsi', 'CSS0035178' => 'camsi', 'CSS0035260' => 'camsi', 'CSS0035316' => 'camsi', 'CSS0035347' => 'camsi', 'CSS0035360' => 'camsi', 'CSS0035380' => 'camsi', 'CSS0035429' => 'camsi', 'CSS0035446' => 'camsi', 'CSS0035737' => 'camsi', 'CSS0035852' => 'camsi', 'CSS0035967' => 'camsi', 'CSS0036001' => 'camsi', 'CSS0036044' => 'camsi', 'CSS0036221' => 'camsi', 'CSS0036333' => 'camsi', 'CSS0036435' => 'camsi', 'CSS0036843' => 'camsi', 'CSS0036846' => 'camsi', 'CSS0037097' => 'camsi', 'CSS0037263' => 'camsi', 'CSS0037370' => 'camsi', 'CSS0037410' => 'camsi', 'CSS0037449' => 'camsi', 'CSS0037603' => 'camsi', 'CSS0037851' => 'camsi', 'CSS0037891' => 'camsi', 'CSS0037996' => 'camsi', 'CSS0038222' => 'camsi', 'CSS0038433' => 'camsi', 'CSS0038441' => 'camsi', 'CSS0038718' => 'camsi', 'CSS0038890' => 'camsi', 'CSS0039049' => 'camsi', 'CSS0039145' => 'camsi', 'CSS0039243' => 'camsi', 'CSS0039294' => 'camsi', 'CSS0039324' => 'camsi', 'CSS0039376' => 'camsi', 'CSS0039475' => 'camsi', 'CSS0039539' => 'camsi', 'CSS0039546' => 'camsi', 'CSS0039567' => 'camsi', 'CSS0039599' => 'camsi', 'CSS0039763' => 'camsi', 'CSS0039863' => 'camsi', 'CSS0040107' => 'camsi', 'CSS0040124' => 'camsi', 'CSS0040151' => 'camsi', 'CSS0040165' => 'camsi', 'CSS0040309' => 'camsi', 'CSS0040318' => 'camsi', 'CSS0040347' => 'camsi', 'CSS0040371' => 'camsi', 'CSS0040456' => 'camsi', 'CSS0040551' => 'camsi', 'CSS0040975' => 'camsi', 'CSS0040981' => 'camsi', 'CSS0041299' => 'camsi', 'CSS0041493' => 'camsi', 'CSS0041658' => 'camsi', 'CSS0041899' => 'camsi', 'CSS0041927' => 'camsi', 'CSS0042016' => 'camsi', 'CSS0042034' => 'camsi', 'CSS0042103' => 'camsi', 'CSS0042172' => 'camsi', 'CSS0042198' => 'camsi', 'CSS0042201' => 'camsi', 'CSS0042308' => 'camsi', 'CSS0042329' => 'camsi', 'CSS0042348' => 'camsi', 'CSS0042349' => 'camsi', 'CSS0042489' => 'camsi', 'CSS0042575' => 'camsi', 'CSS0042624' => 'camsi', 'CSS0042660' => 'camsi', 'CSS0042694' => 'camsi', 'CSS0042995' => 'camsi', 'CSS0043079' => 'camsi', 'CSS0043165' => 'camsi', 'CSS0043171' => 'camsi', 'CSS0043314' => 'camsi', 'CSS0043361' => 'camsi', 'CSS0043375' => 'camsi', 'CSS0043518' => 'camsi', 'CSS0043536' => 'camsi', 'CSS0043678' => 'camsi', 'CSS0043765' => 'camsi', 'CSS0043897' => 'camsi', 'CSS0043944' => 'camsi', 'CSS0044126' => 'camsi', 'CSS0044136' => 'camsi', 'CSS0044179' => 'camsi', 'CSS0044290' => 'camsi', 'CSS0044437' => 'camsi', 'CSS0044502' => 'camsi', 'CSS0044603' => 'camsi', 'CSS0044680' => 'camsi', 'CSS0044685' => 'camsi', 'CSS0044700' => 'camsi', 'CSS0044888' => 'camsi', 'CSS0044923' => 'camsi', 'CSS0044926' => 'camsi', 'CSS0044979' => 'camsi', 'CSS0045049' => 'camsi', 'CSS0045132' => 'camsi', 'CSS0045161' => 'camsi', 'CSS0045219' => 'camsi', 'CSS0045230' => 'camsi', 'CSS0045259' => 'camsi', 'CSS0045324' => 'camsi', 'CSS0045368' => 'camsi', 'CSS0045435' => 'camsi', 'CSS0045856' => 'camsi', 'CSS0045955' => 'camsi', 'CSS0046158' => 'camsi', 'CSS0046334' => 'camsi', 'CSS0046365' => 'camsi', 'CSS0046396' => 'camsi', 'CSS0046400' => 'camsi', 'CSS0046445' => 'camsi', 'CSS0046493' => 'camsi', 'CSS0046640' => 'camsi', 'CSS0046657' => 'camsi', 'CSS0046702' => 'camsi', 'CSS0047208' => 'camsi', 'CSS0047368' => 'camsi', 'CSS0047403' => 'camsi', 'CSS0047417' => 'camsi', 'CSS0047469' => 'camsi', 'CSS0047480' => 'camsi', 'CSS0047482' => 'camsi', 'CSS0047693' => 'camsi', 'CSS0047766' => 'camsi', 'CSS0047866' => 'camsi', 'CSS0047884' => 'camsi', 'CSS0048235' => 'camsi', 'CSS0048383' => 'camsi', 'CSS0048438' => 'camsi', 'CSS0048502' => 'camsi', 'CSS0048546' => 'camsi', 'CSS0048653' => 'camsi', 'CSS0048658' => 'camsi', 'CSS0048729' => 'camsi', 'CSS0048867' => 'camsi', 'CSS0048988' => 'camsi', 'CSS0049053' => 'camsi', 'CSS0049099' => 'camsi', 'CSS0049166' => 'camsi', 'CSS0049174' => 'camsi', 'CSS0049212' => 'camsi', 'CSS0049280' => 'camsi', 'CSS0049391' => 'camsi', 'CSS0049546' => 'camsi', 'CSS0049634' => 'camsi', 'CSS0049655' => 'camsi', 'CSS0049813' => 'camsi', 'CSS0049949' => 'camsi', 'CSS0050009' => 'camsi', 'CSS0050118' => 'camsi', 'CSS0050205' => 'camsi', 'CSS0050275' => 'camsi', 'CSS0050480' => 'camsi', 'CSS0050488' => 'camsi', 'CSS0050497' => 'camsi', 'Dinv03126' => 'din', 'Dinv13140' => 'din', 'Dinv13247' => 'din', 'Dinv14217' => 'din', 'EL10Ac9g22435' => 'bvu', 'FAN20G1200' => 'fan', 'PGR142G2516' => 'pgr', 'Prupe.3G160200' => 'ppe', 'Prupe.5G238200' => 'ppe', 'Prupe.7G047500' => 'ppe', 'QL03p045360' => 'qlo', 'QL05p034369' => 'qlo', 'QL05p034412' => 'qlo', 'QL08p017802' => 'qlo', 'QL08p024762' => 'qlo', 'QL10p026237' => 'qlo', 'QL10p032070' => 'qlo', 'QL11p003821' => 'qlo', 'Rhsim04G0057300' => 'rsi', 'Rhsim05G0049200' => 'rsi', 'Rhsim12G0010400' => 'rsi', 'Rhsim12G0012800' => 'rsi', 'TAR624G0483' => 'tar', 'TAR703G0001' => 'tar', 'vmacro05414' => 'vma', 'vmacro07091' => 'vma', 'vmacro07116' => 'vma', 'vmacro08423' => 'vma', 'vmacro09046' => 'vma', 'vmacro14269' => 'vma', 'vmacro16092' => 'vma', 'vmacro17280' => 'vma', 'vmacro19601' => 'vma' ) $gf_id = 'HOM05D001028' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001028' ) $data_identifier = 'HOM05D001028' $data_type = 'gf_id' $species_gene_counts = array( 'aox' => (int) 11, 'ccan' => (int) 6, 'camsi' => (int) 540, 'din' => (int) 4, 'bvu' => (int) 1, 'fan' => (int) 1, 'pgr' => (int) 1, 'ppe' => (int) 3, 'qlo' => (int) 8, 'rsi' => (int) 4, 'tar' => (int) 2, 'vma' => (int) 9 ) $gf_gene_species = 'vma' $gf_gene_id = 'vmacro19601' $species_info = array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ) $local_species = 'bvu' $disabled = '' $selected = '' $num_hits = (int) 0
Warning (2): count(): Parameter must be an array or an object that implements Countable [APP/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp, line 33]Code Context $disabled = (!array_key_exists($local_species,$species_gene_counts))?"disabled":""; $selected = (isset($selected_species) && array_key_exists($local_species,$selected_species))?"checked='checked'":""; $num_hits = (array_key_exists($local_species,$species_gene_counts))?count($species_gene_counts[$local_species]):0; $viewFile = '/www/bioinformatics01_ro/plaza/_dev_instances/feedback/app/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp' $dataForView = array( 'sidebar_info' => array( 'gf_id' => 'HOM05D001028', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '590', 'num_species' => '12' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'Aqoxy1G01649' => 'aox', 'Aqoxy1G02950' => 'aox', 'Aqoxy2G01005' => 'aox', 'Aqoxy2G01064' => 'aox', 'Aqoxy3G02267' => 'aox', 'Aqoxy3G02617' => 'aox', 'Aqoxy3G02693' => 'aox', 'Aqoxy5G03425' => 'aox', 'Aqoxy6G02164' => 'aox', 'Aqoxy6G02364' => 'aox', 'Aqoxy7G02284' => 'aox', 'Cc00_g09720' => 'ccan', 'Cc00_g21410' => 'ccan', 'Cc00_g31750' => 'ccan', 'Cc00_g34740' => 'ccan', 'Cc04_g16890' => 'ccan', 'Cc11_g03120' => 'ccan', 'CSS0000222' => 'camsi', 'CSS0000265' => 'camsi', 'CSS0000306' => 'camsi', 'CSS0000326' => 'camsi', 'CSS0000530' => 'camsi', 'CSS0000563' => 'camsi', 'CSS0000584' => 'camsi', 'CSS0000684' => 'camsi', 'CSS0001100' => 'camsi', 'CSS0001311' => 'camsi', 'CSS0001343' => 'camsi', 'CSS0001399' => 'camsi', 'CSS0001475' => 'camsi', 'CSS0001506' => 'camsi', 'CSS0001602' => 'camsi', 'CSS0001681' => 'camsi', 'CSS0001874' => 'camsi', 'CSS0001948' => 'camsi', 'CSS0002022' => 'camsi', 'CSS0002230' => 'camsi', 'CSS0002265' => 'camsi', 'CSS0002277' => 'camsi', 'CSS0002462' => 'camsi', 'CSS0002823' => 'camsi', 'CSS0003091' => 'camsi', 'CSS0003162' => 'camsi', 'CSS0003264' => 'camsi', 'CSS0003355' => 'camsi', 'CSS0003378' => 'camsi', 'CSS0003472' => 'camsi', 'CSS0003500' => 'camsi', 'CSS0003640' => 'camsi', 'CSS0003767' => 'camsi', 'CSS0003894' => 'camsi', 'CSS0003952' => 'camsi', 'CSS0003977' => 'camsi', 'CSS0004028' => 'camsi', 'CSS0004117' => 'camsi', 'CSS0004137' => 'camsi', 'CSS0004176' => 'camsi', 'CSS0004265' => 'camsi', 'CSS0004450' => 'camsi', 'CSS0004468' => 'camsi', 'CSS0004488' => 'camsi', 'CSS0004490' => 'camsi', 'CSS0004632' => 'camsi', 'CSS0004790' => 'camsi', 'CSS0004877' => 'camsi', 'CSS0004920' => 'camsi', 'CSS0004969' => 'camsi', 'CSS0005084' => 'camsi', 'CSS0005101' => 'camsi', 'CSS0005271' => 'camsi', 'CSS0005313' => 'camsi', 'CSS0005331' => 'camsi', 'CSS0005368' => 'camsi', 'CSS0005391' => 'camsi', 'CSS0005437' => 'camsi', 'CSS0005515' => 'camsi', 'CSS0005526' => 'camsi', 'CSS0005532' => 'camsi', 'CSS0005595' => 'camsi', 'CSS0005677' => 'camsi', 'CSS0005838' => 'camsi', 'CSS0005988' => 'camsi', 'CSS0006100' => 'camsi', 'CSS0006128' => 'camsi', 'CSS0006293' => 'camsi', 'CSS0006378' => 'camsi', 'CSS0006400' => 'camsi', 'CSS0006441' => 'camsi', 'CSS0006455' => 'camsi', 'CSS0006480' => 'camsi', 'CSS0006483' => 'camsi', 'CSS0006538' => 'camsi', 'CSS0006582' => 'camsi', 'CSS0006632' => 'camsi', 'CSS0006771' => 'camsi', 'CSS0006803' => 'camsi', 'CSS0006852' => 'camsi', 'CSS0006861' => 'camsi', 'CSS0006910' => 'camsi', 'CSS0007037' => 'camsi', 'CSS0007066' => 'camsi', 'CSS0007072' => 'camsi', 'CSS0007109' => 'camsi', 'CSS0007193' => 'camsi', 'CSS0007319' => 'camsi', 'CSS0007336' => 'camsi', 'CSS0007377' => 'camsi', 'CSS0007659' => 'camsi', 'CSS0007701' => 'camsi', 'CSS0007711' => 'camsi', 'CSS0007809' => 'camsi', 'CSS0008045' => 'camsi', 'CSS0008050' => 'camsi', 'CSS0008206' => 'camsi', 'CSS0008251' => 'camsi', 'CSS0008252' => 'camsi', 'CSS0008279' => 'camsi', 'CSS0008482' => 'camsi', 'CSS0008583' => 'camsi', 'CSS0008699' => 'camsi', 'CSS0008798' => 'camsi', 'CSS0008971' => 'camsi', 'CSS0009019' => 'camsi', 'CSS0009191' => 'camsi', 'CSS0009241' => 'camsi', 'CSS0009246' => 'camsi', 'CSS0009399' => 'camsi', 'CSS0009654' => 'camsi', 'CSS0009722' => 'camsi', 'CSS0009920' => 'camsi', 'CSS0009986' => 'camsi', 'CSS0010182' => 'camsi', 'CSS0010202' => 'camsi', 'CSS0010330' => 'camsi', 'CSS0010362' => 'camsi', 'CSS0010456' => 'camsi', 'CSS0010472' => 'camsi', 'CSS0010507' => 'camsi', 'CSS0010512' => 'camsi', 'CSS0010520' => 'camsi', 'CSS0010617' => 'camsi', 'CSS0010706' => 'camsi', 'CSS0010747' => 'camsi', 'CSS0010816' => 'camsi', 'CSS0011020' => 'camsi', 'CSS0011115' => 'camsi', 'CSS0011383' => 'camsi', 'CSS0011491' => 'camsi', 'CSS0011602' => 'camsi', 'CSS0011605' => 'camsi', 'CSS0011625' => 'camsi', 'CSS0011654' => 'camsi', 'CSS0011781' => 'camsi', 'CSS0011853' => 'camsi', 'CSS0011898' => 'camsi', 'CSS0011933' => 'camsi', 'CSS0011996' => 'camsi', 'CSS0012066' => 'camsi', 'CSS0012097' => 'camsi', 'CSS0012108' => 'camsi', 'CSS0012226' => 'camsi', 'CSS0012248' => 'camsi', 'CSS0012331' => 'camsi', 'CSS0012797' => 'camsi', 'CSS0012818' => 'camsi', 'CSS0012904' => 'camsi', 'CSS0013001' => 'camsi', 'CSS0013022' => 'camsi', 'CSS0013172' => 'camsi', 'CSS0013244' => 'camsi', 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'CSS0018304' => 'camsi', 'CSS0018406' => 'camsi', 'CSS0018481' => 'camsi', 'CSS0018511' => 'camsi', 'CSS0018596' => 'camsi', 'CSS0018727' => 'camsi', 'CSS0018751' => 'camsi', 'CSS0018777' => 'camsi', 'CSS0018798' => 'camsi', 'CSS0019137' => 'camsi', 'CSS0019177' => 'camsi', 'CSS0019217' => 'camsi', 'CSS0019361' => 'camsi', 'CSS0019516' => 'camsi', 'CSS0019538' => 'camsi', 'CSS0019560' => 'camsi', 'CSS0019819' => 'camsi', 'CSS0019837' => 'camsi', 'CSS0019915' => 'camsi', 'CSS0019925' => 'camsi', 'CSS0020112' => 'camsi', 'CSS0020160' => 'camsi', 'CSS0020378' => 'camsi', 'CSS0020388' => 'camsi', 'CSS0020452' => 'camsi', 'CSS0020588' => 'camsi', 'CSS0020661' => 'camsi', 'CSS0020886' => 'camsi', 'CSS0020973' => 'camsi', 'CSS0021035' => 'camsi', 'CSS0021111' => 'camsi', 'CSS0021131' => 'camsi', 'CSS0021151' => 'camsi', 'CSS0021228' => 'camsi', 'CSS0021397' => 'camsi', 'CSS0021420' => 'camsi', 'CSS0021464' => 'camsi', 'CSS0021547' => 'camsi', 'CSS0021608' => 'camsi', 'CSS0021740' => 'camsi', 'CSS0021826' => 'camsi', 'CSS0021904' => 'camsi', 'CSS0021941' => 'camsi', 'CSS0022189' => 'camsi', 'CSS0022199' => 'camsi', 'CSS0022502' => 'camsi', 'CSS0022531' => 'camsi', 'CSS0022581' => 'camsi', 'CSS0022612' => 'camsi', 'CSS0022621' => 'camsi', 'CSS0022815' => 'camsi', 'CSS0022936' => 'camsi', 'CSS0022964' => 'camsi', 'CSS0022985' => 'camsi', 'CSS0023002' => 'camsi', 'CSS0023006' => 'camsi', 'CSS0023024' => 'camsi', 'CSS0023489' => 'camsi', 'CSS0023593' => 'camsi', 'CSS0023621' => 'camsi', 'CSS0023743' => 'camsi', 'CSS0023804' => 'camsi', 'CSS0023805' => 'camsi', 'CSS0023908' => 'camsi', 'CSS0023938' => 'camsi', 'CSS0023981' => 'camsi', 'CSS0024027' => 'camsi', 'CSS0024169' => 'camsi', 'CSS0024193' => 'camsi', 'CSS0024269' => 'camsi', 'CSS0024336' => 'camsi', 'CSS0024337' => 'camsi', 'CSS0024548' => 'camsi', 'CSS0024564' => 'camsi', 'CSS0024585' => 'camsi', 'CSS0024738' => 'camsi', 'CSS0024833' => 'camsi', 'CSS0024846' => 'camsi', 'CSS0024957' => 'camsi', 'CSS0024974' => 'camsi', 'CSS0025005' => 'camsi', 'CSS0025235' => 'camsi', 'CSS0025465' => 'camsi', 'CSS0025633' => 'camsi', 'CSS0025688' => 'camsi', 'CSS0025759' => 'camsi', 'CSS0025774' => 'camsi', 'CSS0025801' => 'camsi', 'CSS0025942' => 'camsi', 'CSS0026083' => 'camsi', 'CSS0026194' => 'camsi', 'CSS0026230' => 'camsi', 'CSS0026398' => 'camsi', 'CSS0026419' => 'camsi', 'CSS0026679' => 'camsi', 'CSS0026719' => 'camsi', 'CSS0026795' => 'camsi', 'CSS0026835' => 'camsi', 'CSS0026930' => 'camsi', 'CSS0027053' => 'camsi', 'CSS0027130' => 'camsi', 'CSS0027192' => 'camsi', 'CSS0027454' => 'camsi', 'CSS0027467' => 'camsi', 'CSS0027521' => 'camsi', 'CSS0027662' => 'camsi', 'CSS0027795' => 'camsi', 'CSS0027835' => 'camsi', 'CSS0027966' => 'camsi', 'CSS0028090' => 'camsi', 'CSS0028134' => 'camsi', 'CSS0028205' => 'camsi', 'CSS0028263' => 'camsi', 'CSS0028363' => 'camsi', 'CSS0028598' => 'camsi', 'CSS0029175' => 'camsi', 'CSS0029191' => 'camsi', 'CSS0029424' => 'camsi', 'CSS0029479' => 'camsi', 'CSS0029496' => 'camsi', 'CSS0029633' => 'camsi', 'CSS0029837' => 'camsi', 'CSS0029844' => 'camsi', 'CSS0029863' => 'camsi', 'CSS0029874' => 'camsi', 'CSS0029959' => 'camsi', 'CSS0030001' => 'camsi', 'CSS0030093' => 'camsi', 'CSS0030199' => 'camsi', 'CSS0030200' => 'camsi', 'CSS0030427' => 'camsi', 'CSS0030476' => 'camsi', 'CSS0030636' => 'camsi', 'CSS0030673' => 'camsi', 'CSS0030766' => 'camsi', 'CSS0030775' => 'camsi', 'CSS0030858' => 'camsi', 'CSS0030873' => 'camsi', 'CSS0030929' => 'camsi', 'CSS0031028' => 'camsi', 'CSS0031129' => 'camsi', 'CSS0031164' => 'camsi', 'CSS0031340' => 'camsi', 'CSS0031368' => 'camsi', 'CSS0031395' => 'camsi', 'CSS0031596' => 'camsi', 'CSS0031727' => 'camsi', 'CSS0032011' => 'camsi', 'CSS0032160' => 'camsi', 'CSS0032538' => 'camsi', 'CSS0032576' => 'camsi', 'CSS0032603' => 'camsi', 'CSS0032640' => 'camsi', 'CSS0032704' => 'camsi', 'CSS0032851' => 'camsi', 'CSS0032973' => 'camsi', 'CSS0033048' => 'camsi', 'CSS0033082' => 'camsi', 'CSS0033157' => 'camsi', 'CSS0033253' => 'camsi', 'CSS0033347' => 'camsi', 'CSS0033601' => 'camsi', 'CSS0033820' => 'camsi', 'CSS0033881' => 'camsi', 'CSS0033934' => 'camsi', 'CSS0034143' => 'camsi', 'CSS0034176' => 'camsi', 'CSS0034201' => 'camsi', 'CSS0034269' => 'camsi', 'CSS0034303' => 'camsi', 'CSS0034463' => 'camsi', 'CSS0034470' => 'camsi', 'CSS0034514' => 'camsi', 'CSS0034525' => 'camsi', 'CSS0034726' => 'camsi', 'CSS0034727' => 'camsi', 'CSS0034737' => 'camsi', 'CSS0034768' => 'camsi', 'CSS0034890' => 'camsi', 'CSS0034943' => 'camsi', 'CSS0034957' => 'camsi', 'CSS0034973' => 'camsi', 'CSS0035178' => 'camsi', 'CSS0035260' => 'camsi', 'CSS0035316' => 'camsi', 'CSS0035347' => 'camsi', 'CSS0035360' => 'camsi', 'CSS0035380' => 'camsi', 'CSS0035429' => 'camsi', 'CSS0035446' => 'camsi', 'CSS0035737' => 'camsi', 'CSS0035852' => 'camsi', 'CSS0035967' => 'camsi', 'CSS0036001' => 'camsi', 'CSS0036044' => 'camsi', 'CSS0036221' => 'camsi', 'CSS0036333' => 'camsi', 'CSS0036435' => 'camsi', 'CSS0036843' => 'camsi', 'CSS0036846' => 'camsi', 'CSS0037097' => 'camsi', 'CSS0037263' => 'camsi', 'CSS0037370' => 'camsi', 'CSS0037410' => 'camsi', 'CSS0037449' => 'camsi', 'CSS0037603' => 'camsi', 'CSS0037851' => 'camsi', 'CSS0037891' => 'camsi', 'CSS0037996' => 'camsi', 'CSS0038222' => 'camsi', 'CSS0038433' => 'camsi', 'CSS0038441' => 'camsi', 'CSS0038718' => 'camsi', 'CSS0038890' => 'camsi', 'CSS0039049' => 'camsi', 'CSS0039145' => 'camsi', 'CSS0039243' => 'camsi', 'CSS0039294' => 'camsi', 'CSS0039324' => 'camsi', 'CSS0039376' => 'camsi', 'CSS0039475' => 'camsi', 'CSS0039539' => 'camsi', 'CSS0039546' => 'camsi', 'CSS0039567' => 'camsi', 'CSS0039599' => 'camsi', 'CSS0039763' => 'camsi', 'CSS0039863' => 'camsi', 'CSS0040107' => 'camsi', 'CSS0040124' => 'camsi', 'CSS0040151' => 'camsi', 'CSS0040165' => 'camsi', 'CSS0040309' => 'camsi', 'CSS0040318' => 'camsi', 'CSS0040347' => 'camsi', 'CSS0040371' => 'camsi', 'CSS0040456' => 'camsi', 'CSS0040551' => 'camsi', 'CSS0040975' => 'camsi', 'CSS0040981' => 'camsi', 'CSS0041299' => 'camsi', 'CSS0041493' => 'camsi', 'CSS0041658' => 'camsi', 'CSS0041899' => 'camsi', 'CSS0041927' => 'camsi', 'CSS0042016' => 'camsi', 'CSS0042034' => 'camsi', 'CSS0042103' => 'camsi', 'CSS0042172' => 'camsi', 'CSS0042198' => 'camsi', 'CSS0042201' => 'camsi', 'CSS0042308' => 'camsi', 'CSS0042329' => 'camsi', 'CSS0042348' => 'camsi', 'CSS0042349' => 'camsi', 'CSS0042489' => 'camsi', 'CSS0042575' => 'camsi', 'CSS0042624' => 'camsi', 'CSS0042660' => 'camsi', 'CSS0042694' => 'camsi', 'CSS0042995' => 'camsi', 'CSS0043079' => 'camsi', 'CSS0043165' => 'camsi', 'CSS0043171' => 'camsi', 'CSS0043314' => 'camsi', 'CSS0043361' => 'camsi', 'CSS0043375' => 'camsi', 'CSS0043518' => 'camsi', 'CSS0043536' => 'camsi', 'CSS0043678' => 'camsi', 'CSS0043765' => 'camsi', 'CSS0043897' => 'camsi', 'CSS0043944' => 'camsi', 'CSS0044126' => 'camsi', 'CSS0044136' => 'camsi', 'CSS0044179' => 'camsi', 'CSS0044290' => 'camsi', 'CSS0044437' => 'camsi', 'CSS0044502' => 'camsi', 'CSS0044603' => 'camsi', 'CSS0044680' => 'camsi', 'CSS0044685' => 'camsi', 'CSS0044700' => 'camsi', 'CSS0044888' => 'camsi', 'CSS0044923' => 'camsi', 'CSS0044926' => 'camsi', 'CSS0044979' => 'camsi', 'CSS0045049' => 'camsi', 'CSS0045132' => 'camsi', 'CSS0045161' => 'camsi', 'CSS0045219' => 'camsi', 'CSS0045230' => 'camsi', 'CSS0045259' => 'camsi', 'CSS0045324' => 'camsi', 'CSS0045368' => 'camsi', 'CSS0045435' => 'camsi', 'CSS0045856' => 'camsi', 'CSS0045955' => 'camsi', 'CSS0046158' => 'camsi', 'CSS0046334' => 'camsi', 'CSS0046365' => 'camsi', 'CSS0046396' => 'camsi', 'CSS0046400' => 'camsi', 'CSS0046445' => 'camsi', 'CSS0046493' => 'camsi', 'CSS0046640' => 'camsi', 'CSS0046657' => 'camsi', 'CSS0046702' => 'camsi', 'CSS0047208' => 'camsi', 'CSS0047368' => 'camsi', 'CSS0047403' => 'camsi', 'CSS0047417' => 'camsi', 'CSS0047469' => 'camsi', 'CSS0047480' => 'camsi', 'CSS0047482' => 'camsi', 'CSS0047693' => 'camsi', 'CSS0047766' => 'camsi', 'CSS0047866' => 'camsi', 'CSS0047884' => 'camsi', 'CSS0048235' => 'camsi', 'CSS0048383' => 'camsi', 'CSS0048438' => 'camsi', 'CSS0048502' => 'camsi', 'CSS0048546' => 'camsi', 'CSS0048653' => 'camsi', 'CSS0048658' => 'camsi', 'CSS0048729' => 'camsi', 'CSS0048867' => 'camsi', 'CSS0048988' => 'camsi', 'CSS0049053' => 'camsi', 'CSS0049099' => 'camsi', 'CSS0049166' => 'camsi', 'CSS0049174' => 'camsi', 'CSS0049212' => 'camsi', 'CSS0049280' => 'camsi', 'CSS0049391' => 'camsi', 'CSS0049546' => 'camsi', 'CSS0049634' => 'camsi', 'CSS0049655' => 'camsi', 'CSS0049813' => 'camsi', 'CSS0049949' => 'camsi', 'CSS0050009' => 'camsi', 'CSS0050118' => 'camsi', 'CSS0050205' => 'camsi', 'CSS0050275' => 'camsi', 'CSS0050480' => 'camsi', 'CSS0050488' => 'camsi', 'CSS0050497' => 'camsi', 'Dinv03126' => 'din', 'Dinv13140' => 'din', 'Dinv13247' => 'din', 'Dinv14217' => 'din', 'EL10Ac9g22435' => 'bvu', 'FAN20G1200' => 'fan', 'PGR142G2516' => 'pgr', 'Prupe.3G160200' => 'ppe', 'Prupe.5G238200' => 'ppe', 'Prupe.7G047500' => 'ppe', 'QL03p045360' => 'qlo', 'QL05p034369' => 'qlo', 'QL05p034412' => 'qlo', 'QL08p017802' => 'qlo', 'QL08p024762' => 'qlo', 'QL10p026237' => 'qlo', 'QL10p032070' => 'qlo', 'QL11p003821' => 'qlo', 'Rhsim04G0057300' => 'rsi', 'Rhsim05G0049200' => 'rsi', 'Rhsim12G0010400' => 'rsi', 'Rhsim12G0012800' => 'rsi', 'TAR624G0483' => 'tar', 'TAR703G0001' => 'tar', 'vmacro05414' => 'vma', 'vmacro07091' => 'vma', 'vmacro07116' => 'vma', 'vmacro08423' => 'vma', 'vmacro09046' => 'vma', 'vmacro14269' => 'vma', 'vmacro16092' => 'vma', 'vmacro17280' => 'vma', 'vmacro19601' => 'vma' ), 'gf_id' => 'HOM05D001028', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001028' ), 'data_identifier' => 'HOM05D001028', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001028', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '590', 'num_species' => '12' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'Aqoxy1G01649' => 'aox', 'Aqoxy1G02950' => 'aox', 'Aqoxy2G01005' => 'aox', 'Aqoxy2G01064' => 'aox', 'Aqoxy3G02267' => 'aox', 'Aqoxy3G02617' => 'aox', 'Aqoxy3G02693' => 'aox', 'Aqoxy5G03425' => 'aox', 'Aqoxy6G02164' => 'aox', 'Aqoxy6G02364' => 'aox', 'Aqoxy7G02284' => 'aox', 'Cc00_g09720' => 'ccan', 'Cc00_g21410' => 'ccan', 'Cc00_g31750' => 'ccan', 'Cc00_g34740' => 'ccan', 'Cc04_g16890' => 'ccan', 'Cc11_g03120' => 'ccan', 'CSS0000222' => 'camsi', 'CSS0000265' => 'camsi', 'CSS0000306' => 'camsi', 'CSS0000326' => 'camsi', 'CSS0000530' => 'camsi', 'CSS0000563' => 'camsi', 'CSS0000584' => 'camsi', 'CSS0000684' => 'camsi', 'CSS0001100' => 'camsi', 'CSS0001311' => 'camsi', 'CSS0001343' => 'camsi', 'CSS0001399' => 'camsi', 'CSS0001475' => 'camsi', 'CSS0001506' => 'camsi', 'CSS0001602' => 'camsi', 'CSS0001681' => 'camsi', 'CSS0001874' => 'camsi', 'CSS0001948' => 'camsi', 'CSS0002022' => 'camsi', 'CSS0002230' => 'camsi', 'CSS0002265' => 'camsi', 'CSS0002277' => 'camsi', 'CSS0002462' => 'camsi', 'CSS0002823' => 'camsi', 'CSS0003091' => 'camsi', 'CSS0003162' => 'camsi', 'CSS0003264' => 'camsi', 'CSS0003355' => 'camsi', 'CSS0003378' => 'camsi', 'CSS0003472' => 'camsi', 'CSS0003500' => 'camsi', 'CSS0003640' => 'camsi', 'CSS0003767' => 'camsi', 'CSS0003894' => 'camsi', 'CSS0003952' => 'camsi', 'CSS0003977' => 'camsi', 'CSS0004028' => 'camsi', 'CSS0004117' => 'camsi', 'CSS0004137' => 'camsi', 'CSS0004176' => 'camsi', 'CSS0004265' => 'camsi', 'CSS0004450' => 'camsi', 'CSS0004468' => 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'camsi', 'CSS0019177' => 'camsi', 'CSS0019217' => 'camsi', 'CSS0019361' => 'camsi', 'CSS0019516' => 'camsi', 'CSS0019538' => 'camsi', 'CSS0019560' => 'camsi', 'CSS0019819' => 'camsi', 'CSS0019837' => 'camsi', 'CSS0019915' => 'camsi', 'CSS0019925' => 'camsi', 'CSS0020112' => 'camsi', 'CSS0020160' => 'camsi', 'CSS0020378' => 'camsi', 'CSS0020388' => 'camsi', 'CSS0020452' => 'camsi', 'CSS0020588' => 'camsi', 'CSS0020661' => 'camsi', 'CSS0020886' => 'camsi', 'CSS0020973' => 'camsi', 'CSS0021035' => 'camsi', 'CSS0021111' => 'camsi', 'CSS0021131' => 'camsi', 'CSS0021151' => 'camsi', 'CSS0021228' => 'camsi', 'CSS0021397' => 'camsi', 'CSS0021420' => 'camsi', 'CSS0021464' => 'camsi', 'CSS0021547' => 'camsi', 'CSS0021608' => 'camsi', 'CSS0021740' => 'camsi', 'CSS0021826' => 'camsi', 'CSS0021904' => 'camsi', 'CSS0021941' => 'camsi', 'CSS0022189' => 'camsi', 'CSS0022199' => 'camsi', 'CSS0022502' => 'camsi', 'CSS0022531' => 'camsi', 'CSS0022581' => 'camsi', 'CSS0022612' => 'camsi', 'CSS0022621' => 'camsi', 'CSS0022815' => 'camsi', 'CSS0022936' => 'camsi', 'CSS0022964' => 'camsi', 'CSS0022985' => 'camsi', 'CSS0023002' => 'camsi', 'CSS0023006' => 'camsi', 'CSS0023024' => 'camsi', 'CSS0023489' => 'camsi', 'CSS0023593' => 'camsi', 'CSS0023621' => 'camsi', 'CSS0023743' => 'camsi', 'CSS0023804' => 'camsi', 'CSS0023805' => 'camsi', 'CSS0023908' => 'camsi', 'CSS0023938' => 'camsi', 'CSS0023981' => 'camsi', 'CSS0024027' => 'camsi', 'CSS0024169' => 'camsi', 'CSS0024193' => 'camsi', 'CSS0024269' => 'camsi', 'CSS0024336' => 'camsi', 'CSS0024337' => 'camsi', 'CSS0024548' => 'camsi', 'CSS0024564' => 'camsi', 'CSS0024585' => 'camsi', 'CSS0024738' => 'camsi', 'CSS0024833' => 'camsi', 'CSS0024846' => 'camsi', 'CSS0024957' => 'camsi', 'CSS0024974' => 'camsi', 'CSS0025005' => 'camsi', 'CSS0025235' => 'camsi', 'CSS0025465' => 'camsi', 'CSS0025633' => 'camsi', 'CSS0025688' => 'camsi', 'CSS0025759' => 'camsi', 'CSS0025774' => 'camsi', 'CSS0025801' => 'camsi', 'CSS0025942' => 'camsi', 'CSS0026083' => 'camsi', 'CSS0026194' => 'camsi', 'CSS0026230' => 'camsi', 'CSS0026398' => 'camsi', 'CSS0026419' => 'camsi', 'CSS0026679' => 'camsi', 'CSS0026719' => 'camsi', 'CSS0026795' => 'camsi', 'CSS0026835' => 'camsi', 'CSS0026930' => 'camsi', 'CSS0027053' => 'camsi', 'CSS0027130' => 'camsi', 'CSS0027192' => 'camsi', 'CSS0027454' => 'camsi', 'CSS0027467' => 'camsi', 'CSS0027521' => 'camsi', 'CSS0027662' => 'camsi', 'CSS0027795' => 'camsi', 'CSS0027835' => 'camsi', 'CSS0027966' => 'camsi', 'CSS0028090' => 'camsi', 'CSS0028134' => 'camsi', 'CSS0028205' => 'camsi', 'CSS0028263' => 'camsi', 'CSS0028363' => 'camsi', 'CSS0028598' => 'camsi', 'CSS0029175' => 'camsi', 'CSS0029191' => 'camsi', 'CSS0029424' => 'camsi', 'CSS0029479' => 'camsi', 'CSS0029496' => 'camsi', 'CSS0029633' => 'camsi', 'CSS0029837' => 'camsi', 'CSS0029844' => 'camsi', 'CSS0029863' => 'camsi', 'CSS0029874' => 'camsi', 'CSS0029959' => 'camsi', 'CSS0030001' => 'camsi', 'CSS0030093' => 'camsi', 'CSS0030199' => 'camsi', 'CSS0030200' => 'camsi', 'CSS0030427' => 'camsi', 'CSS0030476' => 'camsi', 'CSS0030636' => 'camsi', 'CSS0030673' => 'camsi', 'CSS0030766' => 'camsi', 'CSS0030775' => 'camsi', 'CSS0030858' => 'camsi', 'CSS0030873' => 'camsi', 'CSS0030929' => 'camsi', 'CSS0031028' => 'camsi', 'CSS0031129' => 'camsi', 'CSS0031164' => 'camsi', 'CSS0031340' => 'camsi', 'CSS0031368' => 'camsi', 'CSS0031395' => 'camsi', 'CSS0031596' => 'camsi', 'CSS0031727' => 'camsi', 'CSS0032011' => 'camsi', 'CSS0032160' => 'camsi', 'CSS0032538' => 'camsi', 'CSS0032576' => 'camsi', 'CSS0032603' => 'camsi', 'CSS0032640' => 'camsi', 'CSS0032704' => 'camsi', 'CSS0032851' => 'camsi', 'CSS0032973' => 'camsi', 'CSS0033048' => 'camsi', 'CSS0033082' => 'camsi', 'CSS0033157' => 'camsi', 'CSS0033253' => 'camsi', 'CSS0033347' => 'camsi', 'CSS0033601' => 'camsi', 'CSS0033820' => 'camsi', 'CSS0033881' => 'camsi', 'CSS0033934' => 'camsi', 'CSS0034143' => 'camsi', 'CSS0034176' => 'camsi', 'CSS0034201' => 'camsi', 'CSS0034269' => 'camsi', 'CSS0034303' => 'camsi', 'CSS0034463' => 'camsi', 'CSS0034470' => 'camsi', 'CSS0034514' => 'camsi', 'CSS0034525' => 'camsi', 'CSS0034726' => 'camsi', 'CSS0034727' => 'camsi', 'CSS0034737' => 'camsi', 'CSS0034768' => 'camsi', 'CSS0034890' => 'camsi', 'CSS0034943' => 'camsi', 'CSS0034957' => 'camsi', 'CSS0034973' => 'camsi', 'CSS0035178' => 'camsi', 'CSS0035260' => 'camsi', 'CSS0035316' => 'camsi', 'CSS0035347' => 'camsi', 'CSS0035360' => 'camsi', 'CSS0035380' => 'camsi', 'CSS0035429' => 'camsi', 'CSS0035446' => 'camsi', 'CSS0035737' => 'camsi', 'CSS0035852' => 'camsi', 'CSS0035967' => 'camsi', 'CSS0036001' => 'camsi', 'CSS0036044' => 'camsi', 'CSS0036221' => 'camsi', 'CSS0036333' => 'camsi', 'CSS0036435' => 'camsi', 'CSS0036843' => 'camsi', 'CSS0036846' => 'camsi', 'CSS0037097' => 'camsi', 'CSS0037263' => 'camsi', 'CSS0037370' => 'camsi', 'CSS0037410' => 'camsi', 'CSS0037449' => 'camsi', 'CSS0037603' => 'camsi', 'CSS0037851' => 'camsi', 'CSS0037891' => 'camsi', 'CSS0037996' => 'camsi', 'CSS0038222' => 'camsi', 'CSS0038433' => 'camsi', 'CSS0038441' => 'camsi', 'CSS0038718' => 'camsi', 'CSS0038890' => 'camsi', 'CSS0039049' => 'camsi', 'CSS0039145' => 'camsi', 'CSS0039243' => 'camsi', 'CSS0039294' => 'camsi', 'CSS0039324' => 'camsi', 'CSS0039376' => 'camsi', 'CSS0039475' => 'camsi', 'CSS0039539' => 'camsi', 'CSS0039546' => 'camsi', 'CSS0039567' => 'camsi', 'CSS0039599' => 'camsi', 'CSS0039763' => 'camsi', 'CSS0039863' => 'camsi', 'CSS0040107' => 'camsi', 'CSS0040124' => 'camsi', 'CSS0040151' => 'camsi', 'CSS0040165' => 'camsi', 'CSS0040309' => 'camsi', 'CSS0040318' => 'camsi', 'CSS0040347' => 'camsi', 'CSS0040371' => 'camsi', 'CSS0040456' => 'camsi', 'CSS0040551' => 'camsi', 'CSS0040975' => 'camsi', 'CSS0040981' => 'camsi', 'CSS0041299' => 'camsi', 'CSS0041493' => 'camsi', 'CSS0041658' => 'camsi', 'CSS0041899' => 'camsi', 'CSS0041927' => 'camsi', 'CSS0042016' => 'camsi', 'CSS0042034' => 'camsi', 'CSS0042103' => 'camsi', 'CSS0042172' => 'camsi', 'CSS0042198' => 'camsi', 'CSS0042201' => 'camsi', 'CSS0042308' => 'camsi', 'CSS0042329' => 'camsi', 'CSS0042348' => 'camsi', 'CSS0042349' => 'camsi', 'CSS0042489' => 'camsi', 'CSS0042575' => 'camsi', 'CSS0042624' => 'camsi', 'CSS0042660' => 'camsi', 'CSS0042694' => 'camsi', 'CSS0042995' => 'camsi', 'CSS0043079' => 'camsi', 'CSS0043165' => 'camsi', 'CSS0043171' => 'camsi', 'CSS0043314' => 'camsi', 'CSS0043361' => 'camsi', 'CSS0043375' => 'camsi', 'CSS0043518' => 'camsi', 'CSS0043536' => 'camsi', 'CSS0043678' => 'camsi', 'CSS0043765' => 'camsi', 'CSS0043897' => 'camsi', 'CSS0043944' => 'camsi', 'CSS0044126' => 'camsi', 'CSS0044136' => 'camsi', 'CSS0044179' => 'camsi', 'CSS0044290' => 'camsi', 'CSS0044437' => 'camsi', 'CSS0044502' => 'camsi', 'CSS0044603' => 'camsi', 'CSS0044680' => 'camsi', 'CSS0044685' => 'camsi', 'CSS0044700' => 'camsi', 'CSS0044888' => 'camsi', 'CSS0044923' => 'camsi', 'CSS0044926' => 'camsi', 'CSS0044979' => 'camsi', 'CSS0045049' => 'camsi', 'CSS0045132' => 'camsi', 'CSS0045161' => 'camsi', 'CSS0045219' => 'camsi', 'CSS0045230' => 'camsi', 'CSS0045259' => 'camsi', 'CSS0045324' => 'camsi', 'CSS0045368' => 'camsi', 'CSS0045435' => 'camsi', 'CSS0045856' => 'camsi', 'CSS0045955' => 'camsi', 'CSS0046158' => 'camsi', 'CSS0046334' => 'camsi', 'CSS0046365' => 'camsi', 'CSS0046396' => 'camsi', 'CSS0046400' => 'camsi', 'CSS0046445' => 'camsi', 'CSS0046493' => 'camsi', 'CSS0046640' => 'camsi', 'CSS0046657' => 'camsi', 'CSS0046702' => 'camsi', 'CSS0047208' => 'camsi', 'CSS0047368' => 'camsi', 'CSS0047403' => 'camsi', 'CSS0047417' => 'camsi', 'CSS0047469' => 'camsi', 'CSS0047480' => 'camsi', 'CSS0047482' => 'camsi', 'CSS0047693' => 'camsi', 'CSS0047766' => 'camsi', 'CSS0047866' => 'camsi', 'CSS0047884' => 'camsi', 'CSS0048235' => 'camsi', 'CSS0048383' => 'camsi', 'CSS0048438' => 'camsi', 'CSS0048502' => 'camsi', 'CSS0048546' => 'camsi', 'CSS0048653' => 'camsi', 'CSS0048658' => 'camsi', 'CSS0048729' => 'camsi', 'CSS0048867' => 'camsi', 'CSS0048988' => 'camsi', 'CSS0049053' => 'camsi', 'CSS0049099' => 'camsi', 'CSS0049166' => 'camsi', 'CSS0049174' => 'camsi', 'CSS0049212' => 'camsi', 'CSS0049280' => 'camsi', 'CSS0049391' => 'camsi', 'CSS0049546' => 'camsi', 'CSS0049634' => 'camsi', 'CSS0049655' => 'camsi', 'CSS0049813' => 'camsi', 'CSS0049949' => 'camsi', 'CSS0050009' => 'camsi', 'CSS0050118' => 'camsi', 'CSS0050205' => 'camsi', 'CSS0050275' => 'camsi', 'CSS0050480' => 'camsi', 'CSS0050488' => 'camsi', 'CSS0050497' => 'camsi', 'Dinv03126' => 'din', 'Dinv13140' => 'din', 'Dinv13247' => 'din', 'Dinv14217' => 'din', 'EL10Ac9g22435' => 'bvu', 'FAN20G1200' => 'fan', 'PGR142G2516' => 'pgr', 'Prupe.3G160200' => 'ppe', 'Prupe.5G238200' => 'ppe', 'Prupe.7G047500' => 'ppe', 'QL03p045360' => 'qlo', 'QL05p034369' => 'qlo', 'QL05p034412' => 'qlo', 'QL08p017802' => 'qlo', 'QL08p024762' => 'qlo', 'QL10p026237' => 'qlo', 'QL10p032070' => 'qlo', 'QL11p003821' => 'qlo', 'Rhsim04G0057300' => 'rsi', 'Rhsim05G0049200' => 'rsi', 'Rhsim12G0010400' => 'rsi', 'Rhsim12G0012800' => 'rsi', 'TAR624G0483' => 'tar', 'TAR703G0001' => 'tar', 'vmacro05414' => 'vma', 'vmacro07091' => 'vma', 'vmacro07116' => 'vma', 'vmacro08423' => 'vma', 'vmacro09046' => 'vma', 'vmacro14269' => 'vma', 'vmacro16092' => 'vma', 'vmacro17280' => 'vma', 'vmacro19601' => 'vma' ) $gf_id = 'HOM05D001028' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001028' ) $data_identifier = 'HOM05D001028' $data_type = 'gf_id' $species_gene_counts = array( 'aox' => (int) 11, 'ccan' => (int) 6, 'camsi' => (int) 540, 'din' => (int) 4, 'bvu' => (int) 1, 'fan' => (int) 1, 'pgr' => (int) 1, 'ppe' => (int) 3, 'qlo' => (int) 8, 'rsi' => (int) 4, 'tar' => (int) 2, 'vma' => (int) 9 ) $gf_gene_species = 'vma' $gf_gene_id = 'vmacro19601' $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' => 'HOM05D001028', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '590', 'num_species' => '12' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'Aqoxy1G01649' => 'aox', 'Aqoxy1G02950' => 'aox', 'Aqoxy2G01005' => 'aox', 'Aqoxy2G01064' => 'aox', 'Aqoxy3G02267' => 'aox', 'Aqoxy3G02617' => 'aox', 'Aqoxy3G02693' => 'aox', 'Aqoxy5G03425' => 'aox', 'Aqoxy6G02164' => 'aox', 'Aqoxy6G02364' => 'aox', 'Aqoxy7G02284' => 'aox', 'Cc00_g09720' => 'ccan', 'Cc00_g21410' => 'ccan', 'Cc00_g31750' => 'ccan', 'Cc00_g34740' => 'ccan', 'Cc04_g16890' => 'ccan', 'Cc11_g03120' => 'ccan', 'CSS0000222' => 'camsi', 'CSS0000265' => 'camsi', 'CSS0000306' => 'camsi', 'CSS0000326' => 'camsi', 'CSS0000530' => 'camsi', 'CSS0000563' => 'camsi', 'CSS0000584' => 'camsi', 'CSS0000684' => 'camsi', 'CSS0001100' => 'camsi', 'CSS0001311' => 'camsi', 'CSS0001343' => 'camsi', 'CSS0001399' => 'camsi', 'CSS0001475' => 'camsi', 'CSS0001506' => 'camsi', 'CSS0001602' => 'camsi', 'CSS0001681' => 'camsi', 'CSS0001874' => 'camsi', 'CSS0001948' => 'camsi', 'CSS0002022' => 'camsi', 'CSS0002230' => 'camsi', 'CSS0002265' => 'camsi', 'CSS0002277' => 'camsi', 'CSS0002462' => 'camsi', 'CSS0002823' => 'camsi', 'CSS0003091' => 'camsi', 'CSS0003162' => 'camsi', 'CSS0003264' => 'camsi', 'CSS0003355' => 'camsi', 'CSS0003378' => 'camsi', 'CSS0003472' => 'camsi', 'CSS0003500' => 'camsi', 'CSS0003640' => 'camsi', 'CSS0003767' => 'camsi', 'CSS0003894' => 'camsi', 'CSS0003952' => 'camsi', 'CSS0003977' => 'camsi', 'CSS0004028' => 'camsi', 'CSS0004117' => 'camsi', 'CSS0004137' => 'camsi', 'CSS0004176' => 'camsi', 'CSS0004265' => 'camsi', 'CSS0004450' => 'camsi', 'CSS0004468' => 'camsi', 'CSS0004488' => 'camsi', 'CSS0004490' => 'camsi', 'CSS0004632' => 'camsi', 'CSS0004790' => 'camsi', 'CSS0004877' => 'camsi', 'CSS0004920' => 'camsi', 'CSS0004969' => 'camsi', 'CSS0005084' => 'camsi', 'CSS0005101' => 'camsi', 'CSS0005271' => 'camsi', 'CSS0005313' => 'camsi', 'CSS0005331' => 'camsi', 'CSS0005368' => 'camsi', 'CSS0005391' => 'camsi', 'CSS0005437' => 'camsi', 'CSS0005515' => 'camsi', 'CSS0005526' => 'camsi', 'CSS0005532' => 'camsi', 'CSS0005595' => 'camsi', 'CSS0005677' => 'camsi', 'CSS0005838' => 'camsi', 'CSS0005988' => 'camsi', 'CSS0006100' => 'camsi', 'CSS0006128' => 'camsi', 'CSS0006293' => 'camsi', 'CSS0006378' => 'camsi', 'CSS0006400' => 'camsi', 'CSS0006441' => 'camsi', 'CSS0006455' => 'camsi', 'CSS0006480' => 'camsi', 'CSS0006483' => 'camsi', 'CSS0006538' => 'camsi', 'CSS0006582' => 'camsi', 'CSS0006632' => 'camsi', 'CSS0006771' => 'camsi', 'CSS0006803' => 'camsi', 'CSS0006852' => 'camsi', 'CSS0006861' => 'camsi', 'CSS0006910' => 'camsi', 'CSS0007037' => 'camsi', 'CSS0007066' => 'camsi', 'CSS0007072' => 'camsi', 'CSS0007109' => 'camsi', 'CSS0007193' => 'camsi', 'CSS0007319' => 'camsi', 'CSS0007336' => 'camsi', 'CSS0007377' => 'camsi', 'CSS0007659' => 'camsi', 'CSS0007701' => 'camsi', 'CSS0007711' => 'camsi', 'CSS0007809' => 'camsi', 'CSS0008045' => 'camsi', 'CSS0008050' => 'camsi', 'CSS0008206' => 'camsi', 'CSS0008251' => 'camsi', 'CSS0008252' => 'camsi', 'CSS0008279' => 'camsi', 'CSS0008482' => 'camsi', 'CSS0008583' => 'camsi', 'CSS0008699' => 'camsi', 'CSS0008798' => 'camsi', 'CSS0008971' => 'camsi', 'CSS0009019' => 'camsi', 'CSS0009191' => 'camsi', 'CSS0009241' => 'camsi', 'CSS0009246' => 'camsi', 'CSS0009399' => 'camsi', 'CSS0009654' => 'camsi', 'CSS0009722' => 'camsi', 'CSS0009920' => 'camsi', 'CSS0009986' => 'camsi', 'CSS0010182' => 'camsi', 'CSS0010202' => 'camsi', 'CSS0010330' => 'camsi', 'CSS0010362' => 'camsi', 'CSS0010456' => 'camsi', 'CSS0010472' => 'camsi', 'CSS0010507' => 'camsi', 'CSS0010512' => 'camsi', 'CSS0010520' => 'camsi', 'CSS0010617' => 'camsi', 'CSS0010706' => 'camsi', 'CSS0010747' => 'camsi', 'CSS0010816' => 'camsi', 'CSS0011020' => 'camsi', 'CSS0011115' => 'camsi', 'CSS0011383' => 'camsi', 'CSS0011491' => 'camsi', 'CSS0011602' => 'camsi', 'CSS0011605' => 'camsi', 'CSS0011625' => 'camsi', 'CSS0011654' => 'camsi', 'CSS0011781' => 'camsi', 'CSS0011853' => 'camsi', 'CSS0011898' => 'camsi', 'CSS0011933' => 'camsi', 'CSS0011996' => 'camsi', 'CSS0012066' => 'camsi', 'CSS0012097' => 'camsi', 'CSS0012108' => 'camsi', 'CSS0012226' => 'camsi', 'CSS0012248' => 'camsi', 'CSS0012331' => 'camsi', 'CSS0012797' => 'camsi', 'CSS0012818' => 'camsi', 'CSS0012904' => 'camsi', 'CSS0013001' => 'camsi', 'CSS0013022' => 'camsi', 'CSS0013172' => 'camsi', 'CSS0013244' => 'camsi', 'CSS0013267' => 'camsi', 'CSS0013275' => 'camsi', 'CSS0013324' => 'camsi', 'CSS0013334' => 'camsi', 'CSS0013394' => 'camsi', 'CSS0013549' => 'camsi', 'CSS0013689' => 'camsi', 'CSS0014026' => 'camsi', 'CSS0014049' => 'camsi', 'CSS0014144' => 'camsi', 'CSS0014354' => 'camsi', 'CSS0014579' => 'camsi', 'CSS0014648' => 'camsi', 'CSS0014902' => 'camsi', 'CSS0014979' => 'camsi', 'CSS0015278' => 'camsi', 'CSS0015310' => 'camsi', 'CSS0015364' => 'camsi', 'CSS0015455' => 'camsi', 'CSS0015693' => 'camsi', 'CSS0015774' => 'camsi', 'CSS0015795' => 'camsi', 'CSS0015952' => 'camsi', 'CSS0016104' => 'camsi', 'CSS0016241' => 'camsi', 'CSS0016303' => 'camsi', 'CSS0016490' => 'camsi', 'CSS0016832' => 'camsi', 'CSS0016845' => 'camsi', 'CSS0016914' => 'camsi', 'CSS0016946' => 'camsi', 'CSS0017102' => 'camsi', 'CSS0017193' => 'camsi', 'CSS0017528' => 'camsi', 'CSS0017619' => 'camsi', 'CSS0017679' => 'camsi', 'CSS0017816' => 'camsi', 'CSS0017880' => 'camsi', 'CSS0018106' => 'camsi', 'CSS0018162' => 'camsi', 'CSS0018304' => 'camsi', 'CSS0018406' => 'camsi', 'CSS0018481' => 'camsi', 'CSS0018511' => 'camsi', 'CSS0018596' => 'camsi', 'CSS0018727' => 'camsi', 'CSS0018751' => 'camsi', 'CSS0018777' => 'camsi', 'CSS0018798' => 'camsi', 'CSS0019137' => 'camsi', 'CSS0019177' => 'camsi', 'CSS0019217' => 'camsi', 'CSS0019361' => 'camsi', 'CSS0019516' => 'camsi', 'CSS0019538' => 'camsi', 'CSS0019560' => 'camsi', 'CSS0019819' => 'camsi', 'CSS0019837' => 'camsi', 'CSS0019915' => 'camsi', 'CSS0019925' => 'camsi', 'CSS0020112' => 'camsi', 'CSS0020160' => 'camsi', 'CSS0020378' => 'camsi', 'CSS0020388' => 'camsi', 'CSS0020452' => 'camsi', 'CSS0020588' => 'camsi', 'CSS0020661' => 'camsi', 'CSS0020886' => 'camsi', 'CSS0020973' => 'camsi', 'CSS0021035' => 'camsi', 'CSS0021111' => 'camsi', 'CSS0021131' => 'camsi', 'CSS0021151' => 'camsi', 'CSS0021228' => 'camsi', 'CSS0021397' => 'camsi', 'CSS0021420' => 'camsi', 'CSS0021464' => 'camsi', 'CSS0021547' => 'camsi', 'CSS0021608' => 'camsi', 'CSS0021740' => 'camsi', 'CSS0021826' => 'camsi', 'CSS0021904' => 'camsi', 'CSS0021941' => 'camsi', 'CSS0022189' => 'camsi', 'CSS0022199' => 'camsi', 'CSS0022502' => 'camsi', 'CSS0022531' => 'camsi', 'CSS0022581' => 'camsi', 'CSS0022612' => 'camsi', 'CSS0022621' => 'camsi', 'CSS0022815' => 'camsi', 'CSS0022936' => 'camsi', 'CSS0022964' => 'camsi', 'CSS0022985' => 'camsi', 'CSS0023002' => 'camsi', 'CSS0023006' => 'camsi', 'CSS0023024' => 'camsi', 'CSS0023489' => 'camsi', 'CSS0023593' => 'camsi', 'CSS0023621' => 'camsi', 'CSS0023743' => 'camsi', 'CSS0023804' => 'camsi', 'CSS0023805' => 'camsi', 'CSS0023908' => 'camsi', 'CSS0023938' => 'camsi', 'CSS0023981' => 'camsi', 'CSS0024027' => 'camsi', 'CSS0024169' => 'camsi', 'CSS0024193' => 'camsi', 'CSS0024269' => 'camsi', 'CSS0024336' => 'camsi', 'CSS0024337' => 'camsi', 'CSS0024548' => 'camsi', 'CSS0024564' => 'camsi', 'CSS0024585' => 'camsi', 'CSS0024738' => 'camsi', 'CSS0024833' => 'camsi', 'CSS0024846' => 'camsi', 'CSS0024957' => 'camsi', 'CSS0024974' => 'camsi', 'CSS0025005' => 'camsi', 'CSS0025235' => 'camsi', 'CSS0025465' => 'camsi', 'CSS0025633' => 'camsi', 'CSS0025688' => 'camsi', 'CSS0025759' => 'camsi', 'CSS0025774' => 'camsi', 'CSS0025801' => 'camsi', 'CSS0025942' => 'camsi', 'CSS0026083' => 'camsi', 'CSS0026194' => 'camsi', 'CSS0026230' => 'camsi', 'CSS0026398' => 'camsi', 'CSS0026419' => 'camsi', 'CSS0026679' => 'camsi', 'CSS0026719' => 'camsi', 'CSS0026795' => 'camsi', 'CSS0026835' => 'camsi', 'CSS0026930' => 'camsi', 'CSS0027053' => 'camsi', 'CSS0027130' => 'camsi', 'CSS0027192' => 'camsi', 'CSS0027454' => 'camsi', 'CSS0027467' => 'camsi', 'CSS0027521' => 'camsi', 'CSS0027662' => 'camsi', 'CSS0027795' => 'camsi', 'CSS0027835' => 'camsi', 'CSS0027966' => 'camsi', 'CSS0028090' => 'camsi', 'CSS0028134' => 'camsi', 'CSS0028205' => 'camsi', 'CSS0028263' => 'camsi', 'CSS0028363' => 'camsi', 'CSS0028598' => 'camsi', 'CSS0029175' => 'camsi', 'CSS0029191' => 'camsi', 'CSS0029424' => 'camsi', 'CSS0029479' => 'camsi', 'CSS0029496' => 'camsi', 'CSS0029633' => 'camsi', 'CSS0029837' => 'camsi', 'CSS0029844' => 'camsi', 'CSS0029863' => 'camsi', 'CSS0029874' => 'camsi', 'CSS0029959' => 'camsi', 'CSS0030001' => 'camsi', 'CSS0030093' => 'camsi', 'CSS0030199' => 'camsi', 'CSS0030200' => 'camsi', 'CSS0030427' => 'camsi', 'CSS0030476' => 'camsi', 'CSS0030636' => 'camsi', 'CSS0030673' => 'camsi', 'CSS0030766' => 'camsi', 'CSS0030775' => 'camsi', 'CSS0030858' => 'camsi', 'CSS0030873' => 'camsi', 'CSS0030929' => 'camsi', 'CSS0031028' => 'camsi', 'CSS0031129' => 'camsi', 'CSS0031164' => 'camsi', 'CSS0031340' => 'camsi', 'CSS0031368' => 'camsi', 'CSS0031395' => 'camsi', 'CSS0031596' => 'camsi', 'CSS0031727' => 'camsi', 'CSS0032011' => 'camsi', 'CSS0032160' => 'camsi', 'CSS0032538' => 'camsi', 'CSS0032576' => 'camsi', 'CSS0032603' => 'camsi', 'CSS0032640' => 'camsi', 'CSS0032704' => 'camsi', 'CSS0032851' => 'camsi', 'CSS0032973' => 'camsi', 'CSS0033048' => 'camsi', 'CSS0033082' => 'camsi', 'CSS0033157' => 'camsi', 'CSS0033253' => 'camsi', 'CSS0033347' => 'camsi', 'CSS0033601' => 'camsi', 'CSS0033820' => 'camsi', 'CSS0033881' => 'camsi', 'CSS0033934' => 'camsi', 'CSS0034143' => 'camsi', 'CSS0034176' => 'camsi', 'CSS0034201' => 'camsi', 'CSS0034269' => 'camsi', 'CSS0034303' => 'camsi', 'CSS0034463' => 'camsi', 'CSS0034470' => 'camsi', 'CSS0034514' => 'camsi', 'CSS0034525' => 'camsi', 'CSS0034726' => 'camsi', 'CSS0034727' => 'camsi', 'CSS0034737' => 'camsi', 'CSS0034768' => 'camsi', 'CSS0034890' => 'camsi', 'CSS0034943' => 'camsi', 'CSS0034957' => 'camsi', 'CSS0034973' => 'camsi', 'CSS0035178' => 'camsi', 'CSS0035260' => 'camsi', 'CSS0035316' => 'camsi', 'CSS0035347' => 'camsi', 'CSS0035360' => 'camsi', 'CSS0035380' => 'camsi', 'CSS0035429' => 'camsi', 'CSS0035446' => 'camsi', 'CSS0035737' => 'camsi', 'CSS0035852' => 'camsi', 'CSS0035967' => 'camsi', 'CSS0036001' => 'camsi', 'CSS0036044' => 'camsi', 'CSS0036221' => 'camsi', 'CSS0036333' => 'camsi', 'CSS0036435' => 'camsi', 'CSS0036843' => 'camsi', 'CSS0036846' => 'camsi', 'CSS0037097' => 'camsi', 'CSS0037263' => 'camsi', 'CSS0037370' => 'camsi', 'CSS0037410' => 'camsi', 'CSS0037449' => 'camsi', 'CSS0037603' => 'camsi', 'CSS0037851' => 'camsi', 'CSS0037891' => 'camsi', 'CSS0037996' => 'camsi', 'CSS0038222' => 'camsi', 'CSS0038433' => 'camsi', 'CSS0038441' => 'camsi', 'CSS0038718' => 'camsi', 'CSS0038890' => 'camsi', 'CSS0039049' => 'camsi', 'CSS0039145' => 'camsi', 'CSS0039243' => 'camsi', 'CSS0039294' => 'camsi', 'CSS0039324' => 'camsi', 'CSS0039376' => 'camsi', 'CSS0039475' => 'camsi', 'CSS0039539' => 'camsi', 'CSS0039546' => 'camsi', 'CSS0039567' => 'camsi', 'CSS0039599' => 'camsi', 'CSS0039763' => 'camsi', 'CSS0039863' => 'camsi', 'CSS0040107' => 'camsi', 'CSS0040124' => 'camsi', 'CSS0040151' => 'camsi', 'CSS0040165' => 'camsi', 'CSS0040309' => 'camsi', 'CSS0040318' => 'camsi', 'CSS0040347' => 'camsi', 'CSS0040371' => 'camsi', 'CSS0040456' => 'camsi', 'CSS0040551' => 'camsi', 'CSS0040975' => 'camsi', 'CSS0040981' => 'camsi', 'CSS0041299' => 'camsi', 'CSS0041493' => 'camsi', 'CSS0041658' => 'camsi', 'CSS0041899' => 'camsi', 'CSS0041927' => 'camsi', 'CSS0042016' => 'camsi', 'CSS0042034' => 'camsi', 'CSS0042103' => 'camsi', 'CSS0042172' => 'camsi', 'CSS0042198' => 'camsi', 'CSS0042201' => 'camsi', 'CSS0042308' => 'camsi', 'CSS0042329' => 'camsi', 'CSS0042348' => 'camsi', 'CSS0042349' => 'camsi', 'CSS0042489' => 'camsi', 'CSS0042575' => 'camsi', 'CSS0042624' => 'camsi', 'CSS0042660' => 'camsi', 'CSS0042694' => 'camsi', 'CSS0042995' => 'camsi', 'CSS0043079' => 'camsi', 'CSS0043165' => 'camsi', 'CSS0043171' => 'camsi', 'CSS0043314' => 'camsi', 'CSS0043361' => 'camsi', 'CSS0043375' => 'camsi', 'CSS0043518' => 'camsi', 'CSS0043536' => 'camsi', 'CSS0043678' => 'camsi', 'CSS0043765' => 'camsi', 'CSS0043897' => 'camsi', 'CSS0043944' => 'camsi', 'CSS0044126' => 'camsi', 'CSS0044136' => 'camsi', 'CSS0044179' => 'camsi', 'CSS0044290' => 'camsi', 'CSS0044437' => 'camsi', 'CSS0044502' => 'camsi', 'CSS0044603' => 'camsi', 'CSS0044680' => 'camsi', 'CSS0044685' => 'camsi', 'CSS0044700' => 'camsi', 'CSS0044888' => 'camsi', 'CSS0044923' => 'camsi', 'CSS0044926' => 'camsi', 'CSS0044979' => 'camsi', 'CSS0045049' => 'camsi', 'CSS0045132' => 'camsi', 'CSS0045161' => 'camsi', 'CSS0045219' => 'camsi', 'CSS0045230' => 'camsi', 'CSS0045259' => 'camsi', 'CSS0045324' => 'camsi', 'CSS0045368' => 'camsi', 'CSS0045435' => 'camsi', 'CSS0045856' => 'camsi', 'CSS0045955' => 'camsi', 'CSS0046158' => 'camsi', 'CSS0046334' => 'camsi', 'CSS0046365' => 'camsi', 'CSS0046396' => 'camsi', 'CSS0046400' => 'camsi', 'CSS0046445' => 'camsi', 'CSS0046493' => 'camsi', 'CSS0046640' => 'camsi', 'CSS0046657' => 'camsi', 'CSS0046702' => 'camsi', 'CSS0047208' => 'camsi', 'CSS0047368' => 'camsi', 'CSS0047403' => 'camsi', 'CSS0047417' => 'camsi', 'CSS0047469' => 'camsi', 'CSS0047480' => 'camsi', 'CSS0047482' => 'camsi', 'CSS0047693' => 'camsi', 'CSS0047766' => 'camsi', 'CSS0047866' => 'camsi', 'CSS0047884' => 'camsi', 'CSS0048235' => 'camsi', 'CSS0048383' => 'camsi', 'CSS0048438' => 'camsi', 'CSS0048502' => 'camsi', 'CSS0048546' => 'camsi', 'CSS0048653' => 'camsi', 'CSS0048658' => 'camsi', 'CSS0048729' => 'camsi', 'CSS0048867' => 'camsi', 'CSS0048988' => 'camsi', 'CSS0049053' => 'camsi', 'CSS0049099' => 'camsi', 'CSS0049166' => 'camsi', 'CSS0049174' => 'camsi', 'CSS0049212' => 'camsi', 'CSS0049280' => 'camsi', 'CSS0049391' => 'camsi', 'CSS0049546' => 'camsi', 'CSS0049634' => 'camsi', 'CSS0049655' => 'camsi', 'CSS0049813' => 'camsi', 'CSS0049949' => 'camsi', 'CSS0050009' => 'camsi', 'CSS0050118' => 'camsi', 'CSS0050205' => 'camsi', 'CSS0050275' => 'camsi', 'CSS0050480' => 'camsi', 'CSS0050488' => 'camsi', 'CSS0050497' => 'camsi', 'Dinv03126' => 'din', 'Dinv13140' => 'din', 'Dinv13247' => 'din', 'Dinv14217' => 'din', 'EL10Ac9g22435' => 'bvu', 'FAN20G1200' => 'fan', 'PGR142G2516' => 'pgr', 'Prupe.3G160200' => 'ppe', 'Prupe.5G238200' => 'ppe', 'Prupe.7G047500' => 'ppe', 'QL03p045360' => 'qlo', 'QL05p034369' => 'qlo', 'QL05p034412' => 'qlo', 'QL08p017802' => 'qlo', 'QL08p024762' => 'qlo', 'QL10p026237' => 'qlo', 'QL10p032070' => 'qlo', 'QL11p003821' => 'qlo', 'Rhsim04G0057300' => 'rsi', 'Rhsim05G0049200' => 'rsi', 'Rhsim12G0010400' => 'rsi', 'Rhsim12G0012800' => 'rsi', 'TAR624G0483' => 'tar', 'TAR703G0001' => 'tar', 'vmacro05414' => 'vma', 'vmacro07091' => 'vma', 'vmacro07116' => 'vma', 'vmacro08423' => 'vma', 'vmacro09046' => 'vma', 'vmacro14269' => 'vma', 'vmacro16092' => 'vma', 'vmacro17280' => 'vma', 'vmacro19601' => 'vma' ), 'gf_id' => 'HOM05D001028', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001028' ), 'data_identifier' => 'HOM05D001028', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001028', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '590', 'num_species' => '12' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'Aqoxy1G01649' => 'aox', 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'CSS0035852' => 'camsi', 'CSS0035967' => 'camsi', 'CSS0036001' => 'camsi', 'CSS0036044' => 'camsi', 'CSS0036221' => 'camsi', 'CSS0036333' => 'camsi', 'CSS0036435' => 'camsi', 'CSS0036843' => 'camsi', 'CSS0036846' => 'camsi', 'CSS0037097' => 'camsi', 'CSS0037263' => 'camsi', 'CSS0037370' => 'camsi', 'CSS0037410' => 'camsi', 'CSS0037449' => 'camsi', 'CSS0037603' => 'camsi', 'CSS0037851' => 'camsi', 'CSS0037891' => 'camsi', 'CSS0037996' => 'camsi', 'CSS0038222' => 'camsi', 'CSS0038433' => 'camsi', 'CSS0038441' => 'camsi', 'CSS0038718' => 'camsi', 'CSS0038890' => 'camsi', 'CSS0039049' => 'camsi', 'CSS0039145' => 'camsi', 'CSS0039243' => 'camsi', 'CSS0039294' => 'camsi', 'CSS0039324' => 'camsi', 'CSS0039376' => 'camsi', 'CSS0039475' => 'camsi', 'CSS0039539' => 'camsi', 'CSS0039546' => 'camsi', 'CSS0039567' => 'camsi', 'CSS0039599' => 'camsi', 'CSS0039763' => 'camsi', 'CSS0039863' => 'camsi', 'CSS0040107' => 'camsi', 'CSS0040124' => 'camsi', 'CSS0040151' => 'camsi', 'CSS0040165' => 'camsi', 'CSS0040309' => 'camsi', 'CSS0040318' => 'camsi', 'CSS0040347' => 'camsi', 'CSS0040371' => 'camsi', 'CSS0040456' => 'camsi', 'CSS0040551' => 'camsi', 'CSS0040975' => 'camsi', 'CSS0040981' => 'camsi', 'CSS0041299' => 'camsi', 'CSS0041493' => 'camsi', 'CSS0041658' => 'camsi', 'CSS0041899' => 'camsi', 'CSS0041927' => 'camsi', 'CSS0042016' => 'camsi', 'CSS0042034' => 'camsi', 'CSS0042103' => 'camsi', 'CSS0042172' => 'camsi', 'CSS0042198' => 'camsi', 'CSS0042201' => 'camsi', 'CSS0042308' => 'camsi', 'CSS0042329' => 'camsi', 'CSS0042348' => 'camsi', 'CSS0042349' => 'camsi', 'CSS0042489' => 'camsi', 'CSS0042575' => 'camsi', 'CSS0042624' => 'camsi', 'CSS0042660' => 'camsi', 'CSS0042694' => 'camsi', 'CSS0042995' => 'camsi', 'CSS0043079' => 'camsi', 'CSS0043165' => 'camsi', 'CSS0043171' => 'camsi', 'CSS0043314' => 'camsi', 'CSS0043361' => 'camsi', 'CSS0043375' => 'camsi', 'CSS0043518' => 'camsi', 'CSS0043536' => 'camsi', 'CSS0043678' => 'camsi', 'CSS0043765' => 'camsi', 'CSS0043897' => 'camsi', 'CSS0043944' => 'camsi', 'CSS0044126' => 'camsi', 'CSS0044136' => 'camsi', 'CSS0044179' => 'camsi', 'CSS0044290' => 'camsi', 'CSS0044437' => 'camsi', 'CSS0044502' => 'camsi', 'CSS0044603' => 'camsi', 'CSS0044680' => 'camsi', 'CSS0044685' => 'camsi', 'CSS0044700' => 'camsi', 'CSS0044888' => 'camsi', 'CSS0044923' => 'camsi', 'CSS0044926' => 'camsi', 'CSS0044979' => 'camsi', 'CSS0045049' => 'camsi', 'CSS0045132' => 'camsi', 'CSS0045161' => 'camsi', 'CSS0045219' => 'camsi', 'CSS0045230' => 'camsi', 'CSS0045259' => 'camsi', 'CSS0045324' => 'camsi', 'CSS0045368' => 'camsi', 'CSS0045435' => 'camsi', 'CSS0045856' => 'camsi', 'CSS0045955' => 'camsi', 'CSS0046158' => 'camsi', 'CSS0046334' => 'camsi', 'CSS0046365' => 'camsi', 'CSS0046396' => 'camsi', 'CSS0046400' => 'camsi', 'CSS0046445' => 'camsi', 'CSS0046493' => 'camsi', 'CSS0046640' => 'camsi', 'CSS0046657' => 'camsi', 'CSS0046702' => 'camsi', 'CSS0047208' => 'camsi', 'CSS0047368' => 'camsi', 'CSS0047403' => 'camsi', 'CSS0047417' => 'camsi', 'CSS0047469' => 'camsi', 'CSS0047480' => 'camsi', 'CSS0047482' => 'camsi', 'CSS0047693' => 'camsi', 'CSS0047766' => 'camsi', 'CSS0047866' => 'camsi', 'CSS0047884' => 'camsi', 'CSS0048235' => 'camsi', 'CSS0048383' => 'camsi', 'CSS0048438' => 'camsi', 'CSS0048502' => 'camsi', 'CSS0048546' => 'camsi', 'CSS0048653' => 'camsi', 'CSS0048658' => 'camsi', 'CSS0048729' => 'camsi', 'CSS0048867' => 'camsi', 'CSS0048988' => 'camsi', 'CSS0049053' => 'camsi', 'CSS0049099' => 'camsi', 'CSS0049166' => 'camsi', 'CSS0049174' => 'camsi', 'CSS0049212' => 'camsi', 'CSS0049280' => 'camsi', 'CSS0049391' => 'camsi', 'CSS0049546' => 'camsi', 'CSS0049634' => 'camsi', 'CSS0049655' => 'camsi', 'CSS0049813' => 'camsi', 'CSS0049949' => 'camsi', 'CSS0050009' => 'camsi', 'CSS0050118' => 'camsi', 'CSS0050205' => 'camsi', 'CSS0050275' => 'camsi', 'CSS0050480' => 'camsi', 'CSS0050488' => 'camsi', 'CSS0050497' => 'camsi', 'Dinv03126' => 'din', 'Dinv13140' => 'din', 'Dinv13247' => 'din', 'Dinv14217' => 'din', 'EL10Ac9g22435' => 'bvu', 'FAN20G1200' => 'fan', 'PGR142G2516' => 'pgr', 'Prupe.3G160200' => 'ppe', 'Prupe.5G238200' => 'ppe', 'Prupe.7G047500' => 'ppe', 'QL03p045360' => 'qlo', 'QL05p034369' => 'qlo', 'QL05p034412' => 'qlo', 'QL08p017802' => 'qlo', 'QL08p024762' => 'qlo', 'QL10p026237' => 'qlo', 'QL10p032070' => 'qlo', 'QL11p003821' => 'qlo', 'Rhsim04G0057300' => 'rsi', 'Rhsim05G0049200' => 'rsi', 'Rhsim12G0010400' => 'rsi', 'Rhsim12G0012800' => 'rsi', 'TAR624G0483' => 'tar', 'TAR703G0001' => 'tar', 'vmacro05414' => 'vma', 'vmacro07091' => 'vma', 'vmacro07116' => 'vma', 'vmacro08423' => 'vma', 'vmacro09046' => 'vma', 'vmacro14269' => 'vma', 'vmacro16092' => 'vma', 'vmacro17280' => 'vma', 'vmacro19601' => 'vma' ) $gf_id = 'HOM05D001028' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001028' ) $data_identifier = 'HOM05D001028' $data_type = 'gf_id' $species_gene_counts = array( 'aox' => (int) 11, 'ccan' => (int) 6, 'camsi' => (int) 540, 'din' => (int) 4, 'bvu' => (int) 1, 'fan' => (int) 1, 'pgr' => (int) 1, 'ppe' => (int) 3, 'qlo' => (int) 8, 'rsi' => (int) 4, 'tar' => (int) 2, 'vma' => (int) 9 ) $gf_gene_species = 'vma' $gf_gene_id = 'vmacro19601' $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' => 'HOM05D001028', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '590', 'num_species' => '12' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'Aqoxy1G01649' => 'aox', 'Aqoxy1G02950' => 'aox', 'Aqoxy2G01005' => 'aox', 'Aqoxy2G01064' => 'aox', 'Aqoxy3G02267' => 'aox', 'Aqoxy3G02617' => 'aox', 'Aqoxy3G02693' => 'aox', 'Aqoxy5G03425' => 'aox', 'Aqoxy6G02164' => 'aox', 'Aqoxy6G02364' => 'aox', 'Aqoxy7G02284' => 'aox', 'Cc00_g09720' => 'ccan', 'Cc00_g21410' => 'ccan', 'Cc00_g31750' => 'ccan', 'Cc00_g34740' => 'ccan', 'Cc04_g16890' => 'ccan', 'Cc11_g03120' => 'ccan', 'CSS0000222' => 'camsi', 'CSS0000265' => 'camsi', 'CSS0000306' => 'camsi', 'CSS0000326' => 'camsi', 'CSS0000530' => 'camsi', 'CSS0000563' => 'camsi', 'CSS0000584' => 'camsi', 'CSS0000684' => 'camsi', 'CSS0001100' => 'camsi', 'CSS0001311' => 'camsi', 'CSS0001343' => 'camsi', 'CSS0001399' => 'camsi', 'CSS0001475' => 'camsi', 'CSS0001506' => 'camsi', 'CSS0001602' => 'camsi', 'CSS0001681' => 'camsi', 'CSS0001874' => 'camsi', 'CSS0001948' => 'camsi', 'CSS0002022' => 'camsi', 'CSS0002230' => 'camsi', 'CSS0002265' => 'camsi', 'CSS0002277' => 'camsi', 'CSS0002462' => 'camsi', 'CSS0002823' => 'camsi', 'CSS0003091' => 'camsi', 'CSS0003162' => 'camsi', 'CSS0003264' => 'camsi', 'CSS0003355' => 'camsi', 'CSS0003378' => 'camsi', 'CSS0003472' => 'camsi', 'CSS0003500' => 'camsi', 'CSS0003640' => 'camsi', 'CSS0003767' => 'camsi', 'CSS0003894' => 'camsi', 'CSS0003952' => 'camsi', 'CSS0003977' => 'camsi', 'CSS0004028' => 'camsi', 'CSS0004117' => 'camsi', 'CSS0004137' => 'camsi', 'CSS0004176' => 'camsi', 'CSS0004265' => 'camsi', 'CSS0004450' => 'camsi', 'CSS0004468' => 'camsi', 'CSS0004488' => 'camsi', 'CSS0004490' => 'camsi', 'CSS0004632' => 'camsi', 'CSS0004790' => 'camsi', 'CSS0004877' => 'camsi', 'CSS0004920' => 'camsi', 'CSS0004969' => 'camsi', 'CSS0005084' => 'camsi', 'CSS0005101' => 'camsi', 'CSS0005271' => 'camsi', 'CSS0005313' => 'camsi', 'CSS0005331' => 'camsi', 'CSS0005368' => 'camsi', 'CSS0005391' => 'camsi', 'CSS0005437' => 'camsi', 'CSS0005515' => 'camsi', 'CSS0005526' => 'camsi', 'CSS0005532' => 'camsi', 'CSS0005595' => 'camsi', 'CSS0005677' => 'camsi', 'CSS0005838' => 'camsi', 'CSS0005988' => 'camsi', 'CSS0006100' => 'camsi', 'CSS0006128' => 'camsi', 'CSS0006293' => 'camsi', 'CSS0006378' => 'camsi', 'CSS0006400' => 'camsi', 'CSS0006441' => 'camsi', 'CSS0006455' => 'camsi', 'CSS0006480' => 'camsi', 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'CSS0009986' => 'camsi', 'CSS0010182' => 'camsi', 'CSS0010202' => 'camsi', 'CSS0010330' => 'camsi', 'CSS0010362' => 'camsi', 'CSS0010456' => 'camsi', 'CSS0010472' => 'camsi', 'CSS0010507' => 'camsi', 'CSS0010512' => 'camsi', 'CSS0010520' => 'camsi', 'CSS0010617' => 'camsi', 'CSS0010706' => 'camsi', 'CSS0010747' => 'camsi', 'CSS0010816' => 'camsi', 'CSS0011020' => 'camsi', 'CSS0011115' => 'camsi', 'CSS0011383' => 'camsi', 'CSS0011491' => 'camsi', 'CSS0011602' => 'camsi', 'CSS0011605' => 'camsi', 'CSS0011625' => 'camsi', 'CSS0011654' => 'camsi', 'CSS0011781' => 'camsi', 'CSS0011853' => 'camsi', 'CSS0011898' => 'camsi', 'CSS0011933' => 'camsi', 'CSS0011996' => 'camsi', 'CSS0012066' => 'camsi', 'CSS0012097' => 'camsi', 'CSS0012108' => 'camsi', 'CSS0012226' => 'camsi', 'CSS0012248' => 'camsi', 'CSS0012331' => 'camsi', 'CSS0012797' => 'camsi', 'CSS0012818' => 'camsi', 'CSS0012904' => 'camsi', 'CSS0013001' => 'camsi', 'CSS0013022' => 'camsi', 'CSS0013172' => 'camsi', 'CSS0013244' => 'camsi', 'CSS0013267' => 'camsi', 'CSS0013275' => 'camsi', 'CSS0013324' => 'camsi', 'CSS0013334' => 'camsi', 'CSS0013394' => 'camsi', 'CSS0013549' => 'camsi', 'CSS0013689' => 'camsi', 'CSS0014026' => 'camsi', 'CSS0014049' => 'camsi', 'CSS0014144' => 'camsi', 'CSS0014354' => 'camsi', 'CSS0014579' => 'camsi', 'CSS0014648' => 'camsi', 'CSS0014902' => 'camsi', 'CSS0014979' => 'camsi', 'CSS0015278' => 'camsi', 'CSS0015310' => 'camsi', 'CSS0015364' => 'camsi', 'CSS0015455' => 'camsi', 'CSS0015693' => 'camsi', 'CSS0015774' => 'camsi', 'CSS0015795' => 'camsi', 'CSS0015952' => 'camsi', 'CSS0016104' => 'camsi', 'CSS0016241' => 'camsi', 'CSS0016303' => 'camsi', 'CSS0016490' => 'camsi', 'CSS0016832' => 'camsi', 'CSS0016845' => 'camsi', 'CSS0016914' => 'camsi', 'CSS0016946' => 'camsi', 'CSS0017102' => 'camsi', 'CSS0017193' => 'camsi', 'CSS0017528' => 'camsi', 'CSS0017619' => 'camsi', 'CSS0017679' => 'camsi', 'CSS0017816' => 'camsi', 'CSS0017880' => 'camsi', 'CSS0018106' => 'camsi', 'CSS0018162' => 'camsi', 'CSS0018304' => 'camsi', 'CSS0018406' => 'camsi', 'CSS0018481' => 'camsi', 'CSS0018511' => 'camsi', 'CSS0018596' => 'camsi', 'CSS0018727' => 'camsi', 'CSS0018751' => 'camsi', 'CSS0018777' => 'camsi', 'CSS0018798' => 'camsi', 'CSS0019137' => 'camsi', 'CSS0019177' => 'camsi', 'CSS0019217' => 'camsi', 'CSS0019361' => 'camsi', 'CSS0019516' => 'camsi', 'CSS0019538' => 'camsi', 'CSS0019560' => 'camsi', 'CSS0019819' => 'camsi', 'CSS0019837' => 'camsi', 'CSS0019915' => 'camsi', 'CSS0019925' => 'camsi', 'CSS0020112' => 