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' => 'HOM05D007912',
'msa_exists' => array(
'full' => true,
'edited' => true
),
'tree_exists' => true,
'num_genes' => '81',
'num_species' => '1'
),
'sidebar' => 'gene_family_sidebar',
'navigation_bar_info' => array(
'num_colinearity_runs' => (int) 1,
'num_colinearity_with_dating_runs' => (int) 0,
'num_functional_clusters_runs' => (int) 6,
'has_pan_genomes' => false
),
'allowed_extra_sequences_types' => array(
'aa' => 'Protein',
'dna' => 'DNA'
),
'allowed_editing_methods' => array(
'column' => 'Positions only',
'row' => 'Genes only',
'column_row' => 'Positions and Genes',
'none' => 'No editing'
),
'allowed_tree_programs' => array(
'fasttree' => 'FastTree',
'iqtree' => 'IQ-TREE (includes model testing)',
'raxml' => 'RAxML',
'phyml' => 'PhyML'
),
'allowed_msa_programs' => array(
'muscle' => 'MUSCLE',
'mafft' => 'MAFFT'
),
'allowed_number_blasthits' => array(
(int) 0 => 'all',
(int) 1 => (int) 20,
(int) 2 => (int) 10,
(int) 3 => (int) 5,
(int) 4 => (int) 1
),
'gf_genes' => array(
'Sc01g0005460' => 'sci',
'Sc01g0005490' => 'sci',
'Sc01g0005850' => 'sci',
'Sc01g0006390' => 'sci',
'Sc01g0006550' => 'sci',
'Sc01g0006690' => 'sci',
'Sc02g0004160' => 'sci',
'Sc02g0004480' => 'sci',
'Sc02g0004790' => 'sci',
'Sc02g0004810' => 'sci',
'Sc02g0004860' => 'sci',
'Sc02g0004890' => 'sci',
'Sc02g0004930' => 'sci',
'Sc02g0004970' => 'sci',
'Sc02g0004980' => 'sci',
'Sc02g0005270' => 'sci',
'Sc02g0005760' => 'sci',
'Sc03g0004300' => 'sci',
'Sc03g0004870' => 'sci',
'Sc03g0005210' => 'sci',
'Sc03g0005380' => 'sci',
'Sc04g0004730' => 'sci',
'Sc04g0004840' => 'sci',
'Sc05g0003960' => 'sci',
'Sc05g0004290' => 'sci',
'Sc05g0004430' => 'sci',
'Sc05g0004480' => 'sci',
'Sc05g0004680' => 'sci',
'Sc05g0004710' => 'sci',
'Sc05g0005050' => 'sci',
'Sc05g0005690' => 'sci',
'Sc06g0004250' => 'sci',
'Sc06g0004280' => 'sci',
'Sc07g0004510' => 'sci',
'Sc07g0004870' => 'sci',
'Sc07g0005080' => 'sci',
'Sc08g0004760' => 'sci',
'Sc08g0005440' => 'sci',
'Sc08g0005480' => 'sci',
'Sc09g0007100' => 'sci',
'Sc10g0006910' => 'sci',
'Sc10g0007100' => 'sci',
'Sc10g0007130' => 'sci',
'Sc10g0007340' => 'sci',
'Sc11g0003920' => 'sci',
'Sc11g0004150' => 'sci',
'Sc11g0004200' => 'sci',
'Sc11g0004270' => 'sci',
'Sc12g0007100' => 'sci',
'Sc12g0007630' => 'sci',
'Sc12g0008150' => 'sci',
'Sc12g0008170' => 'sci',
'Sc12g0008230' => 'sci',
'Sc13g0007430' => 'sci',
'Sc13g0008210' => 'sci',
'Sc13g0008360' => 'sci',
'Sc14g0002490' => 'sci',
'Sc14g0002790' => 'sci',
'Sc14g0002800' => 'sci',
'Sc14g0003270' => 'sci',
'Sc14g0004880' => 'sci',
'Sc15g0002320' => 'sci',
'Sc17g0002860' => 'sci',
'Sc17g0003130' => 'sci',
'Sc17g0003150' => 'sci',
'Sc17g0003260' => 'sci',
'Sc17g0003520' => 'sci',
'Sc17g0003650' => 'sci',
'Sc18g0005300' => 'sci',
'Sc20g0002780' => 'sci',
'Sc21g0003860' => 'sci',
'Sc22g0004270' => 'sci',
'Sc22g0004320' => 'sci',
'Sc22g0004420' => 'sci',
'Sc23g0003790' => 'sci',
'Sc24g0001130' => 'sci',
'Sc24g0001190' => 'sci',
'Sc24g0001210' => 'sci',
'Sc24g0001220' => 'sci',
'Sc25g0003180' => 'sci',
'Sc26g0003020' => 'sci'
),
'gf_id' => 'HOM05D007912',
'gf_types_information' => array(
'HOMFAM' => array(
'id' => 'HOMFAM',
'name' => 'Homologous gene family',
'gene_type' => 'coding',
'parent_id' => '',
'ancestry' => 'homology'
),
'ORTHOFAM' => array(
'id' => 'ORTHOFAM',
'name' => 'Orthologous gene family',
'gene_type' => 'coding',
'parent_id' => 'HOMFAM',
'ancestry' => 'orthology'
)
),
'gf_types_configuration' => array(
'HOMFAM' => array(
'order' => '1',
'show_parentless_subfamilies' => 'false',
'show_table' => 'true',
'show_orphan' => false
),
'ORTHOFAM' => array(
'order' => '2',
'show_parentless_subfamilies' => 'false',
'show_table' => 'true',
'show_orphan' => false
)
),
'all_species' => array(
'acertr' => array(
'species' => 'acertr',
'common_name' => 'Acer truncatum',
'tax_id' => '47965',
'version' => 'v2.0'
),
'ach' => array(
'species' => 'ach',
'common_name' => 'Actinidia chinensis',
'tax_id' => '3625',
'version' => 'V3.0'
),
'aar' => array(
'species' => 'aar',