'camsi', 'CSS0020160' => 'camsi', 'CSS0020378' => 'camsi', 'CSS0020388' => 'camsi', 'CSS0020452' => 'camsi', 'CSS0020588' => 'camsi', 'CSS0020661' => 'camsi', 'CSS0020886' => 'camsi', 'CSS0020973' => 'camsi', 'CSS0021035' => 'camsi', 'CSS0021111' => 'camsi', 'CSS0021131' => 'camsi', 'CSS0021151' => 'camsi', 'CSS0021228' => 'camsi', 'CSS0021397' => 'camsi', 'CSS0021420' => 'camsi', 'CSS0021464' => 'camsi', 'CSS0021547' => 'camsi', 'CSS0021608' => 'camsi', 'CSS0021740' => 'camsi', 'CSS0021826' => 'camsi', 'CSS0021904' => 'camsi', 'CSS0021941' => 'camsi', 'CSS0022189' => 'camsi', 'CSS0022199' => 'camsi', 'CSS0022502' => 'camsi', 'CSS0022531' => 'camsi', 'CSS0022581' => 'camsi', 'CSS0022612' => 'camsi', 'CSS0022621' => 'camsi', 'CSS0022815' => 'camsi', 'CSS0022936' => 'camsi', 'CSS0022964' => 'camsi', 'CSS0022985' => 'camsi', 'CSS0023002' => 'camsi', 'CSS0023006' => 'camsi', 'CSS0023024' => 'camsi', 'CSS0023489' => 'camsi', 'CSS0023593' => 'camsi', 'CSS0023621' => 'camsi', 'CSS0023743' => 'camsi', 'CSS0023804' => 'camsi', 'CSS0023805' => 'camsi', 'CSS0023908' => 'camsi', 'CSS0023938' => 'camsi', 'CSS0023981' => 'camsi', 'CSS0024027' => 'camsi', 'CSS0024169' => 'camsi', 'CSS0024193' => 'camsi', 'CSS0024269' => 'camsi', 'CSS0024336' => 'camsi', 'CSS0024337' => 'camsi', 'CSS0024548' => 'camsi', 'CSS0024564' => 'camsi', 'CSS0024585' => 'camsi', 'CSS0024738' => 'camsi', 'CSS0024833' => 'camsi', 'CSS0024846' => 'camsi', 'CSS0024957' => 'camsi', 'CSS0024974' => 'camsi', 'CSS0025005' => 'camsi', 'CSS0025235' => 'camsi', 'CSS0025465' => 'camsi', 'CSS0025633' => 'camsi', 'CSS0025688' => 'camsi', 'CSS0025759' => 'camsi', 'CSS0025774' => 'camsi', 'CSS0025801' => 'camsi', 'CSS0025942' => 'camsi', 'CSS0026083' => 'camsi', 'CSS0026194' => 'camsi', 'CSS0026230' => 'camsi', 'CSS0026398' => 'camsi', 'CSS0026419' => 'camsi', 'CSS0026679' => 'camsi', 'CSS0026719' => 'camsi', 'CSS0026795' => 'camsi', 'CSS0026835' => 'camsi', 'CSS0026930' => 'camsi', 'CSS0027053' => 'camsi', 'CSS0027130' => 'camsi', 'CSS0027192' => 'camsi', 'CSS0027454' => 'camsi', 'CSS0027467' => 'camsi', 'CSS0027521' => 'camsi', 'CSS0027662' => 'camsi', 'CSS0027795' => 'camsi', 'CSS0027835' => 'camsi', 'CSS0027966' => 'camsi', 'CSS0028090' => 'camsi', 'CSS0028134' => 'camsi', 'CSS0028205' => 'camsi', 'CSS0028263' => 'camsi', 'CSS0028363' => 'camsi', 'CSS0028598' => 'camsi', 'CSS0029175' => 'camsi', 'CSS0029191' => 'camsi', 'CSS0029424' => 'camsi', 'CSS0029479' => 'camsi', 'CSS0029496' => 'camsi', 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'CSS0033347' => 'camsi', 'CSS0033601' => 'camsi', 'CSS0033820' => 'camsi', 'CSS0033881' => 'camsi', 'CSS0033934' => 'camsi', 'CSS0034143' => 'camsi', 'CSS0034176' => 'camsi', 'CSS0034201' => 'camsi', 'CSS0034269' => 'camsi', 'CSS0034303' => 'camsi', 'CSS0034463' => 'camsi', 'CSS0034470' => 'camsi', 'CSS0034514' => 'camsi', 'CSS0034525' => 'camsi', 'CSS0034726' => 'camsi', 'CSS0034727' => 'camsi', 'CSS0034737' => 'camsi', 'CSS0034768' => 'camsi', 'CSS0034890' => 'camsi', 'CSS0034943' => 'camsi', 'CSS0034957' => 'camsi', 'CSS0034973' => 'camsi', 'CSS0035178' => 'camsi', 'CSS0035260' => 'camsi', 'CSS0035316' => 'camsi', 'CSS0035347' => 'camsi', 'CSS0035360' => 'camsi', 'CSS0035380' => 'camsi', 'CSS0035429' => 'camsi', 'CSS0035446' => 'camsi', 'CSS0035737' => 'camsi', 'CSS0035852' => 'camsi', 'CSS0035967' => 'camsi', 'CSS0036001' => 'camsi', 'CSS0036044' => 'camsi', 'CSS0036221' => 'camsi', 'CSS0036333' => 'camsi', 'CSS0036435' => 'camsi', 'CSS0036843' => 'camsi', 'CSS0036846' => 'camsi', 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'CSS0044685' => 'camsi', 'CSS0044700' => 'camsi', 'CSS0044888' => 'camsi', 'CSS0044923' => 'camsi', 'CSS0044926' => 'camsi', 'CSS0044979' => 'camsi', 'CSS0045049' => 'camsi', 'CSS0045132' => 'camsi', 'CSS0045161' => 'camsi', 'CSS0045219' => 'camsi', 'CSS0045230' => 'camsi', 'CSS0045259' => 'camsi', 'CSS0045324' => 'camsi', 'CSS0045368' => 'camsi', 'CSS0045435' => 'camsi', 'CSS0045856' => 'camsi', 'CSS0045955' => 'camsi', 'CSS0046158' => 'camsi', 'CSS0046334' => 'camsi', 'CSS0046365' => 'camsi', 'CSS0046396' => 'camsi', 'CSS0046400' => 'camsi', 'CSS0046445' => 'camsi', 'CSS0046493' => 'camsi', 'CSS0046640' => 'camsi', 'CSS0046657' => 'camsi', 'CSS0046702' => 'camsi', 'CSS0047208' => 'camsi', 'CSS0047368' => 'camsi', 'CSS0047403' => 'camsi', 'CSS0047417' => 'camsi', 'CSS0047469' => 'camsi', 'CSS0047480' => 'camsi', 'CSS0047482' => 'camsi', 'CSS0047693' => 'camsi', 'CSS0047766' => 'camsi', 'CSS0047866' => 'camsi', 'CSS0047884' => 'camsi', 'CSS0048235' => 'camsi', 'CSS0048383' => 'camsi', 'CSS0048438' => 'camsi', 'CSS0048502' => 'camsi', 'CSS0048546' => 'camsi', 'CSS0048653' => 'camsi', 'CSS0048658' => 'camsi', 'CSS0048729' => 'camsi', 'CSS0048867' => 'camsi', 'CSS0048988' => 'camsi', 'CSS0049053' => 'camsi', 'CSS0049099' => 'camsi', 'CSS0049166' => 'camsi', 'CSS0049174' => 'camsi', 'CSS0049212' => 'camsi', 'CSS0049280' => 'camsi', 'CSS0049391' => 'camsi', 'CSS0049546' => 'camsi', 'CSS0049634' => 'camsi', 'CSS0049655' => 'camsi', 'CSS0049813' => 'camsi', 'CSS0049949' => 'camsi', 'CSS0050009' => 'camsi', 'CSS0050118' => 'camsi', 'CSS0050205' => 'camsi', 'CSS0050275' => 'camsi', 'CSS0050480' => 'camsi', 'CSS0050488' => 'camsi', 'CSS0050497' => 'camsi', 'Dinv03126' => 'din', 'Dinv13140' => 'din', 'Dinv13247' => 'din', 'Dinv14217' => 'din', 'EL10Ac9g22435' => 'bvu', 'FAN20G1200' => 'fan', 'PGR142G2516' => 'pgr', 'Prupe.3G160200' => 'ppe', 'Prupe.5G238200' => 'ppe', 'Prupe.7G047500' => 'ppe', 'QL03p045360' => 'qlo', 'QL05p034369' => 'qlo', 'QL05p034412' => 'qlo', 'QL08p017802' => 'qlo', 'QL08p024762' => 'qlo', 'QL10p026237' => 'qlo', 'QL10p032070' => 'qlo', 'QL11p003821' => 'qlo', 'Rhsim04G0057300' => 'rsi', 'Rhsim05G0049200' => 'rsi', 'Rhsim12G0010400' => 'rsi', 'Rhsim12G0012800' => 'rsi', 'TAR624G0483' => 'tar', 'TAR703G0001' => 'tar', 'vmacro05414' => 'vma', 'vmacro07091' => 'vma', 'vmacro07116' => 'vma', 'vmacro08423' => 'vma', 'vmacro09046' => 'vma', 'vmacro14269' => 'vma', 'vmacro16092' => 'vma', 'vmacro17280' => 'vma', 'vmacro19601' => 'vma' ), 'gf_id' => 'HOM05D001028', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001028' ), 'data_identifier' => 'HOM05D001028', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001028', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '590', 'num_species' => '12' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'Aqoxy1G01649' => 'aox', 'Aqoxy1G02950' => 'aox', 'Aqoxy2G01005' => 'aox', 'Aqoxy2G01064' => 'aox', 'Aqoxy3G02267' => 'aox', 'Aqoxy3G02617' => 'aox', 'Aqoxy3G02693' => 'aox', 'Aqoxy5G03425' => 'aox', 'Aqoxy6G02164' => 'aox', 'Aqoxy6G02364' => 'aox', 'Aqoxy7G02284' => 'aox', 'Cc00_g09720' => 'ccan', 'Cc00_g21410' => 'ccan', 'Cc00_g31750' => 'ccan', 'Cc00_g34740' => 'ccan', 'Cc04_g16890' => 'ccan', 'Cc11_g03120' => 'ccan', 'CSS0000222' => 'camsi', 'CSS0000265' => 'camsi', 'CSS0000306' => 'camsi', 'CSS0000326' => 'camsi', 'CSS0000530' => 'camsi', 'CSS0000563' => 'camsi', 'CSS0000584' => 'camsi', 'CSS0000684' => 'camsi', 'CSS0001100' => 'camsi', 'CSS0001311' => 'camsi', 'CSS0001343' => 'camsi', 'CSS0001399' => 'camsi', 'CSS0001475' => 'camsi', 'CSS0001506' => 'camsi', 'CSS0001602' => 'camsi', 'CSS0001681' => 'camsi', 'CSS0001874' => 'camsi', 'CSS0001948' => 'camsi', 'CSS0002022' => 'camsi', 'CSS0002230' => 'camsi', 'CSS0002265' => 'camsi', 'CSS0002277' => 'camsi', 'CSS0002462' => 'camsi', 'CSS0002823' => 'camsi', 'CSS0003091' => 'camsi', 'CSS0003162' => 'camsi', 'CSS0003264' => 'camsi', 'CSS0003355' => 'camsi', 'CSS0003378' => 'camsi', 'CSS0003472' => 'camsi', 'CSS0003500' => 'camsi', 'CSS0003640' => 'camsi', 'CSS0003767' => 'camsi', 'CSS0003894' => 'camsi', 'CSS0003952' => 'camsi', 'CSS0003977' => 'camsi', 'CSS0004028' => 'camsi', 'CSS0004117' => 'camsi', 'CSS0004137' => 'camsi', 'CSS0004176' => 'camsi', 'CSS0004265' => 'camsi', 'CSS0004450' => 'camsi', 'CSS0004468' => 'camsi', 'CSS0004488' => 'camsi', 'CSS0004490' => 'camsi', 'CSS0004632' => 'camsi', 'CSS0004790' => 'camsi', 'CSS0004877' => 'camsi', 'CSS0004920' => 'camsi', 'CSS0004969' => 'camsi', 'CSS0005084' => 'camsi', 'CSS0005101' => 'camsi', 'CSS0005271' => 'camsi', 'CSS0005313' => 'camsi', 'CSS0005331' => 'camsi', 'CSS0005368' => 'camsi', 'CSS0005391' => 'camsi', 'CSS0005437' => 'camsi', 'CSS0005515' => 'camsi', 'CSS0005526' => 'camsi', 'CSS0005532' => 'camsi', 'CSS0005595' => 'camsi', 'CSS0005677' => 'camsi', 'CSS0005838' => 'camsi', 'CSS0005988' => 'camsi', 'CSS0006100' => 'camsi', 'CSS0006128' => 'camsi', 'CSS0006293' => 'camsi', 'CSS0006378' => 'camsi', 'CSS0006400' => 'camsi', 'CSS0006441' => 'camsi', 'CSS0006455' => 'camsi', 'CSS0006480' => 'camsi', 'CSS0006483' => 'camsi', 'CSS0006538' => 'camsi', 'CSS0006582' => 'camsi', 'CSS0006632' => 'camsi', 'CSS0006771' => 'camsi', 'CSS0006803' => 'camsi', 'CSS0006852' => 'camsi', 'CSS0006861' => 'camsi', 'CSS0006910' => 'camsi', 'CSS0007037' => 'camsi', 'CSS0007066' => 'camsi', 'CSS0007072' => 'camsi', 'CSS0007109' => 'camsi', 'CSS0007193' => 'camsi', 'CSS0007319' => 'camsi', 'CSS0007336' => 'camsi', 'CSS0007377' => 'camsi', 'CSS0007659' => 'camsi', 'CSS0007701' => 'camsi', 'CSS0007711' => 'camsi', 'CSS0007809' => 'camsi', 'CSS0008045' => 'camsi', 'CSS0008050' => 'camsi', 'CSS0008206' => 'camsi', 'CSS0008251' => 'camsi', 'CSS0008252' => 'camsi', 'CSS0008279' => 'camsi', 'CSS0008482' => 'camsi', 'CSS0008583' => 'camsi', 'CSS0008699' => 'camsi', 'CSS0008798' => 'camsi', 'CSS0008971' => 'camsi', 'CSS0009019' => 'camsi', 'CSS0009191' => 'camsi', 'CSS0009241' => 'camsi', 'CSS0009246' => 'camsi', 'CSS0009399' => 'camsi', 'CSS0009654' => 'camsi', 'CSS0009722' => 'camsi', 'CSS0009920' => 'camsi', 'CSS0009986' => 'camsi', 'CSS0010182' => 'camsi', 'CSS0010202' => 'camsi', 'CSS0010330' => 'camsi', 'CSS0010362' => 'camsi', 'CSS0010456' => 'camsi', 'CSS0010472' => 'camsi', 'CSS0010507' => 'camsi', 'CSS0010512' => 'camsi', 'CSS0010520' => 'camsi', 'CSS0010617' => 'camsi', 'CSS0010706' => 'camsi', 'CSS0010747' => 'camsi', 'CSS0010816' => 'camsi', 'CSS0011020' => 'camsi', 'CSS0011115' => 'camsi', 'CSS0011383' => 'camsi', 'CSS0011491' => 'camsi', 'CSS0011602' => 'camsi', 'CSS0011605' => 'camsi', 'CSS0011625' => 'camsi', 'CSS0011654' => 'camsi', 'CSS0011781' => 'camsi', 'CSS0011853' => 'camsi', 'CSS0011898' => 'camsi', 'CSS0011933' => 'camsi', 'CSS0011996' => 'camsi', 'CSS0012066' => 'camsi', 'CSS0012097' => 'camsi', 'CSS0012108' => 'camsi', 'CSS0012226' => 'camsi', 'CSS0012248' => 'camsi', 'CSS0012331' => 'camsi', 'CSS0012797' => 'camsi', 'CSS0012818' => 'camsi', 'CSS0012904' => 'camsi', 'CSS0013001' => 'camsi', 'CSS0013022' => 'camsi', 'CSS0013172' => 'camsi', 'CSS0013244' => 'camsi', 'CSS0013267' => 'camsi', 'CSS0013275' => 'camsi', 'CSS0013324' => 'camsi', 'CSS0013334' => 'camsi', 'CSS0013394' => 'camsi', 'CSS0013549' => 'camsi', 'CSS0013689' => 'camsi', 'CSS0014026' => 'camsi', 'CSS0014049' => 'camsi', 'CSS0014144' => 'camsi', 'CSS0014354' => 'camsi', 'CSS0014579' => 'camsi', 'CSS0014648' => 'camsi', 'CSS0014902' => 'camsi', 'CSS0014979' => 'camsi', 'CSS0015278' => 'camsi', 'CSS0015310' => 'camsi', 'CSS0015364' => 'camsi', 'CSS0015455' => 'camsi', 'CSS0015693' => 'camsi', 'CSS0015774' => 'camsi', 'CSS0015795' => 'camsi', 'CSS0015952' => 'camsi', 'CSS0016104' => 'camsi', 'CSS0016241' => 'camsi', 'CSS0016303' => 'camsi', 'CSS0016490' => 'camsi', 'CSS0016832' => 'camsi', 'CSS0016845' => 'camsi', 'CSS0016914' => 'camsi', 'CSS0016946' => 'camsi', 'CSS0017102' => 'camsi', 'CSS0017193' => 'camsi', 'CSS0017528' => 'camsi', 'CSS0017619' => 'camsi', 'CSS0017679' => 'camsi', 'CSS0017816' => 'camsi', 'CSS0017880' => 'camsi', 'CSS0018106' => 'camsi', 'CSS0018162' => 'camsi', 'CSS0018304' => 'camsi', 'CSS0018406' => 'camsi', 'CSS0018481' => 'camsi', 'CSS0018511' => 'camsi', 'CSS0018596' => 'camsi', 'CSS0018727' => 'camsi', 'CSS0018751' => 'camsi', 'CSS0018777' => 'camsi', 'CSS0018798' => 'camsi', 'CSS0019137' => 'camsi', 'CSS0019177' => 'camsi', 'CSS0019217' => 'camsi', 'CSS0019361' => 'camsi', 'CSS0019516' => 'camsi', 'CSS0019538' => 'camsi', 'CSS0019560' => 'camsi', 'CSS0019819' => 'camsi', 'CSS0019837' => 'camsi', 'CSS0019915' => 'camsi', 'CSS0019925' => 'camsi', 'CSS0020112' => 'camsi', 'CSS0020160' => 'camsi', 'CSS0020378' => 'camsi', 'CSS0020388' => 'camsi', 'CSS0020452' => 'camsi', 'CSS0020588' => 'camsi', 'CSS0020661' => 'camsi', 'CSS0020886' => 'camsi', 'CSS0020973' => 'camsi', 'CSS0021035' => 'camsi', 'CSS0021111' => 'camsi', 'CSS0021131' => 'camsi', 'CSS0021151' => 'camsi', 'CSS0021228' => 'camsi', 'CSS0021397' => 'camsi', 'CSS0021420' => 'camsi', 'CSS0021464' => 'camsi', 'CSS0021547' => 'camsi', 'CSS0021608' => 'camsi', 'CSS0021740' => 'camsi', 'CSS0021826' => 'camsi', 'CSS0021904' => 'camsi', 'CSS0021941' => 'camsi', 'CSS0022189' => 'camsi', 'CSS0022199' => 'camsi', 'CSS0022502' => 'camsi', 'CSS0022531' => 'camsi', 'CSS0022581' => 'camsi', 'CSS0022612' => 'camsi', 'CSS0022621' => 'camsi', 'CSS0022815' => 'camsi', 'CSS0022936' => 'camsi', 'CSS0022964' => 'camsi', 'CSS0022985' => 'camsi', 'CSS0023002' => 'camsi', 'CSS0023006' => 'camsi', 'CSS0023024' => 'camsi', 'CSS0023489' => 'camsi', 'CSS0023593' => 'camsi', 'CSS0023621' => 'camsi', 'CSS0023743' => 'camsi', 'CSS0023804' => 'camsi', 'CSS0023805' => 'camsi', 'CSS0023908' => 'camsi', 'CSS0023938' => 'camsi', 'CSS0023981' => 'camsi', 'CSS0024027' => 'camsi', 'CSS0024169' => 'camsi', 'CSS0024193' => 'camsi', 'CSS0024269' => 'camsi', 'CSS0024336' => 'camsi', 'CSS0024337' => 'camsi', 'CSS0024548' => 'camsi', 'CSS0024564' => 'camsi', 'CSS0024585' => 'camsi', 'CSS0024738' => 'camsi', 'CSS0024833' => 'camsi', 'CSS0024846' => 'camsi', 'CSS0024957' => 'camsi', 'CSS0024974' => 'camsi', 'CSS0025005' => 'camsi', 'CSS0025235' => 'camsi', 'CSS0025465' => 'camsi', 'CSS0025633' => 'camsi', 'CSS0025688' => 'camsi', 'CSS0025759' => 'camsi', 'CSS0025774' => 'camsi', 'CSS0025801' => 'camsi', 'CSS0025942' => 'camsi', 'CSS0026083' => 'camsi', 'CSS0026194' => 'camsi', 'CSS0026230' => 'camsi', 'CSS0026398' => 'camsi', 'CSS0026419' => 'camsi', 'CSS0026679' => 'camsi', 'CSS0026719' => 'camsi', 'CSS0026795' => 'camsi', 'CSS0026835' => 'camsi', 'CSS0026930' => 'camsi', 'CSS0027053' => 'camsi', 'CSS0027130' => 'camsi', 'CSS0027192' => 'camsi', 'CSS0027454' => 'camsi', 'CSS0027467' => 'camsi', 'CSS0027521' => 'camsi', 'CSS0027662' => 'camsi', 'CSS0027795' => 'camsi', 'CSS0027835' => 'camsi', 'CSS0027966' => 'camsi', 'CSS0028090' => 'camsi', 'CSS0028134' => 'camsi', 'CSS0028205' => 'camsi', 'CSS0028263' => 'camsi', 'CSS0028363' => 'camsi', 'CSS0028598' => 'camsi', 'CSS0029175' => 'camsi', 'CSS0029191' => 'camsi', 'CSS0029424' => 'camsi', 'CSS0029479' => 'camsi', 'CSS0029496' => 'camsi', 'CSS0029633' => 'camsi', 'CSS0029837' => 'camsi', 'CSS0029844' => 'camsi', 'CSS0029863' => 'camsi', 'CSS0029874' => 'camsi', 'CSS0029959' => 'camsi', 'CSS0030001' => 'camsi', 'CSS0030093' => 'camsi', 'CSS0030199' => 'camsi', 'CSS0030200' => 'camsi', 'CSS0030427' => 'camsi', 'CSS0030476' => 'camsi', 'CSS0030636' => 'camsi', 'CSS0030673' => 'camsi', 'CSS0030766' => 'camsi', 'CSS0030775' => 'camsi', 'CSS0030858' => 'camsi', 'CSS0030873' => 'camsi', 'CSS0030929' => 'camsi', 'CSS0031028' => 'camsi', 'CSS0031129' => 'camsi', 'CSS0031164' => 'camsi', 'CSS0031340' => 'camsi', 'CSS0031368' => 'camsi', 'CSS0031395' => 'camsi', 'CSS0031596' => 'camsi', 'CSS0031727' => 'camsi', 'CSS0032011' => 'camsi', 'CSS0032160' => 'camsi', 'CSS0032538' => 'camsi', 'CSS0032576' => 'camsi', 'CSS0032603' => 'camsi', 'CSS0032640' => 'camsi', 'CSS0032704' => 'camsi', 'CSS0032851' => 'camsi', 'CSS0032973' => 'camsi', 'CSS0033048' => 'camsi', 'CSS0033082' => 'camsi', 'CSS0033157' => 'camsi', 'CSS0033253' => 'camsi', 'CSS0033347' => 'camsi', 'CSS0033601' => 'camsi', 'CSS0033820' => 'camsi', 'CSS0033881' => 'camsi', 'CSS0033934' => 'camsi', 'CSS0034143' => 'camsi', 'CSS0034176' => 'camsi', 'CSS0034201' => 'camsi', 'CSS0034269' => 'camsi', 'CSS0034303' => 'camsi', 'CSS0034463' => 'camsi', 'CSS0034470' => 'camsi', 'CSS0034514' => 'camsi', 'CSS0034525' => 'camsi', 'CSS0034726' => 'camsi', 'CSS0034727' => 'camsi', 'CSS0034737' => 'camsi', 'CSS0034768' => 'camsi', 'CSS0034890' => 'camsi', 'CSS0034943' => 'camsi', 'CSS0034957' => 'camsi', 'CSS0034973' => 'camsi', 'CSS0035178' => 'camsi', 'CSS0035260' => 'camsi', 'CSS0035316' => 'camsi', 'CSS0035347' => 'camsi', 'CSS0035360' => 'camsi', 'CSS0035380' => 'camsi', 'CSS0035429' => 'camsi', 'CSS0035446' => 'camsi', 'CSS0035737' => 'camsi', 'CSS0035852' => 'camsi', 'CSS0035967' => 'camsi', 'CSS0036001' => 'camsi', 'CSS0036044' => 'camsi', 'CSS0036221' => 'camsi', 'CSS0036333' => 'camsi', 'CSS0036435' => 'camsi', 'CSS0036843' => 'camsi', 'CSS0036846' => 'camsi', 'CSS0037097' => 'camsi', 'CSS0037263' => 'camsi', 'CSS0037370' => 'camsi', 'CSS0037410' => 'camsi', 'CSS0037449' => 'camsi', 'CSS0037603' => 'camsi', 'CSS0037851' => 'camsi', 'CSS0037891' => 'camsi', 'CSS0037996' => 'camsi', 'CSS0038222' => 'camsi', 'CSS0038433' => 'camsi', 'CSS0038441' => 'camsi', 'CSS0038718' => 'camsi', 'CSS0038890' => 'camsi', 'CSS0039049' => 'camsi', 'CSS0039145' => 'camsi', 'CSS0039243' => 'camsi', 'CSS0039294' => 'camsi', 'CSS0039324' => 'camsi', 'CSS0039376' => 'camsi', 'CSS0039475' => 'camsi', 'CSS0039539' => 'camsi', 'CSS0039546' => 'camsi', 'CSS0039567' => 'camsi', 'CSS0039599' => 'camsi', 'CSS0039763' => 'camsi', 'CSS0039863' => 'camsi', 'CSS0040107' => 'camsi', 'CSS0040124' => 'camsi', 'CSS0040151' => 'camsi', 'CSS0040165' => 'camsi', 'CSS0040309' => 'camsi', 'CSS0040318' => 'camsi', 'CSS0040347' => 'camsi', 'CSS0040371' => 'camsi', 'CSS0040456' => 'camsi', 'CSS0040551' => 'camsi', 'CSS0040975' => 'camsi', 'CSS0040981' => 'camsi', 'CSS0041299' => 'camsi', 'CSS0041493' => 'camsi', 'CSS0041658' => 'camsi', 'CSS0041899' => 'camsi', 'CSS0041927' => 'camsi', 'CSS0042016' => 'camsi', 'CSS0042034' => 'camsi', 'CSS0042103' => 'camsi', 'CSS0042172' => 'camsi', 'CSS0042198' => 'camsi', 'CSS0042201' => 'camsi', 'CSS0042308' => 'camsi', 'CSS0042329' => 'camsi', 'CSS0042348' => 'camsi', 'CSS0042349' => 'camsi', 'CSS0042489' => 'camsi', 'CSS0042575' => 'camsi', 'CSS0042624' => 'camsi', 'CSS0042660' => 'camsi', 'CSS0042694' => 'camsi', 'CSS0042995' => 'camsi', 'CSS0043079' => 'camsi', 'CSS0043165' => 'camsi', 'CSS0043171' => 'camsi', 'CSS0043314' => 'camsi', 'CSS0043361' => 'camsi', 'CSS0043375' => 'camsi', 'CSS0043518' => 'camsi', 'CSS0043536' => 'camsi', 'CSS0043678' => 'camsi', 'CSS0043765' => 'camsi', 'CSS0043897' => 'camsi', 'CSS0043944' => 'camsi', 'CSS0044126' => 'camsi', 'CSS0044136' => 'camsi', 'CSS0044179' => 'camsi', 'CSS0044290' => 'camsi', 'CSS0044437' => 'camsi', 'CSS0044502' => 'camsi', 'CSS0044603' => 'camsi', 'CSS0044680' => 'camsi', 'CSS0044685' => 'camsi', 'CSS0044700' => 'camsi', 'CSS0044888' => 'camsi', 'CSS0044923' => 'camsi', 'CSS0044926' => 'camsi', 'CSS0044979' => 'camsi', 'CSS0045049' => 'camsi', 'CSS0045132' => 'camsi', 'CSS0045161' => 'camsi', 'CSS0045219' => 'camsi', 'CSS0045230' => 'camsi', 'CSS0045259' => 'camsi', 'CSS0045324' => 'camsi', 'CSS0045368' => 'camsi', 'CSS0045435' => 'camsi', 'CSS0045856' => 'camsi', 'CSS0045955' => 'camsi', 'CSS0046158' => 'camsi', 'CSS0046334' => 'camsi', 'CSS0046365' => 'camsi', 'CSS0046396' => 'camsi', 'CSS0046400' => 'camsi', 'CSS0046445' => 'camsi', 'CSS0046493' => 'camsi', 'CSS0046640' => 'camsi', 'CSS0046657' => 'camsi', 'CSS0046702' => 'camsi', 'CSS0047208' => 'camsi', 'CSS0047368' => 'camsi', 'CSS0047403' => 'camsi', 'CSS0047417' => 'camsi', 'CSS0047469' => 'camsi', 'CSS0047480' => 'camsi', 'CSS0047482' => 'camsi', 'CSS0047693' => 'camsi', 'CSS0047766' => 'camsi', 'CSS0047866' => 'camsi', 'CSS0047884' => 'camsi', 'CSS0048235' => 'camsi', 'CSS0048383' => 'camsi', 'CSS0048438' => 'camsi', 'CSS0048502' => 'camsi', 'CSS0048546' => 'camsi', 'CSS0048653' => 'camsi', 'CSS0048658' => 'camsi', 'CSS0048729' => 'camsi', 'CSS0048867' => 'camsi', 'CSS0048988' => 'camsi', 'CSS0049053' => 'camsi', 'CSS0049099' => 'camsi', 'CSS0049166' => 'camsi', 'CSS0049174' => 'camsi', 'CSS0049212' => 'camsi', 'CSS0049280' => 'camsi', 'CSS0049391' => 'camsi', 'CSS0049546' => 'camsi', 'CSS0049634' => 'camsi', 'CSS0049655' => 'camsi', 'CSS0049813' => 'camsi', 'CSS0049949' => 'camsi', 'CSS0050009' => 'camsi', 'CSS0050118' => 'camsi', 'CSS0050205' => 'camsi', 'CSS0050275' => 'camsi', 'CSS0050480' => 'camsi', 'CSS0050488' => 'camsi', 'CSS0050497' => 'camsi', 'Dinv03126' => 'din', 'Dinv13140' => 'din', 'Dinv13247' => 'din', 'Dinv14217' => 'din', 'EL10Ac9g22435' => 'bvu', 'FAN20G1200' => 'fan', 'PGR142G2516' => 'pgr', 'Prupe.3G160200' => 'ppe', 'Prupe.5G238200' => 'ppe', 'Prupe.7G047500' => 'ppe', 'QL03p045360' => 'qlo', 'QL05p034369' => 'qlo', 'QL05p034412' => 'qlo', 'QL08p017802' => 'qlo', 'QL08p024762' => 'qlo', 'QL10p026237' => 'qlo', 'QL10p032070' => 'qlo', 'QL11p003821' => 'qlo', 'Rhsim04G0057300' => 'rsi', 'Rhsim05G0049200' => 'rsi', 'Rhsim12G0010400' => 'rsi', 'Rhsim12G0012800' => 'rsi', 'TAR624G0483' => 'tar', 'TAR703G0001' => 'tar', 'vmacro05414' => 'vma', 'vmacro07091' => 'vma', 'vmacro07116' => 'vma', 'vmacro08423' => 'vma', 'vmacro09046' => 'vma', 'vmacro14269' => 'vma', 'vmacro16092' => 'vma', 'vmacro17280' => 'vma', 'vmacro19601' => 'vma' ) $gf_id = 'HOM05D001028' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001028' ) $data_identifier = 'HOM05D001028' $data_type = 'gf_id' $species_gene_counts = array( 'aox' => (int) 11, 'ccan' => (int) 6, 'camsi' => (int) 540, 'din' => (int) 4, 'bvu' => (int) 1, 'fan' => (int) 1, 'pgr' => (int) 1, 'ppe' => (int) 3, 'qlo' => (int) 8, 'rsi' => (int) 4, 'tar' => (int) 2, 'vma' => (int) 9 ) $gf_gene_species = 'vma' $gf_gene_id = 'vmacro19601' $species_info = array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ) $local_species = 'ccan' $disabled = '' $selected = '' $num_hits = (int) 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' => 'HOM05D001028', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '590', 'num_species' => '12' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'Aqoxy1G01649' => 'aox', 'Aqoxy1G02950' => 'aox', 'Aqoxy2G01005' => 'aox', 'Aqoxy2G01064' => 'aox', 'Aqoxy3G02267' => 'aox', 'Aqoxy3G02617' => 'aox', 'Aqoxy3G02693' => 'aox', 'Aqoxy5G03425' => 'aox', 'Aqoxy6G02164' => 'aox', 'Aqoxy6G02364' => 'aox', 'Aqoxy7G02284' => 'aox', 'Cc00_g09720' => 'ccan', 'Cc00_g21410' => 'ccan', 'Cc00_g31750' => 'ccan', 'Cc00_g34740' => 'ccan', 'Cc04_g16890' => 'ccan', 'Cc11_g03120' => 'ccan', 'CSS0000222' => 'camsi', 'CSS0000265' => 'camsi', 'CSS0000306' => 'camsi', 'CSS0000326' => 'camsi', 'CSS0000530' => 'camsi', 'CSS0000563' => 'camsi', 'CSS0000584' => 'camsi', 'CSS0000684' => 'camsi', 'CSS0001100' => 'camsi', 'CSS0001311' => 'camsi', 'CSS0001343' => 'camsi', 'CSS0001399' => 'camsi', 'CSS0001475' => 'camsi', 'CSS0001506' => 'camsi', 'CSS0001602' => 'camsi', 'CSS0001681' => 'camsi', 'CSS0001874' => 'camsi', 'CSS0001948' => 'camsi', 'CSS0002022' => 'camsi', 'CSS0002230' => 'camsi', 'CSS0002265' => 'camsi', 'CSS0002277' => 'camsi', 'CSS0002462' => 'camsi', 'CSS0002823' => 'camsi', 'CSS0003091' => 'camsi', 'CSS0003162' => 'camsi', 'CSS0003264' => 'camsi', 'CSS0003355' => 'camsi', 'CSS0003378' => 'camsi', 'CSS0003472' => 'camsi', 'CSS0003500' => 'camsi', 'CSS0003640' => 'camsi', 'CSS0003767' => 'camsi', 'CSS0003894' => 'camsi', 'CSS0003952' => 'camsi', 'CSS0003977' => 'camsi', 'CSS0004028' => 'camsi', 'CSS0004117' => 'camsi', 'CSS0004137' => 'camsi', 'CSS0004176' => 'camsi', 'CSS0004265' => 'camsi', 'CSS0004450' => 'camsi', 'CSS0004468' => 'camsi', 'CSS0004488' => 'camsi', 'CSS0004490' => 'camsi', 'CSS0004632' => 'camsi', 'CSS0004790' => 'camsi', 'CSS0004877' => 'camsi', 'CSS0004920' => 'camsi', 'CSS0004969' => 'camsi', 'CSS0005084' => 'camsi', 'CSS0005101' => 'camsi', 'CSS0005271' => 'camsi', 'CSS0005313' => 'camsi', 'CSS0005331' => 'camsi', 'CSS0005368' => 'camsi', 'CSS0005391' => 'camsi', 'CSS0005437' => 'camsi', 'CSS0005515' => 'camsi', 'CSS0005526' => 'camsi', 'CSS0005532' => 'camsi', 'CSS0005595' => 'camsi', 'CSS0005677' => 'camsi', 'CSS0005838' => 'camsi', 'CSS0005988' => 'camsi', 'CSS0006100' => 'camsi', 'CSS0006128' => 'camsi', 'CSS0006293' => 'camsi', 'CSS0006378' => 'camsi', 'CSS0006400' => 'camsi', 'CSS0006441' => 'camsi', 'CSS0006455' => 'camsi', 'CSS0006480' => 'camsi', 'CSS0006483' => 'camsi', 'CSS0006538' => 'camsi', 'CSS0006582' => 'camsi', 'CSS0006632' => 'camsi', 'CSS0006771' => 'camsi', 'CSS0006803' => 'camsi', 'CSS0006852' => 'camsi', 'CSS0006861' => 'camsi', 'CSS0006910' => 'camsi', 'CSS0007037' => 'camsi', 'CSS0007066' => 'camsi', 'CSS0007072' => 'camsi', 'CSS0007109' => 'camsi', 'CSS0007193' => 'camsi', 'CSS0007319' => 'camsi', 'CSS0007336' => 'camsi', 'CSS0007377' => 'camsi', 'CSS0007659' => 'camsi', 'CSS0007701' => 'camsi', 'CSS0007711' => 'camsi', 'CSS0007809' => 'camsi', 'CSS0008045' => 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array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001028' ), 'data_identifier' => 'HOM05D001028', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001028', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '590', 'num_species' => '12' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'Aqoxy1G01649' => 'aox', 'Aqoxy1G02950' => 'aox', 'Aqoxy2G01005' => 'aox', 'Aqoxy2G01064' => 'aox', 'Aqoxy3G02267' => 'aox', 'Aqoxy3G02617' => 'aox', 'Aqoxy3G02693' => 'aox', 'Aqoxy5G03425' => 'aox', 'Aqoxy6G02164' => 'aox', 'Aqoxy6G02364' => 'aox', 'Aqoxy7G02284' => 'aox', 'Cc00_g09720' => 'ccan', 'Cc00_g21410' => 'ccan', 'Cc00_g31750' => 'ccan', 'Cc00_g34740' => 'ccan', 'Cc04_g16890' => 'ccan', 'Cc11_g03120' => 'ccan', 'CSS0000222' => 'camsi', 'CSS0000265' => 'camsi', 'CSS0000306' => 'camsi', 'CSS0000326' => 'camsi', 'CSS0000530' => 'camsi', 'CSS0000563' => 'camsi', 'CSS0000584' => 'camsi', 'CSS0000684' => 'camsi', 'CSS0001100' => 'camsi', 'CSS0001311' => 'camsi', 'CSS0001343' => 'camsi', 'CSS0001399' => 'camsi', 'CSS0001475' => 'camsi', 'CSS0001506' => 'camsi', 'CSS0001602' => 'camsi', 'CSS0001681' => 'camsi', 'CSS0001874' => 'camsi', 'CSS0001948' => 'camsi', 'CSS0002022' => 'camsi', 'CSS0002230' => 'camsi', 'CSS0002265' => 'camsi', 'CSS0002277' => 'camsi', 'CSS0002462' => 'camsi', 'CSS0002823' => 'camsi', 'CSS0003091' => 'camsi', 'CSS0003162' => 'camsi', 'CSS0003264' => 'camsi', 'CSS0003355' => 'camsi', 'CSS0003378' => 'camsi', 'CSS0003472' => 'camsi', 'CSS0003500' => 'camsi', 'CSS0003640' => 'camsi', 'CSS0003767' => 'camsi', 'CSS0003894' => 'camsi', 'CSS0003952' => 'camsi', 'CSS0003977' => 'camsi', 'CSS0004028' => 'camsi', 'CSS0004117' => 'camsi', 'CSS0004137' => 'camsi', 'CSS0004176' => 'camsi', 'CSS0004265' => 'camsi', 'CSS0004450' => 'camsi', 'CSS0004468' => 'camsi', 'CSS0004488' => 'camsi', 'CSS0004490' => 'camsi', 'CSS0004632' => 'camsi', 'CSS0004790' => 'camsi', 'CSS0004877' => 'camsi', 'CSS0004920' => 'camsi', 'CSS0004969' => 'camsi', 'CSS0005084' => 'camsi', 'CSS0005101' => 'camsi', 'CSS0005271' => 'camsi', 'CSS0005313' => 'camsi', 'CSS0005331' => 'camsi', 'CSS0005368' => 'camsi', 'CSS0005391' => 'camsi', 'CSS0005437' => 'camsi', 'CSS0005515' => 'camsi', 'CSS0005526' => 'camsi', 'CSS0005532' => 'camsi', 'CSS0005595' => 'camsi', 'CSS0005677' => 'camsi', 'CSS0005838' => 'camsi', 'CSS0005988' => 'camsi', 'CSS0006100' => 'camsi', 'CSS0006128' => 'camsi', 'CSS0006293' => 'camsi', 'CSS0006378' => 'camsi', 'CSS0006400' => 'camsi', 'CSS0006441' => 'camsi', 'CSS0006455' => 'camsi', 'CSS0006480' => 'camsi', 'CSS0006483' => 'camsi', 'CSS0006538' => 'camsi', 'CSS0006582' => 'camsi', 'CSS0006632' => 'camsi', 'CSS0006771' => 'camsi', 'CSS0006803' => 'camsi', 'CSS0006852' => 'camsi', 'CSS0006861' => 'camsi', 'CSS0006910' => 'camsi', 'CSS0007037' => 'camsi', 'CSS0007066' => 'camsi', 'CSS0007072' => 'camsi', 'CSS0007109' => 'camsi', 'CSS0007193' => 'camsi', 'CSS0007319' => 'camsi', 'CSS0007336' => 'camsi', 'CSS0007377' => 'camsi', 'CSS0007659' => 'camsi', 'CSS0007701' => 'camsi', 'CSS0007711' => 'camsi', 'CSS0007809' => 'camsi', 'CSS0008045' => 'camsi', 'CSS0008050' => 'camsi', 'CSS0008206' => 'camsi', 'CSS0008251' => 'camsi', 'CSS0008252' => 'camsi', 'CSS0008279' => 'camsi', 'CSS0008482' => 'camsi', 'CSS0008583' => 'camsi', 'CSS0008699' => 'camsi', 'CSS0008798' => 'camsi', 'CSS0008971' => 'camsi', 'CSS0009019' => 'camsi', 'CSS0009191' => 'camsi', 'CSS0009241' => 'camsi', 'CSS0009246' => 'camsi', 'CSS0009399' => 'camsi', 'CSS0009654' => 'camsi', 'CSS0009722' => 'camsi', 'CSS0009920' => 'camsi', 'CSS0009986' => 'camsi', 'CSS0010182' => 'camsi', 'CSS0010202' => 'camsi', 'CSS0010330' => 'camsi', 'CSS0010362' => 'camsi', 'CSS0010456' => 'camsi', 'CSS0010472' => 'camsi', 'CSS0010507' => 'camsi', 'CSS0010512' => 'camsi', 'CSS0010520' => 'camsi', 'CSS0010617' => 'camsi', 'CSS0010706' => 'camsi', 'CSS0010747' => 'camsi', 'CSS0010816' => 'camsi', 'CSS0011020' => 'camsi', 'CSS0011115' => 'camsi', 'CSS0011383' => 'camsi', 'CSS0011491' => 'camsi', 'CSS0011602' => 'camsi', 'CSS0011605' => 'camsi', 'CSS0011625' => 'camsi', 'CSS0011654' => 'camsi', 'CSS0011781' => 'camsi', 'CSS0011853' => 'camsi', 'CSS0011898' => 'camsi', 'CSS0011933' => 'camsi', 'CSS0011996' => 'camsi', 'CSS0012066' => 'camsi', 'CSS0012097' => 'camsi', 'CSS0012108' => 'camsi', 'CSS0012226' => 'camsi', 'CSS0012248' => 'camsi', 'CSS0012331' => 'camsi', 'CSS0012797' => 'camsi', 'CSS0012818' => 'camsi', 'CSS0012904' => 'camsi', 'CSS0013001' => 'camsi', 'CSS0013022' => 'camsi', 'CSS0013172' => 'camsi', 'CSS0013244' => 'camsi', 'CSS0013267' => 'camsi', 'CSS0013275' => 'camsi', 'CSS0013324' => 'camsi', 'CSS0013334' => 'camsi', 'CSS0013394' => 'camsi', 'CSS0013549' => 'camsi', 'CSS0013689' => 'camsi', 'CSS0014026' => 'camsi', 'CSS0014049' => 'camsi', 'CSS0014144' => 'camsi', 'CSS0014354' => 'camsi', 'CSS0014579' => 'camsi', 'CSS0014648' => 'camsi', 'CSS0014902' => 'camsi', 'CSS0014979' => 'camsi', 'CSS0015278' => 'camsi', 'CSS0015310' => 'camsi', 'CSS0015364' => 'camsi', 'CSS0015455' => 'camsi', 'CSS0015693' => 'camsi', 'CSS0015774' => 'camsi', 'CSS0015795' => 'camsi', 'CSS0015952' => 'camsi', 'CSS0016104' => 'camsi', 'CSS0016241' => 'camsi', 'CSS0016303' => 'camsi', 'CSS0016490' => 'camsi', 'CSS0016832' => 'camsi', 'CSS0016845' => 'camsi', 'CSS0016914' => 'camsi', 'CSS0016946' => 'camsi', 'CSS0017102' => 'camsi', 'CSS0017193' => 'camsi', 'CSS0017528' => 'camsi', 'CSS0017619' => 'camsi', 'CSS0017679' => 'camsi', 'CSS0017816' => 'camsi', 'CSS0017880' => 'camsi', 'CSS0018106' => 'camsi', 'CSS0018162' => 'camsi', 'CSS0018304' => 'camsi', 'CSS0018406' => 'camsi', 'CSS0018481' => 'camsi', 'CSS0018511' => 'camsi', 'CSS0018596' => 'camsi', 'CSS0018727' => 'camsi', 'CSS0018751' => 'camsi', 'CSS0018777' => 'camsi', 'CSS0018798' => 'camsi', 'CSS0019137' => 'camsi', 'CSS0019177' => 'camsi', 'CSS0019217' => 'camsi', 'CSS0019361' => 'camsi', 'CSS0019516' => 'camsi', 'CSS0019538' => 'camsi', 'CSS0019560' => 'camsi', 'CSS0019819' => 'camsi', 'CSS0019837' => 'camsi', 'CSS0019915' => 'camsi', 'CSS0019925' => 'camsi', 'CSS0020112' => 'camsi', 'CSS0020160' => 'camsi', 'CSS0020378' => 'camsi', 'CSS0020388' => 'camsi', 'CSS0020452' => 'camsi', 'CSS0020588' => 'camsi', 'CSS0020661' => 'camsi', 'CSS0020886' => 'camsi', 'CSS0020973' => 'camsi', 'CSS0021035' => 'camsi', 'CSS0021111' => 'camsi', 'CSS0021131' => 'camsi', 'CSS0021151' => 'camsi', 'CSS0021228' => 'camsi', 'CSS0021397' => 'camsi', 'CSS0021420' => 'camsi', 'CSS0021464' => 'camsi', 'CSS0021547' => 'camsi', 'CSS0021608' => 'camsi', 'CSS0021740' => 'camsi', 'CSS0021826' => 'camsi', 'CSS0021904' => 'camsi', 'CSS0021941' => 'camsi', 'CSS0022189' => 'camsi', 'CSS0022199' => 'camsi', 'CSS0022502' => 'camsi', 'CSS0022531' => 'camsi', 'CSS0022581' => 'camsi', 'CSS0022612' => 'camsi', 'CSS0022621' => 'camsi', 'CSS0022815' => 'camsi', 'CSS0022936' => 'camsi', 'CSS0022964' => 'camsi', 'CSS0022985' => 'camsi', 'CSS0023002' => 'camsi', 'CSS0023006' => 'camsi', 'CSS0023024' => 'camsi', 'CSS0023489' => 'camsi', 'CSS0023593' => 'camsi', 'CSS0023621' => 'camsi', 'CSS0023743' => 'camsi', 'CSS0023804' => 'camsi', 'CSS0023805' => 'camsi', 'CSS0023908' => 'camsi', 'CSS0023938' => 'camsi', 'CSS0023981' => 'camsi', 'CSS0024027' => 'camsi', 'CSS0024169' => 'camsi', 'CSS0024193' => 'camsi', 'CSS0024269' => 'camsi', 'CSS0024336' => 'camsi', 'CSS0024337' => 'camsi', 'CSS0024548' => 'camsi', 'CSS0024564' => 'camsi', 'CSS0024585' => 'camsi', 'CSS0024738' => 'camsi', 'CSS0024833' => 'camsi', 'CSS0024846' => 'camsi', 'CSS0024957' => 'camsi', 'CSS0024974' => 'camsi', 'CSS0025005' => 'camsi', 'CSS0025235' => 'camsi', 'CSS0025465' => 'camsi', 'CSS0025633' => 'camsi', 'CSS0025688' => 'camsi', 'CSS0025759' => 'camsi', 'CSS0025774' => 'camsi', 'CSS0025801' => 'camsi', 'CSS0025942' => 'camsi', 'CSS0026083' => 'camsi', 'CSS0026194' => 'camsi', 'CSS0026230' => 'camsi', 'CSS0026398' => 'camsi', 'CSS0026419' => 'camsi', 'CSS0026679' => 'camsi', 'CSS0026719' => 'camsi', 'CSS0026795' => 'camsi', 'CSS0026835' => 'camsi', 'CSS0026930' => 'camsi', 'CSS0027053' => 'camsi', 'CSS0027130' => 'camsi', 'CSS0027192' => 'camsi', 'CSS0027454' => 'camsi', 'CSS0027467' => 'camsi', 'CSS0027521' => 'camsi', 'CSS0027662' => 'camsi', 'CSS0027795' => 'camsi', 'CSS0027835' => 'camsi', 'CSS0027966' => 'camsi', 'CSS0028090' => 'camsi', 'CSS0028134' => 'camsi', 'CSS0028205' => 'camsi', 'CSS0028263' => 'camsi', 'CSS0028363' => 'camsi', 'CSS0028598' => 'camsi', 'CSS0029175' => 'camsi', 'CSS0029191' => 'camsi', 'CSS0029424' => 'camsi', 'CSS0029479' => 'camsi', 'CSS0029496' => 'camsi', 'CSS0029633' => 'camsi', 'CSS0029837' => 'camsi', 'CSS0029844' => 'camsi', 'CSS0029863' => 'camsi', 'CSS0029874' => 'camsi', 'CSS0029959' => 'camsi', 'CSS0030001' => 'camsi', 'CSS0030093' => 'camsi', 'CSS0030199' => 'camsi', 'CSS0030200' => 'camsi', 'CSS0030427' => 'camsi', 'CSS0030476' => 'camsi', 'CSS0030636' => 'camsi', 'CSS0030673' => 'camsi', 'CSS0030766' => 'camsi', 'CSS0030775' => 'camsi', 'CSS0030858' => 'camsi', 'CSS0030873' => 'camsi', 'CSS0030929' => 'camsi', 'CSS0031028' => 'camsi', 'CSS0031129' => 'camsi', 'CSS0031164' => 'camsi', 'CSS0031340' => 'camsi', 'CSS0031368' => 'camsi', 'CSS0031395' => 'camsi', 'CSS0031596' => 'camsi', 'CSS0031727' => 'camsi', 'CSS0032011' => 'camsi', 'CSS0032160' => 'camsi', 'CSS0032538' => 'camsi', 'CSS0032576' => 'camsi', 'CSS0032603' => 'camsi', 'CSS0032640' => 'camsi', 'CSS0032704' => 'camsi', 'CSS0032851' => 'camsi', 'CSS0032973' => 'camsi', 'CSS0033048' => 'camsi', 'CSS0033082' => 'camsi', 'CSS0033157' => 'camsi', 'CSS0033253' => 'camsi', 'CSS0033347' => 'camsi', 'CSS0033601' => 'camsi', 'CSS0033820' => 'camsi', 'CSS0033881' => 'camsi', 'CSS0033934' => 'camsi', 'CSS0034143' => 'camsi', 'CSS0034176' => 'camsi', 'CSS0034201' => 'camsi', 'CSS0034269' => 'camsi', 'CSS0034303' => 'camsi', 'CSS0034463' => 'camsi', 'CSS0034470' => 'camsi', 'CSS0034514' => 'camsi', 'CSS0034525' => 'camsi', 'CSS0034726' => 'camsi', 'CSS0034727' => 'camsi', 'CSS0034737' => 'camsi', 'CSS0034768' => 'camsi', 'CSS0034890' => 'camsi', 'CSS0034943' => 'camsi', 'CSS0034957' => 'camsi', 'CSS0034973' => 'camsi', 'CSS0035178' => 'camsi', 'CSS0035260' => 'camsi', 'CSS0035316' => 'camsi', 'CSS0035347' => 'camsi', 'CSS0035360' => 'camsi', 'CSS0035380' => 'camsi', 'CSS0035429' => 'camsi', 'CSS0035446' => 'camsi', 'CSS0035737' => 'camsi', 'CSS0035852' => 'camsi', 'CSS0035967' => 'camsi', 'CSS0036001' => 'camsi', 'CSS0036044' => 'camsi', 'CSS0036221' => 'camsi', 'CSS0036333' => 'camsi', 'CSS0036435' => 'camsi', 'CSS0036843' => 'camsi', 'CSS0036846' => 'camsi', 'CSS0037097' => 'camsi', 'CSS0037263' => 'camsi', 'CSS0037370' => 'camsi', 'CSS0037410' => 'camsi', 'CSS0037449' => 'camsi', 'CSS0037603' => 'camsi', 'CSS0037851' => 'camsi', 'CSS0037891' => 'camsi', 'CSS0037996' => 'camsi', 'CSS0038222' => 'camsi', 'CSS0038433' => 'camsi', 'CSS0038441' => 'camsi', 'CSS0038718' => 'camsi', 'CSS0038890' => 'camsi', 'CSS0039049' => 'camsi', 'CSS0039145' => 'camsi', 'CSS0039243' => 'camsi', 'CSS0039294' => 'camsi', 'CSS0039324' => 'camsi', 'CSS0039376' => 'camsi', 'CSS0039475' => 'camsi', 'CSS0039539' => 'camsi', 'CSS0039546' => 'camsi', 'CSS0039567' => 'camsi', 'CSS0039599' => 'camsi', 'CSS0039763' => 'camsi', 'CSS0039863' => 'camsi', 'CSS0040107' => 'camsi', 'CSS0040124' => 'camsi', 'CSS0040151' => 'camsi', 'CSS0040165' => 'camsi', 'CSS0040309' => 'camsi', 'CSS0040318' => 'camsi', 'CSS0040347' => 'camsi', 'CSS0040371' => 'camsi', 'CSS0040456' => 'camsi', 'CSS0040551' => 'camsi', 'CSS0040975' => 'camsi', 'CSS0040981' => 'camsi', 'CSS0041299' => 'camsi', 'CSS0041493' => 'camsi', 'CSS0041658' => 'camsi', 'CSS0041899' => 'camsi', 'CSS0041927' => 'camsi', 'CSS0042016' => 'camsi', 'CSS0042034' => 'camsi', 'CSS0042103' => 'camsi', 'CSS0042172' => 'camsi', 'CSS0042198' => 'camsi', 'CSS0042201' => 'camsi', 'CSS0042308' => 'camsi', 'CSS0042329' => 'camsi', 'CSS0042348' => 'camsi', 'CSS0042349' => 'camsi', 'CSS0042489' => 'camsi', 'CSS0042575' => 'camsi', 'CSS0042624' => 'camsi', 'CSS0042660' => 'camsi', 'CSS0042694' => 'camsi', 'CSS0042995' => 'camsi', 'CSS0043079' => 'camsi', 'CSS0043165' => 'camsi', 'CSS0043171' => 'camsi', 'CSS0043314' => 'camsi', 'CSS0043361' => 'camsi', 'CSS0043375' => 'camsi', 'CSS0043518' => 'camsi', 'CSS0043536' => 'camsi', 'CSS0043678' => 'camsi', 'CSS0043765' => 'camsi', 'CSS0043897' => 'camsi', 'CSS0043944' => 'camsi', 'CSS0044126' => 'camsi', 'CSS0044136' => 'camsi', 'CSS0044179' => 'camsi', 'CSS0044290' => 'camsi', 'CSS0044437' => 'camsi', 'CSS0044502' => 'camsi', 'CSS0044603' => 'camsi', 'CSS0044680' => 'camsi', 'CSS0044685' => 'camsi', 'CSS0044700' => 'camsi', 'CSS0044888' => 'camsi', 'CSS0044923' => 'camsi', 'CSS0044926' => 'camsi', 'CSS0044979' => 'camsi', 'CSS0045049' => 'camsi', 'CSS0045132' => 'camsi', 'CSS0045161' => 'camsi', 'CSS0045219' => 'camsi', 'CSS0045230' => 'camsi', 'CSS0045259' => 'camsi', 'CSS0045324' => 'camsi', 'CSS0045368' => 'camsi', 'CSS0045435' => 'camsi', 'CSS0045856' => 'camsi', 'CSS0045955' => 'camsi', 'CSS0046158' => 'camsi', 'CSS0046334' => 'camsi', 'CSS0046365' => 'camsi', 'CSS0046396' => 'camsi', 'CSS0046400' => 'camsi', 'CSS0046445' => 'camsi', 'CSS0046493' => 'camsi', 'CSS0046640' => 'camsi', 'CSS0046657' => 'camsi', 'CSS0046702' => 'camsi', 'CSS0047208' => 'camsi', 'CSS0047368' => 'camsi', 'CSS0047403' => 'camsi', 'CSS0047417' => 'camsi', 'CSS0047469' => 'camsi', 'CSS0047480' => 'camsi', 'CSS0047482' => 'camsi', 'CSS0047693' => 'camsi', 'CSS0047766' => 'camsi', 'CSS0047866' => 'camsi', 'CSS0047884' => 'camsi', 'CSS0048235' => 'camsi', 'CSS0048383' => 'camsi', 'CSS0048438' => 'camsi', 'CSS0048502' => 'camsi', 'CSS0048546' => 'camsi', 'CSS0048653' => 'camsi', 'CSS0048658' => 'camsi', 'CSS0048729' => 'camsi', 'CSS0048867' => 'camsi', 'CSS0048988' => 'camsi', 'CSS0049053' => 'camsi', 'CSS0049099' => 'camsi', 'CSS0049166' => 'camsi', 'CSS0049174' => 'camsi', 'CSS0049212' => 'camsi', 'CSS0049280' => 'camsi', 'CSS0049391' => 'camsi', 'CSS0049546' => 'camsi', 'CSS0049634' => 'camsi', 'CSS0049655' => 'camsi', 'CSS0049813' => 'camsi', 'CSS0049949' => 'camsi', 'CSS0050009' => 'camsi', 'CSS0050118' => 'camsi', 'CSS0050205' => 'camsi', 'CSS0050275' => 'camsi', 'CSS0050480' => 'camsi', 'CSS0050488' => 'camsi', 'CSS0050497' => 'camsi', 'Dinv03126' => 'din', 'Dinv13140' => 'din', 'Dinv13247' => 'din', 'Dinv14217' => 'din', 'EL10Ac9g22435' => 'bvu', 'FAN20G1200' => 'fan', 'PGR142G2516' => 'pgr', 'Prupe.3G160200' => 'ppe', 'Prupe.5G238200' => 'ppe', 'Prupe.7G047500' => 'ppe', 'QL03p045360' => 'qlo', 'QL05p034369' => 'qlo', 'QL05p034412' => 'qlo', 'QL08p017802' => 'qlo', 'QL08p024762' => 'qlo', 'QL10p026237' => 'qlo', 'QL10p032070' => 'qlo', 'QL11p003821' => 'qlo', 'Rhsim04G0057300' => 'rsi', 'Rhsim05G0049200' => 'rsi', 'Rhsim12G0010400' => 'rsi', 'Rhsim12G0012800' => 'rsi', 'TAR624G0483' => 'tar', 'TAR703G0001' => 'tar', 'vmacro05414' => 'vma', 'vmacro07091' => 'vma', 'vmacro07116' => 'vma', 'vmacro08423' => 'vma', 'vmacro09046' => 'vma', 'vmacro14269' => 'vma', 'vmacro16092' => 'vma', 'vmacro17280' => 'vma', 'vmacro19601' => 'vma' ) $gf_id = 'HOM05D001028' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001028' ) $data_identifier = 'HOM05D001028' $data_type = 'gf_id' $species_gene_counts = array( 'aox' => (int) 11, 'ccan' => (int) 6, 'camsi' => (int) 540, 'din' => (int) 4, 'bvu' => (int) 1, 'fan' => (int) 1, 'pgr' => (int) 1, 'ppe' => (int) 3, 'qlo' => (int) 8, 'rsi' => (int) 4, 'tar' => (int) 2, 'vma' => (int) 9 ) $gf_gene_species = 'vma' $gf_gene_id = 'vmacro19601' $species_info = array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ) $local_species = 'ccan' $disabled = '' $selected = '' $num_hits = (int) 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' => 'HOM05D001028', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '590', 'num_species' => '12' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'Aqoxy1G01649' => 'aox', 'Aqoxy1G02950' => 'aox', 'Aqoxy2G01005' => 'aox', 'Aqoxy2G01064' => 'aox', 'Aqoxy3G02267' => 'aox', 'Aqoxy3G02617' => 'aox', 'Aqoxy3G02693' => 'aox', 'Aqoxy5G03425' => 'aox', 'Aqoxy6G02164' => 'aox', 'Aqoxy6G02364' => 'aox', 'Aqoxy7G02284' => 'aox', 'Cc00_g09720' => 'ccan', 'Cc00_g21410' => 'ccan', 'Cc00_g31750' => 'ccan', 'Cc00_g34740' => 'ccan', 'Cc04_g16890' => 'ccan', 'Cc11_g03120' => 'ccan', 'CSS0000222' => 'camsi', 'CSS0000265' => 'camsi', 'CSS0000306' => 'camsi', 'CSS0000326' => 'camsi', 'CSS0000530' => 'camsi', 'CSS0000563' => 'camsi', 'CSS0000584' => 'camsi', 'CSS0000684' => 'camsi', 'CSS0001100' => 'camsi', 'CSS0001311' => 'camsi', 'CSS0001343' => 'camsi', 'CSS0001399' => 'camsi', 'CSS0001475' => 'camsi', 'CSS0001506' => 'camsi', 'CSS0001602' => 'camsi', 'CSS0001681' => 'camsi', 'CSS0001874' => 'camsi', 'CSS0001948' => 'camsi', 'CSS0002022' => 'camsi', 'CSS0002230' => 'camsi', 'CSS0002265' => 'camsi', 'CSS0002277' => 'camsi', 'CSS0002462' => 'camsi', 'CSS0002823' => 'camsi', 'CSS0003091' => 'camsi', 'CSS0003162' => 'camsi', 'CSS0003264' => 'camsi', 'CSS0003355' => 'camsi', 'CSS0003378' => 'camsi', 'CSS0003472' => 'camsi', 'CSS0003500' => 'camsi', 'CSS0003640' => 'camsi', 'CSS0003767' => 'camsi', 'CSS0003894' => 'camsi', 'CSS0003952' => 'camsi', 'CSS0003977' => 'camsi', 'CSS0004028' => 'camsi', 'CSS0004117' => 'camsi', 'CSS0004137' => 'camsi', 'CSS0004176' => 'camsi', 'CSS0004265' => 'camsi', 'CSS0004450' => 'camsi', 'CSS0004468' => 'camsi', 'CSS0004488' => 'camsi', 'CSS0004490' => 'camsi', 'CSS0004632' => 'camsi', 'CSS0004790' => 'camsi', 'CSS0004877' => 'camsi', 'CSS0004920' => 'camsi', 'CSS0004969' => 'camsi', 'CSS0005084' => 'camsi', 'CSS0005101' => 'camsi', 'CSS0005271' => 'camsi', 'CSS0005313' => 'camsi', 'CSS0005331' => 'camsi', 'CSS0005368' => 'camsi', 'CSS0005391' => 'camsi', 'CSS0005437' => 'camsi', 'CSS0005515' => 'camsi', 'CSS0005526' => 'camsi', 'CSS0005532' => 'camsi', 'CSS0005595' => 'camsi', 'CSS0005677' => 'camsi', 'CSS0005838' => 'camsi', 'CSS0005988' => 'camsi', 'CSS0006100' => 'camsi', 'CSS0006128' => 'camsi', 'CSS0006293' => 'camsi', 'CSS0006378' => 'camsi', 'CSS0006400' => 'camsi', 'CSS0006441' => 'camsi', 'CSS0006455' => 'camsi', 'CSS0006480' => 'camsi', 'CSS0006483' => 'camsi', 'CSS0006538' => 'camsi', 'CSS0006582' => 'camsi', 'CSS0006632' => 'camsi', 'CSS0006771' => 'camsi', 'CSS0006803' => 'camsi', 'CSS0006852' => 'camsi', 'CSS0006861' => 'camsi', 'CSS0006910' => 'camsi', 'CSS0007037' => 'camsi', 'CSS0007066' => 'camsi', 'CSS0007072' => 'camsi', 'CSS0007109' => 'camsi', 'CSS0007193' => 'camsi', 'CSS0007319' => 'camsi', 'CSS0007336' => 'camsi', 'CSS0007377' => 'camsi', 'CSS0007659' => 'camsi', 'CSS0007701' => 'camsi', 'CSS0007711' => 'camsi', 'CSS0007809' => 'camsi', 'CSS0008045' => 'camsi', 'CSS0008050' => 'camsi', 'CSS0008206' => 'camsi', 'CSS0008251' => 'camsi', 'CSS0008252' => 'camsi', 'CSS0008279' => 'camsi', 'CSS0008482' => 'camsi', 'CSS0008583' => 'camsi', 'CSS0008699' => 'camsi', 'CSS0008798' => 'camsi', 'CSS0008971' => 'camsi', 'CSS0009019' => 'camsi', 'CSS0009191' => 'camsi', 'CSS0009241' => 'camsi', 'CSS0009246' => 'camsi', 'CSS0009399' => 'camsi', 'CSS0009654' => 'camsi', 'CSS0009722' => 'camsi', 'CSS0009920' => 'camsi', 'CSS0009986' => 'camsi', 'CSS0010182' => 'camsi', 'CSS0010202' => 'camsi', 'CSS0010330' => 'camsi', 'CSS0010362' => 'camsi', 'CSS0010456' => 'camsi', 'CSS0010472' => 'camsi', 'CSS0010507' => 'camsi', 'CSS0010512' => 'camsi', 'CSS0010520' => 'camsi', 'CSS0010617' => 'camsi', 'CSS0010706' => 'camsi', 'CSS0010747' => 'camsi', 'CSS0010816' => 'camsi', 'CSS0011020' => 'camsi', 'CSS0011115' => 'camsi', 'CSS0011383' => 'camsi', 'CSS0011491' => 'camsi', 'CSS0011602' => 'camsi', 'CSS0011605' => 'camsi', 'CSS0011625' => 'camsi', 'CSS0011654' => 'camsi', 'CSS0011781' => 'camsi', 'CSS0011853' => 'camsi', 'CSS0011898' => 'camsi', 'CSS0011933' => 'camsi', 'CSS0011996' => 'camsi', 'CSS0012066' => 'camsi', 'CSS0012097' => 'camsi', 'CSS0012108' => 'camsi', 'CSS0012226' => 'camsi', 'CSS0012248' => 'camsi', 'CSS0012331' => 'camsi', 'CSS0012797' => 'camsi', 'CSS0012818' => 'camsi', 'CSS0012904' => 'camsi', 'CSS0013001' => 'camsi', 'CSS0013022' => 'camsi', 'CSS0013172' => 'camsi', 'CSS0013244' => 'camsi', 'CSS0013267' => 'camsi', 'CSS0013275' => 'camsi', 'CSS0013324' => 'camsi', 'CSS0013334' => 'camsi', 'CSS0013394' => 'camsi', 'CSS0013549' => 'camsi', 'CSS0013689' => 'camsi', 'CSS0014026' => 'camsi', 'CSS0014049' => 'camsi', 'CSS0014144' => 'camsi', 'CSS0014354' => 'camsi', 'CSS0014579' => 'camsi', 'CSS0014648' => 'camsi', 'CSS0014902' => 'camsi', 'CSS0014979' => 'camsi', 'CSS0015278' => 'camsi', 'CSS0015310' => 'camsi', 'CSS0015364' => 'camsi', 'CSS0015455' => 'camsi', 'CSS0015693' => 'camsi', 'CSS0015774' => 'camsi', 'CSS0015795' => 'camsi', 'CSS0015952' => 'camsi', 'CSS0016104' => 'camsi', 'CSS0016241' => 'camsi', 'CSS0016303' => 'camsi', 'CSS0016490' => 'camsi', 'CSS0016832' => 'camsi', 'CSS0016845' => 'camsi', 'CSS0016914' => 'camsi', 'CSS0016946' => 'camsi', 'CSS0017102' => 'camsi', 'CSS0017193' => 'camsi', 'CSS0017528' => 'camsi', 'CSS0017619' => 'camsi', 'CSS0017679' => 'camsi', 'CSS0017816' => 'camsi', 'CSS0017880' => 'camsi', 'CSS0018106' => 'camsi', 'CSS0018162' => 'camsi', 'CSS0018304' => 'camsi', 'CSS0018406' => 'camsi', 'CSS0018481' => 'camsi', 'CSS0018511' => 'camsi', 'CSS0018596' => 'camsi', 'CSS0018727' => 'camsi', 'CSS0018751' => 'camsi', 'CSS0018777' => 'camsi', 'CSS0018798' => 'camsi', 'CSS0019137' => 'camsi', 'CSS0019177' => 'camsi', 'CSS0019217' => 'camsi', 'CSS0019361' => 'camsi', 'CSS0019516' => 'camsi', 'CSS0019538' => 'camsi', 'CSS0019560' => 'camsi', 'CSS0019819' => 'camsi', 'CSS0019837' => 'camsi', 'CSS0019915' => 'camsi', 'CSS0019925' => 'camsi', 'CSS0020112' => 'camsi', 'CSS0020160' => 'camsi', 'CSS0020378' => 'camsi', 'CSS0020388' => 'camsi', 'CSS0020452' => 'camsi', 'CSS0020588' => 'camsi', 'CSS0020661' => 'camsi', 'CSS0020886' => 'camsi', 'CSS0020973' => 'camsi', 'CSS0021035' => 'camsi', 'CSS0021111' => 'camsi', 'CSS0021131' => 'camsi', 'CSS0021151' => 'camsi', 'CSS0021228' => 'camsi', 'CSS0021397' => 'camsi', 'CSS0021420' => 'camsi', 'CSS0021464' => 'camsi', 'CSS0021547' => 'camsi', 'CSS0021608' => 'camsi', 'CSS0021740' => 'camsi', 'CSS0021826' => 'camsi', 'CSS0021904' => 'camsi', 'CSS0021941' => 'camsi', 'CSS0022189' => 'camsi', 'CSS0022199' => 'camsi', 'CSS0022502' => 'camsi', 'CSS0022531' => 'camsi', 'CSS0022581' => 'camsi', 'CSS0022612' => 'camsi', 'CSS0022621' => 'camsi', 'CSS0022815' => 'camsi', 'CSS0022936' => 'camsi', 'CSS0022964' => 'camsi', 'CSS0022985' => 'camsi', 'CSS0023002' => 'camsi', 'CSS0023006' => 'camsi', 'CSS0023024' => 'camsi', 'CSS0023489' => 'camsi', 'CSS0023593' => 'camsi', 'CSS0023621' => 'camsi', 'CSS0023743' => 'camsi', 'CSS0023804' => 'camsi', 'CSS0023805' => 'camsi', 'CSS0023908' => 'camsi', 'CSS0023938' => 'camsi', 'CSS0023981' => 'camsi', 'CSS0024027' => 'camsi', 'CSS0024169' => 'camsi', 'CSS0024193' => 'camsi', 'CSS0024269' => 'camsi', 'CSS0024336' => 'camsi', 'CSS0024337' => 'camsi', 'CSS0024548' => 'camsi', 'CSS0024564' => 'camsi', 'CSS0024585' => 'camsi', 'CSS0024738' => 'camsi', 'CSS0024833' => 'camsi', 'CSS0024846' => 'camsi', 'CSS0024957' => 'camsi', 'CSS0024974' => 'camsi', 'CSS0025005' => 'camsi', 'CSS0025235' => 'camsi', 'CSS0025465' => 'camsi', 'CSS0025633' => 'camsi', 'CSS0025688' => 'camsi', 'CSS0025759' => 'camsi', 'CSS0025774' => 'camsi', 'CSS0025801' => 'camsi', 'CSS0025942' => 'camsi', 'CSS0026083' => 'camsi', 'CSS0026194' => 'camsi', 'CSS0026230' => 'camsi', 'CSS0026398' => 'camsi', 'CSS0026419' => 'camsi', 'CSS0026679' => 'camsi', 'CSS0026719' => 'camsi', 'CSS0026795' => 'camsi', 'CSS0026835' => 'camsi', 'CSS0026930' => 'camsi', 'CSS0027053' => 'camsi', 'CSS0027130' => 'camsi', 'CSS0027192' => 'camsi', 'CSS0027454' => 'camsi', 'CSS0027467' => 'camsi', 'CSS0027521' => 'camsi', 'CSS0027662' => 'camsi', 'CSS0027795' => 'camsi', 'CSS0027835' => 'camsi', 'CSS0027966' => 'camsi', 'CSS0028090' => 'camsi', 'CSS0028134' => 'camsi', 'CSS0028205' => 'camsi', 'CSS0028263' => 'camsi', 'CSS0028363' => 'camsi', 'CSS0028598' => 'camsi', 'CSS0029175' => 'camsi', 'CSS0029191' => 'camsi', 'CSS0029424' => 'camsi', 'CSS0029479' => 'camsi', 'CSS0029496' => 'camsi', 'CSS0029633' => 'camsi', 'CSS0029837' => 'camsi', 'CSS0029844' => 'camsi', 'CSS0029863' => 'camsi', 'CSS0029874' => 'camsi', 'CSS0029959' => 'camsi', 'CSS0030001' => 'camsi', 'CSS0030093' => 'camsi', 'CSS0030199' => 'camsi', 'CSS0030200' => 'camsi', 'CSS0030427' => 'camsi', 'CSS0030476' => 'camsi', 'CSS0030636' => 'camsi', 'CSS0030673' => 'camsi', 'CSS0030766' => 'camsi', 'CSS0030775' => 'camsi', 'CSS0030858' => 'camsi', 'CSS0030873' => 'camsi', 'CSS0030929' => 'camsi', 'CSS0031028' => 'camsi', 'CSS0031129' => 'camsi', 'CSS0031164' => 'camsi', 'CSS0031340' => 'camsi', 'CSS0031368' => 'camsi', 'CSS0031395' => 'camsi', 'CSS0031596' => 'camsi', 'CSS0031727' => 'camsi', 'CSS0032011' => 'camsi', 'CSS0032160' => 'camsi', 'CSS0032538' => 'camsi', 'CSS0032576' => 'camsi', 'CSS0032603' => 'camsi', 'CSS0032640' => 'camsi', 'CSS0032704' => 'camsi', 'CSS0032851' => 'camsi', 'CSS0032973' => 'camsi', 'CSS0033048' => 'camsi', 'CSS0033082' => 'camsi', 'CSS0033157' => 'camsi', 'CSS0033253' => 'camsi', 'CSS0033347' => 'camsi', 'CSS0033601' => 'camsi', 'CSS0033820' => 'camsi', 'CSS0033881' => 'camsi', 'CSS0033934' => 'camsi', 'CSS0034143' => 'camsi', 'CSS0034176' => 'camsi', 'CSS0034201' => 'camsi', 'CSS0034269' => 'camsi', 'CSS0034303' => 'camsi', 'CSS0034463' => 'camsi', 'CSS0034470' => 'camsi', 'CSS0034514' => 'camsi', 'CSS0034525' => 'camsi', 'CSS0034726' => 'camsi', 'CSS0034727' => 'camsi', 'CSS0034737' => 'camsi', 'CSS0034768' => 'camsi', 'CSS0034890' => 'camsi', 'CSS0034943' => 'camsi', 'CSS0034957' => 'camsi', 'CSS0034973' => 'camsi', 'CSS0035178' => 'camsi', 'CSS0035260' => 'camsi', 'CSS0035316' => 'camsi', 'CSS0035347' => 'camsi', 'CSS0035360' => 'camsi', 'CSS0035380' => 'camsi', 'CSS0035429' => 'camsi', 'CSS0035446' => 'camsi', 'CSS0035737' => 'camsi', 'CSS0035852' => 'camsi', 'CSS0035967' => 'camsi', 'CSS0036001' => 'camsi', 'CSS0036044' => 'camsi', 'CSS0036221' => 'camsi', 'CSS0036333' => 'camsi', 'CSS0036435' => 'camsi', 'CSS0036843' => 'camsi', 'CSS0036846' => 'camsi', 'CSS0037097' => 'camsi', 'CSS0037263' => 'camsi', 'CSS0037370' => 'camsi', 'CSS0037410' => 'camsi', 'CSS0037449' => 'camsi', 'CSS0037603' => 'camsi', 'CSS0037851' => 'camsi', 'CSS0037891' => 'camsi', 'CSS0037996' => 'camsi', 'CSS0038222' => 'camsi', 'CSS0038433' => 'camsi', 'CSS0038441' => 'camsi', 'CSS0038718' => 'camsi', 'CSS0038890' => 'camsi', 'CSS0039049' => 'camsi', 'CSS0039145' => 'camsi', 'CSS0039243' => 'camsi', 'CSS0039294' => 'camsi', 'CSS0039324' => 'camsi', 'CSS0039376' => 'camsi', 'CSS0039475' => 'camsi', 'CSS0039539' => 'camsi', 'CSS0039546' => 'camsi', 'CSS0039567' => 'camsi', 'CSS0039599' => 'camsi', 'CSS0039763' => 'camsi', 'CSS0039863' => 'camsi', 'CSS0040107' => 'camsi', 'CSS0040124' => 'camsi', 'CSS0040151' => 'camsi', 'CSS0040165' => 'camsi', 'CSS0040309' => 'camsi', 'CSS0040318' => 'camsi', 'CSS0040347' => 'camsi', 'CSS0040371' => 'camsi', 'CSS0040456' => 'camsi', 'CSS0040551' => 'camsi', 'CSS0040975' => 'camsi', 'CSS0040981' => 'camsi', 'CSS0041299' => 'camsi', 'CSS0041493' => 'camsi', 'CSS0041658' => 'camsi', 'CSS0041899' => 'camsi', 'CSS0041927' => 'camsi', 'CSS0042016' => 'camsi', 'CSS0042034' => 'camsi', 'CSS0042103' => 'camsi', 'CSS0042172' => 'camsi', 'CSS0042198' => 'camsi', 'CSS0042201' => 'camsi', 'CSS0042308' => 'camsi', 'CSS0042329' => 'camsi', 'CSS0042348' => 'camsi', 'CSS0042349' => 'camsi', 'CSS0042489' => 'camsi', 'CSS0042575' => 'camsi', 'CSS0042624' => 'camsi', 'CSS0042660' => 'camsi', 'CSS0042694' => 'camsi', 'CSS0042995' => 'camsi', 'CSS0043079' => 'camsi', 'CSS0043165' => 'camsi', 'CSS0043171' => 'camsi', 'CSS0043314' => 'camsi', 'CSS0043361' => 'camsi', 'CSS0043375' => 'camsi', 'CSS0043518' => 'camsi', 'CSS0043536' => 'camsi', 'CSS0043678' => 'camsi', 'CSS0043765' => 'camsi', 'CSS0043897' => 'camsi', 'CSS0043944' => 'camsi', 'CSS0044126' => 'camsi', 'CSS0044136' => 'camsi', 'CSS0044179' => 'camsi', 'CSS0044290' => 'camsi', 'CSS0044437' => 'camsi', 'CSS0044502' => 'camsi', 'CSS0044603' => 'camsi', 'CSS0044680' => 'camsi', 'CSS0044685' => 'camsi', 'CSS0044700' => 'camsi', 'CSS0044888' => 'camsi', 'CSS0044923' => 'camsi', 'CSS0044926' => 'camsi', 'CSS0044979' => 'camsi', 'CSS0045049' => 'camsi', 'CSS0045132' => 'camsi', 'CSS0045161' => 'camsi', 'CSS0045219' => 'camsi', 'CSS0045230' => 'camsi', 'CSS0045259' => 'camsi', 'CSS0045324' => 'camsi', 'CSS0045368' => 'camsi', 'CSS0045435' => 'camsi', 'CSS0045856' => 'camsi', 'CSS0045955' => 'camsi', 'CSS0046158' => 'camsi', 'CSS0046334' => 'camsi', 'CSS0046365' => 'camsi', 'CSS0046396' => 'camsi', 'CSS0046400' => 'camsi', 'CSS0046445' => 'camsi', 'CSS0046493' => 'camsi', 'CSS0046640' => 'camsi', 'CSS0046657' => 'camsi', 'CSS0046702' => 'camsi', 'CSS0047208' => 'camsi', 'CSS0047368' => 'camsi', 'CSS0047403' => 'camsi', 'CSS0047417' => 'camsi', 'CSS0047469' => 'camsi', 'CSS0047480' => 'camsi', 'CSS0047482' => 'camsi', 'CSS0047693' => 'camsi', 'CSS0047766' => 'camsi', 'CSS0047866' => 'camsi', 'CSS0047884' => 'camsi', 'CSS0048235' => 'camsi', 'CSS0048383' => 'camsi', 'CSS0048438' => 'camsi', 'CSS0048502' => 'camsi', 'CSS0048546' => 'camsi', 'CSS0048653' => 'camsi', 'CSS0048658' => 'camsi', 'CSS0048729' => 'camsi', 'CSS0048867' => 'camsi', 'CSS0048988' => 'camsi', 'CSS0049053' => 'camsi', 'CSS0049099' => 'camsi', 'CSS0049166' => 'camsi', 'CSS0049174' => 'camsi', 'CSS0049212' => 'camsi', 'CSS0049280' => 'camsi', 'CSS0049391' => 'camsi', 'CSS0049546' => 'camsi', 'CSS0049634' => 'camsi', 'CSS0049655' => 'camsi', 'CSS0049813' => 'camsi', 'CSS0049949' => 'camsi', 'CSS0050009' => 'camsi', 'CSS0050118' => 'camsi', 'CSS0050205' => 'camsi', 'CSS0050275' => 'camsi', 'CSS0050480' => 'camsi', 'CSS0050488' => 'camsi', 'CSS0050497' => 'camsi', 'Dinv03126' => 'din', 'Dinv13140' => 'din', 'Dinv13247' => 'din', 'Dinv14217' => 'din', 'EL10Ac9g22435' => 'bvu', 'FAN20G1200' => 'fan', 'PGR142G2516' => 'pgr', 'Prupe.3G160200' => 'ppe', 'Prupe.5G238200' => 'ppe', 'Prupe.7G047500' => 'ppe', 'QL03p045360' => 'qlo', 'QL05p034369' => 'qlo', 'QL05p034412' => 'qlo', 'QL08p017802' => 'qlo', 'QL08p024762' => 'qlo', 'QL10p026237' => 'qlo', 'QL10p032070' => 'qlo', 'QL11p003821' => 'qlo', 'Rhsim04G0057300' => 'rsi', 'Rhsim05G0049200' => 'rsi', 'Rhsim12G0010400' => 'rsi', 'Rhsim12G0012800' => 'rsi', 'TAR624G0483' => 'tar', 'TAR703G0001' => 'tar', 'vmacro05414' => 'vma', 'vmacro07091' => 'vma', 'vmacro07116' => 'vma', 'vmacro08423' => 'vma', 'vmacro09046' => 'vma', 'vmacro14269' => 'vma', 'vmacro16092' => 'vma', 'vmacro17280' => 'vma', 'vmacro19601' => 'vma' ), 'gf_id' => 'HOM05D001028', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001028' ), 'data_identifier' => 'HOM05D001028', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001028', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '590', 'num_species' => '12' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'Aqoxy1G01649' => 'aox', 'Aqoxy1G02950' => 'aox', 'Aqoxy2G01005' => 'aox', 'Aqoxy2G01064' => 'aox', 'Aqoxy3G02267' => 'aox', 'Aqoxy3G02617' => 'aox', 'Aqoxy3G02693' => 'aox', 'Aqoxy5G03425' => 'aox', 'Aqoxy6G02164' => 'aox', 'Aqoxy6G02364' => 'aox', 'Aqoxy7G02284' => 'aox', 'Cc00_g09720' => 'ccan', 'Cc00_g21410' => 'ccan', 'Cc00_g31750' => 'ccan', 'Cc00_g34740' => 'ccan', 'Cc04_g16890' => 'ccan', 'Cc11_g03120' => 'ccan', 'CSS0000222' => 'camsi', 'CSS0000265' => 'camsi', 'CSS0000306' => 'camsi', 'CSS0000326' => 'camsi', 'CSS0000530' => 'camsi', 'CSS0000563' => 'camsi', 'CSS0000584' => 'camsi', 'CSS0000684' => 'camsi', 'CSS0001100' => 'camsi', 'CSS0001311' => 'camsi', 'CSS0001343' => 'camsi', 'CSS0001399' => 'camsi', 'CSS0001475' => 'camsi', 'CSS0001506' => 'camsi', 'CSS0001602' => 'camsi', 'CSS0001681' => 'camsi', 'CSS0001874' => 'camsi', 'CSS0001948' => 'camsi', 'CSS0002022' => 'camsi', 'CSS0002230' => 'camsi', 'CSS0002265' => 'camsi', 'CSS0002277' => 'camsi', 'CSS0002462' => 'camsi', 'CSS0002823' => 'camsi', 'CSS0003091' => 'camsi', 'CSS0003162' => 'camsi', 'CSS0003264' => 'camsi', 'CSS0003355' => 'camsi', 'CSS0003378' => 'camsi', 'CSS0003472' => 'camsi', 'CSS0003500' => 'camsi', 'CSS0003640' => 'camsi', 'CSS0003767' => 'camsi', 'CSS0003894' => 'camsi', 'CSS0003952' => 'camsi', 'CSS0003977' => 'camsi', 'CSS0004028' => 'camsi', 'CSS0004117' => 'camsi', 'CSS0004137' => 'camsi', 'CSS0004176' => 'camsi', 'CSS0004265' => 'camsi', 'CSS0004450' => 'camsi', 'CSS0004468' => 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'camsi', 