'common_name' => 'Aethionema arabicum',
'tax_id' => '228871',
'version' => 'v3.1'
),
'amhyb' => array(
'species' => 'amhyb',
'common_name' => 'Amaranthus hybridus',
'tax_id' => '3565',
'version' => 'v1.0'
),
'atr' => array(
'species' => 'atr',
'common_name' => 'Amborella trichopoda',
'tax_id' => '13333',
'version' => 'JGI v1.0'
),
'aag' => array(
'species' => 'aag',
'common_name' => 'Anthoceros agrestis',
'tax_id' => '41834',
'version' => 'v1.1'
),
'aox' => array(
'species' => 'aox',
'common_name' => 'Aquilegia oxysepala',
'tax_id' => '432649',
'version' => 'v1.0'
),
'aly' => array(
'species' => 'aly',
'common_name' => 'Arabidopsis lyrata',
'tax_id' => '59689',
'version' => 'JGI v2.1'
),
'ath' => array(
'species' => 'ath',
'common_name' => 'Arabidopsis thaliana',
'tax_id' => '3702',
'version' => 'Araport11'
),
'arhy' => array(
'species' => 'arhy',
'common_name' => 'Arachis hypogaea',
'tax_id' => '3818',
'version' => 'v1.0'
),
'ama' => array(
'species' => 'ama',
'common_name' => 'Avicennia marina',
'tax_id' => '82927',
'version' => 'v1.1 20200527'
),
'bvu' => array(
'species' => 'bvu',
'common_name' => 'Beta vulgaris',
'tax_id' => '161934',
'version' => 'EL10_1.0'
),
'bca' => array(
'species' => 'bca',
'common_name' => 'Brassica carinata',
'tax_id' => '52824',
'version' => 'V1.0'
),
'bna' => array(
'species' => 'bna',
'common_name' => 'Brassica napus',
'tax_id' => '3708',
'version' => 'v2.0'
),
'bol' => array(
'species' => 'bol',
'common_name' => 'Brassica oleracea',
'tax_id' => '109376',
'version' => 'v1.0'
),
'bra' => array(
'species' => 'bra',
'common_name' => 'Brassica rapa',
'tax_id' => '3711',
'version' => 'v1.0'
),
'camsi' => array(
'species' => 'camsi',
'common_name' => 'Camellia sinensis var. sinensis',
'tax_id' => '542762',
'version' => 'CSS_ChrLev_20200506'
),
'cansat' => array(
'species' => 'cansat',
'common_name' => 'Cannabis sativa',
'tax_id' => '3483',
'version' => 'cs10'
),
'cru' => array(
'species' => 'cru',
'common_name' => 'Capsella rubella',
'tax_id' => '81985',
'version' => 'JGI v1.1'
),
'can' => array(
'species' => 'can',
'common_name' => 'Capsicum annuum',
'tax_id' => '4072',
'version' => 'Pepper Genome v2.0'
),
'chi' => array(
'species' => 'chi',
'common_name' => 'Cardamine hirsuta',
'tax_id' => '50463',
'version' => 'v1.0'
),
'cpa' => array(
'species' => 'cpa',
'common_name' => 'Carica papaya',
'tax_id' => '3649',
'version' => 'JGI ASGPB0.4'
),
'cfa' => array(
'species' => 'cfa',
'common_name' => 'Carpinus fangiana',
'tax_id' => '176857',
'version' => 'v1.0'
),
'cil' => array(
'species' => 'cil',
'common_name' => 'Carya illinoinensis',
'tax_id' => '32201',
'version' => 'v1.1'
),
'cde' => array(
'species' => 'cde',
'common_name' => 'Ceratophyllum demersum',
'tax_id' => '4428',
'version' => 'v1.0'
),
'cbr' => array(
'species' => 'cbr',
'common_name' => 'Chara braunii',
'tax_id' => '69332',
'version' => 'Cbr1.0'
),
'cqu' => array(
'species' => 'cqu',
'common_name' => 'Chenopodium quinoa',
'tax_id' => '63459',
'version' => 'KAUST v1.0'
),
'cre' => array(
'species' => 'cre',
'common_name' => 'Chlamydomonas reinhardtii',
'tax_id' => '3055',
'version' => 'JGI v5.5'
),
'car' => array(
'species' => 'car',
'common_name' => 'Cicer arietinum L.',
'tax_id' => '3827',
'version' => 'v3.0'
),
'cla' => array(
'species' => 'cla',
'common_name' => 'Citrullus lanatus',
'tax_id' => '3654',
'version' => 'WCG v2.0'
),
'ccl' => array(
'species' => 'ccl',
'common_name' => 'Citrus clementina',
'tax_id' => '85681',
'version' => 'JGI v1.0'
),
'ccan' => array(
'species' => 'ccan',
'common_name' => 'Coffea canephora',
'tax_id' => '49390',
'version' => 'Coffee Genome Hub v1'
),
'col' => array(
'species' => 'col',
'common_name' => 'Corchorus olitorius',
'tax_id' => '93759',
'version' => 'GenBank v1.0'
),
'cav' => array(
'species' => 'cav',
'common_name' => 'Corylus avellana',
'tax_id' => '13451',
'version' => 'v1.0'
),
'cme' => array(
'species' => 'cme',
'common_name' => 'Cucumis melo',
'tax_id' => '3656',
'version' => 'Melonomics v3.6.1'
),
'csa' => array(
'species' => 'csa',