'CSS0034463' => 'camsi', 'CSS0034470' => 'camsi', 'CSS0034514' => 'camsi', 'CSS0034525' => 'camsi', 'CSS0034726' => 'camsi', 'CSS0034727' => 'camsi', 'CSS0034737' => 'camsi', 'CSS0034768' => 'camsi', 'CSS0034890' => 'camsi', 'CSS0034943' => 'camsi', 'CSS0034957' => 'camsi', 'CSS0034973' => 'camsi', 'CSS0035178' => 'camsi', 'CSS0035260' => 'camsi', 'CSS0035316' => 'camsi', 'CSS0035347' => 'camsi', 'CSS0035360' => 'camsi', 'CSS0035380' => 'camsi', 'CSS0035429' => 'camsi', 'CSS0035446' => 'camsi', 'CSS0035737' => 'camsi', 'CSS0035852' => 'camsi', 'CSS0035967' => 'camsi', 'CSS0036001' => 'camsi', 'CSS0036044' => 'camsi', 'CSS0036221' => 'camsi', 'CSS0036333' => 'camsi', 'CSS0036435' => 'camsi', 'CSS0036843' => 'camsi', 'CSS0036846' => 'camsi', 'CSS0037097' => 'camsi', 'CSS0037263' => 'camsi', 'CSS0037370' => 'camsi', 'CSS0037410' => 'camsi', 'CSS0037449' => 'camsi', 'CSS0037603' => 'camsi', 'CSS0037851' => 'camsi', 'CSS0037891' => 'camsi', 'CSS0037996' => 'camsi', 'CSS0038222' => 'camsi', 'CSS0038433' => 'camsi', 'CSS0038441' => 'camsi', 'CSS0038718' => 'camsi', 'CSS0038890' => 'camsi', 'CSS0039049' => 'camsi', 'CSS0039145' => 'camsi', 'CSS0039243' => 'camsi', 'CSS0039294' => 'camsi', 'CSS0039324' => 'camsi', 'CSS0039376' => 'camsi', 'CSS0039475' => 'camsi', 'CSS0039539' => 'camsi', 'CSS0039546' => 'camsi', 'CSS0039567' => 'camsi', 'CSS0039599' => 'camsi', 'CSS0039763' => 'camsi', 'CSS0039863' => 'camsi', 'CSS0040107' => 'camsi', 'CSS0040124' => 'camsi', 'CSS0040151' => 'camsi', 'CSS0040165' => 'camsi', 'CSS0040309' => 'camsi', 'CSS0040318' => 'camsi', 'CSS0040347' => 'camsi', 'CSS0040371' => 'camsi', 'CSS0040456' => 'camsi', 'CSS0040551' => 'camsi', 'CSS0040975' => 'camsi', 'CSS0040981' => 'camsi', 'CSS0041299' => 'camsi', 'CSS0041493' => 'camsi', 'CSS0041658' => 'camsi', 'CSS0041899' => 'camsi', 'CSS0041927' => 'camsi', 'CSS0042016' => 'camsi', 'CSS0042034' => 'camsi', 'CSS0042103' => 'camsi', 'CSS0042172' => 'camsi', 'CSS0042198' => 'camsi', 'CSS0042201' => 'camsi', 'CSS0042308' => 'camsi', 'CSS0042329' => 'camsi', 'CSS0042348' => 'camsi', 'CSS0042349' => 'camsi', 'CSS0042489' => 'camsi', 'CSS0042575' => 'camsi', 'CSS0042624' => 'camsi', 'CSS0042660' => 'camsi', 'CSS0042694' => 'camsi', 'CSS0042995' => 'camsi', 'CSS0043079' => 'camsi', 'CSS0043165' => 'camsi', 'CSS0043171' => 'camsi', 'CSS0043314' => 'camsi', 'CSS0043361' => 'camsi', 'CSS0043375' => 'camsi', 'CSS0043518' => 'camsi', 'CSS0043536' => 'camsi', 'CSS0043678' => 'camsi', 'CSS0043765' => 'camsi', 'CSS0043897' => 'camsi', 'CSS0043944' => 'camsi', 'CSS0044126' => 'camsi', 'CSS0044136' => 'camsi', 'CSS0044179' => 'camsi', 'CSS0044290' => 'camsi', 'CSS0044437' => 'camsi', 'CSS0044502' => 'camsi', 'CSS0044603' => 'camsi', 'CSS0044680' => 'camsi', 'CSS0044685' => 'camsi', 'CSS0044700' => 'camsi', 'CSS0044888' => 'camsi', 'CSS0044923' => 'camsi', 'CSS0044926' => 'camsi', 'CSS0044979' => 'camsi', 'CSS0045049' => 'camsi', 'CSS0045132' => 'camsi', 'CSS0045161' => 'camsi', 'CSS0045219' => 'camsi', 'CSS0045230' => 'camsi', 'CSS0045259' => 'camsi', 'CSS0045324' => 'camsi', 'CSS0045368' => 'camsi', 'CSS0045435' => 'camsi', 'CSS0045856' => 'camsi', 'CSS0045955' => 'camsi', 'CSS0046158' => 'camsi', 'CSS0046334' => 'camsi', 'CSS0046365' => 'camsi', 'CSS0046396' => 'camsi', 'CSS0046400' => 'camsi', 'CSS0046445' => 'camsi', 'CSS0046493' => 'camsi', 'CSS0046640' => 'camsi', 'CSS0046657' => 'camsi', 'CSS0046702' => 'camsi', 'CSS0047208' => 'camsi', 'CSS0047368' => 'camsi', 'CSS0047403' => 'camsi', 'CSS0047417' => 'camsi', 'CSS0047469' => 'camsi', 'CSS0047480' => 'camsi', 'CSS0047482' => 'camsi', 'CSS0047693' => 'camsi', 'CSS0047766' => 'camsi', 'CSS0047866' => 'camsi', 'CSS0047884' => 'camsi', 'CSS0048235' => 'camsi', 'CSS0048383' => 'camsi', 'CSS0048438' => 'camsi', 'CSS0048502' => 'camsi', 'CSS0048546' => 'camsi', 'CSS0048653' => 'camsi', 'CSS0048658' => 'camsi', 'CSS0048729' => 'camsi', 'CSS0048867' => 'camsi', 'CSS0048988' => 'camsi', 'CSS0049053' => 'camsi', 'CSS0049099' => 'camsi', 'CSS0049166' => 'camsi', 'CSS0049174' => 'camsi', 'CSS0049212' => 'camsi', 'CSS0049280' => 'camsi', 'CSS0049391' => 'camsi', 'CSS0049546' => 'camsi', 'CSS0049634' => 'camsi', 'CSS0049655' => 'camsi', 'CSS0049813' => 'camsi', 'CSS0049949' => 'camsi', 'CSS0050009' => 'camsi', 'CSS0050118' => 'camsi', 'CSS0050205' => 'camsi', 'CSS0050275' => 'camsi', 'CSS0050480' => 'camsi', 'CSS0050488' => 'camsi', 'CSS0050497' => 'camsi', 'Dinv03126' => 'din', 'Dinv13140' => 'din', 'Dinv13247' => 'din', 'Dinv14217' => 'din', 'EL10Ac9g22435' => 'bvu', 'FAN20G1200' => 'fan', 'PGR142G2516' => 'pgr', 'Prupe.3G160200' => 'ppe', 'Prupe.5G238200' => 'ppe', 'Prupe.7G047500' => 'ppe', 'QL03p045360' => 'qlo', 'QL05p034369' => 'qlo', 'QL05p034412' => 'qlo', 'QL08p017802' => 'qlo', 'QL08p024762' => 'qlo', 'QL10p026237' => 'qlo', 'QL10p032070' => 'qlo', 'QL11p003821' => 'qlo', 'Rhsim04G0057300' => 'rsi', 'Rhsim05G0049200' => 'rsi', 'Rhsim12G0010400' => 'rsi', 'Rhsim12G0012800' => 'rsi', 'TAR624G0483' => 'tar', 'TAR703G0001' => 'tar', 'vmacro05414' => 'vma', 'vmacro07091' => 'vma', 'vmacro07116' => 'vma', 'vmacro08423' => 'vma', 'vmacro09046' => 'vma', 'vmacro14269' => 'vma', 'vmacro16092' => 'vma', 'vmacro17280' => 'vma', 'vmacro19601' => 'vma' ) $gf_id = 'HOM05D001028' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001028' ) $data_identifier = 'HOM05D001028' $data_type = 'gf_id' $species_gene_counts = array( 'aox' => (int) 11, 'ccan' => (int) 6, 'camsi' => (int) 540, 'din' => (int) 4, 'bvu' => (int) 1, 'fan' => (int) 1, 'pgr' => (int) 1, 'ppe' => (int) 3, 'qlo' => (int) 8, 'rsi' => (int) 4, 'tar' => (int) 2, 'vma' => (int) 9 ) $gf_gene_species = 'vma' $gf_gene_id = 'vmacro19601' $species_info = array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ) $local_species = 'din' $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' => 'HOM05D001028', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '590', 'num_species' => '12' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'Aqoxy1G01649' => 'aox', 'Aqoxy1G02950' => 'aox', 'Aqoxy2G01005' => 'aox', 'Aqoxy2G01064' => 'aox', 'Aqoxy3G02267' => 'aox', 'Aqoxy3G02617' => 'aox', 'Aqoxy3G02693' => 'aox', 'Aqoxy5G03425' => 'aox', 'Aqoxy6G02164' => 'aox', 'Aqoxy6G02364' => 'aox', 'Aqoxy7G02284' => 'aox', 'Cc00_g09720' => 'ccan', 'Cc00_g21410' => 'ccan', 'Cc00_g31750' => 'ccan', 'Cc00_g34740' => 'ccan', 'Cc04_g16890' => 'ccan', 'Cc11_g03120' => 'ccan', 'CSS0000222' => 'camsi', 'CSS0000265' => 'camsi', 'CSS0000306' => 'camsi', 'CSS0000326' => 'camsi', 'CSS0000530' => 'camsi', 'CSS0000563' => 'camsi', 'CSS0000584' => 'camsi', 'CSS0000684' => 'camsi', 'CSS0001100' => 'camsi', 'CSS0001311' => 'camsi', 'CSS0001343' => 'camsi', 'CSS0001399' => 'camsi', 'CSS0001475' => 'camsi', 'CSS0001506' => 'camsi', 'CSS0001602' => 'camsi', 'CSS0001681' => 'camsi', 'CSS0001874' => 'camsi', 'CSS0001948' => 'camsi', 'CSS0002022' => 'camsi', 'CSS0002230' => 'camsi', 'CSS0002265' => 'camsi', 'CSS0002277' => 'camsi', 'CSS0002462' => 'camsi', 'CSS0002823' => 'camsi', 'CSS0003091' => 'camsi', 'CSS0003162' => 'camsi', 'CSS0003264' => 'camsi', 'CSS0003355' => 'camsi', 'CSS0003378' => 'camsi', 'CSS0003472' => 'camsi', 'CSS0003500' => 'camsi', 'CSS0003640' => 'camsi', 'CSS0003767' => 'camsi', 'CSS0003894' => 'camsi', 'CSS0003952' => 'camsi', 'CSS0003977' => 'camsi', 'CSS0004028' => 'camsi', 'CSS0004117' => 'camsi', 'CSS0004137' => 'camsi', 'CSS0004176' => 'camsi', 'CSS0004265' => 'camsi', 'CSS0004450' => 'camsi', 'CSS0004468' => 'camsi', 'CSS0004488' => 'camsi', 'CSS0004490' => 'camsi', 'CSS0004632' => 'camsi', 'CSS0004790' => 'camsi', 'CSS0004877' => 'camsi', 'CSS0004920' => 'camsi', 'CSS0004969' => 'camsi', 'CSS0005084' => 'camsi', 'CSS0005101' => 'camsi', 'CSS0005271' => 'camsi', 'CSS0005313' => 'camsi', 'CSS0005331' => 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'camsi', 'CSS0020378' => 'camsi', 'CSS0020388' => 'camsi', 'CSS0020452' => 'camsi', 'CSS0020588' => 'camsi', 'CSS0020661' => 'camsi', 'CSS0020886' => 'camsi', 'CSS0020973' => 'camsi', 'CSS0021035' => 'camsi', 'CSS0021111' => 'camsi', 'CSS0021131' => 'camsi', 'CSS0021151' => 'camsi', 'CSS0021228' => 'camsi', 'CSS0021397' => 'camsi', 'CSS0021420' => 'camsi', 'CSS0021464' => 'camsi', 'CSS0021547' => 'camsi', 'CSS0021608' => 'camsi', 'CSS0021740' => 'camsi', 'CSS0021826' => 'camsi', 'CSS0021904' => 'camsi', 'CSS0021941' => 'camsi', 'CSS0022189' => 'camsi', 'CSS0022199' => 'camsi', 'CSS0022502' => 'camsi', 'CSS0022531' => 'camsi', 'CSS0022581' => 'camsi', 'CSS0022612' => 'camsi', 'CSS0022621' => 'camsi', 'CSS0022815' => 'camsi', 'CSS0022936' => 'camsi', 'CSS0022964' => 'camsi', 'CSS0022985' => 'camsi', 'CSS0023002' => 'camsi', 'CSS0023006' => 'camsi', 'CSS0023024' => 'camsi', 'CSS0023489' => 'camsi', 'CSS0023593' => 'camsi', 'CSS0023621' => 'camsi', 'CSS0023743' => 'camsi', 'CSS0023804' => 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'camsi', 'CSS0043171' => 'camsi', 'CSS0043314' => 'camsi', 'CSS0043361' => 'camsi', 'CSS0043375' => 'camsi', 'CSS0043518' => 'camsi', 'CSS0043536' => 'camsi', 'CSS0043678' => 'camsi', 'CSS0043765' => 'camsi', 'CSS0043897' => 'camsi', 'CSS0043944' => 'camsi', 'CSS0044126' => 'camsi', 'CSS0044136' => 'camsi', 'CSS0044179' => 'camsi', 'CSS0044290' => 'camsi', 'CSS0044437' => 'camsi', 'CSS0044502' => 'camsi', 'CSS0044603' => 'camsi', 'CSS0044680' => 'camsi', 'CSS0044685' => 'camsi', 'CSS0044700' => 'camsi', 'CSS0044888' => 'camsi', 'CSS0044923' => 'camsi', 'CSS0044926' => 'camsi', 'CSS0044979' => 'camsi', 'CSS0045049' => 'camsi', 'CSS0045132' => 'camsi', 'CSS0045161' => 'camsi', 'CSS0045219' => 'camsi', 'CSS0045230' => 'camsi', 'CSS0045259' => 'camsi', 'CSS0045324' => 'camsi', 'CSS0045368' => 'camsi', 'CSS0045435' => 'camsi', 'CSS0045856' => 'camsi', 'CSS0045955' => 'camsi', 'CSS0046158' => 'camsi', 'CSS0046334' => 'camsi', 'CSS0046365' => 'camsi', 'CSS0046396' => 'camsi', 'CSS0046400' => 'camsi', 'CSS0046445' => 'camsi', 'CSS0046493' => 'camsi', 'CSS0046640' => 'camsi', 'CSS0046657' => 'camsi', 'CSS0046702' => 'camsi', 'CSS0047208' => 'camsi', 'CSS0047368' => 'camsi', 'CSS0047403' => 'camsi', 'CSS0047417' => 'camsi', 'CSS0047469' => 'camsi', 'CSS0047480' => 'camsi', 'CSS0047482' => 'camsi', 'CSS0047693' => 'camsi', 'CSS0047766' => 'camsi', 'CSS0047866' => 'camsi', 'CSS0047884' => 'camsi', 'CSS0048235' => 'camsi', 'CSS0048383' => 'camsi', 'CSS0048438' => 'camsi', 'CSS0048502' => 'camsi', 'CSS0048546' => 'camsi', 'CSS0048653' => 'camsi', 'CSS0048658' => 'camsi', 'CSS0048729' => 'camsi', 'CSS0048867' => 'camsi', 'CSS0048988' => 'camsi', 'CSS0049053' => 'camsi', 'CSS0049099' => 'camsi', 'CSS0049166' => 'camsi', 'CSS0049174' => 'camsi', 'CSS0049212' => 'camsi', 'CSS0049280' => 'camsi', 'CSS0049391' => 'camsi', 'CSS0049546' => 'camsi', 'CSS0049634' => 'camsi', 'CSS0049655' => 'camsi', 'CSS0049813' => 'camsi', 'CSS0049949' => 'camsi', 'CSS0050009' => 'camsi', 'CSS0050118' => 'camsi', 'CSS0050205' => 'camsi', 'CSS0050275' => 'camsi', 'CSS0050480' => 'camsi', 'CSS0050488' => 'camsi', 'CSS0050497' => 'camsi', 'Dinv03126' => 'din', 'Dinv13140' => 'din', 'Dinv13247' => 'din', 'Dinv14217' => 'din', 'EL10Ac9g22435' => 'bvu', 'FAN20G1200' => 'fan', 'PGR142G2516' => 'pgr', 'Prupe.3G160200' => 'ppe', 'Prupe.5G238200' => 'ppe', 'Prupe.7G047500' => 'ppe', 'QL03p045360' => 'qlo', 'QL05p034369' => 'qlo', 'QL05p034412' => 'qlo', 'QL08p017802' => 'qlo', 'QL08p024762' => 'qlo', 'QL10p026237' => 'qlo', 'QL10p032070' => 'qlo', 'QL11p003821' => 'qlo', 'Rhsim04G0057300' => 'rsi', 'Rhsim05G0049200' => 'rsi', 'Rhsim12G0010400' => 'rsi', 'Rhsim12G0012800' => 'rsi', 'TAR624G0483' => 'tar', 'TAR703G0001' => 'tar', 'vmacro05414' => 'vma', 'vmacro07091' => 'vma', 'vmacro07116' => 'vma', 'vmacro08423' => 'vma', 'vmacro09046' => 'vma', 'vmacro14269' => 'vma', 'vmacro16092' => 'vma', 'vmacro17280' => 'vma', 'vmacro19601' => 'vma' ), 'gf_id' => 'HOM05D001028', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001028' ), 'data_identifier' => 'HOM05D001028', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001028', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '590', 'num_species' => '12' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'Aqoxy1G01649' => 'aox', 'Aqoxy1G02950' => 'aox', 'Aqoxy2G01005' => 'aox', 'Aqoxy2G01064' => 'aox', 'Aqoxy3G02267' => 'aox', 'Aqoxy3G02617' => 'aox', 'Aqoxy3G02693' => 'aox', 'Aqoxy5G03425' => 'aox', 'Aqoxy6G02164' => 'aox', 'Aqoxy6G02364' => 'aox', 'Aqoxy7G02284' => 'aox', 'Cc00_g09720' => 'ccan', 'Cc00_g21410' => 'ccan', 'Cc00_g31750' => 'ccan', 'Cc00_g34740' => 'ccan', 'Cc04_g16890' => 'ccan', 'Cc11_g03120' => 'ccan', 'CSS0000222' => 'camsi', 'CSS0000265' => 'camsi', 'CSS0000306' => 'camsi', 'CSS0000326' => 'camsi', 'CSS0000530' => 'camsi', 'CSS0000563' => 'camsi', 'CSS0000584' => 'camsi', 'CSS0000684' => 'camsi', 'CSS0001100' => 'camsi', 'CSS0001311' => 'camsi', 'CSS0001343' => 'camsi', 'CSS0001399' => 'camsi', 'CSS0001475' => 'camsi', 'CSS0001506' => 'camsi', 'CSS0001602' => 'camsi', 'CSS0001681' => 'camsi', 'CSS0001874' => 'camsi', 'CSS0001948' => 'camsi', 'CSS0002022' => 'camsi', 'CSS0002230' => 'camsi', 'CSS0002265' => 'camsi', 'CSS0002277' => 'camsi', 'CSS0002462' => 'camsi', 'CSS0002823' => 'camsi', 'CSS0003091' => 'camsi', 'CSS0003162' => 'camsi', 'CSS0003264' => 'camsi', 'CSS0003355' => 'camsi', 'CSS0003378' => 'camsi', 'CSS0003472' => 'camsi', 'CSS0003500' => 'camsi', 'CSS0003640' => 'camsi', 'CSS0003767' => 'camsi', 'CSS0003894' => 'camsi', 'CSS0003952' => 'camsi', 'CSS0003977' => 'camsi', 'CSS0004028' => 'camsi', 'CSS0004117' => 'camsi', 'CSS0004137' => 'camsi', 'CSS0004176' => 'camsi', 'CSS0004265' => 'camsi', 'CSS0004450' => 'camsi', 'CSS0004468' => 'camsi', 'CSS0004488' => 'camsi', 'CSS0004490' => 'camsi', 'CSS0004632' => 'camsi', 'CSS0004790' => 'camsi', 'CSS0004877' => 'camsi', 'CSS0004920' => 'camsi', 'CSS0004969' => 'camsi', 'CSS0005084' => 'camsi', 'CSS0005101' => 'camsi', 'CSS0005271' => 'camsi', 'CSS0005313' => 'camsi', 'CSS0005331' => 'camsi', 'CSS0005368' => 'camsi', 'CSS0005391' => 'camsi', 'CSS0005437' => 'camsi', 'CSS0005515' => 'camsi', 'CSS0005526' => 'camsi', 'CSS0005532' => 'camsi', 'CSS0005595' => 'camsi', 'CSS0005677' => 'camsi', 'CSS0005838' => 'camsi', 'CSS0005988' => 'camsi', 'CSS0006100' => 'camsi', 'CSS0006128' => 'camsi', 'CSS0006293' => 'camsi', 'CSS0006378' => 'camsi', 'CSS0006400' => 'camsi', 'CSS0006441' => 'camsi', 'CSS0006455' => 'camsi', 'CSS0006480' => 'camsi', 'CSS0006483' => 'camsi', 'CSS0006538' => 'camsi', 'CSS0006582' => 'camsi', 'CSS0006632' => 'camsi', 'CSS0006771' => 'camsi', 'CSS0006803' => 'camsi', 'CSS0006852' => 'camsi', 'CSS0006861' => 'camsi', 'CSS0006910' => 'camsi', 'CSS0007037' => 'camsi', 'CSS0007066' => 'camsi', 'CSS0007072' => 'camsi', 'CSS0007109' => 'camsi', 'CSS0007193' => 'camsi', 'CSS0007319' => 'camsi', 'CSS0007336' => 'camsi', 'CSS0007377' => 'camsi', 'CSS0007659' => 'camsi', 'CSS0007701' => 'camsi', 'CSS0007711' => 'camsi', 'CSS0007809' => 'camsi', 'CSS0008045' => 'camsi', 'CSS0008050' => 'camsi', 'CSS0008206' => 'camsi', 'CSS0008251' => 'camsi', 'CSS0008252' => 'camsi', 'CSS0008279' => 'camsi', 'CSS0008482' => 'camsi', 'CSS0008583' => 'camsi', 'CSS0008699' => 'camsi', 'CSS0008798' => 'camsi', 'CSS0008971' => 'camsi', 'CSS0009019' => 'camsi', 'CSS0009191' => 'camsi', 'CSS0009241' => 'camsi', 'CSS0009246' => 'camsi', 'CSS0009399' => 'camsi', 'CSS0009654' => 'camsi', 'CSS0009722' => 'camsi', 'CSS0009920' => 'camsi', 'CSS0009986' => 'camsi', 'CSS0010182' => 'camsi', 'CSS0010202' => 'camsi', 'CSS0010330' => 'camsi', 'CSS0010362' => 'camsi', 'CSS0010456' => 'camsi', 'CSS0010472' => 'camsi', 'CSS0010507' => 'camsi', 'CSS0010512' => 'camsi', 'CSS0010520' => 'camsi', 'CSS0010617' => 'camsi', 'CSS0010706' => 'camsi', 'CSS0010747' => 'camsi', 'CSS0010816' => 'camsi', 'CSS0011020' => 'camsi', 'CSS0011115' => 'camsi', 'CSS0011383' => 'camsi', 'CSS0011491' => 'camsi', 'CSS0011602' => 'camsi', 'CSS0011605' => 'camsi', 'CSS0011625' => 'camsi', 'CSS0011654' => 'camsi', 'CSS0011781' => 'camsi', 'CSS0011853' => 'camsi', 'CSS0011898' => 'camsi', 'CSS0011933' => 'camsi', 'CSS0011996' => 'camsi', 'CSS0012066' => 'camsi', 'CSS0012097' => 'camsi', 'CSS0012108' => 'camsi', 'CSS0012226' => 'camsi', 'CSS0012248' => 'camsi', 'CSS0012331' => 'camsi', 'CSS0012797' => 'camsi', 'CSS0012818' => 'camsi', 'CSS0012904' => 'camsi', 'CSS0013001' => 'camsi', 'CSS0013022' => 'camsi', 'CSS0013172' => 'camsi', 'CSS0013244' => 'camsi', 'CSS0013267' => 'camsi', 'CSS0013275' => 'camsi', 'CSS0013324' => 'camsi', 'CSS0013334' => 'camsi', 'CSS0013394' => 'camsi', 'CSS0013549' => 'camsi', 'CSS0013689' => 'camsi', 'CSS0014026' => 'camsi', 'CSS0014049' => 'camsi', 'CSS0014144' => 'camsi', 'CSS0014354' => 'camsi', 'CSS0014579' => 'camsi', 'CSS0014648' => 'camsi', 'CSS0014902' => 'camsi', 'CSS0014979' => 'camsi', 'CSS0015278' => 'camsi', 'CSS0015310' => 'camsi', 'CSS0015364' => 'camsi', 'CSS0015455' => 'camsi', 'CSS0015693' => 'camsi', 'CSS0015774' => 'camsi', 'CSS0015795' => 'camsi', 'CSS0015952' => 'camsi', 'CSS0016104' => 'camsi', 'CSS0016241' => 'camsi', 'CSS0016303' => 'camsi', 'CSS0016490' => 'camsi', 'CSS0016832' => 'camsi', 'CSS0016845' => 'camsi', 'CSS0016914' => 'camsi', 'CSS0016946' => 'camsi', 'CSS0017102' => 'camsi', 'CSS0017193' => 'camsi', 'CSS0017528' => 'camsi', 'CSS0017619' => 'camsi', 'CSS0017679' => 'camsi', 'CSS0017816' => 'camsi', 'CSS0017880' => 'camsi', 'CSS0018106' => 'camsi', 'CSS0018162' => 'camsi', 'CSS0018304' => 'camsi', 'CSS0018406' => 'camsi', 'CSS0018481' => 'camsi', 'CSS0018511' => 'camsi', 'CSS0018596' => 'camsi', 'CSS0018727' => 'camsi', 'CSS0018751' => 'camsi', 'CSS0018777' => 'camsi', 'CSS0018798' => 'camsi', 'CSS0019137' => 'camsi', 'CSS0019177' => 'camsi', 'CSS0019217' => 'camsi', 'CSS0019361' => 'camsi', 'CSS0019516' => 'camsi', 'CSS0019538' => 'camsi', 'CSS0019560' => 'camsi', 'CSS0019819' => 'camsi', 'CSS0019837' => 'camsi', 'CSS0019915' => 'camsi', 'CSS0019925' => 'camsi', 'CSS0020112' => 'camsi', 'CSS0020160' => 'camsi', 'CSS0020378' => 'camsi', 'CSS0020388' => 'camsi', 'CSS0020452' => 'camsi', 'CSS0020588' => 'camsi', 'CSS0020661' => 'camsi', 'CSS0020886' => 'camsi', 'CSS0020973' => 'camsi', 'CSS0021035' => 'camsi', 'CSS0021111' => 'camsi', 'CSS0021131' => 'camsi', 'CSS0021151' => 'camsi', 'CSS0021228' => 'camsi', 'CSS0021397' => 'camsi', 'CSS0021420' => 'camsi', 'CSS0021464' => 'camsi', 'CSS0021547' => 'camsi', 'CSS0021608' => 'camsi', 'CSS0021740' => 'camsi', 'CSS0021826' => 'camsi', 'CSS0021904' => 'camsi', 'CSS0021941' => 'camsi', 'CSS0022189' => 'camsi', 'CSS0022199' => 'camsi', 'CSS0022502' => 'camsi', 'CSS0022531' => 'camsi', 'CSS0022581' => 'camsi', 'CSS0022612' => 'camsi', 'CSS0022621' => 'camsi', 'CSS0022815' => 'camsi', 'CSS0022936' => 'camsi', 'CSS0022964' => 'camsi', 'CSS0022985' => 'camsi', 'CSS0023002' => 'camsi', 'CSS0023006' => 'camsi', 'CSS0023024' => 'camsi', 'CSS0023489' => 'camsi', 'CSS0023593' => 'camsi', 'CSS0023621' => 'camsi', 'CSS0023743' => 'camsi', 'CSS0023804' => 'camsi', 'CSS0023805' => 'camsi', 'CSS0023908' => 'camsi', 'CSS0023938' => 'camsi', 'CSS0023981' => 'camsi', 'CSS0024027' => 'camsi', 'CSS0024169' => 'camsi', 'CSS0024193' => 'camsi', 'CSS0024269' => 'camsi', 'CSS0024336' => 'camsi', 'CSS0024337' => 'camsi', 'CSS0024548' => 'camsi', 'CSS0024564' => 'camsi', 'CSS0024585' => 'camsi', 'CSS0024738' => 'camsi', 'CSS0024833' => 'camsi', 'CSS0024846' => 'camsi', 'CSS0024957' => 'camsi', 'CSS0024974' => 'camsi', 'CSS0025005' => 'camsi', 'CSS0025235' => 'camsi', 'CSS0025465' => 'camsi', 'CSS0025633' => 'camsi', 'CSS0025688' => 'camsi', 'CSS0025759' => 'camsi', 'CSS0025774' => 'camsi', 'CSS0025801' => 'camsi', 'CSS0025942' => 'camsi', 'CSS0026083' => 'camsi', 'CSS0026194' => 'camsi', 'CSS0026230' => 'camsi', 'CSS0026398' => 'camsi', 'CSS0026419' => 'camsi', 'CSS0026679' => 'camsi', 'CSS0026719' => 'camsi', 'CSS0026795' => 'camsi', 'CSS0026835' => 'camsi', 'CSS0026930' => 'camsi', 'CSS0027053' => 'camsi', 'CSS0027130' => 'camsi', 'CSS0027192' => 'camsi', 'CSS0027454' => 'camsi', 'CSS0027467' => 'camsi', 'CSS0027521' => 'camsi', 'CSS0027662' => 'camsi', 'CSS0027795' => 'camsi', 'CSS0027835' => 'camsi', 'CSS0027966' => 'camsi', 'CSS0028090' => 'camsi', 'CSS0028134' => 'camsi', 'CSS0028205' => 'camsi', 'CSS0028263' => 'camsi', 'CSS0028363' => 'camsi', 'CSS0028598' => 'camsi', 'CSS0029175' => 'camsi', 'CSS0029191' => 'camsi', 'CSS0029424' => 'camsi', 'CSS0029479' => 'camsi', 'CSS0029496' => 'camsi', 'CSS0029633' => 'camsi', 'CSS0029837' => 'camsi', 'CSS0029844' => 'camsi', 'CSS0029863' => 'camsi', 'CSS0029874' => 'camsi', 'CSS0029959' => 'camsi', 'CSS0030001' => 'camsi', 'CSS0030093' => 'camsi', 'CSS0030199' => 'camsi', 'CSS0030200' => 'camsi', 'CSS0030427' => 'camsi', 'CSS0030476' => 'camsi', 'CSS0030636' => 'camsi', 'CSS0030673' => 'camsi', 'CSS0030766' => 'camsi', 'CSS0030775' => 'camsi', 'CSS0030858' => 'camsi', 'CSS0030873' => 'camsi', 'CSS0030929' => 'camsi', 'CSS0031028' => 'camsi', 'CSS0031129' => 'camsi', 'CSS0031164' => 'camsi', 'CSS0031340' => 'camsi', 'CSS0031368' => 'camsi', 'CSS0031395' => 'camsi', 'CSS0031596' => 'camsi', 'CSS0031727' => 'camsi', 'CSS0032011' => 'camsi', 'CSS0032160' => 'camsi', 'CSS0032538' => 'camsi', 'CSS0032576' => 'camsi', 'CSS0032603' => 'camsi', 'CSS0032640' => 'camsi', 'CSS0032704' => 'camsi', 'CSS0032851' => 'camsi', 'CSS0032973' => 'camsi', 'CSS0033048' => 'camsi', 'CSS0033082' => 'camsi', 'CSS0033157' => 'camsi', 'CSS0033253' => 'camsi', 'CSS0033347' => 'camsi', 'CSS0033601' => 'camsi', 'CSS0033820' => 'camsi', 'CSS0033881' => 'camsi', 'CSS0033934' => 'camsi', 'CSS0034143' => 'camsi', 'CSS0034176' => 'camsi', 'CSS0034201' => 'camsi', 'CSS0034269' => 'camsi', 'CSS0034303' => 'camsi', 'CSS0034463' => 'camsi', 'CSS0034470' => 'camsi', 'CSS0034514' => 'camsi', 'CSS0034525' => 'camsi', 'CSS0034726' => 'camsi', 'CSS0034727' => 'camsi', 'CSS0034737' => 'camsi', 'CSS0034768' => 'camsi', 'CSS0034890' => 'camsi', 'CSS0034943' => 'camsi', 'CSS0034957' => 'camsi', 'CSS0034973' => 'camsi', 'CSS0035178' => 'camsi', 'CSS0035260' => 'camsi', 'CSS0035316' => 'camsi', 'CSS0035347' => 'camsi', 'CSS0035360' => 'camsi', 'CSS0035380' => 'camsi', 'CSS0035429' => 'camsi', 'CSS0035446' => 'camsi', 'CSS0035737' => 'camsi', 'CSS0035852' => 'camsi', 'CSS0035967' => 'camsi', 'CSS0036001' => 'camsi', 'CSS0036044' => 'camsi', 'CSS0036221' => 'camsi', 'CSS0036333' => 'camsi', 'CSS0036435' => 'camsi', 'CSS0036843' => 'camsi', 'CSS0036846' => 'camsi', 'CSS0037097' => 'camsi', 'CSS0037263' => 'camsi', 'CSS0037370' => 'camsi', 'CSS0037410' => 'camsi', 'CSS0037449' => 'camsi', 'CSS0037603' => 'camsi', 'CSS0037851' => 'camsi', 'CSS0037891' => 'camsi', 'CSS0037996' => 'camsi', 'CSS0038222' => 'camsi', 'CSS0038433' => 'camsi', 'CSS0038441' => 'camsi', 'CSS0038718' => 'camsi', 'CSS0038890' => 'camsi', 'CSS0039049' => 'camsi', 'CSS0039145' => 'camsi', 'CSS0039243' => 'camsi', 'CSS0039294' => 'camsi', 'CSS0039324' => 'camsi', 'CSS0039376' => 'camsi', 'CSS0039475' => 'camsi', 'CSS0039539' => 'camsi', 'CSS0039546' => 'camsi', 'CSS0039567' => 'camsi', 'CSS0039599' => 'camsi', 'CSS0039763' => 'camsi', 'CSS0039863' => 'camsi', 'CSS0040107' => 'camsi', 'CSS0040124' => 'camsi', 'CSS0040151' => 'camsi', 'CSS0040165' => 'camsi', 'CSS0040309' => 'camsi', 'CSS0040318' => 'camsi', 'CSS0040347' => 'camsi', 'CSS0040371' => 'camsi', 'CSS0040456' => 'camsi', 'CSS0040551' => 'camsi', 'CSS0040975' => 'camsi', 'CSS0040981' => 'camsi', 'CSS0041299' => 'camsi', 'CSS0041493' => 'camsi', 'CSS0041658' => 'camsi', 'CSS0041899' => 'camsi', 'CSS0041927' => 'camsi', 'CSS0042016' => 'camsi', 'CSS0042034' => 'camsi', 'CSS0042103' => 'camsi', 'CSS0042172' => 'camsi', 'CSS0042198' => 'camsi', 'CSS0042201' => 'camsi', 'CSS0042308' => 'camsi', 'CSS0042329' => 'camsi', 'CSS0042348' => 'camsi', 'CSS0042349' => 'camsi', 'CSS0042489' => 'camsi', 'CSS0042575' => 'camsi', 'CSS0042624' => 'camsi', 'CSS0042660' => 'camsi', 'CSS0042694' => 'camsi', 'CSS0042995' => 'camsi', 'CSS0043079' => 'camsi', 'CSS0043165' => 'camsi', 'CSS0043171' => 'camsi', 'CSS0043314' => 'camsi', 'CSS0043361' => 'camsi', 'CSS0043375' => 'camsi', 'CSS0043518' => 'camsi', 'CSS0043536' => 'camsi', 'CSS0043678' => 'camsi', 'CSS0043765' => 'camsi', 'CSS0043897' => 'camsi', 'CSS0043944' => 'camsi', 'CSS0044126' => 'camsi', 'CSS0044136' => 'camsi', 'CSS0044179' => 'camsi', 'CSS0044290' => 'camsi', 'CSS0044437' => 'camsi', 'CSS0044502' => 'camsi', 'CSS0044603' => 'camsi', 'CSS0044680' => 'camsi', 'CSS0044685' => 'camsi', 'CSS0044700' => 'camsi', 'CSS0044888' => 'camsi', 'CSS0044923' => 'camsi', 'CSS0044926' => 'camsi', 'CSS0044979' => 'camsi', 'CSS0045049' => 'camsi', 'CSS0045132' => 'camsi', 'CSS0045161' => 'camsi', 'CSS0045219' => 'camsi', 'CSS0045230' => 'camsi', 'CSS0045259' => 'camsi', 'CSS0045324' => 'camsi', 'CSS0045368' => 'camsi', 'CSS0045435' => 'camsi', 'CSS0045856' => 'camsi', 'CSS0045955' => 'camsi', 'CSS0046158' => 'camsi', 'CSS0046334' => 'camsi', 'CSS0046365' => 'camsi', 'CSS0046396' => 'camsi', 'CSS0046400' => 'camsi', 'CSS0046445' => 'camsi', 'CSS0046493' => 'camsi', 'CSS0046640' => 'camsi', 'CSS0046657' => 'camsi', 'CSS0046702' => 'camsi', 'CSS0047208' => 'camsi', 'CSS0047368' => 'camsi', 'CSS0047403' => 'camsi', 'CSS0047417' => 'camsi', 'CSS0047469' => 'camsi', 'CSS0047480' => 'camsi', 'CSS0047482' => 'camsi', 'CSS0047693' => 'camsi', 'CSS0047766' => 'camsi', 'CSS0047866' => 'camsi', 'CSS0047884' => 'camsi', 'CSS0048235' => 'camsi', 'CSS0048383' => 'camsi', 'CSS0048438' => 'camsi', 'CSS0048502' => 'camsi', 'CSS0048546' => 'camsi', 'CSS0048653' => 'camsi', 'CSS0048658' => 'camsi', 'CSS0048729' => 'camsi', 'CSS0048867' => 'camsi', 'CSS0048988' => 'camsi', 'CSS0049053' => 'camsi', 'CSS0049099' => 'camsi', 'CSS0049166' => 'camsi', 'CSS0049174' => 'camsi', 'CSS0049212' => 'camsi', 'CSS0049280' => 'camsi', 'CSS0049391' => 'camsi', 'CSS0049546' => 'camsi', 'CSS0049634' => 'camsi', 'CSS0049655' => 'camsi', 'CSS0049813' => 'camsi', 'CSS0049949' => 'camsi', 'CSS0050009' => 'camsi', 'CSS0050118' => 'camsi', 'CSS0050205' => 'camsi', 'CSS0050275' => 'camsi', 'CSS0050480' => 'camsi', 'CSS0050488' => 'camsi', 'CSS0050497' => 'camsi', 'Dinv03126' => 'din', 'Dinv13140' => 'din', 'Dinv13247' => 'din', 'Dinv14217' => 'din', 'EL10Ac9g22435' => 'bvu', 'FAN20G1200' => 'fan', 'PGR142G2516' => 'pgr', 'Prupe.3G160200' => 'ppe', 'Prupe.5G238200' => 'ppe', 'Prupe.7G047500' => 'ppe', 'QL03p045360' => 'qlo', 'QL05p034369' => 'qlo', 'QL05p034412' => 'qlo', 'QL08p017802' => 'qlo', 'QL08p024762' => 'qlo', 'QL10p026237' => 'qlo', 'QL10p032070' => 'qlo', 'QL11p003821' => 'qlo', 'Rhsim04G0057300' => 'rsi', 'Rhsim05G0049200' => 'rsi', 'Rhsim12G0010400' => 'rsi', 'Rhsim12G0012800' => 'rsi', 'TAR624G0483' => 'tar', 'TAR703G0001' => 'tar', 'vmacro05414' => 'vma', 'vmacro07091' => 'vma', 'vmacro07116' => 'vma', 'vmacro08423' => 'vma', 'vmacro09046' => 'vma', 'vmacro14269' => 'vma', 'vmacro16092' => 'vma', 'vmacro17280' => 'vma', 'vmacro19601' => 'vma' ) $gf_id = 'HOM05D001028' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001028' ) $data_identifier = 'HOM05D001028' $data_type = 'gf_id' $species_gene_counts = array( 'aox' => (int) 11, 'ccan' => (int) 6, 'camsi' => (int) 540, 'din' => (int) 4, 'bvu' => (int) 1, 'fan' => (int) 1, 'pgr' => (int) 1, 'ppe' => (int) 3, 'qlo' => (int) 8, 'rsi' => (int) 4, 'tar' => (int) 2, 'vma' => (int) 9 ) $gf_gene_species = 'vma' $gf_gene_id = 'vmacro19601' $species_info = array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ) $local_species = 'din' $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' => 'HOM05D001028', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '590', 'num_species' => '12' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'Aqoxy1G01649' => 'aox', 'Aqoxy1G02950' => 'aox', 'Aqoxy2G01005' => 'aox', 'Aqoxy2G01064' => 'aox', 'Aqoxy3G02267' => 'aox', 'Aqoxy3G02617' => 'aox', 'Aqoxy3G02693' => 'aox', 'Aqoxy5G03425' => 'aox', 'Aqoxy6G02164' => 'aox', 'Aqoxy6G02364' => 'aox', 'Aqoxy7G02284' => 'aox', 'Cc00_g09720' => 'ccan', 'Cc00_g21410' => 'ccan', 'Cc00_g31750' => 'ccan', 'Cc00_g34740' => 'ccan', 'Cc04_g16890' => 'ccan', 'Cc11_g03120' => 'ccan', 'CSS0000222' => 'camsi', 'CSS0000265' => 'camsi', 'CSS0000306' => 'camsi', 'CSS0000326' => 'camsi', 'CSS0000530' => 'camsi', 'CSS0000563' => 'camsi', 'CSS0000584' => 'camsi', 'CSS0000684' => 'camsi', 'CSS0001100' => 'camsi', 'CSS0001311' => 'camsi', 'CSS0001343' => 'camsi', 'CSS0001399' => 'camsi', 'CSS0001475' => 'camsi', 'CSS0001506' => 'camsi', 'CSS0001602' => 'camsi', 'CSS0001681' => 'camsi', 'CSS0001874' => 'camsi', 'CSS0001948' => 'camsi', 'CSS0002022' => 'camsi', 'CSS0002230' => 'camsi', 'CSS0002265' => 'camsi', 'CSS0002277' => 'camsi', 'CSS0002462' => 'camsi', 'CSS0002823' => 'camsi', 'CSS0003091' => 'camsi', 'CSS0003162' => 'camsi', 'CSS0003264' => 'camsi', 'CSS0003355' => 'camsi', 'CSS0003378' => 'camsi', 'CSS0003472' => 'camsi', 'CSS0003500' => 'camsi', 'CSS0003640' => 'camsi', 'CSS0003767' => 'camsi', 'CSS0003894' => 'camsi', 'CSS0003952' => 'camsi', 'CSS0003977' => 'camsi', 'CSS0004028' => 'camsi', 'CSS0004117' => 'camsi', 'CSS0004137' => 'camsi', 'CSS0004176' => 'camsi', 'CSS0004265' => 'camsi', 'CSS0004450' => 'camsi', 'CSS0004468' => 'camsi', 'CSS0004488' => 'camsi', 'CSS0004490' => 'camsi', 'CSS0004632' => 'camsi', 'CSS0004790' => 'camsi', 'CSS0004877' => 'camsi', 'CSS0004920' => 'camsi', 'CSS0004969' => 'camsi', 'CSS0005084' => 'camsi', 'CSS0005101' => 'camsi', 'CSS0005271' => 'camsi', 'CSS0005313' => 'camsi', 'CSS0005331' => 'camsi', 'CSS0005368' => 'camsi', 'CSS0005391' => 'camsi', 'CSS0005437' => 'camsi', 'CSS0005515' => 'camsi', 'CSS0005526' => 'camsi', 'CSS0005532' => 'camsi', 'CSS0005595' => 'camsi', 'CSS0005677' => 'camsi', 'CSS0005838' => 'camsi', 'CSS0005988' => 'camsi', 'CSS0006100' => 'camsi', 'CSS0006128' => 'camsi', 'CSS0006293' => 'camsi', 'CSS0006378' => 'camsi', 'CSS0006400' => 'camsi', 'CSS0006441' => 'camsi', 'CSS0006455' => 'camsi', 'CSS0006480' => 'camsi', 'CSS0006483' => 'camsi', 'CSS0006538' => 'camsi', 'CSS0006582' => 'camsi', 'CSS0006632' => 'camsi', 'CSS0006771' => 'camsi', 'CSS0006803' => 'camsi', 'CSS0006852' => 'camsi', 'CSS0006861' => 'camsi', 'CSS0006910' => 'camsi', 'CSS0007037' => 'camsi', 'CSS0007066' => 'camsi', 'CSS0007072' => 'camsi', 'CSS0007109' => 'camsi', 'CSS0007193' => 'camsi', 'CSS0007319' => 'camsi', 'CSS0007336' => 'camsi', 'CSS0007377' => 'camsi', 'CSS0007659' => 'camsi', 'CSS0007701' => 'camsi', 'CSS0007711' => 'camsi', 'CSS0007809' => 'camsi', 'CSS0008045' => 'camsi', 'CSS0008050' => 'camsi', 'CSS0008206' => 'camsi', 'CSS0008251' => 'camsi', 'CSS0008252' => 'camsi', 'CSS0008279' => 'camsi', 'CSS0008482' => 'camsi', 'CSS0008583' => 'camsi', 'CSS0008699' => 'camsi', 'CSS0008798' => 'camsi', 'CSS0008971' => 'camsi', 'CSS0009019' => 'camsi', 'CSS0009191' => 'camsi', 'CSS0009241' => 'camsi', 'CSS0009246' => 'camsi', 'CSS0009399' => 'camsi', 'CSS0009654' => 'camsi', 'CSS0009722' => 'camsi', 'CSS0009920' => 'camsi', 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'CSS0018304' => 'camsi', 'CSS0018406' => 'camsi', 'CSS0018481' => 'camsi', 'CSS0018511' => 'camsi', 'CSS0018596' => 'camsi', 'CSS0018727' => 'camsi', 'CSS0018751' => 'camsi', 'CSS0018777' => 'camsi', 'CSS0018798' => 'camsi', 'CSS0019137' => 'camsi', 'CSS0019177' => 'camsi', 'CSS0019217' => 'camsi', 'CSS0019361' => 'camsi', 'CSS0019516' => 'camsi', 'CSS0019538' => 'camsi', 'CSS0019560' => 'camsi', 'CSS0019819' => 'camsi', 'CSS0019837' => 'camsi', 'CSS0019915' => 'camsi', 'CSS0019925' => 'camsi', 'CSS0020112' => 'camsi', 'CSS0020160' => 'camsi', 'CSS0020378' => 'camsi', 'CSS0020388' => 'camsi', 'CSS0020452' => 'camsi', 'CSS0020588' => 'camsi', 'CSS0020661' => 'camsi', 'CSS0020886' => 'camsi', 'CSS0020973' => 'camsi', 'CSS0021035' => 'camsi', 'CSS0021111' => 'camsi', 'CSS0021131' => 'camsi', 'CSS0021151' => 'camsi', 'CSS0021228' => 'camsi', 'CSS0021397' => 'camsi', 'CSS0021420' => 'camsi', 'CSS0021464' => 'camsi', 'CSS0021547' => 'camsi', 'CSS0021608' => 'camsi', 'CSS0021740' => 'camsi', 'CSS0021826' => 'camsi', 'CSS0021904' => 'camsi', 'CSS0021941' => 'camsi', 'CSS0022189' => 'camsi', 'CSS0022199' => 'camsi', 'CSS0022502' => 'camsi', 'CSS0022531' => 'camsi', 'CSS0022581' => 'camsi', 'CSS0022612' => 'camsi', 'CSS0022621' => 'camsi', 'CSS0022815' => 'camsi', 'CSS0022936' => 'camsi', 'CSS0022964' => 'camsi', 'CSS0022985' => 'camsi', 'CSS0023002' => 'camsi', 'CSS0023006' => 'camsi', 'CSS0023024' => 'camsi', 'CSS0023489' => 'camsi', 'CSS0023593' => 'camsi', 'CSS0023621' => 'camsi', 'CSS0023743' => 'camsi', 'CSS0023804' => 'camsi', 'CSS0023805' => 'camsi', 'CSS0023908' => 'camsi', 'CSS0023938' => 'camsi', 'CSS0023981' => 'camsi', 'CSS0024027' => 'camsi', 'CSS0024169' => 'camsi', 'CSS0024193' => 'camsi', 'CSS0024269' => 'camsi', 'CSS0024336' => 'camsi', 'CSS0024337' => 'camsi', 'CSS0024548' => 'camsi', 'CSS0024564' => 'camsi', 'CSS0024585' => 'camsi', 'CSS0024738' => 'camsi', 'CSS0024833' => 'camsi', 'CSS0024846' => 'camsi', 'CSS0024957' => 'camsi', 'CSS0024974' => 'camsi', 'CSS0025005' => 'camsi', 'CSS0025235' => 'camsi', 'CSS0025465' => 'camsi', 'CSS0025633' => 'camsi', 'CSS0025688' => 'camsi', 'CSS0025759' => 'camsi', 'CSS0025774' => 'camsi', 'CSS0025801' => 'camsi', 'CSS0025942' => 'camsi', 'CSS0026083' => 'camsi', 'CSS0026194' => 'camsi', 'CSS0026230' => 'camsi', 'CSS0026398' => 'camsi', 'CSS0026419' => 'camsi', 'CSS0026679' => 'camsi', 'CSS0026719' => 'camsi', 'CSS0026795' => 'camsi', 'CSS0026835' => 'camsi', 'CSS0026930' => 'camsi', 'CSS0027053' => 'camsi', 'CSS0027130' => 'camsi', 'CSS0027192' => 'camsi', 'CSS0027454' => 'camsi', 'CSS0027467' => 'camsi', 'CSS0027521' => 'camsi', 'CSS0027662' => 'camsi', 'CSS0027795' => 'camsi', 'CSS0027835' => 'camsi', 'CSS0027966' => 'camsi', 'CSS0028090' => 'camsi', 'CSS0028134' => 'camsi', 'CSS0028205' => 'camsi', 'CSS0028263' => 'camsi', 'CSS0028363' => 'camsi', 'CSS0028598' => 'camsi', 'CSS0029175' => 'camsi', 'CSS0029191' => 'camsi', 'CSS0029424' => 'camsi', 'CSS0029479' => 'camsi', 'CSS0029496' => 'camsi', 'CSS0029633' => 'camsi', 'CSS0029837' => 'camsi', 'CSS0029844' => 'camsi', 'CSS0029863' => 'camsi', 'CSS0029874' => 'camsi', 'CSS0029959' => 'camsi', 'CSS0030001' => 'camsi', 'CSS0030093' => 'camsi', 'CSS0030199' => 'camsi', 'CSS0030200' => 'camsi', 'CSS0030427' => 'camsi', 'CSS0030476' => 'camsi', 'CSS0030636' => 'camsi', 'CSS0030673' => 'camsi', 'CSS0030766' => 'camsi', 'CSS0030775' => 'camsi', 'CSS0030858' => 'camsi', 'CSS0030873' => 'camsi', 'CSS0030929' => 'camsi', 'CSS0031028' => 'camsi', 'CSS0031129' => 'camsi', 'CSS0031164' => 'camsi', 'CSS0031340' => 'camsi', 'CSS0031368' => 'camsi', 'CSS0031395' => 'camsi', 'CSS0031596' => 'camsi', 'CSS0031727' => 'camsi', 'CSS0032011' => 'camsi', 'CSS0032160' => 'camsi', 'CSS0032538' => 'camsi', 'CSS0032576' => 'camsi', 'CSS0032603' => 'camsi', 'CSS0032640' => 'camsi', 'CSS0032704' => 'camsi', 'CSS0032851' => 'camsi', 'CSS0032973' => 'camsi', 'CSS0033048' => 'camsi', 'CSS0033082' => 'camsi', 'CSS0033157' => 'camsi', 'CSS0033253' => 'camsi', 'CSS0033347' => 'camsi', 'CSS0033601' => 'camsi', 'CSS0033820' => 'camsi', 'CSS0033881' => 'camsi', 'CSS0033934' => 'camsi', 'CSS0034143' => 'camsi', 'CSS0034176' => 'camsi', 'CSS0034201' => 'camsi', 'CSS0034269' => 'camsi', 'CSS0034303' => 'camsi', 'CSS0034463' => 'camsi', 'CSS0034470' => 'camsi', 'CSS0034514' => 'camsi', 'CSS0034525' => 'camsi', 'CSS0034726' => 'camsi', 'CSS0034727' => 'camsi', 'CSS0034737' => 'camsi', 'CSS0034768' => 'camsi', 'CSS0034890' => 'camsi', 'CSS0034943' => 'camsi', 'CSS0034957' => 'camsi', 'CSS0034973' => 'camsi', 'CSS0035178' => 'camsi', 'CSS0035260' => 'camsi', 'CSS0035316' => 'camsi', 'CSS0035347' => 'camsi', 'CSS0035360' => 'camsi', 'CSS0035380' => 'camsi', 'CSS0035429' => 'camsi', 'CSS0035446' => 'camsi', 'CSS0035737' => 'camsi', 'CSS0035852' => 'camsi', 'CSS0035967' => 'camsi', 'CSS0036001' => 'camsi', 'CSS0036044' => 'camsi', 'CSS0036221' => 'camsi', 'CSS0036333' => 'camsi', 'CSS0036435' => 'camsi', 'CSS0036843' => 'camsi', 'CSS0036846' => 'camsi', 'CSS0037097' => 'camsi', 'CSS0037263' => 'camsi', 'CSS0037370' => 'camsi', 'CSS0037410' => 'camsi', 'CSS0037449' => 'camsi', 'CSS0037603' => 'camsi', 'CSS0037851' => 'camsi', 'CSS0037891' => 'camsi', 'CSS0037996' => 'camsi', 'CSS0038222' => 'camsi', 'CSS0038433' => 'camsi', 'CSS0038441' => 'camsi', 'CSS0038718' => 'camsi', 'CSS0038890' => 'camsi', 'CSS0039049' => 'camsi', 'CSS0039145' => 'camsi', 'CSS0039243' => 'camsi', 'CSS0039294' => 'camsi', 'CSS0039324' => 'camsi', 'CSS0039376' => 'camsi', 'CSS0039475' => 'camsi', 'CSS0039539' => 'camsi', 'CSS0039546' => 'camsi', 'CSS0039567' => 'camsi', 'CSS0039599' => 'camsi', 'CSS0039763' => 'camsi', 'CSS0039863' => 'camsi', 'CSS0040107' => 'camsi', 'CSS0040124' => 'camsi', 'CSS0040151' => 'camsi', 'CSS0040165' => 'camsi', 'CSS0040309' => 'camsi', 'CSS0040318' => 'camsi', 'CSS0040347' => 'camsi', 'CSS0040371' => 'camsi', 'CSS0040456' => 'camsi', 'CSS0040551' => 'camsi', 'CSS0040975' => 'camsi', 'CSS0040981' => 'camsi', 'CSS0041299' => 'camsi', 'CSS0041493' => 'camsi', 'CSS0041658' => 'camsi', 'CSS0041899' => 'camsi', 'CSS0041927' => 'camsi', 'CSS0042016' => 'camsi', 'CSS0042034' => 'camsi', 'CSS0042103' => 'camsi', 'CSS0042172' => 'camsi', 'CSS0042198' => 'camsi', 'CSS0042201' => 'camsi', 'CSS0042308' => 'camsi', 'CSS0042329' => 'camsi', 'CSS0042348' => 'camsi', 'CSS0042349' => 'camsi', 'CSS0042489' => 'camsi', 'CSS0042575' => 'camsi', 'CSS0042624' => 'camsi', 'CSS0042660' => 'camsi', 'CSS0042694' => 'camsi', 'CSS0042995' => 'camsi', 'CSS0043079' => 'camsi', 'CSS0043165' => 'camsi', 'CSS0043171' => 'camsi', 'CSS0043314' => 'camsi', 'CSS0043361' => 'camsi', 'CSS0043375' => 'camsi', 'CSS0043518' => 'camsi', 'CSS0043536' => 'camsi', 'CSS0043678' => 'camsi', 'CSS0043765' => 'camsi', 'CSS0043897' => 'camsi', 'CSS0043944' => 'camsi', 'CSS0044126' => 'camsi', 'CSS0044136' => 'camsi', 'CSS0044179' => 'camsi', 'CSS0044290' => 'camsi', 'CSS0044437' => 'camsi', 'CSS0044502' => 'camsi', 'CSS0044603' => 'camsi', 'CSS0044680' => 'camsi', 'CSS0044685' => 'camsi', 'CSS0044700' => 'camsi', 'CSS0044888' => 'camsi', 'CSS0044923' => 'camsi', 'CSS0044926' => 'camsi', 'CSS0044979' => 'camsi', 'CSS0045049' => 'camsi', 'CSS0045132' => 'camsi', 'CSS0045161' => 'camsi', 'CSS0045219' => 'camsi', 'CSS0045230' => 'camsi', 'CSS0045259' => 'camsi', 'CSS0045324' => 'camsi', 'CSS0045368' => 'camsi', 'CSS0045435' => 'camsi', 'CSS0045856' => 'camsi', 'CSS0045955' => 'camsi', 'CSS0046158' => 'camsi', 'CSS0046334' => 'camsi', 'CSS0046365' => 'camsi', 'CSS0046396' => 'camsi', 'CSS0046400' => 'camsi', 'CSS0046445' => 'camsi', 'CSS0046493' => 'camsi', 'CSS0046640' => 'camsi', 'CSS0046657' => 'camsi', 'CSS0046702' => 'camsi', 'CSS0047208' => 'camsi', 'CSS0047368' => 'camsi', 'CSS0047403' => 'camsi', 'CSS0047417' => 'camsi', 'CSS0047469' => 'camsi', 'CSS0047480' => 'camsi', 'CSS0047482' => 'camsi', 'CSS0047693' => 'camsi', 'CSS0047766' => 'camsi', 'CSS0047866' => 'camsi', 'CSS0047884' => 'camsi', 'CSS0048235' => 'camsi', 'CSS0048383' => 'camsi', 'CSS0048438' => 'camsi', 'CSS0048502' => 'camsi', 'CSS0048546' => 'camsi', 'CSS0048653' => 'camsi', 'CSS0048658' => 'camsi', 'CSS0048729' => 'camsi', 'CSS0048867' => 'camsi', 'CSS0048988' => 'camsi', 'CSS0049053' => 'camsi', 'CSS0049099' => 'camsi', 'CSS0049166' => 'camsi', 'CSS0049174' => 'camsi', 'CSS0049212' => 'camsi', 'CSS0049280' => 'camsi', 'CSS0049391' => 'camsi', 'CSS0049546' => 'camsi', 'CSS0049634' => 'camsi', 'CSS0049655' => 'camsi', 'CSS0049813' => 'camsi', 'CSS0049949' => 'camsi', 'CSS0050009' => 'camsi', 'CSS0050118' => 'camsi', 'CSS0050205' => 'camsi', 'CSS0050275' => 'camsi', 'CSS0050480' => 'camsi', 'CSS0050488' => 'camsi', 'CSS0050497' => 'camsi', 'Dinv03126' => 'din', 'Dinv13140' => 'din', 'Dinv13247' => 'din', 'Dinv14217' => 'din', 'EL10Ac9g22435' => 'bvu', 'FAN20G1200' => 'fan', 'PGR142G2516' => 'pgr', 'Prupe.3G160200' => 'ppe', 'Prupe.5G238200' => 'ppe', 'Prupe.7G047500' => 'ppe', 'QL03p045360' => 'qlo', 'QL05p034369' => 'qlo', 'QL05p034412' => 'qlo', 'QL08p017802' => 'qlo', 'QL08p024762' => 'qlo', 'QL10p026237' => 'qlo', 'QL10p032070' => 'qlo', 'QL11p003821' => 'qlo', 'Rhsim04G0057300' => 'rsi', 'Rhsim05G0049200' => 'rsi', 'Rhsim12G0010400' => 'rsi', 'Rhsim12G0012800' => 'rsi', 'TAR624G0483' => 'tar', 'TAR703G0001' => 'tar', 'vmacro05414' => 'vma', 'vmacro07091' => 'vma', 'vmacro07116' => 'vma', 'vmacro08423' => 'vma', 'vmacro09046' => 'vma', 'vmacro14269' => 'vma', 'vmacro16092' => 'vma', 'vmacro17280' => 'vma', 'vmacro19601' => 'vma' ), 'gf_id' => 'HOM05D001028', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001028' ), 'data_identifier' => 'HOM05D001028', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001028', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '590', 'num_species' => '12' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'Aqoxy1G01649' => 'aox', 'Aqoxy1G02950' => 'aox', 'Aqoxy2G01005' => 'aox', 'Aqoxy2G01064' => 'aox', 'Aqoxy3G02267' => 'aox', 'Aqoxy3G02617' => 'aox', 'Aqoxy3G02693' => 'aox', 'Aqoxy5G03425' => 'aox', 'Aqoxy6G02164' => 'aox', 'Aqoxy6G02364' => 'aox', 'Aqoxy7G02284' => 'aox', 'Cc00_g09720' => 'ccan', 'Cc00_g21410' => 'ccan', 'Cc00_g31750' => 'ccan', 'Cc00_g34740' => 'ccan', 'Cc04_g16890' => 'ccan', 'Cc11_g03120' => 'ccan', 'CSS0000222' => 'camsi', 'CSS0000265' => 'camsi', 'CSS0000306' => 'camsi', 'CSS0000326' => 'camsi', 'CSS0000530' => 'camsi', 'CSS0000563' => 'camsi', 'CSS0000584' => 'camsi', 'CSS0000684' => 'camsi', 'CSS0001100' => 'camsi', 'CSS0001311' => 'camsi', 'CSS0001343' => 'camsi', 'CSS0001399' => 'camsi', 'CSS0001475' => 'camsi', 'CSS0001506' => 'camsi', 'CSS0001602' => 'camsi', 'CSS0001681' => 'camsi', 'CSS0001874' => 'camsi', 'CSS0001948' => 'camsi', 'CSS0002022' => 'camsi', 'CSS0002230' => 'camsi', 'CSS0002265' => 'camsi', 'CSS0002277' => 'camsi', 'CSS0002462' => 'camsi', 'CSS0002823' => 'camsi', 'CSS0003091' => 'camsi', 'CSS0003162' => 'camsi', 'CSS0003264' => 'camsi', 'CSS0003355' => 'camsi', 'CSS0003378' => 'camsi', 'CSS0003472' => 'camsi', 'CSS0003500' => 'camsi', 'CSS0003640' => 'camsi', 'CSS0003767' => 'camsi', 'CSS0003894' => 'camsi', 'CSS0003952' => 'camsi', 'CSS0003977' => 'camsi', 'CSS0004028' => 'camsi', 'CSS0004117' => 'camsi', 'CSS0004137' => 'camsi', 'CSS0004176' => 'camsi', 'CSS0004265' => 'camsi', 'CSS0004450' => 'camsi', 'CSS0004468' => 'camsi', 'CSS0004488' => 'camsi', 'CSS0004490' => 'camsi', 'CSS0004632' => 'camsi', 'CSS0004790' => 'camsi', 'CSS0004877' => 'camsi', 'CSS0004920' => 'camsi', 'CSS0004969' => 'camsi', 'CSS0005084' => 'camsi', 'CSS0005101' => 'camsi', 'CSS0005271' => 'camsi', 'CSS0005313' => 'camsi', 'CSS0005331' => 'camsi', 'CSS0005368' => 'camsi', 'CSS0005391' => 'camsi', 'CSS0005437' => 'camsi', 'CSS0005515' => 'camsi', 'CSS0005526' => 'camsi', 'CSS0005532' => 'camsi', 'CSS0005595' => 'camsi', 'CSS0005677' => 'camsi', 'CSS0005838' => 'camsi', 'CSS0005988' => 'camsi', 'CSS0006100' => 'camsi', 'CSS0006128' => 'camsi', 'CSS0006293' => 'camsi', 'CSS0006378' => 'camsi', 'CSS0006400' => 'camsi', 'CSS0006441' => 'camsi', 'CSS0006455' => 'camsi', 'CSS0006480' => 'camsi', 'CSS0006483' => 'camsi', 'CSS0006538' => 'camsi', 'CSS0006582' => 'camsi', 'CSS0006632' => 'camsi', 'CSS0006771' => 'camsi', 'CSS0006803' => 'camsi', 'CSS0006852' => 'camsi', 'CSS0006861' => 'camsi', 'CSS0006910' => 'camsi', 'CSS0007037' => 'camsi', 'CSS0007066' => 'camsi', 'CSS0007072' => 'camsi', 'CSS0007109' => 'camsi', 'CSS0007193' => 'camsi', 'CSS0007319' => 'camsi', 'CSS0007336' => 'camsi', 'CSS0007377' => 'camsi', 'CSS0007659' => 'camsi', 'CSS0007701' => 'camsi', 'CSS0007711' => 'camsi', 'CSS0007809' => 'camsi', 'CSS0008045' => 'camsi', 'CSS0008050' => 'camsi', 'CSS0008206' => 'camsi', 'CSS0008251' => 'camsi', 'CSS0008252' => 'camsi', 'CSS0008279' => 'camsi', 'CSS0008482' => 'camsi', 'CSS0008583' => 'camsi', 'CSS0008699' => 'camsi', 'CSS0008798' => 'camsi', 'CSS0008971' => 'camsi', 'CSS0009019' => 'camsi', 'CSS0009191' => 'camsi', 'CSS0009241' => 'camsi', 'CSS0009246' => 'camsi', 'CSS0009399' => 'camsi', 'CSS0009654' => 'camsi', 'CSS0009722' => 'camsi', 'CSS0009920' => 'camsi', 'CSS0009986' => 'camsi', 'CSS0010182' => 'camsi', 'CSS0010202' => 'camsi', 'CSS0010330' => 'camsi', 'CSS0010362' => 'camsi', 'CSS0010456' => 'camsi', 'CSS0010472' => 'camsi', 'CSS0010507' => 'camsi', 'CSS0010512' => 'camsi', 'CSS0010520' => 'camsi', 'CSS0010617' => 'camsi', 'CSS0010706' => 'camsi', 'CSS0010747' => 'camsi', 'CSS0010816' => 'camsi', 'CSS0011020' => 'camsi', 'CSS0011115' => 'camsi', 'CSS0011383' => 'camsi', 'CSS0011491' => 'camsi', 'CSS0011602' => 'camsi', 'CSS0011605' => 'camsi', 'CSS0011625' => 'camsi', 'CSS0011654' => 'camsi', 'CSS0011781' => 'camsi', 'CSS0011853' => 'camsi', 'CSS0011898' => 'camsi', 'CSS0011933' => 'camsi', 'CSS0011996' => 'camsi', 'CSS0012066' => 'camsi', 'CSS0012097' => 'camsi', 'CSS0012108' => 'camsi', 'CSS0012226' => 'camsi', 'CSS0012248' => 'camsi', 'CSS0012331' => 'camsi', 'CSS0012797' => 'camsi', 'CSS0012818' => 'camsi', 'CSS0012904' => 'camsi', 'CSS0013001' => 'camsi', 'CSS0013022' => 'camsi', 'CSS0013172' => 'camsi', 'CSS0013244' => 'camsi', 'CSS0013267' => 'camsi', 'CSS0013275' => 'camsi', 'CSS0013324' => 'camsi', 'CSS0013334' => 'camsi', 'CSS0013394' => 'camsi', 'CSS0013549' => 'camsi', 'CSS0013689' => 'camsi', 'CSS0014026' => 'camsi', 'CSS0014049' => 'camsi', 'CSS0014144' => 'camsi', 'CSS0014354' => 'camsi', 'CSS0014579' => 'camsi', 'CSS0014648' => 'camsi', 'CSS0014902' => 'camsi', 'CSS0014979' => 'camsi', 'CSS0015278' => 'camsi', 'CSS0015310' => 'camsi', 'CSS0015364' => 'camsi', 'CSS0015455' => 'camsi', 'CSS0015693' => 'camsi', 'CSS0015774' => 'camsi', 'CSS0015795' => 'camsi', 'CSS0015952' => 'camsi', 'CSS0016104' => 'camsi', 'CSS0016241' => 'camsi', 'CSS0016303' => 'camsi', 'CSS0016490' => 'camsi', 'CSS0016832' => 'camsi', 'CSS0016845' => 'camsi', 'CSS0016914' => 'camsi', 'CSS0016946' => 'camsi', 'CSS0017102' => 'camsi', 'CSS0017193' => 'camsi', 'CSS0017528' => 'camsi', 'CSS0017619' => 'camsi', 'CSS0017679' => 'camsi', 'CSS0017816' => 'camsi', 'CSS0017880' => 'camsi', 'CSS0018106' => 'camsi', 'CSS0018162' => 'camsi', 'CSS0018304' => 'camsi', 'CSS0018406' => 'camsi', 'CSS0018481' => 'camsi', 'CSS0018511' => 'camsi', 'CSS0018596' => 'camsi', 'CSS0018727' => 'camsi', 'CSS0018751' => 'camsi', 'CSS0018777' => 'camsi', 'CSS0018798' => 'camsi', 'CSS0019137' => 'camsi', 'CSS0019177' => 'camsi', 'CSS0019217' => 'camsi', 'CSS0019361' => 'camsi', 'CSS0019516' => 'camsi', 'CSS0019538' => 'camsi', 'CSS0019560' => 'camsi', 'CSS0019819' => 'camsi', 'CSS0019837' => 'camsi', 'CSS0019915' => 'camsi', 'CSS0019925' => 'camsi', 'CSS0020112' => 'camsi', 'CSS0020160' => 'camsi', 'CSS0020378' => 'camsi', 'CSS0020388' => 'camsi', 'CSS0020452' => 'camsi', 'CSS0020588' => 'camsi', 'CSS0020661' => 'camsi', 'CSS0020886' => 'camsi', 'CSS0020973' => 'camsi', 'CSS0021035' => 'camsi', 'CSS0021111' => 'camsi', 'CSS0021131' => 'camsi', 'CSS0021151' => 'camsi', 'CSS0021228' => 'camsi', 'CSS0021397' => 'camsi', 'CSS0021420' => 'camsi', 'CSS0021464' => 'camsi', 'CSS0021547' => 'camsi', 'CSS0021608' => 'camsi', 'CSS0021740' => 'camsi', 'CSS0021826' => 'camsi', 'CSS0021904' => 'camsi', 'CSS0021941' => 'camsi', 'CSS0022189' => 'camsi', 'CSS0022199' => 'camsi', 'CSS0022502' => 'camsi', 'CSS0022531' => 'camsi', 'CSS0022581' => 'camsi', 'CSS0022612' => 'camsi', 'CSS0022621' => 'camsi', 'CSS0022815' => 'camsi', 'CSS0022936' => 'camsi', 'CSS0022964' => 'camsi', 'CSS0022985' => 'camsi', 'CSS0023002' => 'camsi', 'CSS0023006' => 'camsi', 'CSS0023024' => 'camsi', 'CSS0023489' => 'camsi', 'CSS0023593' => 'camsi', 'CSS0023621' => 'camsi', 'CSS0023743' => 'camsi', 'CSS0023804' => 'camsi', 'CSS0023805' => 'camsi', 'CSS0023908' => 'camsi', 'CSS0023938' => 'camsi', 'CSS0023981' => 'camsi', 'CSS0024027' => 'camsi', 'CSS0024169' => 'camsi', 'CSS0024193' => 'camsi', 'CSS0024269' => 'camsi', 'CSS0024336' => 'camsi', 'CSS0024337' => 'camsi', 'CSS0024548' => 'camsi', 'CSS0024564' => 'camsi', 'CSS0024585' => 'camsi', 'CSS0024738' => 'camsi', 'CSS0024833' => 'camsi', 'CSS0024846' => 'camsi', 'CSS0024957' => 'camsi', 'CSS0024974' => 'camsi', 'CSS0025005' => 'camsi', 'CSS0025235' => 'camsi', 'CSS0025465' => 'camsi', 'CSS0025633' => 'camsi', 'CSS0025688' => 'camsi', 'CSS0025759' => 'camsi', 'CSS0025774' => 'camsi', 'CSS0025801' => 'camsi', 'CSS0025942' => 'camsi', 'CSS0026083' => 'camsi', 'CSS0026194' => 'camsi', 'CSS0026230' => 'camsi', 'CSS0026398' => 'camsi', 'CSS0026419' => 'camsi', 'CSS0026679' => 'camsi', 'CSS0026719' => 'camsi', 'CSS0026795' => 'camsi', 'CSS0026835' => 'camsi', 'CSS0026930' => 'camsi', 'CSS0027053' => 'camsi', 'CSS0027130' => 'camsi', 'CSS0027192' => 'camsi', 'CSS0027454' => 'camsi', 'CSS0027467' => 'camsi', 'CSS0027521' => 'camsi', 'CSS0027662' => 'camsi', 'CSS0027795' => 'camsi', 'CSS0027835' => 'camsi', 'CSS0027966' => 'camsi', 'CSS0028090' => 'camsi', 'CSS0028134' => 'camsi', 'CSS0028205' => 'camsi', 'CSS0028263' => 'camsi', 'CSS0028363' => 'camsi', 'CSS0028598' => 'camsi', 'CSS0029175' => 'camsi', 'CSS0029191' => 'camsi', 'CSS0029424' => 'camsi', 'CSS0029479' => 'camsi', 'CSS0029496' => 'camsi', 'CSS0029633' => 'camsi', 'CSS0029837' => 'camsi', 'CSS0029844' => 'camsi', 'CSS0029863' => 'camsi', 'CSS0029874' => 'camsi', 'CSS0029959' => 'camsi', 'CSS0030001' => 'camsi', 'CSS0030093' => 'camsi', 'CSS0030199' => 'camsi', 'CSS0030200' => 'camsi', 'CSS0030427' => 'camsi', 'CSS0030476' => 'camsi', 'CSS0030636' => 'camsi', 'CSS0030673' => 'camsi', 'CSS0030766' => 'camsi', 'CSS0030775' => 'camsi', 'CSS0030858' => 'camsi', 'CSS0030873' => 'camsi', 'CSS0030929' => 'camsi', 'CSS0031028' => 'camsi', 'CSS0031129' => 'camsi', 'CSS0031164' => 'camsi', 'CSS0031340' => 'camsi', 'CSS0031368' => 'camsi', 'CSS0031395' => 'camsi', 'CSS0031596' => 'camsi', 'CSS0031727' => 'camsi', 'CSS0032011' => 'camsi', 'CSS0032160' => 'camsi', 'CSS0032538' => 'camsi', 'CSS0032576' => 'camsi', 'CSS0032603' => 'camsi', 'CSS0032640' => 'camsi', 'CSS0032704' => 'camsi', 'CSS0032851' => 'camsi', 'CSS0032973' => 'camsi', 'CSS0033048' => 'camsi', 'CSS0033082' => 'camsi', 'CSS0033157' => 'camsi', 'CSS0033253' => 'camsi', 'CSS0033347' => 'camsi', 'CSS0033601' => 'camsi', 'CSS0033820' => 'camsi', 'CSS0033881' => 'camsi', 'CSS0033934' => 'camsi', 'CSS0034143' => 'camsi', 'CSS0034176' => 'camsi', 'CSS0034201' => 'camsi', 'CSS0034269' => 'camsi', 'CSS0034303' => 'camsi', 'CSS0034463' => 'camsi', 'CSS0034470' => 'camsi', 'CSS0034514' => 'camsi', 'CSS0034525' => 'camsi', 'CSS0034726' => 'camsi', 'CSS0034727' => 'camsi', 'CSS0034737' => 'camsi', 'CSS0034768' => 'camsi', 'CSS0034890' => 'camsi', 'CSS0034943' => 'camsi', 'CSS0034957' => 'camsi', 'CSS0034973' => 'camsi', 'CSS0035178' => 'camsi', 'CSS0035260' => 'camsi', 'CSS0035316' => 'camsi', 'CSS0035347' => 'camsi', 'CSS0035360' => 'camsi', 'CSS0035380' => 'camsi', 'CSS0035429' => 'camsi', 'CSS0035446' => 'camsi', 'CSS0035737' => 'camsi', 'CSS0035852' => 'camsi', 'CSS0035967' => 'camsi', 'CSS0036001' => 'camsi', 'CSS0036044' => 'camsi', 'CSS0036221' => 'camsi', 'CSS0036333' => 'camsi', 'CSS0036435' => 'camsi', 'CSS0036843' => 'camsi', 'CSS0036846' => 'camsi', 'CSS0037097' => 'camsi', 'CSS0037263' => 'camsi', 'CSS0037370' => 'camsi', 'CSS0037410' => 'camsi', 'CSS0037449' => 'camsi', 'CSS0037603' => 'camsi', 'CSS0037851' => 'camsi', 'CSS0037891' => 'camsi', 'CSS0037996' => 'camsi', 'CSS0038222' => 'camsi', 'CSS0038433' => 'camsi', 'CSS0038441' => 'camsi', 'CSS0038718' => 'camsi', 'CSS0038890' => 'camsi', 'CSS0039049' => 'camsi', 'CSS0039145' => 'camsi', 'CSS0039243' => 'camsi', 'CSS0039294' => 'camsi', 'CSS0039324' => 'camsi', 'CSS0039376' => 'camsi', 'CSS0039475' => 'camsi', 'CSS0039539' => 'camsi', 'CSS0039546' => 'camsi', 'CSS0039567' => 'camsi', 'CSS0039599' => 'camsi', 'CSS0039763' => 'camsi', 'CSS0039863' => 'camsi', 'CSS0040107' => 'camsi', 'CSS0040124' => 'camsi', 'CSS0040151' => 'camsi', 'CSS0040165' => 'camsi', 'CSS0040309' => 'camsi', 'CSS0040318' => 'camsi', 'CSS0040347' => 'camsi', 'CSS0040371' => 'camsi', 'CSS0040456' => 'camsi', 'CSS0040551' => 'camsi', 'CSS0040975' => 'camsi', 'CSS0040981' => 'camsi', 'CSS0041299' => 'camsi', 'CSS0041493' => 'camsi', 'CSS0041658' => 'camsi', 'CSS0041899' => 'camsi', 'CSS0041927' => 'camsi', 'CSS0042016' => 'camsi', 'CSS0042034' => 'camsi', 'CSS0042103' => 'camsi', 'CSS0042172' => 'camsi', 'CSS0042198' => 'camsi', 'CSS0042201' => 'camsi', 'CSS0042308' => 'camsi', 'CSS0042329' => 'camsi', 'CSS0042348' => 'camsi', 'CSS0042349' => 'camsi', 'CSS0042489' => 'camsi', 'CSS0042575' => 'camsi', 'CSS0042624' => 'camsi', 'CSS0042660' => 'camsi', 'CSS0042694' => 'camsi', 'CSS0042995' => 'camsi', 'CSS0043079' => 'camsi', 'CSS0043165' => 'camsi', 'CSS0043171' => 'camsi', 'CSS0043314' => 'camsi', 'CSS0043361' => 'camsi', 'CSS0043375' => 'camsi', 'CSS0043518' => 'camsi', 'CSS0043536' => 'camsi', 'CSS0043678' => 'camsi', 'CSS0043765' => 'camsi', 'CSS0043897' => 'camsi', 'CSS0043944' => 'camsi', 'CSS0044126' => 'camsi', 'CSS0044136' => 'camsi', 'CSS0044179' => 'camsi', 'CSS0044290' => 'camsi', 'CSS0044437' => 'camsi', 'CSS0044502' => 'camsi', 'CSS0044603' => 'camsi', 'CSS0044680' => 'camsi', 'CSS0044685' => 'camsi', 'CSS0044700' => 'camsi', 'CSS0044888' => 'camsi', 'CSS0044923' => 'camsi', 'CSS0044926' => 'camsi', 'CSS0044979' => 'camsi', 'CSS0045049' => 'camsi', 'CSS0045132' => 'camsi', 'CSS0045161' => 'camsi', 'CSS0045219' => 'camsi', 'CSS0045230' => 'camsi', 'CSS0045259' => 'camsi', 'CSS0045324' => 'camsi', 'CSS0045368' => 'camsi', 'CSS0045435' => 'camsi', 'CSS0045856' => 'camsi', 'CSS0045955' => 'camsi', 'CSS0046158' => 'camsi', 'CSS0046334' => 'camsi', 'CSS0046365' => 'camsi', 'CSS0046396' => 'camsi', 'CSS0046400' => 'camsi', 'CSS0046445' => 'camsi', 'CSS0046493' => 'camsi', 'CSS0046640' => 'camsi', 'CSS0046657' => 'camsi', 'CSS0046702' => 'camsi', 'CSS0047208' => 'camsi', 'CSS0047368' => 'camsi', 'CSS0047403' => 'camsi', 'CSS0047417' => 'camsi', 'CSS0047469' => 'camsi', 'CSS0047480' => 'camsi', 'CSS0047482' => 'camsi', 'CSS0047693' => 'camsi', 'CSS0047766' => 'camsi', 'CSS0047866' => 'camsi', 'CSS0047884' => 'camsi', 'CSS0048235' => 'camsi', 'CSS0048383' => 'camsi', 'CSS0048438' => 'camsi', 'CSS0048502' => 'camsi', 'CSS0048546' => 'camsi', 'CSS0048653' => 'camsi', 'CSS0048658' => 'camsi', 'CSS0048729' => 'camsi', 'CSS0048867' => 'camsi', 'CSS0048988' => 'camsi', 'CSS0049053' => 'camsi', 'CSS0049099' => 'camsi', 'CSS0049166' => 'camsi', 'CSS0049174' => 'camsi', 'CSS0049212' => 'camsi', 'CSS0049280' => 'camsi', 'CSS0049391' => 'camsi', 'CSS0049546' => 'camsi', 'CSS0049634' => 'camsi', 'CSS0049655' => 'camsi', 'CSS0049813' => 'camsi', 'CSS0049949' => 'camsi', 'CSS0050009' => 'camsi', 'CSS0050118' => 'camsi', 'CSS0050205' => 'camsi', 'CSS0050275' => 'camsi', 'CSS0050480' => 'camsi', 'CSS0050488' => 'camsi', 'CSS0050497' => 'camsi', 'Dinv03126' => 'din', 'Dinv13140' => 'din', 'Dinv13247' => 'din', 'Dinv14217' => 'din', 'EL10Ac9g22435' => 'bvu', 'FAN20G1200' => 'fan', 'PGR142G2516' => 'pgr', 'Prupe.3G160200' => 'ppe', 'Prupe.5G238200' => 'ppe', 'Prupe.7G047500' => 'ppe', 'QL03p045360' => 'qlo', 'QL05p034369' => 'qlo', 'QL05p034412' => 'qlo', 'QL08p017802' => 'qlo', 'QL08p024762' => 'qlo', 'QL10p026237' => 'qlo', 'QL10p032070' => 'qlo', 'QL11p003821' => 'qlo', 'Rhsim04G0057300' => 'rsi', 'Rhsim05G0049200' => 'rsi', 'Rhsim12G0010400' => 'rsi', 'Rhsim12G0012800' => 'rsi', 'TAR624G0483' => 'tar', 'TAR703G0001' => 'tar', 'vmacro05414' => 'vma', 'vmacro07091' => 'vma', 'vmacro07116' => 'vma', 'vmacro08423' => 'vma', 'vmacro09046' => 'vma', 'vmacro14269' => 'vma', 'vmacro16092' => 'vma', 'vmacro17280' => 'vma', 'vmacro19601' => 'vma' ) $gf_id = 'HOM05D001028' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001028' ) $data_identifier = 'HOM05D001028' $data_type = 'gf_id' $species_gene_counts = array( 'aox' => (int) 11, 'ccan' => (int) 6, 'camsi' => (int) 540, 'din' => (int) 4, 'bvu' => (int) 1, 'fan' => (int) 1, 'pgr' => (int) 1, 'ppe' => (int) 3, 'qlo' => (int) 8, 'rsi' => (int) 4, 'tar' => (int) 2, 'vma' => (int) 9 ) $gf_gene_species = 'vma' $gf_gene_id = 'vmacro19601' $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) 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' => 'HOM05D001028', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '590', 'num_species' => '12' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'Aqoxy1G01649' => 'aox', 'Aqoxy1G02950' => 'aox', 'Aqoxy2G01005' => 'aox', 'Aqoxy2G01064' => 'aox', 'Aqoxy3G02267' => 'aox', 'Aqoxy3G02617' => 'aox', 'Aqoxy3G02693' => 'aox', 'Aqoxy5G03425' => 'aox', 'Aqoxy6G02164' => 'aox', 'Aqoxy6G02364' => 'aox', 'Aqoxy7G02284' => 'aox', 'Cc00_g09720' => 'ccan', 'Cc00_g21410' => 'ccan', 'Cc00_g31750' => 'ccan', 'Cc00_g34740' => 'ccan', 'Cc04_g16890' => 'ccan', 'Cc11_g03120' => 'ccan', 'CSS0000222' => 'camsi', 'CSS0000265' => 'camsi', 'CSS0000306' => 'camsi', 'CSS0000326' => 'camsi', 'CSS0000530' => 'camsi', 'CSS0000563' => 'camsi', 'CSS0000584' => 'camsi', 'CSS0000684' => 'camsi', 'CSS0001100' => 'camsi', 'CSS0001311' => 'camsi', 'CSS0001343' => 'camsi', 'CSS0001399' => 'camsi', 'CSS0001475' => 'camsi', 'CSS0001506' => 'camsi', 'CSS0001602' => 'camsi', 'CSS0001681' => 'camsi', 'CSS0001874' => 'camsi', 'CSS0001948' => 'camsi', 'CSS0002022' => 'camsi', 'CSS0002230' => 'camsi', 'CSS0002265' => 'camsi', 'CSS0002277' => 'camsi', 'CSS0002462' => 'camsi', 'CSS0002823' => 'camsi', 