'common_name' => 'Cucumis sativus L.',
'tax_id' => '3659',
'version' => 'v3.0'
),
'dca' => array(
'species' => 'dca',
'common_name' => 'Daucus carota',
'tax_id' => '4039',
'version' => 'JGI v2.0'
),
'din' => array(
'species' => 'din',
'common_name' => 'Davidia involucrata',
'tax_id' => '16924',
'version' => 'v1.0'
),
'dzi' => array(
'species' => 'dzi',
'common_name' => 'Durio zibethinus',
'tax_id' => '66656',
'version' => 'Duzib1.0'
),
'eca' => array(
'species' => 'eca',
'common_name' => 'Erigeron canadensis',
'tax_id' => '72917',
'version' => 'V1.0'
),
'egut' => array(
'species' => 'egut',
'common_name' => 'Erythranthe guttata',
'tax_id' => '4155',
'version' => 'v2.0'
),
'egr' => array(
'species' => 'egr',
'common_name' => 'Eucalyptus grandis',
'tax_id' => '71139',
'version' => 'v2.0'
),
'esa' => array(
'species' => 'esa',
'common_name' => 'Eutrema salsugineum',
'tax_id' => '72664',
'version' => 'v1.0'
),
'fve' => array(
'species' => 'fve',
'common_name' => 'Fragaria vesca',
'tax_id' => '57918',
'version' => 'V4.0.a2'
),
'fan' => array(
'species' => 'fan',
'common_name' => 'Fragaria x ananassa',
'tax_id' => '3747',
'version' => 'V1.0.a1'
),
'gma' => array(
'species' => 'gma',
'common_name' => 'Glycine max',
'tax_id' => '3847',
'version' => 'JGI Wm82.a4.v1'
),
'ghi' => array(
'species' => 'ghi',
'common_name' => 'Gossypium hirsutum',
'tax_id' => '3635',
'version' => 'v2.1'
),
'gra' => array(
'species' => 'gra',
'common_name' => 'Gossypium raimondii',
'tax_id' => '29730',
'version' => 'v2.1'
),
'han' => array(
'species' => 'han',
'common_name' => 'Helianthus annuus',
'tax_id' => '4232',
'version' => 'r1.2'
),
'hma' => array(
'species' => 'hma',
'common_name' => 'Hydrangea macrophylla',
'tax_id' => '23110',
'version' => 'v2.1'
),
'lsa' => array(
'species' => 'lsa',
'common_name' => 'Lactuca sativa',
'tax_id' => '4236',
'version' => 'v8.0'
),
'lonja' => array(
'species' => 'lonja',
'common_name' => 'Lonicera japonica',
'tax_id' => '105884',
'version' => 'v1.0'
),
'lja' => array(
'species' => 'lja',
'common_name' => 'Lotus japonicus',
'tax_id' => '34305',
'version' => 'Lj1.0v1'
),
'lal' => array(
'species' => 'lal',
'common_name' => 'Lupinus albus',
'tax_id' => '3870',
'version' => 'v1.0'
),
'mbi' => array(
'species' => 'mbi',
'common_name' => 'Magnolia biondii',
'tax_id' => '86725',
'version' => 'v1.0'
),
'mdo' => array(
'species' => 'mdo',
'common_name' => 'Malus domestica',
'tax_id' => '3750',
'version' => 'GDDH13 v1.1'
),
'mes' => array(
'species' => 'mes',
'common_name' => 'Manihot esculenta',
'tax_id' => '3983',
'version' => 'v8.1'
),
'mpo' => array(
'species' => 'mpo',
'common_name' => 'Marchantia polymorpha',
'tax_id' => '3197',
'version' => 'JGI v3.1'
),
'mtr' => array(
'species' => 'mtr',
'common_name' => 'Medicago truncatula',
'tax_id' => '3880',
'version' => 'JGI Mt4.0v1'
),
'mco' => array(
'species' => 'mco',
'common_name' => 'Micromonas commoda',
'tax_id' => '296587',
'version' => 'JGI v3.0'
),
'nnu' => array(
'species' => 'nnu',
'common_name' => 'Nelumbo nucifera',
'tax_id' => '4432',
'version' => 'v2.0'
),
'nta' => array(
'species' => 'nta',
'common_name' => 'Nicotiana tabacum',
'tax_id' => '4097',
'version' => 'Edwards2017'
),
'oeu' => array(
'species' => 'oeu',
'common_name' => 'Olea europaea',
'tax_id' => '4146',
'version' => 'v1.0'
),
'osa' => array(
'species' => 'osa',
'common_name' => 'Oryza sativa ssp. japonica',
'tax_id' => '39947',
'version' => 'IRGSP-1.0-2021-05-10'
),
'pso' => array(
'species' => 'pso',
'common_name' => 'Papaver somniferum',
'tax_id' => '3469',
'version' => 'ASM357369v1'
),
'pax' => array(
'species' => 'pax',
'common_name' => 'Petunia axillaris',
'tax_id' => '33119',
'version' => 'Sol Genomics v1.6.2'
),
'pvu' => array(
'species' => 'pvu',
'common_name' => 'Phaseolus vulgaris',
'tax_id' => '3885',
'version' => 'v2.1'
),
'ppa' => array(
'species' => 'ppa',
'common_name' => 'Physcomitrium patens',
'tax_id' => '3218',
'version' => 'JGI v3.3'
),
'psa' => array(
'species' => 'psa',
'common_name' => 'Pisum sativum',
'tax_id' => '3888',
'version' => 'V1.0a'