'CSS0003091' => 'camsi', 'CSS0003162' => 'camsi', 'CSS0003264' => 'camsi', 'CSS0003355' => 'camsi', 'CSS0003378' => 'camsi', 'CSS0003472' => 'camsi', 'CSS0003500' => 'camsi', 'CSS0003640' => 'camsi', 'CSS0003767' => 'camsi', 'CSS0003894' => 'camsi', 'CSS0003952' => 'camsi', 'CSS0003977' => 'camsi', 'CSS0004028' => 'camsi', 'CSS0004117' => 'camsi', 'CSS0004137' => 'camsi', 'CSS0004176' => 'camsi', 'CSS0004265' => 'camsi', 'CSS0004450' => 'camsi', 'CSS0004468' => 'camsi', 'CSS0004488' => 'camsi', 'CSS0004490' => 'camsi', 'CSS0004632' => 'camsi', 'CSS0004790' => 'camsi', 'CSS0004877' => 'camsi', 'CSS0004920' => 'camsi', 'CSS0004969' => 'camsi', 'CSS0005084' => 'camsi', 'CSS0005101' => 'camsi', 'CSS0005271' => 'camsi', 'CSS0005313' => 'camsi', 'CSS0005331' => 'camsi', 'CSS0005368' => 'camsi', 'CSS0005391' => 'camsi', 'CSS0005437' => 'camsi', 'CSS0005515' => 'camsi', 'CSS0005526' => 'camsi', 'CSS0005532' => 'camsi', 'CSS0005595' => 'camsi', 'CSS0005677' => 'camsi', 'CSS0005838' => 'camsi', 'CSS0005988' => 'camsi', 'CSS0006100' => 'camsi', 'CSS0006128' => 'camsi', 'CSS0006293' => 'camsi', 'CSS0006378' => 'camsi', 'CSS0006400' => 'camsi', 'CSS0006441' => 'camsi', 'CSS0006455' => 'camsi', 'CSS0006480' => 'camsi', 'CSS0006483' => 'camsi', 'CSS0006538' => 'camsi', 'CSS0006582' => 'camsi', 'CSS0006632' => 'camsi', 'CSS0006771' => 'camsi', 'CSS0006803' => 'camsi', 'CSS0006852' => 'camsi', 'CSS0006861' => 'camsi', 'CSS0006910' => 'camsi', 'CSS0007037' => 'camsi', 'CSS0007066' => 'camsi', 'CSS0007072' => 'camsi', 'CSS0007109' => 'camsi', 'CSS0007193' => 'camsi', 'CSS0007319' => 'camsi', 'CSS0007336' => 'camsi', 'CSS0007377' => 'camsi', 'CSS0007659' => 'camsi', 'CSS0007701' => 'camsi', 'CSS0007711' => 'camsi', 'CSS0007809' => 'camsi', 'CSS0008045' => 'camsi', 'CSS0008050' => 'camsi', 'CSS0008206' => 'camsi', 'CSS0008251' => 'camsi', 'CSS0008252' => 'camsi', 'CSS0008279' => 'camsi', 'CSS0008482' => 'camsi', 'CSS0008583' => 'camsi', 'CSS0008699' => 'camsi', 'CSS0008798' => 'camsi', 'CSS0008971' => 'camsi', 'CSS0009019' => 'camsi', 'CSS0009191' => 'camsi', 'CSS0009241' => 'camsi', 'CSS0009246' => 'camsi', 'CSS0009399' => 'camsi', 'CSS0009654' => 'camsi', 'CSS0009722' => 'camsi', 'CSS0009920' => 'camsi', 'CSS0009986' => 'camsi', 'CSS0010182' => 'camsi', 'CSS0010202' => 'camsi', 'CSS0010330' => 'camsi', 'CSS0010362' => 'camsi', 'CSS0010456' => 'camsi', 'CSS0010472' => 'camsi', 'CSS0010507' => 'camsi', 'CSS0010512' => 'camsi', 'CSS0010520' => 'camsi', 'CSS0010617' => 'camsi', 'CSS0010706' => 'camsi', 'CSS0010747' => 'camsi', 'CSS0010816' => 'camsi', 'CSS0011020' => 'camsi', 'CSS0011115' => 'camsi', 'CSS0011383' => 'camsi', 'CSS0011491' => 'camsi', 'CSS0011602' => 'camsi', 'CSS0011605' => 'camsi', 'CSS0011625' => 'camsi', 'CSS0011654' => 'camsi', 'CSS0011781' => 'camsi', 'CSS0011853' => 'camsi', 'CSS0011898' => 'camsi', 'CSS0011933' => 'camsi', 'CSS0011996' => 'camsi', 'CSS0012066' => 'camsi', 'CSS0012097' => 'camsi', 'CSS0012108' => 'camsi', 'CSS0012226' => 'camsi', 'CSS0012248' => 'camsi', 'CSS0012331' => 'camsi', 'CSS0012797' => 'camsi', 'CSS0012818' => 'camsi', 'CSS0012904' => 'camsi', 'CSS0013001' => 'camsi', 'CSS0013022' => 'camsi', 'CSS0013172' => 'camsi', 'CSS0013244' => 'camsi', 'CSS0013267' => 'camsi', 'CSS0013275' => 'camsi', 'CSS0013324' => 'camsi', 'CSS0013334' => 'camsi', 'CSS0013394' => 'camsi', 'CSS0013549' => 'camsi', 'CSS0013689' => 'camsi', 'CSS0014026' => 'camsi', 'CSS0014049' => 'camsi', 'CSS0014144' => 'camsi', 'CSS0014354' => 'camsi', 'CSS0014579' => 'camsi', 'CSS0014648' => 'camsi', 'CSS0014902' => 'camsi', 'CSS0014979' => 'camsi', 'CSS0015278' => 'camsi', 'CSS0015310' => 'camsi', 'CSS0015364' => 'camsi', 'CSS0015455' => 'camsi', 'CSS0015693' => 'camsi', 'CSS0015774' => 'camsi', 'CSS0015795' => 'camsi', 'CSS0015952' => 'camsi', 'CSS0016104' => 'camsi', 'CSS0016241' => 'camsi', 'CSS0016303' => 'camsi', 'CSS0016490' => 'camsi', 'CSS0016832' => 'camsi', 'CSS0016845' => 'camsi', 'CSS0016914' => 'camsi', 'CSS0016946' => 'camsi', 'CSS0017102' => 'camsi', 'CSS0017193' => 'camsi', 'CSS0017528' => 'camsi', 'CSS0017619' => 'camsi', 'CSS0017679' => 'camsi', 'CSS0017816' => 'camsi', 'CSS0017880' => 'camsi', 'CSS0018106' => 'camsi', 'CSS0018162' => 'camsi', 'CSS0018304' => 'camsi', 'CSS0018406' => 'camsi', 'CSS0018481' => 'camsi', 'CSS0018511' => 'camsi', 'CSS0018596' => 'camsi', 'CSS0018727' => 'camsi', 'CSS0018751' => 'camsi', 'CSS0018777' => 'camsi', 'CSS0018798' => 'camsi', 'CSS0019137' => 'camsi', 'CSS0019177' => 'camsi', 'CSS0019217' => 'camsi', 'CSS0019361' => 'camsi', 'CSS0019516' => 'camsi', 'CSS0019538' => 'camsi', 'CSS0019560' => 'camsi', 'CSS0019819' => 'camsi', 'CSS0019837' => 'camsi', 'CSS0019915' => 'camsi', 'CSS0019925' => 'camsi', 'CSS0020112' => 'camsi', 'CSS0020160' => 'camsi', 'CSS0020378' => 'camsi', 'CSS0020388' => 'camsi', 'CSS0020452' => 'camsi', 'CSS0020588' => 'camsi', 'CSS0020661' => 'camsi', 'CSS0020886' => 'camsi', 'CSS0020973' => 'camsi', 'CSS0021035' => 'camsi', 'CSS0021111' => 'camsi', 'CSS0021131' => 'camsi', 'CSS0021151' => 'camsi', 'CSS0021228' => 'camsi', 'CSS0021397' => 'camsi', 'CSS0021420' => 'camsi', 'CSS0021464' => 'camsi', 'CSS0021547' => 'camsi', 'CSS0021608' => 'camsi', 'CSS0021740' => 'camsi', 'CSS0021826' => 'camsi', 'CSS0021904' => 'camsi', 'CSS0021941' => 'camsi', 'CSS0022189' => 'camsi', 'CSS0022199' => 'camsi', 'CSS0022502' => 'camsi', 'CSS0022531' => 'camsi', 'CSS0022581' => 'camsi', 'CSS0022612' => 'camsi', 'CSS0022621' => 'camsi', 'CSS0022815' => 'camsi', 'CSS0022936' => 'camsi', 'CSS0022964' => 'camsi', 'CSS0022985' => 'camsi', 'CSS0023002' => 'camsi', 'CSS0023006' => 'camsi', 'CSS0023024' => 'camsi', 'CSS0023489' => 'camsi', 'CSS0023593' => 'camsi', 'CSS0023621' => 'camsi', 'CSS0023743' => 'camsi', 'CSS0023804' => 'camsi', 'CSS0023805' => 'camsi', 'CSS0023908' => 'camsi', 'CSS0023938' => 'camsi', 'CSS0023981' => 'camsi', 'CSS0024027' => 'camsi', 'CSS0024169' => 'camsi', 'CSS0024193' => 'camsi', 'CSS0024269' => 'camsi', 'CSS0024336' => 'camsi', 'CSS0024337' => 'camsi', 'CSS0024548' => 'camsi', 'CSS0024564' => 'camsi', 'CSS0024585' => 'camsi', 'CSS0024738' => 'camsi', 'CSS0024833' => 'camsi', 'CSS0024846' => 'camsi', 'CSS0024957' => 'camsi', 'CSS0024974' => 'camsi', 'CSS0025005' => 'camsi', 'CSS0025235' => 'camsi', 'CSS0025465' => 'camsi', 'CSS0025633' => 'camsi', 'CSS0025688' => 'camsi', 'CSS0025759' => 'camsi', 'CSS0025774' => 'camsi', 'CSS0025801' => 'camsi', 'CSS0025942' => 'camsi', 'CSS0026083' => 'camsi', 'CSS0026194' => 'camsi', 'CSS0026230' => 'camsi', 'CSS0026398' => 'camsi', 'CSS0026419' => 'camsi', 'CSS0026679' => 'camsi', 'CSS0026719' => 'camsi', 'CSS0026795' => 'camsi', 'CSS0026835' => 'camsi', 'CSS0026930' => 'camsi', 'CSS0027053' => 'camsi', 'CSS0027130' => 'camsi', 'CSS0027192' => 'camsi', 'CSS0027454' => 'camsi', 'CSS0027467' => 'camsi', 'CSS0027521' => 'camsi', 'CSS0027662' => 'camsi', 'CSS0027795' => 'camsi', 'CSS0027835' => 'camsi', 'CSS0027966' => 'camsi', 'CSS0028090' => 'camsi', 'CSS0028134' => 'camsi', 'CSS0028205' => 'camsi', 'CSS0028263' => 'camsi', 'CSS0028363' => 'camsi', 'CSS0028598' => 'camsi', 'CSS0029175' => 'camsi', 'CSS0029191' => 'camsi', 'CSS0029424' => 'camsi', 'CSS0029479' => 'camsi', 'CSS0029496' => 'camsi', 'CSS0029633' => 'camsi', 'CSS0029837' => 'camsi', 'CSS0029844' => 'camsi', 'CSS0029863' => 'camsi', 'CSS0029874' => 'camsi', 'CSS0029959' => 'camsi', 'CSS0030001' => 'camsi', 'CSS0030093' => 'camsi', 'CSS0030199' => 'camsi', 'CSS0030200' => 'camsi', 'CSS0030427' => 'camsi', 'CSS0030476' => 'camsi', 'CSS0030636' => 'camsi', 'CSS0030673' => 'camsi', 'CSS0030766' => 'camsi', 'CSS0030775' => 'camsi', 'CSS0030858' => 'camsi', 'CSS0030873' => 'camsi', 'CSS0030929' => 'camsi', 'CSS0031028' => 'camsi', 'CSS0031129' => 'camsi', 'CSS0031164' => 'camsi', 'CSS0031340' => 'camsi', 'CSS0031368' => 'camsi', 'CSS0031395' => 'camsi', 'CSS0031596' => 'camsi', 'CSS0031727' => 'camsi', 'CSS0032011' => 'camsi', 'CSS0032160' => 'camsi', 'CSS0032538' => 'camsi', 'CSS0032576' => 'camsi', 'CSS0032603' => 'camsi', 'CSS0032640' => 'camsi', 'CSS0032704' => 'camsi', 'CSS0032851' => 'camsi', 'CSS0032973' => 'camsi', 'CSS0033048' => 'camsi', 'CSS0033082' => 'camsi', 'CSS0033157' => 'camsi', 'CSS0033253' => 'camsi', 'CSS0033347' => 'camsi', 'CSS0033601' => 'camsi', 'CSS0033820' => 'camsi', 'CSS0033881' => 'camsi', 'CSS0033934' => 'camsi', 'CSS0034143' => 'camsi', 'CSS0034176' => 'camsi', 'CSS0034201' => 'camsi', 'CSS0034269' => 'camsi', 'CSS0034303' => 'camsi', 'CSS0034463' => 'camsi', 'CSS0034470' => 'camsi', 'CSS0034514' => 'camsi', 'CSS0034525' => 'camsi', 'CSS0034726' => 'camsi', 'CSS0034727' => 'camsi', 'CSS0034737' => 'camsi', 'CSS0034768' => 'camsi', 'CSS0034890' => 'camsi', 'CSS0034943' => 'camsi', 'CSS0034957' => 'camsi', 'CSS0034973' => 'camsi', 'CSS0035178' => 'camsi', 'CSS0035260' => 'camsi', 'CSS0035316' => 'camsi', 'CSS0035347' => 'camsi', 'CSS0035360' => 'camsi', 'CSS0035380' => 'camsi', 'CSS0035429' => 'camsi', 'CSS0035446' => 'camsi', 'CSS0035737' => 'camsi', 'CSS0035852' => 'camsi', 'CSS0035967' => 'camsi', 'CSS0036001' => 'camsi', 'CSS0036044' => 'camsi', 'CSS0036221' => 'camsi', 'CSS0036333' => 'camsi', 'CSS0036435' => 'camsi', 'CSS0036843' => 'camsi', 'CSS0036846' => 'camsi', 'CSS0037097' => 'camsi', 'CSS0037263' => 'camsi', 'CSS0037370' => 'camsi', 'CSS0037410' => 'camsi', 'CSS0037449' => 'camsi', 'CSS0037603' => 'camsi', 'CSS0037851' => 'camsi', 'CSS0037891' => 'camsi', 'CSS0037996' => 'camsi', 'CSS0038222' => 'camsi', 'CSS0038433' => 'camsi', 'CSS0038441' => 'camsi', 'CSS0038718' => 'camsi', 'CSS0038890' => 'camsi', 'CSS0039049' => 'camsi', 'CSS0039145' => 'camsi', 'CSS0039243' => 'camsi', 'CSS0039294' => 'camsi', 'CSS0039324' => 'camsi', 'CSS0039376' => 'camsi', 'CSS0039475' => 'camsi', 'CSS0039539' => 'camsi', 'CSS0039546' => 'camsi', 'CSS0039567' => 'camsi', 'CSS0039599' => 'camsi', 'CSS0039763' => 'camsi', 'CSS0039863' => 'camsi', 'CSS0040107' => 'camsi', 'CSS0040124' => 'camsi', 'CSS0040151' => 'camsi', 'CSS0040165' => 'camsi', 'CSS0040309' => 'camsi', 'CSS0040318' => 'camsi', 'CSS0040347' => 'camsi', 'CSS0040371' => 'camsi', 'CSS0040456' => 'camsi', 'CSS0040551' => 'camsi', 'CSS0040975' => 'camsi', 'CSS0040981' => 'camsi', 'CSS0041299' => 'camsi', 'CSS0041493' => 'camsi', 'CSS0041658' => 'camsi', 'CSS0041899' => 'camsi', 'CSS0041927' => 'camsi', 'CSS0042016' => 'camsi', 'CSS0042034' => 'camsi', 'CSS0042103' => 'camsi', 'CSS0042172' => 'camsi', 'CSS0042198' => 'camsi', 'CSS0042201' => 'camsi', 'CSS0042308' => 'camsi', 'CSS0042329' => 'camsi', 'CSS0042348' => 'camsi', 'CSS0042349' => 'camsi', 'CSS0042489' => 'camsi', 'CSS0042575' => 'camsi', 'CSS0042624' => 'camsi', 'CSS0042660' => 'camsi', 'CSS0042694' => 'camsi', 'CSS0042995' => 'camsi', 'CSS0043079' => 'camsi', 'CSS0043165' => 'camsi', 'CSS0043171' => 'camsi', 'CSS0043314' => 'camsi', 'CSS0043361' => 'camsi', 'CSS0043375' => 'camsi', 'CSS0043518' => 'camsi', 'CSS0043536' => 'camsi', 'CSS0043678' => 'camsi', 'CSS0043765' => 'camsi', 'CSS0043897' => 'camsi', 'CSS0043944' => 'camsi', 'CSS0044126' => 'camsi', 'CSS0044136' => 'camsi', 'CSS0044179' => 'camsi', 'CSS0044290' => 'camsi', 'CSS0044437' => 'camsi', 'CSS0044502' => 'camsi', 'CSS0044603' => 'camsi', 'CSS0044680' => 'camsi', 'CSS0044685' => 'camsi', 'CSS0044700' => 'camsi', 'CSS0044888' => 'camsi', 'CSS0044923' => 'camsi', 'CSS0044926' => 'camsi', 'CSS0044979' => 'camsi', 'CSS0045049' => 'camsi', 'CSS0045132' => 'camsi', 'CSS0045161' => 'camsi', 'CSS0045219' => 'camsi', 'CSS0045230' => 'camsi', 'CSS0045259' => 'camsi', 'CSS0045324' => 'camsi', 'CSS0045368' => 'camsi', 'CSS0045435' => 'camsi', 'CSS0045856' => 'camsi', 'CSS0045955' => 'camsi', 'CSS0046158' => 'camsi', 'CSS0046334' => 'camsi', 'CSS0046365' => 'camsi', 'CSS0046396' => 'camsi', 'CSS0046400' => 'camsi', 'CSS0046445' => 'camsi', 'CSS0046493' => 'camsi', 'CSS0046640' => 'camsi', 'CSS0046657' => 'camsi', 'CSS0046702' => 'camsi', 'CSS0047208' => 'camsi', 'CSS0047368' => 'camsi', 'CSS0047403' => 'camsi', 'CSS0047417' => 'camsi', 'CSS0047469' => 'camsi', 'CSS0047480' => 'camsi', 'CSS0047482' => 'camsi', 'CSS0047693' => 'camsi', 'CSS0047766' => 'camsi', 'CSS0047866' => 'camsi', 'CSS0047884' => 'camsi', 'CSS0048235' => 'camsi', 'CSS0048383' => 'camsi', 'CSS0048438' => 'camsi', 'CSS0048502' => 'camsi', 'CSS0048546' => 'camsi', 'CSS0048653' => 'camsi', 'CSS0048658' => 'camsi', 'CSS0048729' => 'camsi', 'CSS0048867' => 'camsi', 'CSS0048988' => 'camsi', 'CSS0049053' => 'camsi', 'CSS0049099' => 'camsi', 'CSS0049166' => 'camsi', 'CSS0049174' => 'camsi', 'CSS0049212' => 'camsi', 'CSS0049280' => 'camsi', 'CSS0049391' => 'camsi', 'CSS0049546' => 'camsi', 'CSS0049634' => 'camsi', 'CSS0049655' => 'camsi', 'CSS0049813' => 'camsi', 'CSS0049949' => 'camsi', 'CSS0050009' => 'camsi', 'CSS0050118' => 'camsi', 'CSS0050205' => 'camsi', 'CSS0050275' => 'camsi', 'CSS0050480' => 'camsi', 'CSS0050488' => 'camsi', 'CSS0050497' => 'camsi', 'Dinv03126' => 'din', 'Dinv13140' => 'din', 'Dinv13247' => 'din', 'Dinv14217' => 'din', 'EL10Ac9g22435' => 'bvu', 'FAN20G1200' => 'fan', 'PGR142G2516' => 'pgr', 'Prupe.3G160200' => 'ppe', 'Prupe.5G238200' => 'ppe', 'Prupe.7G047500' => 'ppe', 'QL03p045360' => 'qlo', 'QL05p034369' => 'qlo', 'QL05p034412' => 'qlo', 'QL08p017802' => 'qlo', 'QL08p024762' => 'qlo', 'QL10p026237' => 'qlo', 'QL10p032070' => 'qlo', 'QL11p003821' => 'qlo', 'Rhsim04G0057300' => 'rsi', 'Rhsim05G0049200' => 'rsi', 'Rhsim12G0010400' => 'rsi', 'Rhsim12G0012800' => 'rsi', 'TAR624G0483' => 'tar', 'TAR703G0001' => 'tar', 'vmacro05414' => 'vma', 'vmacro07091' => 'vma', 'vmacro07116' => 'vma', 'vmacro08423' => 'vma', 'vmacro09046' => 'vma', 'vmacro14269' => 'vma', 'vmacro16092' => 'vma', 'vmacro17280' => 'vma', 'vmacro19601' => 'vma' ), 'gf_id' => 'HOM05D001028', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001028' ), 'data_identifier' => 'HOM05D001028', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001028', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '590', 'num_species' => '12' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'Aqoxy1G01649' => 'aox', 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'CSS0032603' => 'camsi', 'CSS0032640' => 'camsi', 'CSS0032704' => 'camsi', 'CSS0032851' => 'camsi', 'CSS0032973' => 'camsi', 'CSS0033048' => 'camsi', 'CSS0033082' => 'camsi', 'CSS0033157' => 'camsi', 'CSS0033253' => 'camsi', 'CSS0033347' => 'camsi', 'CSS0033601' => 'camsi', 'CSS0033820' => 'camsi', 'CSS0033881' => 'camsi', 'CSS0033934' => 'camsi', 'CSS0034143' => 'camsi', 'CSS0034176' => 'camsi', 'CSS0034201' => 'camsi', 'CSS0034269' => 'camsi', 'CSS0034303' => 'camsi', 'CSS0034463' => 'camsi', 'CSS0034470' => 'camsi', 'CSS0034514' => 'camsi', 'CSS0034525' => 'camsi', 'CSS0034726' => 'camsi', 'CSS0034727' => 'camsi', 'CSS0034737' => 'camsi', 'CSS0034768' => 'camsi', 'CSS0034890' => 'camsi', 'CSS0034943' => 'camsi', 'CSS0034957' => 'camsi', 'CSS0034973' => 'camsi', 'CSS0035178' => 'camsi', 'CSS0035260' => 'camsi', 'CSS0035316' => 'camsi', 'CSS0035347' => 'camsi', 'CSS0035360' => 'camsi', 'CSS0035380' => 'camsi', 'CSS0035429' => 'camsi', 'CSS0035446' => 'camsi', 'CSS0035737' => 'camsi', 'CSS0035852' => 'camsi', 'CSS0035967' => 'camsi', 'CSS0036001' => 'camsi', 'CSS0036044' => 'camsi', 'CSS0036221' => 'camsi', 'CSS0036333' => 'camsi', 'CSS0036435' => 'camsi', 'CSS0036843' => 'camsi', 'CSS0036846' => 'camsi', 'CSS0037097' => 'camsi', 'CSS0037263' => 'camsi', 'CSS0037370' => 'camsi', 'CSS0037410' => 'camsi', 'CSS0037449' => 'camsi', 'CSS0037603' => 'camsi', 'CSS0037851' => 'camsi', 'CSS0037891' => 'camsi', 'CSS0037996' => 'camsi', 'CSS0038222' => 'camsi', 'CSS0038433' => 'camsi', 'CSS0038441' => 'camsi', 'CSS0038718' => 'camsi', 'CSS0038890' => 'camsi', 'CSS0039049' => 'camsi', 'CSS0039145' => 'camsi', 'CSS0039243' => 'camsi', 'CSS0039294' => 'camsi', 'CSS0039324' => 'camsi', 'CSS0039376' => 'camsi', 'CSS0039475' => 'camsi', 'CSS0039539' => 'camsi', 'CSS0039546' => 'camsi', 'CSS0039567' => 'camsi', 'CSS0039599' => 'camsi', 'CSS0039763' => 'camsi', 'CSS0039863' => 'camsi', 'CSS0040107' => 'camsi', 'CSS0040124' => 'camsi', 'CSS0040151' => 'camsi', 'CSS0040165' => 'camsi', 'CSS0040309' => 'camsi', 'CSS0040318' => 'camsi', 'CSS0040347' => 'camsi', 'CSS0040371' => 'camsi', 'CSS0040456' => 'camsi', 'CSS0040551' => 'camsi', 'CSS0040975' => 'camsi', 'CSS0040981' => 'camsi', 'CSS0041299' => 'camsi', 'CSS0041493' => 'camsi', 'CSS0041658' => 'camsi', 'CSS0041899' => 'camsi', 'CSS0041927' => 'camsi', 'CSS0042016' => 'camsi', 'CSS0042034' => 'camsi', 'CSS0042103' => 'camsi', 'CSS0042172' => 'camsi', 'CSS0042198' => 'camsi', 'CSS0042201' => 'camsi', 'CSS0042308' => 'camsi', 'CSS0042329' => 'camsi', 'CSS0042348' => 'camsi', 'CSS0042349' => 'camsi', 'CSS0042489' => 'camsi', 'CSS0042575' => 'camsi', 'CSS0042624' => 'camsi', 'CSS0042660' => 'camsi', 'CSS0042694' => 'camsi', 'CSS0042995' => 'camsi', 'CSS0043079' => 'camsi', 'CSS0043165' => 'camsi', 'CSS0043171' => 'camsi', 'CSS0043314' => 'camsi', 'CSS0043361' => 'camsi', 'CSS0043375' => 'camsi', 'CSS0043518' => 'camsi', 'CSS0043536' => 'camsi', 'CSS0043678' => 'camsi', 'CSS0043765' => 'camsi', 'CSS0043897' => 'camsi', 'CSS0043944' => 'camsi', 'CSS0044126' => 'camsi', 'CSS0044136' => 'camsi', 'CSS0044179' => 'camsi', 'CSS0044290' => 'camsi', 'CSS0044437' => 'camsi', 'CSS0044502' => 'camsi', 'CSS0044603' => 'camsi', 'CSS0044680' => 'camsi', 'CSS0044685' => 'camsi', 'CSS0044700' => 'camsi', 'CSS0044888' => 'camsi', 'CSS0044923' => 'camsi', 'CSS0044926' => 'camsi', 'CSS0044979' => 'camsi', 'CSS0045049' => 'camsi', 'CSS0045132' => 'camsi', 'CSS0045161' => 'camsi', 'CSS0045219' => 'camsi', 'CSS0045230' => 'camsi', 'CSS0045259' => 'camsi', 'CSS0045324' => 'camsi', 'CSS0045368' => 'camsi', 'CSS0045435' => 'camsi', 'CSS0045856' => 'camsi', 'CSS0045955' => 'camsi', 'CSS0046158' => 'camsi', 'CSS0046334' => 'camsi', 'CSS0046365' => 'camsi', 'CSS0046396' => 'camsi', 'CSS0046400' => 'camsi', 'CSS0046445' => 'camsi', 'CSS0046493' => 'camsi', 'CSS0046640' => 'camsi', 'CSS0046657' => 'camsi', 'CSS0046702' => 'camsi', 'CSS0047208' => 'camsi', 'CSS0047368' => 'camsi', 'CSS0047403' => 'camsi', 'CSS0047417' => 'camsi', 'CSS0047469' => 'camsi', 'CSS0047480' => 'camsi', 'CSS0047482' => 'camsi', 'CSS0047693' => 'camsi', 'CSS0047766' => 'camsi', 'CSS0047866' => 'camsi', 'CSS0047884' => 'camsi', 'CSS0048235' => 'camsi', 'CSS0048383' => 'camsi', 'CSS0048438' => 'camsi', 'CSS0048502' => 'camsi', 'CSS0048546' => 'camsi', 'CSS0048653' => 'camsi', 'CSS0048658' => 'camsi', 'CSS0048729' => 'camsi', 'CSS0048867' => 'camsi', 'CSS0048988' => 'camsi', 'CSS0049053' => 'camsi', 'CSS0049099' => 'camsi', 'CSS0049166' => 'camsi', 'CSS0049174' => 'camsi', 'CSS0049212' => 'camsi', 'CSS0049280' => 'camsi', 'CSS0049391' => 'camsi', 'CSS0049546' => 'camsi', 'CSS0049634' => 'camsi', 'CSS0049655' => 'camsi', 'CSS0049813' => 'camsi', 'CSS0049949' => 'camsi', 'CSS0050009' => 'camsi', 'CSS0050118' => 'camsi', 'CSS0050205' => 'camsi', 'CSS0050275' => 'camsi', 'CSS0050480' => 'camsi', 'CSS0050488' => 'camsi', 'CSS0050497' => 'camsi', 'Dinv03126' => 'din', 'Dinv13140' => 'din', 'Dinv13247' => 'din', 'Dinv14217' => 'din', 'EL10Ac9g22435' => 'bvu', 'FAN20G1200' => 'fan', 'PGR142G2516' => 'pgr', 'Prupe.3G160200' => 'ppe', 'Prupe.5G238200' => 'ppe', 'Prupe.7G047500' => 'ppe', 'QL03p045360' => 'qlo', 'QL05p034369' => 'qlo', 'QL05p034412' => 'qlo', 'QL08p017802' => 'qlo', 'QL08p024762' => 'qlo', 'QL10p026237' => 'qlo', 'QL10p032070' => 'qlo', 'QL11p003821' => 'qlo', 'Rhsim04G0057300' => 'rsi', 'Rhsim05G0049200' => 'rsi', 'Rhsim12G0010400' => 'rsi', 'Rhsim12G0012800' => 'rsi', 'TAR624G0483' => 'tar', 'TAR703G0001' => 'tar', 'vmacro05414' => 'vma', 'vmacro07091' => 'vma', 'vmacro07116' => 'vma', 'vmacro08423' => 'vma', 'vmacro09046' => 'vma', 'vmacro14269' => 'vma', 'vmacro16092' => 'vma', 'vmacro17280' => 'vma', 'vmacro19601' => 'vma' ) $gf_id = 'HOM05D001028' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001028' ) $data_identifier = 'HOM05D001028' $data_type = 'gf_id' $species_gene_counts = array( 'aox' => (int) 11, 'ccan' => (int) 6, 'camsi' => (int) 540, 'din' => (int) 4, 'bvu' => (int) 1, 'fan' => (int) 1, 'pgr' => (int) 1, 'ppe' => (int) 3, 'qlo' => (int) 8, 'rsi' => (int) 4, 'tar' => (int) 2, 'vma' => (int) 9 ) $gf_gene_species = 'vma' $gf_gene_id = 'vmacro19601' $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) 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' => 'HOM05D001028', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '590', 'num_species' => '12' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'Aqoxy1G01649' => 'aox', 'Aqoxy1G02950' => 'aox', 'Aqoxy2G01005' => 'aox', 'Aqoxy2G01064' => 'aox', 'Aqoxy3G02267' => 'aox', 'Aqoxy3G02617' => 'aox', 'Aqoxy3G02693' => 'aox', 'Aqoxy5G03425' => 'aox', 'Aqoxy6G02164' => 'aox', 'Aqoxy6G02364' => 'aox', 'Aqoxy7G02284' => 'aox', 'Cc00_g09720' => 'ccan', 'Cc00_g21410' => 'ccan', 'Cc00_g31750' => 'ccan', 'Cc00_g34740' => 'ccan', 'Cc04_g16890' => 'ccan', 'Cc11_g03120' => 'ccan', 'CSS0000222' => 'camsi', 'CSS0000265' => 'camsi', 'CSS0000306' => 'camsi', 'CSS0000326' => 'camsi', 'CSS0000530' => 'camsi', 'CSS0000563' => 'camsi', 'CSS0000584' => 'camsi', 'CSS0000684' => 'camsi', 'CSS0001100' => 'camsi', 'CSS0001311' => 'camsi', 'CSS0001343' => 'camsi', 'CSS0001399' => 'camsi', 'CSS0001475' => 'camsi', 'CSS0001506' => 'camsi', 'CSS0001602' => 'camsi', 'CSS0001681' => 'camsi', 'CSS0001874' => 'camsi', 'CSS0001948' => 'camsi', 'CSS0002022' => 'camsi', 'CSS0002230' => 'camsi', 'CSS0002265' => 'camsi', 'CSS0002277' => 'camsi', 'CSS0002462' => 'camsi', 'CSS0002823' => 'camsi', 'CSS0003091' => 'camsi', 'CSS0003162' => 'camsi', 'CSS0003264' => 'camsi', 'CSS0003355' => 'camsi', 'CSS0003378' => 'camsi', 'CSS0003472' => 'camsi', 'CSS0003500' => 'camsi', 'CSS0003640' => 'camsi', 'CSS0003767' => 'camsi', 'CSS0003894' => 'camsi', 'CSS0003952' => 'camsi', 'CSS0003977' => 'camsi', 'CSS0004028' => 'camsi', 'CSS0004117' => 'camsi', 'CSS0004137' => 'camsi', 'CSS0004176' => 'camsi', 'CSS0004265' => 'camsi', 'CSS0004450' => 'camsi', 'CSS0004468' => 'camsi', 'CSS0004488' => 'camsi', 'CSS0004490' => 'camsi', 'CSS0004632' => 'camsi', 'CSS0004790' => 'camsi', 'CSS0004877' => 'camsi', 'CSS0004920' => 'camsi', 'CSS0004969' => 'camsi', 'CSS0005084' => 'camsi', 'CSS0005101' => 'camsi', 'CSS0005271' => 'camsi', 'CSS0005313' => 'camsi', 'CSS0005331' => 'camsi', 'CSS0005368' => 'camsi', 'CSS0005391' => 'camsi', 'CSS0005437' => 'camsi', 'CSS0005515' => 'camsi', 'CSS0005526' => 'camsi', 'CSS0005532' => 'camsi', 'CSS0005595' => 'camsi', 'CSS0005677' => 'camsi', 'CSS0005838' => 'camsi', 'CSS0005988' => 'camsi', 'CSS0006100' => 'camsi', 'CSS0006128' => 'camsi', 'CSS0006293' => 'camsi', 'CSS0006378' => 'camsi', 'CSS0006400' => 'camsi', 'CSS0006441' => 'camsi', 'CSS0006455' => 'camsi', 'CSS0006480' => 'camsi', 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'CSS0009986' => 'camsi', 'CSS0010182' => 'camsi', 'CSS0010202' => 'camsi', 'CSS0010330' => 'camsi', 'CSS0010362' => 'camsi', 'CSS0010456' => 'camsi', 'CSS0010472' => 'camsi', 'CSS0010507' => 'camsi', 'CSS0010512' => 'camsi', 'CSS0010520' => 'camsi', 'CSS0010617' => 'camsi', 'CSS0010706' => 'camsi', 'CSS0010747' => 'camsi', 'CSS0010816' => 'camsi', 'CSS0011020' => 'camsi', 'CSS0011115' => 'camsi', 'CSS0011383' => 'camsi', 'CSS0011491' => 'camsi', 'CSS0011602' => 'camsi', 'CSS0011605' => 'camsi', 'CSS0011625' => 'camsi', 'CSS0011654' => 'camsi', 'CSS0011781' => 'camsi', 'CSS0011853' => 'camsi', 'CSS0011898' => 'camsi', 'CSS0011933' => 'camsi', 'CSS0011996' => 'camsi', 'CSS0012066' => 'camsi', 'CSS0012097' => 'camsi', 'CSS0012108' => 'camsi', 'CSS0012226' => 'camsi', 'CSS0012248' => 'camsi', 'CSS0012331' => 'camsi', 'CSS0012797' => 'camsi', 'CSS0012818' => 'camsi', 'CSS0012904' => 'camsi', 'CSS0013001' => 'camsi', 'CSS0013022' => 'camsi', 'CSS0013172' => 'camsi', 'CSS0013244' => 'camsi', 'CSS0013267' => 'camsi', 'CSS0013275' => 'camsi', 'CSS0013324' => 'camsi', 'CSS0013334' => 'camsi', 'CSS0013394' => 'camsi', 'CSS0013549' => 'camsi', 'CSS0013689' => 'camsi', 'CSS0014026' => 'camsi', 'CSS0014049' => 'camsi', 'CSS0014144' => 'camsi', 'CSS0014354' => 'camsi', 'CSS0014579' => 'camsi', 'CSS0014648' => 'camsi', 'CSS0014902' => 'camsi', 'CSS0014979' => 'camsi', 'CSS0015278' => 'camsi', 'CSS0015310' => 'camsi', 'CSS0015364' => 'camsi', 'CSS0015455' => 'camsi', 'CSS0015693' => 'camsi', 'CSS0015774' => 'camsi', 'CSS0015795' => 'camsi', 'CSS0015952' => 'camsi', 'CSS0016104' => 'camsi', 'CSS0016241' => 'camsi', 'CSS0016303' => 'camsi', 'CSS0016490' => 'camsi', 'CSS0016832' => 'camsi', 'CSS0016845' => 'camsi', 'CSS0016914' => 'camsi', 'CSS0016946' => 'camsi', 'CSS0017102' => 'camsi', 'CSS0017193' => 'camsi', 'CSS0017528' => 'camsi', 'CSS0017619' => 'camsi', 'CSS0017679' => 'camsi', 'CSS0017816' => 'camsi', 'CSS0017880' => 'camsi', 'CSS0018106' => 'camsi', 'CSS0018162' => 'camsi', 'CSS0018304' => 'camsi', 'CSS0018406' => 'camsi', 'CSS0018481' => 'camsi', 'CSS0018511' => 'camsi', 'CSS0018596' => 'camsi', 'CSS0018727' => 'camsi', 'CSS0018751' => 'camsi', 'CSS0018777' => 'camsi', 'CSS0018798' => 'camsi', 'CSS0019137' => 'camsi', 'CSS0019177' => 'camsi', 'CSS0019217' => 'camsi', 'CSS0019361' => 'camsi', 'CSS0019516' => 'camsi', 'CSS0019538' => 'camsi', 'CSS0019560' => 'camsi', 'CSS0019819' => 'camsi', 'CSS0019837' => 'camsi', 'CSS0019915' => 'camsi', 'CSS0019925' => 'camsi', 'CSS0020112' => 'camsi', 'CSS0020160' => 'camsi', 'CSS0020378' => 'camsi', 'CSS0020388' => 'camsi', 'CSS0020452' => 'camsi', 'CSS0020588' => 'camsi', 'CSS0020661' => 'camsi', 'CSS0020886' => 'camsi', 'CSS0020973' => 'camsi', 'CSS0021035' => 'camsi', 'CSS0021111' => 'camsi', 'CSS0021131' => 'camsi', 'CSS0021151' => 'camsi', 'CSS0021228' => 'camsi', 'CSS0021397' => 'camsi', 'CSS0021420' => 'camsi', 'CSS0021464' => 'camsi', 'CSS0021547' => 'camsi', 'CSS0021608' => 'camsi', 'CSS0021740' => 'camsi', 'CSS0021826' => 'camsi', 'CSS0021904' => 'camsi', 'CSS0021941' => 'camsi', 'CSS0022189' => 'camsi', 'CSS0022199' => 'camsi', 'CSS0022502' => 'camsi', 'CSS0022531' => 'camsi', 'CSS0022581' => 'camsi', 'CSS0022612' => 'camsi', 'CSS0022621' => 'camsi', 'CSS0022815' => 'camsi', 'CSS0022936' => 'camsi', 'CSS0022964' => 'camsi', 'CSS0022985' => 'camsi', 'CSS0023002' => 'camsi', 'CSS0023006' => 'camsi', 'CSS0023024' => 'camsi', 'CSS0023489' => 'camsi', 'CSS0023593' => 'camsi', 'CSS0023621' => 'camsi', 'CSS0023743' => 'camsi', 'CSS0023804' => 'camsi', 'CSS0023805' => 'camsi', 'CSS0023908' => 'camsi', 'CSS0023938' => 'camsi', 'CSS0023981' => 'camsi', 'CSS0024027' => 'camsi', 'CSS0024169' => 'camsi', 'CSS0024193' => 'camsi', 'CSS0024269' => 'camsi', 'CSS0024336' => 'camsi', 'CSS0024337' => 'camsi', 'CSS0024548' => 'camsi', 'CSS0024564' => 'camsi', 'CSS0024585' => 'camsi', 'CSS0024738' => 'camsi', 'CSS0024833' => 'camsi', 'CSS0024846' => 'camsi', 'CSS0024957' => 'camsi', 'CSS0024974' => 'camsi', 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'CSS0041493' => 'camsi', 'CSS0041658' => 'camsi', 'CSS0041899' => 'camsi', 'CSS0041927' => 'camsi', 'CSS0042016' => 'camsi', 'CSS0042034' => 'camsi', 'CSS0042103' => 'camsi', 'CSS0042172' => 'camsi', 'CSS0042198' => 'camsi', 'CSS0042201' => 'camsi', 'CSS0042308' => 'camsi', 'CSS0042329' => 'camsi', 'CSS0042348' => 'camsi', 'CSS0042349' => 'camsi', 'CSS0042489' => 'camsi', 'CSS0042575' => 'camsi', 'CSS0042624' => 'camsi', 'CSS0042660' => 'camsi', 'CSS0042694' => 'camsi', 'CSS0042995' => 'camsi', 'CSS0043079' => 'camsi', 'CSS0043165' => 'camsi', 'CSS0043171' => 'camsi', 'CSS0043314' => 'camsi', 'CSS0043361' => 'camsi', 'CSS0043375' => 'camsi', 'CSS0043518' => 'camsi', 'CSS0043536' => 'camsi', 'CSS0043678' => 'camsi', 'CSS0043765' => 'camsi', 'CSS0043897' => 'camsi', 'CSS0043944' => 'camsi', 'CSS0044126' => 'camsi', 'CSS0044136' => 'camsi', 'CSS0044179' => 'camsi', 'CSS0044290' => 'camsi', 'CSS0044437' => 'camsi', 'CSS0044502' => 'camsi', 'CSS0044603' => 'camsi', 'CSS0044680' => 'camsi', 'CSS0044685' => 'camsi', 'CSS0044700' => 'camsi', 'CSS0044888' => 'camsi', 'CSS0044923' => 'camsi', 'CSS0044926' => 'camsi', 'CSS0044979' => 'camsi', 'CSS0045049' => 'camsi', 'CSS0045132' => 'camsi', 'CSS0045161' => 'camsi', 'CSS0045219' => 'camsi', 'CSS0045230' => 'camsi', 'CSS0045259' => 'camsi', 'CSS0045324' => 'camsi', 'CSS0045368' => 'camsi', 'CSS0045435' => 'camsi', 'CSS0045856' => 'camsi', 'CSS0045955' => 'camsi', 'CSS0046158' => 'camsi', 'CSS0046334' => 'camsi', 'CSS0046365' => 'camsi', 'CSS0046396' => 'camsi', 'CSS0046400' => 'camsi', 'CSS0046445' => 'camsi', 'CSS0046493' => 'camsi', 'CSS0046640' => 'camsi', 'CSS0046657' => 'camsi', 'CSS0046702' => 'camsi', 'CSS0047208' => 'camsi', 'CSS0047368' => 'camsi', 'CSS0047403' => 'camsi', 'CSS0047417' => 'camsi', 'CSS0047469' => 'camsi', 'CSS0047480' => 'camsi', 'CSS0047482' => 'camsi', 'CSS0047693' => 'camsi', 'CSS0047766' => 'camsi', 'CSS0047866' => 'camsi', 'CSS0047884' => 'camsi', 'CSS0048235' => 'camsi', 'CSS0048383' => 'camsi', 'CSS0048438' => 'camsi', 'CSS0048502' => 'camsi', 'CSS0048546' => 'camsi', 'CSS0048653' => 'camsi', 'CSS0048658' => 'camsi', 'CSS0048729' => 'camsi', 'CSS0048867' => 'camsi', 'CSS0048988' => 'camsi', 'CSS0049053' => 'camsi', 'CSS0049099' => 'camsi', 'CSS0049166' => 'camsi', 'CSS0049174' => 'camsi', 'CSS0049212' => 'camsi', 'CSS0049280' => 'camsi', 'CSS0049391' => 'camsi', 'CSS0049546' => 'camsi', 'CSS0049634' => 'camsi', 'CSS0049655' => 'camsi', 'CSS0049813' => 'camsi', 'CSS0049949' => 'camsi', 'CSS0050009' => 'camsi', 'CSS0050118' => 'camsi', 'CSS0050205' => 'camsi', 'CSS0050275' => 'camsi', 'CSS0050480' => 'camsi', 'CSS0050488' => 'camsi', 'CSS0050497' => 'camsi', 'Dinv03126' => 'din', 'Dinv13140' => 'din', 'Dinv13247' => 'din', 'Dinv14217' => 'din', 'EL10Ac9g22435' => 'bvu', 'FAN20G1200' => 'fan', 'PGR142G2516' => 'pgr', 'Prupe.3G160200' => 'ppe', 'Prupe.5G238200' => 'ppe', 'Prupe.7G047500' => 'ppe', 'QL03p045360' => 'qlo', 'QL05p034369' => 'qlo', 'QL05p034412' => 'qlo', 'QL08p017802' => 'qlo', 'QL08p024762' => 'qlo', 'QL10p026237' => 'qlo', 'QL10p032070' => 'qlo', 'QL11p003821' => 'qlo', 'Rhsim04G0057300' => 'rsi', 'Rhsim05G0049200' => 'rsi', 'Rhsim12G0010400' => 'rsi', 'Rhsim12G0012800' => 'rsi', 'TAR624G0483' => 'tar', 'TAR703G0001' => 'tar', 'vmacro05414' => 'vma', 'vmacro07091' => 'vma', 'vmacro07116' => 'vma', 'vmacro08423' => 'vma', 'vmacro09046' => 'vma', 'vmacro14269' => 'vma', 'vmacro16092' => 'vma', 'vmacro17280' => 'vma', 'vmacro19601' => 'vma' ), 'gf_id' => 'HOM05D001028', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001028' ), 'data_identifier' => 'HOM05D001028', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001028', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '590', 'num_species' => '12' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'Aqoxy1G01649' => 'aox', 'Aqoxy1G02950' => 'aox', 'Aqoxy2G01005' => 'aox', 'Aqoxy2G01064' => 'aox', 'Aqoxy3G02267' => 'aox', 'Aqoxy3G02617' => 'aox', 'Aqoxy3G02693' => 'aox', 'Aqoxy5G03425' => 'aox', 'Aqoxy6G02164' => 'aox', 'Aqoxy6G02364' => 'aox', 'Aqoxy7G02284' => 'aox', 'Cc00_g09720' => 'ccan', 'Cc00_g21410' => 'ccan', 'Cc00_g31750' => 'ccan', 'Cc00_g34740' => 'ccan', 'Cc04_g16890' => 'ccan', 'Cc11_g03120' => 'ccan', 'CSS0000222' => 'camsi', 'CSS0000265' => 'camsi', 'CSS0000306' => 'camsi', 'CSS0000326' => 'camsi', 'CSS0000530' => 'camsi', 'CSS0000563' => 'camsi', 'CSS0000584' => 'camsi', 'CSS0000684' => 'camsi', 'CSS0001100' => 'camsi', 'CSS0001311' => 'camsi', 'CSS0001343' => 'camsi', 'CSS0001399' => 'camsi', 'CSS0001475' => 'camsi', 'CSS0001506' => 'camsi', 'CSS0001602' => 'camsi', 'CSS0001681' => 'camsi', 'CSS0001874' => 'camsi', 'CSS0001948' => 'camsi', 'CSS0002022' => 'camsi', 'CSS0002230' => 'camsi', 'CSS0002265' => 'camsi', 'CSS0002277' => 'camsi', 'CSS0002462' => 'camsi', 'CSS0002823' => 'camsi', 'CSS0003091' => 'camsi', 'CSS0003162' => 'camsi', 'CSS0003264' => 'camsi', 'CSS0003355' => 'camsi', 'CSS0003378' => 'camsi', 'CSS0003472' => 'camsi', 'CSS0003500' => 'camsi', 'CSS0003640' => 'camsi', 'CSS0003767' => 'camsi', 'CSS0003894' => 'camsi', 'CSS0003952' => 'camsi', 'CSS0003977' => 'camsi', 'CSS0004028' => 'camsi', 'CSS0004117' => 'camsi', 'CSS0004137' => 'camsi', 'CSS0004176' => 'camsi', 'CSS0004265' => 'camsi', 'CSS0004450' => 'camsi', 'CSS0004468' => 'camsi', 'CSS0004488' => 'camsi', 'CSS0004490' => 'camsi', 'CSS0004632' => 'camsi', 'CSS0004790' => 'camsi', 'CSS0004877' => 'camsi', 'CSS0004920' => 'camsi', 'CSS0004969' => 'camsi', 'CSS0005084' => 'camsi', 'CSS0005101' => 'camsi', 'CSS0005271' => 'camsi', 'CSS0005313' => 'camsi', 'CSS0005331' => 'camsi', 'CSS0005368' => 'camsi', 'CSS0005391' => 'camsi', 'CSS0005437' => 'camsi', 'CSS0005515' => 'camsi', 'CSS0005526' => 'camsi', 'CSS0005532' => 'camsi', 'CSS0005595' => 'camsi', 'CSS0005677' => 'camsi', 'CSS0005838' => 'camsi', 'CSS0005988' => 'camsi', 'CSS0006100' => 'camsi', 'CSS0006128' => 'camsi', 'CSS0006293' => 'camsi', 'CSS0006378' => 'camsi', 'CSS0006400' => 'camsi', 'CSS0006441' => 'camsi', 'CSS0006455' => 'camsi', 'CSS0006480' => 'camsi', 'CSS0006483' => 'camsi', 'CSS0006538' => 'camsi', 'CSS0006582' => 'camsi', 'CSS0006632' => 'camsi', 'CSS0006771' => 'camsi', 'CSS0006803' => 'camsi', 'CSS0006852' => 'camsi', 'CSS0006861' => 'camsi', 'CSS0006910' => 'camsi', 'CSS0007037' => 'camsi', 'CSS0007066' => 'camsi', 'CSS0007072' => 'camsi', 'CSS0007109' => 'camsi', 'CSS0007193' => 'camsi', 'CSS0007319' => 'camsi', 'CSS0007336' => 'camsi', 'CSS0007377' => 'camsi', 'CSS0007659' => 'camsi', 'CSS0007701' => 'camsi', 'CSS0007711' => 'camsi', 'CSS0007809' => 'camsi', 'CSS0008045' => 'camsi', 'CSS0008050' => 'camsi', 'CSS0008206' => 'camsi', 'CSS0008251' => 'camsi', 'CSS0008252' => 'camsi', 'CSS0008279' => 'camsi', 'CSS0008482' => 'camsi', 'CSS0008583' => 'camsi', 'CSS0008699' => 'camsi', 'CSS0008798' => 'camsi', 'CSS0008971' => 'camsi', 'CSS0009019' => 'camsi', 'CSS0009191' => 'camsi', 'CSS0009241' => 'camsi', 'CSS0009246' => 'camsi', 'CSS0009399' => 'camsi', 'CSS0009654' => 'camsi', 'CSS0009722' => 'camsi', 'CSS0009920' => 'camsi', 'CSS0009986' => 'camsi', 'CSS0010182' => 'camsi', 'CSS0010202' => 'camsi', 'CSS0010330' => 'camsi', 'CSS0010362' => 'camsi', 'CSS0010456' => 'camsi', 'CSS0010472' => 'camsi', 'CSS0010507' => 'camsi', 'CSS0010512' => 'camsi', 'CSS0010520' => 'camsi', 'CSS0010617' => 'camsi', 'CSS0010706' => 'camsi', 'CSS0010747' => 'camsi', 'CSS0010816' => 'camsi', 'CSS0011020' => 'camsi', 'CSS0011115' => 'camsi', 'CSS0011383' => 'camsi', 'CSS0011491' => 'camsi', 'CSS0011602' => 'camsi', 'CSS0011605' => 'camsi', 'CSS0011625' => 'camsi', 'CSS0011654' => 'camsi', 'CSS0011781' => 'camsi', 'CSS0011853' => 'camsi', 'CSS0011898' => 'camsi', 'CSS0011933' => 'camsi', 'CSS0011996' => 'camsi', 'CSS0012066' => 'camsi', 'CSS0012097' => 'camsi', 'CSS0012108' => 'camsi', 'CSS0012226' => 'camsi', 'CSS0012248' => 'camsi', 'CSS0012331' => 'camsi', 'CSS0012797' => 'camsi', 'CSS0012818' => 'camsi', 'CSS0012904' => 'camsi', 'CSS0013001' => 'camsi', 'CSS0013022' => 'camsi', 'CSS0013172' => 'camsi', 'CSS0013244' => 'camsi', 'CSS0013267' => 'camsi', 'CSS0013275' => 'camsi', 'CSS0013324' => 'camsi', 'CSS0013334' => 'camsi', 'CSS0013394' => 'camsi', 'CSS0013549' => 'camsi', 'CSS0013689' => 'camsi', 'CSS0014026' => 'camsi', 'CSS0014049' => 'camsi', 'CSS0014144' => 'camsi', 'CSS0014354' => 'camsi', 'CSS0014579' => 'camsi', 'CSS0014648' => 'camsi', 'CSS0014902' => 'camsi', 'CSS0014979' => 'camsi', 'CSS0015278' => 'camsi', 'CSS0015310' => 'camsi', 'CSS0015364' => 'camsi', 'CSS0015455' => 'camsi', 'CSS0015693' => 'camsi', 'CSS0015774' => 'camsi', 'CSS0015795' => 'camsi', 'CSS0015952' => 'camsi', 'CSS0016104' => 'camsi', 'CSS0016241' => 'camsi', 'CSS0016303' => 'camsi', 'CSS0016490' => 'camsi', 'CSS0016832' => 'camsi', 'CSS0016845' => 'camsi', 'CSS0016914' => 'camsi', 'CSS0016946' => 'camsi', 'CSS0017102' => 'camsi', 'CSS0017193' => 'camsi', 'CSS0017528' => 'camsi', 'CSS0017619' => 'camsi', 'CSS0017679' => 'camsi', 'CSS0017816' => 'camsi', 'CSS0017880' => 'camsi', 'CSS0018106' => 'camsi', 'CSS0018162' => 'camsi', 'CSS0018304' => 'camsi', 'CSS0018406' => 'camsi', 'CSS0018481' => 'camsi', 'CSS0018511' => 'camsi', 'CSS0018596' => 'camsi', 'CSS0018727' => 'camsi', 'CSS0018751' => 'camsi', 'CSS0018777' => 'camsi', 'CSS0018798' => 'camsi', 'CSS0019137' => 'camsi', 'CSS0019177' => 'camsi', 'CSS0019217' => 'camsi', 'CSS0019361' => 'camsi', 'CSS0019516' => 'camsi', 'CSS0019538' => 'camsi', 'CSS0019560' => 'camsi', 'CSS0019819' => 'camsi', 'CSS0019837' => 'camsi', 'CSS0019915' => 'camsi', 'CSS0019925' => 'camsi', 'CSS0020112' => 'camsi', 'CSS0020160' => 'camsi', 'CSS0020378' => 'camsi', 'CSS0020388' => 'camsi', 'CSS0020452' => 'camsi', 'CSS0020588' => 'camsi', 'CSS0020661' => 'camsi', 'CSS0020886' => 'camsi', 'CSS0020973' => 'camsi', 'CSS0021035' => 'camsi', 'CSS0021111' => 'camsi', 'CSS0021131' => 'camsi', 'CSS0021151' => 'camsi', 'CSS0021228' => 'camsi', 'CSS0021397' => 'camsi', 'CSS0021420' => 'camsi', 'CSS0021464' => 'camsi', 'CSS0021547' => 'camsi', 'CSS0021608' => 'camsi', 'CSS0021740' => 'camsi', 'CSS0021826' => 'camsi', 'CSS0021904' => 'camsi', 'CSS0021941' => 'camsi', 'CSS0022189' => 'camsi', 'CSS0022199' => 'camsi', 'CSS0022502' => 'camsi', 'CSS0022531' => 'camsi', 'CSS0022581' => 'camsi', 'CSS0022612' => 'camsi', 'CSS0022621' => 'camsi', 'CSS0022815' => 'camsi', 'CSS0022936' => 'camsi', 'CSS0022964' => 'camsi', 'CSS0022985' => 'camsi', 'CSS0023002' => 'camsi', 'CSS0023006' => 'camsi', 'CSS0023024' => 'camsi', 'CSS0023489' => 'camsi', 'CSS0023593' => 'camsi', 'CSS0023621' => 'camsi', 'CSS0023743' => 'camsi', 'CSS0023804' => 'camsi', 'CSS0023805' => 'camsi', 'CSS0023908' => 'camsi', 'CSS0023938' => 'camsi', 'CSS0023981' => 'camsi', 'CSS0024027' => 'camsi', 'CSS0024169' => 'camsi', 'CSS0024193' => 'camsi', 'CSS0024269' => 'camsi', 'CSS0024336' => 'camsi', 'CSS0024337' => 'camsi', 'CSS0024548' => 'camsi', 'CSS0024564' => 'camsi', 'CSS0024585' => 'camsi', 'CSS0024738' => 'camsi', 'CSS0024833' => 'camsi', 'CSS0024846' => 'camsi', 'CSS0024957' => 'camsi', 'CSS0024974' => 'camsi', 'CSS0025005' => 'camsi', 'CSS0025235' => 'camsi', 'CSS0025465' => 'camsi', 'CSS0025633' => 'camsi', 'CSS0025688' => 'camsi', 'CSS0025759' => 'camsi', 'CSS0025774' => 'camsi', 'CSS0025801' => 'camsi', 'CSS0025942' => 'camsi', 'CSS0026083' => 'camsi', 'CSS0026194' => 'camsi', 'CSS0026230' => 'camsi', 'CSS0026398' => 'camsi', 'CSS0026419' => 'camsi', 'CSS0026679' => 'camsi', 'CSS0026719' => 'camsi', 'CSS0026795' => 'camsi', 'CSS0026835' => 'camsi', 'CSS0026930' => 'camsi', 'CSS0027053' => 'camsi', 'CSS0027130' => 'camsi', 'CSS0027192' => 'camsi', 'CSS0027454' => 'camsi', 'CSS0027467' => 'camsi', 'CSS0027521' => 'camsi', 'CSS0027662' => 'camsi', 'CSS0027795' => 'camsi', 'CSS0027835' => 'camsi', 'CSS0027966' => 'camsi', 'CSS0028090' => 'camsi', 'CSS0028134' => 'camsi', 'CSS0028205' => 'camsi', 'CSS0028263' => 'camsi', 'CSS0028363' => 'camsi', 'CSS0028598' => 'camsi', 'CSS0029175' => 'camsi', 'CSS0029191' => 'camsi', 'CSS0029424' => 'camsi', 'CSS0029479' => 'camsi', 'CSS0029496' => 'camsi', 'CSS0029633' => 'camsi', 'CSS0029837' => 'camsi', 'CSS0029844' => 'camsi', 'CSS0029863' => 'camsi', 'CSS0029874' => 'camsi', 'CSS0029959' => 'camsi', 'CSS0030001' => 'camsi', 'CSS0030093' => 'camsi', 'CSS0030199' => 'camsi', 'CSS0030200' => 'camsi', 'CSS0030427' => 'camsi', 'CSS0030476' => 'camsi', 'CSS0030636' => 'camsi', 'CSS0030673' => 'camsi', 'CSS0030766' => 'camsi', 'CSS0030775' => 'camsi', 'CSS0030858' => 'camsi', 'CSS0030873' => 'camsi', 'CSS0030929' => 'camsi', 'CSS0031028' => 'camsi', 'CSS0031129' => 'camsi', 'CSS0031164' => 'camsi', 'CSS0031340' => 'camsi', 'CSS0031368' => 'camsi', 'CSS0031395' => 'camsi', 'CSS0031596' => 'camsi', 'CSS0031727' => 'camsi', 'CSS0032011' => 'camsi', 'CSS0032160' => 'camsi', 'CSS0032538' => 'camsi', 'CSS0032576' => 'camsi', 'CSS0032603' => 'camsi', 'CSS0032640' => 'camsi', 'CSS0032704' => 'camsi', 'CSS0032851' => 'camsi', 'CSS0032973' => 'camsi', 'CSS0033048' => 'camsi', 'CSS0033082' => 'camsi', 'CSS0033157' => 'camsi', 'CSS0033253' => 'camsi', 'CSS0033347' => 'camsi', 'CSS0033601' => 'camsi', 'CSS0033820' => 'camsi', 'CSS0033881' => 'camsi', 'CSS0033934' => 'camsi', 'CSS0034143' => 'camsi', 'CSS0034176' => 'camsi', 'CSS0034201' => 'camsi', 'CSS0034269' => 'camsi', 'CSS0034303' => 'camsi', 'CSS0034463' => 'camsi', 'CSS0034470' => 'camsi', 'CSS0034514' => 'camsi', 'CSS0034525' => 'camsi', 'CSS0034726' => 'camsi', 'CSS0034727' => 'camsi', 'CSS0034737' => 'camsi', 'CSS0034768' => 'camsi', 'CSS0034890' => 'camsi', 'CSS0034943' => 'camsi', 'CSS0034957' => 'camsi', 'CSS0034973' => 'camsi', 'CSS0035178' => 'camsi', 'CSS0035260' => 'camsi', 'CSS0035316' => 'camsi', 'CSS0035347' => 'camsi', 'CSS0035360' => 'camsi', 'CSS0035380' => 'camsi', 'CSS0035429' => 'camsi', 'CSS0035446' => 'camsi', 'CSS0035737' => 'camsi', 'CSS0035852' => 'camsi', 'CSS0035967' => 'camsi', 'CSS0036001' => 'camsi', 'CSS0036044' => 'camsi', 'CSS0036221' => 'camsi', 'CSS0036333' => 'camsi', 'CSS0036435' => 'camsi', 'CSS0036843' => 'camsi', 'CSS0036846' => 'camsi', 'CSS0037097' => 'camsi', 'CSS0037263' => 'camsi', 'CSS0037370' => 'camsi', 'CSS0037410' => 'camsi', 'CSS0037449' => 'camsi', 'CSS0037603' => 'camsi', 'CSS0037851' => 'camsi', 'CSS0037891' => 'camsi', 'CSS0037996' => 'camsi', 'CSS0038222' => 'camsi', 'CSS0038433' => 'camsi', 'CSS0038441' => 'camsi', 'CSS0038718' => 'camsi', 'CSS0038890' => 'camsi', 'CSS0039049' => 'camsi', 'CSS0039145' => 'camsi', 'CSS0039243' => 'camsi', 'CSS0039294' => 'camsi', 'CSS0039324' => 'camsi', 'CSS0039376' => 'camsi', 'CSS0039475' => 'camsi', 'CSS0039539' => 'camsi', 'CSS0039546' => 'camsi', 'CSS0039567' => 'camsi', 'CSS0039599' => 'camsi', 'CSS0039763' => 'camsi', 'CSS0039863' => 'camsi', 'CSS0040107' => 'camsi', 'CSS0040124' => 'camsi', 'CSS0040151' => 'camsi', 'CSS0040165' => 'camsi', 'CSS0040309' => 'camsi', 'CSS0040318' => 'camsi', 'CSS0040347' => 'camsi', 'CSS0040371' => 'camsi', 'CSS0040456' => 'camsi', 'CSS0040551' => 'camsi', 'CSS0040975' => 'camsi', 'CSS0040981' => 'camsi', 'CSS0041299' => 'camsi', 'CSS0041493' => 'camsi', 'CSS0041658' => 'camsi', 'CSS0041899' => 'camsi', 'CSS0041927' => 'camsi', 'CSS0042016' => 'camsi', 'CSS0042034' => 'camsi', 'CSS0042103' => 'camsi', 'CSS0042172' => 'camsi', 'CSS0042198' => 'camsi', 'CSS0042201' => 'camsi', 'CSS0042308' => 'camsi', 'CSS0042329' => 'camsi', 'CSS0042348' => 'camsi', 'CSS0042349' => 'camsi', 'CSS0042489' => 'camsi', 'CSS0042575' => 'camsi', 'CSS0042624' => 'camsi', 'CSS0042660' => 'camsi', 'CSS0042694' => 'camsi', 'CSS0042995' => 'camsi', 'CSS0043079' => 'camsi', 'CSS0043165' => 'camsi', 'CSS0043171' => 'camsi', 'CSS0043314' => 'camsi', 'CSS0043361' => 'camsi', 'CSS0043375' => 'camsi', 'CSS0043518' => 'camsi', 'CSS0043536' => 'camsi', 'CSS0043678' => 'camsi', 'CSS0043765' => 'camsi', 'CSS0043897' => 'camsi', 'CSS0043944' => 'camsi', 'CSS0044126' => 'camsi', 'CSS0044136' => 'camsi', 'CSS0044179' => 'camsi', 'CSS0044290' => 'camsi', 'CSS0044437' => 'camsi', 'CSS0044502' => 'camsi', 'CSS0044603' => 'camsi', 'CSS0044680' => 'camsi', 'CSS0044685' => 'camsi', 'CSS0044700' => 'camsi', 'CSS0044888' => 'camsi', 'CSS0044923' => 'camsi', 'CSS0044926' => 'camsi', 'CSS0044979' => 'camsi', 'CSS0045049' => 'camsi', 'CSS0045132' => 'camsi', 'CSS0045161' => 'camsi', 'CSS0045219' => 'camsi', 'CSS0045230' => 'camsi', 'CSS0045259' => 'camsi', 'CSS0045324' => 'camsi', 'CSS0045368' => 'camsi', 'CSS0045435' => 'camsi', 'CSS0045856' => 'camsi', 'CSS0045955' => 'camsi', 'CSS0046158' => 'camsi', 'CSS0046334' => 'camsi', 'CSS0046365' => 'camsi', 'CSS0046396' => 'camsi', 'CSS0046400' => 'camsi', 'CSS0046445' => 'camsi', 'CSS0046493' => 'camsi', 'CSS0046640' => 'camsi', 'CSS0046657' => 'camsi', 'CSS0046702' => 'camsi', 'CSS0047208' => 'camsi', 'CSS0047368' => 'camsi', 'CSS0047403' => 'camsi', 'CSS0047417' => 'camsi', 'CSS0047469' => 'camsi', 'CSS0047480' => 'camsi', 'CSS0047482' => 'camsi', 'CSS0047693' => 'camsi', 'CSS0047766' => 'camsi', 'CSS0047866' => 'camsi', 'CSS0047884' => 'camsi', 'CSS0048235' => 'camsi', 'CSS0048383' => 'camsi', 'CSS0048438' => 'camsi', 'CSS0048502' => 'camsi', 'CSS0048546' => 'camsi', 'CSS0048653' => 'camsi', 'CSS0048658' => 'camsi', 'CSS0048729' => 'camsi', 'CSS0048867' => 'camsi', 'CSS0048988' => 'camsi', 'CSS0049053' => 'camsi', 'CSS0049099' => 'camsi', 'CSS0049166' => 'camsi', 'CSS0049174' => 'camsi', 'CSS0049212' => 'camsi', 'CSS0049280' => 'camsi', 'CSS0049391' => 'camsi', 'CSS0049546' => 'camsi', 'CSS0049634' => 'camsi', 'CSS0049655' => 'camsi', 'CSS0049813' => 'camsi', 'CSS0049949' => 'camsi', 'CSS0050009' => 'camsi', 'CSS0050118' => 'camsi', 'CSS0050205' => 'camsi', 'CSS0050275' => 'camsi', 'CSS0050480' => 'camsi', 'CSS0050488' => 'camsi', 'CSS0050497' => 'camsi', 'Dinv03126' => 'din', 'Dinv13140' => 'din', 'Dinv13247' => 'din', 'Dinv14217' => 'din', 'EL10Ac9g22435' => 'bvu', 'FAN20G1200' => 'fan', 'PGR142G2516' => 'pgr', 'Prupe.3G160200' => 'ppe', 'Prupe.5G238200' => 'ppe', 'Prupe.7G047500' => 'ppe', 'QL03p045360' => 'qlo', 'QL05p034369' => 'qlo', 'QL05p034412' => 'qlo', 'QL08p017802' => 'qlo', 'QL08p024762' => 'qlo', 'QL10p026237' => 'qlo', 'QL10p032070' => 'qlo', 'QL11p003821' => 'qlo', 'Rhsim04G0057300' => 'rsi', 'Rhsim05G0049200' => 'rsi', 'Rhsim12G0010400' => 'rsi', 'Rhsim12G0012800' => 'rsi', 'TAR624G0483' => 'tar', 'TAR703G0001' => 'tar', 'vmacro05414' => 'vma', 'vmacro07091' => 'vma', 'vmacro07116' => 'vma', 'vmacro08423' => 'vma', 'vmacro09046' => 'vma', 'vmacro14269' => 'vma', 'vmacro16092' => 'vma', 'vmacro17280' => 'vma', 'vmacro19601' => 'vma' ) $gf_id = 'HOM05D001028' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001028' ) $data_identifier = 'HOM05D001028' $data_type = 'gf_id' $species_gene_counts = array( 'aox' => (int) 11, 'ccan' => (int) 6, 'camsi' => (int) 540, 'din' => (int) 4, 'bvu' => (int) 1, 'fan' => (int) 1, 'pgr' => (int) 1, 'ppe' => (int) 3, 'qlo' => (int) 8, 'rsi' => (int) 4, 'tar' => (int) 2, 'vma' => (int) 9 ) $gf_gene_species = 'vma' $gf_gene_id = 'vmacro19601' $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' => 'HOM05D001028', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '590', 'num_species' => '12' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'Aqoxy1G01649' => 'aox', 'Aqoxy1G02950' => 'aox', 'Aqoxy2G01005' => 'aox', 'Aqoxy2G01064' => 'aox', 'Aqoxy3G02267' => 'aox', 'Aqoxy3G02617' => 'aox', 'Aqoxy3G02693' => 'aox', 'Aqoxy5G03425' => 'aox', 'Aqoxy6G02164' => 'aox', 'Aqoxy6G02364' => 'aox', 'Aqoxy7G02284' => 'aox', 'Cc00_g09720' => 'ccan', 'Cc00_g21410' => 'ccan', 'Cc00_g31750' => 'ccan', 'Cc00_g34740' => 'ccan', 'Cc04_g16890' => 'ccan', 'Cc11_g03120' => 'ccan', 'CSS0000222' => 'camsi', 'CSS0000265' => 'camsi', 'CSS0000306' => 'camsi', 'CSS0000326' => 'camsi', 'CSS0000530' => 'camsi', 'CSS0000563' => 'camsi', 'CSS0000584' => 'camsi', 'CSS0000684' => 'camsi', 'CSS0001100' => 'camsi', 'CSS0001311' => 'camsi', 'CSS0001343' => 'camsi', 'CSS0001399' => 'camsi', 'CSS0001475' => 'camsi', 'CSS0001506' => 'camsi', 'CSS0001602' => 'camsi', 'CSS0001681' => 'camsi', 'CSS0001874' => 'camsi', 'CSS0001948' => 'camsi', 'CSS0002022' => 'camsi', 'CSS0002230' => 'camsi', 'CSS0002265' => 'camsi', 'CSS0002277' => 'camsi', 'CSS0002462' => 'camsi', 'CSS0002823' => 'camsi', 'CSS0003091' => 'camsi', 'CSS0003162' => 'camsi', 'CSS0003264' => 'camsi', 'CSS0003355' => 'camsi', 'CSS0003378' => 'camsi', 'CSS0003472' => 'camsi', 'CSS0003500' => 'camsi', 'CSS0003640' => 'camsi', 'CSS0003767' => 'camsi', 'CSS0003894' => 'camsi', 'CSS0003952' => 'camsi', 'CSS0003977' => 'camsi', 'CSS0004028' => 'camsi', 'CSS0004117' => 'camsi', 'CSS0004137' => 'camsi', 'CSS0004176' => 'camsi', 'CSS0004265' => 'camsi', 'CSS0004450' => 'camsi', 'CSS0004468' => 'camsi', 'CSS0004488' => 'camsi', 'CSS0004490' => 'camsi', 'CSS0004632' => 'camsi', 'CSS0004790' => 'camsi', 'CSS0004877' => 'camsi', 'CSS0004920' => 'camsi', 'CSS0004969' => 'camsi', 'CSS0005084' => 'camsi', 'CSS0005101' => 'camsi', 'CSS0005271' => 'camsi', 'CSS0005313' => 'camsi', 'CSS0005331' => 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'camsi', 'CSS0008050' => 'camsi', 'CSS0008206' => 'camsi', 'CSS0008251' => 'camsi', 'CSS0008252' => 'camsi', 'CSS0008279' => 'camsi', 'CSS0008482' => 'camsi', 'CSS0008583' => 'camsi', 'CSS0008699' => 'camsi', 'CSS0008798' => 'camsi', 'CSS0008971' => 'camsi', 'CSS0009019' => 'camsi', 'CSS0009191' => 'camsi', 'CSS0009241' => 'camsi', 'CSS0009246' => 'camsi', 'CSS0009399' => 'camsi', 'CSS0009654' => 'camsi', 'CSS0009722' => 'camsi', 'CSS0009920' => 'camsi', 'CSS0009986' => 'camsi', 'CSS0010182' => 'camsi', 'CSS0010202' => 'camsi', 'CSS0010330' => 'camsi', 'CSS0010362' => 'camsi', 'CSS0010456' => 'camsi', 'CSS0010472' => 'camsi', 'CSS0010507' => 'camsi', 'CSS0010512' => 'camsi', 'CSS0010520' => 'camsi', 'CSS0010617' => 'camsi', 'CSS0010706' => 'camsi', 'CSS0010747' => 'camsi', 'CSS0010816' => 'camsi', 'CSS0011020' => 'camsi', 'CSS0011115' => 'camsi', 'CSS0011383' => 'camsi', 'CSS0011491' => 'camsi', 'CSS0011602' => 'camsi', 'CSS0011605' => 'camsi', 'CSS0011625' => 'camsi', 'CSS0011654' => 'camsi', 'CSS0011781' => 'camsi', 'CSS0011853' => 'camsi', 'CSS0011898' => 'camsi', 'CSS0011933' => 'camsi', 'CSS0011996' => 'camsi', 'CSS0012066' => 'camsi', 'CSS0012097' => 'camsi', 'CSS0012108' => 'camsi', 'CSS0012226' => 'camsi', 'CSS0012248' => 'camsi', 'CSS0012331' => 'camsi', 'CSS0012797' => 'camsi', 'CSS0012818' => 'camsi', 'CSS0012904' => 'camsi', 'CSS0013001' => 'camsi', 'CSS0013022' => 'camsi', 'CSS0013172' => 'camsi', 'CSS0013244' => 'camsi', 'CSS0013267' => 'camsi', 'CSS0013275' => 'camsi', 'CSS0013324' => 'camsi', 'CSS0013334' => 'camsi', 'CSS0013394' => 'camsi', 'CSS0013549' => 'camsi', 'CSS0013689' => 'camsi', 'CSS0014026' => 'camsi', 'CSS0014049' => 'camsi', 'CSS0014144' => 'camsi', 'CSS0014354' => 'camsi', 'CSS0014579' => 'camsi', 'CSS0014648' => 'camsi', 'CSS0014902' => 'camsi', 'CSS0014979' => 'camsi', 'CSS0015278' => 'camsi', 'CSS0015310' => 'camsi', 'CSS0015364' => 'camsi', 'CSS0015455' => 'camsi', 'CSS0015693' => 'camsi', 'CSS0015774' => 'camsi', 'CSS0015795' => 'camsi', 'CSS0015952' => 'camsi', 'CSS0016104' => 'camsi', 'CSS0016241' => 'camsi', 'CSS0016303' => 'camsi', 'CSS0016490' => 'camsi', 'CSS0016832' => 'camsi', 'CSS0016845' => 'camsi', 'CSS0016914' => 'camsi', 'CSS0016946' => 'camsi', 'CSS0017102' => 'camsi', 'CSS0017193' => 'camsi', 'CSS0017528' => 'camsi', 'CSS0017619' => 'camsi', 'CSS0017679' => 'camsi', 'CSS0017816' => 'camsi', 'CSS0017880' => 'camsi', 'CSS0018106' => 'camsi', 'CSS0018162' => 'camsi', 'CSS0018304' => 'camsi', 'CSS0018406' => 'camsi', 'CSS0018481' => 'camsi', 'CSS0018511' => 'camsi', 'CSS0018596' => 'camsi', 'CSS0018727' => 'camsi', 'CSS0018751' => 'camsi', 'CSS0018777' => 'camsi', 'CSS0018798' => 'camsi', 'CSS0019137' => 'camsi', 'CSS0019177' => 'camsi', 'CSS0019217' => 'camsi', 'CSS0019361' => 'camsi', 'CSS0019516' => 'camsi', 'CSS0019538' => 'camsi', 'CSS0019560' => 'camsi', 'CSS0019819' => 'camsi', 'CSS0019837' => 'camsi', 'CSS0019915' => 'camsi', 'CSS0019925' => 'camsi', 'CSS0020112' => 'camsi', 'CSS0020160' => 'camsi', 'CSS0020378' => 'camsi', 'CSS0020388' => 'camsi', 'CSS0020452' => 'camsi', 'CSS0020588' => 'camsi', 'CSS0020661' => 'camsi', 'CSS0020886' => 'camsi', 'CSS0020973' => 'camsi', 'CSS0021035' => 'camsi', 'CSS0021111' => 'camsi', 'CSS0021131' => 'camsi', 'CSS0021151' => 'camsi', 'CSS0021228' => 'camsi', 'CSS0021397' => 'camsi', 'CSS0021420' => 'camsi', 'CSS0021464' => 'camsi', 'CSS0021547' => 'camsi', 'CSS0021608' => 'camsi', 'CSS0021740' => 'camsi', 'CSS0021826' => 'camsi', 'CSS0021904' => 'camsi', 'CSS0021941' => 'camsi', 'CSS0022189' => 'camsi', 'CSS0022199' => 'camsi', 'CSS0022502' => 'camsi', 'CSS0022531' => 'camsi', 'CSS0022581' => 'camsi', 'CSS0022612' => 'camsi', 'CSS0022621' => 'camsi', 'CSS0022815' => 'camsi', 'CSS0022936' => 'camsi', 'CSS0022964' => 'camsi', 'CSS0022985' => 'camsi', 'CSS0023002' => 'camsi', 'CSS0023006' => 'camsi', 'CSS0023024' => 'camsi', 'CSS0023489' => 'camsi', 'CSS0023593' => 'camsi', 'CSS0023621' => 'camsi', 'CSS0023743' => 'camsi', 'CSS0023804' => 'camsi', 'CSS0023805' => 'camsi', 'CSS0023908' => 'camsi', 'CSS0023938' => 'camsi', 'CSS0023981' => 'camsi', 'CSS0024027' => 'camsi', 'CSS0024169' => 'camsi', 'CSS0024193' => 'camsi', 'CSS0024269' => 'camsi', 'CSS0024336' => 'camsi', 'CSS0024337' => 'camsi', 'CSS0024548' => 'camsi', 'CSS0024564' => 'camsi', 'CSS0024585' => 'camsi', 'CSS0024738' => 'camsi', 'CSS0024833' => 'camsi', 'CSS0024846' => 'camsi', 'CSS0024957' => 'camsi', 'CSS0024974' => 'camsi', 'CSS0025005' => 'camsi', 'CSS0025235' => 'camsi', 'CSS0025465' => 'camsi', 'CSS0025633' => 'camsi', 'CSS0025688' => 'camsi', 'CSS0025759' => 'camsi', 'CSS0025774' => 'camsi', 'CSS0025801' => 'camsi', 'CSS0025942' => 'camsi', 'CSS0026083' => 'camsi', 'CSS0026194' => 'camsi', 'CSS0026230' => 'camsi', 'CSS0026398' => 'camsi', 'CSS0026419' => 'camsi', 'CSS0026679' => 'camsi', 'CSS0026719' => 'camsi', 'CSS0026795' => 'camsi', 'CSS0026835' => 'camsi', 'CSS0026930' => 'camsi', 'CSS0027053' => 'camsi', 'CSS0027130' => 'camsi', 'CSS0027192' => 'camsi', 'CSS0027454' => 'camsi', 'CSS0027467' => 'camsi', 'CSS0027521' => 'camsi', 'CSS0027662' => 'camsi', 'CSS0027795' => 'camsi', 'CSS0027835' => 'camsi', 'CSS0027966' => 'camsi', 'CSS0028090' => 'camsi', 'CSS0028134' => 'camsi', 'CSS0028205' => 'camsi', 'CSS0028263' => 'camsi', 'CSS0028363' => 'camsi', 'CSS0028598' => 'camsi', 'CSS0029175' => 'camsi', 'CSS0029191' => 'camsi', 'CSS0029424' => 'camsi', 'CSS0029479' => 'camsi', 'CSS0029496' => 'camsi', 'CSS0029633' => 'camsi', 'CSS0029837' => 'camsi', 'CSS0029844' => 'camsi', 'CSS0029863' => 'camsi', 'CSS0029874' => 'camsi', 'CSS0029959' => 'camsi', 'CSS0030001' => 'camsi', 'CSS0030093' => 'camsi', 'CSS0030199' => 'camsi', 'CSS0030200' => 'camsi', 'CSS0030427' => 'camsi', 'CSS0030476' => 'camsi', 'CSS0030636' => 'camsi', 'CSS0030673' => 'camsi', 'CSS0030766' => 'camsi', 'CSS0030775' => 'camsi', 'CSS0030858' => 'camsi', 'CSS0030873' => 'camsi', 'CSS0030929' => 'camsi', 'CSS0031028' => 'camsi', 'CSS0031129' => 'camsi', 'CSS0031164' => 'camsi', 'CSS0031340' => 'camsi', 'CSS0031368' => 'camsi', 'CSS0031395' => 'camsi', 'CSS0031596' => 'camsi', 'CSS0031727' => 'camsi', 'CSS0032011' => 'camsi', 'CSS0032160' => 'camsi', 'CSS0032538' => 'camsi', 'CSS0032576' => 'camsi', 'CSS0032603' => 'camsi', 'CSS0032640' => 'camsi', 'CSS0032704' => 'camsi', 'CSS0032851' => 'camsi', 'CSS0032973' => 'camsi', 'CSS0033048' => 'camsi', 'CSS0033082' => 'camsi', 'CSS0033157' => 'camsi', 'CSS0033253' => 'camsi', 'CSS0033347' => 'camsi', 'CSS0033601' => 'camsi', 'CSS0033820' => 'camsi', 'CSS0033881' => 'camsi', 'CSS0033934' => 'camsi', 'CSS0034143' => 'camsi', 'CSS0034176' => 'camsi', 'CSS0034201' => 'camsi', 'CSS0034269' => 'camsi', 'CSS0034303' => 'camsi', 'CSS0034463' => 'camsi', 'CSS0034470' => 'camsi', 'CSS0034514' => 'camsi', 'CSS0034525' => 'camsi', 'CSS0034726' => 'camsi', 'CSS0034727' => 'camsi', 'CSS0034737' => 'camsi', 'CSS0034768' => 'camsi', 'CSS0034890' => 'camsi', 'CSS0034943' => 'camsi', 'CSS0034957' => 'camsi', 'CSS0034973' => 'camsi', 'CSS0035178' => 'camsi', 'CSS0035260' => 'camsi', 'CSS0035316' => 'camsi', 'CSS0035347' => 'camsi', 'CSS0035360' => 'camsi', 'CSS0035380' => 'camsi', 'CSS0035429' => 'camsi', 'CSS0035446' => 'camsi', 'CSS0035737' => 'camsi', 'CSS0035852' => 'camsi', 'CSS0035967' => 'camsi', 'CSS0036001' => 'camsi', 'CSS0036044' => 'camsi', 'CSS0036221' => 'camsi', 'CSS0036333' => 'camsi', 'CSS0036435' => 'camsi', 'CSS0036843' => 'camsi', 'CSS0036846' => 'camsi', 'CSS0037097' => 'camsi', 'CSS0037263' => 'camsi', 'CSS0037370' => 'camsi', 'CSS0037410' => 'camsi', 'CSS0037449' => 'camsi', 'CSS0037603' => 'camsi', 'CSS0037851' => 'camsi', 'CSS0037891' => 'camsi', 'CSS0037996' => 'camsi', 'CSS0038222' => 'camsi', 'CSS0038433' => 'camsi', 'CSS0038441' => 'camsi', 'CSS0038718' => 'camsi', 'CSS0038890' => 'camsi', 'CSS0039049' => 'camsi', 'CSS0039145' => 'camsi', 'CSS0039243' => 'camsi', 'CSS0039294' => 'camsi', 'CSS0039324' => 'camsi', 'CSS0039376' => 'camsi', 'CSS0039475' => 'camsi', 'CSS0039539' => 'camsi', 'CSS0039546' => 'camsi', 'CSS0039567' => 'camsi', 'CSS0039599' => 'camsi', 'CSS0039763' => 'camsi', 'CSS0039863' => 'camsi', 'CSS0040107' => 'camsi', 'CSS0040124' => 'camsi', 'CSS0040151' => 'camsi', 'CSS0040165' => 'camsi', 'CSS0040309' => 'camsi', 'CSS0040318' => 'camsi', 'CSS0040347' => 'camsi', 'CSS0040371' => 'camsi', 'CSS0040456' => 'camsi', 'CSS0040551' => 'camsi', 'CSS0040975' => 'camsi', 'CSS0040981' => 'camsi', 'CSS0041299' => 'camsi', 'CSS0041493' => 'camsi', 'CSS0041658' => 'camsi', 'CSS0041899' => 'camsi', 'CSS0041927' => 'camsi', 'CSS0042016' => 'camsi', 'CSS0042034' => 'camsi', 'CSS0042103' => 'camsi', 'CSS0042172' => 'camsi', 'CSS0042198' => 'camsi', 'CSS0042201' => 'camsi', 'CSS0042308' => 'camsi', 'CSS0042329' => 'camsi', 'CSS0042348' => 'camsi', 'CSS0042349' => 'camsi', 'CSS0042489' => 'camsi', 'CSS0042575' => 'camsi', 'CSS0042624' => 'camsi', 'CSS0042660' => 'camsi', 'CSS0042694' => 'camsi', 'CSS0042995' => 'camsi', 'CSS0043079' => 'camsi', 'CSS0043165' => 'camsi', 'CSS0043171' => 'camsi', 'CSS0043314' => 'camsi', 'CSS0043361' => 'camsi', 'CSS0043375' => 'camsi', 'CSS0043518' => 'camsi', 'CSS0043536' => 'camsi', 'CSS0043678' => 'camsi', 'CSS0043765' => 'camsi', 'CSS0043897' => 'camsi', 'CSS0043944' => 'camsi', 'CSS0044126' => 'camsi', 'CSS0044136' => 