),
'ptr' => array(
'species' => 'ptr',
'common_name' => 'Populus trichocarpa',
'tax_id' => '3694',
'version' => 'JGI v4.1'
),
'pco' => array(
'species' => 'pco',
'common_name' => 'Prasinoderma coloniale',
'tax_id' => '156133',
'version' => 'v1.0'
),
'ppe' => array(
'species' => 'ppe',
'common_name' => 'Prunus persica',
'tax_id' => '3760',
'version' => 'v2.1'
),
'pgr' => array(
'species' => 'pgr',
'common_name' => 'Punica granatum',
'tax_id' => '22663',
'version' => 'ASM765513v2'
),
'qlo' => array(
'species' => 'qlo',
'common_name' => 'Quercus lobata',
'tax_id' => '97700',
'version' => 'v3.0'
),
'rsi' => array(
'species' => 'rsi',
'common_name' => 'Rhododendron simsii',
'tax_id' => '118357',
'version' => 'v1.0'
),
'rch' => array(
'species' => 'rch',
'common_name' => 'Rosa chinensis',
'tax_id' => '74649',
'version' => 'v2.0'
),
'sbr' => array(
'species' => 'sbr',
'common_name' => 'Salix brachista',
'tax_id' => '2182728',
'version' => 'v1.0'
),
'sbo' => array(
'species' => 'sbo',
'common_name' => 'Salvia bowleyana',
'tax_id' => '424416',
'version' => 'v1.0'
),
'shi' => array(
'species' => 'shi',
'common_name' => 'Sapria himalayana',
'tax_id' => '289637',
'version' => 'v1.0'
),
'spa' => array(
'species' => 'spa',
'common_name' => 'Schrenkiella parvula',
'tax_id' => '98039',
'version' => 'v2.2'
),
'sed' => array(
'species' => 'sed',
'common_name' => 'Sechium edule',
'tax_id' => '184140',
'version' => 'v1.0'
),
'smo' => array(
'species' => 'smo',
'common_name' => 'Selaginella moellendorffii',
'tax_id' => '88036',
'version' => 'v1.0'
),
'sun' => array(
'species' => 'sun',
'common_name' => 'Selenicereus undatus',
'tax_id' => '176265',
'version' => 'v1.0'
),
'sgi' => array(
'species' => 'sgi',
'common_name' => 'Sequoiadendron giganteum',
'tax_id' => '99814',
'version' => 'V2.0'
),
'sci' => array(
'species' => 'sci',
'common_name' => 'Simmondsia chinensis',
'tax_id' => '3999',
'version' => 'sc1'
),
'sly' => array(
'species' => 'sly',
'common_name' => 'Solanum lycopersicum',
'tax_id' => '4081',
'version' => 'ITAG4.0'
),
'spe' => array(
'species' => 'spe',
'common_name' => 'Solanum pennellii',
'tax_id' => '28526',
'version' => 'V2.0'
),
'stu' => array(
'species' => 'stu',
'common_name' => 'Solanum tuberosum',
'tax_id' => '4113',
'version' => 'JGI v4.03'
),
'sas' => array(
'species' => 'sas',
'common_name' => 'Striga asiatica',
'tax_id' => '4170',
'version' => 'v2.02'
),
'tha' => array(
'species' => 'tha',
'common_name' => 'Tarenaya hassleriana',
'tax_id' => '28532',
'version' => 'RefSeq v1'
),
'tca' => array(
'species' => 'tca',
'common_name' => 'Theobroma cacao',
'tax_id' => '3641',
'version' => 'V2.1'
),
'tpr' => array(
'species' => 'tpr',
'common_name' => 'Trifolium pratense',
'tax_id' => '57577',
'version' => 'V2.0'
),
'twi' => array(
'species' => 'twi',
'common_name' => 'Tripterygium wilfordii',
'tax_id' => '458696',
'version' => 'ASM1340144v1'
),
'tar' => array(
'species' => 'tar',
'common_name' => 'Trochodendron aralioides',
'tax_id' => '4407',
'version' => 'v1.0'
),
'ugi' => array(
'species' => 'ugi',
'common_name' => 'Utricularia gibba',
'tax_id' => '13748',
'version' => 'v1.1F'
),
'vma' => array(
'species' => 'vma',
'common_name' => 'Vaccinium macrocarpon',
'tax_id' => '13750',
'version' => 'V1.0'
),
'vpl' => array(
'species' => 'vpl',
'common_name' => 'Vanilla planifolia',
'tax_id' => '51239',
'version' => 'Elo Vpla-A Principal v1.0'
),
'vmu' => array(
'species' => 'vmu',
'common_name' => 'Vigna mungo',
'tax_id' => '3915',
'version' => 'ASM1342719v1'
),
'vvi' => array(
'species' => 'vvi',
'common_name' => 'Vitis vinifera',
'tax_id' => '29760',
'version' => 'Genoscope.12x'
),
'zma' => array(
'species' => 'zma',
'common_name' => 'Zea mays',
'tax_id' => '4577',
'version' => 'NAM v5.0'
)
),
'allow_async_use' => true,
'sidebar_information' => array(
'type' => 'gf',
'id' => 'HOM05D007912'
),
'data_identifier' => 'HOM05D007912',
'data_type' => 'gf_id'
)
$sidebar_info = array(
'gf_id' => 'HOM05D007912',
'msa_exists' => array(
'full' => true,
'edited' => true
),