'camsi', 'CSS0044179' => 'camsi', 'CSS0044290' => 'camsi', 'CSS0044437' => 'camsi', 'CSS0044502' => 'camsi', 'CSS0044603' => 'camsi', 'CSS0044680' => 'camsi', 'CSS0044685' => 'camsi', 'CSS0044700' => 'camsi', 'CSS0044888' => 'camsi', 'CSS0044923' => 'camsi', 'CSS0044926' => 'camsi', 'CSS0044979' => 'camsi', 'CSS0045049' => 'camsi', 'CSS0045132' => 'camsi', 'CSS0045161' => 'camsi', 'CSS0045219' => 'camsi', 'CSS0045230' => 'camsi', 'CSS0045259' => 'camsi', 'CSS0045324' => 'camsi', 'CSS0045368' => 'camsi', 'CSS0045435' => 'camsi', 'CSS0045856' => 'camsi', 'CSS0045955' => 'camsi', 'CSS0046158' => 'camsi', 'CSS0046334' => 'camsi', 'CSS0046365' => 'camsi', 'CSS0046396' => 'camsi', 'CSS0046400' => 'camsi', 'CSS0046445' => 'camsi', 'CSS0046493' => 'camsi', 'CSS0046640' => 'camsi', 'CSS0046657' => 'camsi', 'CSS0046702' => 'camsi', 'CSS0047208' => 'camsi', 'CSS0047368' => 'camsi', 'CSS0047403' => 'camsi', 'CSS0047417' => 'camsi', 'CSS0047469' => 'camsi', 'CSS0047480' => 'camsi', 'CSS0047482' => 'camsi', 'CSS0047693' => 'camsi', 'CSS0047766' => 'camsi', 'CSS0047866' => 'camsi', 'CSS0047884' => 'camsi', 'CSS0048235' => 'camsi', 'CSS0048383' => 'camsi', 'CSS0048438' => 'camsi', 'CSS0048502' => 'camsi', 'CSS0048546' => 'camsi', 'CSS0048653' => 'camsi', 'CSS0048658' => 'camsi', 'CSS0048729' => 'camsi', 'CSS0048867' => 'camsi', 'CSS0048988' => 'camsi', 'CSS0049053' => 'camsi', 'CSS0049099' => 'camsi', 'CSS0049166' => 'camsi', 'CSS0049174' => 'camsi', 'CSS0049212' => 'camsi', 'CSS0049280' => 'camsi', 'CSS0049391' => 'camsi', 'CSS0049546' => 'camsi', 'CSS0049634' => 'camsi', 'CSS0049655' => 'camsi', 'CSS0049813' => 'camsi', 'CSS0049949' => 'camsi', 'CSS0050009' => 'camsi', 'CSS0050118' => 'camsi', 'CSS0050205' => 'camsi', 'CSS0050275' => 'camsi', 'CSS0050480' => 'camsi', 'CSS0050488' => 'camsi', 'CSS0050497' => 'camsi', 'Dinv03126' => 'din', 'Dinv13140' => 'din', 'Dinv13247' => 'din', 'Dinv14217' => 'din', 'EL10Ac9g22435' => 'bvu', 'FAN20G1200' => 'fan', 'PGR142G2516' => 'pgr', 'Prupe.3G160200' => 'ppe', 'Prupe.5G238200' => 'ppe', 'Prupe.7G047500' => 'ppe', 'QL03p045360' => 'qlo', 'QL05p034369' => 'qlo', 'QL05p034412' => 'qlo', 'QL08p017802' => 'qlo', 'QL08p024762' => 'qlo', 'QL10p026237' => 'qlo', 'QL10p032070' => 'qlo', 'QL11p003821' => 'qlo', 'Rhsim04G0057300' => 'rsi', 'Rhsim05G0049200' => 'rsi', 'Rhsim12G0010400' => 'rsi', 'Rhsim12G0012800' => 'rsi', 'TAR624G0483' => 'tar', 'TAR703G0001' => 'tar', 'vmacro05414' => 'vma', 'vmacro07091' => 'vma', 'vmacro07116' => 'vma', 'vmacro08423' => 'vma', 'vmacro09046' => 'vma', 'vmacro14269' => 'vma', 'vmacro16092' => 'vma', 'vmacro17280' => 'vma', 'vmacro19601' => 'vma' ), 'gf_id' => 'HOM05D001028', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001028' ), 'data_identifier' => 'HOM05D001028', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001028', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '590', 'num_species' => '12' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'Aqoxy1G01649' => 'aox', 'Aqoxy1G02950' => 'aox', 'Aqoxy2G01005' => 'aox', 'Aqoxy2G01064' => 'aox', 'Aqoxy3G02267' => 'aox', 'Aqoxy3G02617' => 'aox', 'Aqoxy3G02693' => 'aox', 'Aqoxy5G03425' => 'aox', 'Aqoxy6G02164' => 'aox', 'Aqoxy6G02364' => 'aox', 'Aqoxy7G02284' => 'aox', 'Cc00_g09720' => 'ccan', 'Cc00_g21410' => 'ccan', 'Cc00_g31750' => 'ccan', 'Cc00_g34740' => 'ccan', 'Cc04_g16890' => 'ccan', 'Cc11_g03120' => 'ccan', 'CSS0000222' => 'camsi', 'CSS0000265' => 'camsi', 'CSS0000306' => 'camsi', 'CSS0000326' => 'camsi', 'CSS0000530' => 'camsi', 'CSS0000563' => 'camsi', 'CSS0000584' => 'camsi', 'CSS0000684' => 'camsi', 'CSS0001100' => 'camsi', 'CSS0001311' => 'camsi', 'CSS0001343' => 'camsi', 'CSS0001399' => 'camsi', 'CSS0001475' => 'camsi', 'CSS0001506' => 'camsi', 'CSS0001602' => 'camsi', 'CSS0001681' => 'camsi', 'CSS0001874' => 'camsi', 'CSS0001948' => 'camsi', 'CSS0002022' => 'camsi', 'CSS0002230' => 'camsi', 'CSS0002265' => 'camsi', 'CSS0002277' => 'camsi', 'CSS0002462' => 'camsi', 'CSS0002823' => 'camsi', 'CSS0003091' => 'camsi', 'CSS0003162' => 'camsi', 'CSS0003264' => 'camsi', 'CSS0003355' => 'camsi', 'CSS0003378' => 'camsi', 'CSS0003472' => 'camsi', 'CSS0003500' => 'camsi', 'CSS0003640' => 'camsi', 'CSS0003767' => 'camsi', 'CSS0003894' => 'camsi', 'CSS0003952' => 'camsi', 'CSS0003977' => 'camsi', 'CSS0004028' => 'camsi', 'CSS0004117' => 'camsi', 'CSS0004137' => 'camsi', 'CSS0004176' => 'camsi', 'CSS0004265' => 'camsi', 'CSS0004450' => 'camsi', 'CSS0004468' => 'camsi', 'CSS0004488' => 'camsi', 'CSS0004490' => 'camsi', 'CSS0004632' => 'camsi', 'CSS0004790' => 'camsi', 'CSS0004877' => 'camsi', 'CSS0004920' => 'camsi', 'CSS0004969' => 'camsi', 'CSS0005084' => 'camsi', 'CSS0005101' => 'camsi', 'CSS0005271' => 'camsi', 'CSS0005313' => 'camsi', 'CSS0005331' => 'camsi', 'CSS0005368' => 'camsi', 'CSS0005391' => 'camsi', 'CSS0005437' => 'camsi', 'CSS0005515' => 'camsi', 'CSS0005526' => 'camsi', 'CSS0005532' => 'camsi', 'CSS0005595' => 'camsi', 'CSS0005677' => 'camsi', 'CSS0005838' => 'camsi', 'CSS0005988' => 'camsi', 'CSS0006100' => 'camsi', 'CSS0006128' => 'camsi', 'CSS0006293' => 'camsi', 'CSS0006378' => 'camsi', 'CSS0006400' => 'camsi', 'CSS0006441' => 'camsi', 'CSS0006455' => 'camsi', 'CSS0006480' => 'camsi', 'CSS0006483' => 'camsi', 'CSS0006538' => 'camsi', 'CSS0006582' => 'camsi', 'CSS0006632' => 'camsi', 'CSS0006771' => 'camsi', 'CSS0006803' => 'camsi', 'CSS0006852' => 'camsi', 'CSS0006861' => 'camsi', 'CSS0006910' => 'camsi', 'CSS0007037' => 'camsi', 'CSS0007066' => 'camsi', 'CSS0007072' => 'camsi', 'CSS0007109' => 'camsi', 'CSS0007193' => 'camsi', 'CSS0007319' => 'camsi', 'CSS0007336' => 'camsi', 'CSS0007377' => 'camsi', 'CSS0007659' => 'camsi', 'CSS0007701' => 'camsi', 'CSS0007711' => 'camsi', 'CSS0007809' => 'camsi', 'CSS0008045' => 'camsi', 'CSS0008050' => 'camsi', 'CSS0008206' => 'camsi', 'CSS0008251' => 'camsi', 'CSS0008252' => 'camsi', 'CSS0008279' => 'camsi', 'CSS0008482' => 'camsi', 'CSS0008583' => 'camsi', 'CSS0008699' => 'camsi', 'CSS0008798' => 'camsi', 'CSS0008971' => 'camsi', 'CSS0009019' => 'camsi', 'CSS0009191' => 'camsi', 'CSS0009241' => 'camsi', 'CSS0009246' => 'camsi', 'CSS0009399' => 'camsi', 'CSS0009654' => 'camsi', 'CSS0009722' => 'camsi', 'CSS0009920' => 'camsi', 'CSS0009986' => 'camsi', 'CSS0010182' => 'camsi', 'CSS0010202' => 'camsi', 'CSS0010330' => 'camsi', 'CSS0010362' => 'camsi', 'CSS0010456' => 'camsi', 'CSS0010472' => 'camsi', 'CSS0010507' => 'camsi', 'CSS0010512' => 'camsi', 'CSS0010520' => 'camsi', 'CSS0010617' => 'camsi', 'CSS0010706' => 'camsi', 'CSS0010747' => 'camsi', 'CSS0010816' => 'camsi', 'CSS0011020' => 'camsi', 'CSS0011115' => 'camsi', 'CSS0011383' => 'camsi', 'CSS0011491' => 'camsi', 'CSS0011602' => 'camsi', 'CSS0011605' => 'camsi', 'CSS0011625' => 'camsi', 'CSS0011654' => 'camsi', 'CSS0011781' => 'camsi', 'CSS0011853' => 'camsi', 'CSS0011898' => 'camsi', 'CSS0011933' => 'camsi', 'CSS0011996' => 'camsi', 'CSS0012066' => 'camsi', 'CSS0012097' => 'camsi', 'CSS0012108' => 'camsi', 'CSS0012226' => 'camsi', 'CSS0012248' => 'camsi', 'CSS0012331' => 'camsi', 'CSS0012797' => 'camsi', 'CSS0012818' => 'camsi', 'CSS0012904' => 'camsi', 'CSS0013001' => 'camsi', 'CSS0013022' => 'camsi', 'CSS0013172' => 'camsi', 'CSS0013244' => 'camsi', 'CSS0013267' => 'camsi', 'CSS0013275' => 'camsi', 'CSS0013324' => 'camsi', 'CSS0013334' => 'camsi', 'CSS0013394' => 'camsi', 'CSS0013549' => 'camsi', 'CSS0013689' => 'camsi', 'CSS0014026' => 'camsi', 'CSS0014049' => 'camsi', 'CSS0014144' => 'camsi', 'CSS0014354' => 'camsi', 'CSS0014579' => 'camsi', 'CSS0014648' => 'camsi', 'CSS0014902' => 'camsi', 'CSS0014979' => 'camsi', 'CSS0015278' => 'camsi', 'CSS0015310' => 'camsi', 'CSS0015364' => 'camsi', 'CSS0015455' => 'camsi', 'CSS0015693' => 'camsi', 'CSS0015774' => 'camsi', 'CSS0015795' => 'camsi', 'CSS0015952' => 'camsi', 'CSS0016104' => 'camsi', 'CSS0016241' => 'camsi', 'CSS0016303' => 'camsi', 'CSS0016490' => 'camsi', 'CSS0016832' => 'camsi', 'CSS0016845' => 'camsi', 'CSS0016914' => 'camsi', 'CSS0016946' => 'camsi', 'CSS0017102' => 'camsi', 'CSS0017193' => 'camsi', 'CSS0017528' => 'camsi', 'CSS0017619' => 'camsi', 'CSS0017679' => 'camsi', 'CSS0017816' => 'camsi', 'CSS0017880' => 'camsi', 'CSS0018106' => 'camsi', 'CSS0018162' => 'camsi', 'CSS0018304' => 'camsi', 'CSS0018406' => 'camsi', 'CSS0018481' => 'camsi', 'CSS0018511' => 'camsi', 'CSS0018596' => 'camsi', 'CSS0018727' => 'camsi', 'CSS0018751' => 'camsi', 'CSS0018777' => 'camsi', 'CSS0018798' => 'camsi', 'CSS0019137' => 'camsi', 'CSS0019177' => 'camsi', 'CSS0019217' => 'camsi', 'CSS0019361' => 'camsi', 'CSS0019516' => 'camsi', 'CSS0019538' => 'camsi', 'CSS0019560' => 'camsi', 'CSS0019819' => 'camsi', 'CSS0019837' => 'camsi', 'CSS0019915' => 'camsi', 'CSS0019925' => 'camsi', 'CSS0020112' => 'camsi', 'CSS0020160' => 'camsi', 'CSS0020378' => 'camsi', 'CSS0020388' => 'camsi', 'CSS0020452' => 'camsi', 'CSS0020588' => 'camsi', 'CSS0020661' => 'camsi', 'CSS0020886' => 'camsi', 'CSS0020973' => 'camsi', 'CSS0021035' => 'camsi', 'CSS0021111' => 'camsi', 'CSS0021131' => 'camsi', 'CSS0021151' => 'camsi', 'CSS0021228' => 'camsi', 'CSS0021397' => 'camsi', 'CSS0021420' => 'camsi', 'CSS0021464' => 'camsi', 'CSS0021547' => 'camsi', 'CSS0021608' => 'camsi', 'CSS0021740' => 'camsi', 'CSS0021826' => 'camsi', 'CSS0021904' => 'camsi', 'CSS0021941' => 'camsi', 'CSS0022189' => 'camsi', 'CSS0022199' => 'camsi', 'CSS0022502' => 'camsi', 'CSS0022531' => 'camsi', 'CSS0022581' => 'camsi', 'CSS0022612' => 'camsi', 'CSS0022621' => 'camsi', 'CSS0022815' => 'camsi', 'CSS0022936' => 'camsi', 'CSS0022964' => 'camsi', 'CSS0022985' => 'camsi', 'CSS0023002' => 'camsi', 'CSS0023006' => 'camsi', 'CSS0023024' => 'camsi', 'CSS0023489' => 'camsi', 'CSS0023593' => 'camsi', 'CSS0023621' => 'camsi', 'CSS0023743' => 'camsi', 'CSS0023804' => 'camsi', 'CSS0023805' => 'camsi', 'CSS0023908' => 'camsi', 'CSS0023938' => 'camsi', 'CSS0023981' => 'camsi', 'CSS0024027' => 'camsi', 'CSS0024169' => 'camsi', 'CSS0024193' => 'camsi', 'CSS0024269' => 'camsi', 'CSS0024336' => 'camsi', 'CSS0024337' => 'camsi', 'CSS0024548' => 'camsi', 'CSS0024564' => 'camsi', 'CSS0024585' => 'camsi', 'CSS0024738' => 'camsi', 'CSS0024833' => 'camsi', 'CSS0024846' => 'camsi', 'CSS0024957' => 'camsi', 'CSS0024974' => 'camsi', 'CSS0025005' => 'camsi', 'CSS0025235' => 'camsi', 'CSS0025465' => 'camsi', 'CSS0025633' => 'camsi', 'CSS0025688' => 'camsi', 'CSS0025759' => 'camsi', 'CSS0025774' => 'camsi', 'CSS0025801' => 'camsi', 'CSS0025942' => 'camsi', 'CSS0026083' => 'camsi', 'CSS0026194' => 'camsi', 'CSS0026230' => 'camsi', 'CSS0026398' => 'camsi', 'CSS0026419' => 'camsi', 'CSS0026679' => 'camsi', 'CSS0026719' => 'camsi', 'CSS0026795' => 'camsi', 'CSS0026835' => 'camsi', 'CSS0026930' => 'camsi', 'CSS0027053' => 'camsi', 'CSS0027130' => 'camsi', 'CSS0027192' => 'camsi', 'CSS0027454' => 'camsi', 'CSS0027467' => 'camsi', 'CSS0027521' => 'camsi', 'CSS0027662' => 'camsi', 'CSS0027795' => 'camsi', 'CSS0027835' => 'camsi', 'CSS0027966' => 'camsi', 'CSS0028090' => 'camsi', 'CSS0028134' => 'camsi', 'CSS0028205' => 'camsi', 'CSS0028263' => 'camsi', 'CSS0028363' => 'camsi', 'CSS0028598' => 'camsi', 'CSS0029175' => 'camsi', 'CSS0029191' => 'camsi', 'CSS0029424' => 'camsi', 'CSS0029479' => 'camsi', 'CSS0029496' => 'camsi', 'CSS0029633' => 'camsi', 'CSS0029837' => 'camsi', 'CSS0029844' => 'camsi', 'CSS0029863' => 'camsi', 'CSS0029874' => 'camsi', 'CSS0029959' => 'camsi', 'CSS0030001' => 'camsi', 'CSS0030093' => 'camsi', 'CSS0030199' => 'camsi', 'CSS0030200' => 'camsi', 'CSS0030427' => 'camsi', 'CSS0030476' => 'camsi', 'CSS0030636' => 'camsi', 'CSS0030673' => 'camsi', 'CSS0030766' => 'camsi', 'CSS0030775' => 'camsi', 'CSS0030858' => 'camsi', 'CSS0030873' => 'camsi', 'CSS0030929' => 'camsi', 'CSS0031028' => 'camsi', 'CSS0031129' => 'camsi', 'CSS0031164' => 'camsi', 'CSS0031340' => 'camsi', 'CSS0031368' => 'camsi', 'CSS0031395' => 'camsi', 'CSS0031596' => 'camsi', 'CSS0031727' => 'camsi', 'CSS0032011' => 'camsi', 'CSS0032160' => 'camsi', 'CSS0032538' => 'camsi', 'CSS0032576' => 'camsi', 'CSS0032603' => 'camsi', 'CSS0032640' => 'camsi', 'CSS0032704' => 'camsi', 'CSS0032851' => 'camsi', 'CSS0032973' => 'camsi', 'CSS0033048' => 'camsi', 'CSS0033082' => 'camsi', 'CSS0033157' => 'camsi', 'CSS0033253' => 'camsi', 'CSS0033347' => 'camsi', 'CSS0033601' => 'camsi', 'CSS0033820' => 'camsi', 'CSS0033881' => 'camsi', 'CSS0033934' => 'camsi', 'CSS0034143' => 'camsi', 'CSS0034176' => 'camsi', 'CSS0034201' => 'camsi', 'CSS0034269' => 'camsi', 'CSS0034303' => 'camsi', 'CSS0034463' => 'camsi', 'CSS0034470' => 'camsi', 'CSS0034514' => 'camsi', 'CSS0034525' => 'camsi', 'CSS0034726' => 'camsi', 'CSS0034727' => 'camsi', 'CSS0034737' => 'camsi', 'CSS0034768' => 'camsi', 'CSS0034890' => 'camsi', 'CSS0034943' => 'camsi', 'CSS0034957' => 'camsi', 'CSS0034973' => 'camsi', 'CSS0035178' => 'camsi', 'CSS0035260' => 'camsi', 'CSS0035316' => 'camsi', 'CSS0035347' => 'camsi', 'CSS0035360' => 'camsi', 'CSS0035380' => 'camsi', 'CSS0035429' => 'camsi', 'CSS0035446' => 'camsi', 'CSS0035737' => 'camsi', 'CSS0035852' => 'camsi', 'CSS0035967' => 'camsi', 'CSS0036001' => 'camsi', 'CSS0036044' => 'camsi', 'CSS0036221' => 'camsi', 'CSS0036333' => 'camsi', 'CSS0036435' => 'camsi', 'CSS0036843' => 'camsi', 'CSS0036846' => 'camsi', 'CSS0037097' => 'camsi', 'CSS0037263' => 'camsi', 'CSS0037370' => 'camsi', 'CSS0037410' => 'camsi', 'CSS0037449' => 'camsi', 'CSS0037603' => 'camsi', 'CSS0037851' => 'camsi', 'CSS0037891' => 'camsi', 'CSS0037996' => 'camsi', 'CSS0038222' => 'camsi', 'CSS0038433' => 'camsi', 'CSS0038441' => 'camsi', 'CSS0038718' => 'camsi', 'CSS0038890' => 'camsi', 'CSS0039049' => 'camsi', 'CSS0039145' => 'camsi', 'CSS0039243' => 'camsi', 'CSS0039294' => 'camsi', 'CSS0039324' => 'camsi', 'CSS0039376' => 'camsi', 'CSS0039475' => 'camsi', 'CSS0039539' => 'camsi', 'CSS0039546' => 'camsi', 'CSS0039567' => 'camsi', 'CSS0039599' => 'camsi', 'CSS0039763' => 'camsi', 'CSS0039863' => 'camsi', 'CSS0040107' => 'camsi', 'CSS0040124' => 'camsi', 'CSS0040151' => 'camsi', 'CSS0040165' => 'camsi', 'CSS0040309' => 'camsi', 'CSS0040318' => 'camsi', 'CSS0040347' => 'camsi', 'CSS0040371' => 'camsi', 'CSS0040456' => 'camsi', 'CSS0040551' => 'camsi', 'CSS0040975' => 'camsi', 'CSS0040981' => 'camsi', 'CSS0041299' => 'camsi', 'CSS0041493' => 'camsi', 'CSS0041658' => 'camsi', 'CSS0041899' => 'camsi', 'CSS0041927' => 'camsi', 'CSS0042016' => 'camsi', 'CSS0042034' => 'camsi', 'CSS0042103' => 'camsi', 'CSS0042172' => 'camsi', 'CSS0042198' => 'camsi', 'CSS0042201' => 'camsi', 'CSS0042308' => 'camsi', 'CSS0042329' => 'camsi', 'CSS0042348' => 'camsi', 'CSS0042349' => 'camsi', 'CSS0042489' => 'camsi', 'CSS0042575' => 'camsi', 'CSS0042624' => 'camsi', 'CSS0042660' => 'camsi', 'CSS0042694' => 'camsi', 'CSS0042995' => 'camsi', 'CSS0043079' => 'camsi', 'CSS0043165' => 'camsi', 'CSS0043171' => 'camsi', 'CSS0043314' => 'camsi', 'CSS0043361' => 'camsi', 'CSS0043375' => 'camsi', 'CSS0043518' => 'camsi', 'CSS0043536' => 'camsi', 'CSS0043678' => 'camsi', 'CSS0043765' => 'camsi', 'CSS0043897' => 'camsi', 'CSS0043944' => 'camsi', 'CSS0044126' => 'camsi', 'CSS0044136' => 'camsi', 'CSS0044179' => 'camsi', 'CSS0044290' => 'camsi', 'CSS0044437' => 'camsi', 'CSS0044502' => 'camsi', 'CSS0044603' => 'camsi', 'CSS0044680' => 'camsi', 'CSS0044685' => 'camsi', 'CSS0044700' => 'camsi', 'CSS0044888' => 'camsi', 'CSS0044923' => 'camsi', 'CSS0044926' => 'camsi', 'CSS0044979' => 'camsi', 'CSS0045049' => 'camsi', 'CSS0045132' => 'camsi', 'CSS0045161' => 'camsi', 'CSS0045219' => 'camsi', 'CSS0045230' => 'camsi', 'CSS0045259' => 'camsi', 'CSS0045324' => 'camsi', 'CSS0045368' => 'camsi', 'CSS0045435' => 'camsi', 'CSS0045856' => 'camsi', 'CSS0045955' => 'camsi', 'CSS0046158' => 'camsi', 'CSS0046334' => 'camsi', 'CSS0046365' => 'camsi', 'CSS0046396' => 'camsi', 'CSS0046400' => 'camsi', 'CSS0046445' => 'camsi', 'CSS0046493' => 'camsi', 'CSS0046640' => 'camsi', 'CSS0046657' => 'camsi', 'CSS0046702' => 'camsi', 'CSS0047208' => 'camsi', 'CSS0047368' => 'camsi', 'CSS0047403' => 'camsi', 'CSS0047417' => 'camsi', 'CSS0047469' => 'camsi', 'CSS0047480' => 'camsi', 'CSS0047482' => 'camsi', 'CSS0047693' => 'camsi', 'CSS0047766' => 'camsi', 'CSS0047866' => 'camsi', 'CSS0047884' => 'camsi', 'CSS0048235' => 'camsi', 'CSS0048383' => 'camsi', 'CSS0048438' => 'camsi', 'CSS0048502' => 'camsi', 'CSS0048546' => 'camsi', 'CSS0048653' => 'camsi', 'CSS0048658' => 'camsi', 'CSS0048729' => 'camsi', 'CSS0048867' => 'camsi', 'CSS0048988' => 'camsi', 'CSS0049053' => 'camsi', 'CSS0049099' => 'camsi', 'CSS0049166' => 'camsi', 'CSS0049174' => 'camsi', 'CSS0049212' => 'camsi', 'CSS0049280' => 'camsi', 'CSS0049391' => 'camsi', 'CSS0049546' => 'camsi', 'CSS0049634' => 'camsi', 'CSS0049655' => 'camsi', 'CSS0049813' => 'camsi', 'CSS0049949' => 'camsi', 'CSS0050009' => 'camsi', 'CSS0050118' => 'camsi', 'CSS0050205' => 'camsi', 'CSS0050275' => 'camsi', 'CSS0050480' => 'camsi', 'CSS0050488' => 'camsi', 'CSS0050497' => 'camsi', 'Dinv03126' => 'din', 'Dinv13140' => 'din', 'Dinv13247' => 'din', 'Dinv14217' => 'din', 'EL10Ac9g22435' => 'bvu', 'FAN20G1200' => 'fan', 'PGR142G2516' => 'pgr', 'Prupe.3G160200' => 'ppe', 'Prupe.5G238200' => 'ppe', 'Prupe.7G047500' => 'ppe', 'QL03p045360' => 'qlo', 'QL05p034369' => 'qlo', 'QL05p034412' => 'qlo', 'QL08p017802' => 'qlo', 'QL08p024762' => 'qlo', 'QL10p026237' => 'qlo', 'QL10p032070' => 'qlo', 'QL11p003821' => 'qlo', 'Rhsim04G0057300' => 'rsi', 'Rhsim05G0049200' => 'rsi', 'Rhsim12G0010400' => 'rsi', 'Rhsim12G0012800' => 'rsi', 'TAR624G0483' => 'tar', 'TAR703G0001' => 'tar', 'vmacro05414' => 'vma', 'vmacro07091' => 'vma', 'vmacro07116' => 'vma', 'vmacro08423' => 'vma', 'vmacro09046' => 'vma', 'vmacro14269' => 'vma', 'vmacro16092' => 'vma', 'vmacro17280' => 'vma', 'vmacro19601' => 'vma' ) $gf_id = 'HOM05D001028' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001028' ) $data_identifier = 'HOM05D001028' $data_type = 'gf_id' $species_gene_counts = array( 'aox' => (int) 11, 'ccan' => (int) 6, 'camsi' => (int) 540, 'din' => (int) 4, 'bvu' => (int) 1, 'fan' => (int) 1, 'pgr' => (int) 1, 'ppe' => (int) 3, 'qlo' => (int) 8, 'rsi' => (int) 4, 'tar' => (int) 2, 'vma' => (int) 9 ) $gf_gene_species = 'vma' $gf_gene_id = 'vmacro19601' $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' => 'HOM05D001028', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '590', 'num_species' => '12' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'Aqoxy1G01649' => 'aox', 'Aqoxy1G02950' => 'aox', 'Aqoxy2G01005' => 'aox', 'Aqoxy2G01064' => 'aox', 'Aqoxy3G02267' => 'aox', 'Aqoxy3G02617' => 'aox', 'Aqoxy3G02693' => 'aox', 'Aqoxy5G03425' => 'aox', 'Aqoxy6G02164' => 'aox', 'Aqoxy6G02364' => 'aox', 'Aqoxy7G02284' => 'aox', 'Cc00_g09720' => 'ccan', 'Cc00_g21410' => 'ccan', 'Cc00_g31750' => 'ccan', 'Cc00_g34740' => 'ccan', 'Cc04_g16890' => 'ccan', 'Cc11_g03120' => 'ccan', 'CSS0000222' => 'camsi', 'CSS0000265' => 'camsi', 'CSS0000306' => 'camsi', 'CSS0000326' => 'camsi', 'CSS0000530' => 'camsi', 'CSS0000563' => 'camsi', 'CSS0000584' => 'camsi', 'CSS0000684' => 'camsi', 'CSS0001100' => 'camsi', 'CSS0001311' => 'camsi', 'CSS0001343' => 'camsi', 'CSS0001399' => 'camsi', 'CSS0001475' => 'camsi', 'CSS0001506' => 'camsi', 'CSS0001602' => 'camsi', 'CSS0001681' => 'camsi', 'CSS0001874' => 'camsi', 'CSS0001948' => 'camsi', 'CSS0002022' => 'camsi', 'CSS0002230' => 'camsi', 'CSS0002265' => 'camsi', 'CSS0002277' => 'camsi', 'CSS0002462' => 'camsi', 'CSS0002823' => 'camsi', 'CSS0003091' => 'camsi', 'CSS0003162' => 'camsi', 'CSS0003264' => 'camsi', 'CSS0003355' => 'camsi', 'CSS0003378' => 'camsi', 'CSS0003472' => 'camsi', 'CSS0003500' => 'camsi', 'CSS0003640' => 'camsi', 'CSS0003767' => 'camsi', 'CSS0003894' => 'camsi', 'CSS0003952' => 'camsi', 'CSS0003977' => 'camsi', 'CSS0004028' => 'camsi', 'CSS0004117' => 'camsi', 'CSS0004137' => 'camsi', 'CSS0004176' => 'camsi', 'CSS0004265' => 'camsi', 'CSS0004450' => 'camsi', 'CSS0004468' => 'camsi', 'CSS0004488' => 'camsi', 'CSS0004490' => 'camsi', 'CSS0004632' => 'camsi', 'CSS0004790' => 'camsi', 'CSS0004877' => 'camsi', 'CSS0004920' => 'camsi', 'CSS0004969' => 'camsi', 'CSS0005084' => 'camsi', 'CSS0005101' => 'camsi', 'CSS0005271' => 'camsi', 'CSS0005313' => 'camsi', 'CSS0005331' => 'camsi', 'CSS0005368' => 'camsi', 'CSS0005391' => 'camsi', 'CSS0005437' => 'camsi', 'CSS0005515' => 'camsi', 'CSS0005526' => 'camsi', 'CSS0005532' => 'camsi', 'CSS0005595' => 'camsi', 'CSS0005677' => 'camsi', 'CSS0005838' => 'camsi', 'CSS0005988' => 'camsi', 'CSS0006100' => 'camsi', 'CSS0006128' => 'camsi', 'CSS0006293' => 'camsi', 'CSS0006378' => 'camsi', 'CSS0006400' => 'camsi', 'CSS0006441' => 'camsi', 'CSS0006455' => 'camsi', 'CSS0006480' => 'camsi', 'CSS0006483' => 'camsi', 'CSS0006538' => 'camsi', 'CSS0006582' => 'camsi', 'CSS0006632' => 'camsi', 'CSS0006771' => 'camsi', 'CSS0006803' => 'camsi', 'CSS0006852' => 'camsi', 'CSS0006861' => 'camsi', 'CSS0006910' => 'camsi', 'CSS0007037' => 'camsi', 'CSS0007066' => 'camsi', 'CSS0007072' => 'camsi', 'CSS0007109' => 'camsi', 'CSS0007193' => 'camsi', 'CSS0007319' => 'camsi', 'CSS0007336' => 'camsi', 'CSS0007377' => 'camsi', 'CSS0007659' => 'camsi', 'CSS0007701' => 'camsi', 'CSS0007711' => 'camsi', 'CSS0007809' => 'camsi', 'CSS0008045' => 'camsi', 'CSS0008050' => 'camsi', 'CSS0008206' => 'camsi', 'CSS0008251' => 'camsi', 'CSS0008252' => 'camsi', 'CSS0008279' => 'camsi', 'CSS0008482' => 'camsi', 'CSS0008583' => 'camsi', 'CSS0008699' => 'camsi', 'CSS0008798' => 'camsi', 'CSS0008971' => 'camsi', 'CSS0009019' => 'camsi', 'CSS0009191' => 'camsi', 'CSS0009241' => 'camsi', 'CSS0009246' => 'camsi', 'CSS0009399' => 'camsi', 'CSS0009654' => 'camsi', 'CSS0009722' => 'camsi', 'CSS0009920' => 'camsi', 'CSS0009986' => 'camsi', 'CSS0010182' => 'camsi', 'CSS0010202' => 'camsi', 'CSS0010330' => 'camsi', 'CSS0010362' => 'camsi', 'CSS0010456' => 'camsi', 'CSS0010472' => 'camsi', 'CSS0010507' => 'camsi', 'CSS0010512' => 'camsi', 'CSS0010520' => 'camsi', 'CSS0010617' => 'camsi', 'CSS0010706' => 'camsi', 'CSS0010747' => 'camsi', 'CSS0010816' => 'camsi', 'CSS0011020' => 'camsi', 'CSS0011115' => 'camsi', 'CSS0011383' => 'camsi', 'CSS0011491' => 'camsi', 'CSS0011602' => 'camsi', 'CSS0011605' => 'camsi', 'CSS0011625' => 'camsi', 'CSS0011654' => 'camsi', 'CSS0011781' => 'camsi', 'CSS0011853' => 'camsi', 'CSS0011898' => 'camsi', 'CSS0011933' => 'camsi', 'CSS0011996' => 'camsi', 'CSS0012066' => 'camsi', 'CSS0012097' => 'camsi', 'CSS0012108' => 'camsi', 'CSS0012226' => 'camsi', 'CSS0012248' => 'camsi', 'CSS0012331' => 'camsi', 'CSS0012797' => 'camsi', 'CSS0012818' => 'camsi', 'CSS0012904' => 'camsi', 'CSS0013001' => 'camsi', 'CSS0013022' => 'camsi', 'CSS0013172' => 'camsi', 'CSS0013244' => 'camsi', 'CSS0013267' => 'camsi', 'CSS0013275' => 'camsi', 'CSS0013324' => 'camsi', 'CSS0013334' => 'camsi', 'CSS0013394' => 'camsi', 'CSS0013549' => 'camsi', 'CSS0013689' => 'camsi', 'CSS0014026' => 'camsi', 'CSS0014049' => 'camsi', 'CSS0014144' => 'camsi', 'CSS0014354' => 'camsi', 'CSS0014579' => 'camsi', 'CSS0014648' => 'camsi', 'CSS0014902' => 'camsi', 'CSS0014979' => 'camsi', 'CSS0015278' => 'camsi', 'CSS0015310' => 'camsi', 'CSS0015364' => 'camsi', 'CSS0015455' => 'camsi', 'CSS0015693' => 'camsi', 'CSS0015774' => 'camsi', 'CSS0015795' => 'camsi', 'CSS0015952' => 'camsi', 'CSS0016104' => 'camsi', 'CSS0016241' => 'camsi', 'CSS0016303' => 'camsi', 'CSS0016490' => 'camsi', 'CSS0016832' => 'camsi', 'CSS0016845' => 'camsi', 'CSS0016914' => 'camsi', 'CSS0016946' => 'camsi', 'CSS0017102' => 'camsi', 'CSS0017193' => 'camsi', 'CSS0017528' => 'camsi', 'CSS0017619' => 'camsi', 'CSS0017679' => 'camsi', 'CSS0017816' => 'camsi', 'CSS0017880' => 'camsi', 'CSS0018106' => 'camsi', 'CSS0018162' => 'camsi', 'CSS0018304' => 'camsi', 'CSS0018406' => 'camsi', 'CSS0018481' => 'camsi', 'CSS0018511' => 'camsi', 'CSS0018596' => 'camsi', 'CSS0018727' => 'camsi', 'CSS0018751' => 'camsi', 'CSS0018777' => 'camsi', 'CSS0018798' => 'camsi', 'CSS0019137' => 'camsi', 'CSS0019177' => 'camsi', 'CSS0019217' => 'camsi', 'CSS0019361' => 'camsi', 'CSS0019516' => 'camsi', 'CSS0019538' => 'camsi', 'CSS0019560' => 'camsi', 'CSS0019819' => 'camsi', 'CSS0019837' => 'camsi', 'CSS0019915' => 'camsi', 'CSS0019925' => 'camsi', 'CSS0020112' => 'camsi', 'CSS0020160' => 'camsi', 'CSS0020378' => 'camsi', 'CSS0020388' => 'camsi', 'CSS0020452' => 'camsi', 'CSS0020588' => 'camsi', 'CSS0020661' => 'camsi', 'CSS0020886' => 'camsi', 'CSS0020973' => 'camsi', 'CSS0021035' => 'camsi', 'CSS0021111' => 'camsi', 'CSS0021131' => 'camsi', 'CSS0021151' => 'camsi', 'CSS0021228' => 'camsi', 'CSS0021397' => 'camsi', 'CSS0021420' => 'camsi', 'CSS0021464' => 'camsi', 'CSS0021547' => 'camsi', 'CSS0021608' => 'camsi', 'CSS0021740' => 'camsi', 'CSS0021826' => 'camsi', 'CSS0021904' => 'camsi', 'CSS0021941' => 'camsi', 'CSS0022189' => 'camsi', 'CSS0022199' => 'camsi', 'CSS0022502' => 'camsi', 'CSS0022531' => 'camsi', 'CSS0022581' => 'camsi', 'CSS0022612' => 'camsi', 'CSS0022621' => 'camsi', 'CSS0022815' => 'camsi', 'CSS0022936' => 'camsi', 'CSS0022964' => 'camsi', 'CSS0022985' => 'camsi', 'CSS0023002' => 'camsi', 'CSS0023006' => 'camsi', 'CSS0023024' => 'camsi', 'CSS0023489' => 'camsi', 'CSS0023593' => 'camsi', 'CSS0023621' => 'camsi', 'CSS0023743' => 'camsi', 'CSS0023804' => 'camsi', 'CSS0023805' => 'camsi', 'CSS0023908' => 'camsi', 'CSS0023938' => 'camsi', 'CSS0023981' => 'camsi', 'CSS0024027' => 'camsi', 'CSS0024169' => 'camsi', 'CSS0024193' => 'camsi', 'CSS0024269' => 'camsi', 'CSS0024336' => 'camsi', 'CSS0024337' => 'camsi', 'CSS0024548' => 'camsi', 'CSS0024564' => 'camsi', 'CSS0024585' => 'camsi', 'CSS0024738' => 'camsi', 'CSS0024833' => 'camsi', 'CSS0024846' => 'camsi', 'CSS0024957' => 'camsi', 'CSS0024974' => 'camsi', 'CSS0025005' => 'camsi', 'CSS0025235' => 'camsi', 'CSS0025465' => 'camsi', 'CSS0025633' => 'camsi', 'CSS0025688' => 'camsi', 'CSS0025759' => 'camsi', 'CSS0025774' => 'camsi', 'CSS0025801' => 'camsi', 'CSS0025942' => 'camsi', 'CSS0026083' => 'camsi', 'CSS0026194' => 'camsi', 'CSS0026230' => 'camsi', 'CSS0026398' => 'camsi', 'CSS0026419' => 'camsi', 'CSS0026679' => 'camsi', 'CSS0026719' => 'camsi', 'CSS0026795' => 'camsi', 'CSS0026835' => 'camsi', 'CSS0026930' => 'camsi', 'CSS0027053' => 'camsi', 'CSS0027130' => 'camsi', 'CSS0027192' => 'camsi', 'CSS0027454' => 'camsi', 'CSS0027467' => 'camsi', 'CSS0027521' => 'camsi', 'CSS0027662' => 'camsi', 'CSS0027795' => 'camsi', 'CSS0027835' => 'camsi', 'CSS0027966' => 'camsi', 'CSS0028090' => 'camsi', 'CSS0028134' => 'camsi', 'CSS0028205' => 'camsi', 'CSS0028263' => 'camsi', 'CSS0028363' => 'camsi', 'CSS0028598' => 'camsi', 'CSS0029175' => 'camsi', 'CSS0029191' => 'camsi', 'CSS0029424' => 'camsi', 'CSS0029479' => 'camsi', 'CSS0029496' => 'camsi', 'CSS0029633' => 'camsi', 'CSS0029837' => 'camsi', 'CSS0029844' => 'camsi', 'CSS0029863' => 'camsi', 'CSS0029874' => 'camsi', 'CSS0029959' => 'camsi', 'CSS0030001' => 'camsi', 'CSS0030093' => 'camsi', 'CSS0030199' => 'camsi', 'CSS0030200' => 'camsi', 'CSS0030427' => 'camsi', 'CSS0030476' => 'camsi', 'CSS0030636' => 'camsi', 'CSS0030673' => 'camsi', 'CSS0030766' => 'camsi', 'CSS0030775' => 'camsi', 'CSS0030858' => 'camsi', 'CSS0030873' => 'camsi', 'CSS0030929' => 'camsi', 'CSS0031028' => 'camsi', 'CSS0031129' => 'camsi', 'CSS0031164' => 'camsi', 'CSS0031340' => 'camsi', 'CSS0031368' => 'camsi', 'CSS0031395' => 'camsi', 'CSS0031596' => 'camsi', 'CSS0031727' => 'camsi', 'CSS0032011' => 'camsi', 'CSS0032160' => 'camsi', 'CSS0032538' => 'camsi', 'CSS0032576' => 'camsi', 'CSS0032603' => 'camsi', 'CSS0032640' => 'camsi', 'CSS0032704' => 'camsi', 'CSS0032851' => 'camsi', 'CSS0032973' => 'camsi', 'CSS0033048' => 'camsi', 'CSS0033082' => 'camsi', 'CSS0033157' => 'camsi', 'CSS0033253' => 'camsi', 'CSS0033347' => 'camsi', 'CSS0033601' => 'camsi', 'CSS0033820' => 'camsi', 'CSS0033881' => 'camsi', 'CSS0033934' => 'camsi', 'CSS0034143' => 'camsi', 'CSS0034176' => 'camsi', 'CSS0034201' => 'camsi', 'CSS0034269' => 'camsi', 'CSS0034303' => 'camsi', 'CSS0034463' => 'camsi', 'CSS0034470' => 'camsi', 'CSS0034514' => 'camsi', 'CSS0034525' => 'camsi', 'CSS0034726' => 'camsi', 'CSS0034727' => 'camsi', 'CSS0034737' => 'camsi', 'CSS0034768' => 'camsi', 'CSS0034890' => 'camsi', 'CSS0034943' => 'camsi', 'CSS0034957' => 'camsi', 'CSS0034973' => 'camsi', 'CSS0035178' => 'camsi', 'CSS0035260' => 'camsi', 'CSS0035316' => 'camsi', 'CSS0035347' => 'camsi', 'CSS0035360' => 'camsi', 'CSS0035380' => 'camsi', 'CSS0035429' => 'camsi', 'CSS0035446' => 'camsi', 'CSS0035737' => 'camsi', 'CSS0035852' => 'camsi', 'CSS0035967' => 'camsi', 'CSS0036001' => 'camsi', 'CSS0036044' => 'camsi', 'CSS0036221' => 'camsi', 'CSS0036333' => 'camsi', 'CSS0036435' => 'camsi', 'CSS0036843' => 'camsi', 'CSS0036846' => 'camsi', 'CSS0037097' => 'camsi', 'CSS0037263' => 'camsi', 'CSS0037370' => 'camsi', 'CSS0037410' => 'camsi', 'CSS0037449' => 'camsi', 'CSS0037603' => 'camsi', 'CSS0037851' => 'camsi', 'CSS0037891' => 'camsi', 'CSS0037996' => 'camsi', 'CSS0038222' => 'camsi', 'CSS0038433' => 'camsi', 'CSS0038441' => 'camsi', 'CSS0038718' => 'camsi', 'CSS0038890' => 'camsi', 'CSS0039049' => 'camsi', 'CSS0039145' => 'camsi', 'CSS0039243' => 'camsi', 'CSS0039294' => 'camsi', 'CSS0039324' => 'camsi', 'CSS0039376' => 'camsi', 'CSS0039475' => 'camsi', 'CSS0039539' => 'camsi', 'CSS0039546' => 'camsi', 'CSS0039567' => 'camsi', 'CSS0039599' => 'camsi', 'CSS0039763' => 'camsi', 'CSS0039863' => 'camsi', 'CSS0040107' => 'camsi', 'CSS0040124' => 'camsi', 'CSS0040151' => 'camsi', 'CSS0040165' => 'camsi', 'CSS0040309' => 'camsi', 'CSS0040318' => 'camsi', 'CSS0040347' => 'camsi', 'CSS0040371' => 'camsi', 'CSS0040456' => 'camsi', 'CSS0040551' => 'camsi', 'CSS0040975' => 'camsi', 'CSS0040981' => 'camsi', 'CSS0041299' => 'camsi', 'CSS0041493' => 'camsi', 'CSS0041658' => 'camsi', 'CSS0041899' => 'camsi', 'CSS0041927' => 'camsi', 'CSS0042016' => 'camsi', 'CSS0042034' => 'camsi', 'CSS0042103' => 'camsi', 'CSS0042172' => 'camsi', 'CSS0042198' => 'camsi', 'CSS0042201' => 'camsi', 'CSS0042308' => 'camsi', 'CSS0042329' => 'camsi', 'CSS0042348' => 'camsi', 'CSS0042349' => 'camsi', 'CSS0042489' => 'camsi', 'CSS0042575' => 'camsi', 'CSS0042624' => 'camsi', 'CSS0042660' => 'camsi', 'CSS0042694' => 'camsi', 'CSS0042995' => 'camsi', 'CSS0043079' => 'camsi', 'CSS0043165' => 'camsi', 'CSS0043171' => 'camsi', 'CSS0043314' => 'camsi', 'CSS0043361' => 'camsi', 'CSS0043375' => 'camsi', 'CSS0043518' => 'camsi', 'CSS0043536' => 'camsi', 'CSS0043678' => 'camsi', 'CSS0043765' => 'camsi', 'CSS0043897' => 'camsi', 'CSS0043944' => 'camsi', 'CSS0044126' => 'camsi', 'CSS0044136' => 'camsi', 'CSS0044179' => 'camsi', 'CSS0044290' => 'camsi', 'CSS0044437' => 'camsi', 'CSS0044502' => 'camsi', 'CSS0044603' => 'camsi', 'CSS0044680' => 'camsi', 'CSS0044685' => 'camsi', 'CSS0044700' => 'camsi', 'CSS0044888' => 'camsi', 'CSS0044923' => 'camsi', 'CSS0044926' => 'camsi', 'CSS0044979' => 'camsi', 'CSS0045049' => 'camsi', 'CSS0045132' => 'camsi', 'CSS0045161' => 'camsi', 'CSS0045219' => 'camsi', 'CSS0045230' => 'camsi', 'CSS0045259' => 'camsi', 'CSS0045324' => 'camsi', 'CSS0045368' => 'camsi', 'CSS0045435' => 'camsi', 'CSS0045856' => 'camsi', 'CSS0045955' => 'camsi', 'CSS0046158' => 'camsi', 'CSS0046334' => 'camsi', 'CSS0046365' => 'camsi', 'CSS0046396' => 'camsi', 'CSS0046400' => 'camsi', 'CSS0046445' => 'camsi', 'CSS0046493' => 'camsi', 'CSS0046640' => 'camsi', 'CSS0046657' => 'camsi', 'CSS0046702' => 'camsi', 'CSS0047208' => 'camsi', 'CSS0047368' => 'camsi', 'CSS0047403' => 'camsi', 'CSS0047417' => 'camsi', 'CSS0047469' => 'camsi', 'CSS0047480' => 'camsi', 'CSS0047482' => 'camsi', 'CSS0047693' => 'camsi', 'CSS0047766' => 'camsi', 'CSS0047866' => 'camsi', 'CSS0047884' => 'camsi', 'CSS0048235' => 'camsi', 'CSS0048383' => 'camsi', 'CSS0048438' => 'camsi', 'CSS0048502' => 'camsi', 'CSS0048546' => 'camsi', 'CSS0048653' => 'camsi', 'CSS0048658' => 'camsi', 'CSS0048729' => 'camsi', 'CSS0048867' => 'camsi', 'CSS0048988' => 'camsi', 'CSS0049053' => 'camsi', 'CSS0049099' => 'camsi', 'CSS0049166' => 'camsi', 'CSS0049174' => 'camsi', 'CSS0049212' => 'camsi', 'CSS0049280' => 'camsi', 'CSS0049391' => 'camsi', 'CSS0049546' => 'camsi', 'CSS0049634' => 'camsi', 'CSS0049655' => 'camsi', 'CSS0049813' => 'camsi', 'CSS0049949' => 'camsi', 'CSS0050009' => 'camsi', 'CSS0050118' => 'camsi', 'CSS0050205' => 'camsi', 'CSS0050275' => 'camsi', 'CSS0050480' => 'camsi', 'CSS0050488' => 'camsi', 'CSS0050497' => 'camsi', 'Dinv03126' => 'din', 'Dinv13140' => 'din', 'Dinv13247' => 'din', 'Dinv14217' => 'din', 'EL10Ac9g22435' => 'bvu', 'FAN20G1200' => 'fan', 'PGR142G2516' => 'pgr', 'Prupe.3G160200' => 'ppe', 'Prupe.5G238200' => 'ppe', 'Prupe.7G047500' => 'ppe', 'QL03p045360' => 'qlo', 'QL05p034369' => 'qlo', 'QL05p034412' => 'qlo', 'QL08p017802' => 'qlo', 'QL08p024762' => 'qlo', 'QL10p026237' => 'qlo', 'QL10p032070' => 'qlo', 'QL11p003821' => 'qlo', 'Rhsim04G0057300' => 'rsi', 'Rhsim05G0049200' => 'rsi', 'Rhsim12G0010400' => 'rsi', 'Rhsim12G0012800' => 'rsi', 'TAR624G0483' => 'tar', 'TAR703G0001' => 'tar', 'vmacro05414' => 'vma', 'vmacro07091' => 'vma', 'vmacro07116' => 'vma', 'vmacro08423' => 'vma', 'vmacro09046' => 'vma', 'vmacro14269' => 'vma', 'vmacro16092' => 'vma', 'vmacro17280' => 'vma', 'vmacro19601' => 'vma' ), 'gf_id' => 'HOM05D001028', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001028' ), 'data_identifier' => 'HOM05D001028', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001028', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '590', 'num_species' => '12' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'Aqoxy1G01649' => 'aox', 'Aqoxy1G02950' => 'aox', 'Aqoxy2G01005' => 'aox', 'Aqoxy2G01064' => 'aox', 'Aqoxy3G02267' => 'aox', 'Aqoxy3G02617' => 'aox', 'Aqoxy3G02693' => 'aox', 'Aqoxy5G03425' => 'aox', 'Aqoxy6G02164' => 'aox', 'Aqoxy6G02364' => 'aox', 'Aqoxy7G02284' => 'aox', 'Cc00_g09720' => 'ccan', 'Cc00_g21410' => 'ccan', 'Cc00_g31750' => 'ccan', 'Cc00_g34740' => 'ccan', 'Cc04_g16890' => 'ccan', 'Cc11_g03120' => 'ccan', 'CSS0000222' => 'camsi', 'CSS0000265' => 'camsi', 'CSS0000306' => 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'camsi', 'CSS0030427' => 'camsi', 'CSS0030476' => 'camsi', 'CSS0030636' => 'camsi', 'CSS0030673' => 'camsi', 'CSS0030766' => 'camsi', 'CSS0030775' => 'camsi', 'CSS0030858' => 'camsi', 'CSS0030873' => 'camsi', 'CSS0030929' => 'camsi', 'CSS0031028' => 'camsi', 'CSS0031129' => 'camsi', 'CSS0031164' => 'camsi', 'CSS0031340' => 'camsi', 'CSS0031368' => 'camsi', 'CSS0031395' => 'camsi', 'CSS0031596' => 'camsi', 'CSS0031727' => 'camsi', 'CSS0032011' => 'camsi', 'CSS0032160' => 'camsi', 'CSS0032538' => 'camsi', 'CSS0032576' => 'camsi', 'CSS0032603' => 'camsi', 'CSS0032640' => 'camsi', 'CSS0032704' => 'camsi', 'CSS0032851' => 'camsi', 'CSS0032973' => 'camsi', 'CSS0033048' => 'camsi', 'CSS0033082' => 'camsi', 'CSS0033157' => 'camsi', 'CSS0033253' => 'camsi', 'CSS0033347' => 'camsi', 'CSS0033601' => 'camsi', 'CSS0033820' => 'camsi', 'CSS0033881' => 'camsi', 'CSS0033934' => 'camsi', 'CSS0034143' => 'camsi', 'CSS0034176' => 'camsi', 'CSS0034201' => 'camsi', 'CSS0034269' => 'camsi', 'CSS0034303' => 'camsi', 'CSS0034463' => 'camsi', 'CSS0034470' => 'camsi', 'CSS0034514' => 'camsi', 'CSS0034525' => 'camsi', 'CSS0034726' => 'camsi', 'CSS0034727' => 'camsi', 'CSS0034737' => 'camsi', 'CSS0034768' => 'camsi', 'CSS0034890' => 'camsi', 'CSS0034943' => 'camsi', 'CSS0034957' => 'camsi', 'CSS0034973' => 'camsi', 'CSS0035178' => 'camsi', 'CSS0035260' => 'camsi', 'CSS0035316' => 'camsi', 'CSS0035347' => 'camsi', 'CSS0035360' => 'camsi', 'CSS0035380' => 'camsi', 'CSS0035429' => 'camsi', 'CSS0035446' => 'camsi', 'CSS0035737' => 'camsi', 'CSS0035852' => 'camsi', 'CSS0035967' => 'camsi', 'CSS0036001' => 'camsi', 'CSS0036044' => 'camsi', 'CSS0036221' => 'camsi', 'CSS0036333' => 'camsi', 'CSS0036435' => 'camsi', 'CSS0036843' => 'camsi', 'CSS0036846' => 'camsi', 'CSS0037097' => 'camsi', 'CSS0037263' => 'camsi', 'CSS0037370' => 'camsi', 'CSS0037410' => 'camsi', 'CSS0037449' => 'camsi', 'CSS0037603' => 'camsi', 'CSS0037851' => 'camsi', 'CSS0037891' => 'camsi', 'CSS0037996' => 'camsi', 'CSS0038222' => 'camsi', 'CSS0038433' => 'camsi', 'CSS0038441' => 'camsi', 'CSS0038718' => 'camsi', 'CSS0038890' => 'camsi', 'CSS0039049' => 'camsi', 'CSS0039145' => 'camsi', 'CSS0039243' => 'camsi', 'CSS0039294' => 'camsi', 'CSS0039324' => 'camsi', 'CSS0039376' => 'camsi', 'CSS0039475' => 'camsi', 'CSS0039539' => 'camsi', 'CSS0039546' => 'camsi', 'CSS0039567' => 'camsi', 'CSS0039599' => 'camsi', 'CSS0039763' => 'camsi', 'CSS0039863' => 'camsi', 'CSS0040107' => 'camsi', 'CSS0040124' => 'camsi', 'CSS0040151' => 'camsi', 'CSS0040165' => 'camsi', 'CSS0040309' => 'camsi', 'CSS0040318' => 'camsi', 'CSS0040347' => 'camsi', 'CSS0040371' => 'camsi', 'CSS0040456' => 'camsi', 'CSS0040551' => 'camsi', 'CSS0040975' => 'camsi', 'CSS0040981' => 'camsi', 'CSS0041299' => 'camsi', 'CSS0041493' => 'camsi', 'CSS0041658' => 'camsi', 'CSS0041899' => 'camsi', 'CSS0041927' => 'camsi', 'CSS0042016' => 'camsi', 'CSS0042034' => 'camsi', 'CSS0042103' => 'camsi', 'CSS0042172' => 'camsi', 'CSS0042198' => 'camsi', 'CSS0042201' => 'camsi', 'CSS0042308' => 'camsi', 'CSS0042329' => 'camsi', 'CSS0042348' => 'camsi', 'CSS0042349' => 'camsi', 'CSS0042489' => 'camsi', 'CSS0042575' => 'camsi', 'CSS0042624' => 'camsi', 'CSS0042660' => 'camsi', 'CSS0042694' => 'camsi', 'CSS0042995' => 'camsi', 'CSS0043079' => 'camsi', 'CSS0043165' => 'camsi', 'CSS0043171' => 'camsi', 'CSS0043314' => 'camsi', 'CSS0043361' => 'camsi', 'CSS0043375' => 'camsi', 'CSS0043518' => 'camsi', 'CSS0043536' => 'camsi', 'CSS0043678' => 'camsi', 'CSS0043765' => 'camsi', 'CSS0043897' => 'camsi', 'CSS0043944' => 'camsi', 'CSS0044126' => 'camsi', 'CSS0044136' => 'camsi', 'CSS0044179' => 'camsi', 'CSS0044290' => 'camsi', 'CSS0044437' => 'camsi', 'CSS0044502' => 'camsi', 'CSS0044603' => 'camsi', 'CSS0044680' => 'camsi', 'CSS0044685' => 'camsi', 'CSS0044700' => 'camsi', 'CSS0044888' => 'camsi', 'CSS0044923' => 'camsi', 'CSS0044926' => 'camsi', 'CSS0044979' => 'camsi', 'CSS0045049' => 'camsi', 'CSS0045132' => 'camsi', 'CSS0045161' => 'camsi', 'CSS0045219' => 'camsi', 'CSS0045230' => 'camsi', 'CSS0045259' => 'camsi', 'CSS0045324' => 'camsi', 'CSS0045368' => 'camsi', 'CSS0045435' => 'camsi', 'CSS0045856' => 'camsi', 'CSS0045955' => 'camsi', 'CSS0046158' => 'camsi', 'CSS0046334' => 'camsi', 'CSS0046365' => 'camsi', 'CSS0046396' => 'camsi', 'CSS0046400' => 'camsi', 'CSS0046445' => 'camsi', 'CSS0046493' => 'camsi', 'CSS0046640' => 'camsi', 'CSS0046657' => 'camsi', 'CSS0046702' => 'camsi', 'CSS0047208' => 'camsi', 'CSS0047368' => 'camsi', 'CSS0047403' => 'camsi', 'CSS0047417' => 'camsi', 'CSS0047469' => 'camsi', 'CSS0047480' => 'camsi', 'CSS0047482' => 'camsi', 'CSS0047693' => 'camsi', 'CSS0047766' => 'camsi', 'CSS0047866' => 'camsi', 'CSS0047884' => 'camsi', 'CSS0048235' => 'camsi', 'CSS0048383' => 'camsi', 'CSS0048438' => 'camsi', 'CSS0048502' => 'camsi', 'CSS0048546' => 'camsi', 'CSS0048653' => 'camsi', 'CSS0048658' => 'camsi', 'CSS0048729' => 'camsi', 'CSS0048867' => 'camsi', 'CSS0048988' => 'camsi', 'CSS0049053' => 'camsi', 'CSS0049099' => 'camsi', 'CSS0049166' => 'camsi', 'CSS0049174' => 'camsi', 'CSS0049212' => 'camsi', 'CSS0049280' => 'camsi', 'CSS0049391' => 'camsi', 'CSS0049546' => 'camsi', 'CSS0049634' => 'camsi', 'CSS0049655' => 'camsi', 'CSS0049813' => 'camsi', 'CSS0049949' => 'camsi', 'CSS0050009' => 'camsi', 'CSS0050118' => 'camsi', 'CSS0050205' => 'camsi', 'CSS0050275' => 'camsi', 'CSS0050480' => 'camsi', 'CSS0050488' => 'camsi', 'CSS0050497' => 'camsi', 'Dinv03126' => 'din', 'Dinv13140' => 'din', 'Dinv13247' => 'din', 'Dinv14217' => 'din', 'EL10Ac9g22435' => 'bvu', 'FAN20G1200' => 'fan', 'PGR142G2516' => 'pgr', 'Prupe.3G160200' => 'ppe', 'Prupe.5G238200' => 'ppe', 'Prupe.7G047500' => 'ppe', 'QL03p045360' => 'qlo', 'QL05p034369' => 'qlo', 'QL05p034412' => 'qlo', 'QL08p017802' => 'qlo', 'QL08p024762' => 'qlo', 'QL10p026237' => 'qlo', 'QL10p032070' => 'qlo', 'QL11p003821' => 'qlo', 'Rhsim04G0057300' => 'rsi', 'Rhsim05G0049200' => 'rsi', 'Rhsim12G0010400' => 'rsi', 'Rhsim12G0012800' => 'rsi', 'TAR624G0483' => 'tar', 'TAR703G0001' => 'tar', 'vmacro05414' => 'vma', 'vmacro07091' => 'vma', 'vmacro07116' => 'vma', 'vmacro08423' => 'vma', 'vmacro09046' => 'vma', 'vmacro14269' => 'vma', 'vmacro16092' => 'vma', 'vmacro17280' => 'vma', 'vmacro19601' => 'vma' ) $gf_id = 'HOM05D001028' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001028' ) $data_identifier = 'HOM05D001028' $data_type = 'gf_id' $species_gene_counts = array( 'aox' => (int) 11, 'ccan' => (int) 6, 'camsi' => (int) 540, 'din' => (int) 4, 'bvu' => (int) 1, 'fan' => (int) 1, 'pgr' => (int) 1, 'ppe' => (int) 3, 'qlo' => (int) 8, 'rsi' => (int) 4, 'tar' => (int) 2, 'vma' => (int) 9 ) $gf_gene_species = 'vma' $gf_gene_id = 'vmacro19601' $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' => 'HOM05D001028', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '590', 'num_species' => '12' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'Aqoxy1G01649' => 'aox', 'Aqoxy1G02950' => 'aox', 'Aqoxy2G01005' => 'aox', 'Aqoxy2G01064' => 'aox', 'Aqoxy3G02267' => 'aox', 'Aqoxy3G02617' => 'aox', 'Aqoxy3G02693' => 'aox', 'Aqoxy5G03425' => 'aox', 'Aqoxy6G02164' => 'aox', 'Aqoxy6G02364' => 'aox', 'Aqoxy7G02284' => 'aox', 'Cc00_g09720' => 'ccan', 'Cc00_g21410' => 'ccan', 'Cc00_g31750' => 'ccan', 'Cc00_g34740' => 'ccan', 'Cc04_g16890' => 'ccan', 'Cc11_g03120' => 'ccan', 'CSS0000222' => 'camsi', 'CSS0000265' => 'camsi', 'CSS0000306' => 'camsi', 'CSS0000326' => 'camsi', 'CSS0000530' => 'camsi', 'CSS0000563' => 'camsi', 'CSS0000584' => 'camsi', 'CSS0000684' => 'camsi', 'CSS0001100' => 'camsi', 'CSS0001311' => 'camsi', 'CSS0001343' => 'camsi', 'CSS0001399' => 'camsi', 'CSS0001475' => 'camsi', 'CSS0001506' => 'camsi', 'CSS0001602' => 'camsi', 'CSS0001681' => 'camsi', 'CSS0001874' => 'camsi', 'CSS0001948' => 'camsi', 'CSS0002022' => 'camsi', 'CSS0002230' => 'camsi', 'CSS0002265' => 'camsi', 'CSS0002277' => 'camsi', 'CSS0002462' => 'camsi', 'CSS0002823' => 'camsi', 'CSS0003091' => 'camsi', 'CSS0003162' => 'camsi', 'CSS0003264' => 'camsi', 'CSS0003355' => 'camsi', 'CSS0003378' => 'camsi', 'CSS0003472' => 'camsi', 'CSS0003500' => 'camsi', 'CSS0003640' => 'camsi', 'CSS0003767' => 'camsi', 'CSS0003894' => 'camsi', 'CSS0003952' => 'camsi', 'CSS0003977' => 'camsi', 'CSS0004028' => 'camsi', 'CSS0004117' => 'camsi', 'CSS0004137' => 'camsi', 'CSS0004176' => 'camsi', 'CSS0004265' => 'camsi', 'CSS0004450' => 'camsi', 'CSS0004468' => 'camsi', 'CSS0004488' => 'camsi', 'CSS0004490' => 'camsi', 'CSS0004632' => 'camsi', 'CSS0004790' => 'camsi', 'CSS0004877' => 'camsi', 'CSS0004920' => 'camsi', 'CSS0004969' => 'camsi', 'CSS0005084' => 'camsi', 'CSS0005101' => 'camsi', 'CSS0005271' => 'camsi', 'CSS0005313' => 'camsi', 'CSS0005331' => 'camsi', 'CSS0005368' => 'camsi', 'CSS0005391' => 'camsi', 'CSS0005437' => 'camsi', 'CSS0005515' => 'camsi', 'CSS0005526' => 'camsi', 'CSS0005532' => 'camsi', 'CSS0005595' => 'camsi', 'CSS0005677' => 'camsi', 'CSS0005838' => 'camsi', 'CSS0005988' => 'camsi', 'CSS0006100' => 'camsi', 'CSS0006128' => 'camsi', 'CSS0006293' => 'camsi', 'CSS0006378' => 'camsi', 'CSS0006400' => 'camsi', 'CSS0006441' => 'camsi', 'CSS0006455' => 'camsi', 'CSS0006480' => 'camsi', 'CSS0006483' => 'camsi', 'CSS0006538' => 'camsi', 'CSS0006582' => 'camsi', 'CSS0006632' => 'camsi', 'CSS0006771' => 'camsi', 'CSS0006803' => 'camsi', 'CSS0006852' => 'camsi', 'CSS0006861' => 'camsi', 'CSS0006910' => 'camsi', 'CSS0007037' => 'camsi', 'CSS0007066' => 'camsi', 'CSS0007072' => 'camsi', 'CSS0007109' => 'camsi', 'CSS0007193' => 'camsi', 'CSS0007319' => 'camsi', 'CSS0007336' => 'camsi', 'CSS0007377' => 'camsi', 'CSS0007659' => 'camsi', 'CSS0007701' => 'camsi', 'CSS0007711' => 'camsi', 'CSS0007809' => 'camsi', 'CSS0008045' => 'camsi', 'CSS0008050' => 'camsi', 'CSS0008206' => 'camsi', 'CSS0008251' => 'camsi', 'CSS0008252' => 'camsi', 'CSS0008279' => 'camsi', 'CSS0008482' => 'camsi', 'CSS0008583' => 'camsi', 'CSS0008699' => 'camsi', 'CSS0008798' => 'camsi', 'CSS0008971' => 'camsi', 'CSS0009019' => 'camsi', 'CSS0009191' => 'camsi', 'CSS0009241' => 'camsi', 'CSS0009246' => 'camsi', 'CSS0009399' => 'camsi', 'CSS0009654' => 'camsi', 'CSS0009722' => 'camsi', 'CSS0009920' => 'camsi', 'CSS0009986' => 'camsi', 'CSS0010182' => 'camsi', 'CSS0010202' => 'camsi', 'CSS0010330' => 'camsi', 'CSS0010362' => 'camsi', 'CSS0010456' => 'camsi', 'CSS0010472' => 'camsi', 'CSS0010507' => 'camsi', 'CSS0010512' => 'camsi', 'CSS0010520' => 'camsi', 'CSS0010617' => 'camsi', 'CSS0010706' => 'camsi', 'CSS0010747' => 'camsi', 'CSS0010816' => 'camsi', 'CSS0011020' => 'camsi', 'CSS0011115' => 'camsi', 'CSS0011383' => 'camsi', 'CSS0011491' => 'camsi', 'CSS0011602' => 'camsi', 'CSS0011605' => 'camsi', 'CSS0011625' => 'camsi', 'CSS0011654' => 'camsi', 'CSS0011781' => 'camsi', 'CSS0011853' => 'camsi', 'CSS0011898' => 'camsi', 'CSS0011933' => 'camsi', 'CSS0011996' => 'camsi', 'CSS0012066' => 'camsi', 'CSS0012097' => 'camsi', 'CSS0012108' => 'camsi', 'CSS0012226' => 'camsi', 'CSS0012248' => 'camsi', 'CSS0012331' => 'camsi', 'CSS0012797' => 'camsi', 'CSS0012818' => 'camsi', 'CSS0012904' => 'camsi', 'CSS0013001' => 'camsi', 'CSS0013022' => 'camsi', 'CSS0013172' => 'camsi', 'CSS0013244' => 'camsi', 'CSS0013267' => 'camsi', 'CSS0013275' => 'camsi', 'CSS0013324' => 'camsi', 'CSS0013334' => 'camsi', 'CSS0013394' => 'camsi', 'CSS0013549' => 'camsi', 'CSS0013689' => 'camsi', 'CSS0014026' => 'camsi', 'CSS0014049' => 'camsi', 'CSS0014144' => 'camsi', 'CSS0014354' => 'camsi', 'CSS0014579' => 'camsi', 'CSS0014648' => 'camsi', 'CSS0014902' => 'camsi', 'CSS0014979' => 'camsi', 'CSS0015278' => 'camsi', 'CSS0015310' => 'camsi', 'CSS0015364' => 'camsi', 'CSS0015455' => 'camsi', 'CSS0015693' => 'camsi', 'CSS0015774' => 'camsi', 'CSS0015795' => 'camsi', 'CSS0015952' => 'camsi', 'CSS0016104' => 'camsi', 'CSS0016241' => 'camsi', 'CSS0016303' => 'camsi', 'CSS0016490' => 'camsi', 'CSS0016832' => 'camsi', 'CSS0016845' => 'camsi', 'CSS0016914' => 'camsi', 'CSS0016946' => 'camsi', 'CSS0017102' => 'camsi', 'CSS0017193' => 'camsi', 'CSS0017528' => 'camsi', 'CSS0017619' => 'camsi', 'CSS0017679' => 'camsi', 'CSS0017816' => 'camsi', 'CSS0017880' => 'camsi', 'CSS0018106' => 'camsi', 'CSS0018162' => 'camsi', 'CSS0018304' => 'camsi', 'CSS0018406' => 'camsi', 'CSS0018481' => 'camsi', 'CSS0018511' => 'camsi', 'CSS0018596' => 'camsi', 'CSS0018727' => 'camsi', 'CSS0018751' => 'camsi', 'CSS0018777' => 'camsi', 'CSS0018798' => 'camsi', 'CSS0019137' => 'camsi', 'CSS0019177' => 'camsi', 'CSS0019217' => 'camsi', 'CSS0019361' => 'camsi', 'CSS0019516' => 'camsi', 'CSS0019538' => 'camsi', 'CSS0019560' => 'camsi', 'CSS0019819' => 'camsi', 'CSS0019837' => 'camsi', 'CSS0019915' => 'camsi', 'CSS0019925' => 'camsi', 'CSS0020112' => 'camsi', 'CSS0020160' => 'camsi', 'CSS0020378' => 'camsi', 'CSS0020388' => 'camsi', 'CSS0020452' => 'camsi', 'CSS0020588' => 'camsi', 'CSS0020661' => 'camsi', 'CSS0020886' => 'camsi', 'CSS0020973' => 'camsi', 'CSS0021035' => 'camsi', 'CSS0021111' => 'camsi', 'CSS0021131' => 'camsi', 'CSS0021151' => 'camsi', 'CSS0021228' => 'camsi', 'CSS0021397' => 'camsi', 'CSS0021420' => 'camsi', 'CSS0021464' => 'camsi', 'CSS0021547' => 'camsi', 'CSS0021608' => 'camsi', 'CSS0021740' => 'camsi', 'CSS0021826' => 'camsi', 'CSS0021904' => 'camsi', 'CSS0021941' => 'camsi', 'CSS0022189' => 'camsi', 'CSS0022199' => 'camsi', 'CSS0022502' => 'camsi', 'CSS0022531' => 'camsi', 'CSS0022581' => 'camsi', 'CSS0022612' => 'camsi', 'CSS0022621' => 'camsi', 'CSS0022815' => 'camsi', 'CSS0022936' => 'camsi', 'CSS0022964' => 'camsi', 'CSS0022985' => 'camsi', 'CSS0023002' => 'camsi', 'CSS0023006' => 'camsi', 'CSS0023024' => 'camsi', 'CSS0023489' => 'camsi', 'CSS0023593' => 'camsi', 'CSS0023621' => 'camsi', 'CSS0023743' => 'camsi', 'CSS0023804' => 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'camsi', 'CSS0035178' => 'camsi', 'CSS0035260' => 'camsi', 'CSS0035316' => 'camsi', 'CSS0035347' => 'camsi', 'CSS0035360' => 'camsi', 'CSS0035380' => 'camsi', 'CSS0035429' => 'camsi', 'CSS0035446' => 'camsi', 'CSS0035737' => 'camsi', 'CSS0035852' => 'camsi', 'CSS0035967' => 'camsi', 'CSS0036001' => 'camsi', 'CSS0036044' => 'camsi', 'CSS0036221' => 'camsi', 'CSS0036333' => 'camsi', 'CSS0036435' => 'camsi', 'CSS0036843' => 'camsi', 'CSS0036846' => 'camsi', 'CSS0037097' => 'camsi', 'CSS0037263' => 'camsi', 'CSS0037370' => 'camsi', 'CSS0037410' => 'camsi', 'CSS0037449' => 'camsi', 'CSS0037603' => 'camsi', 'CSS0037851' => 'camsi', 'CSS0037891' => 'camsi', 'CSS0037996' => 'camsi', 'CSS0038222' => 'camsi', 'CSS0038433' => 'camsi', 'CSS0038441' => 'camsi', 'CSS0038718' => 'camsi', 'CSS0038890' => 'camsi', 'CSS0039049' => 'camsi', 'CSS0039145' => 'camsi', 'CSS0039243' => 'camsi', 'CSS0039294' => 'camsi', 'CSS0039324' => 'camsi', 'CSS0039376' => 'camsi', 'CSS0039475' => 'camsi', 'CSS0039539' => 'camsi', 'CSS0039546' => 'camsi', 'CSS0039567' => 'camsi', 'CSS0039599' => 'camsi', 'CSS0039763' => 'camsi', 'CSS0039863' => 'camsi', 'CSS0040107' => 'camsi', 'CSS0040124' => 'camsi', 'CSS0040151' => 'camsi', 'CSS0040165' => 'camsi', 'CSS0040309' => 'camsi', 'CSS0040318' => 'camsi', 'CSS0040347' => 'camsi', 'CSS0040371' => 'camsi', 'CSS0040456' => 'camsi', 'CSS0040551' => 'camsi', 'CSS0040975' => 'camsi', 'CSS0040981' => 'camsi', 'CSS0041299' => 'camsi', 'CSS0041493' => 'camsi', 'CSS0041658' => 'camsi', 'CSS0041899' => 'camsi', 'CSS0041927' => 'camsi', 'CSS0042016' => 'camsi', 'CSS0042034' => 'camsi', 'CSS0042103' => 'camsi', 'CSS0042172' => 'camsi', 'CSS0042198' => 'camsi', 'CSS0042201' => 'camsi', 'CSS0042308' => 'camsi', 'CSS0042329' => 'camsi', 'CSS0042348' => 'camsi', 'CSS0042349' => 'camsi', 'CSS0042489' => 'camsi', 'CSS0042575' => 'camsi', 'CSS0042624' => 'camsi', 'CSS0042660' => 'camsi', 'CSS0042694' => 'camsi', 'CSS0042995' => 'camsi', 'CSS0043079' => 'camsi', 'CSS0043165' => 'camsi', 'CSS0043171' => 'camsi', 'CSS0043314' => 'camsi', 'CSS0043361' => 'camsi', 'CSS0043375' => 'camsi', 'CSS0043518' => 'camsi', 'CSS0043536' => 'camsi', 'CSS0043678' => 'camsi', 'CSS0043765' => 'camsi', 'CSS0043897' => 'camsi', 'CSS0043944' => 'camsi', 'CSS0044126' => 'camsi', 'CSS0044136' => 'camsi', 'CSS0044179' => 'camsi', 'CSS0044290' => 'camsi', 'CSS0044437' => 'camsi', 'CSS0044502' => 'camsi', 'CSS0044603' => 'camsi', 'CSS0044680' => 'camsi', 'CSS0044685' => 'camsi', 'CSS0044700' => 'camsi', 'CSS0044888' => 'camsi', 'CSS0044923' => 'camsi', 'CSS0044926' => 'camsi', 'CSS0044979' => 'camsi', 'CSS0045049' => 'camsi', 'CSS0045132' => 'camsi', 'CSS0045161' => 'camsi', 'CSS0045219' => 'camsi', 'CSS0045230' => 'camsi', 'CSS0045259' => 'camsi', 'CSS0045324' => 'camsi', 'CSS0045368' => 'camsi', 'CSS0045435' => 'camsi', 'CSS0045856' => 'camsi', 'CSS0045955' => 'camsi', 'CSS0046158' => 'camsi', 'CSS0046334' => 'camsi', 'CSS0046365' => 'camsi', 'CSS0046396' => 'camsi', 'CSS0046400' => 'camsi', 'CSS0046445' => 'camsi', 'CSS0046493' => 'camsi', 'CSS0046640' => 'camsi', 'CSS0046657' => 'camsi', 'CSS0046702' => 'camsi', 'CSS0047208' => 'camsi', 'CSS0047368' => 'camsi', 'CSS0047403' => 'camsi', 'CSS0047417' => 'camsi', 'CSS0047469' => 'camsi', 'CSS0047480' => 'camsi', 'CSS0047482' => 'camsi', 'CSS0047693' => 'camsi', 'CSS0047766' => 'camsi', 'CSS0047866' => 'camsi', 'CSS0047884' => 'camsi', 'CSS0048235' => 'camsi', 'CSS0048383' => 'camsi', 'CSS0048438' => 'camsi', 'CSS0048502' => 'camsi', 'CSS0048546' => 'camsi', 'CSS0048653' => 'camsi', 'CSS0048658' => 'camsi', 'CSS0048729' => 'camsi', 'CSS0048867' => 'camsi', 'CSS0048988' => 'camsi', 'CSS0049053' => 'camsi', 'CSS0049099' => 'camsi', 'CSS0049166' => 'camsi', 'CSS0049174' => 'camsi', 'CSS0049212' => 'camsi', 'CSS0049280' => 'camsi', 'CSS0049391' => 'camsi', 'CSS0049546' => 'camsi', 'CSS0049634' => 'camsi', 'CSS0049655' => 'camsi', 'CSS0049813' => 'camsi', 'CSS0049949' => 'camsi', 'CSS0050009' => 'camsi', 'CSS0050118' => 'camsi', 'CSS0050205' => 'camsi', 'CSS0050275' => 'camsi', 'CSS0050480' => 'camsi', 'CSS0050488' => 'camsi', 'CSS0050497' => 'camsi', 'Dinv03126' => 'din', 'Dinv13140' => 'din', 'Dinv13247' => 'din', 'Dinv14217' => 'din', 'EL10Ac9g22435' => 'bvu', 'FAN20G1200' => 'fan', 'PGR142G2516' => 'pgr', 'Prupe.3G160200' => 'ppe', 'Prupe.5G238200' => 'ppe', 'Prupe.7G047500' => 'ppe', 'QL03p045360' => 'qlo', 'QL05p034369' => 'qlo', 'QL05p034412' => 'qlo', 'QL08p017802' => 'qlo', 'QL08p024762' => 'qlo', 'QL10p026237' => 'qlo', 'QL10p032070' => 'qlo', 'QL11p003821' => 'qlo', 'Rhsim04G0057300' => 'rsi', 'Rhsim05G0049200' => 'rsi', 'Rhsim12G0010400' => 'rsi', 'Rhsim12G0012800' => 'rsi', 'TAR624G0483' => 'tar', 'TAR703G0001' => 'tar', 'vmacro05414' => 'vma', 'vmacro07091' => 'vma', 'vmacro07116' => 'vma', 'vmacro08423' => 'vma', 'vmacro09046' => 'vma', 'vmacro14269' => 'vma', 'vmacro16092' => 'vma', 'vmacro17280' => 'vma', 'vmacro19601' => 'vma' ), 'gf_id' => 'HOM05D001028', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001028' ), 'data_identifier' => 'HOM05D001028', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001028', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '590', 'num_species' => '12' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'Aqoxy1G01649' => 'aox', 'Aqoxy1G02950' => 'aox', 'Aqoxy2G01005' => 'aox', 'Aqoxy2G01064' => 'aox', 'Aqoxy3G02267' => 'aox', 'Aqoxy3G02617' => 'aox', 'Aqoxy3G02693' => 'aox', 'Aqoxy5G03425' => 'aox', 'Aqoxy6G02164' => 'aox', 'Aqoxy6G02364' => 'aox', 'Aqoxy7G02284' => 'aox', 'Cc00_g09720' => 'ccan', 'Cc00_g21410' => 'ccan', 'Cc00_g31750' => 'ccan', 'Cc00_g34740' => 'ccan', 'Cc04_g16890' => 'ccan', 'Cc11_g03120' => 'ccan', 'CSS0000222' => 'camsi', 'CSS0000265' => 'camsi', 'CSS0000306' => 'camsi', 'CSS0000326' => 'camsi', 'CSS0000530' => 'camsi', 'CSS0000563' => 'camsi', 'CSS0000584' => 'camsi', 'CSS0000684' => 'camsi', 'CSS0001100' => 'camsi', 'CSS0001311' => 'camsi', 'CSS0001343' => 'camsi', 'CSS0001399' => 'camsi', 'CSS0001475' => 'camsi', 'CSS0001506' => 'camsi', 'CSS0001602' => 'camsi', 'CSS0001681' => 'camsi', 'CSS0001874' => 'camsi', 'CSS0001948' => 'camsi', 'CSS0002022' => 'camsi', 'CSS0002230' => 'camsi', 'CSS0002265' => 'camsi', 'CSS0002277' => 'camsi', 'CSS0002462' => 'camsi', 'CSS0002823' => 'camsi', 'CSS0003091' => 'camsi', 'CSS0003162' => 'camsi', 'CSS0003264' => 'camsi', 'CSS0003355' => 'camsi', 'CSS0003378' => 'camsi', 'CSS0003472' => 'camsi', 'CSS0003500' => 'camsi', 'CSS0003640' => 'camsi', 'CSS0003767' => 'camsi', 'CSS0003894' => 'camsi', 'CSS0003952' => 'camsi', 'CSS0003977' => 'camsi', 'CSS0004028' => 'camsi', 'CSS0004117' => 'camsi', 'CSS0004137' => 'camsi', 'CSS0004176' => 'camsi', 'CSS0004265' => 'camsi', 'CSS0004450' => 'camsi', 'CSS0004468' => 'camsi', 'CSS0004488' => 'camsi', 'CSS0004490' => 'camsi', 'CSS0004632' => 'camsi', 'CSS0004790' => 'camsi', 'CSS0004877' => 'camsi', 'CSS0004920' => 'camsi', 'CSS0004969' => 'camsi', 'CSS0005084' => 'camsi', 'CSS0005101' => 'camsi', 'CSS0005271' => 'camsi', 'CSS0005313' => 'camsi', 'CSS0005331' => 'camsi', 'CSS0005368' => 'camsi', 'CSS0005391' => 'camsi', 'CSS0005437' => 'camsi', 'CSS0005515' => 'camsi', 'CSS0005526' => 'camsi', 'CSS0005532' => 'camsi', 'CSS0005595' => 'camsi', 'CSS0005677' => 'camsi', 'CSS0005838' => 'camsi', 'CSS0005988' => 'camsi', 'CSS0006100' => 'camsi', 'CSS0006128' => 'camsi', 'CSS0006293' => 'camsi', 'CSS0006378' => 'camsi', 'CSS0006400' => 'camsi', 'CSS0006441' => 'camsi', 'CSS0006455' => 'camsi', 'CSS0006480' => 'camsi', 'CSS0006483' => 'camsi', 'CSS0006538' => 'camsi', 'CSS0006582' => 'camsi', 'CSS0006632' => 'camsi', 'CSS0006771' => 'camsi', 'CSS0006803' => 'camsi', 'CSS0006852' => 'camsi', 'CSS0006861' => 'camsi', 'CSS0006910' => 'camsi', 'CSS0007037' => 'camsi', 'CSS0007066' => 'camsi', 'CSS0007072' => 'camsi', 'CSS0007109' => 'camsi', 'CSS0007193' => 'camsi', 'CSS0007319' => 'camsi', 'CSS0007336' => 'camsi', 'CSS0007377' => 'camsi', 'CSS0007659' => 'camsi', 'CSS0007701' => 'camsi', 'CSS0007711' => 'camsi', 'CSS0007809' => 'camsi', 'CSS0008045' => 'camsi', 'CSS0008050' => 'camsi', 'CSS0008206' => 'camsi', 'CSS0008251' => 'camsi', 'CSS0008252' => 'camsi', 'CSS0008279' => 'camsi', 'CSS0008482' => 'camsi', 'CSS0008583' => 'camsi', 'CSS0008699' => 'camsi', 'CSS0008798' => 'camsi', 'CSS0008971' => 'camsi', 'CSS0009019' => 'camsi', 'CSS0009191' => 'camsi', 'CSS0009241' => 'camsi', 'CSS0009246' => 'camsi', 'CSS0009399' => 'camsi', 'CSS0009654' => 'camsi', 'CSS0009722' => 'camsi', 'CSS0009920' => 'camsi', 'CSS0009986' => 'camsi', 'CSS0010182' => 'camsi', 'CSS0010202' => 'camsi', 'CSS0010330' => 'camsi', 'CSS0010362' => 'camsi', 'CSS0010456' => 'camsi', 'CSS0010472' => 'camsi', 'CSS0010507' => 'camsi', 'CSS0010512' => 'camsi', 'CSS0010520' => 'camsi', 'CSS0010617' => 'camsi', 'CSS0010706' => 'camsi', 'CSS0010747' => 'camsi', 'CSS0010816' => 'camsi', 'CSS0011020' => 'camsi', 'CSS0011115' => 'camsi', 'CSS0011383' => 'camsi', 'CSS0011491' => 'camsi', 'CSS0011602' => 'camsi', 'CSS0011605' => 'camsi', 'CSS0011625' => 'camsi', 'CSS0011654' => 'camsi', 'CSS0011781' => 'camsi', 'CSS0011853' => 'camsi', 'CSS0011898' => 'camsi', 'CSS0011933' => 'camsi', 'CSS0011996' => 'camsi', 'CSS0012066' => 'camsi', 'CSS0012097' => 'camsi', 'CSS0012108' => 'camsi', 'CSS0012226' => 'camsi', 'CSS0012248' => 'camsi', 'CSS0012331' => 'camsi', 'CSS0012797' => 'camsi', 'CSS0012818' => 'camsi', 'CSS0012904' => 'camsi', 'CSS0013001' => 'camsi', 'CSS0013022' => 'camsi', 'CSS0013172' => 'camsi', 'CSS0013244' => 'camsi', 'CSS0013267' => 'camsi', 'CSS0013275' => 'camsi', 'CSS0013324' => 'camsi', 'CSS0013334' => 'camsi', 'CSS0013394' => 'camsi', 'CSS0013549' => 'camsi', 'CSS0013689' => 'camsi', 'CSS0014026' => 'camsi', 'CSS0014049' => 'camsi', 'CSS0014144' => 'camsi', 'CSS0014354' => 'camsi', 'CSS0014579' => 'camsi', 'CSS0014648' => 'camsi', 'CSS0014902' => 'camsi', 'CSS0014979' => 'camsi', 'CSS0015278' => 'camsi', 'CSS0015310' => 'camsi', 'CSS0015364' => 'camsi', 'CSS0015455' => 'camsi', 'CSS0015693' => 'camsi', 'CSS0015774' => 'camsi', 'CSS0015795' => 'camsi', 'CSS0015952' => 'camsi', 'CSS0016104' => 'camsi', 'CSS0016241' => 'camsi', 'CSS0016303' => 'camsi', 'CSS0016490' => 'camsi', 'CSS0016832' => 'camsi', 'CSS0016845' => 'camsi', 'CSS0016914' => 'camsi', 'CSS0016946' => 'camsi', 'CSS0017102' => 'camsi', 'CSS0017193' => 'camsi', 'CSS0017528' => 'camsi', 'CSS0017619' => 'camsi', 'CSS0017679' => 'camsi', 'CSS0017816' => 'camsi', 'CSS0017880' => 'camsi', 'CSS0018106' => 'camsi', 'CSS0018162' => 'camsi', 'CSS0018304' => 'camsi', 'CSS0018406' => 'camsi', 'CSS0018481' => 'camsi', 'CSS0018511' => 'camsi', 'CSS0018596' => 'camsi', 'CSS0018727' => 'camsi', 'CSS0018751' => 'camsi', 'CSS0018777' => 'camsi', 'CSS0018798' => 'camsi', 'CSS0019137' => 'camsi', 'CSS0019177' => 'camsi', 'CSS0019217' => 'camsi', 'CSS0019361' => 'camsi', 'CSS0019516' => 'camsi', 'CSS0019538' => 'camsi', 'CSS0019560' => 'camsi', 'CSS0019819' => 'camsi', 'CSS0019837' => 'camsi', 'CSS0019915' => 'camsi', 'CSS0019925' => 'camsi', 'CSS0020112' => 'camsi', 'CSS0020160' => 'camsi', 'CSS0020378' => 'camsi', 'CSS0020388' => 'camsi', 'CSS0020452' => 'camsi', 'CSS0020588' => 'camsi', 'CSS0020661' => 'camsi', 'CSS0020886' => 'camsi', 'CSS0020973' => 'camsi', 'CSS0021035' => 'camsi', 'CSS0021111' => 'camsi', 'CSS0021131' => 'camsi', 'CSS0021151' => 'camsi', 'CSS0021228' => 'camsi', 'CSS0021397' => 'camsi', 'CSS0021420' => 'camsi', 'CSS0021464' => 'camsi', 'CSS0021547' => 'camsi', 'CSS0021608' => 'camsi', 'CSS0021740' => 'camsi', 'CSS0021826' => 'camsi', 'CSS0021904' => 'camsi', 'CSS0021941' => 'camsi', 'CSS0022189' => 'camsi', 'CSS0022199' => 'camsi', 'CSS0022502' => 'camsi', 'CSS0022531' => 'camsi', 'CSS0022581' => 'camsi', 'CSS0022612' => 'camsi', 'CSS0022621' => 'camsi', 'CSS0022815' => 'camsi', 'CSS0022936' => 'camsi', 'CSS0022964' => 'camsi', 'CSS0022985' => 'camsi', 'CSS0023002' => 'camsi', 'CSS0023006' => 'camsi', 'CSS0023024' => 'camsi', 'CSS0023489' => 'camsi', 'CSS0023593' => 'camsi', 'CSS0023621' => 'camsi', 'CSS0023743' => 'camsi', 'CSS0023804' => 'camsi', 'CSS0023805' => 'camsi', 'CSS0023908' => 'camsi', 'CSS0023938' => 'camsi', 'CSS0023981' => 'camsi', 'CSS0024027' => 'camsi', 'CSS0024169' => 'camsi', 'CSS0024193' => 'camsi', 'CSS0024269' => 'camsi', 'CSS0024336' => 'camsi', 'CSS0024337' => 'camsi', 'CSS0024548' => 'camsi', 'CSS0024564' => 'camsi', 'CSS0024585' => 'camsi', 'CSS0024738' => 'camsi', 'CSS0024833' => 'camsi', 'CSS0024846' => 'camsi', 'CSS0024957' => 'camsi', 'CSS0024974' => 'camsi', 'CSS0025005' => 'camsi', 'CSS0025235' => 'camsi', 'CSS0025465' => 'camsi', 'CSS0025633' => 'camsi', 'CSS0025688' => 'camsi', 'CSS0025759' => 'camsi', 'CSS0025774' => 'camsi', 'CSS0025801' => 'camsi', 'CSS0025942' => 'camsi', 'CSS0026083' => 'camsi', 'CSS0026194' => 'camsi', 'CSS0026230' => 'camsi', 'CSS0026398' => 'camsi', 'CSS0026419' => 'camsi', 'CSS0026679' => 'camsi', 'CSS0026719' => 'camsi', 'CSS0026795' => 'camsi', 'CSS0026835' => 'camsi', 'CSS0026930' => 'camsi', 'CSS0027053' => 'camsi', 'CSS0027130' => 'camsi', 'CSS0027192' => 'camsi', 'CSS0027454' => 'camsi', 'CSS0027467' => 'camsi', 'CSS0027521' => 'camsi', 'CSS0027662' => 'camsi', 'CSS0027795' => 'camsi', 'CSS0027835' => 'camsi', 'CSS0027966' => 'camsi', 'CSS0028090' => 'camsi', 'CSS0028134' => 'camsi', 'CSS0028205' => 'camsi', 'CSS0028263' => 'camsi', 'CSS0028363' => 'camsi', 'CSS0028598' => 'camsi', 'CSS0029175' => 'camsi', 'CSS0029191' => 'camsi', 'CSS0029424' => 'camsi', 'CSS0029479' => 'camsi', 'CSS0029496' => 'camsi', 'CSS0029633' => 'camsi', 'CSS0029837' => 'camsi', 'CSS0029844' => 'camsi', 'CSS0029863' => 'camsi', 'CSS0029874' => 'camsi', 'CSS0029959' => 'camsi', 'CSS0030001' => 'camsi', 'CSS0030093' => 'camsi', 'CSS0030199' => 'camsi', 'CSS0030200' => 'camsi', 'CSS0030427' => 'camsi', 'CSS0030476' => 'camsi', 'CSS0030636' => 'camsi', 'CSS0030673' => 'camsi', 'CSS0030766' => 'camsi', 'CSS0030775' => 'camsi', 'CSS0030858' => 'camsi', 'CSS0030873' => 'camsi', 'CSS0030929' => 'camsi', 'CSS0031028' => 'camsi', 'CSS0031129' => 'camsi', 'CSS0031164' => 'camsi', 'CSS0031340' => 'camsi', 'CSS0031368' => 'camsi', 'CSS0031395' => 'camsi', 'CSS0031596' => 'camsi', 'CSS0031727' => 'camsi', 'CSS0032011' => 'camsi', 'CSS0032160' => 'camsi', 'CSS0032538' => 'camsi', 'CSS0032576' => 'camsi', 'CSS0032603' => 'camsi', 'CSS0032640' => 'camsi', 'CSS0032704' => 'camsi', 'CSS0032851' => 'camsi', 'CSS0032973' => 'camsi', 'CSS0033048' => 'camsi', 'CSS0033082' => 'camsi', 'CSS0033157' => 'camsi', 'CSS0033253' => 'camsi', 'CSS0033347' => 'camsi', 'CSS0033601' => 'camsi', 'CSS0033820' => 'camsi', 'CSS0033881' => 'camsi', 'CSS0033934' => 'camsi', 'CSS0034143' => 'camsi', 'CSS0034176' => 'camsi', 'CSS0034201' => 'camsi', 'CSS0034269' => 'camsi', 'CSS0034303' => 'camsi', 'CSS0034463' => 'camsi', 'CSS0034470' => 'camsi', 'CSS0034514' => 'camsi', 'CSS0034525' => 'camsi', 'CSS0034726' => 'camsi', 'CSS0034727' => 'camsi', 'CSS0034737' => 'camsi', 'CSS0034768' => 'camsi', 'CSS0034890' => 'camsi', 'CSS0034943' => 'camsi', 'CSS0034957' => 'camsi', 'CSS0034973' => 'camsi', 'CSS0035178' => 'camsi', 'CSS0035260' => 'camsi', 'CSS0035316' => 'camsi', 'CSS0035347' => 'camsi', 'CSS0035360' => 'camsi', 'CSS0035380' => 'camsi', 'CSS0035429' => 'camsi', 'CSS0035446' => 'camsi', 'CSS0035737' => 'camsi', 'CSS0035852' => 'camsi', 'CSS0035967' => 'camsi', 'CSS0036001' => 'camsi', 'CSS0036044' => 'camsi', 'CSS0036221' => 'camsi', 'CSS0036333' => 'camsi', 'CSS0036435' => 'camsi', 'CSS0036843' => 'camsi', 'CSS0036846' => 'camsi', 'CSS0037097' => 'camsi', 'CSS0037263' => 'camsi', 'CSS0037370' => 'camsi', 'CSS0037410' => 'camsi', 'CSS0037449' => 'camsi', 'CSS0037603' => 'camsi', 'CSS0037851' => 'camsi', 'CSS0037891' => 'camsi', 'CSS0037996' => 'camsi', 'CSS0038222' => 'camsi', 'CSS0038433' => 'camsi', 'CSS0038441' => 'camsi', 'CSS0038718' => 'camsi', 'CSS0038890' => 'camsi', 'CSS0039049' => 'camsi', 'CSS0039145' => 'camsi', 'CSS0039243' => 'camsi', 'CSS0039294' => 'camsi', 'CSS0039324' => 'camsi', 'CSS0039376' => 'camsi', 'CSS0039475' => 'camsi', 'CSS0039539' => 'camsi', 'CSS0039546' => 'camsi', 'CSS0039567' => 'camsi', 'CSS0039599' => 'camsi', 'CSS0039763' => 'camsi', 'CSS0039863' => 'camsi', 'CSS0040107' => 'camsi', 'CSS0040124' => 'camsi', 'CSS0040151' => 'camsi', 'CSS0040165' => 'camsi', 'CSS0040309' => 'camsi', 'CSS0040318' => 'camsi', 'CSS0040347' => 'camsi', 'CSS0040371' => 'camsi', 'CSS0040456' => 'camsi', 'CSS0040551' => 'camsi', 'CSS0040975' => 'camsi', 'CSS0040981' => 'camsi', 'CSS0041299' => 'camsi', 'CSS0041493' => 'camsi', 'CSS0041658' => 'camsi', 'CSS0041899' => 'camsi', 'CSS0041927' => 'camsi', 'CSS0042016' => 'camsi', 'CSS0042034' => 'camsi', 'CSS0042103' => 'camsi', 'CSS0042172' => 'camsi', 'CSS0042198' => 'camsi', 'CSS0042201' => 'camsi', 'CSS0042308' => 'camsi', 'CSS0042329' => 'camsi', 'CSS0042348' => 'camsi', 'CSS0042349' => 'camsi', 'CSS0042489' => 'camsi', 'CSS0042575' => 'camsi', 'CSS0042624' => 'camsi', 'CSS0042660' => 'camsi', 'CSS0042694' => 'camsi', 'CSS0042995' => 'camsi', 'CSS0043079' => 'camsi', 'CSS0043165' => 'camsi', 'CSS0043171' => 'camsi', 'CSS0043314' => 'camsi', 'CSS0043361' => 'camsi', 'CSS0043375' => 'camsi', 'CSS0043518' => 'camsi', 'CSS0043536' => 'camsi', 'CSS0043678' => 'camsi', 'CSS0043765' => 'camsi', 'CSS0043897' => 'camsi', 'CSS0043944' => 'camsi', 'CSS0044126' => 'camsi', 'CSS0044136' => 'camsi', 'CSS0044179' => 'camsi', 'CSS0044290' => 'camsi', 'CSS0044437' => 'camsi', 'CSS0044502' => 'camsi', 'CSS0044603' => 'camsi', 'CSS0044680' => 'camsi', 'CSS0044685' => 'camsi', 'CSS0044700' => 'camsi', 'CSS0044888' => 'camsi', 'CSS0044923' => 'camsi', 'CSS0044926' => 'camsi', 'CSS0044979' => 'camsi', 'CSS0045049' => 'camsi', 'CSS0045132' => 'camsi', 'CSS0045161' => 'camsi', 'CSS0045219' => 'camsi', 'CSS0045230' => 'camsi', 'CSS0045259' => 'camsi', 'CSS0045324' => 'camsi', 'CSS0045368' => 'camsi', 'CSS0045435' => 'camsi', 'CSS0045856' => 'camsi', 'CSS0045955' => 'camsi', 'CSS0046158' => 'camsi', 'CSS0046334' => 'camsi', 'CSS0046365' => 'camsi', 'CSS0046396' => 'camsi', 'CSS0046400' => 'camsi', 'CSS0046445' => 'camsi', 'CSS0046493' => 'camsi', 'CSS0046640' => 'camsi', 'CSS0046657' => 'camsi', 'CSS0046702' => 'camsi', 'CSS0047208' => 'camsi', 'CSS0047368' => 'camsi', 'CSS0047403' => 'camsi', 'CSS0047417' => 'camsi', 'CSS0047469' => 'camsi', 'CSS0047480' => 'camsi', 'CSS0047482' => 'camsi', 'CSS0047693' => 'camsi', 'CSS0047766' => 'camsi', 'CSS0047866' => 'camsi', 'CSS0047884' => 'camsi', 'CSS0048235' => 'camsi', 'CSS0048383' => 'camsi', 'CSS0048438' => 'camsi', 'CSS0048502' => 'camsi', 'CSS0048546' => 'camsi', 'CSS0048653' => 'camsi', 'CSS0048658' => 'camsi', 'CSS0048729' => 'camsi', 'CSS0048867' => 'camsi', 'CSS0048988' => 'camsi', 'CSS0049053' => 'camsi', 'CSS0049099' => 'camsi', 'CSS0049166' => 'camsi', 'CSS0049174' => 'camsi', 'CSS0049212' => 'camsi', 'CSS0049280' => 'camsi', 'CSS0049391' => 'camsi', 'CSS0049546' => 'camsi', 'CSS0049634' => 'camsi', 'CSS0049655' => 'camsi', 'CSS0049813' => 'camsi', 'CSS0049949' => 'camsi', 'CSS0050009' => 'camsi', 'CSS0050118' => 'camsi', 'CSS0050205' => 'camsi', 'CSS0050275' => 'camsi', 'CSS0050480' => 'camsi', 'CSS0050488' => 'camsi', 'CSS0050497' => 'camsi', 'Dinv03126' => 'din', 'Dinv13140' => 'din', 'Dinv13247' => 'din', 'Dinv14217' => 'din', 'EL10Ac9g22435' => 'bvu', 'FAN20G1200' => 'fan', 'PGR142G2516' => 'pgr', 'Prupe.3G160200' => 'ppe', 'Prupe.5G238200' => 'ppe', 'Prupe.7G047500' => 'ppe', 'QL03p045360' => 'qlo', 'QL05p034369' => 'qlo', 'QL05p034412' => 'qlo', 'QL08p017802' => 'qlo', 'QL08p024762' => 'qlo', 'QL10p026237' => 'qlo', 'QL10p032070' => 'qlo', 'QL11p003821' => 'qlo', 'Rhsim04G0057300' => 'rsi', 'Rhsim05G0049200' => 'rsi', 'Rhsim12G0010400' => 'rsi', 'Rhsim12G0012800' => 'rsi', 'TAR624G0483' => 'tar', 'TAR703G0001' => 'tar', 'vmacro05414' => 'vma', 'vmacro07091' => 'vma', 'vmacro07116' => 'vma', 'vmacro08423' => 'vma', 'vmacro09046' => 'vma', 'vmacro14269' => 'vma', 'vmacro16092' => 'vma', 'vmacro17280' => 'vma', 'vmacro19601' => 'vma' ) $gf_id = 'HOM05D001028' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001028' ) $data_identifier = 'HOM05D001028' $data_type = 'gf_id' $species_gene_counts = array( 'aox' => (int) 11, 'ccan' => (int) 6, 'camsi' => (int) 540, 'din' => (int) 4, 'bvu' => (int) 1, 'fan' => (int) 1, 'pgr' => (int) 1, 'ppe' => (int) 3, 'qlo' => (int) 8, 'rsi' => (int) 4, 'tar' => (int) 2, 'vma' => (int) 9 ) $gf_gene_species = 'vma' $gf_gene_id = 'vmacro19601' $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' => 'HOM05D001028', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '590', 'num_species' => '12' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'Aqoxy1G01649' => 'aox', 'Aqoxy1G02950' => 'aox', 'Aqoxy2G01005' => 'aox', 'Aqoxy2G01064' => 'aox', 'Aqoxy3G02267' => 'aox', 'Aqoxy3G02617' => 'aox', 'Aqoxy3G02693' => 'aox', 'Aqoxy5G03425' => 'aox', 'Aqoxy6G02164' => 'aox', 'Aqoxy6G02364' => 'aox', 'Aqoxy7G02284' => 'aox', 'Cc00_g09720' => 'ccan', 'Cc00_g21410' => 'ccan', 'Cc00_g31750' => 'ccan', 'Cc00_g34740' => 'ccan', 'Cc04_g16890' => 'ccan', 'Cc11_g03120' => 'ccan', 'CSS0000222' => 'camsi', 'CSS0000265' => 'camsi', 'CSS0000306' => 'camsi', 'CSS0000326' => 'camsi', 'CSS0000530' => 'camsi', 'CSS0000563' => 'camsi', 'CSS0000584' => 'camsi', 'CSS0000684' => 'camsi', 'CSS0001100' => 'camsi', 'CSS0001311' => 'camsi', 'CSS0001343' => 'camsi', 'CSS0001399' => 'camsi', 'CSS0001475' => 'camsi', 'CSS0001506' => 'camsi', 'CSS0001602' => 'camsi', 'CSS0001681' => 'camsi', 'CSS0001874' => 'camsi', 'CSS0001948' => 'camsi', 'CSS0002022' => 'camsi', 'CSS0002230' => 'camsi', 'CSS0002265' => 'camsi', 'CSS0002277' => 'camsi', 'CSS0002462' => 'camsi', 'CSS0002823' => 'camsi', 'CSS0003091' => 'camsi', 'CSS0003162' => 'camsi', 'CSS0003264' => 'camsi', 'CSS0003355' => 'camsi', 'CSS0003378' => 'camsi', 'CSS0003472' => 'camsi', 'CSS0003500' => 'camsi', 'CSS0003640' => 'camsi', 'CSS0003767' => 'camsi', 'CSS0003894' => 'camsi', 'CSS0003952' => 'camsi', 'CSS0003977' => 'camsi', 'CSS0004028' => 'camsi', 'CSS0004117' => 'camsi', 'CSS0004137' => 'camsi', 'CSS0004176' => 'camsi', 'CSS0004265' => 'camsi', 'CSS0004450' => 'camsi', 'CSS0004468' => 'camsi', 'CSS0004488' => 'camsi', 'CSS0004490' => 'camsi', 'CSS0004632' => 'camsi', 'CSS0004790' => 'camsi', 'CSS0004877' => 'camsi', 'CSS0004920' => 'camsi', 'CSS0004969' => 'camsi', 'CSS0005084' => 'camsi', 'CSS0005101' => 'camsi', 'CSS0005271' => 'camsi', 'CSS0005313' => 'camsi', 'CSS0005331' => 'camsi', 'CSS0005368' => 'camsi', 'CSS0005391' => 'camsi', 'CSS0005437' => 'camsi', 'CSS0005515' => 'camsi', 'CSS0005526' => 'camsi', 'CSS0005532' => 'camsi', 'CSS0005595' => 'camsi', 'CSS0005677' => 'camsi', 'CSS0005838' => 'camsi', 'CSS0005988' => 'camsi', 'CSS0006100' => 'camsi', 'CSS0006128' => 'camsi', 'CSS0006293' => 'camsi', 'CSS0006378' => 'camsi', 'CSS0006400' => 'camsi', 'CSS0006441' => 'camsi', 'CSS0006455' => 'camsi', 'CSS0006480' => 'camsi', 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'CSS0048438' => 'camsi', 'CSS0048502' => 'camsi', 'CSS0048546' => 'camsi', 'CSS0048653' => 'camsi', 'CSS0048658' => 'camsi', 'CSS0048729' => 'camsi', 'CSS0048867' => 'camsi', 'CSS0048988' => 'camsi', 'CSS0049053' => 'camsi', 'CSS0049099' => 'camsi', 'CSS0049166' => 'camsi', 'CSS0049174' => 'camsi', 'CSS0049212' => 'camsi', 'CSS0049280' => 'camsi', 'CSS0049391' => 'camsi', 'CSS0049546' => 'camsi', 'CSS0049634' => 'camsi', 'CSS0049655' => 'camsi', 'CSS0049813' => 'camsi', 'CSS0049949' => 'camsi', 'CSS0050009' => 'camsi', 'CSS0050118' => 'camsi', 'CSS0050205' => 'camsi', 'CSS0050275' => 'camsi', 'CSS0050480' => 'camsi', 'CSS0050488' => 'camsi', 'CSS0050497' => 'camsi', 'Dinv03126' => 'din', 'Dinv13140' => 'din', 'Dinv13247' => 'din', 'Dinv14217' => 'din', 'EL10Ac9g22435' => 'bvu', 'FAN20G1200' => 'fan', 'PGR142G2516' => 'pgr', 'Prupe.3G160200' => 'ppe', 'Prupe.5G238200' => 'ppe', 'Prupe.7G047500' => 'ppe', 'QL03p045360' => 'qlo', 'QL05p034369' => 'qlo', 'QL05p034412' => 'qlo', 'QL08p017802' => 'qlo', 'QL08p024762' => 'qlo', 'QL10p026237' => 'qlo', 'QL10p032070' => 'qlo', 'QL11p003821' => 'qlo', 'Rhsim04G0057300' => 'rsi', 'Rhsim05G0049200' => 'rsi', 'Rhsim12G0010400' => 'rsi', 'Rhsim12G0012800' => 'rsi', 'TAR624G0483' => 'tar', 'TAR703G0001' => 'tar', 'vmacro05414' => 'vma', 'vmacro07091' => 'vma', 'vmacro07116' => 'vma', 'vmacro08423' => 'vma', 'vmacro09046' => 'vma', 'vmacro14269' => 'vma', 'vmacro16092' => 'vma', 'vmacro17280' => 'vma', 'vmacro19601' => 'vma' ), 'gf_id' => 'HOM05D001028', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001028' ), 'data_identifier' => 'HOM05D001028', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001028', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '590', 'num_species' => '12' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'Aqoxy1G01649' => 'aox', 'Aqoxy1G02950' => 'aox', 'Aqoxy2G01005' => 'aox', 'Aqoxy2G01064' => 'aox', 'Aqoxy3G02267' => 'aox', 'Aqoxy3G02617' => 'aox', 'Aqoxy3G02693' => 'aox', 'Aqoxy5G03425' => 'aox', 'Aqoxy6G02164' => 'aox', 'Aqoxy6G02364' => 'aox', 'Aqoxy7G02284' => 'aox', 'Cc00_g09720' => 'ccan', 'Cc00_g21410' => 'ccan', 'Cc00_g31750' => 'ccan', 'Cc00_g34740' => 'ccan', 'Cc04_g16890' => 'ccan', 'Cc11_g03120' => 'ccan', 'CSS0000222' => 'camsi', 'CSS0000265' => 'camsi', 'CSS0000306' => 'camsi', 'CSS0000326' => 'camsi', 'CSS0000530' => 'camsi', 'CSS0000563' => 'camsi', 'CSS0000584' => 'camsi', 'CSS0000684' => 'camsi', 'CSS0001100' => 'camsi', 'CSS0001311' => 'camsi', 'CSS0001343' => 'camsi', 'CSS0001399' => 'camsi', 'CSS0001475' => 'camsi', 'CSS0001506' => 'camsi', 'CSS0001602' => 'camsi', 'CSS0001681' => 'camsi', 'CSS0001874' => 'camsi', 'CSS0001948' => 'camsi', 'CSS0002022' => 'camsi', 'CSS0002230' => 'camsi', 'CSS0002265' => 'camsi', 'CSS0002277' => 'camsi', 'CSS0002462' => 'camsi', 'CSS0002823' => 'camsi', 'CSS0003091' => 'camsi', 'CSS0003162' => 'camsi', 'CSS0003264' => 'camsi', 'CSS0003355' => 'camsi', 'CSS0003378' => 'camsi', 'CSS0003472' => 'camsi', 'CSS0003500' => 'camsi', 'CSS0003640' => 'camsi', 'CSS0003767' => 'camsi', 'CSS0003894' => 'camsi', 'CSS0003952' => 'camsi', 'CSS0003977' => 'camsi', 'CSS0004028' => 'camsi', 'CSS0004117' => 'camsi', 'CSS0004137' => 'camsi', 'CSS0004176' => 'camsi', 'CSS0004265' => 'camsi', 'CSS0004450' => 'camsi', 'CSS0004468' => 'camsi', 'CSS0004488' => 'camsi', 'CSS0004490' => 'camsi', 'CSS0004632' => 'camsi', 'CSS0004790' => 'camsi', 'CSS0004877' => 'camsi', 'CSS0004920' => 'camsi', 'CSS0004969' => 'camsi', 'CSS0005084' => 'camsi', 'CSS0005101' => 'camsi', 'CSS0005271' => 'camsi', 'CSS0005313' => 'camsi', 'CSS0005331' => 'camsi', 'CSS0005368' => 'camsi', 'CSS0005391' => 'camsi', 'CSS0005437' => 'camsi', 'CSS0005515' => 'camsi', 'CSS0005526' => 'camsi', 'CSS0005532' => 'camsi', 'CSS0005595' => 'camsi', 'CSS0005677' => 'camsi', 'CSS0005838' => 'camsi', 'CSS0005988' => 'camsi', 'CSS0006100' => 'camsi', 'CSS0006128' => 'camsi', 'CSS0006293' => 'camsi', 'CSS0006378' => 'camsi', 'CSS0006400' => 'camsi', 'CSS0006441' => 'camsi', 'CSS0006455' => 'camsi', 'CSS0006480' => 'camsi', 'CSS0006483' => 'camsi', 'CSS0006538' => 'camsi', 'CSS0006582' => 'camsi', 'CSS0006632' => 'camsi', 'CSS0006771' => 'camsi', 'CSS0006803' => 'camsi', 'CSS0006852' => 'camsi', 'CSS0006861' => 'camsi', 'CSS0006910' => 'camsi', 'CSS0007037' => 'camsi', 'CSS0007066' => 'camsi', 'CSS0007072' => 'camsi', 'CSS0007109' => 'camsi', 'CSS0007193' => 'camsi', 'CSS0007319' => 'camsi', 'CSS0007336' => 'camsi', 'CSS0007377' => 'camsi', 'CSS0007659' => 'camsi', 'CSS0007701' => 'camsi', 'CSS0007711' => 'camsi', 'CSS0007809' => 'camsi', 'CSS0008045' => 'camsi', 'CSS0008050' => 'camsi', 'CSS0008206' => 'camsi', 'CSS0008251' => 'camsi', 'CSS0008252' => 'camsi', 'CSS0008279' => 'camsi', 'CSS0008482' => 'camsi', 'CSS0008583' => 'camsi', 'CSS0008699' => 'camsi', 'CSS0008798' => 'camsi', 'CSS0008971' => 'camsi', 'CSS0009019' => 'camsi', 'CSS0009191' => 'camsi', 'CSS0009241' => 'camsi', 'CSS0009246' => 'camsi', 'CSS0009399' => 'camsi', 'CSS0009654' => 'camsi', 'CSS0009722' => 'camsi', 'CSS0009920' => 'camsi', 'CSS0009986' => 'camsi', 'CSS0010182' => 'camsi', 'CSS0010202' => 'camsi', 'CSS0010330' => 'camsi', 'CSS0010362' => 'camsi', 'CSS0010456' => 'camsi', 'CSS0010472' => 'camsi', 'CSS0010507' => 'camsi', 'CSS0010512' => 'camsi', 'CSS0010520' => 'camsi', 'CSS0010617' => 'camsi', 'CSS0010706' => 'camsi', 'CSS0010747' => 'camsi', 'CSS0010816' => 'camsi', 'CSS0011020' => 'camsi', 'CSS0011115' => 'camsi', 'CSS0011383' => 'camsi', 'CSS0011491' => 'camsi', 'CSS0011602' => 'camsi', 'CSS0011605' => 'camsi', 'CSS0011625' => 'camsi', 'CSS0011654' => 'camsi', 'CSS0011781' => 'camsi', 'CSS0011853' => 'camsi', 'CSS0011898' => 'camsi', 'CSS0011933' => 'camsi', 'CSS0011996' => 'camsi', 'CSS0012066' => 'camsi', 'CSS0012097' => 'camsi', 'CSS0012108' => 'camsi', 'CSS0012226' => 'camsi', 'CSS0012248' => 'camsi', 'CSS0012331' => 'camsi', 'CSS0012797' => 'camsi', 'CSS0012818' => 'camsi', 'CSS0012904' => 'camsi', 'CSS0013001' => 'camsi', 'CSS0013022' => 'camsi', 'CSS0013172' => 'camsi', 'CSS0013244' => 'camsi', 'CSS0013267' => 'camsi', 'CSS0013275' => 'camsi', 'CSS0013324' => 'camsi', 'CSS0013334' => 'camsi', 'CSS0013394' => 'camsi', 'CSS0013549' => 'camsi', 'CSS0013689' => 'camsi', 'CSS0014026' => 'camsi', 'CSS0014049' => 'camsi', 'CSS0014144' => 'camsi', 'CSS0014354' => 'camsi', 'CSS0014579' => 'camsi', 'CSS0014648' => 'camsi', 'CSS0014902' => 'camsi', 'CSS0014979' => 'camsi', 'CSS0015278' => 'camsi', 'CSS0015310' => 'camsi', 'CSS0015364' => 'camsi', 'CSS0015455' => 'camsi', 'CSS0015693' => 'camsi', 'CSS0015774' => 'camsi', 'CSS0015795' => 'camsi', 'CSS0015952' => 'camsi', 'CSS0016104' => 'camsi', 'CSS0016241' => 'camsi', 'CSS0016303' => 'camsi', 'CSS0016490' => 'camsi', 'CSS0016832' => 'camsi', 'CSS0016845' => 'camsi', 'CSS0016914' => 'camsi', 'CSS0016946' => 'camsi', 'CSS0017102' => 'camsi', 'CSS0017193' => 'camsi', 'CSS0017528' => 'camsi', 'CSS0017619' => 'camsi', 'CSS0017679' => 'camsi', 'CSS0017816' => 'camsi', 'CSS0017880' => 'camsi', 'CSS0018106' => 'camsi', 'CSS0018162' => 'camsi', 'CSS0018304' => 'camsi', 'CSS0018406' => 'camsi', 'CSS0018481' => 'camsi', 'CSS0018511' => 'camsi', 'CSS0018596' => 'camsi', 'CSS0018727' => 'camsi', 'CSS0018751' => 'camsi', 'CSS0018777' => 'camsi', 'CSS0018798' => 'camsi', 'CSS0019137' => 'camsi', 'CSS0019177' => 'camsi', 'CSS0019217' => 'camsi', 'CSS0019361' => 'camsi', 'CSS0019516' => 'camsi', 'CSS0019538' => 'camsi', 'CSS0019560' => 'camsi', 'CSS0019819' => 'camsi', 'CSS0019837' => 'camsi', 'CSS0019915' => 'camsi', 'CSS0019925' => 'camsi', 'CSS0020112' => 'camsi', 'CSS0020160' => 'camsi', 'CSS0020378' => 'camsi', 'CSS0020388' => 'camsi', 'CSS0020452' => 'camsi', 'CSS0020588' => 'camsi', 'CSS0020661' => 'camsi', 'CSS0020886' => 'camsi', 'CSS0020973' => 'camsi', 'CSS0021035' => 'camsi', 'CSS0021111' => 'camsi', 'CSS0021131' => 'camsi', 'CSS0021151' => 'camsi', 'CSS0021228' => 'camsi', 'CSS0021397' => 'camsi', 'CSS0021420' => 'camsi', 'CSS0021464' => 'camsi', 'CSS0021547' => 'camsi', 'CSS0021608' => 'camsi', 'CSS0021740' => 'camsi', 'CSS0021826' => 'camsi', 'CSS0021904' => 'camsi', 'CSS0021941' => 'camsi', 'CSS0022189' => 'camsi', 'CSS0022199' => 'camsi', 'CSS0022502' => 'camsi', 'CSS0022531' => 'camsi', 'CSS0022581' => 'camsi', 'CSS0022612' => 'camsi', 'CSS0022621' => 'camsi', 'CSS0022815' => 'camsi', 'CSS0022936' => 'camsi', 'CSS0022964' => 'camsi', 'CSS0022985' => 'camsi', 'CSS0023002' => 'camsi', 'CSS0023006' => 'camsi', 'CSS0023024' => 'camsi', 'CSS0023489' => 'camsi', 'CSS0023593' => 'camsi', 'CSS0023621' => 'camsi', 'CSS0023743' => 'camsi', 'CSS0023804' => 'camsi', 'CSS0023805' => 'camsi', 'CSS0023908' => 'camsi', 'CSS0023938' => 'camsi', 'CSS0023981' => 'camsi', 'CSS0024027' => 'camsi', 'CSS0024169' => 'camsi', 'CSS0024193' => 'camsi', 'CSS0024269' => 'camsi', 'CSS0024336' => 'camsi', 'CSS0024337' => 'camsi', 'CSS0024548' => 'camsi', 'CSS0024564' => 'camsi', 'CSS0024585' => 'camsi', 'CSS0024738' => 'camsi', 'CSS0024833' => 'camsi', 'CSS0024846' => 'camsi', 'CSS0024957' => 'camsi', 'CSS0024974' => 'camsi', 'CSS0025005' => 'camsi', 'CSS0025235' => 'camsi', 'CSS0025465' => 'camsi', 'CSS0025633' => 'camsi', 'CSS0025688' => 'camsi', 'CSS0025759' => 'camsi', 'CSS0025774' => 'camsi', 'CSS0025801' => 'camsi', 'CSS0025942' => 'camsi', 'CSS0026083' => 'camsi', 'CSS0026194' => 'camsi', 'CSS0026230' => 'camsi', 'CSS0026398' => 'camsi', 'CSS0026419' => 'camsi', 'CSS0026679' => 'camsi', 'CSS0026719' => 'camsi', 'CSS0026795' => 'camsi', 'CSS0026835' => 'camsi', 'CSS0026930' => 'camsi', 'CSS0027053' => 'camsi', 'CSS0027130' => 'camsi', 'CSS0027192' => 'camsi', 'CSS0027454' => 'camsi', 'CSS0027467' => 'camsi', 'CSS0027521' => 'camsi', 'CSS0027662' => 'camsi', 'CSS0027795' => 'camsi', 'CSS0027835' => 'camsi', 'CSS0027966' => 'camsi', 'CSS0028090' => 'camsi', 'CSS0028134' => 'camsi', 'CSS0028205' => 'camsi', 'CSS0028263' => 'camsi', 'CSS0028363' => 'camsi', 'CSS0028598' => 'camsi', 'CSS0029175' => 'camsi', 'CSS0029191' => 'camsi', 'CSS0029424' => 'camsi', 'CSS0029479' => 'camsi', 'CSS0029496' => 'camsi', 'CSS0029633' => 'camsi', 'CSS0029837' => 'camsi', 'CSS0029844' => 'camsi', 'CSS0029863' => 'camsi', 'CSS0029874' => 'camsi', 'CSS0029959' => 'camsi', 'CSS0030001' => 'camsi', 'CSS0030093' => 'camsi', 'CSS0030199' => 'camsi', 'CSS0030200' => 'camsi', 'CSS0030427' => 'camsi', 'CSS0030476' => 'camsi', 'CSS0030636' => 'camsi', 'CSS0030673' => 'camsi', 'CSS0030766' => 'camsi', 'CSS0030775' => 'camsi', 'CSS0030858' => 'camsi', 'CSS0030873' => 'camsi', 'CSS0030929' => 'camsi', 'CSS0031028' => 'camsi', 'CSS0031129' => 'camsi', 'CSS0031164' => 'camsi', 'CSS0031340' => 'camsi', 'CSS0031368' => 'camsi', 'CSS0031395' => 'camsi', 'CSS0031596' => 'camsi', 'CSS0031727' => 'camsi', 'CSS0032011' => 'camsi', 'CSS0032160' => 'camsi', 'CSS0032538' => 'camsi', 'CSS0032576' => 'camsi', 'CSS0032603' => 'camsi', 'CSS0032640' => 'camsi', 'CSS0032704' => 'camsi', 'CSS0032851' => 'camsi', 'CSS0032973' => 'camsi', 'CSS0033048' => 'camsi', 'CSS0033082' => 'camsi', 'CSS0033157' => 'camsi', 'CSS0033253' => 'camsi', 'CSS0033347' => 'camsi', 'CSS0033601' => 'camsi', 'CSS0033820' => 'camsi', 'CSS0033881' => 'camsi', 'CSS0033934' => 'camsi', 'CSS0034143' => 'camsi', 'CSS0034176' => 'camsi', 'CSS0034201' => 'camsi', 'CSS0034269' => 'camsi', 'CSS0034303' => 'camsi', 'CSS0034463' => 'camsi', 'CSS0034470' => 'camsi', 'CSS0034514' => 'camsi', 'CSS0034525' => 'camsi', 'CSS0034726' => 'camsi', 'CSS0034727' => 'camsi', 'CSS0034737' => 'camsi', 'CSS0034768' => 'camsi', 'CSS0034890' => 'camsi', 'CSS0034943' => 'camsi', 'CSS0034957' => 'camsi', 'CSS0034973' => 'camsi', 'CSS0035178' => 'camsi', 'CSS0035260' => 'camsi', 'CSS0035316' => 'camsi', 'CSS0035347' => 'camsi', 'CSS0035360' => 'camsi', 'CSS0035380' => 'camsi', 'CSS0035429' => 'camsi', 'CSS0035446' => 'camsi', 'CSS0035737' => 'camsi', 'CSS0035852' => 'camsi', 'CSS0035967' => 'camsi', 'CSS0036001' => 'camsi', 'CSS0036044' => 'camsi', 'CSS0036221' => 'camsi', 'CSS0036333' => 'camsi', 'CSS0036435' => 'camsi', 'CSS0036843' => 'camsi', 'CSS0036846' => 'camsi', 'CSS0037097' => 'camsi', 'CSS0037263' => 'camsi', 'CSS0037370' => 'camsi', 'CSS0037410' => 'camsi', 'CSS0037449' => 'camsi', 'CSS0037603' => 'camsi', 'CSS0037851' => 'camsi', 'CSS0037891' => 'camsi', 'CSS0037996' => 'camsi', 'CSS0038222' => 'camsi', 'CSS0038433' => 'camsi', 'CSS0038441' => 'camsi', 'CSS0038718' => 'camsi', 'CSS0038890' => 'camsi', 'CSS0039049' => 'camsi', 'CSS0039145' => 'camsi', 'CSS0039243' => 'camsi', 'CSS0039294' => 'camsi', 'CSS0039324' => 'camsi', 'CSS0039376' => 'camsi', 'CSS0039475' => 'camsi', 'CSS0039539' => 'camsi', 'CSS0039546' => 'camsi', 'CSS0039567' => 'camsi', 'CSS0039599' => 'camsi', 'CSS0039763' => 'camsi', 'CSS0039863' => 'camsi', 'CSS0040107' => 'camsi', 'CSS0040124' => 'camsi', 'CSS0040151' => 'camsi', 'CSS0040165' => 'camsi', 'CSS0040309' => 'camsi', 'CSS0040318' => 'camsi', 'CSS0040347' => 'camsi', 'CSS0040371' => 'camsi', 'CSS0040456' => 'camsi', 'CSS0040551' => 'camsi', 'CSS0040975' => 'camsi', 'CSS0040981' => 'camsi', 'CSS0041299' => 'camsi', 'CSS0041493' => 'camsi', 'CSS0041658' => 'camsi', 'CSS0041899' => 'camsi', 'CSS0041927' => 'camsi', 'CSS0042016' => 'camsi', 'CSS0042034' => 'camsi', 'CSS0042103' => 'camsi', 'CSS0042172' => 'camsi', 'CSS0042198' => 'camsi', 'CSS0042201' => 'camsi', 'CSS0042308' => 'camsi', 'CSS0042329' => 'camsi', 'CSS0042348' => 'camsi', 'CSS0042349' => 'camsi', 'CSS0042489' => 'camsi', 'CSS0042575' => 'camsi', 'CSS0042624' => 'camsi', 'CSS0042660' => 'camsi', 'CSS0042694' => 'camsi', 'CSS0042995' => 'camsi', 'CSS0043079' => 'camsi', 'CSS0043165' => 'camsi', 'CSS0043171' => 'camsi', 'CSS0043314' => 'camsi', 'CSS0043361' => 'camsi', 'CSS0043375' => 'camsi', 'CSS0043518' => 'camsi', 'CSS0043536' => 'camsi', 'CSS0043678' => 'camsi', 'CSS0043765' => 'camsi', 'CSS0043897' => 'camsi', 'CSS0043944' => 'camsi', 'CSS0044126' => 'camsi', 'CSS0044136' => 'camsi', 'CSS0044179' => 'camsi', 'CSS0044290' => 'camsi', 'CSS0044437' => 'camsi', 'CSS0044502' => 'camsi', 'CSS0044603' => 'camsi', 'CSS0044680' => 'camsi', 'CSS0044685' => 'camsi', 'CSS0044700' => 'camsi', 'CSS0044888' => 'camsi', 'CSS0044923' => 'camsi', 'CSS0044926' => 'camsi', 'CSS0044979' => 'camsi', 'CSS0045049' => 'camsi', 'CSS0045132' => 'camsi', 'CSS0045161' => 'camsi', 'CSS0045219' => 'camsi', 'CSS0045230' => 'camsi', 'CSS0045259' => 'camsi', 'CSS0045324' => 'camsi', 'CSS0045368' => 'camsi', 'CSS0045435' => 'camsi', 'CSS0045856' => 'camsi', 'CSS0045955' => 'camsi', 'CSS0046158' => 'camsi', 'CSS0046334' => 'camsi', 'CSS0046365' => 'camsi', 'CSS0046396' => 'camsi', 'CSS0046400' => 'camsi', 'CSS0046445' => 'camsi', 'CSS0046493' => 'camsi', 'CSS0046640' => 'camsi', 'CSS0046657' => 'camsi', 'CSS0046702' => 'camsi', 'CSS0047208' => 'camsi', 'CSS0047368' => 'camsi', 'CSS0047403' => 'camsi', 'CSS0047417' => 'camsi', 'CSS0047469' => 'camsi', 'CSS0047480' => 'camsi', 'CSS0047482' => 'camsi', 'CSS0047693' => 'camsi', 'CSS0047766' => 'camsi', 'CSS0047866' => 'camsi', 'CSS0047884' => 'camsi', 'CSS0048235' => 'camsi', 'CSS0048383' => 'camsi', 'CSS0048438' => 'camsi', 'CSS0048502' => 'camsi', 'CSS0048546' => 'camsi', 'CSS0048653' => 'camsi', 'CSS0048658' => 'camsi', 'CSS0048729' => 'camsi', 'CSS0048867' => 'camsi', 'CSS0048988' => 'camsi', 'CSS0049053' => 'camsi', 'CSS0049099' => 'camsi', 'CSS0049166' => 'camsi', 'CSS0049174' => 'camsi', 'CSS0049212' => 'camsi', 'CSS0049280' => 'camsi', 'CSS0049391' => 'camsi', 'CSS0049546' => 'camsi', 'CSS0049634' => 'camsi', 'CSS0049655' => 'camsi', 'CSS0049813' => 'camsi', 'CSS0049949' => 'camsi', 'CSS0050009' => 'camsi', 'CSS0050118' => 'camsi', 'CSS0050205' => 'camsi', 'CSS0050275' => 'camsi', 'CSS0050480' => 'camsi', 'CSS0050488' => 'camsi', 'CSS0050497' => 'camsi', 'Dinv03126' => 'din', 'Dinv13140' => 'din', 'Dinv13247' => 'din', 'Dinv14217' => 'din', 'EL10Ac9g22435' => 'bvu', 'FAN20G1200' => 'fan', 'PGR142G2516' => 'pgr', 'Prupe.3G160200' => 'ppe', 'Prupe.5G238200' => 'ppe', 'Prupe.7G047500' => 'ppe', 'QL03p045360' => 'qlo', 'QL05p034369' => 'qlo', 'QL05p034412' => 'qlo', 'QL08p017802' => 'qlo', 'QL08p024762' => 'qlo', 'QL10p026237' => 'qlo', 'QL10p032070' => 'qlo', 'QL11p003821' => 'qlo', 'Rhsim04G0057300' => 'rsi', 'Rhsim05G0049200' => 'rsi', 'Rhsim12G0010400' => 'rsi', 'Rhsim12G0012800' => 'rsi', 'TAR624G0483' => 'tar', 'TAR703G0001' => 'tar', 'vmacro05414' => 'vma', 'vmacro07091' => 'vma', 'vmacro07116' => 'vma', 'vmacro08423' => 'vma', 'vmacro09046' => 'vma', 'vmacro14269' => 'vma', 'vmacro16092' => 'vma', 'vmacro17280' => 'vma', 'vmacro19601' => 'vma' ) $gf_id = 'HOM05D001028' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001028' ) $data_identifier = 'HOM05D001028' $data_type = 'gf_id' $species_gene_counts = array( 'aox' => (int) 11, 'ccan' => (int) 6, 'camsi' => (int) 540, 'din' => (int) 4, 'bvu' => (int) 1, 'fan' => (int) 1, 'pgr' => (int) 1, 'ppe' => (int) 3, 'qlo' => (int) 8, 'rsi' => (int) 4, 'tar' => (int) 2, 'vma' => (int) 9 ) $gf_gene_species = 'vma' $gf_gene_id = 'vmacro19601' $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' => 'HOM05D001028', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '590', 'num_species' => '12' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'Aqoxy1G01649' => 'aox', 'Aqoxy1G02950' => 'aox', 'Aqoxy2G01005' => 'aox', 'Aqoxy2G01064' => 'aox', 'Aqoxy3G02267' => 'aox', 'Aqoxy3G02617' => 'aox', 'Aqoxy3G02693' => 'aox', 'Aqoxy5G03425' => 'aox', 'Aqoxy6G02164' => 'aox', 'Aqoxy6G02364' => 'aox', 'Aqoxy7G02284' => 'aox', 'Cc00_g09720' => 'ccan', 'Cc00_g21410' => 'ccan', 'Cc00_g31750' => 'ccan', 'Cc00_g34740' => 'ccan', 'Cc04_g16890' => 'ccan', 'Cc11_g03120' => 'ccan', 'CSS0000222' => 'camsi', 'CSS0000265' => 'camsi', 'CSS0000306' => 'camsi', 'CSS0000326' => 'camsi', 'CSS0000530' => 'camsi', 'CSS0000563' => 'camsi', 'CSS0000584' => 'camsi', 'CSS0000684' => 'camsi', 'CSS0001100' => 'camsi', 'CSS0001311' => 'camsi', 'CSS0001343' => 'camsi', 'CSS0001399' => 'camsi', 'CSS0001475' => 'camsi', 'CSS0001506' => 'camsi', 'CSS0001602' => 'camsi', 'CSS0001681' => 'camsi', 'CSS0001874' => 'camsi', 'CSS0001948' => 'camsi', 'CSS0002022' => 'camsi', 'CSS0002230' => 'camsi', 'CSS0002265' => 'camsi', 'CSS0002277' => 'camsi', 'CSS0002462' => 'camsi', 'CSS0002823' => 'camsi', 'CSS0003091' => 'camsi', 'CSS0003162' => 'camsi', 'CSS0003264' => 'camsi', 'CSS0003355' => 'camsi', 'CSS0003378' => 'camsi', 'CSS0003472' => 'camsi', 'CSS0003500' => 'camsi', 'CSS0003640' => 'camsi', 'CSS0003767' => 'camsi', 'CSS0003894' => 'camsi', 'CSS0003952' => 'camsi', 'CSS0003977' => 'camsi', 'CSS0004028' => 'camsi', 'CSS0004117' => 'camsi', 'CSS0004137' => 'camsi', 'CSS0004176' => 'camsi', 'CSS0004265' => 'camsi', 'CSS0004450' => 'camsi', 'CSS0004468' => 'camsi', 'CSS0004488' => 'camsi', 'CSS0004490' => 'camsi', 'CSS0004632' => 'camsi', 'CSS0004790' => 'camsi', 'CSS0004877' => 'camsi', 'CSS0004920' => 'camsi', 'CSS0004969' => 'camsi', 'CSS0005084' => 'camsi', 'CSS0005101' => 'camsi', 'CSS0005271' => 'camsi', 'CSS0005313' => 'camsi', 'CSS0005331' => 'camsi', 'CSS0005368' => 'camsi', 'CSS0005391' => 'camsi', 'CSS0005437' => 'camsi', 'CSS0005515' => 'camsi', 'CSS0005526' => 'camsi', 'CSS0005532' => 'camsi', 'CSS0005595' => 'camsi', 'CSS0005677' => 'camsi', 'CSS0005838' => 'camsi', 'CSS0005988' => 'camsi', 'CSS0006100' => 'camsi', 'CSS0006128' => 'camsi', 'CSS0006293' => 'camsi', 'CSS0006378' => 'camsi', 'CSS0006400' => 'camsi', 'CSS0006441' => 'camsi', 'CSS0006455' => 'camsi', 'CSS0006480' => 'camsi', 'CSS0006483' => 'camsi', 'CSS0006538' => 'camsi', 'CSS0006582' => 'camsi', 'CSS0006632' => 'camsi', 'CSS0006771' => 'camsi', 'CSS0006803' => 'camsi', 'CSS0006852' => 'camsi', 'CSS0006861' => 'camsi', 'CSS0006910' => 'camsi', 'CSS0007037' => 'camsi', 'CSS0007066' => 'camsi', 'CSS0007072' => 'camsi', 'CSS0007109' => 'camsi', 'CSS0007193' => 'camsi', 'CSS0007319' => 'camsi', 'CSS0007336' => 'camsi', 'CSS0007377' => 'camsi', 'CSS0007659' => 'camsi', 'CSS0007701' => 'camsi', 'CSS0007711' => 'camsi', 'CSS0007809' => 'camsi', 'CSS0008045' => 'camsi', 'CSS0008050' => 'camsi', 'CSS0008206' => 'camsi', 'CSS0008251' => 'camsi', 'CSS0008252' => 'camsi', 'CSS0008279' => 'camsi', 'CSS0008482' => 'camsi', 'CSS0008583' => 'camsi', 'CSS0008699' => 'camsi', 'CSS0008798' => 'camsi', 'CSS0008971' => 'camsi', 'CSS0009019' => 'camsi', 'CSS0009191' => 'camsi', 'CSS0009241' => 'camsi', 'CSS0009246' => 'camsi', 'CSS0009399' => 'camsi', 'CSS0009654' => 'camsi', 'CSS0009722' => 'camsi', 'CSS0009920' => 'camsi', 'CSS0009986' => 'camsi', 'CSS0010182' => 'camsi', 'CSS0010202' => 'camsi', 'CSS0010330' => 'camsi', 'CSS0010362' => 'camsi', 'CSS0010456' => 'camsi', 'CSS0010472' => 'camsi', 'CSS0010507' => 'camsi', 'CSS0010512' => 'camsi', 'CSS0010520' => 'camsi', 'CSS0010617' => 'camsi', 'CSS0010706' => 'camsi', 'CSS0010747' => 'camsi', 'CSS0010816' => 'camsi', 'CSS0011020' => 'camsi', 'CSS0011115' => 'camsi', 'CSS0011383' => 'camsi', 'CSS0011491' => 'camsi', 'CSS0011602' => 'camsi', 'CSS0011605' => 'camsi', 'CSS0011625' => 'camsi', 'CSS0011654' => 'camsi', 'CSS0011781' => 'camsi', 'CSS0011853' => 'camsi', 'CSS0011898' => 'camsi', 'CSS0011933' => 'camsi', 'CSS0011996' => 'camsi', 'CSS0012066' => 'camsi', 'CSS0012097' => 'camsi', 'CSS0012108' => 'camsi', 'CSS0012226' => 'camsi', 'CSS0012248' => 'camsi', 'CSS0012331' => 'camsi', 'CSS0012797' => 'camsi', 'CSS0012818' => 'camsi', 'CSS0012904' => 'camsi', 'CSS0013001' => 'camsi', 'CSS0013022' => 'camsi', 'CSS0013172' => 'camsi', 'CSS0013244' => 'camsi', 'CSS0013267' => 'camsi', 'CSS0013275' => 'camsi', 'CSS0013324' => 'camsi', 'CSS0013334' => 'camsi', 'CSS0013394' => 'camsi', 'CSS0013549' => 'camsi', 'CSS0013689' => 'camsi', 'CSS0014026' => 'camsi', 'CSS0014049' => 'camsi', 'CSS0014144' => 'camsi', 'CSS0014354' => 'camsi', 'CSS0014579' => 'camsi', 'CSS0014648' => 'camsi', 'CSS0014902' => 'camsi', 'CSS0014979' => 'camsi', 'CSS0015278' => 'camsi', 'CSS0015310' => 'camsi', 'CSS0015364' => 'camsi', 'CSS0015455' => 'camsi', 'CSS0015693' => 'camsi', 'CSS0015774' => 'camsi', 'CSS0015795' => 'camsi', 'CSS0015952' => 'camsi', 'CSS0016104' => 'camsi', 'CSS0016241' => 'camsi', 'CSS0016303' => 'camsi', 'CSS0016490' => 'camsi', 'CSS0016832' => 'camsi', 'CSS0016845' => 'camsi', 'CSS0016914' => 'camsi', 'CSS0016946' => 'camsi', 'CSS0017102' => 'camsi', 'CSS0017193' => 'camsi', 'CSS0017528' => 'camsi', 'CSS0017619' => 'camsi', 'CSS0017679' => 'camsi', 'CSS0017816' => 'camsi', 'CSS0017880' => 'camsi', 'CSS0018106' => 'camsi', 'CSS0018162' => 'camsi', 'CSS0018304' => 'camsi', 'CSS0018406' => 'camsi', 'CSS0018481' => 'camsi', 'CSS0018511' => 'camsi', 'CSS0018596' => 'camsi', 'CSS0018727' => 'camsi', 'CSS0018751' => 'camsi', 'CSS0018777' => 'camsi', 'CSS0018798' => 'camsi', 'CSS0019137' => 'camsi', 'CSS0019177' => 'camsi', 'CSS0019217' => 'camsi', 'CSS0019361' => 'camsi', 'CSS0019516' => 'camsi', 'CSS0019538' => 'camsi', 'CSS0019560' => 'camsi', 'CSS0019819' => 'camsi', 'CSS0019837' => 'camsi', 'CSS0019915' => 'camsi', 'CSS0019925' => 'camsi', 'CSS0020112' => 'camsi', 'CSS0020160' => 'camsi', 'CSS0020378' => 'camsi', 'CSS0020388' => 'camsi', 'CSS0020452' => 'camsi', 'CSS0020588' => 'camsi', 'CSS0020661' => 'camsi', 'CSS0020886' => 'camsi', 'CSS0020973' => 'camsi', 'CSS0021035' => 'camsi', 'CSS0021111' => 'camsi', 'CSS0021131' => 'camsi', 'CSS0021151' => 'camsi', 'CSS0021228' => 'camsi', 'CSS0021397' => 'camsi', 'CSS0021420' => 'camsi', 'CSS0021464' => 'camsi', 'CSS0021547' => 'camsi', 'CSS0021608' => 'camsi', 'CSS0021740' => 'camsi', 'CSS0021826' => 'camsi', 'CSS0021904' => 'camsi', 'CSS0021941' => 'camsi', 'CSS0022189' => 'camsi', 'CSS0022199' => 'camsi', 'CSS0022502' => 'camsi', 'CSS0022531' => 'camsi', 'CSS0022581' => 'camsi', 'CSS0022612' => 'camsi', 'CSS0022621' => 'camsi', 'CSS0022815' => 'camsi', 'CSS0022936' => 'camsi', 'CSS0022964' => 'camsi', 'CSS0022985' => 'camsi', 'CSS0023002' => 'camsi', 'CSS0023006' => 'camsi', 'CSS0023024' => 'camsi', 'CSS0023489' => 'camsi', 'CSS0023593' => 'camsi', 'CSS0023621' => 'camsi', 'CSS0023743' => 'camsi', 'CSS0023804' => 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'camsi', 'CSS0031340' => 'camsi', 'CSS0031368' => 'camsi', 'CSS0031395' => 'camsi', 'CSS0031596' => 'camsi', 'CSS0031727' => 'camsi', 'CSS0032011' => 'camsi', 'CSS0032160' => 'camsi', 'CSS0032538' => 'camsi', 'CSS0032576' => 'camsi', 'CSS0032603' => 'camsi', 'CSS0032640' => 'camsi', 'CSS0032704' => 'camsi', 'CSS0032851' => 'camsi', 'CSS0032973' => 'camsi', 'CSS0033048' => 'camsi', 'CSS0033082' => 'camsi', 'CSS0033157' => 'camsi', 'CSS0033253' => 'camsi', 'CSS0033347' => 'camsi', 'CSS0033601' => 'camsi', 'CSS0033820' => 'camsi', 'CSS0033881' => 'camsi', 'CSS0033934' => 'camsi', 'CSS0034143' => 'camsi', 'CSS0034176' => 'camsi', 'CSS0034201' => 'camsi', 'CSS0034269' => 'camsi', 'CSS0034303' => 'camsi', 'CSS0034463' => 'camsi', 'CSS0034470' => 'camsi', 'CSS0034514' => 'camsi', 'CSS0034525' => 'camsi', 'CSS0034726' => 'camsi', 'CSS0034727' => 'camsi', 'CSS0034737' => 'camsi', 'CSS0034768' => 'camsi', 'CSS0034890' => 'camsi', 'CSS0034943' => 'camsi', 'CSS0034957' => 'camsi', 'CSS0034973' => 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'camsi', 'CSS0039546' => 'camsi', 'CSS0039567' => 'camsi', 'CSS0039599' => 'camsi', 'CSS0039763' => 'camsi', 'CSS0039863' => 'camsi', 'CSS0040107' => 'camsi', 'CSS0040124' => 'camsi', 'CSS0040151' => 'camsi', 'CSS0040165' => 'camsi', 'CSS0040309' => 'camsi', 'CSS0040318' => 'camsi', 'CSS0040347' => 'camsi', 'CSS0040371' => 'camsi', 'CSS0040456' => 'camsi', 'CSS0040551' => 'camsi', 'CSS0040975' => 'camsi', 'CSS0040981' => 'camsi', 'CSS0041299' => 'camsi', 'CSS0041493' => 'camsi', 'CSS0041658' => 'camsi', 'CSS0041899' => 'camsi', 'CSS0041927' => 'camsi', 'CSS0042016' => 'camsi', 'CSS0042034' => 'camsi', 'CSS0042103' => 'camsi', 'CSS0042172' => 'camsi', 'CSS0042198' => 'camsi', 'CSS0042201' => 'camsi', 'CSS0042308' => 'camsi', 'CSS0042329' => 'camsi', 'CSS0042348' => 'camsi', 'CSS0042349' => 'camsi', 'CSS0042489' => 'camsi', 'CSS0042575' => 'camsi', 'CSS0042624' => 'camsi', 'CSS0042660' => 'camsi', 'CSS0042694' => 'camsi', 'CSS0042995' => 'camsi', 'CSS0043079' => 'camsi', 'CSS0043165' => 'camsi', 'CSS0043171' => 'camsi', 'CSS0043314' => 'camsi', 'CSS0043361' => 'camsi', 'CSS0043375' => 'camsi', 'CSS0043518' => 'camsi', 'CSS0043536' => 'camsi', 'CSS0043678' => 'camsi', 'CSS0043765' => 'camsi', 'CSS0043897' => 'camsi', 'CSS0043944' => 'camsi', 'CSS0044126' => 'camsi', 'CSS0044136' => 'camsi', 'CSS0044179' => 'camsi', 'CSS0044290' => 'camsi', 'CSS0044437' => 'camsi', 'CSS0044502' => 'camsi', 'CSS0044603' => 'camsi', 'CSS0044680' => 'camsi', 'CSS0044685' => 'camsi', 'CSS0044700' => 'camsi', 'CSS0044888' => 'camsi', 'CSS0044923' => 'camsi', 'CSS0044926' => 'camsi', 'CSS0044979' => 'camsi', 'CSS0045049' => 'camsi', 'CSS0045132' => 'camsi', 'CSS0045161' => 'camsi', 'CSS0045219' => 'camsi', 'CSS0045230' => 'camsi', 'CSS0045259' => 'camsi', 'CSS0045324' => 'camsi', 'CSS0045368' => 'camsi', 'CSS0045435' => 'camsi', 'CSS0045856' => 'camsi', 'CSS0045955' => 'camsi', 'CSS0046158' => 'camsi', 'CSS0046334' => 'camsi', 'CSS0046365' => 'camsi', 'CSS0046396' => 'camsi', 'CSS0046400' => 'camsi', 'CSS0046445' => 'camsi', 'CSS0046493' => 'camsi', 'CSS0046640' => 'camsi', 'CSS0046657' => 'camsi', 'CSS0046702' => 'camsi', 'CSS0047208' => 'camsi', 'CSS0047368' => 'camsi', 'CSS0047403' => 'camsi', 'CSS0047417' => 'camsi', 'CSS0047469' => 'camsi', 'CSS0047480' => 'camsi', 'CSS0047482' => 'camsi', 'CSS0047693' => 'camsi', 'CSS0047766' => 'camsi', 'CSS0047866' => 'camsi', 'CSS0047884' => 'camsi', 'CSS0048235' => 'camsi', 'CSS0048383' => 'camsi', 'CSS0048438' => 'camsi', 'CSS0048502' => 'camsi', 'CSS0048546' => 'camsi', 'CSS0048653' => 'camsi', 'CSS0048658' => 'camsi', 'CSS0048729' => 'camsi', 'CSS0048867' => 'camsi', 'CSS0048988' => 'camsi', 'CSS0049053' => 'camsi', 'CSS0049099' => 'camsi', 'CSS0049166' => 'camsi', 'CSS0049174' => 'camsi', 'CSS0049212' => 'camsi', 'CSS0049280' => 'camsi', 'CSS0049391' => 'camsi', 'CSS0049546' => 'camsi', 'CSS0049634' => 'camsi', 'CSS0049655' => 'camsi', 'CSS0049813' => 'camsi', 'CSS0049949' => 'camsi', 'CSS0050009' => 'camsi', 'CSS0050118' => 'camsi', 'CSS0050205' => 'camsi', 'CSS0050275' => 'camsi', 'CSS0050480' => 'camsi', 'CSS0050488' => 'camsi', 'CSS0050497' => 'camsi', 'Dinv03126' => 'din', 'Dinv13140' => 'din', 'Dinv13247' => 'din', 'Dinv14217' => 'din', 'EL10Ac9g22435' => 'bvu', 'FAN20G1200' => 'fan', 'PGR142G2516' => 'pgr', 'Prupe.3G160200' => 'ppe', 'Prupe.5G238200' => 'ppe', 'Prupe.7G047500' => 'ppe', 'QL03p045360' => 'qlo', 'QL05p034369' => 'qlo', 'QL05p034412' => 'qlo', 'QL08p017802' => 'qlo', 'QL08p024762' => 'qlo', 'QL10p026237' => 'qlo', 'QL10p032070' => 'qlo', 'QL11p003821' => 'qlo', 'Rhsim04G0057300' => 'rsi', 'Rhsim05G0049200' => 'rsi', 'Rhsim12G0010400' => 'rsi', 'Rhsim12G0012800' => 'rsi', 'TAR624G0483' => 'tar', 'TAR703G0001' => 'tar', 'vmacro05414' => 'vma', 'vmacro07091' => 'vma', 'vmacro07116' => 'vma', 'vmacro08423' => 'vma', 'vmacro09046' => 'vma', 'vmacro14269' => 'vma', 'vmacro16092' => 'vma', 'vmacro17280' => 'vma', 'vmacro19601' => 'vma' ), 'gf_id' => 'HOM05D001028', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001028' ), 'data_identifier' => 'HOM05D001028', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001028', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '590', 'num_species' => '12' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'Aqoxy1G01649' => 'aox', 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'CSS0028205' => 'camsi', 'CSS0028263' => 'camsi', 'CSS0028363' => 'camsi', 'CSS0028598' => 'camsi', 'CSS0029175' => 'camsi', 'CSS0029191' => 'camsi', 'CSS0029424' => 'camsi', 'CSS0029479' => 'camsi', 'CSS0029496' => 'camsi', 'CSS0029633' => 'camsi', 'CSS0029837' => 'camsi', 'CSS0029844' => 'camsi', 'CSS0029863' => 'camsi', 'CSS0029874' => 'camsi', 'CSS0029959' => 'camsi', 'CSS0030001' => 'camsi', 'CSS0030093' => 'camsi', 'CSS0030199' => 'camsi', 'CSS0030200' => 'camsi', 'CSS0030427' => 'camsi', 'CSS0030476' => 'camsi', 'CSS0030636' => 'camsi', 'CSS0030673' => 'camsi', 'CSS0030766' => 'camsi', 'CSS0030775' => 'camsi', 'CSS0030858' => 'camsi', 'CSS0030873' => 'camsi', 'CSS0030929' => 'camsi', 'CSS0031028' => 'camsi', 'CSS0031129' => 'camsi', 'CSS0031164' => 'camsi', 'CSS0031340' => 'camsi', 'CSS0031368' => 'camsi', 'CSS0031395' => 'camsi', 'CSS0031596' => 'camsi', 'CSS0031727' => 'camsi', 'CSS0032011' => 'camsi', 'CSS0032160' => 'camsi', 'CSS0032538' => 'camsi', 'CSS0032576' => 'camsi', 'CSS0032603' => 'camsi', 'CSS0032640' => 'camsi', 'CSS0032704' => 'camsi', 'CSS0032851' => 'camsi', 'CSS0032973' => 'camsi', 'CSS0033048' => 'camsi', 'CSS0033082' => 'camsi', 'CSS0033157' => 'camsi', 'CSS0033253' => 'camsi', 'CSS0033347' => 'camsi', 'CSS0033601' => 'camsi', 'CSS0033820' => 'camsi', 'CSS0033881' => 'camsi', 'CSS0033934' => 'camsi', 'CSS0034143' => 'camsi', 'CSS0034176' => 'camsi', 'CSS0034201' => 'camsi', 'CSS0034269' => 'camsi', 'CSS0034303' => 'camsi', 'CSS0034463' => 'camsi', 'CSS0034470' => 'camsi', 'CSS0034514' => 'camsi', 'CSS0034525' => 'camsi', 'CSS0034726' => 'camsi', 'CSS0034727' => 'camsi', 'CSS0034737' => 'camsi', 'CSS0034768' => 'camsi', 'CSS0034890' => 'camsi', 'CSS0034943' => 'camsi', 'CSS0034957' => 'camsi', 'CSS0034973' => 'camsi', 'CSS0035178' => 'camsi', 'CSS0035260' => 'camsi', 'CSS0035316' => 'camsi', 'CSS0035347' => 'camsi', 'CSS0035360' => 'camsi', 'CSS0035380' => 'camsi', 'CSS0035429' => 'camsi', 'CSS0035446' => 'camsi', 'CSS0035737' => 'camsi', 'CSS0035852' => 'camsi', 'CSS0035967' => 'camsi', 'CSS0036001' => 'camsi', 'CSS0036044' => 'camsi', 'CSS0036221' => 'camsi', 'CSS0036333' => 'camsi', 'CSS0036435' => 'camsi', 'CSS0036843' => 'camsi', 'CSS0036846' => 'camsi', 'CSS0037097' => 'camsi', 'CSS0037263' => 'camsi', 'CSS0037370' => 'camsi', 'CSS0037410' => 'camsi', 'CSS0037449' => 'camsi', 'CSS0037603' => 'camsi', 'CSS0037851' => 'camsi', 'CSS0037891' => 'camsi', 'CSS0037996' => 'camsi', 'CSS0038222' => 'camsi', 'CSS0038433' => 'camsi', 'CSS0038441' => 'camsi', 'CSS0038718' => 'camsi', 'CSS0038890' => 'camsi', 'CSS0039049' => 'camsi', 'CSS0039145' => 'camsi', 'CSS0039243' => 'camsi', 'CSS0039294' => 'camsi', 'CSS0039324' => 'camsi', 'CSS0039376' => 'camsi', 'CSS0039475' => 'camsi', 'CSS0039539' => 'camsi', 'CSS0039546' => 'camsi', 'CSS0039567' => 'camsi', 'CSS0039599' => 'camsi', 'CSS0039763' => 'camsi', 'CSS0039863' => 'camsi', 'CSS0040107' => 'camsi', 'CSS0040124' => 'camsi', 'CSS0040151' => 'camsi', 'CSS0040165' => 'camsi', 'CSS0040309' => 'camsi', 'CSS0040318' => 'camsi', 'CSS0040347' => 'camsi', 'CSS0040371' => 'camsi', 'CSS0040456' => 'camsi', 'CSS0040551' => 'camsi', 'CSS0040975' => 'camsi', 'CSS0040981' => 'camsi', 'CSS0041299' => 'camsi', 'CSS0041493' => 'camsi', 'CSS0041658' => 'camsi', 'CSS0041899' => 'camsi', 'CSS0041927' => 'camsi', 'CSS0042016' => 'camsi', 'CSS0042034' => 'camsi', 'CSS0042103' => 'camsi', 'CSS0042172' => 'camsi', 'CSS0042198' => 'camsi', 'CSS0042201' => 'camsi', 'CSS0042308' => 'camsi', 'CSS0042329' => 'camsi', 'CSS0042348' => 'camsi', 'CSS0042349' => 'camsi', 'CSS0042489' => 'camsi', 'CSS0042575' => 'camsi', 'CSS0042624' => 'camsi', 'CSS0042660' => 'camsi', 'CSS0042694' => 'camsi', 'CSS0042995' => 'camsi', 'CSS0043079' => 'camsi', 'CSS0043165' => 'camsi', 'CSS0043171' => 'camsi', 'CSS0043314' => 'camsi', 'CSS0043361' => 'camsi', 'CSS0043375' => 'camsi', 'CSS0043518' => 'camsi', 'CSS0043536' => 'camsi', 'CSS0043678' => 'camsi', 'CSS0043765' => 'camsi', 'CSS0043897' => 'camsi', 'CSS0043944' => 'camsi', 'CSS0044126' => 'camsi', 'CSS0044136' => 'camsi', 'CSS0044179' => 'camsi', 'CSS0044290' => 'camsi', 'CSS0044437' => 'camsi', 'CSS0044502' => 'camsi', 'CSS0044603' => 'camsi', 'CSS0044680' => 'camsi', 'CSS0044685' => 'camsi', 'CSS0044700' => 'camsi', 'CSS0044888' => 'camsi', 'CSS0044923' => 'camsi', 'CSS0044926' => 'camsi', 'CSS0044979' => 'camsi', 'CSS0045049' => 'camsi', 'CSS0045132' => 'camsi', 'CSS0045161' => 'camsi', 'CSS0045219' => 'camsi', 'CSS0045230' => 'camsi', 'CSS0045259' => 'camsi', 'CSS0045324' => 'camsi', 'CSS0045368' => 'camsi', 'CSS0045435' => 'camsi', 'CSS0045856' => 'camsi', 'CSS0045955' => 'camsi', 'CSS0046158' => 'camsi', 'CSS0046334' => 'camsi', 'CSS0046365' => 'camsi', 'CSS0046396' => 'camsi', 'CSS0046400' => 'camsi', 'CSS0046445' => 'camsi', 'CSS0046493' => 'camsi', 'CSS0046640' => 'camsi', 'CSS0046657' => 'camsi', 'CSS0046702' => 'camsi', 'CSS0047208' => 'camsi', 'CSS0047368' => 'camsi', 'CSS0047403' => 'camsi', 'CSS0047417' => 'camsi', 'CSS0047469' => 'camsi', 'CSS0047480' => 'camsi', 'CSS0047482' => 'camsi', 'CSS0047693' => 'camsi', 'CSS0047766' => 'camsi', 'CSS0047866' => 'camsi', 'CSS0047884' => 'camsi', 'CSS0048235' => 'camsi', 'CSS0048383' => 'camsi', 'CSS0048438' => 'camsi', 'CSS0048502' => 'camsi', 'CSS0048546' => 'camsi', 'CSS0048653' => 'camsi', 'CSS0048658' => 'camsi', 'CSS0048729' => 'camsi', 'CSS0048867' => 'camsi', 'CSS0048988' => 'camsi', 'CSS0049053' => 'camsi', 'CSS0049099' => 'camsi', 'CSS0049166' => 'camsi', 'CSS0049174' => 'camsi', 'CSS0049212' => 'camsi', 'CSS0049280' => 'camsi', 'CSS0049391' => 'camsi', 'CSS0049546' => 'camsi', 'CSS0049634' => 'camsi', 'CSS0049655' => 'camsi', 'CSS0049813' => 'camsi', 'CSS0049949' => 'camsi', 'CSS0050009' => 'camsi', 'CSS0050118' => 'camsi', 'CSS0050205' => 'camsi', 'CSS0050275' => 'camsi', 'CSS0050480' => 'camsi', 'CSS0050488' => 'camsi', 'CSS0050497' => 'camsi', 'Dinv03126' => 'din', 'Dinv13140' => 'din', 'Dinv13247' => 'din', 'Dinv14217' => 'din', 'EL10Ac9g22435' => 'bvu', 'FAN20G1200' => 'fan', 'PGR142G2516' => 'pgr', 'Prupe.3G160200' => 'ppe', 'Prupe.5G238200' => 'ppe', 'Prupe.7G047500' => 'ppe', 'QL03p045360' => 'qlo', 'QL05p034369' => 'qlo', 'QL05p034412' => 'qlo', 'QL08p017802' => 'qlo', 'QL08p024762' => 'qlo', 'QL10p026237' => 'qlo', 'QL10p032070' => 'qlo', 'QL11p003821' => 'qlo', 'Rhsim04G0057300' => 'rsi', 'Rhsim05G0049200' => 'rsi', 'Rhsim12G0010400' => 'rsi', 'Rhsim12G0012800' => 'rsi', 'TAR624G0483' => 'tar', 'TAR703G0001' => 'tar', 'vmacro05414' => 'vma', 'vmacro07091' => 'vma', 'vmacro07116' => 'vma', 'vmacro08423' => 'vma', 'vmacro09046' => 'vma', 'vmacro14269' => 'vma', 'vmacro16092' => 'vma', 'vmacro17280' => 'vma', 'vmacro19601' => 'vma' ) $gf_id = 'HOM05D001028' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001028' ) $data_identifier = 'HOM05D001028' $data_type = 'gf_id' $species_gene_counts = array( 'aox' => (int) 11, 'ccan' => (int) 6, 'camsi' => (int) 540, 'din' => (int) 4, 'bvu' => (int) 1, 'fan' => (int) 1, 'pgr' => (int) 1, 'ppe' => (int) 3, 'qlo' => (int) 8, 'rsi' => (int) 4, 'tar' => (int) 2, 'vma' => (int) 9 ) $gf_gene_species = 'vma' $gf_gene_id = 'vmacro19601' $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' => 'HOM05D001028', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '590', 'num_species' => '12' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'Aqoxy1G01649' => 'aox', 'Aqoxy1G02950' => 'aox', 'Aqoxy2G01005' => 'aox', 'Aqoxy2G01064' => 'aox', 'Aqoxy3G02267' => 'aox', 'Aqoxy3G02617' => 'aox', 'Aqoxy3G02693' => 'aox', 'Aqoxy5G03425' => 'aox', 'Aqoxy6G02164' => 'aox', 'Aqoxy6G02364' => 'aox', 'Aqoxy7G02284' => 'aox', 'Cc00_g09720' => 'ccan', 'Cc00_g21410' => 'ccan', 'Cc00_g31750' => 'ccan', 'Cc00_g34740' => 'ccan', 'Cc04_g16890' => 'ccan', 'Cc11_g03120' => 'ccan', 'CSS0000222' => 'camsi', 'CSS0000265' => 'camsi', 'CSS0000306' => 'camsi', 'CSS0000326' => 'camsi', 'CSS0000530' => 'camsi', 'CSS0000563' => 'camsi', 'CSS0000584' => 'camsi', 'CSS0000684' => 'camsi', 'CSS0001100' => 'camsi', 'CSS0001311' => 'camsi', 'CSS0001343' => 'camsi', 'CSS0001399' => 'camsi', 'CSS0001475' => 'camsi', 'CSS0001506' => 'camsi', 'CSS0001602' => 'camsi', 'CSS0001681' => 'camsi', 'CSS0001874' => 'camsi', 'CSS0001948' => 'camsi', 'CSS0002022' => 'camsi', 'CSS0002230' => 'camsi', 'CSS0002265' => 'camsi', 'CSS0002277' => 'camsi', 'CSS0002462' => 'camsi', 'CSS0002823' => 'camsi', 'CSS0003091' => 'camsi', 'CSS0003162' => 'camsi', 'CSS0003264' => 'camsi', 'CSS0003355' => 'camsi', 'CSS0003378' => 'camsi', 'CSS0003472' => 'camsi', 'CSS0003500' => 'camsi', 'CSS0003640' => 'camsi', 'CSS0003767' => 'camsi', 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'CSS0009986' => 'camsi', 'CSS0010182' => 'camsi', 'CSS0010202' => 'camsi', 'CSS0010330' => 'camsi', 'CSS0010362' => 'camsi', 'CSS0010456' => 'camsi', 'CSS0010472' => 'camsi', 'CSS0010507' => 'camsi', 'CSS0010512' => 'camsi', 'CSS0010520' => 'camsi', 'CSS0010617' => 'camsi', 'CSS0010706' => 'camsi', 'CSS0010747' => 'camsi', 'CSS0010816' => 'camsi', 'CSS0011020' => 'camsi', 'CSS0011115' => 'camsi', 'CSS0011383' => 'camsi', 'CSS0011491' => 'camsi', 'CSS0011602' => 'camsi', 'CSS0011605' => 'camsi', 'CSS0011625' => 'camsi', 'CSS0011654' => 'camsi', 'CSS0011781' => 'camsi', 'CSS0011853' => 'camsi', 'CSS0011898' => 'camsi', 'CSS0011933' => 'camsi', 'CSS0011996' => 'camsi', 'CSS0012066' => 'camsi', 'CSS0012097' => 'camsi', 'CSS0012108' => 'camsi', 'CSS0012226' => 'camsi', 'CSS0012248' => 'camsi', 'CSS0012331' => 'camsi', 'CSS0012797' => 'camsi', 'CSS0012818' => 'camsi', 'CSS0012904' => 'camsi', 'CSS0013001' => 'camsi', 'CSS0013022' => 'camsi', 'CSS0013172' => 'camsi', 'CSS0013244' => 'camsi', 'CSS0013267' => 'camsi', 'CSS0013275' => 'camsi', 'CSS0013324' => 'camsi', 'CSS0013334' => 'camsi', 'CSS0013394' => 'camsi', 'CSS0013549' => 'camsi', 'CSS0013689' => 'camsi', 'CSS0014026' => 'camsi', 'CSS0014049' => 'camsi', 'CSS0014144' => 'camsi', 'CSS0014354' => 'camsi', 'CSS0014579' => 'camsi', 'CSS0014648' => 'camsi', 'CSS0014902' => 'camsi', 'CSS0014979' => 'camsi', 'CSS0015278' => 'camsi', 'CSS0015310' => 'camsi', 'CSS0015364' => 'camsi', 'CSS0015455' => 'camsi', 'CSS0015693' => 'camsi', 'CSS0015774' => 'camsi', 'CSS0015795' => 'camsi', 'CSS0015952' => 'camsi', 'CSS0016104' => 'camsi', 'CSS0016241' => 'camsi', 'CSS0016303' => 'camsi', 'CSS0016490' => 'camsi', 'CSS0016832' => 'camsi', 'CSS0016845' => 'camsi', 'CSS0016914' => 'camsi', 'CSS0016946' => 'camsi', 'CSS0017102' => 'camsi', 'CSS0017193' => 'camsi', 'CSS0017528' => 'camsi', 'CSS0017619' => 'camsi', 'CSS0017679' => 'camsi', 'CSS0017816' => 'camsi', 'CSS0017880' => 'camsi', 'CSS0018106' => 'camsi', 'CSS0018162' => 'camsi', 'CSS0018304' => 'camsi', 'CSS0018406' => 'camsi', 'CSS0018481' => 'camsi', 'CSS0018511' => 'camsi', 'CSS0018596' => 'camsi', 'CSS0018727' => 'camsi', 'CSS0018751' => 'camsi', 'CSS0018777' => 'camsi', 'CSS0018798' => 'camsi', 'CSS0019137' => 'camsi', 'CSS0019177' => 'camsi', 'CSS0019217' => 'camsi', 'CSS0019361' => 'camsi', 'CSS0019516' => 'camsi', 'CSS0019538' => 'camsi', 'CSS0019560' => 'camsi', 'CSS0019819' => 'camsi', 'CSS0019837' => 'camsi', 'CSS0019915' => 'camsi', 'CSS0019925' => 'camsi', 'CSS0020112' => 'camsi', 'CSS0020160' => 'camsi', 'CSS0020378' => 'camsi', 'CSS0020388' => 'camsi', 'CSS0020452' => 'camsi', 'CSS0020588' => 'camsi', 'CSS0020661' => 'camsi', 'CSS0020886' => 'camsi', 'CSS0020973' => 'camsi', 'CSS0021035' => 'camsi', 'CSS0021111' => 'camsi', 'CSS0021131' => 'camsi', 'CSS0021151' => 'camsi', 'CSS0021228' => 'camsi', 'CSS0021397' => 'camsi', 'CSS0021420' => 'camsi', 'CSS0021464' => 'camsi', 'CSS0021547' => 'camsi', 'CSS0021608' => 'camsi', 'CSS0021740' => 'camsi', 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'CSS0037097' => 'camsi', 'CSS0037263' => 'camsi', 'CSS0037370' => 'camsi', 'CSS0037410' => 'camsi', 'CSS0037449' => 'camsi', 'CSS0037603' => 'camsi', 'CSS0037851' => 'camsi', 'CSS0037891' => 'camsi', 'CSS0037996' => 'camsi', 'CSS0038222' => 'camsi', 'CSS0038433' => 'camsi', 'CSS0038441' => 'camsi', 'CSS0038718' => 'camsi', 'CSS0038890' => 'camsi', 'CSS0039049' => 'camsi', 'CSS0039145' => 'camsi', 'CSS0039243' => 'camsi', 'CSS0039294' => 'camsi', 'CSS0039324' => 'camsi', 'CSS0039376' => 'camsi', 'CSS0039475' => 'camsi', 'CSS0039539' => 'camsi', 'CSS0039546' => 'camsi', 'CSS0039567' => 'camsi', 'CSS0039599' => 'camsi', 'CSS0039763' => 'camsi', 'CSS0039863' => 'camsi', 'CSS0040107' => 'camsi', 'CSS0040124' => 'camsi', 'CSS0040151' => 'camsi', 'CSS0040165' => 'camsi', 'CSS0040309' => 'camsi', 'CSS0040318' => 'camsi', 'CSS0040347' => 'camsi', 'CSS0040371' => 'camsi', 'CSS0040456' => 'camsi', 'CSS0040551' => 'camsi', 'CSS0040975' => 'camsi', 'CSS0040981' => 'camsi', 'CSS0041299' => 'camsi', 'CSS0041493' => 'camsi', 'CSS0041658' => 'camsi', 'CSS0041899' => 'camsi', 'CSS0041927' => 'camsi', 'CSS0042016' => 'camsi', 'CSS0042034' => 'camsi', 'CSS0042103' => 'camsi', 'CSS0042172' => 'camsi', 'CSS0042198' => 'camsi', 'CSS0042201' => 'camsi', 'CSS0042308' => 'camsi', 'CSS0042329' => 'camsi', 'CSS0042348' => 'camsi', 'CSS0042349' => 'camsi', 'CSS0042489' => 'camsi', 'CSS0042575' => 'camsi', 'CSS0042624' => 'camsi', 'CSS0042660' => 'camsi', 'CSS0042694' => 'camsi', 'CSS0042995' => 'camsi', 'CSS0043079' => 'camsi', 'CSS0043165' => 'camsi', 'CSS0043171' => 'camsi', 'CSS0043314' => 'camsi', 'CSS0043361' => 'camsi', 'CSS0043375' => 'camsi', 'CSS0043518' => 'camsi', 'CSS0043536' => 'camsi', 'CSS0043678' => 'camsi', 'CSS0043765' => 'camsi', 'CSS0043897' => 'camsi', 'CSS0043944' => 'camsi', 'CSS0044126' => 'camsi', 'CSS0044136' => 'camsi', 'CSS0044179' => 'camsi', 'CSS0044290' => 'camsi', 'CSS0044437' => 'camsi', 'CSS0044502' => 'camsi', 'CSS0044603' => 'camsi', 'CSS0044680' => 'camsi', 'CSS0044685' => 'camsi', 'CSS0044700' => 'camsi', 'CSS0044888' => 'camsi', 'CSS0044923' => 'camsi', 'CSS0044926' => 'camsi', 'CSS0044979' => 'camsi', 'CSS0045049' => 'camsi', 'CSS0045132' => 'camsi', 'CSS0045161' => 'camsi', 'CSS0045219' => 'camsi', 'CSS0045230' => 'camsi', 'CSS0045259' => 'camsi', 'CSS0045324' => 'camsi', 'CSS0045368' => 'camsi', 'CSS0045435' => 'camsi', 'CSS0045856' => 'camsi', 'CSS0045955' => 'camsi', 'CSS0046158' => 'camsi', 'CSS0046334' => 'camsi', 'CSS0046365' => 'camsi', 'CSS0046396' => 'camsi', 'CSS0046400' => 'camsi', 'CSS0046445' => 'camsi', 'CSS0046493' => 'camsi', 'CSS0046640' => 'camsi', 