'tree_exists' => true,
'num_genes' => '81',
'num_species' => '1'
)
$sidebar = 'gene_family_sidebar'
$navigation_bar_info = array(
'num_colinearity_runs' => (int) 1,
'num_colinearity_with_dating_runs' => (int) 0,
'num_functional_clusters_runs' => (int) 6,
'has_pan_genomes' => false
)
$allowed_extra_sequences_types = array(
'aa' => 'Protein',
'dna' => 'DNA'
)
$allowed_editing_methods = array(
'column' => 'Positions only',
'row' => 'Genes only',
'column_row' => 'Positions and Genes',
'none' => 'No editing'
)
$allowed_tree_programs = array(
'fasttree' => 'FastTree',
'iqtree' => 'IQ-TREE (includes model testing)',
'raxml' => 'RAxML',
'phyml' => 'PhyML'
)
$allowed_msa_programs = array(
'muscle' => 'MUSCLE',
'mafft' => 'MAFFT'
)
$allowed_number_blasthits = array(
(int) 0 => 'all',
(int) 1 => (int) 20,
(int) 2 => (int) 10,
(int) 3 => (int) 5,
(int) 4 => (int) 1
)
$gf_genes = array(
'Sc01g0005460' => 'sci',
'Sc01g0005490' => 'sci',
'Sc01g0005850' => 'sci',
'Sc01g0006390' => 'sci',
'Sc01g0006550' => 'sci',
'Sc01g0006690' => 'sci',
'Sc02g0004160' => 'sci',
'Sc02g0004480' => 'sci',
'Sc02g0004790' => 'sci',
'Sc02g0004810' => 'sci',
'Sc02g0004860' => 'sci',
'Sc02g0004890' => 'sci',
'Sc02g0004930' => 'sci',
'Sc02g0004970' => 'sci',
'Sc02g0004980' => 'sci',
'Sc02g0005270' => 'sci',
'Sc02g0005760' => 'sci',
'Sc03g0004300' => 'sci',
'Sc03g0004870' => 'sci',
'Sc03g0005210' => 'sci',
'Sc03g0005380' => 'sci',
'Sc04g0004730' => 'sci',
'Sc04g0004840' => 'sci',
'Sc05g0003960' => 'sci',
'Sc05g0004290' => 'sci',
'Sc05g0004430' => 'sci',
'Sc05g0004480' => 'sci',
'Sc05g0004680' => 'sci',
'Sc05g0004710' => 'sci',
'Sc05g0005050' => 'sci',
'Sc05g0005690' => 'sci',
'Sc06g0004250' => 'sci',
'Sc06g0004280' => 'sci',
'Sc07g0004510' => 'sci',
'Sc07g0004870' => 'sci',
'Sc07g0005080' => 'sci',
'Sc08g0004760' => 'sci',
'Sc08g0005440' => 'sci',
'Sc08g0005480' => 'sci',
'Sc09g0007100' => 'sci',
'Sc10g0006910' => 'sci',
'Sc10g0007100' => 'sci',
'Sc10g0007130' => 'sci',
'Sc10g0007340' => 'sci',
'Sc11g0003920' => 'sci',
'Sc11g0004150' => 'sci',
'Sc11g0004200' => 'sci',
'Sc11g0004270' => 'sci',
'Sc12g0007100' => 'sci',
'Sc12g0007630' => 'sci',
'Sc12g0008150' => 'sci',
'Sc12g0008170' => 'sci',
'Sc12g0008230' => 'sci',
'Sc13g0007430' => 'sci',
'Sc13g0008210' => 'sci',
'Sc13g0008360' => 'sci',
'Sc14g0002490' => 'sci',
'Sc14g0002790' => 'sci',
'Sc14g0002800' => 'sci',
'Sc14g0003270' => 'sci',
'Sc14g0004880' => 'sci',
'Sc15g0002320' => 'sci',
'Sc17g0002860' => 'sci',
'Sc17g0003130' => 'sci',
'Sc17g0003150' => 'sci',
'Sc17g0003260' => 'sci',
'Sc17g0003520' => 'sci',
'Sc17g0003650' => 'sci',
'Sc18g0005300' => 'sci',
'Sc20g0002780' => 'sci',
'Sc21g0003860' => 'sci',
'Sc22g0004270' => 'sci',
'Sc22g0004320' => 'sci',
'Sc22g0004420' => 'sci',
'Sc23g0003790' => 'sci',
'Sc24g0001130' => 'sci',
'Sc24g0001190' => 'sci',
'Sc24g0001210' => 'sci',
'Sc24g0001220' => 'sci',
'Sc25g0003180' => 'sci',
'Sc26g0003020' => 'sci'
)
$gf_id = 'HOM05D007912'
$gf_types_information = array(
'HOMFAM' => array(
'id' => 'HOMFAM',
'name' => 'Homologous gene family',
'gene_type' => 'coding',
'parent_id' => '',
'ancestry' => 'homology'
),
'ORTHOFAM' => array(
'id' => 'ORTHOFAM',
'name' => 'Orthologous gene family',
'gene_type' => 'coding',
'parent_id' => 'HOMFAM',
'ancestry' => 'orthology'
)
)
$gf_types_configuration = array(
'HOMFAM' => array(
'order' => '1',
'show_parentless_subfamilies' => 'false',
'show_table' => 'true',
'show_orphan' => false
),
'ORTHOFAM' => array(
'order' => '2',
'show_parentless_subfamilies' => 'false',
'show_table' => 'true',
'show_orphan' => false
)
)
$all_species = array(
'acertr' => array(
'species' => 'acertr',
'common_name' => 'Acer truncatum',
'tax_id' => '47965',
'version' => 'v2.0'
),
'ach' => array(
'species' => 'ach',
'common_name' => 'Actinidia chinensis',
'tax_id' => '3625',
'version' => 'V3.0'
),
'aar' => array(
'species' => 'aar',
'common_name' => 'Aethionema arabicum',
'tax_id' => '228871',
'version' => 'v3.1'
),
'amhyb' => array(
'species' => 'amhyb',
'common_name' => 'Amaranthus hybridus',
'tax_id' => '3565',