'CSS0046657' => 'camsi', 'CSS0046702' => 'camsi', 'CSS0047208' => 'camsi', 'CSS0047368' => 'camsi', 'CSS0047403' => 'camsi', 'CSS0047417' => 'camsi', 'CSS0047469' => 'camsi', 'CSS0047480' => 'camsi', 'CSS0047482' => 'camsi', 'CSS0047693' => 'camsi', 'CSS0047766' => 'camsi', 'CSS0047866' => 'camsi', 'CSS0047884' => 'camsi', 'CSS0048235' => 'camsi', 'CSS0048383' => 'camsi', 'CSS0048438' => 'camsi', 'CSS0048502' => 'camsi', 'CSS0048546' => 'camsi', 'CSS0048653' => 'camsi', 'CSS0048658' => 'camsi', 'CSS0048729' => 'camsi', 'CSS0048867' => 'camsi', 'CSS0048988' => 'camsi', 'CSS0049053' => 'camsi', 'CSS0049099' => 'camsi', 'CSS0049166' => 'camsi', 'CSS0049174' => 'camsi', 'CSS0049212' => 'camsi', 'CSS0049280' => 'camsi', 'CSS0049391' => 'camsi', 'CSS0049546' => 'camsi', 'CSS0049634' => 'camsi', 'CSS0049655' => 'camsi', 'CSS0049813' => 'camsi', 'CSS0049949' => 'camsi', 'CSS0050009' => 'camsi', 'CSS0050118' => 'camsi', 'CSS0050205' => 'camsi', 'CSS0050275' => 'camsi', 'CSS0050480' => 'camsi', 'CSS0050488' => 'camsi', 'CSS0050497' => 'camsi', 'Dinv03126' => 'din', 'Dinv13140' => 'din', 'Dinv13247' => 'din', 'Dinv14217' => 'din', 'EL10Ac9g22435' => 'bvu', 'FAN20G1200' => 'fan', 'PGR142G2516' => 'pgr', 'Prupe.3G160200' => 'ppe', 'Prupe.5G238200' => 'ppe', 'Prupe.7G047500' => 'ppe', 'QL03p045360' => 'qlo', 'QL05p034369' => 'qlo', 'QL05p034412' => 'qlo', 'QL08p017802' => 'qlo', 'QL08p024762' => 'qlo', 'QL10p026237' => 'qlo', 'QL10p032070' => 'qlo', 'QL11p003821' => 'qlo', 'Rhsim04G0057300' => 'rsi', 'Rhsim05G0049200' => 'rsi', 'Rhsim12G0010400' => 'rsi', 'Rhsim12G0012800' => 'rsi', 'TAR624G0483' => 'tar', 'TAR703G0001' => 'tar', 'vmacro05414' => 'vma', 'vmacro07091' => 'vma', 'vmacro07116' => 'vma', 'vmacro08423' => 'vma', 'vmacro09046' => 'vma', 'vmacro14269' => 'vma', 'vmacro16092' => 'vma', 'vmacro17280' => 'vma', 'vmacro19601' => 'vma' ), 'gf_id' => 'HOM05D001028', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001028' ), 'data_identifier' => 'HOM05D001028', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001028', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '590', 'num_species' => '12' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'Aqoxy1G01649' => 'aox', 'Aqoxy1G02950' => 'aox', 'Aqoxy2G01005' => 'aox', 'Aqoxy2G01064' => 'aox', 'Aqoxy3G02267' => 'aox', 'Aqoxy3G02617' => 'aox', 'Aqoxy3G02693' => 'aox', 'Aqoxy5G03425' => 'aox', 'Aqoxy6G02164' => 'aox', 'Aqoxy6G02364' => 'aox', 'Aqoxy7G02284' => 'aox', 'Cc00_g09720' => 'ccan', 'Cc00_g21410' => 'ccan', 'Cc00_g31750' => 'ccan', 'Cc00_g34740' => 'ccan', 'Cc04_g16890' => 'ccan', 'Cc11_g03120' => 'ccan', 'CSS0000222' => 'camsi', 'CSS0000265' => 'camsi', 'CSS0000306' => 'camsi', 'CSS0000326' => 'camsi', 'CSS0000530' => 'camsi', 'CSS0000563' => 'camsi', 'CSS0000584' => 'camsi', 'CSS0000684' => 'camsi', 'CSS0001100' => 'camsi', 'CSS0001311' => 'camsi', 'CSS0001343' => 'camsi', 'CSS0001399' => 'camsi', 'CSS0001475' => 'camsi', 'CSS0001506' => 'camsi', 'CSS0001602' => 'camsi', 'CSS0001681' => 'camsi', 'CSS0001874' => 'camsi', 'CSS0001948' => 'camsi', 'CSS0002022' => 'camsi', 'CSS0002230' => 'camsi', 'CSS0002265' => 'camsi', 'CSS0002277' => 'camsi', 'CSS0002462' => 'camsi', 'CSS0002823' => 'camsi', 'CSS0003091' => 'camsi', 'CSS0003162' => 'camsi', 'CSS0003264' => 'camsi', 'CSS0003355' => 'camsi', 'CSS0003378' => 'camsi', 'CSS0003472' => 'camsi', 'CSS0003500' => 'camsi', 'CSS0003640' => 'camsi', 'CSS0003767' => 'camsi', 'CSS0003894' => 'camsi', 'CSS0003952' => 'camsi', 'CSS0003977' => 'camsi', 'CSS0004028' => 'camsi', 'CSS0004117' => 'camsi', 'CSS0004137' => 'camsi', 'CSS0004176' => 'camsi', 'CSS0004265' => 'camsi', 'CSS0004450' => 'camsi', 'CSS0004468' => 'camsi', 'CSS0004488' => 'camsi', 'CSS0004490' => 'camsi', 'CSS0004632' => 'camsi', 'CSS0004790' => 'camsi', 'CSS0004877' => 'camsi', 'CSS0004920' => 'camsi', 'CSS0004969' => 'camsi', 'CSS0005084' => 'camsi', 'CSS0005101' => 'camsi', 'CSS0005271' => 'camsi', 'CSS0005313' => 'camsi', 'CSS0005331' => 'camsi', 'CSS0005368' => 'camsi', 'CSS0005391' => 'camsi', 'CSS0005437' => 'camsi', 'CSS0005515' => 'camsi', 'CSS0005526' => 'camsi', 'CSS0005532' => 'camsi', 'CSS0005595' => 'camsi', 'CSS0005677' => 'camsi', 'CSS0005838' => 'camsi', 'CSS0005988' => 'camsi', 'CSS0006100' => 'camsi', 'CSS0006128' => 'camsi', 'CSS0006293' => 'camsi', 'CSS0006378' => 'camsi', 'CSS0006400' => 'camsi', 'CSS0006441' => 'camsi', 'CSS0006455' => 'camsi', 'CSS0006480' => 'camsi', 'CSS0006483' => 'camsi', 'CSS0006538' => 'camsi', 'CSS0006582' => 'camsi', 'CSS0006632' => 'camsi', 'CSS0006771' => 'camsi', 'CSS0006803' => 'camsi', 'CSS0006852' => 'camsi', 'CSS0006861' => 'camsi', 'CSS0006910' => 'camsi', 'CSS0007037' => 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'camsi', 'CSS0010617' => 'camsi', 'CSS0010706' => 'camsi', 'CSS0010747' => 'camsi', 'CSS0010816' => 'camsi', 'CSS0011020' => 'camsi', 'CSS0011115' => 'camsi', 'CSS0011383' => 'camsi', 'CSS0011491' => 'camsi', 'CSS0011602' => 'camsi', 'CSS0011605' => 'camsi', 'CSS0011625' => 'camsi', 'CSS0011654' => 'camsi', 'CSS0011781' => 'camsi', 'CSS0011853' => 'camsi', 'CSS0011898' => 'camsi', 'CSS0011933' => 'camsi', 'CSS0011996' => 'camsi', 'CSS0012066' => 'camsi', 'CSS0012097' => 'camsi', 'CSS0012108' => 'camsi', 'CSS0012226' => 'camsi', 'CSS0012248' => 'camsi', 'CSS0012331' => 'camsi', 'CSS0012797' => 'camsi', 'CSS0012818' => 'camsi', 'CSS0012904' => 'camsi', 'CSS0013001' => 'camsi', 'CSS0013022' => 'camsi', 'CSS0013172' => 'camsi', 'CSS0013244' => 'camsi', 'CSS0013267' => 'camsi', 'CSS0013275' => 'camsi', 'CSS0013324' => 'camsi', 'CSS0013334' => 'camsi', 'CSS0013394' => 'camsi', 'CSS0013549' => 'camsi', 'CSS0013689' => 'camsi', 'CSS0014026' => 'camsi', 'CSS0014049' => 'camsi', 'CSS0014144' => 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'camsi', 'CSS0045230' => 'camsi', 'CSS0045259' => 'camsi', 'CSS0045324' => 'camsi', 'CSS0045368' => 'camsi', 'CSS0045435' => 'camsi', 'CSS0045856' => 'camsi', 'CSS0045955' => 'camsi', 'CSS0046158' => 'camsi', 'CSS0046334' => 'camsi', 'CSS0046365' => 'camsi', 'CSS0046396' => 'camsi', 'CSS0046400' => 'camsi', 'CSS0046445' => 'camsi', 'CSS0046493' => 'camsi', 'CSS0046640' => 'camsi', 'CSS0046657' => 'camsi', 'CSS0046702' => 'camsi', 'CSS0047208' => 'camsi', 'CSS0047368' => 'camsi', 'CSS0047403' => 'camsi', 'CSS0047417' => 'camsi', 'CSS0047469' => 'camsi', 'CSS0047480' => 'camsi', 'CSS0047482' => 'camsi', 'CSS0047693' => 'camsi', 'CSS0047766' => 'camsi', 'CSS0047866' => 'camsi', 'CSS0047884' => 'camsi', 'CSS0048235' => 'camsi', 'CSS0048383' => 'camsi', 'CSS0048438' => 'camsi', 'CSS0048502' => 'camsi', 'CSS0048546' => 'camsi', 'CSS0048653' => 'camsi', 'CSS0048658' => 'camsi', 'CSS0048729' => 'camsi', 'CSS0048867' => 'camsi', 'CSS0048988' => 'camsi', 'CSS0049053' => 'camsi', 'CSS0049099' => 'camsi', 'CSS0049166' => 'camsi', 'CSS0049174' => 'camsi', 'CSS0049212' => 'camsi', 'CSS0049280' => 'camsi', 'CSS0049391' => 'camsi', 'CSS0049546' => 'camsi', 'CSS0049634' => 'camsi', 'CSS0049655' => 'camsi', 'CSS0049813' => 'camsi', 'CSS0049949' => 'camsi', 'CSS0050009' => 'camsi', 'CSS0050118' => 'camsi', 'CSS0050205' => 'camsi', 'CSS0050275' => 'camsi', 'CSS0050480' => 'camsi', 'CSS0050488' => 'camsi', 'CSS0050497' => 'camsi', 'Dinv03126' => 'din', 'Dinv13140' => 'din', 'Dinv13247' => 'din', 'Dinv14217' => 'din', 'EL10Ac9g22435' => 'bvu', 'FAN20G1200' => 'fan', 'PGR142G2516' => 'pgr', 'Prupe.3G160200' => 'ppe', 'Prupe.5G238200' => 'ppe', 'Prupe.7G047500' => 'ppe', 'QL03p045360' => 'qlo', 'QL05p034369' => 'qlo', 'QL05p034412' => 'qlo', 'QL08p017802' => 'qlo', 'QL08p024762' => 'qlo', 'QL10p026237' => 'qlo', 'QL10p032070' => 'qlo', 'QL11p003821' => 'qlo', 'Rhsim04G0057300' => 'rsi', 'Rhsim05G0049200' => 'rsi', 'Rhsim12G0010400' => 'rsi', 'Rhsim12G0012800' => 'rsi', 'TAR624G0483' => 'tar', 'TAR703G0001' => 'tar', 'vmacro05414' => 'vma', 'vmacro07091' => 'vma', 'vmacro07116' => 'vma', 'vmacro08423' => 'vma', 'vmacro09046' => 'vma', 'vmacro14269' => 'vma', 'vmacro16092' => 'vma', 'vmacro17280' => 'vma', 'vmacro19601' => 'vma' ) $gf_id = 'HOM05D001028' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001028' ) $data_identifier = 'HOM05D001028' $data_type = 'gf_id' $species_gene_counts = array( 'aox' => (int) 11, 'ccan' => (int) 6, 'camsi' => (int) 540, 'din' => (int) 4, 'bvu' => (int) 1, 'fan' => (int) 1, 'pgr' => (int) 1, 'ppe' => (int) 3, 'qlo' => (int) 8, 'rsi' => (int) 4, 'tar' => (int) 2, 'vma' => (int) 9 ) $gf_gene_species = 'vma' $gf_gene_id = 'vmacro19601' $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' => 'HOM05D001028', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '590', 'num_species' => '12' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'Aqoxy1G01649' => 'aox', 'Aqoxy1G02950' => 'aox', 'Aqoxy2G01005' => 'aox', 'Aqoxy2G01064' => 'aox', 'Aqoxy3G02267' => 'aox', 'Aqoxy3G02617' => 'aox', 'Aqoxy3G02693' => 'aox', 'Aqoxy5G03425' => 'aox', 'Aqoxy6G02164' => 'aox', 'Aqoxy6G02364' => 'aox', 'Aqoxy7G02284' => 'aox', 'Cc00_g09720' => 'ccan', 'Cc00_g21410' => 'ccan', 'Cc00_g31750' => 'ccan', 'Cc00_g34740' => 'ccan', 'Cc04_g16890' => 'ccan', 'Cc11_g03120' => 'ccan', 'CSS0000222' => 'camsi', 'CSS0000265' => 'camsi', 'CSS0000306' => 'camsi', 'CSS0000326' => 'camsi', 'CSS0000530' => 'camsi', 'CSS0000563' => 'camsi', 'CSS0000584' => 'camsi', 'CSS0000684' => 'camsi', 'CSS0001100' => 'camsi', 'CSS0001311' => 'camsi', 'CSS0001343' => 'camsi', 'CSS0001399' => 'camsi', 'CSS0001475' => 'camsi', 'CSS0001506' => 'camsi', 'CSS0001602' => 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array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001028' ), 'data_identifier' => 'HOM05D001028', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001028', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '590', 'num_species' => '12' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'Aqoxy1G01649' => 'aox', 'Aqoxy1G02950' => 'aox', 'Aqoxy2G01005' => 'aox', 'Aqoxy2G01064' => 'aox', 'Aqoxy3G02267' => 'aox', 'Aqoxy3G02617' => 'aox', 'Aqoxy3G02693' => 'aox', 'Aqoxy5G03425' => 'aox', 'Aqoxy6G02164' => 'aox', 'Aqoxy6G02364' => 'aox', 'Aqoxy7G02284' => 'aox', 'Cc00_g09720' => 'ccan', 'Cc00_g21410' => 'ccan', 'Cc00_g31750' => 'ccan', 'Cc00_g34740' => 'ccan', 'Cc04_g16890' => 'ccan', 'Cc11_g03120' => 'ccan', 'CSS0000222' => 'camsi', 'CSS0000265' => 'camsi', 'CSS0000306' => 'camsi', 'CSS0000326' => 'camsi', 'CSS0000530' => 'camsi', 'CSS0000563' => 'camsi', 'CSS0000584' => 'camsi', 'CSS0000684' => 'camsi', 'CSS0001100' => 'camsi', 'CSS0001311' => 'camsi', 'CSS0001343' => 'camsi', 'CSS0001399' => 'camsi', 'CSS0001475' => 'camsi', 'CSS0001506' => 'camsi', 'CSS0001602' => 'camsi', 'CSS0001681' => 'camsi', 'CSS0001874' => 'camsi', 'CSS0001948' => 'camsi', 'CSS0002022' => 'camsi', 'CSS0002230' => 'camsi', 'CSS0002265' => 'camsi', 'CSS0002277' => 'camsi', 'CSS0002462' => 'camsi', 'CSS0002823' => 'camsi', 'CSS0003091' => 'camsi', 'CSS0003162' => 'camsi', 'CSS0003264' => 'camsi', 'CSS0003355' => 'camsi', 'CSS0003378' => 'camsi', 'CSS0003472' => 'camsi', 'CSS0003500' => 'camsi', 'CSS0003640' => 'camsi', 'CSS0003767' => 'camsi', 'CSS0003894' => 'camsi', 'CSS0003952' => 'camsi', 'CSS0003977' => 'camsi', 'CSS0004028' => 'camsi', 'CSS0004117' => 'camsi', 'CSS0004137' => 'camsi', 'CSS0004176' => 'camsi', 'CSS0004265' => 'camsi', 'CSS0004450' => 'camsi', 'CSS0004468' => 'camsi', 'CSS0004488' => 'camsi', 'CSS0004490' => 'camsi', 'CSS0004632' => 'camsi', 'CSS0004790' => 'camsi', 'CSS0004877' => 'camsi', 'CSS0004920' => 'camsi', 'CSS0004969' => 'camsi', 'CSS0005084' => 'camsi', 'CSS0005101' => 'camsi', 'CSS0005271' => 'camsi', 'CSS0005313' => 'camsi', 'CSS0005331' => 'camsi', 'CSS0005368' => 'camsi', 'CSS0005391' => 'camsi', 'CSS0005437' => 'camsi', 'CSS0005515' => 'camsi', 'CSS0005526' => 'camsi', 'CSS0005532' => 'camsi', 'CSS0005595' => 'camsi', 'CSS0005677' => 'camsi', 'CSS0005838' => 'camsi', 'CSS0005988' => 'camsi', 'CSS0006100' => 'camsi', 'CSS0006128' => 'camsi', 'CSS0006293' => 'camsi', 'CSS0006378' => 'camsi', 'CSS0006400' => 'camsi', 'CSS0006441' => 'camsi', 'CSS0006455' => 'camsi', 'CSS0006480' => 'camsi', 'CSS0006483' => 'camsi', 'CSS0006538' => 'camsi', 'CSS0006582' => 'camsi', 'CSS0006632' => 'camsi', 'CSS0006771' => 'camsi', 'CSS0006803' => 'camsi', 'CSS0006852' => 'camsi', 'CSS0006861' => 'camsi', 'CSS0006910' => 'camsi', 'CSS0007037' => 'camsi', 'CSS0007066' => 'camsi', 'CSS0007072' => 'camsi', 'CSS0007109' => 'camsi', 'CSS0007193' => 'camsi', 'CSS0007319' => 'camsi', 'CSS0007336' => 'camsi', 'CSS0007377' => 'camsi', 'CSS0007659' => 'camsi', 'CSS0007701' => 'camsi', 'CSS0007711' => 'camsi', 'CSS0007809' => 'camsi', 'CSS0008045' => 'camsi', 'CSS0008050' => 'camsi', 'CSS0008206' => 'camsi', 'CSS0008251' => 'camsi', 'CSS0008252' => 'camsi', 'CSS0008279' => 'camsi', 'CSS0008482' => 'camsi', 'CSS0008583' => 'camsi', 'CSS0008699' => 'camsi', 'CSS0008798' => 'camsi', 'CSS0008971' => 'camsi', 'CSS0009019' => 'camsi', 'CSS0009191' => 'camsi', 'CSS0009241' => 'camsi', 'CSS0009246' => 'camsi', 'CSS0009399' => 'camsi', 'CSS0009654' => 'camsi', 'CSS0009722' => 'camsi', 'CSS0009920' => 'camsi', 'CSS0009986' => 'camsi', 'CSS0010182' => 'camsi', 'CSS0010202' => 'camsi', 'CSS0010330' => 'camsi', 'CSS0010362' => 'camsi', 'CSS0010456' => 'camsi', 'CSS0010472' => 'camsi', 'CSS0010507' => 'camsi', 'CSS0010512' => 'camsi', 'CSS0010520' => 'camsi', 'CSS0010617' => 'camsi', 'CSS0010706' => 'camsi', 'CSS0010747' => 'camsi', 'CSS0010816' => 'camsi', 'CSS0011020' => 'camsi', 'CSS0011115' => 'camsi', 'CSS0011383' => 'camsi', 'CSS0011491' => 'camsi', 'CSS0011602' => 'camsi', 'CSS0011605' => 'camsi', 'CSS0011625' => 'camsi', 'CSS0011654' => 'camsi', 'CSS0011781' => 'camsi', 'CSS0011853' => 'camsi', 'CSS0011898' => 'camsi', 'CSS0011933' => 'camsi', 'CSS0011996' => 'camsi', 'CSS0012066' => 'camsi', 'CSS0012097' => 'camsi', 'CSS0012108' => 'camsi', 'CSS0012226' => 'camsi', 'CSS0012248' => 'camsi', 'CSS0012331' => 'camsi', 'CSS0012797' => 'camsi', 'CSS0012818' => 'camsi', 'CSS0012904' => 'camsi', 'CSS0013001' => 'camsi', 'CSS0013022' => 'camsi', 'CSS0013172' => 'camsi', 'CSS0013244' => 'camsi', 'CSS0013267' => 'camsi', 'CSS0013275' => 'camsi', 'CSS0013324' => 'camsi', 'CSS0013334' => 'camsi', 'CSS0013394' => 'camsi', 'CSS0013549' => 'camsi', 'CSS0013689' => 'camsi', 'CSS0014026' => 'camsi', 'CSS0014049' => 'camsi', 'CSS0014144' => 'camsi', 'CSS0014354' => 'camsi', 'CSS0014579' => 'camsi', 'CSS0014648' => 'camsi', 'CSS0014902' => 'camsi', 'CSS0014979' => 'camsi', 'CSS0015278' => 'camsi', 'CSS0015310' => 'camsi', 'CSS0015364' => 'camsi', 'CSS0015455' => 'camsi', 'CSS0015693' => 'camsi', 'CSS0015774' => 'camsi', 'CSS0015795' => 'camsi', 'CSS0015952' => 'camsi', 'CSS0016104' => 'camsi', 'CSS0016241' => 'camsi', 'CSS0016303' => 'camsi', 'CSS0016490' => 'camsi', 'CSS0016832' => 'camsi', 'CSS0016845' => 'camsi', 'CSS0016914' => 'camsi', 'CSS0016946' => 'camsi', 'CSS0017102' => 'camsi', 'CSS0017193' => 'camsi', 'CSS0017528' => 'camsi', 'CSS0017619' => 'camsi', 'CSS0017679' => 'camsi', 'CSS0017816' => 'camsi', 'CSS0017880' => 'camsi', 'CSS0018106' => 'camsi', 'CSS0018162' => 'camsi', 'CSS0018304' => 'camsi', 'CSS0018406' => 'camsi', 'CSS0018481' => 'camsi', 'CSS0018511' => 'camsi', 'CSS0018596' => 'camsi', 'CSS0018727' => 'camsi', 'CSS0018751' => 'camsi', 'CSS0018777' => 'camsi', 'CSS0018798' => 'camsi', 'CSS0019137' => 'camsi', 'CSS0019177' => 'camsi', 'CSS0019217' => 'camsi', 'CSS0019361' => 'camsi', 'CSS0019516' => 'camsi', 'CSS0019538' => 'camsi', 'CSS0019560' => 'camsi', 'CSS0019819' => 'camsi', 'CSS0019837' => 'camsi', 'CSS0019915' => 'camsi', 'CSS0019925' => 'camsi', 'CSS0020112' => 'camsi', 'CSS0020160' => 'camsi', 'CSS0020378' => 'camsi', 'CSS0020388' => 'camsi', 'CSS0020452' => 'camsi', 'CSS0020588' => 'camsi', 'CSS0020661' => 'camsi', 'CSS0020886' => 'camsi', 'CSS0020973' => 'camsi', 'CSS0021035' => 'camsi', 'CSS0021111' => 'camsi', 'CSS0021131' => 'camsi', 'CSS0021151' => 'camsi', 'CSS0021228' => 'camsi', 'CSS0021397' => 'camsi', 'CSS0021420' => 'camsi', 'CSS0021464' => 'camsi', 'CSS0021547' => 'camsi', 'CSS0021608' => 'camsi', 'CSS0021740' => 'camsi', 'CSS0021826' => 'camsi', 'CSS0021904' => 'camsi', 'CSS0021941' => 'camsi', 'CSS0022189' => 'camsi', 'CSS0022199' => 'camsi', 'CSS0022502' => 'camsi', 'CSS0022531' => 'camsi', 'CSS0022581' => 'camsi', 'CSS0022612' => 'camsi', 'CSS0022621' => 'camsi', 'CSS0022815' => 'camsi', 'CSS0022936' => 'camsi', 'CSS0022964' => 'camsi', 'CSS0022985' => 'camsi', 'CSS0023002' => 'camsi', 'CSS0023006' => 'camsi', 'CSS0023024' => 'camsi', 'CSS0023489' => 'camsi', 'CSS0023593' => 'camsi', 'CSS0023621' => 'camsi', 'CSS0023743' => 'camsi', 'CSS0023804' => 'camsi', 'CSS0023805' => 'camsi', 'CSS0023908' => 'camsi', 'CSS0023938' => 'camsi', 'CSS0023981' => 'camsi', 'CSS0024027' => 'camsi', 'CSS0024169' => 'camsi', 'CSS0024193' => 'camsi', 'CSS0024269' => 'camsi', 'CSS0024336' => 'camsi', 'CSS0024337' => 'camsi', 'CSS0024548' => 'camsi', 'CSS0024564' => 'camsi', 'CSS0024585' => 'camsi', 'CSS0024738' => 'camsi', 'CSS0024833' => 'camsi', 'CSS0024846' => 'camsi', 'CSS0024957' => 'camsi', 'CSS0024974' => 'camsi', 'CSS0025005' => 'camsi', 'CSS0025235' => 'camsi', 'CSS0025465' => 'camsi', 'CSS0025633' => 'camsi', 'CSS0025688' => 'camsi', 'CSS0025759' => 'camsi', 'CSS0025774' => 'camsi', 'CSS0025801' => 'camsi', 'CSS0025942' => 'camsi', 'CSS0026083' => 'camsi', 'CSS0026194' => 'camsi', 'CSS0026230' => 'camsi', 'CSS0026398' => 'camsi', 'CSS0026419' => 'camsi', 'CSS0026679' => 'camsi', 'CSS0026719' => 'camsi', 'CSS0026795' => 'camsi', 'CSS0026835' => 'camsi', 'CSS0026930' => 'camsi', 'CSS0027053' => 'camsi', 'CSS0027130' => 'camsi', 'CSS0027192' => 'camsi', 'CSS0027454' => 'camsi', 'CSS0027467' => 'camsi', 'CSS0027521' => 'camsi', 'CSS0027662' => 'camsi', 'CSS0027795' => 'camsi', 'CSS0027835' => 'camsi', 'CSS0027966' => 'camsi', 'CSS0028090' => 'camsi', 'CSS0028134' => 'camsi', 'CSS0028205' => 'camsi', 'CSS0028263' => 'camsi', 'CSS0028363' => 'camsi', 'CSS0028598' => 'camsi', 'CSS0029175' => 'camsi', 'CSS0029191' => 'camsi', 'CSS0029424' => 'camsi', 'CSS0029479' => 'camsi', 'CSS0029496' => 'camsi', 'CSS0029633' => 'camsi', 'CSS0029837' => 'camsi', 'CSS0029844' => 'camsi', 'CSS0029863' => 'camsi', 'CSS0029874' => 'camsi', 'CSS0029959' => 'camsi', 'CSS0030001' => 'camsi', 'CSS0030093' => 'camsi', 'CSS0030199' => 'camsi', 'CSS0030200' => 'camsi', 'CSS0030427' => 'camsi', 'CSS0030476' => 'camsi', 'CSS0030636' => 'camsi', 'CSS0030673' => 'camsi', 'CSS0030766' => 'camsi', 'CSS0030775' => 'camsi', 'CSS0030858' => 'camsi', 'CSS0030873' => 'camsi', 'CSS0030929' => 'camsi', 'CSS0031028' => 'camsi', 'CSS0031129' => 'camsi', 'CSS0031164' => 'camsi', 'CSS0031340' => 'camsi', 'CSS0031368' => 'camsi', 'CSS0031395' => 'camsi', 'CSS0031596' => 'camsi', 'CSS0031727' => 'camsi', 'CSS0032011' => 'camsi', 'CSS0032160' => 'camsi', 'CSS0032538' => 'camsi', 'CSS0032576' => 'camsi', 'CSS0032603' => 'camsi', 'CSS0032640' => 'camsi', 'CSS0032704' => 'camsi', 'CSS0032851' => 'camsi', 'CSS0032973' => 'camsi', 'CSS0033048' => 'camsi', 'CSS0033082' => 'camsi', 'CSS0033157' => 'camsi', 'CSS0033253' => 'camsi', 'CSS0033347' => 'camsi', 'CSS0033601' => 'camsi', 'CSS0033820' => 'camsi', 'CSS0033881' => 'camsi', 'CSS0033934' => 'camsi', 'CSS0034143' => 'camsi', 'CSS0034176' => 'camsi', 'CSS0034201' => 'camsi', 'CSS0034269' => 'camsi', 'CSS0034303' => 'camsi', 'CSS0034463' => 'camsi', 'CSS0034470' => 'camsi', 'CSS0034514' => 'camsi', 'CSS0034525' => 'camsi', 'CSS0034726' => 'camsi', 'CSS0034727' => 'camsi', 'CSS0034737' => 'camsi', 'CSS0034768' => 'camsi', 'CSS0034890' => 'camsi', 'CSS0034943' => 'camsi', 'CSS0034957' => 'camsi', 'CSS0034973' => 'camsi', 'CSS0035178' => 'camsi', 'CSS0035260' => 'camsi', 'CSS0035316' => 'camsi', 'CSS0035347' => 'camsi', 'CSS0035360' => 'camsi', 'CSS0035380' => 'camsi', 'CSS0035429' => 'camsi', 'CSS0035446' => 'camsi', 'CSS0035737' => 'camsi', 'CSS0035852' => 'camsi', 'CSS0035967' => 'camsi', 'CSS0036001' => 'camsi', 'CSS0036044' => 'camsi', 'CSS0036221' => 'camsi', 'CSS0036333' => 'camsi', 'CSS0036435' => 'camsi', 'CSS0036843' => 'camsi', 'CSS0036846' => 'camsi', 'CSS0037097' => 'camsi', 'CSS0037263' => 'camsi', 'CSS0037370' => 'camsi', 'CSS0037410' => 'camsi', 'CSS0037449' => 'camsi', 'CSS0037603' => 'camsi', 'CSS0037851' => 'camsi', 'CSS0037891' => 'camsi', 'CSS0037996' => 'camsi', 'CSS0038222' => 'camsi', 'CSS0038433' => 'camsi', 'CSS0038441' => 'camsi', 'CSS0038718' => 'camsi', 'CSS0038890' => 'camsi', 'CSS0039049' => 'camsi', 'CSS0039145' => 'camsi', 'CSS0039243' => 'camsi', 'CSS0039294' => 'camsi', 'CSS0039324' => 'camsi', 'CSS0039376' => 'camsi', 'CSS0039475' => 'camsi', 'CSS0039539' => 'camsi', 'CSS0039546' => 'camsi', 'CSS0039567' => 'camsi', 'CSS0039599' => 'camsi', 'CSS0039763' => 'camsi', 'CSS0039863' => 'camsi', 'CSS0040107' => 'camsi', 'CSS0040124' => 'camsi', 'CSS0040151' => 'camsi', 'CSS0040165' => 'camsi', 'CSS0040309' => 'camsi', 'CSS0040318' => 'camsi', 'CSS0040347' => 'camsi', 'CSS0040371' => 'camsi', 'CSS0040456' => 'camsi', 'CSS0040551' => 'camsi', 'CSS0040975' => 'camsi', 'CSS0040981' => 'camsi', 'CSS0041299' => 'camsi', 'CSS0041493' => 'camsi', 'CSS0041658' => 'camsi', 'CSS0041899' => 'camsi', 'CSS0041927' => 'camsi', 'CSS0042016' => 'camsi', 'CSS0042034' => 'camsi', 'CSS0042103' => 'camsi', 'CSS0042172' => 'camsi', 'CSS0042198' => 'camsi', 'CSS0042201' => 'camsi', 'CSS0042308' => 'camsi', 'CSS0042329' => 'camsi', 'CSS0042348' => 'camsi', 'CSS0042349' => 'camsi', 'CSS0042489' => 'camsi', 'CSS0042575' => 'camsi', 'CSS0042624' => 'camsi', 'CSS0042660' => 'camsi', 'CSS0042694' => 'camsi', 'CSS0042995' => 'camsi', 'CSS0043079' => 'camsi', 'CSS0043165' => 'camsi', 'CSS0043171' => 'camsi', 'CSS0043314' => 'camsi', 'CSS0043361' => 'camsi', 'CSS0043375' => 'camsi', 'CSS0043518' => 'camsi', 'CSS0043536' => 'camsi', 'CSS0043678' => 'camsi', 'CSS0043765' => 'camsi', 'CSS0043897' => 'camsi', 'CSS0043944' => 'camsi', 'CSS0044126' => 'camsi', 'CSS0044136' => 'camsi', 'CSS0044179' => 'camsi', 'CSS0044290' => 'camsi', 'CSS0044437' => 'camsi', 'CSS0044502' => 'camsi', 'CSS0044603' => 'camsi', 'CSS0044680' => 'camsi', 'CSS0044685' => 'camsi', 'CSS0044700' => 'camsi', 'CSS0044888' => 'camsi', 'CSS0044923' => 'camsi', 'CSS0044926' => 'camsi', 'CSS0044979' => 'camsi', 'CSS0045049' => 'camsi', 'CSS0045132' => 'camsi', 'CSS0045161' => 'camsi', 'CSS0045219' => 'camsi', 'CSS0045230' => 'camsi', 'CSS0045259' => 'camsi', 'CSS0045324' => 'camsi', 'CSS0045368' => 'camsi', 'CSS0045435' => 'camsi', 'CSS0045856' => 'camsi', 'CSS0045955' => 'camsi', 'CSS0046158' => 'camsi', 'CSS0046334' => 'camsi', 'CSS0046365' => 'camsi', 'CSS0046396' => 'camsi', 'CSS0046400' => 'camsi', 'CSS0046445' => 'camsi', 'CSS0046493' => 'camsi', 'CSS0046640' => 'camsi', 'CSS0046657' => 'camsi', 'CSS0046702' => 'camsi', 'CSS0047208' => 'camsi', 'CSS0047368' => 'camsi', 'CSS0047403' => 'camsi', 'CSS0047417' => 'camsi', 'CSS0047469' => 'camsi', 'CSS0047480' => 'camsi', 'CSS0047482' => 'camsi', 'CSS0047693' => 'camsi', 'CSS0047766' => 'camsi', 'CSS0047866' => 'camsi', 'CSS0047884' => 'camsi', 'CSS0048235' => 'camsi', 'CSS0048383' => 'camsi', 'CSS0048438' => 'camsi', 'CSS0048502' => 'camsi', 'CSS0048546' => 'camsi', 'CSS0048653' => 'camsi', 'CSS0048658' => 'camsi', 'CSS0048729' => 'camsi', 'CSS0048867' => 'camsi', 'CSS0048988' => 'camsi', 'CSS0049053' => 'camsi', 'CSS0049099' => 'camsi', 'CSS0049166' => 'camsi', 'CSS0049174' => 'camsi', 'CSS0049212' => 'camsi', 'CSS0049280' => 'camsi', 'CSS0049391' => 'camsi', 'CSS0049546' => 'camsi', 'CSS0049634' => 'camsi', 'CSS0049655' => 'camsi', 'CSS0049813' => 'camsi', 'CSS0049949' => 'camsi', 'CSS0050009' => 'camsi', 'CSS0050118' => 'camsi', 'CSS0050205' => 'camsi', 'CSS0050275' => 'camsi', 'CSS0050480' => 'camsi', 'CSS0050488' => 'camsi', 'CSS0050497' => 'camsi', 'Dinv03126' => 'din', 'Dinv13140' => 'din', 'Dinv13247' => 'din', 'Dinv14217' => 'din', 'EL10Ac9g22435' => 'bvu', 'FAN20G1200' => 'fan', 'PGR142G2516' => 'pgr', 'Prupe.3G160200' => 'ppe', 'Prupe.5G238200' => 'ppe', 'Prupe.7G047500' => 'ppe', 'QL03p045360' => 'qlo', 'QL05p034369' => 'qlo', 'QL05p034412' => 'qlo', 'QL08p017802' => 'qlo', 'QL08p024762' => 'qlo', 'QL10p026237' => 'qlo', 'QL10p032070' => 'qlo', 'QL11p003821' => 'qlo', 'Rhsim04G0057300' => 'rsi', 'Rhsim05G0049200' => 'rsi', 'Rhsim12G0010400' => 'rsi', 'Rhsim12G0012800' => 'rsi', 'TAR624G0483' => 'tar', 'TAR703G0001' => 'tar', 'vmacro05414' => 'vma', 'vmacro07091' => 'vma', 'vmacro07116' => 'vma', 'vmacro08423' => 'vma', 'vmacro09046' => 'vma', 'vmacro14269' => 'vma', 'vmacro16092' => 'vma', 'vmacro17280' => 'vma', 'vmacro19601' => 'vma' ) $gf_id = 'HOM05D001028' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001028' ) $data_identifier = 'HOM05D001028' $data_type = 'gf_id' $species_gene_counts = array( 'aox' => (int) 11, 'ccan' => (int) 6, 'camsi' => (int) 540, 'din' => (int) 4, 'bvu' => (int) 1, 'fan' => (int) 1, 'pgr' => (int) 1, 'ppe' => (int) 3, 'qlo' => (int) 8, 'rsi' => (int) 4, 'tar' => (int) 2, 'vma' => (int) 9 ) $gf_gene_species = 'vma' $gf_gene_id = 'vmacro19601' $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' => 'HOM05D001028', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '590', 'num_species' => '12' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'Aqoxy1G01649' => 'aox', 'Aqoxy1G02950' => 'aox', 'Aqoxy2G01005' => 'aox', 'Aqoxy2G01064' => 'aox', 'Aqoxy3G02267' => 'aox', 'Aqoxy3G02617' => 'aox', 'Aqoxy3G02693' => 'aox', 'Aqoxy5G03425' => 'aox', 'Aqoxy6G02164' => 'aox', 'Aqoxy6G02364' => 'aox', 'Aqoxy7G02284' => 'aox', 'Cc00_g09720' => 'ccan', 'Cc00_g21410' => 'ccan', 'Cc00_g31750' => 'ccan', 'Cc00_g34740' => 'ccan', 'Cc04_g16890' => 'ccan', 'Cc11_g03120' => 'ccan', 'CSS0000222' => 'camsi', 'CSS0000265' => 'camsi', 'CSS0000306' => 'camsi', 'CSS0000326' => 'camsi', 'CSS0000530' => 'camsi', 'CSS0000563' => 'camsi', 'CSS0000584' => 'camsi', 'CSS0000684' => 'camsi', 'CSS0001100' => 'camsi', 'CSS0001311' => 'camsi', 'CSS0001343' => 'camsi', 'CSS0001399' => 'camsi', 'CSS0001475' => 'camsi', 'CSS0001506' => 'camsi', 'CSS0001602' => 'camsi', 'CSS0001681' => 'camsi', 'CSS0001874' => 'camsi', 'CSS0001948' => 'camsi', 'CSS0002022' => 'camsi', 'CSS0002230' => 'camsi', 'CSS0002265' => 'camsi', 'CSS0002277' => 'camsi', 'CSS0002462' => 'camsi', 'CSS0002823' => 'camsi', 'CSS0003091' => 'camsi', 'CSS0003162' => 'camsi', 'CSS0003264' => 'camsi', 'CSS0003355' => 'camsi', 'CSS0003378' => 'camsi', 'CSS0003472' => 'camsi', 'CSS0003500' => 'camsi', 'CSS0003640' => 'camsi', 'CSS0003767' => 'camsi', 'CSS0003894' => 'camsi', 'CSS0003952' => 'camsi', 'CSS0003977' => 'camsi', 'CSS0004028' => 'camsi', 'CSS0004117' => 'camsi', 'CSS0004137' => 'camsi', 'CSS0004176' => 'camsi', 'CSS0004265' => 'camsi', 'CSS0004450' => 'camsi', 'CSS0004468' => 'camsi', 'CSS0004488' => 'camsi', 'CSS0004490' => 'camsi', 'CSS0004632' => 'camsi', 'CSS0004790' => 'camsi', 'CSS0004877' => 'camsi', 'CSS0004920' => 'camsi', 'CSS0004969' => 'camsi', 'CSS0005084' => 'camsi', 'CSS0005101' => 'camsi', 'CSS0005271' => 'camsi', 'CSS0005313' => 'camsi', 'CSS0005331' => 'camsi', 'CSS0005368' => 'camsi', 'CSS0005391' => 'camsi', 'CSS0005437' => 'camsi', 'CSS0005515' => 'camsi', 'CSS0005526' => 'camsi', 'CSS0005532' => 'camsi', 'CSS0005595' => 'camsi', 'CSS0005677' => 'camsi', 'CSS0005838' => 'camsi', 'CSS0005988' => 'camsi', 'CSS0006100' => 'camsi', 'CSS0006128' => 'camsi', 'CSS0006293' => 'camsi', 'CSS0006378' => 'camsi', 'CSS0006400' => 'camsi', 'CSS0006441' => 'camsi', 'CSS0006455' => 'camsi', 'CSS0006480' => 'camsi', 'CSS0006483' => 'camsi', 'CSS0006538' => 'camsi', 'CSS0006582' => 'camsi', 'CSS0006632' => 'camsi', 'CSS0006771' => 'camsi', 'CSS0006803' => 'camsi', 'CSS0006852' => 'camsi', 'CSS0006861' => 'camsi', 'CSS0006910' => 'camsi', 'CSS0007037' => 'camsi', 'CSS0007066' => 'camsi', 'CSS0007072' => 'camsi', 'CSS0007109' => 'camsi', 'CSS0007193' => 'camsi', 'CSS0007319' => 'camsi', 'CSS0007336' => 'camsi', 'CSS0007377' => 'camsi', 'CSS0007659' => 'camsi', 'CSS0007701' => 'camsi', 'CSS0007711' => 'camsi', 'CSS0007809' => 'camsi', 'CSS0008045' => 'camsi', 'CSS0008050' => 'camsi', 'CSS0008206' => 'camsi', 'CSS0008251' => 'camsi', 'CSS0008252' => 'camsi', 'CSS0008279' => 'camsi', 'CSS0008482' => 'camsi', 'CSS0008583' => 'camsi', 'CSS0008699' => 'camsi', 'CSS0008798' => 'camsi', 'CSS0008971' => 'camsi', 'CSS0009019' => 'camsi', 'CSS0009191' => 'camsi', 'CSS0009241' => 'camsi', 'CSS0009246' => 'camsi', 'CSS0009399' => 'camsi', 'CSS0009654' => 'camsi', 'CSS0009722' => 'camsi', 'CSS0009920' => 'camsi', 'CSS0009986' => 'camsi', 'CSS0010182' => 'camsi', 'CSS0010202' => 'camsi', 'CSS0010330' => 'camsi', 'CSS0010362' => 'camsi', 'CSS0010456' => 'camsi', 'CSS0010472' => 'camsi', 'CSS0010507' => 'camsi', 'CSS0010512' => 'camsi', 'CSS0010520' => 'camsi', 'CSS0010617' => 'camsi', 'CSS0010706' => 'camsi', 'CSS0010747' => 'camsi', 'CSS0010816' => 'camsi', 'CSS0011020' => 'camsi', 'CSS0011115' => 'camsi', 'CSS0011383' => 'camsi', 'CSS0011491' => 'camsi', 'CSS0011602' => 'camsi', 'CSS0011605' => 'camsi', 'CSS0011625' => 'camsi', 'CSS0011654' => 'camsi', 'CSS0011781' => 'camsi', 'CSS0011853' => 'camsi', 'CSS0011898' => 'camsi', 'CSS0011933' => 'camsi', 'CSS0011996' => 'camsi', 'CSS0012066' => 'camsi', 'CSS0012097' => 'camsi', 'CSS0012108' => 'camsi', 'CSS0012226' => 'camsi', 'CSS0012248' => 'camsi', 'CSS0012331' => 'camsi', 'CSS0012797' => 'camsi', 'CSS0012818' => 'camsi', 'CSS0012904' => 'camsi', 'CSS0013001' => 'camsi', 'CSS0013022' => 'camsi', 'CSS0013172' => 'camsi', 'CSS0013244' => 'camsi', 'CSS0013267' => 'camsi', 'CSS0013275' => 'camsi', 'CSS0013324' => 'camsi', 'CSS0013334' => 'camsi', 'CSS0013394' => 'camsi', 'CSS0013549' => 'camsi', 'CSS0013689' => 'camsi', 'CSS0014026' => 'camsi', 'CSS0014049' => 'camsi', 'CSS0014144' => 'camsi', 'CSS0014354' => 'camsi', 'CSS0014579' => 'camsi', 'CSS0014648' => 'camsi', 'CSS0014902' => 'camsi', 'CSS0014979' => 'camsi', 'CSS0015278' => 'camsi', 'CSS0015310' => 'camsi', 'CSS0015364' => 'camsi', 'CSS0015455' => 'camsi', 'CSS0015693' => 'camsi', 'CSS0015774' => 'camsi', 'CSS0015795' => 'camsi', 'CSS0015952' => 'camsi', 'CSS0016104' => 'camsi', 'CSS0016241' => 'camsi', 'CSS0016303' => 'camsi', 'CSS0016490' => 'camsi', 'CSS0016832' => 'camsi', 'CSS0016845' => 'camsi', 'CSS0016914' => 'camsi', 'CSS0016946' => 'camsi', 'CSS0017102' => 'camsi', 'CSS0017193' => 'camsi', 'CSS0017528' => 'camsi', 'CSS0017619' => 'camsi', 'CSS0017679' => 'camsi', 'CSS0017816' => 'camsi', 'CSS0017880' => 'camsi', 'CSS0018106' => 'camsi', 'CSS0018162' => 'camsi', 'CSS0018304' => 'camsi', 'CSS0018406' => 'camsi', 'CSS0018481' => 'camsi', 'CSS0018511' => 'camsi', 'CSS0018596' => 'camsi', 'CSS0018727' => 'camsi', 'CSS0018751' => 'camsi', 'CSS0018777' => 'camsi', 'CSS0018798' => 'camsi', 'CSS0019137' => 'camsi', 'CSS0019177' => 'camsi', 'CSS0019217' => 'camsi', 'CSS0019361' => 'camsi', 'CSS0019516' => 'camsi', 'CSS0019538' => 'camsi', 'CSS0019560' => 'camsi', 'CSS0019819' => 'camsi', 'CSS0019837' => 'camsi', 'CSS0019915' => 'camsi', 'CSS0019925' => 'camsi', 'CSS0020112' => 'camsi', 'CSS0020160' => 'camsi', 'CSS0020378' => 'camsi', 'CSS0020388' => 'camsi', 'CSS0020452' => 'camsi', 'CSS0020588' => 'camsi', 'CSS0020661' => 'camsi', 'CSS0020886' => 'camsi', 'CSS0020973' => 'camsi', 'CSS0021035' => 'camsi', 'CSS0021111' => 'camsi', 'CSS0021131' => 'camsi', 'CSS0021151' => 'camsi', 'CSS0021228' => 'camsi', 'CSS0021397' => 'camsi', 'CSS0021420' => 'camsi', 'CSS0021464' => 'camsi', 'CSS0021547' => 'camsi', 'CSS0021608' => 'camsi', 'CSS0021740' => 'camsi', 'CSS0021826' => 'camsi', 'CSS0021904' => 'camsi', 'CSS0021941' => 'camsi', 'CSS0022189' => 'camsi', 'CSS0022199' => 'camsi', 'CSS0022502' => 'camsi', 'CSS0022531' => 'camsi', 'CSS0022581' => 'camsi', 'CSS0022612' => 'camsi', 'CSS0022621' => 'camsi', 'CSS0022815' => 'camsi', 'CSS0022936' => 'camsi', 'CSS0022964' => 'camsi', 'CSS0022985' => 'camsi', 'CSS0023002' => 'camsi', 'CSS0023006' => 'camsi', 'CSS0023024' => 'camsi', 'CSS0023489' => 'camsi', 'CSS0023593' => 'camsi', 'CSS0023621' => 'camsi', 'CSS0023743' => 'camsi', 'CSS0023804' => 'camsi', 'CSS0023805' => 'camsi', 'CSS0023908' => 'camsi', 'CSS0023938' => 'camsi', 'CSS0023981' => 'camsi', 'CSS0024027' => 'camsi', 'CSS0024169' => 'camsi', 'CSS0024193' => 'camsi', 'CSS0024269' => 'camsi', 'CSS0024336' => 'camsi', 'CSS0024337' => 'camsi', 'CSS0024548' => 'camsi', 'CSS0024564' => 'camsi', 'CSS0024585' => 'camsi', 'CSS0024738' => 'camsi', 'CSS0024833' => 'camsi', 'CSS0024846' => 'camsi', 'CSS0024957' => 'camsi', 'CSS0024974' => 'camsi', 'CSS0025005' => 'camsi', 'CSS0025235' => 'camsi', 'CSS0025465' => 'camsi', 'CSS0025633' => 'camsi', 'CSS0025688' => 'camsi', 'CSS0025759' => 'camsi', 'CSS0025774' => 'camsi', 'CSS0025801' => 'camsi', 'CSS0025942' => 'camsi', 'CSS0026083' => 'camsi', 'CSS0026194' => 'camsi', 'CSS0026230' => 'camsi', 'CSS0026398' => 'camsi', 'CSS0026419' => 'camsi', 'CSS0026679' => 'camsi', 'CSS0026719' => 'camsi', 'CSS0026795' => 'camsi', 'CSS0026835' => 'camsi', 'CSS0026930' => 'camsi', 'CSS0027053' => 'camsi', 'CSS0027130' => 'camsi', 'CSS0027192' => 'camsi', 'CSS0027454' => 'camsi', 'CSS0027467' => 'camsi', 'CSS0027521' => 'camsi', 'CSS0027662' => 'camsi', 'CSS0027795' => 'camsi', 'CSS0027835' => 'camsi', 'CSS0027966' => 'camsi', 'CSS0028090' => 'camsi', 'CSS0028134' => 'camsi', 'CSS0028205' => 'camsi', 'CSS0028263' => 'camsi', 'CSS0028363' => 'camsi', 'CSS0028598' => 'camsi', 'CSS0029175' => 'camsi', 'CSS0029191' => 'camsi', 'CSS0029424' => 'camsi', 'CSS0029479' => 'camsi', 'CSS0029496' => 'camsi', 'CSS0029633' => 'camsi', 'CSS0029837' => 'camsi', 'CSS0029844' => 'camsi', 'CSS0029863' => 'camsi', 'CSS0029874' => 'camsi', 'CSS0029959' => 'camsi', 'CSS0030001' => 'camsi', 'CSS0030093' => 'camsi', 'CSS0030199' => 'camsi', 'CSS0030200' => 'camsi', 'CSS0030427' => 'camsi', 'CSS0030476' => 'camsi', 'CSS0030636' => 'camsi', 'CSS0030673' => 'camsi', 'CSS0030766' => 'camsi', 'CSS0030775' => 'camsi', 'CSS0030858' => 'camsi', 'CSS0030873' => 'camsi', 'CSS0030929' => 'camsi', 'CSS0031028' => 'camsi', 'CSS0031129' => 'camsi', 'CSS0031164' => 'camsi', 'CSS0031340' => 'camsi', 'CSS0031368' => 'camsi', 'CSS0031395' => 'camsi', 'CSS0031596' => 'camsi', 'CSS0031727' => 'camsi', 'CSS0032011' => 'camsi', 'CSS0032160' => 'camsi', 'CSS0032538' => 'camsi', 'CSS0032576' => 'camsi', 'CSS0032603' => 'camsi', 'CSS0032640' => 'camsi', 'CSS0032704' => 'camsi', 'CSS0032851' => 'camsi', 'CSS0032973' => 'camsi', 'CSS0033048' => 'camsi', 'CSS0033082' => 'camsi', 'CSS0033157' => 'camsi', 'CSS0033253' => 'camsi', 'CSS0033347' => 'camsi', 'CSS0033601' => 'camsi', 'CSS0033820' => 'camsi', 'CSS0033881' => 'camsi', 'CSS0033934' => 'camsi', 'CSS0034143' => 'camsi', 'CSS0034176' => 'camsi', 'CSS0034201' => 'camsi', 'CSS0034269' => 'camsi', 'CSS0034303' => 'camsi', 'CSS0034463' => 'camsi', 'CSS0034470' => 'camsi', 'CSS0034514' => 'camsi', 'CSS0034525' => 'camsi', 'CSS0034726' => 'camsi', 'CSS0034727' => 'camsi', 'CSS0034737' => 'camsi', 'CSS0034768' => 'camsi', 'CSS0034890' => 'camsi', 'CSS0034943' => 'camsi', 'CSS0034957' => 'camsi', 'CSS0034973' => 'camsi', 'CSS0035178' => 'camsi', 'CSS0035260' => 'camsi', 'CSS0035316' => 'camsi', 'CSS0035347' => 'camsi', 'CSS0035360' => 'camsi', 'CSS0035380' => 'camsi', 'CSS0035429' => 'camsi', 'CSS0035446' => 'camsi', 'CSS0035737' => 'camsi', 'CSS0035852' => 'camsi', 'CSS0035967' => 'camsi', 'CSS0036001' => 'camsi', 'CSS0036044' => 'camsi', 'CSS0036221' => 'camsi', 'CSS0036333' => 'camsi', 'CSS0036435' => 'camsi', 'CSS0036843' => 'camsi', 'CSS0036846' => 'camsi', 'CSS0037097' => 'camsi', 'CSS0037263' => 'camsi', 'CSS0037370' => 'camsi', 'CSS0037410' => 'camsi', 'CSS0037449' => 'camsi', 'CSS0037603' => 'camsi', 'CSS0037851' => 'camsi', 'CSS0037891' => 'camsi', 'CSS0037996' => 'camsi', 'CSS0038222' => 'camsi', 'CSS0038433' => 'camsi', 'CSS0038441' => 'camsi', 'CSS0038718' => 'camsi', 'CSS0038890' => 'camsi', 'CSS0039049' => 'camsi', 'CSS0039145' => 'camsi', 'CSS0039243' => 'camsi', 'CSS0039294' => 'camsi', 'CSS0039324' => 'camsi', 'CSS0039376' => 'camsi', 'CSS0039475' => 'camsi', 'CSS0039539' => 'camsi', 'CSS0039546' => 'camsi', 'CSS0039567' => 'camsi', 'CSS0039599' => 'camsi', 'CSS0039763' => 'camsi', 'CSS0039863' => 'camsi', 'CSS0040107' => 'camsi', 'CSS0040124' => 'camsi', 'CSS0040151' => 'camsi', 'CSS0040165' => 'camsi', 'CSS0040309' => 'camsi', 'CSS0040318' => 'camsi', 'CSS0040347' => 'camsi', 'CSS0040371' => 'camsi', 'CSS0040456' => 'camsi', 'CSS0040551' => 'camsi', 'CSS0040975' => 'camsi', 'CSS0040981' => 'camsi', 'CSS0041299' => 'camsi', 'CSS0041493' => 'camsi', 'CSS0041658' => 'camsi', 'CSS0041899' => 'camsi', 'CSS0041927' => 'camsi', 'CSS0042016' => 'camsi', 'CSS0042034' => 'camsi', 'CSS0042103' => 'camsi', 'CSS0042172' => 'camsi', 'CSS0042198' => 'camsi', 'CSS0042201' => 'camsi', 'CSS0042308' => 'camsi', 'CSS0042329' => 'camsi', 'CSS0042348' => 'camsi', 'CSS0042349' => 'camsi', 'CSS0042489' => 'camsi', 'CSS0042575' => 'camsi', 'CSS0042624' => 'camsi', 'CSS0042660' => 'camsi', 'CSS0042694' => 'camsi', 'CSS0042995' => 'camsi', 'CSS0043079' => 'camsi', 'CSS0043165' => 'camsi', 'CSS0043171' => 'camsi', 'CSS0043314' => 'camsi', 'CSS0043361' => 'camsi', 'CSS0043375' => 'camsi', 'CSS0043518' => 'camsi', 'CSS0043536' => 'camsi', 'CSS0043678' => 'camsi', 'CSS0043765' => 'camsi', 'CSS0043897' => 'camsi', 'CSS0043944' => 'camsi', 'CSS0044126' => 'camsi', 'CSS0044136' => 'camsi', 'CSS0044179' => 'camsi', 'CSS0044290' => 'camsi', 'CSS0044437' => 'camsi', 'CSS0044502' => 'camsi', 'CSS0044603' => 'camsi', 'CSS0044680' => 'camsi', 'CSS0044685' => 'camsi', 'CSS0044700' => 'camsi', 'CSS0044888' => 'camsi', 'CSS0044923' => 'camsi', 'CSS0044926' => 'camsi', 'CSS0044979' => 'camsi', 'CSS0045049' => 'camsi', 'CSS0045132' => 'camsi', 'CSS0045161' => 'camsi', 'CSS0045219' => 'camsi', 'CSS0045230' => 'camsi', 'CSS0045259' => 'camsi', 'CSS0045324' => 'camsi', 'CSS0045368' => 'camsi', 'CSS0045435' => 'camsi', 'CSS0045856' => 'camsi', 'CSS0045955' => 'camsi', 'CSS0046158' => 'camsi', 'CSS0046334' => 'camsi', 'CSS0046365' => 'camsi', 'CSS0046396' => 'camsi', 'CSS0046400' => 'camsi', 'CSS0046445' => 'camsi', 'CSS0046493' => 'camsi', 'CSS0046640' => 'camsi', 'CSS0046657' => 'camsi', 'CSS0046702' => 'camsi', 'CSS0047208' => 'camsi', 'CSS0047368' => 'camsi', 'CSS0047403' => 'camsi', 'CSS0047417' => 'camsi', 'CSS0047469' => 'camsi', 'CSS0047480' => 'camsi', 'CSS0047482' => 'camsi', 'CSS0047693' => 'camsi', 'CSS0047766' => 'camsi', 'CSS0047866' => 'camsi', 'CSS0047884' => 'camsi', 'CSS0048235' => 'camsi', 'CSS0048383' => 'camsi', 'CSS0048438' => 'camsi', 'CSS0048502' => 'camsi', 'CSS0048546' => 'camsi', 'CSS0048653' => 'camsi', 'CSS0048658' => 'camsi', 'CSS0048729' => 'camsi', 'CSS0048867' => 'camsi', 'CSS0048988' => 'camsi', 'CSS0049053' => 'camsi', 'CSS0049099' => 'camsi', 'CSS0049166' => 'camsi', 'CSS0049174' => 'camsi', 'CSS0049212' => 'camsi', 'CSS0049280' => 'camsi', 'CSS0049391' => 'camsi', 'CSS0049546' => 'camsi', 'CSS0049634' => 'camsi', 'CSS0049655' => 'camsi', 'CSS0049813' => 'camsi', 'CSS0049949' => 'camsi', 'CSS0050009' => 'camsi', 'CSS0050118' => 'camsi', 'CSS0050205' => 'camsi', 'CSS0050275' => 'camsi', 'CSS0050480' => 'camsi', 'CSS0050488' => 'camsi', 'CSS0050497' => 'camsi', 'Dinv03126' => 'din', 'Dinv13140' => 'din', 'Dinv13247' => 'din', 'Dinv14217' => 'din', 'EL10Ac9g22435' => 'bvu', 'FAN20G1200' => 'fan', 'PGR142G2516' => 'pgr', 'Prupe.3G160200' => 'ppe', 'Prupe.5G238200' => 'ppe', 'Prupe.7G047500' => 'ppe', 'QL03p045360' => 'qlo', 'QL05p034369' => 'qlo', 'QL05p034412' => 'qlo', 'QL08p017802' => 'qlo', 'QL08p024762' => 'qlo', 'QL10p026237' => 'qlo', 'QL10p032070' => 'qlo', 'QL11p003821' => 'qlo', 'Rhsim04G0057300' => 'rsi', 'Rhsim05G0049200' => 'rsi', 'Rhsim12G0010400' => 'rsi', 'Rhsim12G0012800' => 'rsi', 'TAR624G0483' => 'tar', 'TAR703G0001' => 'tar', 'vmacro05414' => 'vma', 'vmacro07091' => 'vma', 'vmacro07116' => 'vma', 'vmacro08423' => 'vma', 'vmacro09046' => 'vma', 'vmacro14269' => 'vma', 'vmacro16092' => 'vma', 'vmacro17280' => 'vma', 'vmacro19601' => 'vma' ), 'gf_id' => 'HOM05D001028', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001028' ), 'data_identifier' => 'HOM05D001028', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001028', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '590', 'num_species' => '12' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'Aqoxy1G01649' => 'aox', 'Aqoxy1G02950' => 'aox', 'Aqoxy2G01005' => 'aox', 'Aqoxy2G01064' => 'aox', 'Aqoxy3G02267' => 'aox', 'Aqoxy3G02617' => 'aox', 'Aqoxy3G02693' => 'aox', 'Aqoxy5G03425' => 'aox', 'Aqoxy6G02164' => 'aox', 'Aqoxy6G02364' => 'aox', 'Aqoxy7G02284' => 'aox', 'Cc00_g09720' => 'ccan', 'Cc00_g21410' => 'ccan', 'Cc00_g31750' => 'ccan', 'Cc00_g34740' => 'ccan', 'Cc04_g16890' => 'ccan', 'Cc11_g03120' => 'ccan', 'CSS0000222' => 'camsi', 'CSS0000265' => 'camsi', 'CSS0000306' => 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'camsi', 'CSS0030427' => 'camsi', 'CSS0030476' => 'camsi', 'CSS0030636' => 'camsi', 'CSS0030673' => 'camsi', 'CSS0030766' => 'camsi', 'CSS0030775' => 'camsi', 'CSS0030858' => 'camsi', 'CSS0030873' => 'camsi', 'CSS0030929' => 'camsi', 'CSS0031028' => 'camsi', 'CSS0031129' => 'camsi', 'CSS0031164' => 'camsi', 'CSS0031340' => 'camsi', 'CSS0031368' => 'camsi', 'CSS0031395' => 'camsi', 'CSS0031596' => 'camsi', 'CSS0031727' => 'camsi', 'CSS0032011' => 'camsi', 'CSS0032160' => 'camsi', 'CSS0032538' => 'camsi', 'CSS0032576' => 'camsi', 'CSS0032603' => 'camsi', 'CSS0032640' => 'camsi', 'CSS0032704' => 'camsi', 'CSS0032851' => 'camsi', 'CSS0032973' => 'camsi', 'CSS0033048' => 'camsi', 'CSS0033082' => 'camsi', 'CSS0033157' => 'camsi', 'CSS0033253' => 'camsi', 'CSS0033347' => 'camsi', 'CSS0033601' => 'camsi', 'CSS0033820' => 'camsi', 'CSS0033881' => 'camsi', 'CSS0033934' => 'camsi', 'CSS0034143' => 'camsi', 'CSS0034176' => 'camsi', 'CSS0034201' => 'camsi', 'CSS0034269' => 'camsi', 'CSS0034303' => 'camsi', 'CSS0034463' => 'camsi', 'CSS0034470' => 'camsi', 'CSS0034514' => 'camsi', 'CSS0034525' => 'camsi', 'CSS0034726' => 'camsi', 'CSS0034727' => 'camsi', 'CSS0034737' => 'camsi', 'CSS0034768' => 'camsi', 'CSS0034890' => 'camsi', 'CSS0034943' => 'camsi', 'CSS0034957' => 'camsi', 'CSS0034973' => 'camsi', 'CSS0035178' => 'camsi', 'CSS0035260' => 'camsi', 'CSS0035316' => 'camsi', 'CSS0035347' => 'camsi', 'CSS0035360' => 'camsi', 'CSS0035380' => 'camsi', 'CSS0035429' => 'camsi', 'CSS0035446' => 'camsi', 'CSS0035737' => 'camsi', 'CSS0035852' => 'camsi', 'CSS0035967' => 'camsi', 'CSS0036001' => 'camsi', 'CSS0036044' => 'camsi', 'CSS0036221' => 'camsi', 'CSS0036333' => 'camsi', 'CSS0036435' => 'camsi', 'CSS0036843' => 'camsi', 'CSS0036846' => 'camsi', 'CSS0037097' => 'camsi', 'CSS0037263' => 'camsi', 'CSS0037370' => 'camsi', 'CSS0037410' => 'camsi', 'CSS0037449' => 'camsi', 'CSS0037603' => 'camsi', 'CSS0037851' => 'camsi', 'CSS0037891' => 'camsi', 'CSS0037996' => 'camsi', 'CSS0038222' => 'camsi', 'CSS0038433' => 'camsi', 'CSS0038441' => 'camsi', 'CSS0038718' => 'camsi', 'CSS0038890' => 'camsi', 'CSS0039049' => 'camsi', 'CSS0039145' => 'camsi', 'CSS0039243' => 'camsi', 'CSS0039294' => 'camsi', 'CSS0039324' => 'camsi', 'CSS0039376' => 'camsi', 'CSS0039475' => 'camsi', 'CSS0039539' => 'camsi', 'CSS0039546' => 'camsi', 'CSS0039567' => 'camsi', 'CSS0039599' => 'camsi', 'CSS0039763' => 'camsi', 'CSS0039863' => 'camsi', 'CSS0040107' => 'camsi', 'CSS0040124' => 'camsi', 'CSS0040151' => 'camsi', 'CSS0040165' => 'camsi', 'CSS0040309' => 'camsi', 'CSS0040318' => 'camsi', 'CSS0040347' => 'camsi', 'CSS0040371' => 'camsi', 'CSS0040456' => 'camsi', 'CSS0040551' => 'camsi', 'CSS0040975' => 'camsi', 'CSS0040981' => 'camsi', 'CSS0041299' => 'camsi', 'CSS0041493' => 'camsi', 'CSS0041658' => 'camsi', 'CSS0041899' => 'camsi', 'CSS0041927' => 'camsi', 'CSS0042016' => 'camsi', 'CSS0042034' => 'camsi', 'CSS0042103' => 'camsi', 'CSS0042172' => 'camsi', 'CSS0042198' => 'camsi', 'CSS0042201' => 'camsi', 'CSS0042308' => 'camsi', 'CSS0042329' => 'camsi', 'CSS0042348' => 'camsi', 'CSS0042349' => 'camsi', 'CSS0042489' => 'camsi', 'CSS0042575' => 'camsi', 'CSS0042624' => 'camsi', 'CSS0042660' => 'camsi', 'CSS0042694' => 'camsi', 'CSS0042995' => 'camsi', 'CSS0043079' => 'camsi', 'CSS0043165' => 'camsi', 'CSS0043171' => 'camsi', 'CSS0043314' => 'camsi', 'CSS0043361' => 'camsi', 'CSS0043375' => 'camsi', 'CSS0043518' => 'camsi', 'CSS0043536' => 'camsi', 'CSS0043678' => 'camsi', 'CSS0043765' => 'camsi', 'CSS0043897' => 'camsi', 'CSS0043944' => 'camsi', 'CSS0044126' => 'camsi', 'CSS0044136' => 'camsi', 'CSS0044179' => 'camsi', 'CSS0044290' => 'camsi', 'CSS0044437' => 'camsi', 'CSS0044502' => 'camsi', 'CSS0044603' => 'camsi', 'CSS0044680' => 'camsi', 'CSS0044685' => 'camsi', 'CSS0044700' => 'camsi', 'CSS0044888' => 'camsi', 'CSS0044923' => 'camsi', 'CSS0044926' => 'camsi', 'CSS0044979' => 'camsi', 'CSS0045049' => 'camsi', 'CSS0045132' => 'camsi', 'CSS0045161' => 'camsi', 'CSS0045219' => 'camsi', 'CSS0045230' => 'camsi', 'CSS0045259' => 'camsi', 'CSS0045324' => 'camsi', 'CSS0045368' => 'camsi', 'CSS0045435' => 'camsi', 'CSS0045856' => 'camsi', 'CSS0045955' => 'camsi', 'CSS0046158' => 'camsi', 'CSS0046334' => 'camsi', 'CSS0046365' => 'camsi', 'CSS0046396' => 'camsi', 'CSS0046400' => 'camsi', 'CSS0046445' => 'camsi', 'CSS0046493' => 'camsi', 'CSS0046640' => 'camsi', 'CSS0046657' => 'camsi', 'CSS0046702' => 'camsi', 'CSS0047208' => 'camsi', 'CSS0047368' => 'camsi', 'CSS0047403' => 'camsi', 'CSS0047417' => 'camsi', 'CSS0047469' => 'camsi', 'CSS0047480' => 'camsi', 'CSS0047482' => 'camsi', 'CSS0047693' => 'camsi', 'CSS0047766' => 'camsi', 'CSS0047866' => 'camsi', 'CSS0047884' => 'camsi', 'CSS0048235' => 'camsi', 'CSS0048383' => 'camsi', 'CSS0048438' => 'camsi', 'CSS0048502' => 'camsi', 'CSS0048546' => 'camsi', 'CSS0048653' => 'camsi', 'CSS0048658' => 'camsi', 'CSS0048729' => 'camsi', 'CSS0048867' => 'camsi', 'CSS0048988' => 'camsi', 'CSS0049053' => 'camsi', 'CSS0049099' => 'camsi', 'CSS0049166' => 'camsi', 'CSS0049174' => 'camsi', 'CSS0049212' => 'camsi', 'CSS0049280' => 'camsi', 'CSS0049391' => 'camsi', 'CSS0049546' => 'camsi', 'CSS0049634' => 'camsi', 'CSS0049655' => 'camsi', 'CSS0049813' => 'camsi', 'CSS0049949' => 'camsi', 'CSS0050009' => 'camsi', 'CSS0050118' => 'camsi', 'CSS0050205' => 'camsi', 'CSS0050275' => 'camsi', 'CSS0050480' => 'camsi', 'CSS0050488' => 'camsi', 'CSS0050497' => 'camsi', 'Dinv03126' => 'din', 'Dinv13140' => 'din', 'Dinv13247' => 'din', 'Dinv14217' => 'din', 'EL10Ac9g22435' => 'bvu', 'FAN20G1200' => 'fan', 'PGR142G2516' => 'pgr', 'Prupe.3G160200' => 'ppe', 'Prupe.5G238200' => 'ppe', 'Prupe.7G047500' => 'ppe', 'QL03p045360' => 'qlo', 'QL05p034369' => 'qlo', 'QL05p034412' => 'qlo', 'QL08p017802' => 'qlo', 'QL08p024762' => 'qlo', 'QL10p026237' => 'qlo', 'QL10p032070' => 'qlo', 'QL11p003821' => 'qlo', 'Rhsim04G0057300' => 'rsi', 'Rhsim05G0049200' => 'rsi', 'Rhsim12G0010400' => 'rsi', 'Rhsim12G0012800' => 'rsi', 'TAR624G0483' => 'tar', 'TAR703G0001' => 'tar', 'vmacro05414' => 'vma', 'vmacro07091' => 'vma', 'vmacro07116' => 'vma', 'vmacro08423' => 'vma', 'vmacro09046' => 'vma', 'vmacro14269' => 'vma', 'vmacro16092' => 'vma', 'vmacro17280' => 'vma', 'vmacro19601' => 'vma' ) $gf_id = 'HOM05D001028' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001028' ) $data_identifier = 'HOM05D001028' $data_type = 'gf_id' $species_gene_counts = array( 'aox' => (int) 11, 'ccan' => (int) 6, 'camsi' => (int) 540, 'din' => (int) 4, 'bvu' => (int) 1, 'fan' => (int) 1, 'pgr' => (int) 1, 'ppe' => (int) 3, 'qlo' => (int) 8, 'rsi' => (int) 4, 'tar' => (int) 2, 'vma' => (int) 9 ) $gf_gene_species = 'vma' $gf_gene_id = 'vmacro19601' $species_info = array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ) $local_species = 'tar' $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' => 'HOM05D001028', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '590', 'num_species' => '12' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'Aqoxy1G01649' => 'aox', 'Aqoxy1G02950' => 'aox', 'Aqoxy2G01005' => 'aox', 'Aqoxy2G01064' => 'aox', 'Aqoxy3G02267' => 'aox', 'Aqoxy3G02617' => 'aox', 'Aqoxy3G02693' => 'aox', 'Aqoxy5G03425' => 'aox', 'Aqoxy6G02164' => 'aox', 'Aqoxy6G02364' => 'aox', 'Aqoxy7G02284' => 'aox', 'Cc00_g09720' => 'ccan', 'Cc00_g21410' => 'ccan', 'Cc00_g31750' => 'ccan', 'Cc00_g34740' => 'ccan', 'Cc04_g16890' => 'ccan', 'Cc11_g03120' => 'ccan', 'CSS0000222' => 'camsi', 'CSS0000265' => 'camsi', 'CSS0000306' => 'camsi', 'CSS0000326' => 'camsi', 'CSS0000530' => 'camsi', 'CSS0000563' => 'camsi', 'CSS0000584' => 'camsi', 'CSS0000684' => 'camsi', 'CSS0001100' => 'camsi', 'CSS0001311' => 'camsi', 'CSS0001343' => 'camsi', 'CSS0001399' => 'camsi', 'CSS0001475' => 'camsi', 'CSS0001506' => 'camsi', 'CSS0001602' => 'camsi', 'CSS0001681' => 'camsi', 'CSS0001874' => 'camsi', 'CSS0001948' => 'camsi', 'CSS0002022' => 'camsi', 'CSS0002230' => 'camsi', 'CSS0002265' => 'camsi', 'CSS0002277' => 'camsi', 'CSS0002462' => 'camsi', 'CSS0002823' => 'camsi', 'CSS0003091' => 'camsi', 'CSS0003162' => 'camsi', 'CSS0003264' => 'camsi', 'CSS0003355' => 'camsi', 'CSS0003378' => 'camsi', 'CSS0003472' => 'camsi', 'CSS0003500' => 'camsi', 'CSS0003640' => 'camsi', 'CSS0003767' => 'camsi', 'CSS0003894' => 'camsi', 'CSS0003952' => 'camsi', 'CSS0003977' => 'camsi', 'CSS0004028' => 'camsi', 'CSS0004117' => 'camsi', 'CSS0004137' => 'camsi', 'CSS0004176' => 'camsi', 'CSS0004265' => 'camsi', 'CSS0004450' => 'camsi', 'CSS0004468' => 'camsi', 'CSS0004488' => 'camsi', 'CSS0004490' => 'camsi', 'CSS0004632' => 'camsi', 'CSS0004790' => 'camsi', 'CSS0004877' => 'camsi', 'CSS0004920' => 'camsi', 'CSS0004969' => 'camsi', 'CSS0005084' => 'camsi', 'CSS0005101' => 'camsi', 'CSS0005271' => 'camsi', 'CSS0005313' => 'camsi', 'CSS0005331' => 'camsi', 'CSS0005368' => 'camsi', 'CSS0005391' => 'camsi', 'CSS0005437' => 'camsi', 'CSS0005515' => 'camsi', 'CSS0005526' => 'camsi', 'CSS0005532' => 'camsi', 'CSS0005595' => 'camsi', 'CSS0005677' => 'camsi', 'CSS0005838' => 'camsi', 'CSS0005988' => 'camsi', 'CSS0006100' => 'camsi', 'CSS0006128' => 'camsi', 'CSS0006293' => 'camsi', 'CSS0006378' => 'camsi', 'CSS0006400' => 'camsi', 'CSS0006441' => 'camsi', 'CSS0006455' => 'camsi', 'CSS0006480' => 'camsi', 'CSS0006483' => 'camsi', 'CSS0006538' => 'camsi', 'CSS0006582' => 'camsi', 'CSS0006632' => 'camsi', 'CSS0006771' => 'camsi', 'CSS0006803' => 'camsi', 'CSS0006852' => 'camsi', 'CSS0006861' => 'camsi', 'CSS0006910' => 'camsi', 'CSS0007037' => 'camsi', 'CSS0007066' => 'camsi', 'CSS0007072' => 'camsi', 'CSS0007109' => 'camsi', 'CSS0007193' => 'camsi', 'CSS0007319' => 'camsi', 'CSS0007336' => 'camsi', 'CSS0007377' => 'camsi', 'CSS0007659' => 'camsi', 'CSS0007701' => 'camsi', 'CSS0007711' => 'camsi', 'CSS0007809' => 'camsi', 'CSS0008045' => 'camsi', 'CSS0008050' => 'camsi', 'CSS0008206' => 'camsi', 'CSS0008251' => 'camsi', 'CSS0008252' => 'camsi', 'CSS0008279' => 'camsi', 'CSS0008482' => 'camsi', 'CSS0008583' => 'camsi', 'CSS0008699' => 'camsi', 'CSS0008798' => 'camsi', 'CSS0008971' => 'camsi', 'CSS0009019' => 'camsi', 'CSS0009191' => 'camsi', 'CSS0009241' => 'camsi', 'CSS0009246' => 'camsi', 'CSS0009399' => 'camsi', 'CSS0009654' => 'camsi', 'CSS0009722' => 'camsi', 'CSS0009920' => 'camsi', 'CSS0009986' => 'camsi', 'CSS0010182' => 'camsi', 'CSS0010202' => 'camsi', 'CSS0010330' => 'camsi', 'CSS0010362' => 'camsi', 'CSS0010456' => 'camsi', 'CSS0010472' => 'camsi', 'CSS0010507' => 'camsi', 'CSS0010512' => 'camsi', 'CSS0010520' => 'camsi', 'CSS0010617' => 'camsi', 'CSS0010706' => 'camsi', 'CSS0010747' => 'camsi', 'CSS0010816' => 'camsi', 'CSS0011020' => 'camsi', 'CSS0011115' => 'camsi', 'CSS0011383' => 'camsi', 'CSS0011491' => 'camsi', 'CSS0011602' => 'camsi', 'CSS0011605' => 'camsi', 'CSS0011625' => 'camsi', 'CSS0011654' => 'camsi', 'CSS0011781' => 'camsi', 'CSS0011853' => 'camsi', 'CSS0011898' => 'camsi', 'CSS0011933' => 'camsi', 'CSS0011996' => 'camsi', 'CSS0012066' => 'camsi', 'CSS0012097' => 'camsi', 'CSS0012108' => 'camsi', 'CSS0012226' => 'camsi', 'CSS0012248' => 'camsi', 'CSS0012331' => 'camsi', 'CSS0012797' => 'camsi', 'CSS0012818' => 'camsi', 'CSS0012904' => 'camsi', 'CSS0013001' => 'camsi', 'CSS0013022' => 'camsi', 'CSS0013172' => 'camsi', 'CSS0013244' => 'camsi', 'CSS0013267' => 'camsi', 'CSS0013275' => 'camsi', 'CSS0013324' => 'camsi', 'CSS0013334' => 'camsi', 'CSS0013394' => 'camsi', 'CSS0013549' => 'camsi', 'CSS0013689' => 'camsi', 'CSS0014026' => 'camsi', 'CSS0014049' => 'camsi', 'CSS0014144' => 'camsi', 'CSS0014354' => 'camsi', 'CSS0014579' => 'camsi', 'CSS0014648' => 'camsi', 'CSS0014902' => 'camsi', 'CSS0014979' => 'camsi', 'CSS0015278' => 'camsi', 'CSS0015310' => 'camsi', 'CSS0015364' => 'camsi', 'CSS0015455' => 'camsi', 'CSS0015693' => 'camsi', 'CSS0015774' => 'camsi', 'CSS0015795' => 'camsi', 'CSS0015952' => 'camsi', 'CSS0016104' => 'camsi', 'CSS0016241' => 'camsi', 'CSS0016303' => 'camsi', 'CSS0016490' => 'camsi', 'CSS0016832' => 'camsi', 'CSS0016845' => 'camsi', 'CSS0016914' => 'camsi', 'CSS0016946' => 'camsi', 'CSS0017102' => 'camsi', 'CSS0017193' => 'camsi', 'CSS0017528' => 'camsi', 'CSS0017619' => 'camsi', 'CSS0017679' => 'camsi', 'CSS0017816' => 'camsi', 'CSS0017880' => 'camsi', 'CSS0018106' => 'camsi', 'CSS0018162' => 'camsi', 'CSS0018304' => 'camsi', 'CSS0018406' => 'camsi', 'CSS0018481' => 'camsi', 'CSS0018511' => 'camsi', 'CSS0018596' => 'camsi', 'CSS0018727' => 'camsi', 'CSS0018751' => 'camsi', 'CSS0018777' => 'camsi', 'CSS0018798' => 'camsi', 'CSS0019137' => 'camsi', 'CSS0019177' => 'camsi', 'CSS0019217' => 'camsi', 'CSS0019361' => 'camsi', 'CSS0019516' => 'camsi', 'CSS0019538' => 'camsi', 'CSS0019560' => 'camsi', 'CSS0019819' => 'camsi', 'CSS0019837' => 'camsi', 'CSS0019915' => 'camsi', 'CSS0019925' => 'camsi', 'CSS0020112' => 'camsi', 'CSS0020160' => 'camsi', 'CSS0020378' => 'camsi', 'CSS0020388' => 'camsi', 'CSS0020452' => 'camsi', 'CSS0020588' => 'camsi', 'CSS0020661' => 'camsi', 'CSS0020886' => 'camsi', 'CSS0020973' => 'camsi', 'CSS0021035' => 'camsi', 'CSS0021111' => 'camsi', 'CSS0021131' => 'camsi', 'CSS0021151' => 'camsi', 'CSS0021228' => 'camsi', 'CSS0021397' => 'camsi', 'CSS0021420' => 'camsi', 'CSS0021464' => 'camsi', 'CSS0021547' => 'camsi', 'CSS0021608' => 'camsi', 'CSS0021740' => 'camsi', 'CSS0021826' => 'camsi', 'CSS0021904' => 'camsi', 'CSS0021941' => 'camsi', 'CSS0022189' => 'camsi', 'CSS0022199' => 'camsi', 'CSS0022502' => 'camsi', 'CSS0022531' => 'camsi', 'CSS0022581' => 'camsi', 'CSS0022612' => 'camsi', 'CSS0022621' => 'camsi', 'CSS0022815' => 'camsi', 'CSS0022936' => 'camsi', 'CSS0022964' => 'camsi', 'CSS0022985' => 'camsi', 'CSS0023002' => 'camsi', 'CSS0023006' => 'camsi', 'CSS0023024' => 'camsi', 'CSS0023489' => 'camsi', 'CSS0023593' => 'camsi', 'CSS0023621' => 'camsi', 'CSS0023743' => 'camsi', 'CSS0023804' => 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'camsi', 'CSS0035178' => 'camsi', 'CSS0035260' => 'camsi', 'CSS0035316' => 'camsi', 'CSS0035347' => 'camsi', 'CSS0035360' => 'camsi', 'CSS0035380' => 'camsi', 'CSS0035429' => 'camsi', 'CSS0035446' => 'camsi', 'CSS0035737' => 'camsi', 'CSS0035852' => 'camsi', 'CSS0035967' => 'camsi', 'CSS0036001' => 'camsi', 'CSS0036044' => 'camsi', 'CSS0036221' => 'camsi', 'CSS0036333' => 'camsi', 'CSS0036435' => 'camsi', 'CSS0036843' => 'camsi', 'CSS0036846' => 'camsi', 'CSS0037097' => 'camsi', 'CSS0037263' => 'camsi', 'CSS0037370' => 'camsi', 'CSS0037410' => 'camsi', 'CSS0037449' => 'camsi', 'CSS0037603' => 'camsi', 'CSS0037851' => 'camsi', 'CSS0037891' => 'camsi', 'CSS0037996' => 'camsi', 'CSS0038222' => 'camsi', 'CSS0038433' => 'camsi', 'CSS0038441' => 'camsi', 'CSS0038718' => 'camsi', 'CSS0038890' => 'camsi', 'CSS0039049' => 'camsi', 'CSS0039145' => 'camsi', 'CSS0039243' => 'camsi', 'CSS0039294' => 'camsi', 'CSS0039324' => 'camsi', 'CSS0039376' => 'camsi', 'CSS0039475' => 'camsi', 'CSS0039539' => 'camsi', 'CSS0039546' => 'camsi', 'CSS0039567' => 'camsi', 'CSS0039599' => 'camsi', 'CSS0039763' => 'camsi', 'CSS0039863' => 'camsi', 'CSS0040107' => 'camsi', 'CSS0040124' => 'camsi', 'CSS0040151' => 'camsi', 'CSS0040165' => 'camsi', 'CSS0040309' => 'camsi', 'CSS0040318' => 'camsi', 'CSS0040347' => 'camsi', 'CSS0040371' => 'camsi', 'CSS0040456' => 'camsi', 'CSS0040551' => 'camsi', 'CSS0040975' => 'camsi', 'CSS0040981' => 'camsi', 'CSS0041299' => 'camsi', 'CSS0041493' => 'camsi', 'CSS0041658' => 'camsi', 'CSS0041899' => 'camsi', 'CSS0041927' => 'camsi', 'CSS0042016' => 'camsi', 'CSS0042034' => 'camsi', 'CSS0042103' => 'camsi', 'CSS0042172' => 'camsi', 'CSS0042198' => 'camsi', 'CSS0042201' => 'camsi', 'CSS0042308' => 'camsi', 'CSS0042329' => 'camsi', 'CSS0042348' => 'camsi', 'CSS0042349' => 'camsi', 'CSS0042489' => 'camsi', 'CSS0042575' => 'camsi', 'CSS0042624' => 'camsi', 'CSS0042660' => 'camsi', 'CSS0042694' => 'camsi', 'CSS0042995' => 'camsi', 'CSS0043079' => 'camsi', 'CSS0043165' => 'camsi', 'CSS0043171' => 'camsi', 'CSS0043314' => 'camsi', 'CSS0043361' => 'camsi', 'CSS0043375' => 'camsi', 'CSS0043518' => 'camsi', 'CSS0043536' => 'camsi', 'CSS0043678' => 'camsi', 'CSS0043765' => 'camsi', 'CSS0043897' => 'camsi', 'CSS0043944' => 'camsi', 'CSS0044126' => 'camsi', 'CSS0044136' => 'camsi', 'CSS0044179' => 'camsi', 'CSS0044290' => 'camsi', 'CSS0044437' => 'camsi', 'CSS0044502' => 'camsi', 'CSS0044603' => 'camsi', 'CSS0044680' => 'camsi', 'CSS0044685' => 'camsi', 'CSS0044700' => 'camsi', 'CSS0044888' => 'camsi', 'CSS0044923' => 'camsi', 'CSS0044926' => 