'version' => 'v1.0'
),
'atr' => array(
'species' => 'atr',
'common_name' => 'Amborella trichopoda',
'tax_id' => '13333',
'version' => 'JGI v1.0'
),
'aag' => array(
'species' => 'aag',
'common_name' => 'Anthoceros agrestis',
'tax_id' => '41834',
'version' => 'v1.1'
),
'aox' => array(
'species' => 'aox',
'common_name' => 'Aquilegia oxysepala',
'tax_id' => '432649',
'version' => 'v1.0'
),
'aly' => array(
'species' => 'aly',
'common_name' => 'Arabidopsis lyrata',
'tax_id' => '59689',
'version' => 'JGI v2.1'
),
'ath' => array(
'species' => 'ath',
'common_name' => 'Arabidopsis thaliana',
'tax_id' => '3702',
'version' => 'Araport11'
),
'arhy' => array(
'species' => 'arhy',
'common_name' => 'Arachis hypogaea',
'tax_id' => '3818',
'version' => 'v1.0'
),
'ama' => array(
'species' => 'ama',
'common_name' => 'Avicennia marina',
'tax_id' => '82927',
'version' => 'v1.1 20200527'
),
'bvu' => array(
'species' => 'bvu',
'common_name' => 'Beta vulgaris',
'tax_id' => '161934',
'version' => 'EL10_1.0'
),
'bca' => array(
'species' => 'bca',
'common_name' => 'Brassica carinata',
'tax_id' => '52824',
'version' => 'V1.0'
),
'bna' => array(
'species' => 'bna',
'common_name' => 'Brassica napus',
'tax_id' => '3708',
'version' => 'v2.0'
),
'bol' => array(
'species' => 'bol',
'common_name' => 'Brassica oleracea',
'tax_id' => '109376',
'version' => 'v1.0'
),
'bra' => array(
'species' => 'bra',
'common_name' => 'Brassica rapa',
'tax_id' => '3711',
'version' => 'v1.0'
),
'camsi' => array(
'species' => 'camsi',
'common_name' => 'Camellia sinensis var. sinensis',
'tax_id' => '542762',
'version' => 'CSS_ChrLev_20200506'
),
'cansat' => array(
'species' => 'cansat',
'common_name' => 'Cannabis sativa',
'tax_id' => '3483',
'version' => 'cs10'
),
'cru' => array(
'species' => 'cru',
'common_name' => 'Capsella rubella',
'tax_id' => '81985',
'version' => 'JGI v1.1'
),
'can' => array(
'species' => 'can',
'common_name' => 'Capsicum annuum',
'tax_id' => '4072',
'version' => 'Pepper Genome v2.0'
),
'chi' => array(
'species' => 'chi',
'common_name' => 'Cardamine hirsuta',
'tax_id' => '50463',
'version' => 'v1.0'
),
'cpa' => array(
'species' => 'cpa',
'common_name' => 'Carica papaya',
'tax_id' => '3649',
'version' => 'JGI ASGPB0.4'
),
'cfa' => array(
'species' => 'cfa',
'common_name' => 'Carpinus fangiana',
'tax_id' => '176857',
'version' => 'v1.0'
),
'cil' => array(
'species' => 'cil',
'common_name' => 'Carya illinoinensis',
'tax_id' => '32201',
'version' => 'v1.1'
),
'cde' => array(
'species' => 'cde',
'common_name' => 'Ceratophyllum demersum',
'tax_id' => '4428',
'version' => 'v1.0'
),
'cbr' => array(
'species' => 'cbr',
'common_name' => 'Chara braunii',
'tax_id' => '69332',
'version' => 'Cbr1.0'
),
'cqu' => array(
'species' => 'cqu',
'common_name' => 'Chenopodium quinoa',
'tax_id' => '63459',
'version' => 'KAUST v1.0'
),
'cre' => array(
'species' => 'cre',
'common_name' => 'Chlamydomonas reinhardtii',
'tax_id' => '3055',
'version' => 'JGI v5.5'
),
'car' => array(
'species' => 'car',
'common_name' => 'Cicer arietinum L.',
'tax_id' => '3827',
'version' => 'v3.0'
),
'cla' => array(
'species' => 'cla',
'common_name' => 'Citrullus lanatus',
'tax_id' => '3654',
'version' => 'WCG v2.0'
),
'ccl' => array(
'species' => 'ccl',
'common_name' => 'Citrus clementina',
'tax_id' => '85681',
'version' => 'JGI v1.0'
),
'ccan' => array(
'species' => 'ccan',
'common_name' => 'Coffea canephora',
'tax_id' => '49390',
'version' => 'Coffee Genome Hub v1'
),
'col' => array(
'species' => 'col',
'common_name' => 'Corchorus olitorius',
'tax_id' => '93759',
'version' => 'GenBank v1.0'
),
'cav' => array(
'species' => 'cav',
'common_name' => 'Corylus avellana',
'tax_id' => '13451',
'version' => 'v1.0'
),
'cme' => array(
'species' => 'cme',
'common_name' => 'Cucumis melo',
'tax_id' => '3656',
'version' => 'Melonomics v3.6.1'
),
'csa' => array(
'species' => 'csa',
'common_name' => 'Cucumis sativus L.',
'tax_id' => '3659',
'version' => 'v3.0'
),
'dca' => array(
'species' => 'dca',
'common_name' => 'Daucus carota',
'tax_id' => '4039',
'version' => 'JGI v2.0'
),
'din' => array(
'species' => 'din',
'common_name' => 'Davidia involucrata',
'tax_id' => '16924',
'version' => 'v1.0'
),
'dzi' => array(
'species' => 'dzi',
'common_name' => 'Durio zibethinus',
'tax_id' => '66656',
'version' => 'Duzib1.0'
),
'eca' => array(
'species' => 'eca',
'common_name' => 'Erigeron canadensis',
'tax_id' => '72917',
'version' => 'V1.0'
),
'egut' => array(
'species' => 'egut',
'common_name' => 'Erythranthe guttata',
'tax_id' => '4155',
'version' => 'v2.0'
),
'egr' => array(
'species' => 'egr',
'common_name' => 'Eucalyptus grandis',
'tax_id' => '71139',
'version' => 'v2.0'
),
'esa' => array(
'species' => 'esa',
'common_name' => 'Eutrema salsugineum',
'tax_id' => '72664',
'version' => 'v1.0'
),
'fve' => array(
'species' => 'fve',
'common_name' => 'Fragaria vesca',
'tax_id' => '57918',
'version' => 'V4.0.a2'
),
'fan' => array(
'species' => 'fan',
'common_name' => 'Fragaria x ananassa',
'tax_id' => '3747',
'version' => 'V1.0.a1'
),
'gma' => array(
'species' => 'gma',
'common_name' => 'Glycine max',
'tax_id' => '3847',
'version' => 'JGI Wm82.a4.v1'
),
'ghi' => array(
'species' => 'ghi',
'common_name' => 'Gossypium hirsutum',
'tax_id' => '3635',
'version' => 'v2.1'
),
'gra' => array(
'species' => 'gra',
'common_name' => 'Gossypium raimondii',
'tax_id' => '29730',
'version' => 'v2.1'
),
'han' => array(
'species' => 'han',
'common_name' => 'Helianthus annuus',
'tax_id' => '4232',
'version' => 'r1.2'
),
'hma' => array(
'species' => 'hma',
'common_name' => 'Hydrangea macrophylla',
'tax_id' => '23110',
'version' => 'v2.1'
),
'lsa' => array(
'species' => 'lsa',
'common_name' => 'Lactuca sativa',
'tax_id' => '4236',
'version' => 'v8.0'
),
'lonja' => array(
'species' => 'lonja',
'common_name' => 'Lonicera japonica',
'tax_id' => '105884',
'version' => 'v1.0'
),
'lja' => array(
'species' => 'lja',
'common_name' => 'Lotus japonicus',
'tax_id' => '34305',
'version' => 'Lj1.0v1'
),
'lal' => array(
'species' => 'lal',
'common_name' => 'Lupinus albus',
'tax_id' => '3870',
'version' => 'v1.0'
),
'mbi' => array(
'species' => 'mbi',
'common_name' => 'Magnolia biondii',
'tax_id' => '86725',
'version' => 'v1.0'
),
'mdo' => array(
'species' => 'mdo',
'common_name' => 'Malus domestica',
'tax_id' => '3750',
'version' => 'GDDH13 v1.1'
),
'mes' => array(
'species' => 'mes',
'common_name' => 'Manihot esculenta',
'tax_id' => '3983',
'version' => 'v8.1'
),
'mpo' => array(
'species' => 'mpo',
'common_name' => 'Marchantia polymorpha',
'tax_id' => '3197',
'version' => 'JGI v3.1'
),
'mtr' => array(
'species' => 'mtr',
'common_name' => 'Medicago truncatula',
'tax_id' => '3880',
'version' => 'JGI Mt4.0v1'
),
'mco' => array(
'species' => 'mco',
'common_name' => 'Micromonas commoda',
'tax_id' => '296587',
'version' => 'JGI v3.0'
),
'nnu' => array(
'species' => 'nnu',
'common_name' => 'Nelumbo nucifera',
'tax_id' => '4432',
'version' => 'v2.0'
),
'nta' => array(
'species' => 'nta',
'common_name' => 'Nicotiana tabacum',
'tax_id' => '4097',
'version' => 'Edwards2017'
),
'oeu' => array(
'species' => 'oeu',
'common_name' => 'Olea europaea',
'tax_id' => '4146',
'version' => 'v1.0'
),
'osa' => array(
'species' => 'osa',
'common_name' => 'Oryza sativa ssp. japonica',
'tax_id' => '39947',
'version' => 'IRGSP-1.0-2021-05-10'
),
'pso' => array(
'species' => 'pso',
'common_name' => 'Papaver somniferum',
'tax_id' => '3469',
'version' => 'ASM357369v1'
),
'pax' => array(
'species' => 'pax',
'common_name' => 'Petunia axillaris',
'tax_id' => '33119',
'version' => 'Sol Genomics v1.6.2'
),
'pvu' => array(
'species' => 'pvu',
'common_name' => 'Phaseolus vulgaris',
'tax_id' => '3885',
'version' => 'v2.1'
),
'ppa' => array(
'species' => 'ppa',
'common_name' => 'Physcomitrium patens',
'tax_id' => '3218',
'version' => 'JGI v3.3'
),
'psa' => array(
'species' => 'psa',
'common_name' => 'Pisum sativum',
'tax_id' => '3888',
'version' => 'V1.0a'
),
'ptr' => array(
'species' => 'ptr',
'common_name' => 'Populus trichocarpa',
'tax_id' => '3694',
'version' => 'JGI v4.1'
),
'pco' => array(
'species' => 'pco',