'camsi', 'CSS0044979' => 'camsi', 'CSS0045049' => 'camsi', 'CSS0045132' => 'camsi', 'CSS0045161' => 'camsi', 'CSS0045219' => 'camsi', 'CSS0045230' => 'camsi', 'CSS0045259' => 'camsi', 'CSS0045324' => 'camsi', 'CSS0045368' => 'camsi', 'CSS0045435' => 'camsi', 'CSS0045856' => 'camsi', 'CSS0045955' => 'camsi', 'CSS0046158' => 'camsi', 'CSS0046334' => 'camsi', 'CSS0046365' => 'camsi', 'CSS0046396' => 'camsi', 'CSS0046400' => 'camsi', 'CSS0046445' => 'camsi', 'CSS0046493' => 'camsi', 'CSS0046640' => 'camsi', 'CSS0046657' => 'camsi', 'CSS0046702' => 'camsi', 'CSS0047208' => 'camsi', 'CSS0047368' => 'camsi', 'CSS0047403' => 'camsi', 'CSS0047417' => 'camsi', 'CSS0047469' => 'camsi', 'CSS0047480' => 'camsi', 'CSS0047482' => 'camsi', 'CSS0047693' => 'camsi', 'CSS0047766' => 'camsi', 'CSS0047866' => 'camsi', 'CSS0047884' => 'camsi', 'CSS0048235' => 'camsi', 'CSS0048383' => 'camsi', 'CSS0048438' => 'camsi', 'CSS0048502' => 'camsi', 'CSS0048546' => 'camsi', 'CSS0048653' => 'camsi', 'CSS0048658' => 'camsi', 'CSS0048729' => 'camsi', 'CSS0048867' => 'camsi', 'CSS0048988' => 'camsi', 'CSS0049053' => 'camsi', 'CSS0049099' => 'camsi', 'CSS0049166' => 'camsi', 'CSS0049174' => 'camsi', 'CSS0049212' => 'camsi', 'CSS0049280' => 'camsi', 'CSS0049391' => 'camsi', 'CSS0049546' => 'camsi', 'CSS0049634' => 'camsi', 'CSS0049655' => 'camsi', 'CSS0049813' => 'camsi', 'CSS0049949' => 'camsi', 'CSS0050009' => 'camsi', 'CSS0050118' => 'camsi', 'CSS0050205' => 'camsi', 'CSS0050275' => 'camsi', 'CSS0050480' => 'camsi', 'CSS0050488' => 'camsi', 'CSS0050497' => 'camsi', 'Dinv03126' => 'din', 'Dinv13140' => 'din', 'Dinv13247' => 'din', 'Dinv14217' => 'din', 'EL10Ac9g22435' => 'bvu', 'FAN20G1200' => 'fan', 'PGR142G2516' => 'pgr', 'Prupe.3G160200' => 'ppe', 'Prupe.5G238200' => 'ppe', 'Prupe.7G047500' => 'ppe', 'QL03p045360' => 'qlo', 'QL05p034369' => 'qlo', 'QL05p034412' => 'qlo', 'QL08p017802' => 'qlo', 'QL08p024762' => 'qlo', 'QL10p026237' => 'qlo', 'QL10p032070' => 'qlo', 'QL11p003821' => 'qlo', 'Rhsim04G0057300' => 'rsi', 'Rhsim05G0049200' => 'rsi', 'Rhsim12G0010400' => 'rsi', 'Rhsim12G0012800' => 'rsi', 'TAR624G0483' => 'tar', 'TAR703G0001' => 'tar', 'vmacro05414' => 'vma', 'vmacro07091' => 'vma', 'vmacro07116' => 'vma', 'vmacro08423' => 'vma', 'vmacro09046' => 'vma', 'vmacro14269' => 'vma', 'vmacro16092' => 'vma', 'vmacro17280' => 'vma', 'vmacro19601' => 'vma' ), 'gf_id' => 'HOM05D001028', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001028' ), 'data_identifier' => 'HOM05D001028', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001028', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '590', 'num_species' => '12' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'Aqoxy1G01649' => 'aox', 'Aqoxy1G02950' => 'aox', 'Aqoxy2G01005' => 'aox', 'Aqoxy2G01064' => 'aox', 'Aqoxy3G02267' => 'aox', 'Aqoxy3G02617' => 'aox', 'Aqoxy3G02693' => 'aox', 'Aqoxy5G03425' => 'aox', 'Aqoxy6G02164' => 'aox', 'Aqoxy6G02364' => 'aox', 'Aqoxy7G02284' => 'aox', 'Cc00_g09720' => 'ccan', 'Cc00_g21410' => 'ccan', 'Cc00_g31750' => 'ccan', 'Cc00_g34740' => 'ccan', 'Cc04_g16890' => 'ccan', 'Cc11_g03120' => 'ccan', 'CSS0000222' => 'camsi', 'CSS0000265' => 'camsi', 'CSS0000306' => 'camsi', 'CSS0000326' => 'camsi', 'CSS0000530' => 'camsi', 'CSS0000563' => 'camsi', 'CSS0000584' => 'camsi', 'CSS0000684' => 'camsi', 'CSS0001100' => 'camsi', 'CSS0001311' => 'camsi', 'CSS0001343' => 'camsi', 'CSS0001399' => 'camsi', 'CSS0001475' => 'camsi', 'CSS0001506' => 'camsi', 'CSS0001602' => 'camsi', 'CSS0001681' => 'camsi', 'CSS0001874' => 'camsi', 'CSS0001948' => 'camsi', 'CSS0002022' => 'camsi', 'CSS0002230' => 'camsi', 'CSS0002265' => 'camsi', 'CSS0002277' => 'camsi', 'CSS0002462' => 'camsi', 'CSS0002823' => 'camsi', 'CSS0003091' => 'camsi', 'CSS0003162' => 'camsi', 'CSS0003264' => 'camsi', 'CSS0003355' => 'camsi', 'CSS0003378' => 'camsi', 'CSS0003472' => 'camsi', 'CSS0003500' => 'camsi', 'CSS0003640' => 'camsi', 'CSS0003767' => 'camsi', 'CSS0003894' => 'camsi', 'CSS0003952' => 'camsi', 'CSS0003977' => 'camsi', 'CSS0004028' => 'camsi', 'CSS0004117' => 'camsi', 'CSS0004137' => 'camsi', 'CSS0004176' => 'camsi', 'CSS0004265' => 'camsi', 'CSS0004450' => 'camsi', 'CSS0004468' => 'camsi', 'CSS0004488' => 'camsi', 'CSS0004490' => 'camsi', 'CSS0004632' => 'camsi', 'CSS0004790' => 'camsi', 'CSS0004877' => 'camsi', 'CSS0004920' => 'camsi', 'CSS0004969' => 'camsi', 'CSS0005084' => 'camsi', 'CSS0005101' => 'camsi', 'CSS0005271' => 'camsi', 'CSS0005313' => 'camsi', 'CSS0005331' => 'camsi', 'CSS0005368' => 'camsi', 'CSS0005391' => 'camsi', 'CSS0005437' => 'camsi', 'CSS0005515' => 'camsi', 'CSS0005526' => 'camsi', 'CSS0005532' => 'camsi', 'CSS0005595' => 'camsi', 'CSS0005677' => 'camsi', 'CSS0005838' => 'camsi', 'CSS0005988' => 'camsi', 'CSS0006100' => 'camsi', 'CSS0006128' => 'camsi', 'CSS0006293' => 'camsi', 'CSS0006378' => 'camsi', 'CSS0006400' => 'camsi', 'CSS0006441' => 'camsi', 'CSS0006455' => 'camsi', 'CSS0006480' => 'camsi', 'CSS0006483' => 'camsi', 'CSS0006538' => 'camsi', 'CSS0006582' => 'camsi', 'CSS0006632' => 'camsi', 'CSS0006771' => 'camsi', 'CSS0006803' => 'camsi', 'CSS0006852' => 'camsi', 'CSS0006861' => 'camsi', 'CSS0006910' => 'camsi', 'CSS0007037' => 'camsi', 'CSS0007066' => 'camsi', 'CSS0007072' => 'camsi', 'CSS0007109' => 'camsi', 'CSS0007193' => 'camsi', 'CSS0007319' => 'camsi', 'CSS0007336' => 'camsi', 'CSS0007377' => 'camsi', 'CSS0007659' => 'camsi', 'CSS0007701' => 'camsi', 'CSS0007711' => 'camsi', 'CSS0007809' => 'camsi', 'CSS0008045' => 'camsi', 'CSS0008050' => 'camsi', 'CSS0008206' => 'camsi', 'CSS0008251' => 'camsi', 'CSS0008252' => 'camsi', 'CSS0008279' => 'camsi', 'CSS0008482' => 'camsi', 'CSS0008583' => 'camsi', 'CSS0008699' => 'camsi', 'CSS0008798' => 'camsi', 'CSS0008971' => 'camsi', 'CSS0009019' => 'camsi', 'CSS0009191' => 'camsi', 'CSS0009241' => 'camsi', 'CSS0009246' => 'camsi', 'CSS0009399' => 'camsi', 'CSS0009654' => 'camsi', 'CSS0009722' => 'camsi', 'CSS0009920' => 'camsi', 'CSS0009986' => 'camsi', 'CSS0010182' => 'camsi', 'CSS0010202' => 'camsi', 'CSS0010330' => 'camsi', 'CSS0010362' => 'camsi', 'CSS0010456' => 'camsi', 'CSS0010472' => 'camsi', 'CSS0010507' => 'camsi', 'CSS0010512' => 'camsi', 'CSS0010520' => 'camsi', 'CSS0010617' => 'camsi', 'CSS0010706' => 'camsi', 'CSS0010747' => 'camsi', 'CSS0010816' => 'camsi', 'CSS0011020' => 'camsi', 'CSS0011115' => 'camsi', 'CSS0011383' => 'camsi', 'CSS0011491' => 'camsi', 'CSS0011602' => 'camsi', 'CSS0011605' => 'camsi', 'CSS0011625' => 'camsi', 'CSS0011654' => 'camsi', 'CSS0011781' => 'camsi', 'CSS0011853' => 'camsi', 'CSS0011898' => 'camsi', 'CSS0011933' => 'camsi', 'CSS0011996' => 'camsi', 'CSS0012066' => 'camsi', 'CSS0012097' => 'camsi', 'CSS0012108' => 'camsi', 'CSS0012226' => 'camsi', 'CSS0012248' => 'camsi', 'CSS0012331' => 'camsi', 'CSS0012797' => 'camsi', 'CSS0012818' => 'camsi', 'CSS0012904' => 'camsi', 'CSS0013001' => 'camsi', 'CSS0013022' => 'camsi', 'CSS0013172' => 'camsi', 'CSS0013244' => 'camsi', 'CSS0013267' => 'camsi', 'CSS0013275' => 'camsi', 'CSS0013324' => 'camsi', 'CSS0013334' => 'camsi', 'CSS0013394' => 'camsi', 'CSS0013549' => 'camsi', 'CSS0013689' => 'camsi', 'CSS0014026' => 'camsi', 'CSS0014049' => 'camsi', 'CSS0014144' => 'camsi', 'CSS0014354' => 'camsi', 'CSS0014579' => 'camsi', 'CSS0014648' => 'camsi', 'CSS0014902' => 'camsi', 'CSS0014979' => 'camsi', 'CSS0015278' => 'camsi', 'CSS0015310' => 'camsi', 'CSS0015364' => 'camsi', 'CSS0015455' => 'camsi', 'CSS0015693' => 'camsi', 'CSS0015774' => 'camsi', 'CSS0015795' => 'camsi', 'CSS0015952' => 'camsi', 'CSS0016104' => 'camsi', 'CSS0016241' => 'camsi', 'CSS0016303' => 'camsi', 'CSS0016490' => 'camsi', 'CSS0016832' => 'camsi', 'CSS0016845' => 'camsi', 'CSS0016914' => 'camsi', 'CSS0016946' => 'camsi', 'CSS0017102' => 'camsi', 'CSS0017193' => 'camsi', 'CSS0017528' => 'camsi', 'CSS0017619' => 'camsi', 'CSS0017679' => 'camsi', 'CSS0017816' => 'camsi', 'CSS0017880' => 'camsi', 'CSS0018106' => 'camsi', 'CSS0018162' => 'camsi', 'CSS0018304' => 'camsi', 'CSS0018406' => 'camsi', 'CSS0018481' => 'camsi', 'CSS0018511' => 'camsi', 'CSS0018596' => 'camsi', 'CSS0018727' => 'camsi', 'CSS0018751' => 'camsi', 'CSS0018777' => 'camsi', 'CSS0018798' => 'camsi', 'CSS0019137' => 'camsi', 'CSS0019177' => 'camsi', 'CSS0019217' => 'camsi', 'CSS0019361' => 'camsi', 'CSS0019516' => 'camsi', 'CSS0019538' => 'camsi', 'CSS0019560' => 'camsi', 'CSS0019819' => 'camsi', 'CSS0019837' => 'camsi', 'CSS0019915' => 'camsi', 'CSS0019925' => 'camsi', 'CSS0020112' => 'camsi', 'CSS0020160' => 'camsi', 'CSS0020378' => 'camsi', 'CSS0020388' => 'camsi', 'CSS0020452' => 'camsi', 'CSS0020588' => 'camsi', 'CSS0020661' => 'camsi', 'CSS0020886' => 'camsi', 'CSS0020973' => 'camsi', 'CSS0021035' => 'camsi', 'CSS0021111' => 'camsi', 'CSS0021131' => 'camsi', 'CSS0021151' => 'camsi', 'CSS0021228' => 'camsi', 'CSS0021397' => 'camsi', 'CSS0021420' => 'camsi', 'CSS0021464' => 'camsi', 'CSS0021547' => 'camsi', 'CSS0021608' => 'camsi', 'CSS0021740' => 'camsi', 'CSS0021826' => 'camsi', 'CSS0021904' => 'camsi', 'CSS0021941' => 'camsi', 'CSS0022189' => 'camsi', 'CSS0022199' => 'camsi', 'CSS0022502' => 'camsi', 'CSS0022531' => 'camsi', 'CSS0022581' => 'camsi', 'CSS0022612' => 'camsi', 'CSS0022621' => 'camsi', 'CSS0022815' => 'camsi', 'CSS0022936' => 'camsi', 'CSS0022964' => 'camsi', 'CSS0022985' => 'camsi', 'CSS0023002' => 'camsi', 'CSS0023006' => 'camsi', 'CSS0023024' => 'camsi', 'CSS0023489' => 'camsi', 'CSS0023593' => 'camsi', 'CSS0023621' => 'camsi', 'CSS0023743' => 'camsi', 'CSS0023804' => 'camsi', 'CSS0023805' => 'camsi', 'CSS0023908' => 'camsi', 'CSS0023938' => 'camsi', 'CSS0023981' => 'camsi', 'CSS0024027' => 'camsi', 'CSS0024169' => 'camsi', 'CSS0024193' => 'camsi', 'CSS0024269' => 'camsi', 'CSS0024336' => 'camsi', 'CSS0024337' => 'camsi', 'CSS0024548' => 'camsi', 'CSS0024564' => 'camsi', 'CSS0024585' => 'camsi', 'CSS0024738' => 'camsi', 'CSS0024833' => 'camsi', 'CSS0024846' => 'camsi', 'CSS0024957' => 'camsi', 'CSS0024974' => 'camsi', 'CSS0025005' => 'camsi', 'CSS0025235' => 'camsi', 'CSS0025465' => 'camsi', 'CSS0025633' => 'camsi', 'CSS0025688' => 'camsi', 'CSS0025759' => 'camsi', 'CSS0025774' => 'camsi', 'CSS0025801' => 'camsi', 'CSS0025942' => 'camsi', 'CSS0026083' => 'camsi', 'CSS0026194' => 'camsi', 'CSS0026230' => 'camsi', 'CSS0026398' => 'camsi', 'CSS0026419' => 'camsi', 'CSS0026679' => 'camsi', 'CSS0026719' => 'camsi', 'CSS0026795' => 'camsi', 'CSS0026835' => 'camsi', 'CSS0026930' => 'camsi', 'CSS0027053' => 'camsi', 'CSS0027130' => 'camsi', 'CSS0027192' => 'camsi', 'CSS0027454' => 'camsi', 'CSS0027467' => 'camsi', 'CSS0027521' => 'camsi', 'CSS0027662' => 'camsi', 'CSS0027795' => 'camsi', 'CSS0027835' => 'camsi', 'CSS0027966' => 'camsi', 'CSS0028090' => 'camsi', 'CSS0028134' => 'camsi', 'CSS0028205' => 'camsi', 'CSS0028263' => 'camsi', 'CSS0028363' => 'camsi', 'CSS0028598' => 'camsi', 'CSS0029175' => 'camsi', 'CSS0029191' => 'camsi', 'CSS0029424' => 'camsi', 'CSS0029479' => 'camsi', 'CSS0029496' => 'camsi', 'CSS0029633' => 'camsi', 'CSS0029837' => 'camsi', 'CSS0029844' => 'camsi', 'CSS0029863' => 'camsi', 'CSS0029874' => 'camsi', 'CSS0029959' => 'camsi', 'CSS0030001' => 'camsi', 'CSS0030093' => 'camsi', 'CSS0030199' => 'camsi', 'CSS0030200' => 'camsi', 'CSS0030427' => 'camsi', 'CSS0030476' => 'camsi', 'CSS0030636' => 'camsi', 'CSS0030673' => 'camsi', 'CSS0030766' => 'camsi', 'CSS0030775' => 'camsi', 'CSS0030858' => 'camsi', 'CSS0030873' => 'camsi', 'CSS0030929' => 'camsi', 'CSS0031028' => 'camsi', 'CSS0031129' => 'camsi', 'CSS0031164' => 'camsi', 'CSS0031340' => 'camsi', 'CSS0031368' => 'camsi', 'CSS0031395' => 'camsi', 'CSS0031596' => 'camsi', 'CSS0031727' => 'camsi', 'CSS0032011' => 'camsi', 'CSS0032160' => 'camsi', 'CSS0032538' => 'camsi', 'CSS0032576' => 'camsi', 'CSS0032603' => 'camsi', 'CSS0032640' => 'camsi', 'CSS0032704' => 'camsi', 'CSS0032851' => 'camsi', 'CSS0032973' => 'camsi', 'CSS0033048' => 'camsi', 'CSS0033082' => 'camsi', 'CSS0033157' => 'camsi', 'CSS0033253' => 'camsi', 'CSS0033347' => 'camsi', 'CSS0033601' => 'camsi', 'CSS0033820' => 'camsi', 'CSS0033881' => 'camsi', 'CSS0033934' => 'camsi', 'CSS0034143' => 'camsi', 'CSS0034176' => 'camsi', 'CSS0034201' => 'camsi', 'CSS0034269' => 'camsi', 'CSS0034303' => 'camsi', 'CSS0034463' => 'camsi', 'CSS0034470' => 'camsi', 'CSS0034514' => 'camsi', 'CSS0034525' => 'camsi', 'CSS0034726' => 'camsi', 'CSS0034727' => 'camsi', 'CSS0034737' => 'camsi', 'CSS0034768' => 'camsi', 'CSS0034890' => 'camsi', 'CSS0034943' => 'camsi', 'CSS0034957' => 'camsi', 'CSS0034973' => 'camsi', 'CSS0035178' => 'camsi', 'CSS0035260' => 'camsi', 'CSS0035316' => 'camsi', 'CSS0035347' => 'camsi', 'CSS0035360' => 'camsi', 'CSS0035380' => 'camsi', 'CSS0035429' => 'camsi', 'CSS0035446' => 'camsi', 'CSS0035737' => 'camsi', 'CSS0035852' => 'camsi', 'CSS0035967' => 'camsi', 'CSS0036001' => 'camsi', 'CSS0036044' => 'camsi', 'CSS0036221' => 'camsi', 'CSS0036333' => 'camsi', 'CSS0036435' => 'camsi', 'CSS0036843' => 'camsi', 'CSS0036846' => 'camsi', 'CSS0037097' => 'camsi', 'CSS0037263' => 'camsi', 'CSS0037370' => 'camsi', 'CSS0037410' => 'camsi', 'CSS0037449' => 'camsi', 'CSS0037603' => 'camsi', 'CSS0037851' => 'camsi', 'CSS0037891' => 'camsi', 'CSS0037996' => 'camsi', 'CSS0038222' => 'camsi', 'CSS0038433' => 'camsi', 'CSS0038441' => 'camsi', 'CSS0038718' => 'camsi', 'CSS0038890' => 'camsi', 'CSS0039049' => 'camsi', 'CSS0039145' => 'camsi', 'CSS0039243' => 'camsi', 'CSS0039294' => 'camsi', 'CSS0039324' => 'camsi', 'CSS0039376' => 'camsi', 'CSS0039475' => 'camsi', 'CSS0039539' => 'camsi', 'CSS0039546' => 'camsi', 'CSS0039567' => 'camsi', 'CSS0039599' => 'camsi', 'CSS0039763' => 'camsi', 'CSS0039863' => 'camsi', 'CSS0040107' => 'camsi', 'CSS0040124' => 'camsi', 'CSS0040151' => 'camsi', 'CSS0040165' => 'camsi', 'CSS0040309' => 'camsi', 'CSS0040318' => 'camsi', 'CSS0040347' => 'camsi', 'CSS0040371' => 'camsi', 'CSS0040456' => 'camsi', 'CSS0040551' => 'camsi', 'CSS0040975' => 'camsi', 'CSS0040981' => 'camsi', 'CSS0041299' => 'camsi', 'CSS0041493' => 'camsi', 'CSS0041658' => 'camsi', 'CSS0041899' => 'camsi', 'CSS0041927' => 'camsi', 'CSS0042016' => 'camsi', 'CSS0042034' => 'camsi', 'CSS0042103' => 'camsi', 'CSS0042172' => 'camsi', 'CSS0042198' => 'camsi', 'CSS0042201' => 'camsi', 'CSS0042308' => 'camsi', 'CSS0042329' => 'camsi', 'CSS0042348' => 'camsi', 'CSS0042349' => 'camsi', 'CSS0042489' => 'camsi', 'CSS0042575' => 'camsi', 'CSS0042624' => 'camsi', 'CSS0042660' => 'camsi', 'CSS0042694' => 'camsi', 'CSS0042995' => 'camsi', 'CSS0043079' => 'camsi', 'CSS0043165' => 'camsi', 'CSS0043171' => 'camsi', 'CSS0043314' => 'camsi', 'CSS0043361' => 'camsi', 'CSS0043375' => 'camsi', 'CSS0043518' => 'camsi', 'CSS0043536' => 'camsi', 'CSS0043678' => 'camsi', 'CSS0043765' => 'camsi', 'CSS0043897' => 'camsi', 'CSS0043944' => 'camsi', 'CSS0044126' => 'camsi', 'CSS0044136' => 'camsi', 'CSS0044179' => 'camsi', 'CSS0044290' => 'camsi', 'CSS0044437' => 'camsi', 'CSS0044502' => 'camsi', 'CSS0044603' => 'camsi', 'CSS0044680' => 'camsi', 'CSS0044685' => 'camsi', 'CSS0044700' => 'camsi', 'CSS0044888' => 'camsi', 'CSS0044923' => 'camsi', 'CSS0044926' => 'camsi', 'CSS0044979' => 'camsi', 'CSS0045049' => 'camsi', 'CSS0045132' => 'camsi', 'CSS0045161' => 'camsi', 'CSS0045219' => 'camsi', 'CSS0045230' => 'camsi', 'CSS0045259' => 'camsi', 'CSS0045324' => 'camsi', 'CSS0045368' => 'camsi', 'CSS0045435' => 'camsi', 'CSS0045856' => 'camsi', 'CSS0045955' => 'camsi', 'CSS0046158' => 'camsi', 'CSS0046334' => 'camsi', 'CSS0046365' => 'camsi', 'CSS0046396' => 'camsi', 'CSS0046400' => 'camsi', 'CSS0046445' => 'camsi', 'CSS0046493' => 'camsi', 'CSS0046640' => 'camsi', 'CSS0046657' => 'camsi', 'CSS0046702' => 'camsi', 'CSS0047208' => 'camsi', 'CSS0047368' => 'camsi', 'CSS0047403' => 'camsi', 'CSS0047417' => 'camsi', 'CSS0047469' => 'camsi', 'CSS0047480' => 'camsi', 'CSS0047482' => 'camsi', 'CSS0047693' => 'camsi', 'CSS0047766' => 'camsi', 'CSS0047866' => 'camsi', 'CSS0047884' => 'camsi', 'CSS0048235' => 'camsi', 'CSS0048383' => 'camsi', 'CSS0048438' => 'camsi', 'CSS0048502' => 'camsi', 'CSS0048546' => 'camsi', 'CSS0048653' => 'camsi', 'CSS0048658' => 'camsi', 'CSS0048729' => 'camsi', 'CSS0048867' => 'camsi', 'CSS0048988' => 'camsi', 'CSS0049053' => 'camsi', 'CSS0049099' => 'camsi', 'CSS0049166' => 'camsi', 'CSS0049174' => 'camsi', 'CSS0049212' => 'camsi', 'CSS0049280' => 'camsi', 'CSS0049391' => 'camsi', 'CSS0049546' => 'camsi', 'CSS0049634' => 'camsi', 'CSS0049655' => 'camsi', 'CSS0049813' => 'camsi', 'CSS0049949' => 'camsi', 'CSS0050009' => 'camsi', 'CSS0050118' => 'camsi', 'CSS0050205' => 'camsi', 'CSS0050275' => 'camsi', 'CSS0050480' => 'camsi', 'CSS0050488' => 'camsi', 'CSS0050497' => 'camsi', 'Dinv03126' => 'din', 'Dinv13140' => 'din', 'Dinv13247' => 'din', 'Dinv14217' => 'din', 'EL10Ac9g22435' => 'bvu', 'FAN20G1200' => 'fan', 'PGR142G2516' => 'pgr', 'Prupe.3G160200' => 'ppe', 'Prupe.5G238200' => 'ppe', 'Prupe.7G047500' => 'ppe', 'QL03p045360' => 'qlo', 'QL05p034369' => 'qlo', 'QL05p034412' => 'qlo', 'QL08p017802' => 'qlo', 'QL08p024762' => 'qlo', 'QL10p026237' => 'qlo', 'QL10p032070' => 'qlo', 'QL11p003821' => 'qlo', 'Rhsim04G0057300' => 'rsi', 'Rhsim05G0049200' => 'rsi', 'Rhsim12G0010400' => 'rsi', 'Rhsim12G0012800' => 'rsi', 'TAR624G0483' => 'tar', 'TAR703G0001' => 'tar', 'vmacro05414' => 'vma', 'vmacro07091' => 'vma', 'vmacro07116' => 'vma', 'vmacro08423' => 'vma', 'vmacro09046' => 'vma', 'vmacro14269' => 'vma', 'vmacro16092' => 'vma', 'vmacro17280' => 'vma', 'vmacro19601' => 'vma' ) $gf_id = 'HOM05D001028' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001028' ) $data_identifier = 'HOM05D001028' $data_type = 'gf_id' $species_gene_counts = array( 'aox' => (int) 11, 'ccan' => (int) 6, 'camsi' => (int) 540, 'din' => (int) 4, 'bvu' => (int) 1, 'fan' => (int) 1, 'pgr' => (int) 1, 'ppe' => (int) 3, 'qlo' => (int) 8, 'rsi' => (int) 4, 'tar' => (int) 2, 'vma' => (int) 9 ) $gf_gene_species = 'vma' $gf_gene_id = 'vmacro19601' $species_info = array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ) $local_species = 'tar' $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' => 'HOM05D001028', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '590', 'num_species' => '12' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'Aqoxy1G01649' => 'aox', 'Aqoxy1G02950' => 'aox', 'Aqoxy2G01005' => 'aox', 'Aqoxy2G01064' => 'aox', 'Aqoxy3G02267' => 'aox', 'Aqoxy3G02617' => 'aox', 'Aqoxy3G02693' => 'aox', 'Aqoxy5G03425' => 'aox', 'Aqoxy6G02164' => 'aox', 'Aqoxy6G02364' => 'aox', 'Aqoxy7G02284' => 'aox', 'Cc00_g09720' => 'ccan', 'Cc00_g21410' => 'ccan', 'Cc00_g31750' => 'ccan', 'Cc00_g34740' => 'ccan', 'Cc04_g16890' => 'ccan', 'Cc11_g03120' => 'ccan', 'CSS0000222' => 'camsi', 'CSS0000265' => 'camsi', 'CSS0000306' => 'camsi', 'CSS0000326' => 'camsi', 'CSS0000530' => 'camsi', 'CSS0000563' => 'camsi', 'CSS0000584' => 'camsi', 'CSS0000684' => 'camsi', 'CSS0001100' => 'camsi', 'CSS0001311' => 'camsi', 'CSS0001343' => 'camsi', 'CSS0001399' => 'camsi', 'CSS0001475' => 'camsi', 'CSS0001506' => 'camsi', 'CSS0001602' => 'camsi', 'CSS0001681' => 'camsi', 'CSS0001874' => 'camsi', 'CSS0001948' => 'camsi', 'CSS0002022' => 'camsi', 'CSS0002230' => 'camsi', 'CSS0002265' => 'camsi', 'CSS0002277' => 'camsi', 'CSS0002462' => 'camsi', 'CSS0002823' => 'camsi', 'CSS0003091' => 'camsi', 'CSS0003162' => 'camsi', 'CSS0003264' => 'camsi', 'CSS0003355' => 'camsi', 'CSS0003378' => 'camsi', 'CSS0003472' => 'camsi', 'CSS0003500' => 'camsi', 'CSS0003640' => 'camsi', 'CSS0003767' => 'camsi', 'CSS0003894' => 'camsi', 'CSS0003952' => 'camsi', 'CSS0003977' => 'camsi', 'CSS0004028' => 'camsi', 'CSS0004117' => 'camsi', 'CSS0004137' => 'camsi', 'CSS0004176' => 'camsi', 'CSS0004265' => 'camsi', 'CSS0004450' => 'camsi', 'CSS0004468' => 'camsi', 'CSS0004488' => 'camsi', 'CSS0004490' => 'camsi', 'CSS0004632' => 'camsi', 'CSS0004790' => 'camsi', 'CSS0004877' => 'camsi', 'CSS0004920' => 'camsi', 'CSS0004969' => 'camsi', 'CSS0005084' => 'camsi', 'CSS0005101' => 'camsi', 'CSS0005271' => 'camsi', 'CSS0005313' => 'camsi', 'CSS0005331' => 'camsi', 'CSS0005368' => 'camsi', 'CSS0005391' => 'camsi', 'CSS0005437' => 'camsi', 'CSS0005515' => 'camsi', 'CSS0005526' => 'camsi', 'CSS0005532' => 'camsi', 'CSS0005595' => 'camsi', 'CSS0005677' => 'camsi', 'CSS0005838' => 'camsi', 'CSS0005988' => 'camsi', 'CSS0006100' => 'camsi', 'CSS0006128' => 'camsi', 'CSS0006293' => 'camsi', 'CSS0006378' => 'camsi', 'CSS0006400' => 'camsi', 'CSS0006441' => 'camsi', 'CSS0006455' => 'camsi', 'CSS0006480' => 'camsi', 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'CSS0048438' => 'camsi', 'CSS0048502' => 'camsi', 'CSS0048546' => 'camsi', 'CSS0048653' => 'camsi', 'CSS0048658' => 'camsi', 'CSS0048729' => 'camsi', 'CSS0048867' => 'camsi', 'CSS0048988' => 'camsi', 'CSS0049053' => 'camsi', 'CSS0049099' => 'camsi', 'CSS0049166' => 'camsi', 'CSS0049174' => 'camsi', 'CSS0049212' => 'camsi', 'CSS0049280' => 'camsi', 'CSS0049391' => 'camsi', 'CSS0049546' => 'camsi', 'CSS0049634' => 'camsi', 'CSS0049655' => 'camsi', 'CSS0049813' => 'camsi', 'CSS0049949' => 'camsi', 'CSS0050009' => 'camsi', 'CSS0050118' => 'camsi', 'CSS0050205' => 'camsi', 'CSS0050275' => 'camsi', 'CSS0050480' => 'camsi', 'CSS0050488' => 'camsi', 'CSS0050497' => 'camsi', 'Dinv03126' => 'din', 'Dinv13140' => 'din', 'Dinv13247' => 'din', 'Dinv14217' => 'din', 'EL10Ac9g22435' => 'bvu', 'FAN20G1200' => 'fan', 'PGR142G2516' => 'pgr', 'Prupe.3G160200' => 'ppe', 'Prupe.5G238200' => 'ppe', 'Prupe.7G047500' => 'ppe', 'QL03p045360' => 'qlo', 'QL05p034369' => 'qlo', 'QL05p034412' => 'qlo', 'QL08p017802' => 'qlo', 'QL08p024762' => 'qlo', 'QL10p026237' => 'qlo', 'QL10p032070' => 'qlo', 'QL11p003821' => 'qlo', 'Rhsim04G0057300' => 'rsi', 'Rhsim05G0049200' => 'rsi', 'Rhsim12G0010400' => 'rsi', 'Rhsim12G0012800' => 'rsi', 'TAR624G0483' => 'tar', 'TAR703G0001' => 'tar', 'vmacro05414' => 'vma', 'vmacro07091' => 'vma', 'vmacro07116' => 'vma', 'vmacro08423' => 'vma', 'vmacro09046' => 'vma', 'vmacro14269' => 'vma', 'vmacro16092' => 'vma', 'vmacro17280' => 'vma', 'vmacro19601' => 'vma' ), 'gf_id' => 'HOM05D001028', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001028' ), 'data_identifier' => 'HOM05D001028', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001028', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '590', 'num_species' => '12' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'Aqoxy1G01649' => 'aox', 'Aqoxy1G02950' => 'aox', 'Aqoxy2G01005' => 'aox', 'Aqoxy2G01064' => 'aox', 'Aqoxy3G02267' => 'aox', 'Aqoxy3G02617' => 'aox', 'Aqoxy3G02693' => 'aox', 'Aqoxy5G03425' => 'aox', 'Aqoxy6G02164' => 'aox', 'Aqoxy6G02364' => 'aox', 'Aqoxy7G02284' => 'aox', 'Cc00_g09720' => 'ccan', 'Cc00_g21410' => 'ccan', 'Cc00_g31750' => 'ccan', 'Cc00_g34740' => 'ccan', 'Cc04_g16890' => 'ccan', 'Cc11_g03120' => 'ccan', 'CSS0000222' => 'camsi', 'CSS0000265' => 'camsi', 'CSS0000306' => 'camsi', 'CSS0000326' => 'camsi', 'CSS0000530' => 'camsi', 'CSS0000563' => 'camsi', 'CSS0000584' => 'camsi', 'CSS0000684' => 'camsi', 'CSS0001100' => 'camsi', 'CSS0001311' => 'camsi', 'CSS0001343' => 'camsi', 'CSS0001399' => 'camsi', 'CSS0001475' => 'camsi', 'CSS0001506' => 'camsi', 'CSS0001602' => 'camsi', 'CSS0001681' => 'camsi', 'CSS0001874' => 'camsi', 'CSS0001948' => 'camsi', 'CSS0002022' => 'camsi', 'CSS0002230' => 'camsi', 'CSS0002265' => 'camsi', 'CSS0002277' => 'camsi', 'CSS0002462' => 'camsi', 'CSS0002823' => 'camsi', 'CSS0003091' => 'camsi', 'CSS0003162' => 'camsi', 'CSS0003264' => 'camsi', 'CSS0003355' => 'camsi', 'CSS0003378' => 'camsi', 'CSS0003472' => 'camsi', 'CSS0003500' => 'camsi', 'CSS0003640' => 'camsi', 'CSS0003767' => 'camsi', 'CSS0003894' => 'camsi', 'CSS0003952' => 'camsi', 'CSS0003977' => 'camsi', 'CSS0004028' => 'camsi', 'CSS0004117' => 'camsi', 'CSS0004137' => 'camsi', 'CSS0004176' => 'camsi', 'CSS0004265' => 'camsi', 'CSS0004450' => 'camsi', 'CSS0004468' => 'camsi', 'CSS0004488' => 'camsi', 'CSS0004490' => 'camsi', 'CSS0004632' => 'camsi', 'CSS0004790' => 'camsi', 'CSS0004877' => 'camsi', 'CSS0004920' => 'camsi', 'CSS0004969' => 'camsi', 'CSS0005084' => 'camsi', 'CSS0005101' => 'camsi', 'CSS0005271' => 'camsi', 'CSS0005313' => 'camsi', 'CSS0005331' => 'camsi', 'CSS0005368' => 'camsi', 'CSS0005391' => 'camsi', 'CSS0005437' => 'camsi', 'CSS0005515' => 'camsi', 'CSS0005526' => 'camsi', 'CSS0005532' => 'camsi', 'CSS0005595' => 'camsi', 'CSS0005677' => 'camsi', 'CSS0005838' => 'camsi', 'CSS0005988' => 'camsi', 'CSS0006100' => 'camsi', 'CSS0006128' => 'camsi', 'CSS0006293' => 'camsi', 'CSS0006378' => 'camsi', 'CSS0006400' => 'camsi', 'CSS0006441' => 'camsi', 'CSS0006455' => 'camsi', 'CSS0006480' => 'camsi', 'CSS0006483' => 'camsi', 'CSS0006538' => 'camsi', 'CSS0006582' => 'camsi', 'CSS0006632' => 'camsi', 'CSS0006771' => 'camsi', 'CSS0006803' => 'camsi', 'CSS0006852' => 'camsi', 'CSS0006861' => 'camsi', 'CSS0006910' => 'camsi', 'CSS0007037' => 'camsi', 'CSS0007066' => 'camsi', 'CSS0007072' => 'camsi', 'CSS0007109' => 'camsi', 'CSS0007193' => 'camsi', 'CSS0007319' => 'camsi', 'CSS0007336' => 'camsi', 'CSS0007377' => 'camsi', 'CSS0007659' => 'camsi', 'CSS0007701' => 'camsi', 'CSS0007711' => 'camsi', 'CSS0007809' => 'camsi', 'CSS0008045' => 'camsi', 'CSS0008050' => 'camsi', 'CSS0008206' => 'camsi', 'CSS0008251' => 'camsi', 'CSS0008252' => 'camsi', 'CSS0008279' => 'camsi', 'CSS0008482' => 'camsi', 'CSS0008583' => 'camsi', 'CSS0008699' => 'camsi', 'CSS0008798' => 'camsi', 'CSS0008971' => 'camsi', 'CSS0009019' => 'camsi', 'CSS0009191' => 'camsi', 'CSS0009241' => 'camsi', 'CSS0009246' => 'camsi', 'CSS0009399' => 'camsi', 'CSS0009654' => 'camsi', 'CSS0009722' => 'camsi', 'CSS0009920' => 'camsi', 'CSS0009986' => 'camsi', 'CSS0010182' => 'camsi', 'CSS0010202' => 'camsi', 'CSS0010330' => 'camsi', 'CSS0010362' => 'camsi', 'CSS0010456' => 'camsi', 'CSS0010472' => 'camsi', 'CSS0010507' => 'camsi', 'CSS0010512' => 'camsi', 'CSS0010520' => 'camsi', 'CSS0010617' => 'camsi', 'CSS0010706' => 'camsi', 'CSS0010747' => 'camsi', 'CSS0010816' => 'camsi', 'CSS0011020' => 'camsi', 'CSS0011115' => 'camsi', 'CSS0011383' => 'camsi', 'CSS0011491' => 'camsi', 'CSS0011602' => 'camsi', 'CSS0011605' => 'camsi', 'CSS0011625' => 'camsi', 'CSS0011654' => 'camsi', 'CSS0011781' => 'camsi', 'CSS0011853' => 'camsi', 'CSS0011898' => 'camsi', 'CSS0011933' => 'camsi', 'CSS0011996' => 'camsi', 'CSS0012066' => 'camsi', 'CSS0012097' => 'camsi', 'CSS0012108' => 'camsi', 'CSS0012226' => 'camsi', 'CSS0012248' => 'camsi', 'CSS0012331' => 'camsi', 'CSS0012797' => 'camsi', 'CSS0012818' => 'camsi', 'CSS0012904' => 'camsi', 'CSS0013001' => 'camsi', 'CSS0013022' => 'camsi', 'CSS0013172' => 'camsi', 'CSS0013244' => 'camsi', 'CSS0013267' => 'camsi', 'CSS0013275' => 'camsi', 'CSS0013324' => 'camsi', 'CSS0013334' => 'camsi', 'CSS0013394' => 'camsi', 'CSS0013549' => 'camsi', 'CSS0013689' => 'camsi', 'CSS0014026' => 'camsi', 'CSS0014049' => 'camsi', 'CSS0014144' => 'camsi', 'CSS0014354' => 'camsi', 'CSS0014579' => 'camsi', 'CSS0014648' => 'camsi', 'CSS0014902' => 'camsi', 'CSS0014979' => 'camsi', 'CSS0015278' => 'camsi', 'CSS0015310' => 'camsi', 'CSS0015364' => 'camsi', 'CSS0015455' => 'camsi', 'CSS0015693' => 'camsi', 'CSS0015774' => 'camsi', 'CSS0015795' => 'camsi', 'CSS0015952' => 'camsi', 'CSS0016104' => 'camsi', 'CSS0016241' => 'camsi', 'CSS0016303' => 'camsi', 'CSS0016490' => 'camsi', 'CSS0016832' => 'camsi', 'CSS0016845' => 'camsi', 'CSS0016914' => 'camsi', 'CSS0016946' => 'camsi', 'CSS0017102' => 'camsi', 'CSS0017193' => 'camsi', 'CSS0017528' => 'camsi', 'CSS0017619' => 'camsi', 'CSS0017679' => 'camsi', 'CSS0017816' => 'camsi', 'CSS0017880' => 'camsi', 'CSS0018106' => 'camsi', 'CSS0018162' => 'camsi', 'CSS0018304' => 'camsi', 'CSS0018406' => 'camsi', 'CSS0018481' => 'camsi', 'CSS0018511' => 'camsi', 'CSS0018596' => 'camsi', 'CSS0018727' => 'camsi', 'CSS0018751' => 'camsi', 'CSS0018777' => 'camsi', 'CSS0018798' => 'camsi', 'CSS0019137' => 'camsi', 'CSS0019177' => 'camsi', 'CSS0019217' => 'camsi', 'CSS0019361' => 'camsi', 'CSS0019516' => 'camsi', 'CSS0019538' => 'camsi', 'CSS0019560' => 'camsi', 'CSS0019819' => 'camsi', 'CSS0019837' => 'camsi', 'CSS0019915' => 'camsi', 'CSS0019925' => 'camsi', 'CSS0020112' => 'camsi', 'CSS0020160' => 'camsi', 'CSS0020378' => 'camsi', 'CSS0020388' => 'camsi', 'CSS0020452' => 'camsi', 'CSS0020588' => 'camsi', 'CSS0020661' => 'camsi', 'CSS0020886' => 'camsi', 'CSS0020973' => 'camsi', 'CSS0021035' => 'camsi', 'CSS0021111' => 'camsi', 'CSS0021131' => 'camsi', 'CSS0021151' => 'camsi', 'CSS0021228' => 'camsi', 'CSS0021397' => 'camsi', 'CSS0021420' => 'camsi', 'CSS0021464' => 'camsi', 'CSS0021547' => 'camsi', 'CSS0021608' => 'camsi', 'CSS0021740' => 'camsi', 'CSS0021826' => 'camsi', 'CSS0021904' => 'camsi', 'CSS0021941' => 'camsi', 'CSS0022189' => 'camsi', 'CSS0022199' => 'camsi', 'CSS0022502' => 'camsi', 'CSS0022531' => 'camsi', 'CSS0022581' => 'camsi', 'CSS0022612' => 'camsi', 'CSS0022621' => 'camsi', 'CSS0022815' => 'camsi', 'CSS0022936' => 'camsi', 'CSS0022964' => 'camsi', 'CSS0022985' => 'camsi', 'CSS0023002' => 'camsi', 'CSS0023006' => 'camsi', 'CSS0023024' => 'camsi', 'CSS0023489' => 'camsi', 'CSS0023593' => 'camsi', 'CSS0023621' => 'camsi', 'CSS0023743' => 'camsi', 'CSS0023804' => 'camsi', 'CSS0023805' => 'camsi', 'CSS0023908' => 'camsi', 'CSS0023938' => 'camsi', 'CSS0023981' => 'camsi', 'CSS0024027' => 'camsi', 'CSS0024169' => 'camsi', 'CSS0024193' => 'camsi', 'CSS0024269' => 'camsi', 'CSS0024336' => 'camsi', 'CSS0024337' => 'camsi', 'CSS0024548' => 'camsi', 'CSS0024564' => 'camsi', 'CSS0024585' => 'camsi', 'CSS0024738' => 'camsi', 'CSS0024833' => 'camsi', 'CSS0024846' => 'camsi', 'CSS0024957' => 'camsi', 'CSS0024974' => 'camsi', 'CSS0025005' => 'camsi', 'CSS0025235' => 'camsi', 'CSS0025465' => 'camsi', 'CSS0025633' => 'camsi', 'CSS0025688' => 'camsi', 'CSS0025759' => 'camsi', 'CSS0025774' => 'camsi', 'CSS0025801' => 'camsi', 'CSS0025942' => 'camsi', 'CSS0026083' => 'camsi', 'CSS0026194' => 'camsi', 'CSS0026230' => 'camsi', 'CSS0026398' => 'camsi', 'CSS0026419' => 'camsi', 'CSS0026679' => 'camsi', 'CSS0026719' => 'camsi', 'CSS0026795' => 'camsi', 'CSS0026835' => 'camsi', 'CSS0026930' => 'camsi', 'CSS0027053' => 'camsi', 'CSS0027130' => 'camsi', 'CSS0027192' => 'camsi', 'CSS0027454' => 'camsi', 'CSS0027467' => 'camsi', 'CSS0027521' => 'camsi', 'CSS0027662' => 'camsi', 'CSS0027795' => 'camsi', 'CSS0027835' => 'camsi', 'CSS0027966' => 'camsi', 'CSS0028090' => 'camsi', 'CSS0028134' => 'camsi', 'CSS0028205' => 'camsi', 'CSS0028263' => 'camsi', 'CSS0028363' => 'camsi', 'CSS0028598' => 'camsi', 'CSS0029175' => 'camsi', 'CSS0029191' => 'camsi', 'CSS0029424' => 'camsi', 'CSS0029479' => 'camsi', 'CSS0029496' => 'camsi', 'CSS0029633' => 'camsi', 'CSS0029837' => 'camsi', 'CSS0029844' => 'camsi', 'CSS0029863' => 'camsi', 'CSS0029874' => 'camsi', 'CSS0029959' => 'camsi', 'CSS0030001' => 'camsi', 'CSS0030093' => 'camsi', 'CSS0030199' => 'camsi', 'CSS0030200' => 'camsi', 'CSS0030427' => 'camsi', 'CSS0030476' => 'camsi', 'CSS0030636' => 'camsi', 'CSS0030673' => 'camsi', 'CSS0030766' => 'camsi', 'CSS0030775' => 'camsi', 'CSS0030858' => 'camsi', 'CSS0030873' => 'camsi', 'CSS0030929' => 'camsi', 'CSS0031028' => 'camsi', 'CSS0031129' => 'camsi', 'CSS0031164' => 'camsi', 'CSS0031340' => 'camsi', 'CSS0031368' => 'camsi', 'CSS0031395' => 'camsi', 'CSS0031596' => 'camsi', 'CSS0031727' => 'camsi', 'CSS0032011' => 'camsi', 'CSS0032160' => 'camsi', 'CSS0032538' => 'camsi', 'CSS0032576' => 'camsi', 'CSS0032603' => 'camsi', 'CSS0032640' => 'camsi', 'CSS0032704' => 'camsi', 'CSS0032851' => 'camsi', 'CSS0032973' => 'camsi', 'CSS0033048' => 'camsi', 'CSS0033082' => 'camsi', 'CSS0033157' => 'camsi', 'CSS0033253' => 'camsi', 'CSS0033347' => 'camsi', 'CSS0033601' => 'camsi', 'CSS0033820' => 'camsi', 'CSS0033881' => 'camsi', 'CSS0033934' => 'camsi', 'CSS0034143' => 'camsi', 'CSS0034176' => 'camsi', 'CSS0034201' => 'camsi', 'CSS0034269' => 'camsi', 'CSS0034303' => 'camsi', 'CSS0034463' => 'camsi', 'CSS0034470' => 'camsi', 'CSS0034514' => 'camsi', 'CSS0034525' => 'camsi', 'CSS0034726' => 'camsi', 'CSS0034727' => 'camsi', 'CSS0034737' => 'camsi', 'CSS0034768' => 'camsi', 'CSS0034890' => 'camsi', 'CSS0034943' => 'camsi', 'CSS0034957' => 'camsi', 'CSS0034973' => 'camsi', 'CSS0035178' => 'camsi', 'CSS0035260' => 'camsi', 'CSS0035316' => 'camsi', 'CSS0035347' => 'camsi', 'CSS0035360' => 'camsi', 'CSS0035380' => 'camsi', 'CSS0035429' => 'camsi', 'CSS0035446' => 'camsi', 'CSS0035737' => 'camsi', 'CSS0035852' => 'camsi', 'CSS0035967' => 'camsi', 'CSS0036001' => 'camsi', 'CSS0036044' => 'camsi', 'CSS0036221' => 'camsi', 'CSS0036333' => 'camsi', 'CSS0036435' => 'camsi', 'CSS0036843' => 'camsi', 'CSS0036846' => 'camsi', 'CSS0037097' => 'camsi', 'CSS0037263' => 'camsi', 'CSS0037370' => 'camsi', 'CSS0037410' => 'camsi', 'CSS0037449' => 'camsi', 'CSS0037603' => 'camsi', 'CSS0037851' => 'camsi', 'CSS0037891' => 'camsi', 'CSS0037996' => 'camsi', 'CSS0038222' => 'camsi', 'CSS0038433' => 'camsi', 'CSS0038441' => 'camsi', 'CSS0038718' => 'camsi', 'CSS0038890' => 'camsi', 'CSS0039049' => 'camsi', 'CSS0039145' => 'camsi', 'CSS0039243' => 'camsi', 'CSS0039294' => 'camsi', 'CSS0039324' => 'camsi', 'CSS0039376' => 'camsi', 'CSS0039475' => 'camsi', 'CSS0039539' => 'camsi', 'CSS0039546' => 'camsi', 'CSS0039567' => 'camsi', 'CSS0039599' => 'camsi', 'CSS0039763' => 'camsi', 'CSS0039863' => 'camsi', 'CSS0040107' => 'camsi', 'CSS0040124' => 'camsi', 'CSS0040151' => 'camsi', 'CSS0040165' => 'camsi', 'CSS0040309' => 'camsi', 'CSS0040318' => 'camsi', 'CSS0040347' => 'camsi', 'CSS0040371' => 'camsi', 'CSS0040456' => 'camsi', 'CSS0040551' => 'camsi', 'CSS0040975' => 'camsi', 'CSS0040981' => 'camsi', 'CSS0041299' => 'camsi', 'CSS0041493' => 'camsi', 'CSS0041658' => 'camsi', 'CSS0041899' => 'camsi', 'CSS0041927' => 'camsi', 'CSS0042016' => 'camsi', 'CSS0042034' => 'camsi', 'CSS0042103' => 'camsi', 'CSS0042172' => 'camsi', 'CSS0042198' => 'camsi', 'CSS0042201' => 'camsi', 'CSS0042308' => 'camsi', 'CSS0042329' => 'camsi', 'CSS0042348' => 'camsi', 'CSS0042349' => 'camsi', 'CSS0042489' => 'camsi', 'CSS0042575' => 'camsi', 'CSS0042624' => 'camsi', 'CSS0042660' => 'camsi', 'CSS0042694' => 'camsi', 'CSS0042995' => 'camsi', 'CSS0043079' => 'camsi', 'CSS0043165' => 'camsi', 'CSS0043171' => 'camsi', 'CSS0043314' => 'camsi', 'CSS0043361' => 'camsi', 'CSS0043375' => 'camsi', 'CSS0043518' => 'camsi', 'CSS0043536' => 'camsi', 'CSS0043678' => 'camsi', 'CSS0043765' => 'camsi', 'CSS0043897' => 'camsi', 'CSS0043944' => 'camsi', 'CSS0044126' => 'camsi', 'CSS0044136' => 'camsi', 'CSS0044179' => 'camsi', 'CSS0044290' => 'camsi', 'CSS0044437' => 'camsi', 'CSS0044502' => 'camsi', 'CSS0044603' => 'camsi', 'CSS0044680' => 'camsi', 'CSS0044685' => 'camsi', 'CSS0044700' => 'camsi', 'CSS0044888' => 'camsi', 'CSS0044923' => 'camsi', 'CSS0044926' => 'camsi', 'CSS0044979' => 'camsi', 'CSS0045049' => 'camsi', 'CSS0045132' => 'camsi', 'CSS0045161' => 'camsi', 'CSS0045219' => 'camsi', 'CSS0045230' => 'camsi', 'CSS0045259' => 'camsi', 'CSS0045324' => 'camsi', 'CSS0045368' => 'camsi', 'CSS0045435' => 'camsi', 'CSS0045856' => 'camsi', 'CSS0045955' => 'camsi', 'CSS0046158' => 'camsi', 'CSS0046334' => 'camsi', 'CSS0046365' => 'camsi', 'CSS0046396' => 'camsi', 'CSS0046400' => 'camsi', 'CSS0046445' => 'camsi', 'CSS0046493' => 'camsi', 'CSS0046640' => 'camsi', 'CSS0046657' => 'camsi', 'CSS0046702' => 'camsi', 'CSS0047208' => 'camsi', 'CSS0047368' => 'camsi', 'CSS0047403' => 'camsi', 'CSS0047417' => 'camsi', 'CSS0047469' => 'camsi', 'CSS0047480' => 'camsi', 'CSS0047482' => 'camsi', 'CSS0047693' => 'camsi', 'CSS0047766' => 'camsi', 'CSS0047866' => 'camsi', 'CSS0047884' => 'camsi', 'CSS0048235' => 'camsi', 'CSS0048383' => 'camsi', 'CSS0048438' => 'camsi', 'CSS0048502' => 'camsi', 'CSS0048546' => 'camsi', 'CSS0048653' => 'camsi', 'CSS0048658' => 'camsi', 'CSS0048729' => 'camsi', 'CSS0048867' => 'camsi', 'CSS0048988' => 'camsi', 'CSS0049053' => 'camsi', 'CSS0049099' => 'camsi', 'CSS0049166' => 'camsi', 'CSS0049174' => 'camsi', 'CSS0049212' => 'camsi', 'CSS0049280' => 'camsi', 'CSS0049391' => 'camsi', 'CSS0049546' => 'camsi', 'CSS0049634' => 'camsi', 'CSS0049655' => 'camsi', 'CSS0049813' => 'camsi', 'CSS0049949' => 'camsi', 'CSS0050009' => 'camsi', 'CSS0050118' => 'camsi', 'CSS0050205' => 'camsi', 'CSS0050275' => 'camsi', 'CSS0050480' => 'camsi', 'CSS0050488' => 'camsi', 'CSS0050497' => 'camsi', 'Dinv03126' => 'din', 'Dinv13140' => 'din', 'Dinv13247' => 'din', 'Dinv14217' => 'din', 'EL10Ac9g22435' => 'bvu', 'FAN20G1200' => 'fan', 'PGR142G2516' => 'pgr', 'Prupe.3G160200' => 'ppe', 'Prupe.5G238200' => 'ppe', 'Prupe.7G047500' => 'ppe', 'QL03p045360' => 'qlo', 'QL05p034369' => 'qlo', 'QL05p034412' => 'qlo', 'QL08p017802' => 'qlo', 'QL08p024762' => 'qlo', 'QL10p026237' => 'qlo', 'QL10p032070' => 'qlo', 'QL11p003821' => 'qlo', 'Rhsim04G0057300' => 'rsi', 'Rhsim05G0049200' => 'rsi', 'Rhsim12G0010400' => 'rsi', 'Rhsim12G0012800' => 'rsi', 'TAR624G0483' => 'tar', 'TAR703G0001' => 'tar', 'vmacro05414' => 'vma', 'vmacro07091' => 'vma', 'vmacro07116' => 'vma', 'vmacro08423' => 'vma', 'vmacro09046' => 'vma', 'vmacro14269' => 'vma', 'vmacro16092' => 'vma', 'vmacro17280' => 'vma', 'vmacro19601' => 'vma' ) $gf_id = 'HOM05D001028' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001028' ) $data_identifier = 'HOM05D001028' $data_type = 'gf_id' $species_gene_counts = array( 'aox' => (int) 11, 'ccan' => (int) 6, 'camsi' => (int) 540, 'din' => (int) 4, 'bvu' => (int) 1, 'fan' => (int) 1, 'pgr' => (int) 1, 'ppe' => (int) 3, 'qlo' => (int) 8, 'rsi' => (int) 4, 'tar' => (int) 2, 'vma' => (int) 9 ) $gf_gene_species = 'vma' $gf_gene_id = 'vmacro19601' $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' => 'HOM05D001028', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '590', 'num_species' => '12' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'Aqoxy1G01649' => 'aox', 'Aqoxy1G02950' => 'aox', 'Aqoxy2G01005' => 'aox', 'Aqoxy2G01064' => 'aox', 'Aqoxy3G02267' => 'aox', 'Aqoxy3G02617' => 'aox', 'Aqoxy3G02693' => 'aox', 'Aqoxy5G03425' => 'aox', 'Aqoxy6G02164' => 'aox', 'Aqoxy6G02364' => 'aox', 'Aqoxy7G02284' => 'aox', 'Cc00_g09720' => 'ccan', 'Cc00_g21410' => 'ccan', 'Cc00_g31750' => 'ccan', 'Cc00_g34740' => 'ccan', 'Cc04_g16890' => 'ccan', 'Cc11_g03120' => 'ccan', 'CSS0000222' => 'camsi', 'CSS0000265' => 'camsi', 'CSS0000306' => 'camsi', 'CSS0000326' => 'camsi', 'CSS0000530' => 'camsi', 'CSS0000563' => 'camsi', 'CSS0000584' => 'camsi', 'CSS0000684' => 'camsi', 'CSS0001100' => 'camsi', 'CSS0001311' => 'camsi', 'CSS0001343' => 'camsi', 'CSS0001399' => 'camsi', 'CSS0001475' => 'camsi', 'CSS0001506' => 'camsi', 'CSS0001602' => 'camsi', 'CSS0001681' => 'camsi', 'CSS0001874' => 'camsi', 'CSS0001948' => 'camsi', 'CSS0002022' => 'camsi', 'CSS0002230' => 'camsi', 'CSS0002265' => 'camsi', 'CSS0002277' => 'camsi', 'CSS0002462' => 'camsi', 'CSS0002823' => 'camsi', 'CSS0003091' => 'camsi', 'CSS0003162' => 'camsi', 'CSS0003264' => 'camsi', 'CSS0003355' => 'camsi', 'CSS0003378' => 'camsi', 'CSS0003472' => 'camsi', 'CSS0003500' => 'camsi', 'CSS0003640' => 'camsi', 'CSS0003767' => 'camsi', 'CSS0003894' => 'camsi', 'CSS0003952' => 'camsi', 'CSS0003977' => 'camsi', 'CSS0004028' => 'camsi', 'CSS0004117' => 'camsi', 'CSS0004137' => 'camsi', 'CSS0004176' => 'camsi', 'CSS0004265' => 'camsi', 'CSS0004450' => 'camsi', 'CSS0004468' => 'camsi', 'CSS0004488' => 'camsi', 'CSS0004490' => 'camsi', 'CSS0004632' => 'camsi', 'CSS0004790' => 'camsi', 'CSS0004877' => 'camsi', 'CSS0004920' => 'camsi', 'CSS0004969' => 'camsi', 'CSS0005084' => 'camsi', 'CSS0005101' => 'camsi', 'CSS0005271' => 'camsi', 'CSS0005313' => 'camsi', 'CSS0005331' => 'camsi', 'CSS0005368' => 'camsi', 'CSS0005391' => 'camsi', 'CSS0005437' => 'camsi', 'CSS0005515' => 'camsi', 'CSS0005526' => 'camsi', 'CSS0005532' => 'camsi', 'CSS0005595' => 'camsi', 'CSS0005677' => 'camsi', 'CSS0005838' => 'camsi', 'CSS0005988' => 'camsi', 'CSS0006100' => 'camsi', 'CSS0006128' => 'camsi', 'CSS0006293' => 'camsi', 'CSS0006378' => 'camsi', 'CSS0006400' => 'camsi', 'CSS0006441' => 'camsi', 'CSS0006455' => 'camsi', 'CSS0006480' => 'camsi', 'CSS0006483' => 'camsi', 'CSS0006538' => 'camsi', 'CSS0006582' => 'camsi', 'CSS0006632' => 'camsi', 'CSS0006771' => 'camsi', 'CSS0006803' => 'camsi', 'CSS0006852' => 'camsi', 'CSS0006861' => 'camsi', 'CSS0006910' => 'camsi', 'CSS0007037' => 'camsi', 'CSS0007066' => 'camsi', 'CSS0007072' => 'camsi', 'CSS0007109' => 'camsi', 'CSS0007193' => 'camsi', 'CSS0007319' => 'camsi', 'CSS0007336' => 'camsi', 'CSS0007377' => 'camsi', 'CSS0007659' => 'camsi', 'CSS0007701' => 'camsi', 'CSS0007711' => 'camsi', 'CSS0007809' => 'camsi', 'CSS0008045' => 'camsi', 'CSS0008050' => 'camsi', 'CSS0008206' => 'camsi', 'CSS0008251' => 'camsi', 'CSS0008252' => 'camsi', 'CSS0008279' => 'camsi', 'CSS0008482' => 'camsi', 'CSS0008583' => 'camsi', 'CSS0008699' => 'camsi', 'CSS0008798' => 'camsi', 'CSS0008971' => 'camsi', 'CSS0009019' => 'camsi', 'CSS0009191' => 'camsi', 'CSS0009241' => 'camsi', 'CSS0009246' => 'camsi', 'CSS0009399' => 'camsi', 'CSS0009654' => 'camsi', 'CSS0009722' => 'camsi', 'CSS0009920' => 'camsi', 'CSS0009986' => 'camsi', 'CSS0010182' => 'camsi', 'CSS0010202' => 'camsi', 'CSS0010330' => 'camsi', 'CSS0010362' => 'camsi', 'CSS0010456' => 'camsi', 'CSS0010472' => 'camsi', 'CSS0010507' => 'camsi', 'CSS0010512' => 'camsi', 'CSS0010520' => 'camsi', 'CSS0010617' => 'camsi', 'CSS0010706' => 'camsi', 'CSS0010747' => 'camsi', 'CSS0010816' => 'camsi', 'CSS0011020' => 'camsi', 'CSS0011115' => 'camsi', 'CSS0011383' => 'camsi', 'CSS0011491' => 'camsi', 'CSS0011602' => 'camsi', 'CSS0011605' => 'camsi', 'CSS0011625' => 'camsi', 'CSS0011654' => 'camsi', 'CSS0011781' => 'camsi', 'CSS0011853' => 'camsi', 'CSS0011898' => 'camsi', 'CSS0011933' => 'camsi', 'CSS0011996' => 'camsi', 'CSS0012066' => 'camsi', 'CSS0012097' => 'camsi', 'CSS0012108' => 'camsi', 'CSS0012226' => 'camsi', 'CSS0012248' => 'camsi', 'CSS0012331' => 'camsi', 'CSS0012797' => 'camsi', 'CSS0012818' => 'camsi', 'CSS0012904' => 'camsi', 'CSS0013001' => 'camsi', 'CSS0013022' => 'camsi', 'CSS0013172' => 'camsi', 'CSS0013244' => 'camsi', 'CSS0013267' => 'camsi', 'CSS0013275' => 'camsi', 'CSS0013324' => 'camsi', 'CSS0013334' => 'camsi', 'CSS0013394' => 'camsi', 'CSS0013549' => 'camsi', 'CSS0013689' => 'camsi', 'CSS0014026' => 'camsi', 'CSS0014049' => 'camsi', 'CSS0014144' => 'camsi', 'CSS0014354' => 'camsi', 'CSS0014579' => 'camsi', 'CSS0014648' => 'camsi', 'CSS0014902' => 'camsi', 'CSS0014979' => 'camsi', 'CSS0015278' => 'camsi', 'CSS0015310' => 'camsi', 'CSS0015364' => 'camsi', 'CSS0015455' => 'camsi', 'CSS0015693' => 'camsi', 'CSS0015774' => 'camsi', 'CSS0015795' => 'camsi', 'CSS0015952' => 'camsi', 'CSS0016104' => 'camsi', 'CSS0016241' => 'camsi', 'CSS0016303' => 'camsi', 'CSS0016490' => 'camsi', 'CSS0016832' => 'camsi', 'CSS0016845' => 'camsi', 'CSS0016914' => 'camsi', 'CSS0016946' => 'camsi', 'CSS0017102' => 'camsi', 'CSS0017193' => 'camsi', 'CSS0017528' => 'camsi', 'CSS0017619' => 'camsi', 'CSS0017679' => 'camsi', 'CSS0017816' => 'camsi', 'CSS0017880' => 'camsi', 'CSS0018106' => 'camsi', 'CSS0018162' => 'camsi', 'CSS0018304' => 'camsi', 'CSS0018406' => 'camsi', 'CSS0018481' => 'camsi', 'CSS0018511' => 'camsi', 'CSS0018596' => 'camsi', 'CSS0018727' => 'camsi', 'CSS0018751' => 'camsi', 'CSS0018777' => 'camsi', 'CSS0018798' => 'camsi', 'CSS0019137' => 'camsi', 'CSS0019177' => 'camsi', 'CSS0019217' => 'camsi', 'CSS0019361' => 'camsi', 'CSS0019516' => 'camsi', 'CSS0019538' => 'camsi', 'CSS0019560' => 'camsi', 'CSS0019819' => 'camsi', 'CSS0019837' => 'camsi', 'CSS0019915' => 'camsi', 'CSS0019925' => 'camsi', 'CSS0020112' => 'camsi', 'CSS0020160' => 'camsi', 'CSS0020378' => 'camsi', 'CSS0020388' => 'camsi', 'CSS0020452' => 'camsi', 'CSS0020588' => 'camsi', 'CSS0020661' => 'camsi', 'CSS0020886' => 'camsi', 'CSS0020973' => 'camsi', 'CSS0021035' => 'camsi', 'CSS0021111' => 'camsi', 'CSS0021131' => 'camsi', 'CSS0021151' => 'camsi', 'CSS0021228' => 'camsi', 'CSS0021397' => 'camsi', 'CSS0021420' => 'camsi', 'CSS0021464' => 'camsi', 'CSS0021547' => 'camsi', 'CSS0021608' => 'camsi', 'CSS0021740' => 'camsi', 'CSS0021826' => 'camsi', 'CSS0021904' => 'camsi', 'CSS0021941' => 'camsi', 'CSS0022189' => 'camsi', 'CSS0022199' => 'camsi', 'CSS0022502' => 'camsi', 'CSS0022531' => 'camsi', 'CSS0022581' => 'camsi', 'CSS0022612' => 'camsi', 'CSS0022621' => 'camsi', 'CSS0022815' => 'camsi', 'CSS0022936' => 'camsi', 'CSS0022964' => 'camsi', 'CSS0022985' => 'camsi', 'CSS0023002' => 'camsi', 'CSS0023006' => 'camsi', 'CSS0023024' => 'camsi', 'CSS0023489' => 'camsi', 'CSS0023593' => 'camsi', 'CSS0023621' => 'camsi', 'CSS0023743' => 'camsi', 'CSS0023804' => 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'camsi', 'CSS0031340' => 'camsi', 'CSS0031368' => 'camsi', 'CSS0031395' => 'camsi', 'CSS0031596' => 'camsi', 'CSS0031727' => 'camsi', 'CSS0032011' => 'camsi', 'CSS0032160' => 'camsi', 'CSS0032538' => 'camsi', 'CSS0032576' => 'camsi', 'CSS0032603' => 'camsi', 'CSS0032640' => 'camsi', 'CSS0032704' => 'camsi', 'CSS0032851' => 'camsi', 'CSS0032973' => 'camsi', 'CSS0033048' => 'camsi', 'CSS0033082' => 'camsi', 'CSS0033157' => 'camsi', 'CSS0033253' => 'camsi', 'CSS0033347' => 'camsi', 'CSS0033601' => 'camsi', 'CSS0033820' => 'camsi', 'CSS0033881' => 'camsi', 'CSS0033934' => 'camsi', 'CSS0034143' => 'camsi', 'CSS0034176' => 'camsi', 'CSS0034201' => 'camsi', 'CSS0034269' => 'camsi', 'CSS0034303' => 'camsi', 'CSS0034463' => 'camsi', 'CSS0034470' => 'camsi', 'CSS0034514' => 'camsi', 'CSS0034525' => 'camsi', 'CSS0034726' => 'camsi', 'CSS0034727' => 'camsi', 'CSS0034737' => 'camsi', 'CSS0034768' => 'camsi', 'CSS0034890' => 'camsi', 'CSS0034943' => 'camsi', 'CSS0034957' => 'camsi', 'CSS0034973' => 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'camsi', 'CSS0039546' => 'camsi', 'CSS0039567' => 'camsi', 'CSS0039599' => 'camsi', 'CSS0039763' => 'camsi', 'CSS0039863' => 'camsi', 'CSS0040107' => 'camsi', 'CSS0040124' => 'camsi', 'CSS0040151' => 'camsi', 'CSS0040165' => 'camsi', 'CSS0040309' => 'camsi', 'CSS0040318' => 'camsi', 'CSS0040347' => 'camsi', 'CSS0040371' => 'camsi', 'CSS0040456' => 'camsi', 'CSS0040551' => 'camsi', 'CSS0040975' => 'camsi', 'CSS0040981' => 'camsi', 'CSS0041299' => 'camsi', 'CSS0041493' => 'camsi', 'CSS0041658' => 'camsi', 'CSS0041899' => 'camsi', 'CSS0041927' => 'camsi', 'CSS0042016' => 'camsi', 'CSS0042034' => 'camsi', 'CSS0042103' => 'camsi', 'CSS0042172' => 'camsi', 'CSS0042198' => 'camsi', 'CSS0042201' => 'camsi', 'CSS0042308' => 'camsi', 'CSS0042329' => 'camsi', 'CSS0042348' => 'camsi', 'CSS0042349' => 'camsi', 'CSS0042489' => 'camsi', 'CSS0042575' => 'camsi', 'CSS0042624' => 'camsi', 'CSS0042660' => 'camsi', 'CSS0042694' => 'camsi', 'CSS0042995' => 'camsi', 'CSS0043079' => 'camsi', 'CSS0043165' => 'camsi', 'CSS0043171' => 'camsi', 'CSS0043314' => 'camsi', 'CSS0043361' => 'camsi', 'CSS0043375' => 'camsi', 'CSS0043518' => 'camsi', 'CSS0043536' => 'camsi', 'CSS0043678' => 'camsi', 'CSS0043765' => 'camsi', 'CSS0043897' => 'camsi', 'CSS0043944' => 'camsi', 'CSS0044126' => 'camsi', 'CSS0044136' => 'camsi', 'CSS0044179' => 'camsi', 'CSS0044290' => 'camsi', 'CSS0044437' => 'camsi', 'CSS0044502' => 'camsi', 'CSS0044603' => 'camsi', 'CSS0044680' => 'camsi', 'CSS0044685' => 'camsi', 'CSS0044700' => 'camsi', 'CSS0044888' => 'camsi', 'CSS0044923' => 'camsi', 'CSS0044926' => 'camsi', 'CSS0044979' => 'camsi', 'CSS0045049' => 'camsi', 'CSS0045132' => 'camsi', 'CSS0045161' => 'camsi', 'CSS0045219' => 'camsi', 'CSS0045230' => 'camsi', 'CSS0045259' => 'camsi', 'CSS0045324' => 'camsi', 'CSS0045368' => 'camsi', 'CSS0045435' => 'camsi', 'CSS0045856' => 'camsi', 'CSS0045955' => 'camsi', 'CSS0046158' => 'camsi', 'CSS0046334' => 'camsi', 'CSS0046365' => 'camsi', 'CSS0046396' => 'camsi', 'CSS0046400' => 'camsi', 'CSS0046445' => 'camsi', 'CSS0046493' => 'camsi', 'CSS0046640' => 'camsi', 'CSS0046657' => 'camsi', 'CSS0046702' => 'camsi', 'CSS0047208' => 'camsi', 'CSS0047368' => 'camsi', 'CSS0047403' => 'camsi', 'CSS0047417' => 'camsi', 'CSS0047469' => 'camsi', 'CSS0047480' => 'camsi', 'CSS0047482' => 'camsi', 'CSS0047693' => 'camsi', 'CSS0047766' => 'camsi', 'CSS0047866' => 'camsi', 'CSS0047884' => 'camsi', 'CSS0048235' => 'camsi', 'CSS0048383' => 'camsi', 'CSS0048438' => 'camsi', 'CSS0048502' => 'camsi', 'CSS0048546' => 'camsi', 'CSS0048653' => 'camsi', 'CSS0048658' => 'camsi', 'CSS0048729' => 'camsi', 'CSS0048867' => 'camsi', 'CSS0048988' => 'camsi', 'CSS0049053' => 'camsi', 'CSS0049099' => 'camsi', 'CSS0049166' => 'camsi', 'CSS0049174' => 'camsi', 'CSS0049212' => 'camsi', 'CSS0049280' => 'camsi', 'CSS0049391' => 'camsi', 'CSS0049546' => 'camsi', 'CSS0049634' => 'camsi', 'CSS0049655' => 'camsi', 'CSS0049813' => 'camsi', 'CSS0049949' => 'camsi', 'CSS0050009' => 'camsi', 'CSS0050118' => 'camsi', 'CSS0050205' => 'camsi', 'CSS0050275' => 'camsi', 'CSS0050480' => 'camsi', 'CSS0050488' => 'camsi', 'CSS0050497' => 'camsi', 'Dinv03126' => 'din', 'Dinv13140' => 'din', 'Dinv13247' => 'din', 'Dinv14217' => 'din', 'EL10Ac9g22435' => 'bvu', 'FAN20G1200' => 'fan', 'PGR142G2516' => 'pgr', 'Prupe.3G160200' => 'ppe', 'Prupe.5G238200' => 'ppe', 'Prupe.7G047500' => 'ppe', 'QL03p045360' => 'qlo', 'QL05p034369' => 'qlo', 'QL05p034412' => 'qlo', 'QL08p017802' => 'qlo', 'QL08p024762' => 'qlo', 'QL10p026237' => 'qlo', 'QL10p032070' => 'qlo', 'QL11p003821' => 'qlo', 'Rhsim04G0057300' => 'rsi', 'Rhsim05G0049200' => 'rsi', 'Rhsim12G0010400' => 'rsi', 'Rhsim12G0012800' => 'rsi', 'TAR624G0483' => 'tar', 'TAR703G0001' => 'tar', 'vmacro05414' => 'vma', 'vmacro07091' => 'vma', 'vmacro07116' => 'vma', 'vmacro08423' => 'vma', 'vmacro09046' => 'vma', 'vmacro14269' => 'vma', 'vmacro16092' => 'vma', 'vmacro17280' => 'vma', 'vmacro19601' => 'vma' ), 'gf_id' => 'HOM05D001028', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001028' ), 'data_identifier' => 'HOM05D001028', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001028', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '590', 'num_species' => '12' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'Aqoxy1G01649' => 'aox', 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'CSS0028205' => 'camsi', 'CSS0028263' => 'camsi', 'CSS0028363' => 'camsi', 'CSS0028598' => 'camsi', 'CSS0029175' => 'camsi', 'CSS0029191' => 'camsi', 'CSS0029424' => 'camsi', 'CSS0029479' => 'camsi', 'CSS0029496' => 'camsi', 'CSS0029633' => 'camsi', 'CSS0029837' => 'camsi', 'CSS0029844' => 'camsi', 'CSS0029863' => 'camsi', 'CSS0029874' => 'camsi', 'CSS0029959' => 'camsi', 'CSS0030001' => 'camsi', 'CSS0030093' => 'camsi', 'CSS0030199' => 'camsi', 'CSS0030200' => 'camsi', 'CSS0030427' => 'camsi', 'CSS0030476' => 'camsi', 'CSS0030636' => 'camsi', 'CSS0030673' => 'camsi', 'CSS0030766' => 'camsi', 'CSS0030775' => 'camsi', 'CSS0030858' => 'camsi', 'CSS0030873' => 'camsi', 'CSS0030929' => 'camsi', 'CSS0031028' => 'camsi', 'CSS0031129' => 'camsi', 'CSS0031164' => 'camsi', 'CSS0031340' => 'camsi', 'CSS0031368' => 'camsi', 'CSS0031395' => 'camsi', 'CSS0031596' => 'camsi', 'CSS0031727' => 'camsi', 'CSS0032011' => 'camsi', 'CSS0032160' => 'camsi', 'CSS0032538' => 'camsi', 'CSS0032576' => 'camsi', 'CSS0032603' => 'camsi', 'CSS0032640' => 'camsi', 'CSS0032704' => 'camsi', 'CSS0032851' => 'camsi', 'CSS0032973' => 'camsi', 'CSS0033048' => 'camsi', 'CSS0033082' => 'camsi', 'CSS0033157' => 'camsi', 'CSS0033253' => 'camsi', 'CSS0033347' => 'camsi', 'CSS0033601' => 'camsi', 'CSS0033820' => 'camsi', 'CSS0033881' => 'camsi', 'CSS0033934' => 'camsi', 'CSS0034143' => 'camsi', 'CSS0034176' => 'camsi', 'CSS0034201' => 'camsi', 'CSS0034269' => 'camsi', 'CSS0034303' => 'camsi', 'CSS0034463' => 'camsi', 'CSS0034470' => 'camsi', 'CSS0034514' => 'camsi', 'CSS0034525' => 'camsi', 'CSS0034726' => 'camsi', 'CSS0034727' => 'camsi', 'CSS0034737' => 'camsi', 'CSS0034768' => 'camsi', 'CSS0034890' => 'camsi', 'CSS0034943' => 'camsi', 'CSS0034957' => 'camsi', 'CSS0034973' => 'camsi', 'CSS0035178' => 'camsi', 'CSS0035260' => 'camsi', 'CSS0035316' => 'camsi', 'CSS0035347' => 'camsi', 'CSS0035360' => 'camsi', 'CSS0035380' => 'camsi', 'CSS0035429' => 'camsi', 'CSS0035446' => 'camsi', 'CSS0035737' => 'camsi', 'CSS0035852' => 'camsi', 'CSS0035967' => 'camsi', 'CSS0036001' => 'camsi', 'CSS0036044' => 'camsi', 'CSS0036221' => 'camsi', 'CSS0036333' => 'camsi', 'CSS0036435' => 'camsi', 'CSS0036843' => 'camsi', 'CSS0036846' => 'camsi', 'CSS0037097' => 'camsi', 'CSS0037263' => 'camsi', 'CSS0037370' => 'camsi', 'CSS0037410' => 'camsi', 'CSS0037449' => 'camsi', 'CSS0037603' => 'camsi', 'CSS0037851' => 'camsi', 'CSS0037891' => 'camsi', 'CSS0037996' => 'camsi', 'CSS0038222' => 'camsi', 'CSS0038433' => 'camsi', 'CSS0038441' => 'camsi', 'CSS0038718' => 'camsi', 'CSS0038890' => 'camsi', 'CSS0039049' => 'camsi', 'CSS0039145' => 'camsi', 'CSS0039243' => 'camsi', 'CSS0039294' => 'camsi', 'CSS0039324' => 'camsi', 'CSS0039376' => 'camsi', 'CSS0039475' => 'camsi', 'CSS0039539' => 'camsi', 'CSS0039546' => 'camsi', 'CSS0039567' => 'camsi', 'CSS0039599' => 'camsi', 'CSS0039763' => 'camsi', 'CSS0039863' => 'camsi', 'CSS0040107' => 'camsi', 'CSS0040124' => 'camsi', 'CSS0040151' => 'camsi', 'CSS0040165' => 'camsi', 'CSS0040309' => 'camsi', 'CSS0040318' => 'camsi', 'CSS0040347' => 'camsi', 'CSS0040371' => 'camsi', 'CSS0040456' => 'camsi', 'CSS0040551' => 'camsi', 'CSS0040975' => 'camsi', 'CSS0040981' => 'camsi', 'CSS0041299' => 'camsi', 'CSS0041493' => 'camsi', 'CSS0041658' => 'camsi', 'CSS0041899' => 'camsi', 'CSS0041927' => 'camsi', 'CSS0042016' => 'camsi', 'CSS0042034' => 'camsi', 'CSS0042103' => 'camsi', 'CSS0042172' => 'camsi', 'CSS0042198' => 'camsi', 'CSS0042201' => 'camsi', 'CSS0042308' => 'camsi', 'CSS0042329' => 'camsi', 'CSS0042348' => 'camsi', 'CSS0042349' => 'camsi', 'CSS0042489' => 'camsi', 'CSS0042575' => 'camsi', 'CSS0042624' => 'camsi', 'CSS0042660' => 'camsi', 'CSS0042694' => 'camsi', 'CSS0042995' => 'camsi', 'CSS0043079' => 'camsi', 'CSS0043165' => 'camsi', 'CSS0043171' => 'camsi', 'CSS0043314' => 'camsi', 'CSS0043361' => 'camsi', 'CSS0043375' => 'camsi', 'CSS0043518' => 'camsi', 'CSS0043536' => 'camsi', 'CSS0043678' => 'camsi', 'CSS0043765' => 'camsi', 'CSS0043897' => 'camsi', 'CSS0043944' => 'camsi', 'CSS0044126' => 'camsi', 'CSS0044136' => 'camsi', 'CSS0044179' => 'camsi', 'CSS0044290' => 'camsi', 'CSS0044437' => 'camsi', 'CSS0044502' => 'camsi', 'CSS0044603' => 'camsi', 'CSS0044680' => 'camsi', 'CSS0044685' => 'camsi', 'CSS0044700' => 'camsi', 'CSS0044888' => 'camsi', 'CSS0044923' => 'camsi', 'CSS0044926' => 'camsi', 'CSS0044979' => 'camsi', 'CSS0045049' => 'camsi', 'CSS0045132' => 'camsi', 'CSS0045161' => 'camsi', 'CSS0045219' => 'camsi', 'CSS0045230' => 'camsi', 'CSS0045259' => 'camsi', 'CSS0045324' => 'camsi', 'CSS0045368' => 'camsi', 'CSS0045435' => 'camsi', 'CSS0045856' => 'camsi', 'CSS0045955' => 'camsi', 'CSS0046158' => 'camsi', 'CSS0046334' => 'camsi', 'CSS0046365' => 'camsi', 'CSS0046396' => 'camsi', 'CSS0046400' => 'camsi', 'CSS0046445' => 'camsi', 'CSS0046493' => 'camsi', 'CSS0046640' => 'camsi', 'CSS0046657' => 'camsi', 'CSS0046702' => 'camsi', 'CSS0047208' => 'camsi', 'CSS0047368' => 'camsi', 'CSS0047403' => 'camsi', 'CSS0047417' => 'camsi', 'CSS0047469' => 'camsi', 'CSS0047480' => 'camsi', 'CSS0047482' => 'camsi', 'CSS0047693' => 'camsi', 'CSS0047766' => 'camsi', 'CSS0047866' => 'camsi', 'CSS0047884' => 'camsi', 'CSS0048235' => 'camsi', 'CSS0048383' => 'camsi', 'CSS0048438' => 'camsi', 'CSS0048502' => 'camsi', 'CSS0048546' => 'camsi', 'CSS0048653' => 'camsi', 'CSS0048658' => 'camsi', 'CSS0048729' => 'camsi', 'CSS0048867' => 'camsi', 'CSS0048988' => 'camsi', 'CSS0049053' => 'camsi', 'CSS0049099' => 'camsi', 'CSS0049166' => 'camsi', 'CSS0049174' => 'camsi', 'CSS0049212' => 'camsi', 'CSS0049280' => 'camsi', 'CSS0049391' => 'camsi', 'CSS0049546' => 'camsi', 'CSS0049634' => 'camsi', 'CSS0049655' => 'camsi', 'CSS0049813' => 'camsi', 'CSS0049949' => 'camsi', 'CSS0050009' => 'camsi', 'CSS0050118' => 'camsi', 'CSS0050205' => 'camsi', 'CSS0050275' => 'camsi', 'CSS0050480' => 'camsi', 'CSS0050488' => 'camsi', 'CSS0050497' => 'camsi', 'Dinv03126' => 'din', 'Dinv13140' => 'din', 'Dinv13247' => 'din', 'Dinv14217' => 'din', 'EL10Ac9g22435' => 'bvu', 'FAN20G1200' => 'fan', 'PGR142G2516' => 'pgr', 'Prupe.3G160200' => 'ppe', 'Prupe.5G238200' => 'ppe', 'Prupe.7G047500' => 'ppe', 'QL03p045360' => 'qlo', 'QL05p034369' => 'qlo', 'QL05p034412' => 'qlo', 'QL08p017802' => 'qlo', 'QL08p024762' => 'qlo', 'QL10p026237' => 'qlo', 'QL10p032070' => 'qlo', 'QL11p003821' => 'qlo', 'Rhsim04G0057300' => 'rsi', 'Rhsim05G0049200' => 'rsi', 'Rhsim12G0010400' => 'rsi', 'Rhsim12G0012800' => 'rsi', 'TAR624G0483' => 'tar', 'TAR703G0001' => 'tar', 'vmacro05414' => 'vma', 'vmacro07091' => 'vma', 'vmacro07116' => 'vma', 'vmacro08423' => 'vma', 'vmacro09046' => 'vma', 'vmacro14269' => 'vma', 'vmacro16092' => 'vma', 'vmacro17280' => 'vma', 'vmacro19601' => 'vma' ) $gf_id = 'HOM05D001028' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001028' ) $data_identifier = 'HOM05D001028' $data_type = 'gf_id' $species_gene_counts = array( 'aox' => (int) 11, 'ccan' => (int) 6, 'camsi' => (int) 540, 'din' => (int) 4, 'bvu' => (int) 1, 'fan' => (int) 1, 'pgr' => (int) 1, 'ppe' => (int) 3, 'qlo' => (int) 8, 'rsi' => (int) 4, 'tar' => (int) 2, 'vma' => (int) 9 ) $gf_gene_species = 'vma' $gf_gene_id = 'vmacro19601' $species_info = array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ) $local_species = 'vma' $disabled = '' $selected = '' $num_hits = (int) 0