'common_name' => 'Prasinoderma coloniale',
'tax_id' => '156133',
'version' => 'v1.0'
),
'ppe' => array(
'species' => 'ppe',
'common_name' => 'Prunus persica',
'tax_id' => '3760',
'version' => 'v2.1'
),
'pgr' => array(
'species' => 'pgr',
'common_name' => 'Punica granatum',
'tax_id' => '22663',
'version' => 'ASM765513v2'
),
'qlo' => array(
'species' => 'qlo',
'common_name' => 'Quercus lobata',
'tax_id' => '97700',
'version' => 'v3.0'
),
'rsi' => array(
'species' => 'rsi',
'common_name' => 'Rhododendron simsii',
'tax_id' => '118357',
'version' => 'v1.0'
),
'rch' => array(
'species' => 'rch',
'common_name' => 'Rosa chinensis',
'tax_id' => '74649',
'version' => 'v2.0'
),
'sbr' => array(
'species' => 'sbr',
'common_name' => 'Salix brachista',
'tax_id' => '2182728',
'version' => 'v1.0'
),
'sbo' => array(
'species' => 'sbo',
'common_name' => 'Salvia bowleyana',
'tax_id' => '424416',
'version' => 'v1.0'
),
'shi' => array(
'species' => 'shi',
'common_name' => 'Sapria himalayana',
'tax_id' => '289637',
'version' => 'v1.0'
),
'spa' => array(
'species' => 'spa',
'common_name' => 'Schrenkiella parvula',
'tax_id' => '98039',
'version' => 'v2.2'
),
'sed' => array(
'species' => 'sed',
'common_name' => 'Sechium edule',
'tax_id' => '184140',
'version' => 'v1.0'
),
'smo' => array(
'species' => 'smo',
'common_name' => 'Selaginella moellendorffii',
'tax_id' => '88036',
'version' => 'v1.0'
),
'sun' => array(
'species' => 'sun',
'common_name' => 'Selenicereus undatus',
'tax_id' => '176265',
'version' => 'v1.0'
),
'sgi' => array(
'species' => 'sgi',
'common_name' => 'Sequoiadendron giganteum',
'tax_id' => '99814',
'version' => 'V2.0'
),
'sci' => array(
'species' => 'sci',
'common_name' => 'Simmondsia chinensis',
'tax_id' => '3999',
'version' => 'sc1'
),
'sly' => array(
'species' => 'sly',
'common_name' => 'Solanum lycopersicum',
'tax_id' => '4081',
'version' => 'ITAG4.0'
),
'spe' => array(
'species' => 'spe',
'common_name' => 'Solanum pennellii',
'tax_id' => '28526',
'version' => 'V2.0'
),
'stu' => array(
'species' => 'stu',
'common_name' => 'Solanum tuberosum',
'tax_id' => '4113',
'version' => 'JGI v4.03'
),
'sas' => array(
'species' => 'sas',
'common_name' => 'Striga asiatica',
'tax_id' => '4170',
'version' => 'v2.02'
),
'tha' => array(
'species' => 'tha',
'common_name' => 'Tarenaya hassleriana',
'tax_id' => '28532',
'version' => 'RefSeq v1'
),
'tca' => array(
'species' => 'tca',
'common_name' => 'Theobroma cacao',
'tax_id' => '3641',
'version' => 'V2.1'
),
'tpr' => array(
'species' => 'tpr',
'common_name' => 'Trifolium pratense',
'tax_id' => '57577',
'version' => 'V2.0'
),
'twi' => array(
'species' => 'twi',
'common_name' => 'Tripterygium wilfordii',
'tax_id' => '458696',
'version' => 'ASM1340144v1'
),
'tar' => array(
'species' => 'tar',
'common_name' => 'Trochodendron aralioides',
'tax_id' => '4407',
'version' => 'v1.0'
),
'ugi' => array(
'species' => 'ugi',
'common_name' => 'Utricularia gibba',
'tax_id' => '13748',
'version' => 'v1.1F'
),
'vma' => array(
'species' => 'vma',
'common_name' => 'Vaccinium macrocarpon',
'tax_id' => '13750',
'version' => 'V1.0'
),
'vpl' => array(
'species' => 'vpl',
'common_name' => 'Vanilla planifolia',
'tax_id' => '51239',
'version' => 'Elo Vpla-A Principal v1.0'
),
'vmu' => array(
'species' => 'vmu',
'common_name' => 'Vigna mungo',
'tax_id' => '3915',
'version' => 'ASM1342719v1'
),
'vvi' => array(
'species' => 'vvi',
'common_name' => 'Vitis vinifera',
'tax_id' => '29760',
'version' => 'Genoscope.12x'
),
'zma' => array(
'species' => 'zma',
'common_name' => 'Zea mays',
'tax_id' => '4577',
'version' => 'NAM v5.0'
)
)
$allow_async_use = true
$sidebar_information = array(
'type' => 'gf',
'id' => 'HOM05D007912'
)
$data_identifier = 'HOM05D007912'
$data_type = 'gf_id'
$species_gene_counts = array(
'sci' => (int) 81
)
$gf_gene_species = 'sci'
$gf_gene_id = 'Sc26g0003020'
$species_info = array(
'species' => 'sci',
'common_name' => 'Simmondsia chinensis',
'tax_id' => '3999',
'version' => 'sc1'
)
$local_species = 'sci'
$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